@article{cho_principles_2018,
	title = {Principles of {Systems} {Biology}, {No}. 31},
	volume = {7},
	copyright = {All rights reserved},
	issn = {2405-4712},
	doi = {10.1016/j.cels.2018.08.005},
	abstract = {This month: selected work from the 2018 RECOMB meeting, organized by Ecole Polytechnique and held last April in Paris.},
	language = {eng},
	number = {2},
	journal = {Cell Systems},
	author = {Cho, Hyunghoon and Berger, Bonnie and Peng, Jian and Galitzine, Cyril and Vitek, Olga and Beltran, Pierre M. Jean and Cristea, Ileana M. and Görtler, Franziska and Solbrig, Stefan and Wettig, Tilo and Oefner, Peter J. and Spang, Rainer and Altenbuchinger, Michael and Basso, Rebecca Sarto and Hochbaum, Dorit and Vandin, Fabio and Silverbush, Dana and Cristea, Simona and Yanovich, Gali and Geiger, Tamar and Beerenwinkel, Niko and Sharan, Roded and Zhou, Zhemin and Luhmann, Nina and Alikhan, Nabil-Fareed and Achtman, Mark},
	month = aug,
	year = {2018},
	pmid = {30138580},
	note = {0 citations (Crossref) [2022-06-30]},
	keywords = {Alikhan},
	pages = {133--135},
	file = {Full Text:/usr/users/QIB_fr005/alikhan/Zotero/storage/Q635MWFU/Cho et al. - 2018 - Principles of Systems Biology, No. 31.pdf:application/pdf},
}

@article{zhou_grapetree:_2018,
	title = {{GrapeTree}: visualization of core genomic relationships among 100,000 bacterial pathogens},
	volume = {28},
	copyright = {Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International Licence (CC-BY-NC-ND)},
	issn = {1549-5469},
	shorttitle = {{GrapeTree}},
	doi = {10.1101/gr.232397.117},
	abstract = {Current methods struggle to reconstruct and visualize the genomic relationships of large numbers of bacterial genomes. GrapeTree facilitates the analyses of large numbers of allelic profiles by a static "GrapeTree Layout" algorithm that supports interactive visualizations of large trees within a web browser window. GrapeTree also implements a novel minimum spanning tree algorithm (MSTree V2) to reconstruct genetic relationships despite high levels of missing data. GrapeTree is a stand-alone package for investigating phylogenetic trees plus associated metadata and is also integrated into EnteroBase to facilitate cutting edge navigation of genomic relationships among bacterial pathogens.},
	language = {eng},
	number = {9},
	journal = {Genome Research},
	author = {Zhou, Zhemin and Alikhan, Nabil-Fareed and Sergeant, Martin J. and Luhmann, Nina and Vaz, Cátia and Francisco, Alexandre P. and Carriço, João André and Achtman, Mark},
	year = {2018},
	pmid = {30049790},
	pmcid = {PMC6120633},
	note = {307 citations (Crossref) [2022-06-30]},
	keywords = {Alikhan, Alleles, Bacteria, DNA Barcoding, Taxonomic, Genome, Bacterial, Phylogeny, Software},
	pages = {1395--1404},
	file = {Full Text:/usr/users/QIB_fr005/alikhan/Zotero/storage/42NDRSNZ/Zhou et al. - 2018 - GrapeTree visualization of core genomic relations.pdf:application/pdf;Full Text:/usr/users/QIB_fr005/alikhan/Zotero/storage/YRZMDYLD/Zhou et al. - 2018 - GrapeTree visualization of core genomic relations.pdf:application/pdf},
}

@article{alikhan_genomic_2018,
	title = {A genomic overview of the population structure of {Salmonella}},
	volume = {14},
	copyright = {All rights reserved},
	issn = {1553-7404},
	doi = {10.1371/journal.pgen.1007261},
	abstract = {For many decades, Salmonella enterica has been subdivided by serological properties into serovars or further subdivided for epidemiological tracing by a variety of diagnostic tests with higher resolution. Recently, it has been proposed that so-called eBurst groups (eBGs) based on the alleles of seven housekeeping genes (legacy multilocus sequence typing [MLST]) corresponded to natural populations and could replace serotyping. However, this approach lacks the resolution needed for epidemiological tracing and the existence of natural populations had not been independently validated by independent criteria. Here, we describe EnteroBase, a web-based platform that assembles draft genomes from Illumina short reads in the public domain or that are uploaded by users. EnteroBase implements legacy MLST as well as ribosomal gene MLST (rMLST), core genome MLST (cgMLST), and whole genome MLST (wgMLST) and currently contains over 100,000 assembled genomes from Salmonella. It also provides graphical tools for visual interrogation of these genotypes and those based on core single nucleotide polymorphisms (SNPs). eBGs based on legacy MLST are largely consistent with eBGs based on rMLST, thus demonstrating that these correspond to natural populations. rMLST also facilitated the selection of representative genotypes for SNP analyses of the entire breadth of diversity within Salmonella. In contrast, cgMLST provides the resolution needed for epidemiological investigations. These observations show that genomic genotyping, with the assistance of EnteroBase, can be applied at all levels of diversity within the Salmonella genus.},
	language = {eng},
	number = {4},
	journal = {PLoS genetics},
	author = {Alikhan, Nabil-Fareed and Zhou, Zhemin and Sergeant, Martin J. and Achtman, Mark},
	year = {2018},
	pmid = {29621240},
	pmcid = {PMC5886390},
	note = {315 citations (Crossref) [2022-06-30]},
	keywords = {Alikhan, Databases, Genetic, Genome, Bacterial, Multilocus Sequence Typing, Phylogeny, Polymorphism, Single Nucleotide, Salmonella},
	pages = {e1007261},
	file = {Full Text:/usr/users/QIB_fr005/alikhan/Zotero/storage/F2KFFY9C/Alikhan et al. - 2018 - A genomic overview of the population structure of .pdf:application/pdf},
}

@article{pearce_comparative_2018,
	title = {Comparative analysis of core genome {MLST} and {SNP} typing within a {European} {Salmonella} serovar {Enteritidis} outbreak},
	volume = {274},
	copyright = {Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International Licence (CC-BY-NC-ND)},
	issn = {1879-3460},
	doi = {10.1016/j.ijfoodmicro.2018.02.023},
	abstract = {Multi-country outbreaks of foodborne bacterial disease present challenges in their detection, tracking, and notification. As food is increasingly distributed across borders, such outbreaks are becoming more common. This increases the need for high-resolution, accessible, and replicable isolate typing schemes. Here we evaluate a core genome multilocus typing (cgMLST) scheme for the high-resolution reproducible typing of Salmonella enterica (S. enterica) isolates, by its application to a large European outbreak of S. enterica serovar Enteritidis. This outbreak had been extensively characterised using single nucleotide polymorphism (SNP)-based approaches. The cgMLST analysis was congruent with the original SNP-based analysis, the epidemiological data, and whole genome MLST (wgMLST) analysis. Combination of the cgMLST and epidemiological data confirmed that the genetic diversity among the isolates predated the outbreak, and was likely present at the infection source. There was consequently no link between country of isolation and genetic diversity, but the cgMLST clusters were congruent with date of isolation. Furthermore, comparison with publicly available Enteritidis isolate data demonstrated that the cgMLST scheme presented is highly scalable, enabling outbreaks to be contextualised within the Salmonella genus. The cgMLST scheme is therefore shown to be a standardised and scalable typing method, which allows Salmonella outbreaks to be analysed and compared across laboratories and jurisdictions.},
	language = {eng},
	journal = {International Journal of Food Microbiology},
	author = {Pearce, Madison E. and Alikhan, Nabil-Fareed and Dallman, Timothy J. and Zhou, Zhemin and Grant, Kathie and Maiden, Martin C. J.},
	month = jun,
	year = {2018},
	pmid = {29574242},
	pmcid = {PMC5899760},
	note = {86 citations (Crossref) [2022-06-30]},
	keywords = {Alikhan, Animals, Core genome multilocus sequence typing (cgMLST), Foodborne Diseases, Genetic Variation, Genome, Bacterial, Multilocus Sequence Typing, Outbreak, Phylogeny, Polymorphism, Single Nucleotide, Salmonella, Salmonella enteritidis, Salmonella Infections, Animal, Single nucleotide polymorphisms (SNPs), Whole-genome sequencing (wgs)},
	pages = {1--11},
	file = {Full Text:/usr/users/QIB_fr005/alikhan/Zotero/storage/PE94PG5J/Pearce et al. - 2018 - Comparative analysis of core genome MLST and SNP t.pdf:application/pdf},
}

@article{page_comparison_2017,
	title = {Comparison of classical multi-locus sequence typing software for next-generation sequencing data},
	volume = {3},
	copyright = {Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International Licence (CC-BY-NC-ND)},
	issn = {2057-5858},
	doi = {10.1099/mgen.0.000124},
	abstract = {Multi-locus sequence typing (MLST) is a widely used method for categorizing bacteria. Increasingly, MLST is being performed using next-generation sequencing (NGS) data by reference laboratories and for clinical diagnostics. Many software applications have been developed to calculate sequence types from NGS data; however, there has been no comprehensive review to date on these methods. We have compared eight of these applications against real and simulated data, and present results on: (1) the accuracy of each method against traditional typing methods, (2) the performance on real outbreak datasets, (3) the impact of contamination and varying depth of coverage, and (4) the computational resource requirements.},
	language = {eng},
	number = {8},
	journal = {Microbial Genomics},
	author = {Page, Andrew J. and Alikhan, Nabil-Fareed and Carleton, Heather A. and Seemann, Torsten and Keane, Jacqueline A. and Katz, Lee S.},
	year = {2017},
	pmid = {29026660},
	pmcid = {PMC5610716},
	note = {21 citations (Crossref) [2022-06-30]},
	keywords = {Alikhan, Bacteria, Bacterial Typing Techniques, Databases, Factual, Genome, Bacterial, MLST, multi-locus sequence typing, Multilocus Sequence Typing, next-generation sequencing, Software, software comparison},
	pages = {e000124},
	file = {Full Text:/usr/users/QIB_fr005/alikhan/Zotero/storage/EGZEY2HY/Page et al. - 2017 - Comparison of classical multi-locus sequence typin.pdf:application/pdf},
}

@article{wailan_mechanisms_2016,
	title = {Mechanisms {Involved} in acquisition of \textit{bla}$_{\textrm{{NDM}}}$ {Genes} by {IncA}/{C2} and {IncFIIY} {Plasmids}},
	volume = {60},
	copyright = {All rights reserved},
	issn = {1098-6596},
	doi = {10.1128/AAC.00368-16},
	abstract = {blaNDM genes confer carbapenem resistance and have been identified on transferable plasmids belonging to different incompatibility (Inc) groups. Here we present the complete sequences of four plasmids carrying a blaNDM gene, pKP1-NDM-1, pEC2-NDM-3, pECL3-NDM-1, and pEC4-NDM-6, from four clinical samples originating from four different patients. Different plasmids carry segments that align to different parts of the blaNDM region found on Acinetobacter plasmids. pKP1-NDM-1 and pEC2-NDM-3, from Klebsiella pneumoniae and Escherichia coli, respectively, were identified as type 1 IncA/C2 plasmids with almost identical backbones. Different regions carrying blaNDM are inserted in different locations in the antibiotic resistance island known as ARI-A, and ISCR1 may have been involved in the acquisition of blaNDM-3 by pEC2-NDM-3. pECL3-NDM-1 and pEC4-NDM-6, from Enterobacter cloacae and E. coli, respectively, have similar IncFIIY backbones, but different regions carrying blaNDM are found in different locations. Tn3-derived inverted-repeat transposable elements (TIME) appear to have been involved in the acquisition of blaNDM-6 by pEC4-NDM-6 and the rmtC 16S rRNA methylase gene by IncFIIY plasmids. Characterization of these plasmids further demonstrates that even very closely related plasmids may have acquired blaNDM genes by different mechanisms. These findings also illustrate the complex relationships between antimicrobial resistance genes, transposable elements, and plasmids and provide insights into the possible routes for transmission of blaNDM genes among species of the Enterobacteriaceae family.},
	language = {eng},
	number = {7},
	journal = {Antimicrobial Agents and Chemotherapy},
	author = {Wailan, Alexander M. and Sidjabat, Hanna E. and Yam, Wan Keat and Alikhan, Nabil-Fareed and Petty, Nicola K. and Sartor, Anna L. and Williamson, Deborah A. and Forde, Brian M. and Schembri, Mark A. and Beatson, Scott A. and Paterson, David L. and Walsh, Timothy R. and Partridge, Sally R.},
	year = {2016},
	pmid = {27114281},
	pmcid = {PMC4914633},
	note = {34 citations (Crossref) [2022-06-30]},
	keywords = {Acinetobacter, Alikhan, Anti-Bacterial Agents, beta-Lactamases, Carbapenems, DNA Transposable Elements, Drug Resistance, Multiple, Bacterial, Enterobacter cloacae, Escherichia coli, Klebsiella pneumoniae, Microbial Sensitivity Tests, Plasmids, RNA, Ribosomal, 16S},
	pages = {4082--4088},
	file = {Full Text:/usr/users/QIB_fr005/alikhan/Zotero/storage/NCTDQNX6/Wailan et al. - 2016 - Mechanisms Involved in Acquisition of blaNDM Genes.pdf:application/pdf},
}

@article{beatson_molecular_2015,
	title = {Molecular analysis of asymptomatic bacteriuria {Escherichia} coli strain {VR50} reveals adaptation to the urinary tract by gene acquisition},
	volume = {83},
	copyright = {All rights reserved},
	issn = {1098-5522},
	doi = {10.1128/IAI.02810-14},
	abstract = {Urinary tract infections (UTIs) are among the most common infectious diseases of humans, with Escherichia coli responsible for {\textgreater}80\% of all cases. One extreme of UTI is asymptomatic bacteriuria (ABU), which occurs as an asymptomatic carrier state that resembles commensalism. To understand the evolution and molecular mechanisms that underpin ABU, the genome of the ABU E. coli strain VR50 was sequenced. Analysis of the complete genome indicated that it most resembles E. coli K-12, with the addition of a 94-kb genomic island (GI-VR50-pheV), eight prophages, and multiple plasmids. GI-VR50-pheV has a mosaic structure and contains genes encoding a number of UTI-associated virulence factors, namely, Afa (afimbrial adhesin), two autotransporter proteins (Ag43 and Sat), and aerobactin. We demonstrated that the presence of this island in VR50 confers its ability to colonize the murine bladder, as a VR50 mutant with GI-VR50-pheV deleted was attenuated in a mouse model of UTI in vivo. We established that Afa is the island-encoded factor responsible for this phenotype using two independent deletion (Afa operon and AfaE adhesin) mutants. E. coli VR50afa and VR50afaE displayed significantly decreased ability to adhere to human bladder epithelial cells. In the mouse model of UTI, VR50afa and VR50afaE displayed reduced bladder colonization compared to wild-type VR50, similar to the colonization level of the GI-VR50-pheV mutant. Our study suggests that E. coli VR50 is a commensal-like strain that has acquired fitness factors that facilitate colonization of the human bladder.},
	language = {eng},
	number = {5},
	journal = {Infection and Immunity},
	author = {Beatson, Scott A. and Ben Zakour, Nouri L. and Totsika, Makrina and Forde, Brian M. and Watts, Rebecca E. and Mabbett, Amanda N. and Szubert, Jan M. and Sarkar, Sohinee and Phan, Minh-Duy and Peters, Kate M. and Petty, Nicola K. and Alikhan, Nabil-Fareed and Sullivan, Mitchell J. and Gawthorne, Jayde A. and Stanton-Cook, Mitchell and Nhu, Nguyen Thi Khanh and Chong, Teik Min and Yin, Wai-Fong and Chan, Kok-Gan and Hancock, Viktoria and Ussery, David W. and Ulett, Glen C. and Schembri, Mark A.},
	month = may,
	year = {2015},
	pmid = {25667270},
	pmcid = {PMC4399054},
	note = {20 citations (Crossref) [2022-06-30]},
	keywords = {Adaptation, Biological, Adult, Alikhan, Animals, Bacterial Adhesion, Bacteriuria, Carrier State, Cell Line, DNA, Bacterial, Epithelial Cells, Escherichia coli, Escherichia coli Infections, Evolution, Molecular, Female, Genome, Bacterial, Humans, Mice, Inbred C57BL, Models, Animal, Molecular Sequence Data, Sequence Analysis, DNA, Urinary Tract},
	pages = {1749--1764},
	file = {Full Text:/usr/users/QIB_fr005/alikhan/Zotero/storage/K8XDM6Z3/Beatson et al. - 2015 - Molecular analysis of asymptomatic bacteriuria Esc.pdf:application/pdf},
}

@article{alikhan_blast_2011,
	title = {{BLAST} {Ring} {Image} {Generator} ({BRIG}): simple prokaryote genome comparisons},
	volume = {12},
	copyright = {Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International Licence (CC-BY-NC-ND)},
	issn = {1471-2164},
	shorttitle = {{BLAST} {Ring} {Image} {Generator} ({BRIG})},
	doi = {10.1186/1471-2164-12-402},
	abstract = {BACKGROUND: Visualisation of genome comparisons is invaluable for helping to determine genotypic differences between closely related prokaryotes. New visualisation and abstraction methods are required in order to improve the validation, interpretation and communication of genome sequence information; especially with the increasing amount of data arising from next-generation sequencing projects. Visualising a prokaryote genome as a circular image has become a powerful means of displaying informative comparisons of one genome to a number of others. Several programs, imaging libraries and internet resources already exist for this purpose, however, most are either limited in the number of comparisons they can show, are unable to adequately utilise draft genome sequence data, or require a knowledge of command-line scripting for implementation. Currently, there is no freely available desktop application that enables users to rapidly visualise comparisons between hundreds of draft or complete genomes in a single image.
RESULTS: BLAST Ring Image Generator (BRIG) can generate images that show multiple prokaryote genome comparisons, without an arbitrary limit on the number of genomes compared. The output image shows similarity between a central reference sequence and other sequences as a set of concentric rings, where BLAST matches are coloured on a sliding scale indicating a defined percentage identity. Images can also include draft genome assembly information to show read coverage, assembly breakpoints and collapsed repeats. In addition, BRIG supports the mapping of unassembled sequencing reads against one or more central reference sequences. Many types of custom data and annotations can be shown using BRIG, making it a versatile approach for visualising a range of genomic comparison data. BRIG is readily accessible to any user, as it assumes no specialist computational knowledge and will perform all required file parsing and BLAST comparisons automatically.
CONCLUSIONS: There is a clear need for a user-friendly program that can produce genome comparisons for a large number of prokaryote genomes with an emphasis on rapidly utilising unfinished or unassembled genome data. Here we present BRIG, a cross-platform application that enables the interactive generation of comparative genomic images via a simple graphical-user interface. BRIG is freely available for all operating systems at http://sourceforge.net/projects/brig/.},
	language = {eng},
	journal = {BMC genomics},
	author = {Alikhan, Nabil-Fareed and Petty, Nicola K. and Ben Zakour, Nouri L. and Beatson, Scott A.},
	month = aug,
	year = {2011},
	pmid = {21824423},
	pmcid = {PMC3163573},
	note = {1707 citations (Crossref) [2022-06-30]},
	keywords = {Alikhan, Computer Graphics, Genome, Archaeal, Genome, Bacterial, Genomics, Software, User-Computer Interface},
	pages = {402},
	file = {Full Text:/usr/users/QIB_fr005/alikhan/Zotero/storage/5DN4ENQ8/Alikhan et al. - 2011 - BLAST Ring Image Generator (BRIG) simple prokaryo.pdf:application/pdf},
}

@article{merhi_replacement_2022,
	title = {Replacement of the {Alpha} variant of {SARS}-{CoV}-2 by the {Delta} variant in {Lebanon} between {April} and {June} 2021},
	volume = {8},
	issn = {2057-5858},
	url = {https://www.microbiologyresearch.org/content/journal/mgen/10.1099/mgen.0.000838},
	doi = {10.1099/mgen.0.000838},
	abstract = {The COVID-19 pandemic continues to expand globally, with case numbers rising in many areas of the world, including the Eastern Mediterranean Region. Lebanon experienced its largest wave of COVID-19 infections from January to April 2021. Limited genomic surveillance was undertaken, with just 26 SARS-CoV-2 genomes available for this period, nine of which were from travellers from Lebanon detected by other countries. Additional genome sequencing is thus needed to allow surveillance of variants in circulation. In total, 905 SARS-CoV-2 genomes were sequenced using the ARTIC protocol. The genomes were derived from SARS-CoV-2-positive samples, selected retrospectively from the sentinel COVID-19 surveillance network, to capture diversity of location, sampling time, sex, nationality and age. Although 16 PANGO lineages were circulating in Lebanon in January 2021, by February there were just four, with the Alpha variant accounting for 97 \% of samples. In the following 2 months, all samples contained the Alpha variant. However, this had changed dramatically by June and July 2021, when all samples belonged to the Delta variant. This study documents a ten-fold increase in the number of SARS-CoV-2 genomes available from Lebanon. The Alpha variant, first detected in the UK, rapidly swept through Lebanon, causing the country's largest wave to date, which peaked in January 2021. The Alpha variant was introduced to Lebanon multiple times despite travel restrictions, but the source of these introductions remains uncertain. The Delta variant was detected in Gambia in travellers from Lebanon in mid-May, suggesting community transmission in Lebanon several weeks before this variant was detected in the country. Prospective sequencing in June/July 2021 showed that the Delta variant had completely replaced the Alpha variant in under 6 weeks.},
	language = {en},
	number = {7},
	urldate = {2022-09-28},
	journal = {Microbial Genomics},
	author = {Merhi, Georgi and Trotter, Alexander J. and de Oliveira Martins, Leonardo and Koweyes, Jad and Le-Viet, Thanh and Abou Naja, Hala and Al Buaini, Mona and Prosolek, Sophie J. and Alikhan, Nabil-Fareed and Lott, Martin and Tohmeh, Tatiana and Badran, Bassam and Jupp, Orla J. and Gardner, Sarah and Felgate, Matthew W. and Makin, Kate A. and Wilkinson, Janine M. and Stanley, Rachael and Sesay, Abdul K. and Webber, Mark A. and Davidson, Rose K. and Ghosn, Nada and Pallen, Mark and Hasan, Hamad and Page, Andrew J. and Tokajian, Sima},
	month = jul,
	year = {2022},
	file = {Submitted Version:/usr/users/QIB_fr005/alikhan/Zotero/storage/PTMFL9NA/Merhi et al. - 2022 - Replacement of the Alpha variant of SARS-CoV-2 by .pdf:application/pdf},
}

@article{xiaoli_benchmark_2022,
	title = {Benchmark datasets for {SARS}-{CoV}-2 surveillance bioinformatics},
	volume = {10},
	issn = {2167-8359},
	url = {https://peerj.com/articles/13821},
	doi = {10.7717/peerj.13821},
	abstract = {Background
              Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the cause of coronavirus disease 2019 (COVID-19), has spread globally and is being surveilled with an international genome sequencing effort. Surveillance consists of sample acquisition, library preparation, and whole genome sequencing. This has necessitated a classification scheme detailing Variants of Concern (VOC) and Variants of Interest (VOI), and the rapid expansion of bioinformatics tools for sequence analysis. These bioinformatic tools are means for major actionable results: maintaining quality assurance and checks, defining population structure, performing genomic epidemiology, and inferring lineage to allow reliable and actionable identification and classification. Additionally, the pandemic has required public health laboratories to reach high throughput proficiency in sequencing library preparation and downstream data analysis rapidly. However, both processes can be limited by a lack of a standardized sequence dataset.
            
            
              Methods
              We identified six SARS-CoV-2 sequence datasets from recent publications, public databases and internal resources. In addition, we created a method to mine public databases to identify representative genomes for these datasets. Using this novel method, we identified several genomes as either VOI/VOC representatives or non-VOI/VOC representatives. To describe each dataset, we utilized a previously published datasets format, which describes accession information and whole dataset information. Additionally, a script from the same publication has been enhanced to download and verify all data from this study.
            
            
              Results
              
                The benchmark datasets focus on the two most widely used sequencing platforms: long read sequencing data from the Oxford Nanopore Technologies platform and short read sequencing data from the Illumina platform. There are six datasets: three were derived from recent publications; two were derived from data mining public databases to answer common questions not covered by published datasets; one unique dataset representing common sequence failures was obtained by rigorously scrutinizing data that did not pass quality checks. The dataset summary table, data mining script and quality control (QC) values for all sequence data are publicly available on GitHub:
                https://github.com/CDCgov/datasets-sars-cov-2
                .
              
            
            
              Discussion
              The datasets presented here were generated to help public health laboratories build sequencing and bioinformatics capacity, benchmark different workflows and pipelines, and calibrate QC thresholds to ensure sequencing quality. Together, improvements in these areas support accurate and timely outbreak investigation and surveillance, providing actionable data for pandemic management. Furthermore, these publicly available and standardized benchmark data will facilitate the development and adjudication of new pipelines.},
	language = {en},
	urldate = {2022-09-28},
	journal = {PeerJ},
	author = {Xiaoli, Lingzi and Hagey, Jill V. and Park, Daniel J. and Gulvik, Christopher A. and Young, Erin L. and Alikhan, Nabil-Fareed and Lawsin, Adrian and Hassell, Norman and Knipe, Kristen and Oakeson, Kelly F. and Retchless, Adam C. and Shakya, Migun and Lo, Chien-Chi and Chain, Patrick and Page, Andrew J. and Metcalf, Benjamin J. and Su, Michelle and Rowell, Jessica and Vidyaprakash, Eshaw and Paden, Clinton R. and Huang, Andrew D. and Roellig, Dawn and Patel, Ketan and Winglee, Kathryn and Weigand, Michael R. and Katz, Lee S.},
	month = sep,
	year = {2022},
	pages = {e13821},
	file = {Full Text:/usr/users/QIB_fr005/alikhan/Zotero/storage/MDVKT65A/Xiaoli et al. - 2022 - Benchmark datasets for SARS-CoV-2 surveillance bio.pdf:application/pdf},
}

@article{pallen_naming_2022,
	title = {Naming the unnamed: over 65,000 {Candidatus} names for unnamed {Archaea} and {Bacteria} in the {Genome} {Taxonomy} {Database}},
	volume = {72},
	issn = {1466-5026, 1466-5034},
	shorttitle = {Naming the unnamed},
	url = {https://www.microbiologyresearch.org/content/journal/ijsem/10.1099/ijsem.0.005482},
	doi = {10.1099/ijsem.0.005482},
	abstract = {Thousands of new bacterial and archaeal species and higher-level taxa are discovered each year through the analysis of genomes and metagenomes. The Genome Taxonomy Database (GTDB) provides hierarchical sequence-based descriptions and classifications for new and as-yet-unnamed taxa. However, bacterial nomenclature, as currently configured, cannot keep up with the need for new well-formed names. Instead, microbiologists have been forced to use hard-to-remember alphanumeric placeholder labels. Here, we exploit an approach to the generation of well-formed arbitrary Latinate names at a scale sufficient to name tens of thousands of unnamed taxa within GTDB. These newly created names represent an important resource for the microbiology community, facilitating communication between bioinformaticians, microbiologists and taxonomists, while populating the emerging landscape of microbial taxonomic and functional discovery with accessible and memorable linguistic labels.},
	language = {en},
	number = {9},
	urldate = {2022-09-28},
	journal = {International Journal of Systematic and Evolutionary Microbiology},
	author = {Pallen, Mark J. and Rodriguez-R, Luis M. and Alikhan, Nabil-Fareed},
	month = sep,
	year = {2022},
	file = {Submitted Version:/usr/users/QIB_fr005/alikhan/Zotero/storage/FETE9F7B/Pallen et al. - 2022 - Naming the unnamed over 65,000 Candidatus names f.pdf:application/pdf},
}

@article{de_silva_impact_2021,
	title = {The impact of viral mutations on recognition by {SARS}-{CoV}-2 specific {T} cells},
	volume = {24},
	copyright = {Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International Licence (CC-BY-NC-ND)},
	issn = {25890042},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S2589004221013225},
	doi = {10.1016/j.isci.2021.103353},
	abstract = {We identify amino acid variants within dominant SARS-CoV-2 T cell epitopes by interrogating global sequence data. Several variants within nucleocapsid and ORF3a epitopes have arisen independently in multiple lineages and result in loss of recognition by epitope-specific T cells assessed by IFN-γ and cytotoxic killing assays. Complete loss of T cell responsiveness was seen due to Q213K in the A∗01:01-restricted CD8+ ORF3a epitope FTSDYYQLY207-215; due to P13L, P13S, and P13T in the B∗27:05-restricted CD8+ nucleocapsid epitope QRNAPRITF9-17; and due to T362I and P365S in the A∗03:01/A∗11:01-restricted CD8+ nucleocapsid epitope KTFPPTEPK361-369. CD8+ T cell lines unable to recognize variant epitopes have diverse T cell receptor repertoires. These data demonstrate the potential for T cell evasion and highlight the need for ongoing surveillance for variants capable of escaping T cell as well as humoral immunity.},
	language = {en},
	number = {11},
	urldate = {2022-05-13},
	journal = {iScience},
	author = {de Silva, Thushan I. and Liu, Guihai and Lindsey, Benjamin B. and Dong, Danning and Moore, Shona C. and Hsu, Nienyun Sharon and Shah, Dhruv and Wellington, Dannielle and Mentzer, Alexander J. and Angyal, Adrienn and Brown, Rebecca and Parker, Matthew D. and Ying, Zixi and Yao, Xuan and Turtle, Lance and Dunachie, Susanna and Maini, Mala K. and Ogg, Graham and Knight, Julian C. and Peng, Yanchun and Rowland-Jones, Sarah L. and Dong, Tao and Aanensen, David M. and Abudahab, Khalil and Adams, Helen and Adams, Alexander and Afifi, Safiah and Aggarwal, Dinesh and Ahmad, Shazaad S.Y. and Aigrain, Louise and Alcolea-Medina, Adela and Alikhan, Nabil-Fareed and Allara, Elias and Amato, Roberto and Annett, Tara and Aplin, Stephen and Ariani, Cristina V. and Asad, Hibo and Ash, Amy and Ashfield, Paula and Ashford, Fiona and Atkinson, Laura and Attwood, Stephen W. and Auckland, Cressida and Aydin, Alp and Baker, David J. and Baker, Paul and Balcazar, Carlos E. and Ball, Jonathan and Barrett, Jeffrey C. and Barrow, Magdalena and Barton, Edward and Bashton, Matthew and Bassett, Andrew R. and Batra, Rahul and Baxter, Chris and Bayzid, Nadua and Beaver, Charlotte and Beckett, Angela H. and Beckwith, Shaun M. and Bedford, Luke and Beer, Robert and Beggs, Andrew and Bellis, Katherine L. and Berry, Louise and Bertolusso, Beatrice and Best, Angus and Betteridge, Emma and Bibby, David and Bicknell, Kelly and Binns, Debbie and Birchley, Alec and Bird, Paul W. and Bishop, Chloe and Blacow, Rachel and Blakey, Victoria and Blane, Beth and Bolt, Frances and Bonfield, James and Bonner, Stephen and Bonsall, David and Boswell, Tim and Bosworth, Andrew and Bourgeois, Yann and Boyd, Olivia and Bradley, Declan T. and Breen, Cassie and Bresner, Catherine and Breuer, Judith and Bridgett, Stephen and Bronner, Iraad F. and Brooks, Ellena and Broos, Alice and Brown, Julianne R. and Bucca, Giselda and Buchan, Sarah L. and Buck, David and Bull, Matthew and Burns, Phillipa J. and Burton-Fanning, Shirelle and Byaruhanga, Timothy and Byott, Matthew and Campbell, Sharon and Carabelli, Alessandro M. and Cargill, James S. and Carlile, Matthew and Carvalho, Silvia F. and Casey, Anna and Castigador, Anibolina and Catalan, Jana and Chalker, Vicki and Chaloner, Nicola J. and Chand, Meera and Chappell, Joseph G. and Charalampous, Themoula and Chatterton, Wendy and Chaudhry, Yasmin and Churcher, Carol M. and Clark, Gemma and Clarke, Phillip and Cogger, Benjamin J. and Cole, Kevin and Collins, Jennifer and Colquhoun, Rachel and Connor, Thomas R. and Cook, Kate F. and Coombes, Jason and Corden, Sally and Cormie, Claire and Cortes, Nicholas and Cotic, Marius and Cotton, Seb and Cottrell, Simon and Coupland, Lindsay and Cox, MacGregor and Cox, Alison and Craine, Noel and Crawford, Liam and Cross, Aidan and Crown, Matthew R. and Crudgington, Dorian and Cumley, Nicola and Curran, Tanya and Curran, Martin D. and da Silva Filipe, Ana and Dabrera, Gavin and Darby, Alistair C. and Davidson, Rose K. and Davies, Alisha and Davies, Robert M. and Davis, Thomas and de Angelis, Daniela and De Lacy, Elen and de Oliveira Martins, Leonardo and Debebe, Johnny and Denton-Smith, Rebecca and Dervisevic, Samir and Dewar, Rebecca and Dey, Jayasree and Dias, Joana and Dobie, Donald and Dorman, Matthew J. and Downing, Fatima and Driscoll, Megan and du Plessis, Louis and Duckworth, Nichola and Durham, Jillian and Eastick, Kirstine and Easton, Lisa J. and Eccles, Richard and Edgeworth, Jonathan and Edwards, Sue and El Bouzidi, Kate and Eldirdiri, Sahar and Ellaby, Nicholas and Elliott, Scott and Eltringham, Gary and Ensell, Leah and Erkiert, Michelle J. and Zamudio, Marina Escalera and Essex, Sarah and Evans, Johnathan M. and Evans, Cariad and Everson, William and Fairley, Derek J. and Fallon, Karlie and Fanaie, Arezou and Farr, Ben W. and Fearn, Christopher and Feltwell, Theresa and Ferguson, Lynne and Fina, Laia and Flaviani, Flavia and Fleming, Vicki M. and Forrest, Sally and Foster-Nyarko, Ebenezer and Foulkes, Benjamin H. and Foulser, Luke and Fragakis, Mireille and Frampton, Dan and Francois, Sarah and Fraser, Christophe and Freeman, Timothy M. and Fryer, Helen and Fuchs, Marc and Fuller, William and Gajee, Kavitha and Galai, Katerina and Gallagher, Abbie and Gallagher, Eileen and Gallagher, Michael D. and Gallis, Marta and Gaskin, Amy and Gatica-Wilcox, Bree and Geidelberg, Lily and Gemmell, Matthew and Georgana, Iliana and George, Ryan P. and Gifford, Laura and Gilbert, Lauren and Girgis, Sophia T. and Glaysher, Sharon and Goldstein, Emily J. and Golubchik, Tanya and Gomes, Andrea N. and Gonçalves, Sónia and Goodfellow, Ian G. and Goodwin, Scott and Goudarzi, Salman and Gourtovaia, Marina and Graham, Clive and Graham, Lee and Grant, Paul R. and Green, Luke R. and Green, Angie and Greenaway, Jane and Gregory, Richard and Guest, Martyn and Gunson, Rory N. and Gupta, Ravi K. and Gutierrez, Bernardo and Haldenby, Sam T. and Hamilton, William L. and Hansford, Samantha E. and Haque, Tanzina and Harris, Kathryn A. and Harrison, Ian and Harrison, Ewan M. and Hart, Jennifer and Hartley, John A. and Harvey, William T. and Harvey, Matthew and Hassan-Ibrahim, Mohammed O. and Heaney, Judith and Helmer, Thomas and Henderson, John H. and Hesketh, Andrew R. and Hey, Jessica and Heyburn, David and Higginson, Ellen E. and Hill, Verity and Hill, Jack D. and Hilson, Rachel A. and Hilvers, Ember and Holden, Matthew T.G. and Hollis, Amy and Holmes, Christopher W. and Holmes, Nadine and Holmes, Alison H. and Hopes, Richard and Hornsby, Hailey R. and Hosmillo, Myra and Houlihan, Catherine and Howson-Wells, Hannah C. and Hubb, Jonathan and Huckson, Hannah and Hughes, Warwick and Hughes, Joseph and Hughes, Margaret and Hutchings, Stephanie and Idle, Giles and Illingworth, Chris J. and Impey, Robert and Irish-Tavares, Dianne and Iturriza-Gomara, Miren and Izuagbe, Rhys and Jackson, Chris and Jackson, Ben and Jackson, Leigh M. and Jackson, Kathryn A. and Jackson, David K. and Jahun, Aminu S. and James, Victoria and James, Keith and Jeanes, Christopher and Jeffries, Aaron R. and Jeremiah, Sarah and Jermy, Andrew and John, Michaela and Johnson, Rob and Johnson, Kate and Johnston, Ian and Jones, Owen and Jones, Sophie and Jones, Hannah and Jones, Christopher R. and Jones, Neil and Joseph, Amelia and Judges, Sarah and Kay, Gemma L. and Kay, Sally and Keatley, Jon-Paul and Keeley, Alexander J. and Kenyon, Anita and Kermack, Leanne M. and Khakh, Manjinder and Kidd, Stephen P. and Kimuli, Maimuna and Kirk, Stuart and Kitchen, Christine and Kitchman, Katie and Knight, Bridget A. and Koshy, Cherian and Kraemer, Moritz U.G. and Kumziene-Summerhayes, Sara and Kwiatkowski, Dominic and Lackenby, Angie and Laing, Kenneth G. and Lampejo, Temi and Langford, Cordelia F. and Lavin, Deborah and Lawton, Andrew I. and Lee, Jack and Lee, David and Lensing, Stefanie V. and Leonard, Steven and Levett, Lisa J. and Le-Viet, Thanh and Lewis, Jonathan and Lewis, Kevin and Liddle, Jennifier and Liggett, Steven and Lillie, Patrick J. and Lister, Michelle M. and Livett, Rich and Lo, Stephanie and Loman, Nicholas J. and Loose, Matthew W. and Louka, Stavroula F. and Loveson, Katie F. and Lowdon, Sarah and Lowe, Hannah and Lowe, Helen L. and Lucaci, Anita O. and Ludden, Catherine and Lynch, Jessica and Lyons, Ronan A. and Lythgoe, Katrina and Machin, Nicholas W. and MacIntyre-Cockett, George and Mack, Andrew and Macklin, Ben and Maclean, Alasdair and Macnaughton, Emily and Madona, Pinglawathee and Maes, Mailis and Maftei, Laurentiu and Mahanama, Adhyana I.K. and Mahungu, Tabitha W. and Mair, Daniel and Maksimovic, Joshua and Malone, Cassandra S. and Maloney, Daniel and Manesis, Nikos and Manley, Robin and Mantzouratou, Anna and Marchbank, Angela and Mariappan, Arun and Martincorena, Inigo and Martinez Nunez, Rocio T. and Mather, Alison E. and Maxwell, Patrick and Mayhew, Megan and Mbisa, Tamyo and McCann, Clare M. and McCarthy, Shane A. and McCluggage, Kathryn and McClure, Patrick C. and McCrone, J.T. and McHugh, Martin P. and McKenna, James P. and McKerr, Caoimhe and McManus, Georgina M. and McMurray, Claire L. and McMurray, Claire and McNally, Alan and Meadows, Lizzie and Medd, Nathan and Megram, Oliver and Menegazzo, Mirko and Merrick, Ian and Michell, Stephen L. and Michelsen, Michelle L. and Mirfenderesky, Mariyam and Mirza, Jeremy and Miskelly, Julia and Moles-Garcia, Emma and Moll, Robin J. and Molnar, Zoltan and Monahan, Irene M. and Mondani, Matteo and Mookerjee, Siddharth and Moore, Christopher and Moore, Jonathan and Moore, Nathan and Moore, Catherine and Morcrette, Helen and Morgan, Sian and Morgan, Mari and Mori, Matilde and Morriss, Arthur and Moses, Samuel and Mower, Craig and Muir, Peter and Mukaddas, Afrida and Munemo, Florence and Munn, Robert and Murray, Abigail and Murray, Leanne J. and Murray, Darren R. and Mutingwende, Manasa and Myers, Richard and Nastouli, Eleni and Nebbia, Gaia and Nelson, Andrew and Nelson, Charlotte and Nicholls, Sam and Nichols, Jenna and Nicodemi, Roberto and Nomikou, Kyriaki and O’Grady, Justin and O'Brien, Sarah and Odedra, Mina and Ohemeng-Kumi, Natasha and Oliver, Karen and Orton, Richard J. and Osman, Husam and {xeine O'Toole} and Pacchiarini, Nicole and Padgett, Debra and Page, Andrew J. and Park, Emily J. and Park, Naomi R. and Parmar, Surendra and Partridge, David G. and Pascall, David and Patel, Amita and Patel, Bindi and Paterson, Steve and Payne, Brendan A.I. and Peacock, Sharon J. and Pearson, Clare and Pelosi, Emanuela and Percival, Benita and Perkins, Jon and Perry, Malorie and Pinckert, Malte L. and Platt, Steven and Podplomyk, Olga and Pohare, Manoj and Pond, Marcus and Pope, Cassie F. and Poplawski, Radoslaw and Powell, Jessica and Poyner, Jennifer and Prestwood, Liam and Price, Anna and Price, James R. and Prieto, Jacqui A. and Pritchard, David T. and Prosolek, Sophie J. and Pugh, Georgia and Pusok, Monika and Pybus, Oliver G. and Pymont, Hannah M. and Quail, Michael A. and Quick, Joshua and Radulescu, Clara and Raghwani, Jayna and Ragonnet-Cronin, Manon and Rainbow, Lucille and Rajan, Diana and Rajatileka, Shavanthi and Ramadan, Newara A. and Rambaut, Andrew and Ramble, John and Randell, Paul A. and Randell, Paul and Ratcliffe, Liz and Raviprakash, Veena and Raza, Mohammad and Redshaw, Nicholas M. and Rey, Sara and Reynolds, Nicola and Richter, Alex and Robertson, David L. and Robinson, Esther and Robson, Samuel C. and Rogan, Fiona and Rooke, Stefan and Rowe, Will and Roy, Sunando and Rudder, Steven and Ruis, Chris and Rushton, Steven and Ryan, Felicity and Saeed, Kordo and Samaraweera, Buddhini and Sambles, Christine M. and Sanderson, Roy and Sanderson, Theo and Sang, Fei and Sass, Thea and Scher, Emily and Scott, Garren and Scott, Carol and Sehmi, Jasveen and Shaaban, Sharif and Shah, Divya and Shaw, Jessica and Shelest, Ekaterina and Shepherd, James G. and Sheridan, Liz A. and Sheriff, Nicola and Shirley, Lesley and Sillitoe, John and Silviera, Siona and Simpson, David A. and Singh, Aditi and Singleton, Dawn and Skvortsov, Timofey and Sloan, Tim J. and Sluga, Graciela and Smith, Ken and Smith, Kim S. and Smith, Perminder and Smith, Darren L. and Smith, Louise and Smith, Colin P. and Smith, Nikki and Smollett, Katherine L. and Snell, Luke B. and Somassa, Thomas and Southgate, Joel and Spellman, Karla and Spencer Chapman, Michael H. and Spurgin, Lewis G. and Spyer, Moira J. and Stanley, Rachael and Stanley, William and Stanton, Thomas D. and Starinskij, Igor and Stockton, Joanne and Stonehouse, Susanne and Storey, Nathaniel and Studholme, David J. and Sudhanva, Malur and Swindells, Emma and Taha, Yusri and Tan, Ngee Keong and Tang, Julian W. and Tang, Miao and Taylor, Ben E.W. and Taylor, Joshua F. and Taylor, Sarah and Temperton, Ben and Templeton, Kate E. and Thomas, Claire and Thomson, Laura and Thomson, Emma C. and Thornton, Alicia and Thurston, Scott A.J. and Todd, John A. and Tomb, Rachael and Tong, Lily and Tonkin-Hill, Gerry and Torok, M. Estee and Tovar-Corona, Jaime M. and Trebes, Amy and Trotter, Alexander J. and Tsatsani, Ioulia and Turnbull, Robyn and Twohig, Katherine A. and Umpleby, Helen and Underwood, Anthony P. and Vamos, Edith E. and Vasylyeva, Tetyana I. and Vattipally, Sreenu and Vernet, Gabrielle and Vipond, Barry B. and Volz, Erik M. and Walsh, Sarah and Wang, Dennis and Warne, Ben and Warwick-Dugdale, Joanna and Wastnedge, Elizabeth and Watkins, Joanne and Watson, Louisa K. and Waugh, Sheila and Webster, Hermione J. and Weldon, Danni and Westwick, Elaine and Whalley, Thomas and Wheeler, Helen and Whitehead, Mark and Whiteley, Max and Whitwham, Andrew and Wierzbicki, Claudia and Willford, Nicholas J. and Williams, Lesley-Anne and Williams, Rebecca and Williams, Cheryl and Williams, Chris and Williams, Charlotte A. and Williams, Rachel J. and Williams, Thomas and Williams, Catryn and Williamson, Kathleen A. and Wilson-Davies, Eleri and Witele, Eric and Withell, Karen T. and Witney, Adam A. and Wolverson, Paige and Wong, Nick and Workman, Trudy and Wright, Victoria and Wright, Derek W. and Wyatt, Tim and Wyllie, Sarah and Xu-McCrae, Li and Yavus, Mehmet and Yaze, Geraldine and Yeats, Corin A. and Yebra, Gonzalo and Yew, Wen C. and Young, Gregory R. and Young, Jamie and Zarebski, Alex E. and Zhang, Peijun and Baillie, J. Kenneth and Semple, Malcolm G. and Openshaw, Peter J.M. and Carson, Gail and Alex, Beatrice and Andrikopoulos, Petros and Bach, Benjamin and Barclay, Wendy S. and Bogaert, Debby and Chand, Meera and Chechi, Kanta and Cooke, Graham S. and da Silva Filipe, Ana and Docherty, Annemarie B. and Correia, Gonçalo dos Santos and Dumas, Marc-Emmanuel and Dunning, Jake and Fletcher, Tom and Green, Christopher A. and Greenhalf, William and Griffin, Julian L. and Gupta, Rishi K. and Harrison, Ewen M. and Hiscox, Julian A. and Wai Ho, Antonia Ying and Horby, Peter W. and Ijaz, Samreen and Khoo, Saye and Klenerman, Paul and Law, Andrew and Lewis, Matthew R. and Liggi, Sonia and Lim, Wei Shen and Maslen, Lynn and Mentzer, Alexander J. and Merson, Laura and Meynert, Alison M. and Noursadeghi, Mahdad and Olanipekun, Michael and Osagie, Anthonia and Palmarini, Massimo and Palmieri, Carlo and Paxton, William A. and Pollakis, Georgios and Price, Nicholas and Rambaut, Andrew and Robertson, David L. and Russell, Clark D. and Sancho-Shimizu, Vanessa and Sands, Caroline J. and Scott, Janet T. and Sigfrid, Louise and Solomon, Tom and Sriskandan, Shiranee and Stuart, David and Summers, Charlotte and Swann, Olivia V. and Takats, Zoltan and Takis, Panteleimon and Tedder, Richard S. and Thompson, A.A. Roger and Thomson, Emma C. and Thwaites, Ryan S. and Zambon, Maria and Hardwick, Hayley and Donohue, Chloe and Griffiths, Fiona and Oosthuyzen, Wilna and Donegan, Cara and Spencer, Rebecca G. and Dalton, Jo and Girvan, Michelle and Saviciute, Egle and Roberts, Stephanie and Harrison, Janet and Marsh, Laura and Connor, Marie and Halpin, Sophie and Jackson, Clare and Gamble, Carrol and Plotkin, Daniel and Lee, James and Leeming, Gary and Law, Andrew and Wham, Murray and Clohisey, Sara and Hendry, Ross and Scott-Brown, James and Shaw, Victoria and McDonald, Sarah E. and Keating, Seán and Ahmed, Katie A. and Armstrong, Jane A. and Ashworth, Milton and Asiimwe, Innocent G. and Bakshi, Siddharth and Barlow, Samantha L. and Booth, Laura and Brennan, Benjamin and Bullock, Katie and Catterall, Benjamin W.A. and Clark, Jordan J. and Clarke, Emily A. and Cole, Sarah and Cooper, Louise and Cox, Helen and Davis, Christopher and Dincarslan, Oslem and Dunn, Chris and Dyer, Philip and Elliott, Angela and Evans, Anthony and Finch, Lorna and Fisher, Lewis W.S. and Foster, Terry and Garcia-Dorival, Isabel and Gunning, Philip and Hartley, Catherine and Jensen, Rebecca L. and Jones, Christopher B. and Jones, Trevor R. and Khandaker, Shadia and King, Katharine and Kiy, Robyn T. and Koukorava, Chrysa and Lake, Annette and Lant, Suzannah and Latawiec, Diane and Lavelle-Langham, Lara and Lefteri, Daniella and Lett, Lauren and Livoti, Lucia A. and Mancini, Maria and McDonald, Sarah and McEvoy, Laurence and McLauchlan, John and Metelmann, Soeren and Miah, Nahida S. and Middleton, Joanna and Mitchell, Joyce and Moore, Shona C. and Murphy, Ellen G. and Penrice-Randal, Rebekah and Pilgrim, Jack and Prince, Tessa and Reynolds, Will and Ridley, P. Matthew and Sales, Debby and Shaw, Victoria E. and Shears, Rebecca K. and Small, Benjamin and Subramaniam, Krishanthi S. and Szemiel, Agnieska and Taggart, Aislynn and Tanianis-Hughes, Jolanta and Thomas, Jordan and Trochu, Erwan and van Tonder, Libby and Wilcock, Eve and Zhang, J. Eunice and Flaherty, Lisa and Maziere, Nicole and Cass, Emily and Carracedo, Alejandra Doce and Carlucci, Nicola and Holmes, Anthony and Massey, Hannah and Murphy, Lee and Wrobel, Nicola and McCafferty, Sarah and Morrice, Kirstie and MacLean, Alan and Adeniji, Kayode and Agranoff, Daniel and Agwuh, Ken and Ail, Dhiraj and Aldera, Erin L. and Alegria, Ana and Allen, Sam and Angus, Brian and Ashish, Abdul and Atkinson, Dougal and Bari, Shahedal and Barlow, Gavin and Barnass, Stella and Barrett, Nicholas and Bassford, Christopher and Basude, Sneha and Baxter, David and Beadsworth, Michael and Bernatoniene, Jolanta and Berridge, John and Berry, Colin and Best, Nicola and Bothma, Pieter and Chadwick, David and Brittain-Long, Robin and Bulteel, Naomi and Burden, Tom and Burtenshaw, Andrew and Caruth, Vikki and Chadwick, David and Chambler, Duncan and Chee, Nigel and Child, Jenny and Chukkambotla, Srikanth and Clark, Tom and Collini, Paul and Cosgrove, Catherine and Cupitt, Jason and Cutino-Moguel, Maria-Teresa and Dark, Paul and Dawson, Chris and Dervisevic, Samir and Donnison, Phil and Douthwaite, Sam and Drummond, Andrew and DuRand, Ingrid and Dushianthan, Ahilanadan and Dyer, Tristan and Evans, Cariad and Eziefula, Chi and Fegan, Chrisopher and Finn, Adam and Fullerton, Duncan and Garg, Sanjeev and Garg, Sanjeev and Garg, Atul and Gkrania-Klotsas, Effrossyni and Godden, Jo and Goldsmith, Arthur and Graham, Clive and Hardy, Elaine and Hartshorn, Stuart and Harvey, Daniel and Havalda, Peter and Hawcutt, Daniel B. and Hobrok, Maria and Hodgson, Luke and Hormis, Anil and Jacobs, Michael and Jain, Susan and Jennings, Paul and Kaliappan, Agilan and Kasipandian, Vidya and Kegg, Stephen and Kelsey, Michael and Kendall, Jason and Kerrison, Caroline and Kerslake, Ian and Koch, Oliver and Koduri, Gouri and Koshy, George and Laha, Shondipon and Laird, Steven and Larkin, Susan and Leiner, Tamas and Lillie, Patrick and Limb, James and Linnett, Vanessa and Little, Jeff and Lyttle, Mark and MacMahon, Michael and MacNaughton, Emily and Mankregod, Ravish and Masson, Huw and Matovu, Elijah and McCullough, Katherine and McEwen, Ruth and Meda, Manjula and Mills, Gary and Minton, Jane and Mirfenderesky, Mariyam and Mohandas, Kavya and Mok, Quen and Moon, James and Moore, Elinoor and Morgan, Patrick and Morris, Craig and Mortimore, Katherine and Moses, Samuel and Mpenge, Mbiye and Mulla, Rohinton and Murphy, Michael and Nagel, Megan and Nagarajan, Thapas and Nelson, Mark and Norris, Lillian and O'Shea, Matthew K. and Otahal, Igor and Ostermann, Marlies and Pais, Mark and Palmieri, Carlo and Panchatsharam, Selva and Papakonstantinou, Danai and Paraiso, Hassan and Patel, Brij and Pattison, Natalie and Pepperell, Justin and Peters, Mark and Phull, Mandeep and Pintus, Stefania and Pooni, Jagtur Singh and Planche, Tim and Post, Frank and Price, David and Prout, Rachel and Rae, Nikolas and Reschreiter, Henrik and Reynolds, Tim and Richardson, Neil and Roberts, Mark and Roberts, Devender and Rose, Alistair and Rousseau, Guy and Ruge, Bobby and Ryan, Brendan and Saluja, Taranprit and Schmid, Matthias L. and Shah, Aarti and Shanmuga, Prad and Sharma, Anil and Shawcross, Anna and Sizer, Jeremy and Shankar-Hari, Manu and Smith, Richard and Snelson, Catherine and Spittle, Nick and Staines, Nikki and Stambach, Tom and Stewart, Richard and Subudhi, Pradeep and Szakmany, Tamas and Tatham, Kate and Thomas, Jo and Thompson, Chris and Thompson, Robert and Tridente, Ascanio and Tupper-Carey, Darell and Twagira, Mary and Vallotton, Nick and Vancheeswaran, Rama and Vincent-Smith, Lisa and Visuvanathan, Shico and Vuylsteke, Alan and Waddy, Sam and Wake, Rachel and Walden, Andrew and Welters, Ingeborg and Whitehouse, Tony and Whittaker, Paul and Whittington, Ashley and Papineni, Padmasayee and Wijesinghe, Meme and Williams, Martin and Wilson, Lawrence and Cole, Sarah and Winchester, Stephen and Wiselka, Martin and Wolverson, Adam and Wootton, Daniel G. and Workman, Andrew and Yates, Bryan and Young, Peter},
	month = nov,
	year = {2021},
	pmid = {34729465},
	pmcid = {PMC8552693},
	note = {7 citations (Crossref) [2022-06-30]},
	pages = {103353},
	file = {Full Text:/usr/users/QIB_fr005/alikhan/Zotero/storage/J75MYN5J/de Silva et al. - 2021 - The impact of viral mutations on recognition by SA.pdf:application/pdf},
}

@article{zhou_enterobase_2020,
	title = {The {EnteroBase} user's guide, with case studies on \textit{{Salmonella}} transmissions, \textit{{Yersinia} pestis} phylogeny, and \textit{{Escherichia}} core genomic diversity},
	volume = {30},
	copyright = {Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International Licence (CC-BY-NC-ND)},
	issn = {1088-9051, 1549-5469},
	url = {http://genome.cshlp.org/lookup/doi/10.1101/gr.251678.119},
	doi = {10.1101/gr.251678.119},
	abstract = {EnteroBase is an integrated software environment that supports the identification of global population structures within several bacterial genera that include pathogens. Here, we provide an overview of how EnteroBase works, what it can do, and its future prospects. EnteroBase has currently assembled more than 300,000 genomes from Illumina short reads from
              Salmonella
              ,
              Escherichia
              ,
              Yersinia
              ,
              Clostridioides
              ,
              Helicobacter
              ,
              Vibrio
              , and
              Moraxella
              and genotyped those assemblies by core genome multilocus sequence typing (cgMLST). Hierarchical clustering of cgMLST sequence types allows mapping a new bacterial strain to predefined population structures at multiple levels of resolution within a few hours after uploading its short reads. Case Study 1 illustrates this process for local transmissions of
              Salmonella enterica
              serovar Agama between neighboring social groups of badgers and humans. EnteroBase also supports single nucleotide polymorphism (SNP) calls from both genomic assemblies and after extraction from metagenomic sequences, as illustrated by Case Study 2 which summarizes the microevolution of
              Yersinia pestis
              over the last 5000 years of pandemic plague. EnteroBase can also provide a global overview of the genomic diversity within an entire genus, as illustrated by Case Study 3, which presents a novel, global overview of the population structure of all of the species, subspecies, and clades within
              Escherichia
              .},
	language = {en},
	number = {1},
	urldate = {2022-05-13},
	journal = {Genome Research},
	author = {Zhou, Zhemin and Alikhan, Nabil-Fareed and Mohamed, Khaled and Fan, Yulei and {the Agama Study Group} and Achtman, Mark},
	month = jan,
	year = {2020},
	pmid = {31809257},
	pmcid = {PMC6961584},
	note = {281 citations (Crossref) [2022-06-30]},
	pages = {138--152},
	file = {Full Text:/usr/users/QIB_fr005/alikhan/Zotero/storage/JJAG66SU/Zhou et al. - 2020 - The EnteroBase user's guide, with case studies on .pdf:application/pdf},
}

@article{sarwar_sars-cov-2_2021,
	title = {{SARS}-{CoV}-2 variants of concern dominate in {Lahore}, {Pakistan} in {April} 2021},
	volume = {7},
	copyright = {Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International Licence (CC-BY-NC-ND)},
	issn = {2057-5858},
	url = {https://www.microbiologyresearch.org/content/journal/mgen/10.1099/mgen.0.000693},
	doi = {10.1099/mgen.0.000693},
	abstract = {The SARS-CoV-2 pandemic continues to expand globally, with case numbers rising in many areas of the world, including the Indian sub-continent. Pakistan has one of the world’s largest populations, of over 200 million people and is experiencing a severe third wave of infections caused by SARS-CoV-2 that began in March 2021. In Pakistan, during the third wave until now only 12 SARS-CoV-2 genomes have been collected and among these nine are from Islamabad. This highlights the need for more genome sequencing to allow surveillance of variants in circulation. In fact, more genomes are available among travellers with a travel history from Pakistan, than from within the country itself. We thus aimed to provide a snapshot assessment of circulating lineages in Lahore and surrounding areas with a combined population of 11.1 million. Within a week of April 2021, 102 samples were sequenced. The samples were randomly collected from two hospitals with a diagnostic PCR cutoff value of less than 25 cycles. Analysis of the lineages shows that the Alpha variant of concern (first identified in the UK) dominates, accounting for 97.9 \% (97/99) of cases, with the Beta variant of concern (first identified in South Africa) accounting for 2.0 \% (2/99) of cases. No other lineages were observed. In depth analysis of the Alpha lineages indicated multiple separate introductions and subsequent establishment within the region. Eight samples were identical to genomes observed in Europe (seven UK, one Switzerland), indicating recent transmission. Genomes of other samples show evidence that these have evolved, indicating sustained transmission over a period of time either within Pakistan or other countries with low-density genome sequencing. Vaccines remain effective against Alpha, however, the low level of Beta against which some vaccines are less effective demonstrates the requirement for continued prospective genomic surveillance.},
	language = {en},
	number = {11},
	urldate = {2022-05-13},
	journal = {Microbial Genomics},
	author = {Sarwar, Muhammad Bilal and Yasir, Muhammad and Alikhan, Nabil-Fareed and Afzal, Nadeem and de Oliveira Martins, Leonardo and Le Viet, Thanh and Trotter, Alexander J. and Prosolek, Sophie J. and Kay, Gemma L. and Foster-Nyarko, Ebenezer and Rudder, Steven and Baker, David J. and Muntaha, Sidra Tul and Roman, Muhammad and Webber, Mark A. and Shafiq, Almina and Shabbir, Bilquis and Akram, Javed and Page, Andrew J. and Jahan, Shah},
	month = nov,
	year = {2021},
	pmid = {34846280},
	pmcid = {PMC8743565},
	note = {0 citations (Crossref) [2022-06-30]},
	file = {Full Text:/usr/users/QIB_fr005/alikhan/Zotero/storage/7RSGHPNA/Sarwar et al. - 2021 - SARS-CoV-2 variants of concern dominate in Lahore,.pdf:application/pdf},
}

@article{meng_recurrent_2021,
	title = {Recurrent emergence of {SARS}-{CoV}-2 spike deletion {H69}/{V70} and its role in the {Alpha} variant {B}.1.1.7},
	volume = {35},
	copyright = {Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International Licence (CC-BY-NC-ND)},
	issn = {22111247},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S221112472100663X},
	doi = {10.1016/j.celrep.2021.109292},
	abstract = {We report severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike ΔH69/V70 in multiple independent lineages, often occurring after acquisition of receptor binding motif replacements such as N439K and Y453F, known to increase binding affinity to the ACE2 receptor and confer antibody escape. In vitro, we show that, although ΔH69/V70 itself is not an antibody evasion mechanism, it increases infectivity associated with enhanced incorporation of cleaved spike into virions. ΔH69/V70 is able to partially rescue infectivity of spike proteins that have acquired N439K and Y453F escape mutations by increased spike incorporation. In addition, replacement of the H69 and V70 residues in the Alpha variant B.1.1.7 spike (where ΔH69/V70 occurs naturally) impairs spike incorporation and entry efficiency of the B.1.1.7 spike pseudotyped virus. Alpha variant B.1.1.7 spike mediates faster kinetics of cell-cell fusion than wild-type Wuhan-1 D614G, dependent on ΔH69/V70. Therefore, as ΔH69/V70 compensates for immune escape mutations that impair infectivity, continued surveillance for deletions with functional effects is warranted.},
	language = {en},
	number = {13},
	urldate = {2022-05-13},
	journal = {Cell Reports},
	author = {Meng, Bo and Kemp, Steven A. and Papa, Guido and Datir, Rawlings and Ferreira, Isabella A.T.M. and Marelli, Sara and Harvey, William T. and Lytras, Spyros and Mohamed, Ahmed and Gallo, Giulia and Thakur, Nazia and Collier, Dami A. and Mlcochova, Petra and Duncan, Lidia M. and Carabelli, Alessandro M. and Kenyon, Julia C. and Lever, Andrew M. and De Marco, Anna and Saliba, Christian and Culap, Katja and Cameroni, Elisabetta and Matheson, Nicholas J. and Piccoli, Luca and Corti, Davide and James, Leo C. and Robertson, David L. and Bailey, Dalan and Gupta, Ravindra K. and Robson, Samuel C. and Loman, Nicholas J. and Connor, Thomas R. and Golubchik, Tanya and Martinez Nunez, Rocio T. and Ludden, Catherine and Corden, Sally and Johnston, Ian and Bonsall, David and Smith, Colin P. and Awan, Ali R. and Bucca, Giselda and Torok, M. Estee and Saeed, Kordo and Prieto, Jacqui A. and Jackson, David K. and Hamilton, William L. and Snell, Luke B. and Moore, Catherine and Harrison, Ewan M. and Goncalves, Sonia and Fairley, Derek J. and Loose, Matthew W. and Watkins, Joanne and Livett, Rich and Moses, Samuel and Amato, Roberto and Nicholls, Sam and Bull, Matthew and Smith, Darren L. and Barrett, Jeff and Aanensen, David M. and Curran, Martin D. and Parmar, Surendra and Aggarwal, Dinesh and Shepherd, James G. and Parker, Matthew D. and Glaysher, Sharon and Bashton, Matthew and Underwood, Anthony P. and Pacchiarini, Nicole and Loveson, Katie F. and Templeton, Kate E. and Langford, Cordelia F. and Sillitoe, John and de Silva, Thushan I. and Wang, Dennis and Kwiatkowski, Dominic and Rambaut, Andrew and O’Grady, Justin and Cottrell, Simon and Holden, Matthew T.G. and Thomson, Emma C. and Osman, Husam and Andersson, Monique and Chauhan, Anoop J. and Hassan-Ibrahim, Mohammed O. and Lawniczak, Mara and Alderton, Alex and Chand, Meera and Constantinidou, Chrystala and Unnikrishnan, Meera and Darby, Alistair C. and Hiscox, Julian A. and Paterson, Steve and Martincorena, Inigo and Volz, Erik M. and Page, Andrew J. and Pybus, Oliver G. and Bassett, Andrew R. and Ariani, Cristina V. and Chapman, Michael H. Spencer and Li, Kathy K. and Shah, Rajiv N. and Jesudason, Natasha G. and Taha, Yusri and McHugh, Martin P. and Dewar, Rebecca and Jahun, Aminu S. and McMurray, Claire and Pandey, Sarojini and McKenna, James P. and Nelson, Andrew and Young, Gregory R. and McCann, Clare M. and Elliott, Scott and Lowe, Hannah and Temperton, Ben and Roy, Sunando and Price, Anna and Rey, Sara and Wyles, Matthew and Rooke, Stefan and Shaaban, Sharif and de Cesare, Mariateresa and Letchford, Laura and Silveira, Siona and Pelosi, Emanuela and Wilson-Davies, Eleri and Hosmillo, Myra and O’Toole, Áine and Hesketh, Andrew R. and Stark, Richard and du Plessis, Louis and Ruis, Chris and Adams, Helen and Bourgeois, Yann and Michell, Stephen L. and Gramatopoulos, Dimitris and Edgeworth, Jonathan and Breuer, Judith and Todd, John A. and Fraser, Christophe and Buck, David and John, Michaela and Kay, Gemma L. and Palmer, Steve and Peacock, Sharon J. and Heyburn, David and Weldon, Danni and Robinson, Esther and McNally, Alan and Muir, Peter and Vipond, Ian B. and Boyes, John and Sivaprakasam, Venkat and Salluja, Tranprit and Dervisevic, Samir and Meader, Emma J. and Park, Naomi R. and Oliver, Karen and Jeffries, Aaron R. and Ott, Sascha and da Silva Filipe, Ana and Simpson, David A. and Williams, Chris and Masoli, Jane A.H. and Knight, Bridget A. and Jones, Christopher R. and Koshy, Cherian and Ash, Amy and Casey, Anna and Bosworth, Andrew and Ratcliffe, Liz and Xu-McCrae, Li and Pymont, Hannah M. and Hutchings, Stephanie and Berry, Lisa and Jones, Katie and Halstead, Fenella and Davis, Thomas and Holmes, Christopher and Iturriza-Gomara, Miren and Lucaci, Anita O. and Randell, Paul Anthony and Cox, Alison and Madona, Pinglawathee and Harris, Kathryn Ann and Brown, Julianne Rose and Mahungu, Tabitha W. and Irish-Tavares, Dianne and Haque, Tanzina and Hart, Jennifer and Witele, Eric and Fenton, Melisa Louise and Liggett, Steven and Graham, Clive and Swindells, Emma and Collins, Jennifer and Eltringham, Gary and Campbell, Sharon and McClure, Patrick C. and Clark, Gemma and Sloan, Tim J. and Jones, Carl and Lynch, Jessica and Warne, Ben and Leonard, Steven and Durham, Jillian and Williams, Thomas and Haldenby, Sam T. and Storey, Nathaniel and Alikhan, Nabil-Fareed and Holmes, Nadine and Moore, Christopher and Carlile, Matthew and Perry, Malorie and Craine, Noel and Lyons, Ronan A. and Beckett, Angela H. and Goudarzi, Salman and Fearn, Christopher and Cook, Kate and Dent, Hannah and Paul, Hannah and Davies, Robert and Blane, Beth and Girgis, Sophia T. and Beale, Mathew A. and Bellis, Katherine L. and Dorman, Matthew J. and Drury, Eleanor and Kane, Leanne and Kay, Sally and McGuigan, Samantha and Nelson, Rachel and Prestwood, Liam and Rajatileka, Shavanthi and Batra, Rahul and Williams, Rachel J. and Kristiansen, Mark and Green, Angie and Justice, Anita and Mahanama, Adhyana I.K. and Samaraweera, Buddhini and Hadjirin, Nazreen F. and Quick, Joshua and Poplawski, Radoslaw and Kermack, Leanne M. and Reynolds, Nicola and Hall, Grant and Chaudhry, Yasmin and Pinckert, Malte L. and Georgana, Iliana and Moll, Robin J. and Thornton, Alicia and Myers, Richard and Stockton, Joanne and Williams, Charlotte A. and Yew, Wen C. and Trotter, Alexander J. and Trebes, Amy and MacIntyre-Cockett, George and Birchley, Alec and Adams, Alexander and Plimmer, Amy and Gatica-Wilcox, Bree and McKerr, Caoimhe and Hilvers, Ember and Jones, Hannah and Asad, Hibo and Coombes, Jason and Evans, Johnathan M. and Fina, Laia and Gilbert, Lauren and Graham, Lee and Cronin, Michelle and Kumziene-Summerhayes, Sara and Taylor, Sarah and Jones, Sophie and Groves, Danielle C. and Zhang, Peijun and Gallis, Marta and Louka, Stavroula F. and Starinskij, Igor and Jackson, Chris and Gourtovaia, Marina and Tonkin-Hill, Gerry and Lewis, Kevin and Tovar-Corona, Jaime M. and James, Keith and Baxter, Laura and Alam, Mohammad T. and Orton, Richard J. and Hughes, Joseph and Vattipally, Sreenu and Ragonnet-Cronin, Manon and Nascimento, Fabricia F. and Jorgensen, David and Boyd, Olivia and Geidelberg, Lily and Zarebski, Alex E. and Raghwani, Jayna and Kraemer, Moritz U.G. and Southgate, Joel and Lindsey, Benjamin B. and Freeman, Timothy M. and Keatley, Jon-Paul and Singer, Joshua B. and de Oliveira Martins, Leonardo and Yeats, Corin A. and Abudahab, Khalil and Taylor, Ben E.W. and Menegazzo, Mirko and Danesh, John and Hogsden, Wendy and Eldirdiri, Sahar and Kenyon, Anita and Mason, Jenifer and Robinson, Trevor I. and Holmes, Alison and Price, James and Hartley, John A. and Curran, Tanya and Mather, Alison E. and Shankar, Giri and Jones, Rachel and Howe, Robin and Morgan, Sian and Wastenge, Elizabeth and Chapman, Michael R. and Mookerjee, Siddharth and Stanley, Rachael and Smith, Wendy and Peto, Timothy and Eyre, David and Crook, Derrick and Vernet, Gabrielle and Kitchen, Christine and Gulliver, Huw and Merrick, Ian and Guest, Martyn and Munn, Robert and Bradley, Declan T. and Wyatt, Tim and Beaver, Charlotte and Foulser, Luke and Palmer, Sophie and Churcher, Carol M. and Brooks, Ellena and Smith, Kim S. and Galai, Katerina and McManus, Georgina M. and Bolt, Frances and Coll, Francesc and Meadows, Lizzie and Attwood, Stephen W. and Davies, Alisha and De Lacy, Elen and Downing, Fatima and Edwards, Sue and Scarlett, Garry P. and Jeremiah, Sarah and Smith, Nikki and Leek, Danielle and Sridhar, Sushmita and Forrest, Sally and Cormie, Claire and Gill, Harmeet K. and Dias, Joana and Higginson, Ellen E. and Maes, Mailis and Young, Jamie and Wantoch, Michelle and Jamrozy, Dorota and Lo, Stephanie and Patel, Minal and Hill, Verity and Bewshea, Claire M. and Ellard, Sian and Auckland, Cressida and Harrison, Ian and Bishop, Chloe and Chalker, Vicki and Richter, Alex and Beggs, Andrew and Best, Angus and Percival, Benita and Mirza, Jeremy and Megram, Oliver and Mayhew, Megan and Crawford, Liam and Ashcroft, Fiona and Moles-Garcia, Emma and Cumley, Nicola and Hopes, Richard and Asamaphan, Patawee and Niebel, Marc O. and Gunson, Rory N. and Bradley, Amanda and Maclean, Alasdair and Mollett, Guy and Blacow, Rachel and Bird, Paul and Helmer, Thomas and Fallon, Karlie and Tang, Julian and Hale, Antony D. and Macfarlane-Smith, Louissa R. and Harper, Katherine L. and Carden, Holli and Machin, Nicholas W. and Jackson, Kathryn A. and Ahmad, Shazaad S.Y. and George, Ryan P. and Turtle, Lance and O’Toole, Elaine and Watts, Joanne and Breen, Cassie and Cowell, Angela and Alcolea-Medina, Adela and Charalampous, Themoula and Patel, Amita and Levett, Lisa J. and Heaney, Judith and Rowan, Aileen and Taylor, Graham P. and Shah, Divya and Atkinson, Laura and Lee, Jack C.D. and Westhorpe, Adam P. and Jannoo, Riaz and Lowe, Helen L. and Karamani, Angeliki and Ensell, Leah and Chatterton, Wendy and Pusok, Monika and Dadrah, Ashok and Symmonds, Amanda and Sluga, Graciela and Molnar, Zoltan and Baker, Paul and Bonner, Stephen and Essex, Sarah and Barton, Edward and Padgett, Debra and Scott, Garren and Greenaway, Jane and Payne, Brendan A.I. and Burton-Fanning, Shirelle and Waugh, Sheila and Raviprakash, Veena and Sheriff, Nicola and Blakey, Victoria and Williams, Lesley-Anne and Moore, Jonathan and Stonehouse, Susanne and Smith, Louise and Davidson, Rose K. and Bedford, Luke and Coupland, Lindsay and Wright, Victoria and Chappell, Joseph G. and Tsoleridis, Theocharis and Ball, Jonathan and Khakh, Manjinder and Fleming, Vicki M. and Lister, Michelle M. and Howson-Wells, Hannah C. and Berry, Louise and Boswell, Tim and Joseph, Amelia and Willingham, Iona and Duckworth, Nichola and Walsh, Sarah and Wise, Emma and Moore, Nathan and Mori, Matilde and Cortes, Nick and Kidd, Stephen and Williams, Rebecca and Gifford, Laura and Bicknell, Kelly and Wyllie, Sarah and Lloyd, Allyson and Impey, Robert and Malone, Cassandra S. and Cogger, Benjamin J. and Levene, Nick and Monaghan, Lynn and Keeley, Alexander J. and Partridge, David G. and Raza, Mohammad and Evans, Cariad and Johnson, Kate and Betteridge, Emma and Farr, Ben W. and Goodwin, Scott and Quail, Michael A. and Scott, Carol and Shirley, Lesley and Thurston, Scott A.J. and Rajan, Diana and Bronner, Iraad F. and Aigrain, Louise and Redshaw, Nicholas M. and Lensing, Stefanie V. and McCarthy, Shane and Makunin, Alex and Balcazar, Carlos E. and Gallagher, Michael D. and Williamson, Kathleen A. and Stanton, Thomas D. and Michelsen, Michelle L. and Warwick-Dugdale, Joanna and Manley, Robin and Farbos, Audrey and Harrison, James W. and Sambles, Christine M. and Studholme, David J. and Lackenby, Angie and Mbisa, Tamyo and Platt, Steven and Miah, Shahjahan and Bibby, David and Manso, Carmen and Hubb, Jonathan and Dabrera, Gavin and Ramsay, Mary and Bradshaw, Daniel and Schaefer, Ulf and Groves, Natalie and Gallagher, Eileen and Lee, David and Williams, David and Ellaby, Nicholas and Hartman, Hassan and Manesis, Nikos and Patel, Vineet and Ledesma, Juan and Twohig, Katherine A. and Allara, Elias and Pearson, Clare and Cheng, Jeffrey K.J. and Bridgewater, Hannah E. and Frost, Lucy R. and Taylor-Joyce, Grace and Brown, Paul E. and Tong, Lily and Broos, Alice and Mair, Daniel and Nichols, Jenna and Carmichael, Stephen N. and Smollett, Katherine L. and Nomikou, Kyriaki and Aranday-Cortes, Elihu and Johnson, Natasha and Nickbakhsh, Seema and Vamos, Edith E. and Hughes, Margaret and Rainbow, Lucille and Eccles, Richard and Nelson, Charlotte and Whitehead, Mark and Gregory, Richard and Gemmell, Matthew and Wierzbicki, Claudia and Webster, Hermione J. and Fisher, Chloe L. and Signell, Adrian W. and Betancor, Gilberto and Wilson, Harry D. and Nebbia, Gaia and Flaviani, Flavia and Cerda, Alberto C. and Merrill, Tammy V. and Wilson, Rebekah E. and Cotic, Marius and Bayzid, Nadua and Thompson, Thomas and Acheson, Erwan and Rushton, Steven and O’Brien, Sarah and Baker, David J. and Rudder, Steven and Aydin, Alp and Sang, Fei and Debebe, Johnny and Francois, Sarah and Vasylyeva, Tetyana I. and Zamudio, Marina Escalera and Gutierrez, Bernardo and Marchbank, Angela and Maksimovic, Joshua and Spellman, Karla and McCluggage, Kathryn and Morgan, Mari and Beer, Robert and Afifi, Safiah and Workman, Trudy and Fuller, William and Bresner, Catherine and Angyal, Adrienn and Green, Luke R. and Parsons, Paul J. and Tucker, Rachel M. and Brown, Rebecca and Whiteley, Max and Bonfield, James and Puethe, Christoph and Whitwham, Andrew and Liddle, Jennifier and Rowe, Will and Siveroni, Igor and Le-Viet, Thanh and Gaskin, Amy and Johnson, Rob and Abnizova, Irina and Ali, Mozam and Allen, Laura and Anderson, Ralph and Ariani, Cristina and Austin-Guest, Siobhan and Bala, Sendu and Barrett, Jeffrey and Bassett, Andrew and Battleday, Kristina and Beal, James and Beale, Mathew and Bellany, Sam and Bellerby, Tristram and Bellis, Katie and Berger, Duncan and Berriman, Matt and Bevan, Paul and Binley, Simon and Bishop, Jason and Blackburn, Kirsty and Boughton, Nick and Bowker, Sam and Brendler-Spaeth, Timothy and Bronner, Iraad and Brooklyn, Tanya and Buddenborg, Sarah Kay and Bush, Robert and Caetano, Catarina and Cagan, Alex and Carter, Nicola and Cartwright, Joanna and Monteiro, Tiago Carvalho and Chapman, Liz and Chillingworth, Tracey-Jane and Clapham, Peter and Clark, Richard and Clarke, Adrian and Clarke, Catriona and Cole, Daryl and Cook, Elizabeth and Coppola, Maria and Cornell, Linda and Cornwell, Clare and Corton, Craig and Crackett, Abby and Cranage, Alison and Craven, Harriet and Craw, Sarah and Crawford, Mark and Cutts, Tim and Dabrowska, Monika and Davies, Matt and Dawson, Joseph and Day, Callum and Densem, Aiden and Dibling, Thomas and Dockree, Cat and Dodd, David and Dogga, Sunil and Dorman, Matthew and Dougan, Gordon and Dougherty, Martin and Dove, Alexander and Drummond, Lucy and Dudek, Monika and Durrant, Laura and Easthope, Elizabeth and Eckert, Sabine and Ellis, Pete and Farr, Ben and Fenton, Michael and Ferrero, Marcella and Flack, Neil and Fordham, Howerd and Forsythe, Grace and Francis, Matt and Fraser, Audrey and Freeman, Adam and Galvin, Anastasia and Garcia-Casado, Maria and Gedny, Alex and Girgis, Sophia and Glover, James and Gould, Oliver and Gray, Andy and Gray, Emma and Griffiths, Coline and Gu, Yong and Guerin, Florence and Hamilton, Will and Hanks, Hannah and Harrison, Ewan and Harrott, Alexandria and Harry, Edward and Harvison, Julia and Heath, Paul and Hernandez-Koutoucheva, Anastasia and Hobbs, Rhiannon and Holland, Dave and Holmes, Sarah and Hornett, Gary and Hough, Nicholas and Huckle, Liz and Hughes-Hallet, Lena and Hunter, Adam and Inglis, Stephen and Iqbal, Sameena and Jackson, Adam and Jackson, David and Verdejo, Carlos Jimenez and Jones, Matthew and Kallepally, Kalyan and Kay, Keely and Keatley, Jon and Keith, Alan and King, Alison and Kitchin, Lucy and Kleanthous, Matt and Klimekova, Martina and Korlevic, Petra and Krasheninnkova, Ksenia and Lane, Greg and Langford, Cordelia and Laverack, Adam and Law, Katharine and Lensing, Stefanie and Lewis-Wade, Amanah and Liddle, Jennifer and Lin, Quan and Lindsay, Sarah and Linsdell, Sally and Long, Rhona and Lovell, Jamie and Lovell, Jon and Mack, James and Maddison, Mark and Makunin, Aleksei and Mamun, Irfan and Mansfield, Jenny and Marriott, Neil and Martin, Matt and Mayho, Matthew and McClintock, Jo and McHugh, Sandra and MapcMinn, Liz and Meadows, Carl and Mobley, Emily and Moll, Robin and Morra, Maria and Morrow, Leanne and Murie, Kathryn and Nash, Sian and Nathwani, Claire and Naydenova, Plamena and Neaverson, Alexandra and Nerou, Ed and Nicholson, Jon and Nimz, Tabea and Noell, Guillaume G. and O’Meara, Sarah and Ohan, Valeriu and Olney, Charles and Ormond, Doug and Oszlanczi, Agnes and Pang, Yoke Fei and Pardubska, Barbora and Park, Naomi and Parmar, Aaron and Patel, Gaurang and Payne, Maggie and Peacock, Sharon and Petersen, Arabella and Plowman, Deborah and Preston, Tom and Quail, Michael and Rance, Richard and Rawlings, Suzannah and Redshaw, Nicholas and Reynolds, Joe and Reynolds, Mark and Rice, Simon and Richardson, Matt and Roberts, Connor and Robinson, Katrina and Robinson, Melanie and Robinson, David and Rogers, Hazel and Rojo, Eduardo Martin and Roopra, Daljit and Rose, Mark and Rudd, Luke and Sadri, Ramin and Salmon, Nicholas and Saul, David and Schwach, Frank and Seekings, Phil and Simms, Alison and Sinnott, Matt and Sivadasan, Shanthi and Siwek, Bart and Sizer, Dale and Skeldon, Kenneth and Skelton, Jason and Slater-Tunstill, Joanna and Sloper, Lisa and Smerdon, Nathalie and Smith, Chris and Smith, Christen and Smith, James and Smith, Katie and Smith, Michelle and Smith, Sean and Smith, Tina and Sneade, Leighton and Soria, Carmen Diaz and Sousa, Catarina and Souster, Emily and Sparkes, Andrew and Spencer-Chapman, Michael and Squares, Janet and Stanley, Robert and Steed, Claire and Stickland, Tim and Still, Ian and Stratton, Mike and Strickland, Michelle and Swann, Allen and Swiatkowska, Agnieszka and Sycamore, Neil and Swift, Emma and Symons, Edward and Szluha, Suzanne and Taluy, Emma and Tao, Nunu and Taylor, Katy and Taylor, Sam and Thompson, Stacey and Thompson, Mark and Thomson, Mark and Thomson, Nicholas and Thurston, Scott and Toombs, Dee and Topping, Benjamin and Tovar-Corona, Jaime and Ungureanu, Daniel and Uphill, James and Urbanova, Jana and Van, Philip Jansen and Vancollie, Valerie and Voak, Paul and Walker, Danielle and Walker, Matthew and Waller, Matt and Ward, Gary and Weatherhogg, Charlie and Webb, Niki and Wells, Alan and Wells, Eloise and Westwood, Luke and Whipp, Theo and Whiteley, Thomas and Whitton, Georgia and Widaa, Sara and Williams, Mia and Wilson, Mark and Wright, Sean},
	month = jun,
	year = {2021},
	pmid = {34166617},
	pmcid = {PMC8185188},
	note = {183 citations (Crossref) [2022-06-30]},
	pages = {109292},
	file = {Full Text:/usr/users/QIB_fr005/alikhan/Zotero/storage/BHQ3RKRS/Meng et al. - 2021 - Recurrent emergence of SARS-CoV-2 spike deletion H.pdf:application/pdf},
}

@article{zhou_pan-genome_2018,
	title = {Pan-genome {Analysis} of {Ancient} and {Modern} {Salmonella} enterica {Demonstrates} {Genomic} {Stability} of the {Invasive} {Para} {C} {Lineage} for {Millennia}},
	volume = {28},
	copyright = {Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International Licence (CC-BY-NC-ND)},
	issn = {09609822},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0960982218306948},
	doi = {10.1016/j.cub.2018.05.058},
	abstract = {Salmonella enterica serovar Paratyphi C causes enteric (paratyphoid) fever in humans. Its presentation can range from asymptomatic infections of the blood stream to gastrointestinal or urinary tract infection or even a fatal septicemia [1]. Paratyphi C is very rare in Europe and North America except for occasional travelers from South and East Asia or Africa, where the disease is more common [2, 3]. However, early 20th-century observations in Eastern Europe [3, 4] suggest that Paratyphi C enteric fever may once have had a wide-ranging impact on human societies. Here, we describe a draft Paratyphi C genome (Ragna) recovered from the 800-year-old skeleton (SK152) of a young woman in Trondheim, Norway. Paratyphi C sequences were recovered from her teeth and bones, suggesting that she died of enteric fever and demonstrating that these bacteria have long caused invasive salmonellosis in Europeans. Comparative analyses against modern Salmonella genome sequences revealed that Paratyphi C is a clade within the Para C lineage, which also includes serovars Choleraesuis, Typhisuis, and Lomita. Although Paratyphi C only infects humans, Choleraesuis causes septicemia in pigs and boar [5] (and occasionally humans), and Typhisuis causes epidemic swine salmonellosis (chronic paratyphoid) in domestic pigs [2, 3]. These different host specificities likely evolved in Europe over the last ∼4,000 years since the time of their most recent common ancestor (tMRCA) and are possibly associated with the differential acquisitions of two genomic islands, SPI-6 and SPI-7. The tMRCAs of these bacterial clades coincide with the timing of pig domestication in Europe [6].},
	language = {en},
	number = {15},
	urldate = {2022-05-13},
	journal = {Current Biology},
	author = {Zhou, Zhemin and Lundstrøm, Inge and Tran-Dien, Alicia and Duchêne, Sebastián and Alikhan, Nabil-Fareed and Sergeant, Martin J. and Langridge, Gemma and Fotakis, Anna K. and Nair, Satheesh and Stenøien, Hans K. and Hamre, Stian S. and Casjens, Sherwood and Christophersen, Axel and Quince, Christopher and Thomson, Nicholas R. and Weill, François-Xavier and Ho, Simon Y.W. and Gilbert, M. Thomas P. and Achtman, Mark},
	month = aug,
	year = {2018},
	pmid = {30033331},
	pmcid = {PMC6089836},
	note = {49 citations (Crossref) [2022-06-30]},
	pages = {2420--2428.e10},
	file = {Full Text:/usr/users/QIB_fr005/alikhan/Zotero/storage/N9MZEZUJ/Zhou et al. - 2018 - Pan-genome Analysis of Ancient and Modern Salmonel.pdf:application/pdf},
}

@article{foster-nyarko_non-human_2020,
	title = {Non-human primates in the {Gambia} harbour human-associated pathogenic {Escherichia} coli strains},
	volume = {2},
	copyright = {Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International Licence (CC-BY-NC-ND)},
	issn = {2516-8290},
	url = {https://www.microbiologyresearch.org/content/journal/acmi/10.1099/acmi.ac2020.po0781},
	doi = {10.1099/acmi.ac2020.po0781},
	abstract = {Increasing contact between humans and non-human primates provides an opportunity for the transfer of potential pathogens or antimicrobial resistance between different host species. We have investigated genetic diversity and antimicrobial resistance in
              Escherichia coli
              isolates from a range of non-human primates dispersed across the Gambia: patas monkey (n=1), western colobus monkey (n=6), green monkey (n=14) and guinea baboon (n=22). From 43 stools, we recovered 99 isolates. We performed Illumina whole-genome shotgun sequencing on all isolates and nanopore long-read sequencing on isolates with antimicrobial resistance genes. We inferred the evolution of
              E. coli
              in this population using the EnteroBase software environment. We identified 43 sequence types (ten of them novel), spanning five of the eight known phylogroups of
              E. coli
              . Many of the observed sequence types and phylotypes from non-human primates have been associated with human extra-intestinal infection and carry virulence characteristics associated with disease in humans, particularly ST73, ST217 and ST681. However, we found a low prevalence of antimicrobial resistance genes in isolates from non-human primates. Hierarchical clustering showed that ST442 and ST349 from non-human primates are closely related to isolates from human infections, suggesting recent exchange of bacteria between humans and monkeys. Our results are of public health importance, considering the increasing contact between humans and wild primates.},
	language = {en},
	number = {7A},
	urldate = {2022-05-13},
	journal = {Access Microbiology},
	author = {Foster-Nyarko, Ebenezer and Alikhan, Nabil-Fareed and Ravi, Anuradha and Thilliez, Gaëtan and Thomson, Nicholas and Baker, David and Kay, Gemma and D. Cramer, Jennifer and O’Grady, Justin and Antonio, Martin and Pallen, Mark},
	month = jul,
	year = {2020},
	note = {1 citations (Crossref) [2022-06-30]},
}

@article{page_large-scale_2021,
	title = {Large-scale sequencing of {SARS}-{CoV}-2 genomes from one region allows detailed epidemiology and enables local outbreak management},
	volume = {7},
	copyright = {Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International Licence (CC-BY-NC-ND)},
	issn = {2057-5858},
	url = {https://www.microbiologyresearch.org/content/journal/mgen/10.1099/mgen.0.000589},
	doi = {10.1099/mgen.0.000589},
	abstract = {The COVID-19 pandemic has spread rapidly throughout the world. In the UK, the initial peak was in April 2020; in the county of Norfolk (UK) and surrounding areas, which has a stable, low-density population, over 3200 cases were reported between March and August 2020. As part of the activities of the national COVID-19 Genomics Consortium (COG-UK) we undertook whole genome sequencing of the SARS-CoV-2 genomes present in positive clinical samples from the Norfolk region. These samples were collected by four major hospitals, multiple minor hospitals, care facilities and community organizations within Norfolk and surrounding areas. We combined clinical metadata with the sequencing data from regional SARS-CoV-2 genomes to understand the origins, genetic variation, transmission and expansion (spread) of the virus within the region and provide context nationally. Data were fed back into the national effort for pandemic management, whilst simultaneously being used to assist local outbreak analyses. Overall, 1565 positive samples (172 per 100 000 population) from 1376 cases were evaluated; for 140 cases between two and six samples were available providing longitudinal data. This represented 42.6 \% of all positive samples identified by hospital testing in the region and encompassed those with clinical need, and health and care workers and their families. In total, 1035 cases had genome sequences of sufficient quality to provide phylogenetic lineages. These genomes belonged to 26 distinct global lineages, indicating that there were multiple separate introductions into the region. Furthermore, 100 genetically distinct UK lineages were detected demonstrating local evolution, at a rate of {\textasciitilde}2 SNPs per month, and multiple co-occurring lineages as the pandemic progressed. Our analysis: identified a discrete sublineage associated with six care facilities; found no evidence of reinfection in longitudinal samples; ruled out a nosocomial outbreak; identified 16 lineages in key workers which were not in patients, indicating infection control measures were effective; and found the D614G spike protein mutation which is linked to increased transmissibility dominates the samples and rapidly confirmed relatedness of cases in an outbreak at a food processing facility. The large-scale genome sequencing of SARS-CoV-2-positive samples has provided valuable additional data for public health epidemiology in the Norfolk region, and will continue to help identify and untangle hidden transmission chains as the pandemic evolves.},
	language = {en},
	number = {6},
	urldate = {2022-05-13},
	journal = {Microbial Genomics},
	author = {Page, Andrew J. and Mather, Alison E. and Le-Viet, Thanh and Meader, Emma J. and Alikhan, Nabil-Fareed and Kay, Gemma L. and de Oliveira Martins, Leonardo and Aydin, Alp and Baker, David J. and Trotter, Alexander J. and Rudder, Steven and Tedim, Ana P. and Kolyva, Anastasia and Stanley, Rachael and Yasir, Muhammad and Diaz, Maria and Potter, Will and Stuart, Claire and Meadows, Lizzie and Bell, Andrew and Gutierrez, Ana Victoria and Thomson, Nicholas M. and Adriaenssens, Evelien M. and Swingler, Tracey and Gilroy, Rachel A. J. and Griffith, Luke and Sethi, Dheeraj K. and Aggarwal, Dinesh and Brown, Colin S. and Davidson, Rose K. and Kingsley, Robert A. and Bedford, Luke and Coupland, Lindsay J. and Charles, Ian G. and Elumogo, Ngozi and Wain, John and Prakash, Reenesh and Webber, Mark A. and Smith, S. J. Louise and Chand, Meera and Dervisevic, Samir and O’Grady, Justin and {The COVID-19 Genomics UK (COG-UK) Consortium}},
	month = jun,
	year = {2021},
	pmid = {34184982},
	pmcid = {PMC8461472},
	note = {5 citations (Crossref) [2022-06-30]},
	file = {Full Text:/usr/users/QIB_fr005/alikhan/Zotero/storage/XYAF2X25/Page et al. - 2021 - Large-scale sequencing of SARS-CoV-2 genomes from .pdf:application/pdf},
}

@article{kanteh_invasive_2021,
	title = {Invasive atypical non-typhoidal {Salmonella} serovars in {The} {Gambia}},
	volume = {7},
	copyright = {Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International Licence (CC-BY-NC-ND)},
	issn = {2057-5858},
	url = {https://www.microbiologyresearch.org/content/journal/mgen/10.1099/mgen.0.000677},
	doi = {10.1099/mgen.0.000677},
	abstract = {Invasive non-typhoidal
              
                
                  Salmonella
                
              
              (iNTS) disease continues to be a significant public health problem in sub-Saharan Africa. Common clinical misdiagnosis, antimicrobial resistance, high case fatality and lack of a vaccine make iNTS a priority for global health research. Using whole genome sequence analysis of 164 invasive
              
                
                  Salmonella
                
              
              isolates obtained through population-based surveillance between 2008 and 2016, we conducted genomic analysis of the serovars causing invasive
              
                
                  Salmonella
                
              
              diseases in rural Gambia. The incidence of iNTS varied over time. The proportion of atypical serovars causing disease increased over time from 40 to 65 \% compared to the typical serovars Enteritidis and Typhimurium that decreased from 30 to 12 \%. Overall iNTS case fatality was 10\%, but case fatality associated with atypical iNTS alone was 10 \%. Genetic virulence factors were identified in 14/70 (20 \%) typical serovars and 45/68 (66 \%) of the atypical serovars and were associated with: invasion, proliferation and/or translocation (Clade A); and host colonization and immune modulation (Clade G). Among Enteritidis isolates, 33/40 were resistant to four or more of the antimicrobials tested, except ciprofloxacin, to which all isolates were susceptible. Resistance was low in Typhimurium isolates, but all 16 isolates were resistant to gentamicin. The increase in incidence and proportion of iNTS disease caused by atypical serovars is concerning. The increased proportion of atypical serovars and the high associated case fatality may be related to acquisition of specific genetic virulence factors. These factors may provide a selective advantage to the atypical serovars. Investigations should be conducted elsewhere in Africa to identify potential changes in the distribution of iNTS serovars and the extent of these virulence elements.},
	language = {en},
	number = {11},
	urldate = {2022-05-13},
	journal = {Microbial Genomics},
	author = {Kanteh, Abdoulie and Sesay, Abdul Karim and Alikhan, Nabil-Fareed and Ikumapayi, Usman Nurudeen and Salaudeen, Rasheed and Manneh, Jarra and Olatunji, Yekini and Page, Andrew J. and Mackenzie, Grant},
	month = nov,
	year = {2021},
	note = {2 citations (Crossref) [2022-06-30]},
	file = {Accepted Version:/usr/users/QIB_fr005/alikhan/Zotero/storage/2YRZQBUL/Kanteh et al. - 2021 - Invasive atypical non-typhoidal Salmonella serovar.pdf:application/pdf},
}

@article{barylski_ictv_2020,
	title = {{ICTV} {Virus} {Taxonomy} {Profile}: {Herelleviridae}},
	volume = {101},
	copyright = {Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International Licence (CC-BY-NC-ND)},
	issn = {0022-1317, 1465-2099},
	shorttitle = {{ICTV} {Virus} {Taxonomy} {Profile}},
	url = {https://www.microbiologyresearch.org/content/journal/jgv/10.1099/jgv.0.001392},
	doi = {10.1099/jgv.0.001392},
	abstract = {Members of the family Herelleviridae are bacterial viruses infecting members of the phylum Firmicutes. The virions have myovirus morphology and virus genomes comprise a linear dsDNA of 125–170 kb. This is a summary of the International Committee on Taxonomy of Viruses (ICTV) Report on the family Herelleviridae, which is available at ictv.global/report/herelleviridae.},
	language = {en},
	number = {4},
	urldate = {2022-05-13},
	journal = {Journal of General Virology},
	author = {Barylski, Jakub and Kropinski, Andrew M. and Alikhan, Nabil-Fareed and Adriaenssens, Evelien M. and {ICTV Report Consortium}},
	month = apr,
	year = {2020},
	pmid = {32022658},
	pmcid = {PMC7414437},
	note = {19 citations (Crossref) [2022-06-30]},
	pages = {362--363},
}

@article{achtman_genomic_2021,
	title = {Genomic diversity of {Salmonella} enterica -{The} {UoWUCC} {10K} genomes project},
	volume = {5},
	copyright = {Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International Licence (CC-BY-NC-ND)},
	issn = {2398-502X},
	url = {https://wellcomeopenresearch.org/articles/5-223/v2},
	doi = {10.12688/wellcomeopenres.16291.2},
	abstract = {Most publicly available genomes of  Salmonella enterica  are from human disease in the US and the UK, or from domesticated animals in the US. Here we describe a historical collection of 10,000 strains isolated between 1891-2010 in 73 different countries. They encompass a broad range of sources, ranging from rivers through reptiles to the diversity of all S. enterica isolated on the island of Ireland between 2000 and 2005. Genomic DNA was isolated, and sequenced by Illumina short read sequencing.

 The short reads are publicly available in the Short Reads Archive. They were also uploaded to EnteroBase, which assembled and annotated draft genomes. 9769 draft genomes which passed quality control were genotyped with multiple levels of multilocus sequence typing, and used to predict serovars. Genomes were assigned to hierarchical clusters on the basis of numbers of pair-wise allelic differences in core genes, which were mapped to genetic Lineages within phylogenetic trees.
            
 The University of Warwick/University College Cork (UoWUCC) project greatly extends the geographic sources, dates and core genomic diversity of publicly available S. enterica genomes. We illustrate these features by an overview of core genomic Lineages within 33,000 publicly available Salmonella genomes whose strains were isolated before 2011. We also present detailed examinations of HC400, HC900 and HC2000 hierarchical clusters within exemplar Lineages, including serovars Typhimurium, Enteritidis and Mbandaka. These analyses confirm the polyphyletic nature of multiple serovars while showing that discrete clusters with geographical specificity can be reliably recognized by hierarchical clustering approaches. The results also demonstrate that the genomes sequenced here provide an important counterbalance to the sampling bias which is so dominant in current genomic sequencing.},
	language = {en},
	urldate = {2022-05-13},
	journal = {Wellcome Open Research},
	author = {Achtman, Mark and Zhou, Zhemin and Alikhan, Nabil-Fareed and Tyne, William and Parkhill, Julian and Cormican, Martin and Chiou, Chien-Shun and Torpdahl, Mia and Litrup, Eva and Prendergast, Deirdre M. and Moore, John E. and Strain, Sam and Kornschober, Christian and Meinersmann, Richard and Uesbeck, Alexandra and Weill, François-Xavier and Coffey, Aidan and Andrews-Polymenis, Helene and Curtiss rd, Roy and Fanning, Séamus},
	month = feb,
	year = {2021},
	pmid = {33614977},
	pmcid = {PMC7869069},
	note = {6 citations (Crossref) [2022-06-30]},
	pages = {223},
	file = {Full Text:/usr/users/QIB_fr005/alikhan/Zotero/storage/PRPDHBMQ/Achtman et al. - 2021 - Genomic diversity of Salmonella enterica -The UoWU.pdf:application/pdf},
}

@article{twohig_hospital_2022,
	title = {Hospital admission and emergency care attendance risk for {SARS}-{CoV}-2 delta ({B}.1.617.2) compared with alpha ({B}.1.1.7) variants of concern: a cohort study},
	volume = {22},
	copyright = {Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International Licence (CC-BY-NC-ND)},
	issn = {14733099},
	shorttitle = {Hospital admission and emergency care attendance risk for {SARS}-{CoV}-2 delta ({B}.1.617.2) compared with alpha ({B}.1.1.7) variants of concern},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S1473309921004758},
	doi = {10.1016/S1473-3099(21)00475-8},
	abstract = {Background
The SARS-CoV-2 delta (B.1.617.2) variant was first detected in England in March, 2021. It has since rapidly become the predominant lineage, owing to high transmissibility. It is suspected that the delta variant is associated with more severe disease than the previously dominant alpha (B.1.1.7) variant. We aimed to characterise the severity of the delta variant compared with the alpha variant by determining the relative risk of hospital attendance outcomes.
Methods
This cohort study was done among all patients with COVID-19 in England between March 29 and May 23, 2021, who were identified as being infected with either the alpha or delta SARS-CoV-2 variant through whole-genome sequencing. Individual-level data on these patients were linked to routine health-care datasets on vaccination, emergency care attendance, hospital admission, and mortality (data from Public Health England's Second Generation Surveillance System and COVID-19-associated deaths dataset; the National Immunisation Management System; and NHS Digital Secondary Uses Services and Emergency Care Data Set). The risk for hospital admission and emergency care attendance were compared between patients with sequencing-confirmed delta and alpha variants for the whole cohort and by vaccination status subgroups. Stratified Cox regression was used to adjust for age, sex, ethnicity, deprivation, recent international travel, area of residence, calendar week, and vaccination status.
Findings
Individual-level data on 43 338 COVID-19-positive patients (8682 with the delta variant, 34 656 with the alpha variant; median age 31 years [IQR 17–43]) were included in our analysis. 196 (2·3\%) patients with the delta variant versus 764 (2·2\%) patients with the alpha variant were admitted to hospital within 14 days after the specimen was taken (adjusted hazard ratio [HR] 2·26 [95\% CI 1·32–3·89]). 498 (5·7\%) patients with the delta variant versus 1448 (4·2\%) patients with the alpha variant were admitted to hospital or attended emergency care within 14 days (adjusted HR 1·45 [1·08–1·95]). Most patients were unvaccinated (32 078 [74·0\%] across both groups). The HRs for vaccinated patients with the delta variant versus the alpha variant (adjusted HR for hospital admission 1·94 [95\% CI 0·47–8·05] and for hospital admission or emergency care attendance 1·58 [0·69–3·61]) were similar to the HRs for unvaccinated patients (2·32 [1·29–4·16] and 1·43 [1·04–1·97]; p=0·82 for both) but the precision for the vaccinated subgroup was low.
Interpretation
This large national study found a higher hospital admission or emergency care attendance risk for patients with COVID-19 infected with the delta variant compared with the alpha variant. Results suggest that outbreaks of the delta variant in unvaccinated populations might lead to a greater burden on health-care services than the alpha variant.},
	language = {en},
	number = {1},
	urldate = {2022-05-13},
	journal = {The Lancet Infectious Diseases},
	author = {Twohig, Katherine A and Nyberg, Tommy and Zaidi, Asad and Thelwall, Simon and Sinnathamby, Mary A and Aliabadi, Shirin and Seaman, Shaun R and Harris, Ross J and Hope, Russell and Lopez-Bernal, Jamie and Gallagher, Eileen and Charlett, Andre and De Angelis, Daniela and Presanis, Anne M and Dabrera, Gavin and Koshy, Cherian and Ash, Amy and Wise, Emma and Moore, Nathan and Mori, Matilde and Cortes, Nick and Lynch, Jessica and Kidd, Stephen and Fairley, Derek and Curran, Tanya and McKenna, James and Adams, Helen and Fraser, Christophe and Golubchik, Tanya and Bonsall, David and Hassan-Ibrahim, Mohammed and Malone, Cassandra and Cogger, Benjamin and Wantoch, Michelle and Reynolds, Nicola and Warne, Ben and Maksimovic, Joshua and Spellman, Karla and McCluggage, Kathryn and John, Michaela and Beer, Robert and Afifi, Safiah and Morgan, Sian and Marchbank, Angela and Price, Anna and Kitchen, Christine and Gulliver, Huw and Merrick, Ian and Southgate, Joel and Guest, Martyn and Munn, Robert and Workman, Trudy and Connor, Thomas and Fuller, William and Bresner, Catherine and Snell, Luke and Patel, Amita and Charalampous, Themoula and Nebbia, Gaia and Batra, Rahul and Edgeworth, Jonathan and Robson, Samuel and Beckett, Angela and Aanensen, David and Underwood, Anthony and Yeats, Corin and Abudahab, Khalil and Taylor, Ben and Menegazzo, Mirko and Clark, Gemma and Smith, Wendy and Khakh, Manjinder and Fleming, Vicki and Lister, Michelle and Howson-Wells, Hannah and Berry, Louise and Boswell, Tim and Joseph, Amelia and Willingham, Iona and Jones, Carl and Holmes, Christopher and Bird, Paul and Helmer, Thomas and Fallon, Karlie and Tang, Julian and Raviprakash, Veena and Campbell, Sharon and Sheriff, Nicola and Blakey, Victoria and Williams, Lesley-Anne and Loose, Matthew and Holmes, Nadine and Moore, Christopher and Carlile, Matthew and Wright, Victoria and Sang, Fei and Debebe, Johnny and Coll, Francesc and Signell, Adrian and Betancor, Gilberto and Wilson, Harry and Eldirdiri, Sahar and Kenyon, Anita and Davis, Thomas and Pybus, Oliver and du Plessis, Louis and Zarebski, Alex and Raghwani, Jayna and Kraemer, Moritz and Francois, Sarah and Attwood, Stephen and Vasylyeva, Tetyana and Escalera Zamudio, Marina and Gutierrez, Bernardo and Torok, M. Estee and Hamilton, William and Goodfellow, Ian and Hall, Grant and Jahun, Aminu and Chaudhry, Yasmin and Hosmillo, Myra and Pinckert, Malte and Georgana, Iliana and Moses, Samuel and Lowe, Hannah and Bedford, Luke and Moore, Jonathan and Stonehouse, Susanne and Fisher, Chloe and Awan, Ali and BoYes, John and Breuer, Judith and Harris, Kathryn and Brown, Julianne and Shah, Divya and Atkinson, Laura and Lee, Jack and Storey, Nathaniel and Flaviani, Flavia and Alcolea-Medina, Adela and Williams, Rebecca and Vernet, Gabrielle and Chapman, Michael and Levett, Lisa and Heaney, Judith and Chatterton, Wendy and Pusok, Monika and Xu-McCrae, Li and Smith, Darren and Bashton, Matthew and Young, Gregory and Holmes, Alison and Randell, Paul and Cox, Alison and Madona, Pinglawathee and Bolt, Frances and Price, James and Mookerjee, Siddharth and Ragonnet-Cronin, Manon and F. Nascimento, Fabricia and Jorgensen, David and Siveroni, Igor and Johnson, Rob and Boyd, Olivia and Geidelberg, Lily and Volz, Erik and Rowan, Aileen and Taylor, Graham and Smollett, Katherine and Loman, Nicholas and Quick, Joshua and McMurray, Claire and Stockton, Joanne and Nicholls, Sam and Rowe, Will and Poplawski, Radoslaw and McNally, Alan and Martinez Nunez, Rocio and Mason, Jenifer and Robinson, Trevor and O'Toole, Elaine and Watts, Joanne and Breen, Cassie and Cowell, Angela and Sluga, Graciela and Machin, Nicholas and Ahmad, Shazaad and George, Ryan and Halstead, Fenella and Sivaprakasam, Venkat and Hogsden, Wendy and Illingworth, Chris and Jackson, Chris and Thomson, Emma and Shepherd, James and Asamaphan, Patawee and Niebel, Marc and Li, Kathy and Shah, Rajiv and Jesudason, Natasha and Tong, Lily and Broos, Alice and Mair, Daniel and Nichols, Jenna and Carmichael, Stephen and Nomikou, Kyriaki and Aranday-Cortes, Elihu and Johnson, Natasha and Starinskij, Igor and da Silva Filipe, Ana and Robertson, David and Orton, Richard and Hughes, Joseph and Vattipally, Sreenu and Singer, Joshua and Nickbakhsh, Seema and Hale, Antony and Macfarlane-Smith, Louissa and Harper, Katherine and Carden, Holli and Taha, Yusri and Payne, Brendan and Burton-Fanning, Shirelle and Waugh, Sheila and Collins, Jennifer and Eltringham, Gary and Rushton, Steven and O'Brien, Sarah and Bradley, Amanda and Maclean, Alasdair and Mollett, Guy and Blacow, Rachel and Templeton, Kate and McHugh, Martin and Dewar, Rebecca and Wastenge, Elizabeth and Dervisevic, Samir and Stanley, Rachael and Meader, Emma and Coupland, Lindsay and Smith, Louise and Graham, Clive and Barton, Edward and Padgett, Debra and Scott, Garren and Swindells, Emma and Greenaway, Jane and Nelson, Andrew and McCann, Clare and Yew, Wen and Andersson, Monique and Peto, Timothy and Justice, Anita and Eyre, David and Crook, Derrick and Sloan, Tim and Duckworth, Nichola and Walsh, Sarah and Chauhan, Anoop and Glaysher, Sharon and Bicknell, Kelly and Wyllie, Sarah and Elliott, Scott and Lloyd, Allyson and Impey, Robert and Levene, Nick and Monaghan, Lynn and Bradley, Declan and Wyatt, Tim and Allara, Elias and Pearson, Clare and Osman, Husam and Bosworth, Andrew and Robinson, Esther and Muir, Peter and Vipond, Ian and Hopes, Richard and Pymont, Hannah and Hutchings, Stephanie and Curran, Martin and Parmar, Surendra and Lackenby, Angie and Mbisa, Tamyo and Platt, Steven and Miah, Shahjahan and Bibby, David and Manso, Carmen and Hubb, Jonathan and Chand, Meera and Dabrera, Gavin and Ramsay, Mary and Bradshaw, Daniel and Thornton, Alicia and Myers, Richard and Schaefer, Ulf and Groves, Natalie and Gallagher, Eileen and Lee, David and Williams, David and Ellaby, Nicholas and Harrison, Ian and Hartman, Hassan and Manesis, Nikos and Patel, Vineet and Bishop, Chloe and Chalker, Vicki and Ledesma, Juan and Twohig, Katherine and Holden, Matthew and Shaaban, Sharif and Birchley, Alec and Adams, Alexander and Davies, Alisha and Gaskin, Amy and Plimmer, Amy and Gatica-Wilcox, Bree and McKerr, Caoimhe and Moore, Catherine and Williams, Chris and Heyburn, David and De Lacy, Elen and Hilvers, Ember and Downing, Fatima and Shankar, Giri and Jones, Hannah and Asad, Hibo and Coombes, Jason and Watkins, Joanne and Evans, Johnathan and Fina, Laia and Gifford, Laura and Gilbert, Lauren and Graham, Lee and Perry, Malorie and Morgan, Mari and Bull, Matthew and Cronin, Michelle and Pacchiarini, Nicole and Craine, Noel and Jones, Rachel and Howe, Robin and Corden, Sally and Rey, Sara and Kumziene-SummerhaYes, Sara and Taylor, Sarah and Cottrell, Simon and Jones, Sophie and Edwards, Sue and O'Grady, Justin and Page, Andrew and Mather, Alison and Baker, David and Rudder, Steven and Aydin, Alp and Kay, Gemma and Trotter, Alexander and Alikhan, Nabil-Fareed and de Oliveira Martins, Leonardo and Le-Viet, Thanh and Meadows, Lizzie and Casey, Anna and Ratcliffe, Liz and Simpson, David and Molnar, Zoltan and Thompson, Thomas and Acheson, Erwan and Masoli, Jane and Knight, Bridget and Ellard, Sian and Auckland, Cressida and Jones, Christopher and Mahungu, Tabitha and Irish-Tavares, Dianne and Haque, Tanzina and Hart, Jennifer and Witele, Eric and Fenton, Melisa and Dadrah, Ashok and Symmonds, Amanda and Saluja, Tranprit and Bourgeois, Yann and Scarlett, Garry and Loveson, Katie and Goudarzi, Salman and Fearn, Christopher and Cook, Kate and Dent, Hannah and Paul, Hannah and Partridge, David and Raza, Mohammad and Evans, Cariad and Johnson, Kate and Liggett, Steven and Baker, Paul and Bonner, Stephen and Essex, Sarah and Lyons, Ronan and Saeed, Kordo and Mahanama, Adhyana and Samaraweera, Buddhini and Silveira, Siona and Pelosi, Emanuela and Wilson-Davies, Eleri and Williams, Rachel and Kristiansen, Mark and Roy, Sunando and Williams, Charlotte and Cotic, Marius and Bayzid, Nadua and Westhorpe, Adam and Hartley, John and Jannoo, Riaz and Lowe, Helen and Karamani, Angeliki and Ensell, Leah and Prieto, Jacqui and Jeremiah, Sarah and Grammatopoulos, Dimitris and Pandey, Sarojini and Berry, Lisa and Jones, Katie and Richter, Alex and Beggs, Andrew and Best, Angus and Percival, Benita and Mirza, Jeremy and Megram, Oliver and Mayhew, Megan and Crawford, Liam and Ashcroft, Fiona and Moles-Garcia, Emma and Cumley, Nicola and Smith, Colin and Bucca, Giselda and Hesketh, Andrew and Blane, Beth and Girgis, Sophia and Leek, Danielle and Sridhar, Sushmita and Forrest, Sally and Cormie, Claire and Gill, Harmeet and Dias, Joana and Higginson, Ellen and Maes, Mailis and Young, Jamie and Kermack, Leanne and Gupta, Ravi and Ludden, Catherine and Peacock, Sharon and Palmer, Sophie and Churcher, Carol and Hadjirin, Nazreen and Carabelli, Alessandro and Brooks, Ellena and Smith, Kim and Galai, Katerina and McManus, Georgina and Ruis, Chris and Davidson, Rose and Rambaut, Andrew and Williams, Thomas and Balcazar, Carlos and Gallagher, Michael and O'Toole, Áine and Rooke, Stefan and Hill, Verity and Williamson, Kathleen and Stanton, Thomas and Michell, Stephen and Bewshea, Claire and Temperton, Ben and Michelsen, Michelle and Warwick-Dugdale, Joanna and Manley, Robin and Farbos, Audrey and Harrison, James and Sambles, Christine and Studholme, David and Jeffries, Aaron and Jackson, Leigh and Darby, Alistair and Hiscox, Julian and Paterson, Steve and Iturriza-Gomara, Miren and Jackson, Kathryn and Lucaci, Anita and Vamos, Edith and Hughes, Margaret and Rainbow, Lucille and Eccles, Richard and Nelson, Charlotte and Whitehead, Mark and Turtle, Lance and Haldenby, Sam and Gregory, Richard and Gemmell, Matthew and Wierzbicki, Claudia and Webster, Hermione and de Silva, Thushan and Smith, Nikki and Angyal, Adrienn and Lindsey, Benjamin and Groves, Danielle and Green, Luke and Wang, Dennis and Freeman, Timothy and Parker, Matthew and Keeley, Alexander and Parsons, Paul and Tucker, Rachel and Brown, Rebecca and Wyles, Matthew and Whiteley, Max and Zhang, Peijun and Gallis, Marta and Louka, Stavroula and Constantinidou, Chrystala and Unnikrishnan, Meera and Ott, Sascha and Cheng, Jeffrey and Bridgewater, Hannah and Frost, Lucy and Taylor-Joyce, Grace and Stark, Richard and Baxter, Laura and Alam, Mohammad and Brown, Paul and Aggarwal, Dinesh and Cerda, Alberto and Merrill, Tammy and Wilson, Rebekah and McClure, Patrick and Chappell, Joseph and Tsoleridis, Theocharis and Ball, Jonathan and Buck, David and Todd, John and Green, Angie and Trebes, Amy and MacIntyre-Cockett, George and de Cesare, Mariateresa and Alderton, Alex and Amato, Roberto and Ariani, Cristina and Beale, Mathew and Beaver, Charlotte and Bellis, Katherine and Betteridge, Emma and Bonfield, James and Danesh, John and Dorman, Matthew and Drury, Eleanor and Farr, Ben and Foulser, Luke and Goncalves, Sonia and Goodwin, Scott and Gourtovaia, Marina and Harrison, Ewan and Jackson, David and Jamrozy, Dorota and Johnston, Ian and Kane, Leanne and Kay, Sally and Keatley, Jon-Paul and Kwiatkowski, Dominic and Langford, Cordelia and Lawniczak, Mara and Letchford, Laura and Livett, Rich and Lo, Stephanie and Martincorena, Inigo and McGuigan, Samantha and Nelson, Rachel and Palmer, Steve and Park, Naomi and Patel, Minal and Prestwood, Liam and Puethe, Christoph and Quail, Michael and Rajatileka, Shavanthi and Scott, Carol and Shirley, Lesley and Sillitoe, John and Spencer Chapman, Michael and Thurston, Scott and Tonkin-Hill, Gerry and Weldon, Danni and Rajan, Diana and Bronner, Iraad and Aigrain, Louise and Redshaw, Nicholas and Lensing, Stefanie and Davies, Robert and Whitwham, Andrew and Liddle, Jennifier and Lewis, Kevin and Tovar-Corona, Jaime and Leonard, Steven and Durham, Jillian and Bassett, Andrew and McCarthy, Shane and Moll, Robin and James, Keith and Oliver, Karen and Makunin, Alex and Barrett, Jeff and Gunson, Rory},
	month = jan,
	year = {2022},
	pmid = {34461056},
	pmcid = {PMC8397301},
	note = {196 citations (Crossref) [2022-06-30]},
	pages = {35--42},
	file = {Full Text:/usr/users/QIB_fr005/alikhan/Zotero/storage/LWGPGXQP/Twohig et al. - 2022 - Hospital admission and emergency care attendance r.pdf:application/pdf},
}

@article{foster-nyarko_genomic_2021,
	title = {Genomic diversity of \textit{{Escherichia} coli} from healthy children in rural {Gambia}},
	volume = {9},
	copyright = {Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International Licence (CC-BY-NC-ND)},
	issn = {2167-8359},
	url = {https://peerj.com/articles/10572},
	doi = {10.7717/peerj.10572},
	abstract = {Little is known about the genomic diversity of
              Escherichia coli
              in healthy children from sub-Saharan Africa, even though this is pertinent to understanding bacterial evolution and ecology and their role in infection. We isolated and whole-genome sequenced up to five colonies of faecal
              E. coli
              from 66 asymptomatic children aged three-to-five years in rural Gambia (n = 88 isolates from 21 positive stools). We identified 56 genotypes, with an average of 2.7 genotypes per host. These were spread over 37 seven-allele sequence types and the
              E. coli
              phylogroups A, B1, B2, C, D, E, F and
              Escherichia
              cryptic clade I. Immigration events accounted for three-quarters of the diversity within our study population, while one-quarter of variants appeared to have arisen from within-host evolution. Several isolates encode putative virulence factors commonly found in Enteropathogenic and Enteroaggregative
              E. coli,
              and 53\% of the isolates encode resistance to three or more classes of antimicrobials. Thus, resident
              E. coli
              in these children may constitute reservoirs of virulence- and resistance-associated genes. Moreover, several study strains were closely related to isolates that caused disease in humans or originated from livestock. Our results suggest that within-host evolution plays a minor role in the generation of diversity compared to independent immigration and the establishment of strains among our study population. Also, this study adds significantly to the number of commensal
              E. coli
              genomes, a group that has been traditionally underrepresented in the sequencing of this species.},
	language = {en},
	urldate = {2022-05-13},
	journal = {PeerJ},
	author = {Foster-Nyarko, Ebenezer and Alikhan, Nabil-Fareed and Ikumapayi, Usman N. and Sarwar, Golam and Okoi, Catherine and Tientcheu, Peggy-Estelle Maguiagueu and Defernez, Marianne and O’Grady, Justin and Antonio, Martin and Pallen, Mark J.},
	month = jan,
	year = {2021},
	note = {4 citations (Crossref) [2022-06-30]},
	pages = {e10572},
	file = {Full Text:/usr/users/QIB_fr005/alikhan/Zotero/storage/WM2R8VUV/Foster-Nyarko et al. - 2021 - Genomic diversity of Escherichia coli from .pdf:application/pdf},
}

@article{beatson_genome_2011,
	title = {Genome {Sequence} of the {Emerging} {Pathogen} \textit{{Aeromonas} caviae}},
	volume = {193},
	copyright = {Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International Licence (CC-BY-NC-ND)},
	issn = {0021-9193, 1098-5530},
	url = {https://journals.asm.org/doi/10.1128/JB.01337-10},
	doi = {10.1128/JB.01337-10},
	abstract = {ABSTRACT
            
              Aeromonas caviae
              is a Gram-negative, motile and rod-shaped facultative anaerobe that is increasingly being recognized as a cause of diarrhea in children. Here we present the first genome sequence of an
              A. caviae
              strain that was isolated as the sole pathogen from a child with profuse diarrhea.},
	language = {en},
	number = {5},
	urldate = {2022-05-13},
	journal = {Journal of Bacteriology},
	author = {Beatson, Scott A. and das Graças de Luna, Maria and Bachmann, Nathan L. and Alikhan, Nabil-Fareed and Hanks, Kirstin R. and Sullivan, Mitchell J. and Wee, Bryan A. and Freitas-Almeida, Angela C. and dos Santos, Paula A. and de Melo, Janyne T. B. and Squire, Derrick J. P. and Cunningham, Adam F. and Fitzgerald, J. Ross and Henderson, Ian R.},
	month = mar,
	year = {2011},
	pmcid = {PMC3067608},
	pmid = {21183677},
	note = {30 citations (Crossref) [2022-06-30]},
	pages = {1286--1287},
	file = {Full Text:/usr/users/QIB_fr005/alikhan/Zotero/storage/THWSVLZL/Beatson et al. - 2011 - Genome Sequence of the Emerging Pathogen Aeromo.pdf:application/pdf},
}

@article{chen_genome-wide_2019,
	title = {Genome-wide {Identification} and {Characterization} of a {Superfamily} of {Bacterial} {Extracellular} {Contractile} {Injection} {Systems}},
	volume = {29},
	copyright = {Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International Licence (CC-BY-NC-ND)},
	issn = {22111247},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S2211124719311581},
	doi = {10.1016/j.celrep.2019.08.096},
	abstract = {Several phage-tail-like nanomachines were shown to play an important role in the interactions between bacteria and their eukaryotic hosts. These apparatuses appear to represent a new injection paradigm. Here, with three verified extracellular contractile injection systems (eCISs), a protein profile and genomic context-based iterative approach was applied to identify 631 eCIS-like loci from the 11,699 publicly available complete bacterial genomes. The eCIS superfamily, which is phylogenetically diverse and sub-divided into six families, is distributed among Gram-negative and -positive bacteria in addition to archaea. Our results show that very few bacteria are seen to possess intact operons of both eCIS and type VI secretion systems (T6SSs). An open access online database of all detected eCIS-like loci is presented to facilitate future studies. The presence of this bacterial injection machine in a multitude of organisms suggests that it may play an important ecological role in the life cycles of many bacteria.},
	language = {en},
	number = {2},
	urldate = {2022-05-13},
	journal = {Cell Reports},
	author = {Chen, Lihong and Song, Nan and Liu, Bo and Zhang, Nan and Alikhan, Nabil-Fareed and Zhou, Zhemin and Zhou, Yanyan and Zhou, Siyu and Zheng, Dandan and Chen, Mingxing and Hapeshi, Alexia and Healey, Joseph and Waterfield, Nicholas R. and Yang, Jian and Yang, Guowei},
	month = oct,
	year = {2019},
	pmid = {31597107},
	pmcid = {PMC6899500},
	note = {22 citations (Crossref) [2022-06-30]},
	pages = {511--521.e2},
	file = {Full Text:/usr/users/QIB_fr005/alikhan/Zotero/storage/9FDRTUVT/Chen et al. - 2019 - Genome-wide Identification and Characterization of.pdf:application/pdf},
}

@article{foster-nyarko_gambian_2020,
	title = {Gambian poultry isolates from hyperendemic group of {AMR} {Escherichia} coli strains in sub-{Saharan} {Africa}},
	volume = {2},
	copyright = {Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International Licence (CC-BY-NC-ND)},
	issn = {2516-8290},
	url = {https://www.microbiologyresearch.org/content/journal/acmi/10.1099/acmi.ac2020.po0824},
	doi = {10.1099/acmi.ac2020.po0824},
	abstract = {Chickens and guinea fowl are commonly reared in Gambian homes as affordable sources of protein. Using standard microbiological techniques, we obtained 68 caecal isolates of
              Escherichia coli
              from ten chickens and nine guinea fowl in rural Gambia. After Illumina whole-genome sequencing, 28 sequence types were detected in the isolates (four of them novel), of which ST155 was the most common (22/68, 32\%). These strains span four of the eight main phylogroups of
              E. coli
              , with phylogroups B1 and A being most prevalent. Nearly a third of the isolates harboured at least one antimicrobial resistance gene, while most of the ST155 isolates (14/22, 64\%) encoded resistance to ≥3 classes of clinically relevant antibiotics, as well as putative virulence factors, suggesting pathogenic potential in humans. Furthermore, hierarchical clustering revealed that several Gambian poultry strains were closely related to isolates from humans. Although the ST155 lineage is common in poultry from Africa and South America, the Gambian ST155 isolates sit within a tight genomic cluster (100 alleles difference) of strains from poultry and livestock in sub-Saharan Africa (the Gambia, Uganda and Kenya). Continued surveillance of
              E. coli
              and other potential pathogens in rural backyard poultry from sub-Saharan Africa is warranted.},
	language = {en},
	number = {7A},
	urldate = {2022-05-13},
	journal = {Access Microbiology},
	author = {Foster-Nyarko, Ebenezer and Alikhan, Nabil-Fareed and Ravi, Anuradha and Thomson, Nicholas and Jarju, Sheikh and Secka, Arss and Antonio, Martin and J. Pallen, Mark},
	month = jul,
	year = {2020},
	note = {0 citations (Crossref) [2022-06-30]},
}

@article{gilroy_extensive_2021,
	title = {Extensive microbial diversity within the chicken gut microbiome revealed by metagenomics and culture},
	volume = {9},
	copyright = {Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International Licence (CC-BY-NC-ND)},
	issn = {2167-8359},
	url = {https://peerj.com/articles/10941},
	doi = {10.7717/peerj.10941},
	abstract = {Background
              The chicken is the most abundant food animal in the world. However, despite its importance, the chicken gut microbiome remains largely undefined. Here, we exploit culture-independent and culture-dependent approaches to reveal extensive taxonomic diversity within this complex microbial community.
            
            
              Results
              
                We performed metagenomic sequencing of fifty chicken faecal samples from two breeds and analysed these, alongside all (
                n
                = 582) relevant publicly available chicken metagenomes, to cluster over 20 million non-redundant genes and to construct over 5,500 metagenome-assembled bacterial genomes. In addition, we recovered nearly 600 bacteriophage genomes. This represents the most comprehensive view of taxonomic diversity within the chicken gut microbiome to date, encompassing hundreds of novel candidate bacterial genera and species. To provide a stable, clear and memorable nomenclature for novel species, we devised a scalable combinatorial system for the creation of hundreds of well-formed Latin binomials. We cultured and genome-sequenced bacterial isolates from chicken faeces, documenting over forty novel species, together with three species from the genus
                Escherichia
                , including the newly named species
                Escherichia whittamii
                .
              
            
            
              Conclusions
              Our metagenomic and culture-based analyses provide new insights into the bacterial, archaeal and bacteriophage components of the chicken gut microbiome. The resulting datasets expand the known diversity of the chicken gut microbiome and provide a key resource for future high-resolution taxonomic and functional studies on the chicken gut microbiome.},
	language = {en},
	urldate = {2022-05-13},
	journal = {PeerJ},
	author = {Gilroy, Rachel and Ravi, Anuradha and Getino, Maria and Pursley, Isabella and Horton, Daniel L. and Alikhan, Nabil-Fareed and Baker, Dave and Gharbi, Karim and Hall, Neil and Watson, Mick and Adriaenssens, Evelien M. and Foster-Nyarko, Ebenezer and Jarju, Sheikh and Secka, Arss and Antonio, Martin and Oren, Aharon and Chaudhuri, Roy R. and La Ragione, Roberto and Hildebrand, Falk and Pallen, Mark J.},
	month = apr,
	year = {2021},
	note = {24 citations (Crossref) [2022-06-30]},
	pages = {e10941},
	file = {Full Text:/usr/users/QIB_fr005/alikhan/Zotero/storage/M9MK9UVD/Gilroy et al. - 2021 - Extensive microbial diversity within the chicken g.pdf:application/pdf},
}

@article{griffiths_future-proofing_2022,
	title = {Future-proofing and maximizing the utility of metadata: {The} {PHA4GE} {SARS}-{CoV}-2 contextual data specification package},
	volume = {11},
	copyright = {Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International Licence (CC-BY-NC-ND)},
	issn = {2047-217X},
	shorttitle = {Future-proofing and maximizing the utility of metadata},
	url = {https://academic.oup.com/gigascience/article/doi/10.1093/gigascience/giac003/6529104},
	doi = {10.1093/gigascience/giac003},
	abstract = {Abstract
            
              Background
              The Public Health Alliance for Genomic Epidemiology (PHA4GE) (https://pha4ge.org) is a global coalition that is actively working to establish consensus standards, document and share best practices, improve the availability of critical bioinformatics tools and resources, and advocate for greater openness, interoperability, accessibility, and reproducibility in public health microbial bioinformatics. In the face of the current pandemic, PHA4GE has identified a need for a fit-for-purpose, open-source SARS-CoV-2 contextual data standard.
            
            
              Results
              As such, we have developed a SARS-CoV-2 contextual data specification package based on harmonizable, publicly available community standards. The specification can be implemented via a collection template, as well as an array of protocols and tools to support both the harmonization and submission of sequence data and contextual information to public biorepositories.
            
            
              Conclusions
              Well-structured, rich contextual data add value, promote reuse, and enable aggregation and integration of disparate datasets. Adoption of the proposed standard and practices will better enable interoperability between datasets and systems, improve the consistency and utility of generated data, and ultimately facilitate novel insights and discoveries in SARS-CoV-2 and COVID-19. The package is now supported by the NCBI’s BioSample database.},
	language = {en},
	urldate = {2022-05-13},
	journal = {GigaScience},
	author = {Griffiths, Emma J and Timme, Ruth E and Mendes, Catarina Inês and Page, Andrew J and Alikhan, Nabil-Fareed and Fornika, Dan and Maguire, Finlay and Campos, Josefina and Park, Daniel and Olawoye, Idowu B and Oluniyi, Paul E and Anderson, Dominique and Christoffels, Alan and da Silva, Anders Gonçalves and Cameron, Rhiannon and Dooley, Damion and Katz, Lee S and Black, Allison and Karsch-Mizrachi, Ilene and Barrett, Tanya and Johnston, Anjanette and Connor, Thomas R and Nicholls, Samuel M and Witney, Adam A and Tyson, Gregory H and Tausch, Simon H and Raphenya, Amogelang R and Alcock, Brian and Aanensen, David M and Hodcroft, Emma and Hsiao, William W L and Vasconcelos, Ana Tereza R and MacCannell, Duncan R},
	month = feb,
	year = {2022},
	pmid = {35169842},
	pmcid = {PMC8847733},
	note = {1 citations (Crossref) [2022-06-30]},
	pages = {giac003},
	file = {Full Text:/usr/users/QIB_fr005/alikhan/Zotero/storage/EZVS8IM7/Griffiths et al. - 2022 - Future-proofing and maximizing the utility of meta.pdf:application/pdf},
}

@article{bawn_evolution_2020,
	title = {Evolution of {Salmonella} enterica serotype {Typhimurium} driven by anthropogenic selection and niche adaptation},
	volume = {16},
	copyright = {Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International Licence (CC-BY-NC-ND)},
	issn = {1553-7404},
	url = {https://dx.plos.org/10.1371/journal.pgen.1008850},
	doi = {10.1371/journal.pgen.1008850},
	abstract = {Salmonella enterica serotype Typhimurium (S. Typhimurium) is a leading cause of gastroenteritis and bacteraemia worldwide, and a model organism for the study of host-pathogen interactions. Two S. Typhimurium strains (SL1344 and ATCC14028) are widely used to study host-pathogen interactions, yet genotypic variation results in strains with diverse host range, pathogenicity and risk to food safety. The population structure of diverse strains of S. Typhimurium revealed a major phylogroup of predominantly sequence type 19 (ST19) and a minor phylogroup of ST36. The major phylogroup had a population structure with two high order clades (α and β) and multiple subclades on extended internal branches, that exhibited distinct signatures of host adaptation and anthropogenic selection. Clade α contained a number of subclades composed of strains from well characterized epidemics in domesticated animals, while clade β contained multiple subclades associated with wild avian species. The contrasting epidemiology of strains in clade α and β was reflected by the distinct distribution of antimicrobial resistance (AMR) genes, accumulation of hypothetically disrupted coding sequences (HDCS), and signatures of functional diversification. These observations were consistent with elevated anthropogenic selection of clade α lineages from adaptation to circulation in populations of domesticated livestock, and the predisposition of clade β lineages to undergo adaptation to an invasive lifestyle by a process of convergent evolution with of host adapted Salmonella serotypes. Gene flux was predominantly driven by acquisition and recombination of prophage and associated cargo genes, with only occasional loss of these elements. The acquisition of large chromosomally-encoded genetic islands was limited, but notably, a feature of two recent pandemic clones (DT104 and monophasic S. Typhimurium ST34) of clade α (SGI-1 and SGI-4).},
	language = {en},
	number = {6},
	urldate = {2022-05-13},
	journal = {PLOS Genetics},
	author = {Bawn, Matt and Alikhan, Nabil-Fareed and Thilliez, Gaëtan and Kirkwood, Mark and Wheeler, Nicole E. and Petrovska, Liljana and Dallman, Timothy J. and Adriaenssens, Evelien M. and Hall, Neil and Kingsley, Robert A.},
	editor = {Didelot, Xavier},
	month = jun,
	year = {2020},
	pmid = {32511244},
	pmcid = {PMC7302871},
	note = {18 citations (Crossref) [2022-06-30]},
	pages = {e1008850},
	file = {Full Text:/usr/users/QIB_fr005/alikhan/Zotero/storage/ZJTB4SNT/Bawn et al. - 2020 - Evolution of Salmonella enterica serotype Typhimur.pdf:application/pdf},
}

@article{volz_evaluating_2021,
	title = {Evaluating the {Effects} of {SARS}-{CoV}-2 {Spike} {Mutation} {D614G} on {Transmissibility} and {Pathogenicity}},
	volume = {184},
	copyright = {Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International Licence (CC-BY-NC-ND)},
	issn = {00928674},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0092867420315373},
	doi = {10.1016/j.cell.2020.11.020},
	abstract = {Global dispersal and increasing frequency of the SARS-CoV-2 spike protein variant D614G are suggestive of a selective advantage but may also be due to a random founder effect. We investigate the hypothesis for positive selection of spike D614G in the United Kingdom using more than 25,000 whole genome SARS-CoV-2 sequences. Despite the availability of a large dataset, well represented by both spike 614 variants, not all approaches showed a conclusive signal of positive selection. Population genetic analysis indicates that 614G increases in frequency relative to 614D in a manner consistent with a selective advantage. We do not find any indication that patients infected with the spike 614G variant have higher COVID-19 mortality or clinical severity, but 614G is associated with higher viral load and younger age of patients. Significant differences in growth and size of 614G phylogenetic clusters indicate a need for continued study of this variant.},
	language = {en},
	number = {1},
	urldate = {2022-05-13},
	journal = {Cell},
	author = {Volz, Erik and Hill, Verity and McCrone, John T. and Price, Anna and Jorgensen, David and O’Toole, Áine and Southgate, Joel and Johnson, Robert and Jackson, Ben and Nascimento, Fabricia F. and Rey, Sara M. and Nicholls, Samuel M. and Colquhoun, Rachel M. and da Silva Filipe, Ana and Shepherd, James and Pascall, David J. and Shah, Rajiv and Jesudason, Natasha and Li, Kathy and Jarrett, Ruth and Pacchiarini, Nicole and Bull, Matthew and Geidelberg, Lily and Siveroni, Igor and Goodfellow, Ian and Loman, Nicholas J. and Pybus, Oliver G. and Robertson, David L. and Thomson, Emma C. and Rambaut, Andrew and Connor, Thomas R. and Koshy, Cherian and Wise, Emma and Cortes, Nick and Lynch, Jessica and Kidd, Stephen and Mori, Matilde and Fairley, Derek J. and Curran, Tanya and McKenna, James P. and Adams, Helen and Fraser, Christophe and Golubchik, Tanya and Bonsall, David and Moore, Catrin and Caddy, Sarah L. and Khokhar, Fahad A. and Wantoch, Michelle and Reynolds, Nicola and Warne, Ben and Maksimovic, Joshua and Spellman, Karla and McCluggage, Kathryn and John, Michaela and Beer, Robert and Afifi, Safiah and Morgan, Sian and Marchbank, Angela and Price, Anna and Kitchen, Christine and Gulliver, Huw and Merrick, Ian and Southgate, Joel and Guest, Martyn and Munn, Robert and Workman, Trudy and Connor, Thomas R. and Fuller, William and Bresner, Catherine and Snell, Luke B. and Charalampous, Themoula and Nebbia, Gaia and Batra, Rahul and Edgeworth, Jonathan and Robson, Samuel C. and Beckett, Angela and Loveson, Katie F. and Aanensen, David M. and Underwood, Anthony P. and Yeats, Corin A. and Abudahab, Khalil and Taylor, Ben E.W. and Menegazzo, Mirko and Clark, Gemma and Smith, Wendy and Khakh, Manjinder and Fleming, Vicki M. and Lister, Michelle M. and Howson-Wells, Hannah C. and Berry, Louise and Boswell, Tim and Joseph, Amelia and Willingham, Iona and Bird, Paul and Helmer, Thomas and Fallon, Karlie and Holmes, Christopher and Tang, Julian and Raviprakash, Veena and Campbell, Sharon and Sheriff, Nicola and Loose, Matthew W. and Holmes, Nadine and Moore, Christopher and Carlile, Matthew and Wright, Victoria and Sang, Fei and Debebe, Johnny and Coll, Francesc and Signell, Adrian W. and Betancor, Gilberto and Wilson, Harry D. and Feltwell, Theresa and Houldcroft, Charlotte J. and Eldirdiri, Sahar and Kenyon, Anita and Davis, Thomas and Pybus, Oliver and du Plessis, Louis and Zarebski, Alex and Raghwani, Jayna and Kraemer, Moritz and Francois, Sarah and Attwood, Stephen and Vasylyeva, Tetyana and Torok, M. Estee and Hamilton, William L. and Goodfellow, Ian G. and Hall, Grant and Jahun, Aminu S. and Chaudhry, Yasmin and Hosmillo, Myra and Pinckert, Malte L. and Georgana, Iliana and Yakovleva, Anna and Meredith, Luke W. and Moses, Samuel and Lowe, Hannah and Ryan, Felicity and Fisher, Chloe L. and Awan, Ali R. and Boyes, John and Breuer, Judith and Harris, Kathryn Ann and Brown, Julianne Rose and Shah, Divya and Atkinson, Laura and Lee, Jack C.D. and Alcolea-Medina, Adela and Moore, Nathan and Cortes, Nicholas and Williams, Rebecca and Chapman, Michael R. and Levett, Lisa J. and Heaney, Judith and Smith, Darren L. and Bashton, Matthew and Young, Gregory R. and Allan, John and Loh, Joshua and Randell, Paul A. and Cox, Alison and Madona, Pinglawathee and Holmes, Alison and Bolt, Frances and Price, James and Mookerjee, Siddharth and Rowan, Aileen and Taylor, Graham P. and Ragonnet-Cronin, Manon and Nascimento, Fabricia F. and Jorgensen, David and Siveroni, Igor and Johnson, Rob and Boyd, Olivia and Geidelberg, Lily and Volz, Erik M. and Brunker, Kirstyn and Smollett, Katherine L. and Loman, Nicholas J. and Quick, Joshua and McMurray, Claire and Stockton, Joanne and Nicholls, Sam and Rowe, Will and Poplawski, Radoslaw and Martinez-Nunez, Rocio T. and Mason, Jenifer and Robinson, Trevor I. and O'Toole, Elaine and Watts, Joanne and Breen, Cassie and Cowell, Angela and Ludden, Catherine and Sluga, Graciela and Machin, Nicholas W. and Ahmad, Shazaad S.Y. and George, Ryan P. and Halstead, Fenella and Sivaprakasam, Venkat and Thomson, Emma C. and Shepherd, James G. and Asamaphan, Patawee and Niebel, Marc O. and Li, Kathy K. and Shah, Rajiv N. and Jesudason, Natasha G. and Parr, Yasmin A. and Tong, Lily and Broos, Alice and Mair, Daniel and Nichols, Jenna and Carmichael, Stephen N. and Nomikou, Kyriaki and Aranday-Cortes, Elihu and Johnson, Natasha and Starinskij, Igor and da Silva Filipe, Ana and Robertson, David L. and Orton, Richard J. and Hughes, Joseph and Vattipally, Sreenu and Singer, Joshua B. and Hale, Antony D. and Macfarlane-Smith, Louissa R. and Harper, Katherine L. and Taha, Yusri and Payne, Brendan A.I. and Burton-Fanning, Shirelle and Waugh, Sheila and Collins, Jennifer and Eltringham, Gary and Templeton, Kate E. and McHugh, Martin P. and Dewar, Rebecca and Wastenge, Elizabeth and Dervisevic, Samir and Stanley, Rachael and Prakash, Reenesh and Stuart, Claire and Elumogo, Ngozi and Sethi, Dheeraj K. and Meader, Emma J. and Coupland, Lindsay J. and Potter, Will and Graham, Clive and Barton, Edward and Padgett, Debra and Scott, Garren and Swindells, Emma and Greenaway, Jane and Nelson, Andrew and Yew, Wen C. and Resende Silva, Paola C. and Andersson, Monique and Shaw, Robert and Peto, Timothy and Justice, Anita and Eyre, David and Crooke, Derrick and Hoosdally, Sarah and Sloan, Tim J. and Duckworth, Nichola and Walsh, Sarah and Chauhan, Anoop J. and Glaysher, Sharon and Bicknell, Kelly and Wyllie, Sarah and Butcher, Ethan and Elliott, Scott and Lloyd, Allyson and Impey, Robert and Levene, Nick and Monaghan, Lynn and Bradley, Declan T. and Allara, Elias and Pearson, Clare and Muir, Peter and Vipond, Ian B. and Hopes, Richard and Pymont, Hannah M. and Hutchings, Stephanie and Curran, Martin D. and Parmar, Surendra and Lackenby, Angie and Mbisa, Tamyo and Platt, Steven and Miah, Shahjahan and Bibby, David and Manso, Carmen and Hubb, Jonathan and Chand, Meera and Dabrera, Gavin and Ramsay, Mary and Bradshaw, Daniel and Thornton, Alicia and Myers, Richard and Schaefer, Ulf and Groves, Natalie and Gallagher, Eileen and Lee, David and Williams, David and Ellaby, Nicholas and Harrison, Ian and Hartman, Hassan and Manesis, Nikos and Patel, Vineet and Bishop, Chloe and Chalker, Vicki and Osman, Husam and Bosworth, Andrew and Robinson, Esther and Holden, Matthew T.G. and Shaaban, Sharif and Birchley, Alec and Adams, Alexander and Davies, Alisha and Gaskin, Amy and Plimmer, Amy and Gatica-Wilcox, Bree and McKerr, Caoimhe and Moore, Catherine and Williams, Chris and Heyburn, David and De Lacy, Elen and Hilvers, Ember and Downing, Fatima and Shankar, Giri and Jones, Hannah and Asad, Hibo and Coombes, Jason and Watkins, Joanne and Evans, Johnathan M. and Fina, Laia and Gifford, Laura and Gilbert, Lauren and Graham, Lee and Perry, Malorie and Morgan, Mari and Bull, Matthew and Cronin, Michelle and Pacchiarini, Nicole and Craine, Noel and Jones, Rachel and Howe, Robin and Corden, Sally and Rey, Sara and Kumziene-Summerhayes, Sara and Taylor, Sarah and Cottrell, Simon and Jones, Sophie and Edwards, Sue and O’Grady, Justin and Page, Andrew J. and Wain, John and Webber, Mark A. and Mather, Alison E. and Baker, David J. and Rudder, Steven and Yasir, Muhammad and Thomson, Nicholas M. and Aydin, Alp and Tedim, Ana P. and Kay, Gemma L. and Trotter, Alexander J. and Gilroy, Rachel A.J. and Alikhan, Nabil-Fareed and de Oliveira Martins, Leonardo and Le-Viet, Thanh and Meadows, Lizzie and Kolyva, Anastasia and Diaz, Maria and Bell, Andrew and Gutierrez, Ana Victoria and Charles, Ian G. and Adriaenssens, Evelien M. and Kingsley, Robert A. and Casey, Anna and Simpson, David A. and Molnar, Zoltan and Thompson, Thomas and Acheson, Erwan and Masoli, Jane A.H. and Knight, Bridget A. and Hattersley, Andrew and Ellard, Sian and Auckland, Cressida and Mahungu, Tabitha W. and Irish-Tavares, Dianne and Haque, Tanzina and Bourgeois, Yann and Scarlett, Garry P. and Partridge, David G. and Raza, Mohammad and Evans, Cariad and Johnson, Kate and Liggett, Steven and Baker, Paul and Essex, Sarah and Lyons, Ronan A. and Caller, Laura G. and Castellano, Sergi and Williams, Rachel J. and Kristiansen, Mark and Roy, Sunando and Williams, Charlotte A. and Dyal, Patricia L. and Tutill, Helena J. and Panchbhaya, Yasmin N. and Forrest, Leysa M. and Niola, Paola and Findlay, Jacqueline and Brooks, Tony T. and Gavriil, Artemis and Mestek-Boukhibar, Lamia and Weeks, Sam and Pandey, Sarojini and Berry, Lisa and Jones, Katie and Richter, Alex and Beggs, Andrew and Smith, Colin P. and Bucca, Giselda and Hesketh, Andrew R. and Harrison, Ewan M. and Peacock, Sharon J. and Palmer, Sophie and Churcher, Carol M. and Bellis, Katherine L. and Girgis, Sophia T. and Naydenova, Plamena and Blane, Beth and Sridhar, Sushmita and Ruis, Chris and Forrest, Sally and Cormie, Claire and Gill, Harmeet K. and Dias, Joana and Higginson, Ellen E. and Maes, Mailis and Young, Jamie and Kermack, Leanne M. and Hadjirin, Nazreen F. and Aggarwal, Dinesh and Griffith, Luke and Swingler, Tracey and Davidson, Rose K. and Rambaut, Andrew and Williams, Thomas and Balcazar, Carlos E. and Gallagher, Michael D. and O'Toole, Áine and Rooke, Stefan and Jackson, Ben and Colquhoun, Rachel and Ashworth, Jordan and Hill, Verity and McCrone, J.T. and Scher, Emily and Yu, Xiaoyu and Williamson, Kathleen A. and Stanton, Thomas D. and Michell, Stephen L. and Bewshea, Claire M. and Temperton, Ben and Michelsen, Michelle L. and Warwick-Dugdale, Joanna and Manley, Robin and Farbos, Audrey and Harrison, James W. and Sambles, Christine M. and Studholme, David J. and Jeffries, Aaron R. and Darby, Alistair C. and Hiscox, Julian A. and Paterson, Steve and Iturriza-Gomara, Miren and Jackson, Kathryn A. and Lucaci, Anita O. and Vamos, Edith E. and Hughes, Margaret and Rainbow, Lucille and Eccles, Richard and Nelson, Charlotte and Whitehead, Mark and Turtle, Lance and Haldenby, Sam T. and Gregory, Richard and Gemmell, Matthew and Kwiatkowski, Dominic and de Silva, Thushan I. and Smith, Nikki and Angyal, Adrienn and Lindsey, Benjamin B. and Groves, Danielle C. and Green, Luke R. and Wang, Dennis and Freeman, Timothy M. and Parker, Matthew D. and Keeley, Alexander J. and Parsons, Paul J. and Tucker, Rachel M. and Brown, Rebecca and Wyles, Matthew and Constantinidou, Chrystala and Unnikrishnan, Meera and Ott, Sascha and Cheng, Jeffrey K.J. and Bridgewater, Hannah E. and Frost, Lucy R. and Taylor-Joyce, Grace and Stark, Richard and Baxter, Laura and Alam, Mohammad T. and Brown, Paul E. and McClure, Patrick C. and Chappell, Joseph G. and Tsoleridis, Theocharis and Ball, Jonathan and Gramatopoulos, Dimitris and Buck, David and Todd, John A. and Green, Angie and Trebes, Amy and MacIntyre-Cockett, George and de Cesare, Mariateresa and Langford, Cordelia and Alderton, Alex and Amato, Roberto and Goncalves, Sonia and Jackson, David K. and Johnston, Ian and Sillitoe, John and Palmer, Steve and Lawniczak, Mara and Berriman, Matt and Danesh, John and Livett, Rich and Shirley, Lesley and Farr, Ben and Quail, Mike and Thurston, Scott and Park, Naomi and Betteridge, Emma and Weldon, Danni and Goodwin, Scott and Nelson, Rachel and Beaver, Charlotte and Letchford, Laura and Jackson, David A. and Foulser, Luke and McMinn, Liz and Prestwood, Liam and Kay, Sally and Kane, Leanne and Dorman, Matthew J. and Martincorena, Inigo and Puethe, Christoph and Keatley, Jon-Paul and Tonkin-Hill, Gerry and Smith, Christen and Jamrozy, Dorota and Beale, Mathew A. and Patel, Minal and Ariani, Cristina and Spencer-Chapman, Michael and Drury, Eleanor and Lo, Stephanie and Rajatileka, Shavanthi and Scott, Carol and James, Keith and Buddenborg, Sarah K. and Berger, Duncan J. and Patel, Gaurang and Garcia-Casado, Maria V. and Dibling, Thomas and McGuigan, Samantha and Rogers, Hazel A. and Hunter, Adam D. and Souster, Emily and Neaverson, Alexandra S.},
	month = jan,
	year = {2021},
	pmid = {33275900},
	pmcid = {PMC7674007},
	note = {555 citations (Crossref) [2022-06-30]},
	pages = {64--75.e11},
	file = {Full Text:/usr/users/QIB_fr005/alikhan/Zotero/storage/GYHK8W5Q/Volz et al. - 2021 - Evaluating the Effects of SARS-CoV-2 Spike Mutatio.pdf:application/pdf},
}

@article{key_emergence_2020,
	title = {Emergence of human-adapted {Salmonella} enterica is linked to the {Neolithization} process},
	volume = {4},
	copyright = {Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International Licence (CC-BY-NC-ND)},
	issn = {2397-334X},
	url = {http://www.nature.com/articles/s41559-020-1106-9},
	doi = {10.1038/s41559-020-1106-9},
	abstract = {It has been hypothesized that the Neolithic transition towards an agricultural and pastoralist economy facilitated the emergence of human-adapted pathogens. Here, we recovered eight Salmonella enterica subsp. enterica genomes from human skeletons of transitional foragers, pastoralists and agropastoralists in western Eurasia that were up to 6,500 yr old. Despite the high genetic diversity of S. enterica, all ancient bacterial genomes clustered in a single previously uncharacterized branch that contains S. enterica adapted to multiple mammalian species. All ancient bacterial genomes from prehistoric (agro-)pastoralists fall within a part of this branch that also includes the human-specific S. enterica Paratyphi C, illustrating the evolution of a human pathogen over a period of 5,000 yr. Bacterial genomic comparisons suggest that the earlier ancient strains were not host specific, differed in pathogenic potential and experienced convergent pseudogenization that accompanied their downstream host adaptation. These observations support the concept that the emergence of human-adapted S. enterica is linked to human cultural transformations.},
	language = {en},
	number = {3},
	urldate = {2022-05-13},
	journal = {Nature Ecology \& Evolution},
	author = {Key, Felix M. and Posth, Cosimo and Esquivel-Gomez, Luis R. and Hübler, Ron and Spyrou, Maria A. and Neumann, Gunnar U. and Furtwängler, Anja and Sabin, Susanna and Burri, Marta and Wissgott, Antje and Lankapalli, Aditya Kumar and Vågene, Åshild J. and Meyer, Matthias and Nagel, Sarah and Tukhbatova, Rezeda and Khokhlov, Aleksandr and Chizhevsky, Andrey and Hansen, Svend and Belinsky, Andrey B. and Kalmykov, Alexey and Kantorovich, Anatoly R. and Maslov, Vladimir E. and Stockhammer, Philipp W. and Vai, Stefania and Zavattaro, Monica and Riga, Alessandro and Caramelli, David and Skeates, Robin and Beckett, Jessica and Gradoli, Maria Giuseppina and Steuri, Noah and Hafner, Albert and Ramstein, Marianne and Siebke, Inga and Lösch, Sandra and Erdal, Yilmaz Selim and Alikhan, Nabil-Fareed and Zhou, Zhemin and Achtman, Mark and Bos, Kirsten and Reinhold, Sabine and Haak, Wolfgang and Kühnert, Denise and Herbig, Alexander and Krause, Johannes},
	month = mar,
	year = {2020},
	pmid = {32094538},
	pmcid = {PMC7186082},
	note = {39 citations (Crossref) [2022-06-30]},
	pages = {324--333},
}

@article{rasheed_emergence_2020,
	title = {Emergence of {Resistance} to {Fluoroquinolones} and {Third}-{Generation} {Cephalosporins} in {Salmonella} {Typhi} in {Lahore}, {Pakistan}},
	volume = {8},
	copyright = {Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International Licence (CC-BY-NC-ND)},
	issn = {2076-2607},
	url = {https://www.mdpi.com/2076-2607/8/9/1336},
	doi = {10.3390/microorganisms8091336},
	abstract = {Extensively drug-resistant (XDR) Salmonella Typhi has been reported in Sindh province of Pakistan since 2016. The potential for further spread is of serious concern as remaining treatment options are severely limited. We report the phenotypic and genotypic characterization of 27 XDR S. Typhi isolated from patients attending Jinnah Hospital, Lahore, Pakistan. Isolates were identified by biochemical profiling; antimicrobial susceptibility was determined by a modified Kirby–Bauer method. These findings were confirmed using Illumina whole genome nucleotide sequence data. All sequences were compared to the outbreak strain from Southern Pakistan and typed using the S. Typhi genotyping scheme. All isolates were confirmed by a sequence analysis to harbor an IncY plasmid and the CTX-M-15 ceftriaxone resistance determinant. All isolates were of the same genotypic background as the outbreak strain from Sindh province. We report the first emergence of XDR S. Typhi in Punjab province of Pakistan confirmed by whole genome sequencing.},
	language = {en},
	number = {9},
	urldate = {2022-05-13},
	journal = {Microorganisms},
	author = {Rasheed, Farhan and Saeed, Muhammad and Alikhan, Nabil-Fareed and Baker, David and Khurshid, Mohsin and Ainsworth, Emma V. and Turner, A. Keith and Imran, Ambereen Anwar and Rasool, Muhammad Hidayat and Saqalein, Muhammad and Nisar, Muhammad Atif and Fayyaz ur Rehman, Muhammad and Wain, John and Yasir, Muhammad and Langridge, Gemma C. and Ikram, Aamer},
	month = sep,
	year = {2020},
	pmid = {32883020},
	pmcid = {PMC7564241},
	note = {15 citations (Crossref) [2022-06-30]},
	pages = {1336},
	file = {Full Text:/usr/users/QIB_fr005/alikhan/Zotero/storage/BQN36SLV/Rasheed et al. - 2020 - Emergence of Resistance to Fluoroquinolones and Th.pdf:application/pdf},
}

@article{alikhan_dynamics_2022,
	title = {Dynamics of {Salmonella} enterica and antimicrobial resistance in the {Brazilian} poultry industry and global impacts on public health},
	volume = {18},
	issn = {1553-7404},
	url = {https://dx.plos.org/10.1371/journal.pgen.1010174},
	doi = {10.1371/journal.pgen.1010174},
	abstract = {Non-typhoidal
              Salmonella enterica
              is a common cause of diarrhoeal disease; in humans, consumption of contaminated poultry meat is believed to be a major source. Brazil is the world’s largest exporter of chicken meat globally, and previous studies have indicated the introduction of
              Salmonella
              serovars through imported food products from Brazil. Here we provide an in-depth genomic characterisation and evolutionary analysis to investigate the most prevalent serovars and antimicrobial resistance (AMR) in Brazilian chickens and assess the impact to public health of products contaminated with
              S
              .
              enterica
              imported into the United Kingdom from Brazil. To do so, we examine 183
              Salmonella
              genomes from chickens in Brazil and 357 genomes from humans, domestic poultry and imported Brazilian poultry products isolated in the United Kingdom.
              S
              .
              enterica
              serovars Heidelberg and Minnesota were the most prevalent serovars in Brazil and in meat products imported from Brazil into the UK. We extended our analysis to include 1,259 publicly available
              Salmonella
              Heidelberg and
              Salmonella
              Minnesota genomes for context. The Brazil genomes form clades distinct from global isolates, with temporal analysis suggesting emergence of these
              Salmonella
              Heidelberg and
              Salmonella
              Minnesota clades in the early 2000s, around the time of the 2003 introduction of the Enteritidis vaccine in Brazilian poultry. Analysis showed genomes within the
              Salmonella
              Heidelberg and
              Salmonella
              Minnesota clades shared resistance to sulphonamides, tetracyclines and beta-lactams conferred by
              sul2
              ,
              tetA
              and
              bla
              CMY-2
              genes, not widely observed in other co-circulating serovars despite similar selection pressures. The
              sul2
              and
              tetA
              genes were concomitantly carried on IncC plasmids, whereas
              bla
              CMY-2
              was either co-located with the
              sul2
              and
              tetA
              genes on IncC plasmids or independently on IncI1 plasmids. Long-term surveillance data collected in the UK showed no increase in the incidence of
              Salmonella
              Heidelberg or
              Salmonella
              Minnesota in human cases of clinical disease in the UK following the increase of these two serovars in Brazilian poultry. In addition, almost all of the small number of UK-derived genomes which cluster with the Brazilian poultry-derived sequences could either be attributed to human cases with a recent history of foreign travel or were from imported Brazilian food products. These findings indicate that even should
              Salmonella
              from imported Brazilian poultry products reach UK consumers, they are very unlikely to be causing disease. No evidence of the Brazilian strains of
              Salmonella
              Heidelberg or
              Salmonella
              Minnesota were observed in UK domestic chickens. These findings suggest that introduction of the
              Salmonella
              Enteritidis vaccine, in addition to increasing antimicrobial use, could have resulted in replacement of salmonellae in Brazilian poultry flocks with serovars that are more drug resistant, but less associated with disease in humans in the UK. The plasmids conferring resistance to beta-lactams, sulphonamides and tetracyclines likely conferred a competitive advantage to the
              Salmonella
              Minnesota and
              Salmonella
              Heidelberg serovars in this setting of high antimicrobial use, but the apparent lack of transfer to other serovars present in the same setting suggests barriers to horizontal gene transfer that could be exploited in intervention strategies to reduce AMR. The insights obtained reinforce the importance of One Health genomic surveillance.},
	language = {en},
	number = {6},
	urldate = {2022-06-07},
	journal = {PLOS Genetics},
	author = {Alikhan, Nabil-Fareed and Moreno, Luisa Zanolli and Castellanos, Luis Ricardo and Chattaway, Marie Anne and McLauchlin, Jim and Lodge, Martin and O’Grady, Justin and Zamudio, Roxana and Doughty, Emma and Petrovska, Liljana and Cunha, Marcos Paulo Vieira and Knöbl, Terezinha and Moreno, Andrea Micke and Mather, Alison E.},
	editor = {Didelot, Xavier},
	month = jun,
	year = {2022},
	note = {0 citations (Crossref) [2022-06-30]},
	pages = {e1010174},
	file = {Full Text:/usr/users/QIB_fr005/alikhan/Zotero/storage/Z88DX57U/Alikhan et al. - 2022 - Dynamics of Salmonella enterica and antimicrobial .pdf:application/pdf},
}

@article{baker_coronahit_2021,
	title = {{CoronaHiT}: high-throughput sequencing of {SARS}-{CoV}-2 genomes},
	volume = {13},
	copyright = {Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International Licence (CC-BY-NC-ND)},
	issn = {1756-994X},
	shorttitle = {{CoronaHiT}},
	url = {https://genomemedicine.biomedcentral.com/articles/10.1186/s13073-021-00839-5},
	doi = {10.1186/s13073-021-00839-5},
	abstract = {Abstract
            We present CoronaHiT, a platform and throughput flexible method for sequencing SARS-CoV-2 genomes (≤ 96 on MinION or {\textgreater} 96 on Illumina NextSeq) depending on changing requirements experienced during the pandemic. CoronaHiT uses transposase-based library preparation of ARTIC PCR products. Method performance was demonstrated by sequencing 2 plates containing 95 and 59 SARS-CoV-2 genomes on nanopore and Illumina platforms and comparing to the ARTIC LoCost nanopore method. Of the 154 samples sequenced using all 3 methods, ≥ 90\% genome coverage was obtained for 64.3\% using ARTIC LoCost, 71.4\% using CoronaHiT-ONT and 76.6\% using CoronaHiT-Illumina, with almost identical clustering on a maximum likelihood tree. This protocol will aid the rapid expansion of SARS-CoV-2 genome sequencing globally.},
	language = {en},
	number = {1},
	urldate = {2022-05-13},
	journal = {Genome Medicine},
	author = {Baker, Dave J. and Aydin, Alp and Le-Viet, Thanh and Kay, Gemma L. and Rudder, Steven and de Oliveira Martins, Leonardo and Tedim, Ana P. and Kolyva, Anastasia and Diaz, Maria and Alikhan, Nabil-Fareed and Meadows, Lizzie and Bell, Andrew and Gutierrez, Ana Victoria and Trotter, Alexander J. and Thomson, Nicholas M. and Gilroy, Rachel and Griffith, Luke and Adriaenssens, Evelien M. and Stanley, Rachael and Charles, Ian G. and Elumogo, Ngozi and Wain, John and Prakash, Reenesh and Meader, Emma and Mather, Alison E. and Webber, Mark A. and Dervisevic, Samir and Page, Andrew J. and O’Grady, Justin},
	month = dec,
	year = {2021},
	pmid = {33563320},
	pmcid = {PMC7871948},
	note = {48 citations (Crossref) [2022-06-30]},
	pages = {21},
	file = {Full Text:/usr/users/QIB_fr005/alikhan/Zotero/storage/87WUBKGL/Baker et al. - 2021 - CoronaHiT high-throughput sequencing of SARS-CoV-.pdf:application/pdf},
}

@article{eales_characterising_2022,
	title = {Characterising the persistence of {RT}-{PCR} positivity and incidence in a community survey of {SARS}-{CoV}-2},
	volume = {7},
	issn = {2398-502X},
	url = {https://wellcomeopenresearch.org/articles/7-102/v1},
	doi = {10.12688/wellcomeopenres.17723.1},
	abstract = {Background:
              The REal-time Assessment of Community Transmission-1 (REACT-1) study has provided unbiased estimates of swab-positivity in England approximately monthly since May 2020 using RT-PCR testing of self-administered throat and nose swabs. However, estimating infection incidence requires an understanding of the persistence of RT-PCR swab-positivity in the community.
            
            
              Methods:
              During round 8 of REACT-1 from 6 January to 22 January 2021, we collected up to two additional swabs from 896 initially RT-PCR positive individuals approximately 6 and 9 days after their initial swab.
            
            
              Results:
              Test sensitivity and duration of positivity were estimated using an exponential decay model, for all participants and for subsets by initial N-gene cycle threshold (Ct) value, symptom status, lineage and age. A P-spline model was used to estimate infection incidence for the entire duration of the REACT-1 study. REACT-1 test sensitivity was estimated at 0.79 (0.77, 0.81) with median duration of positivity at 9.7 (8.9, 10.6) days. We found greater duration of positivity in those exhibiting symptoms, with low N-gene Ct values, or infected with the Alpha variant. Test sensitivity was found to be higher for those who were pre-symptomatic or with low N-gene Ct values. Compared to swab-positivity, our estimates of infection incidence included sharper features with evident transient increases around the time of changes in social distancing measures.
            
            
              Conclusions:
              These results validate previous efforts to estimate incidence of SARS-CoV-2 from swab-positivity data and provide a reliable means to obtain community infection estimates to inform policy response.},
	language = {en},
	urldate = {2022-05-13},
	journal = {Wellcome Open Research},
	author = {Eales, Oliver and Walters, Caroline E. and Wang, Haowei and Haw, David and Ainslie, Kylie E. C. and Atchison, Christina J. and Page, Andrew J. and Prosolek, Sophie and Trotter, Alexander J. and Le Viet, Thanh and Alikhan, Nabil-Fareed and Jackson, Leigh M. and Ludden, Catherine and {COVID-19 Genomics UK Consortium} and Ashby, Deborah and Donnelly, Christl A. and Cooke, Graham and Barclay, Wendy and Ward, Helen and Darzi, Ara and Elliott, Paul and Riley, Steven},
	month = mar,
	year = {2022},
	note = {2 citations (Crossref) [2022-06-30]},
	pages = {102},
	file = {Full Text:/usr/users/QIB_fr005/alikhan/Zotero/storage/GTABVRE4/Eales et al. - 2022 - Characterising the persistence of RT-PCR positivit.pdf:application/pdf},
}

@article{snell_combined_2022,
	title = {Combined epidemiological and genomic analysis of nosocomial {SARS}-{CoV}-2 infection early in the pandemic and the role of unidentified cases in transmission},
	volume = {28},
	copyright = {Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International Licence (CC-BY-NC-ND)},
	issn = {1198743X},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S1198743X21004353},
	doi = {10.1016/j.cmi.2021.07.040},
	abstract = {To analyse nosocomial transmission in the early stages of the coronavirus 2019 (COVID-19) pandemic at a large multisite healthcare institution. Nosocomial incidence is linked with infection control interventions.
Methods
Viral genome sequence and epidemiological data were analysed for 574 consecutive patients, including 86 nosocomial cases, with a positive PCR test for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) during the first 19 days of the pandemic.
Results
Forty-four putative transmission clusters were found through epidemiological analysis; these included 234 cases and all 86 nosocomial cases. SARS-CoV-2 genome sequences were obtained from 168/234 (72\%) of these cases in epidemiological clusters, including 77/86 nosocomial cases (90\%). Only 75/168 (45\%) of epidemiologically linked, sequenced cases were not refuted by applying genomic data, creating 14 final clusters accounting for 59/77 sequenced nosocomial cases (77\%). Viral haplotypes from these clusters were enriched 1–14x (median 4x) compared to the community. Three factors implicated unidentified cases in transmission: (a) community-onset or indeterminate cases were absent in 7/14 clusters (50\%), (b) four clusters (29\%) had additional evidence of cryptic transmission, and (c) in three clusters (21\%) diagnosis of the earliest case was delayed, which may have facilitated transmission. Nosocomial cases decreased to low levels (0–2 per day) despite continuing high numbers of admissions of community-onset SARS-CoV-2 cases (40–50 per day) and before the impact of introducing universal face masks and banning hospital visitors.
Conclusion
Genomics was necessary to accurately resolve transmission clusters. Our data support unidentified cases—such as healthcare workers or asymptomatic patients—as important vectors of transmission. Evidence is needed to ascertain whether routine screening increases case ascertainment and limits nosocomial transmission.},
	language = {en},
	number = {1},
	urldate = {2022-05-13},
	journal = {Clinical Microbiology and Infection},
	author = {Snell, Luke B. and Fisher, Chloe L. and Taj, Usman and Stirrup, Oliver and Merrick, Blair and Alcolea-Medina, Adela and Charalampous, Themoula and Signell, Adrian W. and Wilson, Harry D. and Betancor, Gilberto and Kia Ik, Mark Tan and Cunningham, Emma and Cliff, Penelope R. and Pickering, Suzanne and Galao, Rui Pedro and Batra, Rahul and Neil, Stuart J.D. and Malim, Michael H. and Doores, Katie J. and Douthwaite, Sam T. and Nebbia, Gaia and Edgeworth, Jonathan D. and Awan, Ali R.},
	month = jan,
	year = {2022},
	pmid = {34400345},
	pmcid = {PMC8361005},
	note = {4 citations (Crossref) [2022-06-30]},
	pages = {93--100},
	file = {Full Text:/usr/users/QIB_fr005/alikhan/Zotero/storage/DMNJKGWD/Snell et al. - 2022 - Combined epidemiological and genomic analysis of n.pdf:application/pdf},
}

@article{graham_changes_2021,
	title = {Changes in symptomatology, reinfection, and transmissibility associated with the {SARS}-{CoV}-2 variant {B}.1.1.7: an ecological study},
	volume = {6},
	copyright = {Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International Licence (CC-BY-NC-ND)},
	issn = {24682667},
	shorttitle = {Changes in symptomatology, reinfection, and transmissibility associated with the {SARS}-{CoV}-2 variant {B}.1.1.7},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S2468266721000554},
	doi = {10.1016/S2468-2667(21)00055-4},
	abstract = {The SARS-CoV-2 variant B.1.1.7 was first identified in December, 2020, in England. We aimed to investigate whether increases in the proportion of infections with this variant are associated with differences in symptoms or disease course, reinfection rates, or transmissibility.},
	language = {en},
	number = {5},
	urldate = {2022-05-13},
	journal = {The Lancet Public Health},
	author = {Graham, Mark S and Sudre, Carole H and May, Anna and Antonelli, Michela and Murray, Benjamin and Varsavsky, Thomas and Kläser, Kerstin and Canas, Liane S and Molteni, Erika and Modat, Marc and Drew, David A and Nguyen, Long H and Polidori, Lorenzo and Selvachandran, Somesh and Hu, Christina and Capdevila, Joan and Hammers, Alexander and Chan, Andrew T and Wolf, Jonathan and Spector, Tim D and Steves, Claire J and Ourselin, Sebastien and Koshy, Cherian and Ash, Amy and Wise, Emma and Moore, Nathan and Mori, Matilde and Cortes, Nick and Lynch, Jessica and Kidd, Stephen and Fairley, Derek J and Curran, Tanya and McKenna, James P and Adams, Helen and Fraser, Christophe and Golubchik, Tanya and Bonsall, David and Hassan-Ibrahim, Mohammed O and Malone, Cassandra S and Cogger, Benjamin J and Wantoch, Michelle and Reynolds, Nicola and Warne, Ben and Maksimovic, Joshua and Spellman, Karla and McCluggage, Kathryn and John, Michaela and Beer, Robert and Afifi, Safiah and Morgan, Sian and Marchbank, Angela and Price, Anna and Kitchen, Christine and Gulliver, Huw and Merrick, Ian and Southgate, Joel and Guest, Martyn and Munn, Robert and Workman, Trudy and Connor, Thomas R and Fuller, William and Bresner, Catherine and Snell, Luke B and Patel, Amita and Charalampous, Themoula and Nebbia, Gaia and Batra, Rahul and Edgeworth, Jonathan and Robson, Samuel C and Beckett, Angela H and Aanensen, David M and Underwood, Anthony P and Yeats, Corin A and Abudahab, Khalil and Taylor, Ben EW and Menegazzo, Mirko and Clark, Gemma and Smith, Wendy and Khakh, Manjinder and Fleming, Vicki M and Lister, Michelle M and Howson-Wells, Hannah C and Berry, Louise and Boswell, Tim and Joseph, Amelia and Willingham, Iona and Jones, Carl and Holmes, Christopher and Bird, Paul and Helmer, Thomas and Fallon, Karlie and Tang, Julian and Raviprakash, Veena and Campbell, Sharon and Sheriff, Nicola and Blakey, Victoria and Williams, Lesley-Anne and Loose, Matthew W and Holmes, Nadine and Moore, Christopher and Carlile, Matthew and Wright, Victoria and Sang, Fei and Debebe, Johnny and Coll, Francesc and Signell, Adrian W and Betancor, Gilberto and Wilson, Harry D and Eldirdiri, Sahar and Kenyon, Anita and Davis, Thomas and Pybus, Oliver G and du Plessis, Louis and Zarebski, Alex E and Raghwani, Jayna and Kraemer, Moritz UG and Francois, Sarah and Attwood, Stephen W and Vasylyeva, Tetyana I and Escalera Zamudio, Marina and Gutierrez, Bernardo and Torok, M. Estee and Hamilton, William L and Goodfellow, Ian G and Hall, Grant and Jahun, Aminu S and Chaudhry, Yasmin and Hosmillo, Myra and Pinckert, Malte L and Georgana, Iliana and Moses, Samuel and Lowe, Hannah and Bedford, Luke and Moore, Jonathan and Stonehouse, Susanne and Fisher, Chloe L and Awan, Ali R and BoYes, John and Breuer, Judith and Harris, Kathryn Ann and Brown, Julianne Rose and Shah, Divya and Atkinson, Laura and Lee, Jack CD and Storey, Nathaniel and Flaviani, Flavia and Alcolea-Medina, Adela and Williams, Rebecca and Vernet, Gabrielle and Chapman, Michael R and Levett, Lisa J and Heaney, Judith and Chatterton, Wendy and Pusok, Monika and Xu-McCrae, Li and Smith, Darren L and Bashton, Matthew and Young, Gregory R and Holmes, Alison and Randell, Paul Anthony and Cox, Alison and Madona, Pinglawathee and Bolt, Frances and Price, James and Mookerjee, Siddharth and Ragonnet-Cronin, Manon and Nascimento, Fabricia F. and Jorgensen, David and Siveroni, Igor and Johnson, Rob and Boyd, Olivia and Geidelberg, Lily and Volz, Erik M and Rowan, Aileen and Taylor, Graham P and Smollett, Katherine L and Loman, Nicholas J and Quick, Joshua and McMurray, Claire and Stockton, Joanne and Nicholls, Sam and Rowe, Will and Poplawski, Radoslaw and McNally, Alan and Martinez Nunez, Rocio T and Mason, Jenifer and Robinson, Trevor I and O'Toole, Elaine and Watts, Joanne and Breen, Cassie and Cowell, Angela and Sluga, Graciela and Machin, Nicholas W and Ahmad, Shazaad S Y and George, Ryan P and Halstead, Fenella and Sivaprakasam, Venkat and Hogsden, Wendy and Illingworth, Chris J and Jackson, Chris and Thomson, Emma C and Shepherd, James G and Asamaphan, Patawee and Niebel, Marc O and Li, Kathy K and Shah, Rajiv N and Jesudason, Natasha G and Tong, Lily and Broos, Alice and Mair, Daniel and Nichols, Jenna and Carmichael, Stephen N and Nomikou, Kyriaki and Aranday-Cortes, Elihu and Johnson, Natasha and Starinskij, Igor and da Silva Filipe, Ana and Robertson, David L and Orton, Richard J and Hughes, Joseph and Vattipally, Sreenu and Singer, Joshua B and Nickbakhsh, Seema and Hale, Antony D and Macfarlane-Smith, Louissa R and Harper, Katherine L and Carden, Holli and Taha, Yusri and Payne, Brendan AI and Burton-Fanning, Shirelle and Waugh, Sheila and Collins, Jennifer and Eltringham, Gary and Rushton, Steven and O'Brien, Sarah and Bradley, Amanda and Maclean, Alasdair and Mollett, Guy and Blacow, Rachel and Templeton, Kate E and McHugh, Martin P and Dewar, Rebecca and Wastenge, Elizabeth and Dervisevic, Samir and Stanley, Rachael and Meader, Emma J and Coupland, Lindsay and Smith, Louise and Graham, Clive and Barton, Edward and Padgett, Debra and Scott, Garren and Swindells, Emma and Greenaway, Jane and Nelson, Andrew and McCann, Clare M and Yew, Wen C and Andersson, Monique and Peto, Timothy and Justice, Anita and Eyre, David and Crook, Derrick and Sloan, Tim J and Duckworth, Nichola and Walsh, Sarah and Chauhan, Anoop J and Glaysher, Sharon and Bicknell, Kelly and Wyllie, Sarah and Elliott, Scott and Lloyd, Allyson and Impey, Robert and Levene, Nick and Monaghan, Lynn and Bradley, Declan T and Wyatt, Tim and Allara, Elias and Pearson, Clare and Osman, Husam and Bosworth, Andrew and Robinson, Esther and Muir, Peter and Vipond, Ian B and Hopes, Richard and Pymont, Hannah M and Hutchings, Stephanie and Curran, Martin D and Parmar, Surendra and Lackenby, Angie and Mbisa, Tamyo and Platt, Steven and Miah, Shahjahan and Bibby, David and Manso, Carmen and Hubb, Jonathan and Chand, Meera and Dabrera, Gavin and Ramsay, Mary and Bradshaw, Daniel and Thornton, Alicia and Myers, Richard and Schaefer, Ulf and Groves, Natalie and Gallagher, Eileen and Lee, David and Williams, David and Ellaby, Nicholas and Harrison, Ian and Hartman, Hassan and Manesis, Nikos and Patel, Vineet and Bishop, Chloe and Chalker, Vicki and Ledesma, Juan and Twohig, Katherine A and Holden, Matthew T.G. and Shaaban, Sharif and Birchley, Alec and Adams, Alexander and Davies, Alisha and Gaskin, Amy and Plimmer, Amy and Gatica-Wilcox, Bree and McKerr, Caoimhe and Moore, Catherine and Williams, Chris and Heyburn, David and De Lacy, Elen and Hilvers, Ember and Downing, Fatima and Shankar, Giri and Jones, Hannah and Asad, Hibo and Coombes, Jason and Watkins, Joanne and Evans, Johnathan M and Fina, Laia and Gifford, Laura and Gilbert, Lauren and Graham, Lee and Perry, Malorie and Morgan, Mari and Bull, Matthew and Cronin, Michelle and Pacchiarini, Nicole and Craine, Noel and Jones, Rachel and Howe, Robin and Corden, Sally and Rey, Sara and Kumziene-SummerhaYes, Sara and Taylor, Sarah and Cottrell, Simon and Jones, Sophie and Edwards, Sue and O'Grady, Justin and Page, Andrew J and Mather, Alison E and Baker, David J and Rudder, Steven and Aydin, Alp and Kay, Gemma L and Trotter, Alexander J and Alikhan, Nabil-Fareed and de Oliveira Martins, Leonardo and Le-Viet, Thanh and Meadows, Lizzie and Casey, Anna and Ratcliffe, Liz and Simpson, David A and Molnar, Zoltan and Thompson, Thomas and Acheson, Erwan and Masoli, Jane AH and Knight, Bridget A and Ellard, Sian and Auckland, Cressida and Jones, Christopher R and Mahungu, Tabitha W and Irish-Tavares, Dianne and Haque, Tanzina and Hart, Jennifer and Witele, Eric and Fenton, Melisa Louise and Dadrah, Ashok and Symmonds, Amanda and Saluja, Tranprit and Bourgeois, Yann and Scarlett, Garry P and Loveson, Katie F and Goudarzi, Salman and Fearn, Christopher and Cook, Kate and Dent, Hannah and Paul, Hannah and Partridge, David G and Raza, Mohammad and Evans, Cariad and Johnson, Kate and Liggett, Steven and Baker, Paul and Bonner, Stephen and Essex, Sarah and Lyons, Ronan A and Saeed, Kordo and Mahanama, Adhyana I.K and Samaraweera, Buddhini and Silveira, Siona and Pelosi, Emanuela and Wilson-Davies, Eleri and Williams, Rachel J and Kristiansen, Mark and Roy, Sunando and Williams, Charlotte A and Cotic, Marius and Bayzid, Nadua and Westhorpe, Adam P and Hartley, John A and Jannoo, Riaz and Lowe, Helen L and Karamani, Angeliki and Ensell, Leah and Prieto, Jacqui A and Jeremiah, Sarah and Grammatopoulos, Dimitris and Pandey, Sarojini and Berry, Lisa and Jones, Katie and Richter, Alex and Beggs, Andrew and Best, Angus and Percival, Benita and Mirza, Jeremy and Megram, Oliver and Mayhew, Megan and Crawford, Liam and Ashcroft, Fiona and Moles-Garcia, Emma and Cumley, Nicola and Smith, Colin P and Bucca, Giselda and Hesketh, Andrew R and Blane, Beth and Girgis, Sophia T and Leek, Danielle and Sridhar, Sushmita and Forrest, Sally and Cormie, Claire and Gill, Harmeet K and Dias, Joana and Higginson, Ellen E and Maes, Mailis and Young, Jamie and Kermack, Leanne M and Gupta, Ravi Kumar and Ludden, Catherine and Peacock, Sharon J and Palmer, Sophie and Churcher, Carol M and Hadjirin, Nazreen F and Carabelli, Alessandro M and Brooks, Ellena and Smith, Kim S and Galai, Katerina and McManus, Georgina M and Ruis, Chris and Davidson, Rose K and Rambaut, Andrew and Williams, Thomas and Balcazar, Carlos E and Gallagher, Michael D and O'Toole, Áine and Rooke, Stefan and Hill, Verity and Williamson, Kathleen A and Stanton, Thomas D and Michell, Stephen L and Bewshea, Claire M and Temperton, Ben and Michelsen, Michelle L and Warwick-Dugdale, Joanna and Manley, Robin and Farbos, Audrey and Harrison, James W and Sambles, Christine M and Studholme, David J and Jeffries, Aaron R and Darby, Alistair C and Hiscox, Julian A and Paterson, Steve and Iturriza-Gomara, Miren and Jackson, Kathryn A and Lucaci, Anita O and Vamos, Edith E and Hughes, Margaret and Rainbow, Lucille and Eccles, Richard and Nelson, Charlotte and Whitehead, Mark and Turtle, Lance and Haldenby, Sam T and Gregory, Richard and Gemmell, Matthew and Wierzbicki, Claudia and Webster, Hermione J and de Silva, Thushan I and Smith, Nikki and Angyal, Adrienn and Lindsey, Benjamin B and Groves, Danielle C and Green, Luke R and Wang, Dennis and Freeman, Timothy M and Parker, Matthew D and Keeley, Alexander J and Parsons, Paul J and Tucker, Rachel M and Brown, Rebecca and Wyles, Matthew and Whiteley, Max and Zhang, Peijun and Gallis, Marta and Louka, Stavroula F and Constantinidou, Chrystala and Unnikrishnan, Meera and Ott, Sascha and Cheng, Jeffrey K.J. and Bridgewater, Hannah E. and Frost, Lucy R. and Taylor-Joyce, Grace and Stark, Richard and Baxter, Laura and Alam, Mohammad T. and Brown, Paul E and Aggarwal, Dinesh and Cerda, Alberto C and Merrill, Tammy V and Wilson, Rebekah E and McClure, Patrick C and Chappell, Joseph G and Tsoleridis, Theocharis and Ball, Jonathan and Buck, David and Todd, John A and Green, Angie and Trebes, Amy and MacIntyre-Cockett, George and de Cesare, Mariateresa and Alderton, Alex and Amato, Roberto and Ariani, Cristina V and Beale, Mathew A and Beaver, Charlotte and Bellis, Katherine L and Betteridge, Emma and Bonfield, James and Danesh, John and Dorman, Matthew J and Drury, Eleanor and Farr, Ben W and Foulser, Luke and Goncalves, Sonia and Goodwin, Scott and Gourtovaia, Marina and Harrison, Ewan M and Jackson, David K and Jamrozy, Dorota and Johnston, Ian and Kane, Leanne and Kay, Sally and Keatley, Jon-Paul and Kwiatkowski, Dominic and Langford, Cordelia F and Lawniczak, Mara and Letchford, Laura and Livett, Rich and Lo, Stephanie and Martincorena, Inigo and McGuigan, Samantha and Nelson, Rachel and Palmer, Steve and Park, Naomi R and Patel, Minal and Prestwood, Liam and Puethe, Christoph and Quail, Michael A and Rajatileka, Shavanthi and Scott, Carol and Shirley, Lesley and Sillitoe, John and Spencer Chapman, Michael H and Thurston, Scott AJ and Tonkin-Hill, Gerry and Weldon, Danni and Rajan, Diana and Bronner, Iraad F and Aigrain, Louise and Redshaw, Nicholas M and Lensing, Stefanie V and Davies, Robert and Whitwham, Andrew and Liddle, Jennifier and Lewis, Kevin and Tovar-Corona, Jaime M and Leonard, Steven and Durham, Jillian and Bassett, Andrew R and McCarthy, Shane and Moll, Robin J and James, Keith and Oliver, Karen and Makunin, Alex and Barrett, Jeff and Gunson, Rory N},
	month = may,
	year = {2021},
	note = {171 citations (Crossref) [2022-06-30]},
	pages = {e335--e345},
	file = {Full Text:/usr/users/QIB_fr005/alikhan/Zotero/storage/HBFKBDFL/Graham et al. - 2021 - Changes in symptomatology, reinfection, and transm.pdf:application/pdf},
}

@incollection{raphael_accurate_2018,
	address = {Cham},
	title = {Accurate {Reconstruction} of {Microbial} {Strains} from {Metagenomic} {Sequencing} {Using} {Representative} {Reference} {Genomes}},
	volume = {10812},
	copyright = {Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International Licence (CC-BY-NC-ND)},
	isbn = {978-3-319-89928-2 978-3-319-89929-9},
	url = {http://link.springer.com/10.1007/978-3-319-89929-9_15},
	abstract = {Exploring the genetic diversity of microbes within the environment through metagenomic sequencing first requires classifying these reads into taxonomic groups. Current methods compare these sequencing data with existing biased and limited reference databases. Several recent evaluation studies demonstrate that current methods either lack sufficient sensitivity for species-level assignments or suffer from false positives, overestimating the number of species in the metagenome. Both are especially problematic for the identification of low-abundance microbial species, e. g. detecting pathogens in ancient metagenomic samples. We present a new method, SPARSE, which improves taxonomic assignments of metagenomic reads. SPARSE balances existing biased reference databases by grouping reference genomes into similarity-based hierarchical clusters, implemented as an efficient incremental data structure. SPARSE assigns reads to these clusters using a probabilistic model, which specifically penalizes non-specific mappings of reads from unknown sources and hence reduces false-positive assignments. Our evaluation on simulated datasets from two recent evaluation studies demonstrated the improved precision of SPARSE in comparison to other methods for species-level classification. In a third simulation, our method successfully differentiated multiple co-existing Escherichia coli strains from the same sample. In real archaeological datasets, SPARSE identified ancient pathogens with ≤0.02\% abundance, consistent with published findings that required additional sequencing data. In these datasets, other methods either missed targeted pathogens or reported non-existent ones.},
	urldate = {2022-05-13},
	booktitle = {Research in {Computational} {Molecular} {Biology}},
	publisher = {Springer International Publishing},
	author = {Zhou, Zhemin and Luhmann, Nina and Alikhan, Nabil-Fareed and Quince, Christopher and Achtman, Mark},
	editor = {Raphael, Benjamin J.},
	year = {2018},
	doi = {10.1007/978-3-319-89929-9_15},
	note = {Series Title: Lecture Notes in Computer Science},
	pages = {225--240},
	file = {Submitted Version:/usr/users/QIB_fr005/alikhan/Zotero/storage/AJ8SYGJF/Zhou et al. - 2018 - Accurate Reconstruction of Microbial Strains from .pdf:application/pdf},
}

@techreport{alikhan_defining_2021,
	type = {preprint},
	title = {Defining the analytical and clinical sensitivity of the {ARTIC} method for the detection of {SARS}-{CoV}-2},
	copyright = {Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International Licence (CC-BY-NC-ND)},
	url = {http://medrxiv.org/lookup/doi/10.1101/2021.10.09.21264695},
	abstract = {Abstract
          
            The SARS-CoV-2 ARTIC amplicon protocol is the most widely used genome sequencing method for SARS-CoV-2, accounting for over 43\% of publicly-available genome sequences. The protocol utilises 98 primers to amplify ∼400bp fragments of the SARS-CoV-2 genome covering all 30,000 bases. Understanding the analytical performance metrics of this protocol will improve how the data is used and interpreted. Different concentrations of SARS-CoV-2 control material were used to establish the limit of detection (LoD) of the ARTIC protocol. Results demonstrated the LoD was a minimum of 25-50 virus particles per mL. The sensitivity of ARTIC was comparable to the published sensitivities of commercial diagnostics assays and could therefore be used to confirm diagnostic testing results. A set of over 3,600 clinical samples from three UK regions were then evaluated to compare the protocols performance to clinical diagnostic assays (Roche Lightcycler 480 II, AusDiagnostics, Roche Cobas, Hologic Panther, Corman RdRp, Roche Flow, ABI QuantStudio 5, Seegene Nimbus, Qiagen Rotorgene, Abbott M2000, Thermo TaqPath, Xpert). We developed a Python tool, RonaLDO, to perform this validation (available under the GNU GPL3 open-source licence from
            https://github.com/quadram-institute-bioscience/ronaldo
            ). Positives detected by diagnostic platforms were generally supported by sequencing data; platforms that used RT-qPCR were the best predictors of whether the sample would subsequently sequence successfully. To maximise success of sample sequencing for phylogenetic analysis, samples with Ct {\textless}31 should be chosen. For diagnostic tests that do not provide a quantifiable Ct value, adding a quantification step is recommended. The ARTIC SARS-CoV-2 sequencing protocol is highly sensitive, capable of detecting SARS-CoV-2 in samples with Cts in the high 30s. However, to routinely obtain whole genome coverage, samples with Ct {\textless}31 are recommended. Comparing different virus detection methods close to their LoD was challenging and significant discordance was observed.},
	language = {en},
	urldate = {2022-05-13},
	institution = {Infectious Diseases (except HIV/AIDS)},
	author = {Alikhan, Nabil-Fareed and Quick, Joshua and Trotter, Alexander J. and Robson, Samuel C. and Bashton, Matthew and Kay, Gemma L. and Loose, Matt and Rooke, Stefan and McHugh, Martin and Darby, Alistair C and Nicholls, Samuel M. and Loman, Nicholas J. and {The COVID-19 Genomics UK (COG-UK) consortium} and Dervisevic, Samir and Page, Andrew J. and O’Grady, Justin},
	month = oct,
	year = {2021},
	doi = {10.1101/2021.10.09.21264695},
	file = {Submitted Version:/usr/users/QIB_fr005/alikhan/Zotero/storage/BSV2BBN9/Alikhan et al. - 2021 - Defining the analytical and clinical sensitivity o.pdf:application/pdf},
}

@techreport{foster-nyarko_within-host_2019,
	type = {preprint},
	title = {Within-{Host} {Diversity} and {Vertical} {Transmission} of {Group} {B} \textit{{Streptococcus}} {Among} {Mother}-infant {Dyads} in {The} {Gambia}},
	copyright = {Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International Licence (CC-BY-NC-ND)},
	url = {http://biorxiv.org/lookup/doi/10.1101/760512},
	abstract = {Abstract
          
            Introduction
            
              Understanding mother-to-infant transmission of Group B
              Streptococcus
              (GBS) is vital to the prevention and control of GBS disease. We investigated the transmission and phylogenetic relationships of mothers colonised by GBS and their infants in a peri-urban setting in The Gambia.
            
          
          
            Methods
            We collected nasopharyngeal swabs from 35 mother-infant dyads at weekly intervals from birth until six weeks post-partum. GBS was isolated by conventional microbiology techniques. Whole-genome sequencing was performed on GBS isolates from one mother-infant dyad (dyad 17).
          
          
            Results
            We recovered 85 GBS isolates from the 245 nasopharyngeal swabs. GBS was isolated from 16.33\% and 18.37\% of sampled mothers and infants, respectively. In 87\% of cultured swabs, the culture status of an infant agreed with that of the mother (Kappa p-value {\textless}0.001). In dyad 17, phylogenetic analysis revealed within-host strain diversity in the mother and clone to her infant.
          
          
            Conclusion
            GBS colonisation in mothers presents a significant risk of colonisation in their infants. We confirm vertical transmission from mother to child in dyad 17, accompanied by within-host diversity.},
	language = {en},
	urldate = {2022-05-13},
	institution = {Microbiology},
	author = {Foster-Nyarko, Ebenezer and Senghore, Madikay and Kwambana-Adams, Brenda A. and Alikhan, Nabil-Fareed and Ravi, Anuradha and Jafali, James and Jawneh, Kaddijatou and Jah, Amara and Jarju, Maimuna and Ceesay, Fatima and Bojang, Sainabou and Worwui, Archibald and Odutola, Aderonke and Ogundare, Ezra and Pallen, Mark J. and Ota, Martin and Antonio, Martin},
	month = sep,
	year = {2019},
	doi = {10.1101/760512},
	file = {Submitted Version:/usr/users/QIB_fr005/alikhan/Zotero/storage/VSZI26A5/Foster-Nyarko et al. - 2019 - Within-Host Diversity and Vertical Transmission of.pdf:application/pdf},
}

@techreport{page_rapid_2020,
	type = {preprint},
	title = {Rapid \textit{{Mycobacterium} tuberculosis} spoligotyping from uncorrected long reads using {Galru}},
	copyright = {Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International Licence (CC-BY-NC-ND)},
	url = {http://biorxiv.org/lookup/doi/10.1101/2020.05.31.126490},
	abstract = {Abstract
          
            Spoligotyping of
            Mycobacterium tuberculosis
            provides a subspecies classification of this major human pathogen. Spoligotypes can be predicted from short read genome sequencing data; however, no methods exist for long read sequence data such as from Nanopore or PacBio. We present a novel software package Galru, which can rapidly detect the spoligotype of a
            Mycobacterium tuberculosis
            sample from as little as a single uncorrected long read. It allows for near real-time spoligotyping from long read data as it is being sequenced, giving rapid sample typing. We compare it to the existing state of the art software and find it performs identically to the results obtained from short read sequencing data. Galru is freely available from
            https://github.com/quadram-institute-bioscience/galru
            under the GPLv3 open source licence.},
	language = {en},
	urldate = {2022-05-13},
	institution = {Bioinformatics},
	author = {Page, Andrew J. and Alikhan, Nabil-Fareed and Strinden, Michael and Le Viet, Thanh and Skvortsov, Timofey},
	month = jun,
	year = {2020},
	doi = {10.1101/2020.05.31.126490},
	file = {Submitted Version:/usr/users/QIB_fr005/alikhan/Zotero/storage/ILZRPHX9/Page et al. - 2020 - Rapid Mycobacterium tuberculosis spoligotyp.pdf:application/pdf},
}

@techreport{alikhan_multiple_2019,
	type = {preprint},
	title = {Multiple evolutionary trajectories for non-{O157} {Shiga} toxigenic \textit{{Escherichia} coli}},
	copyright = {Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International Licence (CC-BY-NC-ND)},
	url = {http://biorxiv.org/lookup/doi/10.1101/549998},
	abstract = {Abstract
          
            Background
            
              Shiga toxigenic
              Escherichia coli
              (STEC) is an emerging global pathogen and remains a major cause of food-borne illness with more severe symptoms including hemorrhagic colitis and hemolytic-uremic syndrome. Since the characterization of the archetypal STEC serotype,
              E. coli
              O157:H7, more than 250 STEC serotypes have been defined. Many of these non-O157 STEC are associated with clinical cases of equal severity as O157. In this study, we utilize whole genome sequencing of 44 STEC strains from eight serogroups associated with human infection to establish their evolutionary relationships and contrast this with their virulence gene profiles and established typing methods.
            
          
          
            Results
            
              Our phylogenomic analysis delineated these STEC strains into seven distinct lineages, each with a characteristic repertoire of virulence factors. Some lineages included commensal or other
              E. coli
              pathotypes. Multiple independent acquisitions of the Locus for Enterocyte Effacement were identified, each associated with a distinct repertoire of effector genes. Lineages were inconsistent with O-antigen typing in several instances, consistent with lateral gene transfer within the O-antigen locus. STEC lineages could be defined by the conservation of clustered regularly interspaced short palindromic repeats (CRISPRs), however, no CRISPR profile could differentiate STEC from other
              E. coli
              strains. Six genomic regions (ranging from 500 bp - 10 kbp) were found to be conserved across all STEC in this dataset and may dictate interactions with Stx phage lysogeny.
            
          
          
            Conclusions
            
              The genomic analyses reported here present non-O157 STEC as a diverse group of pathogenic
              E. coli
              emerging from multiple lineages that independently acquired mobile genetic elements that promote pathogenesis.},
	language = {en},
	urldate = {2022-05-13},
	institution = {Microbiology},
	author = {Alikhan, Nabil-Fareed and Bachmann, Nathan L. and Zakour, Nouri L. Ben and Petty, Nicola K. and Stanton-Cook, Mitchell and Gawthorne, Jayde A. and Easton, Donna M. and Mahony, Timothy J. and Cobbold, Rowland and Schembri, Mark A. and Beatson, Scott A.},
	month = feb,
	year = {2019},
	doi = {10.1101/549998},
	file = {Full Text:/usr/users/QIB_fr005/alikhan/Zotero/storage/SBH6ZQXE/Alikhan et al. - 2019 - Multiple evolutionary trajectories for non-O157 Sh.pdf:application/pdf},
}

@techreport{riley_react-1_2021,
	type = {preprint},
	title = {{REACT}-1 round 12 report: resurgence of {SARS}-{CoV}-2 infections in {England} associated with increased frequency of the {Delta} variant},
	copyright = {Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International Licence (CC-BY-NC-ND)},
	shorttitle = {{REACT}-1 round 12 report},
	url = {http://medrxiv.org/lookup/doi/10.1101/2021.06.17.21259103},
	abstract = {Abstract
          
            Background
            England entered a third national lockdown from 6 January 2021 due to the COVID-19 pandemic. Despite a successful vaccine rollout during the first half of 2021, cases and hospitalisations have started to increase since the end of May as the SARS-CoV-2 Delta (B.1.617.2) variant increases in frequency. The final step of relaxation of COVID-19 restrictions in England has been delayed from 21 June to 19 July 2021.
          
          
            Methods
            The REal-time Assessment of Community Transmision-1 (REACT-1) study measures the prevalence of swab-positivity among random samples of the population of England. Round 12 of REACT-1 obtained self-administered swab collections from participants from 20 May 2021 to 7 June 2021; results are compared with those for round 11, in which swabs were collected from 15 April to 3 May 2021.
          
          
            Results
            Between rounds 11 and 12, national prevalence increased from 0.10\% (0.08\%, 0.13\%) to 0.15\% (0.12\%, 0.18\%). During round 12, we detected exponential growth with a doubling time of 11 (7.1, 23) days and an R number of 1.44 (1.20, 1.73). The highest prevalence was found in the North West at 0.26\% (0.16\%, 0.41\%) compared to 0.05\% (0.02\%, 0.12\%) in the South West. In the North West, the locations of positive samples suggested a cluster in Greater Manchester and the east Lancashire area. Prevalence in those aged 5-49 was 2.5 times higher at 0.20\% (0.16\%, 0.26\%) compared with those aged 50 years and above at 0.08\% (0.06\%, 0.11\%). At the beginning of February 2021, the link between infection rates and hospitalisations and deaths started to weaken, although in late April 2021, infection rates and hospital admissions started to reconverge. When split by age, the weakened link between infection rates and hospitalisations at ages 65 years and above was maintained, while the trends converged below the age of 65 years. The majority of the infections in the younger group occurred in the unvaccinated population or those without a stated vaccine history. We observed the rapid replacement of the Alpha (B.1.1.7) variant of SARS-CoV-2 with the Delta variant during the period covered by rounds 11 and 12 of the study.
          
          
            Discussion
            The extent to which exponential growth continues, or slows down as a consequence of the continued rapid roll-out of the vaccination programme, including to young adults, requires close monitoring. Data on community prevalence are vital to track the course of the epidemic and inform ongoing decisions about the timing of further lifting of restrictions in England.},
	language = {en},
	urldate = {2022-05-13},
	institution = {Infectious Diseases (except HIV/AIDS)},
	author = {Riley, Steven and Wang, Haowei and Eales, Oliver and Haw, David and Walters, Caroline E. and Ainslie, Kylie E. C. and Atchison, Christina and Fronterre, Claudio and Diggle, Peter J. and Page, Andrew J. and Prosolek, Sophie J. and Trotter, Alexander J. and Le Viet, Thanh and Alikhan, Nabil-Fareed and Jackson, Leigh M and Ludden, Catherine and {The COVID-19 Genomics UK (COG-UK) Consortium} and Ashby, Deborah and Donnelly, Christl A. and Cooke, Graham and Barclay, Wendy and Ward, Helen and Darzi, Ara and Elliott, Paul},
	month = jun,
	year = {2021},
	doi = {10.1101/2021.06.17.21259103},
	file = {Submitted Version:/usr/users/QIB_fr005/alikhan/Zotero/storage/ZR692UK4/Riley et al. - 2021 - REACT-1 round 12 report resurgence of SARS-CoV-2 .pdf:application/pdf},
}

@techreport{riley_react-1_2021-1,
	type = {preprint},
	title = {{REACT}-1 round 11 report: low prevalence of {SARS}-{CoV}-2 infection in the community prior to the third step of the {English} roadmap out of lockdown},
	copyright = {Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International Licence (CC-BY-NC-ND)},
	shorttitle = {{REACT}-1 round 11 report},
	url = {http://medrxiv.org/lookup/doi/10.1101/2021.05.13.21257144},
	abstract = {Abstract
          
            Background
            National epidemic dynamics of SARS-CoV-2 infections are being driven by: the degree of recent indoor mixing (both social and workplace), vaccine coverage, intrinsic properties of the circulating lineages, and prior history of infection (via natural immunity). In England, infections, hospitalisations and deaths fell during the first two steps of the “roadmap” for exiting the third national lockdown. The third step of the roadmap in England takes place on 17 May 2021.
          
          
            Methods
            We report the most recent findings on community infections from the REal-time Assessment of Community Transmission-1 (REACT-1) study in which a swab is obtained from a representative cross-sectional sample of the population in England and tested using PCR. Round 11 of REACT-1 commenced self-administered swab-collection on 15 April 2021 and completed collections on 3 May 2021. We compare the results of REACT-1 round 11 to round 10, in which swabs were collected from 11 to 30 March 2021.
          
          
            Results
            Between rounds 10 and 11, prevalence of swab-positivity dropped by 50\% in England from 0.20\% (0.17\%, 0.23\%) to 0.10\% (0.08\%, 0.13\%), with a corresponding R estimate of 0.90 (0.87, 0.94). Rates of swab-positivity fell in the 55 to 64 year old group from 0.17\% (0.12\%, 0.25\%) in round 10 to 0.06\% (0.04\%, 0.11\%) in round 11. Prevalence in round 11 was higher in the 25 to 34 year old group at 0.21\% (0.12\%, 0.38\%) than in the 55 to 64 year olds and also higher in participants of Asian ethnicity at 0.31\% (0.16\%, 0.60\%) compared with white participants at 0.09\% (0.07\%, 0.11\%). Based on sequence data for positive samples for which a lineage could be identified, we estimate that 92.3\% (75.9\%, 97.9\%, n=24) of infections were from the B.1.1.7 lineage compared to 7.7\% (2.1\%, 24.1\%, n=2) from the B.1.617.2 lineage. Both samples from the B.1.617.2 lineage were detected in London from participants not reporting travel in the previous two weeks. Also, allowing for suitable lag periods, the prior close alignment between prevalence of infections and hospitalisations and deaths nationally has diverged.
          
          
            Discussion
            We observed marked reductions in prevalence from March to April and early May 2021 in England reflecting the success of the vaccination programme and despite easing of restrictions during lockdown. However, there is potential upwards pressure on prevalence from the further easing of lockdown regulations and presence of the B.1.617.2 lineage. If prevalence rises in the coming weeks, policy-makers will need to assess the possible impact on hospitalisations and deaths. In addition, consideration should be given to other health and economic impacts if increased levels of community transmission occur.},
	language = {en},
	urldate = {2022-05-13},
	institution = {Epidemiology},
	author = {Riley, Steven and Haw, David and Walters, Caroline E. and Wang, Haowei and Eales, Oliver and Ainslie, Kylie E. C. and Atchison, Christina and Fronterre, Claudio and Diggle, Peter J. and Page, Andrew J. and Trotter, Alexander J. and Le Viet, Thanh and Alikhan, Nabil-Fareed and O’Grady, Justin and {The COVID-19 Genomics UK (COG-UK) Consortium} and Ashby, Deborah and Donnelly, Christl A. and Cooke, Graham and Barclay, Wendy and Ward, Helen and Darzi, Ara and Elliott, Paul},
	month = may,
	year = {2021},
	doi = {10.1101/2021.05.13.21257144},
	file = {Submitted Version:/usr/users/QIB_fr005/alikhan/Zotero/storage/998C6JBL/Riley et al. - 2021 - REACT-1 round 11 report low prevalence of SARS-Co.pdf:application/pdf},
}

@article{castillo-bravo_clinical_2022,
	title = {Clinical {Performance} of {Direct} {RT}-{PCR} {Testing} of {Raw} {Saliva} for {Detection} of {SARS}-{CoV}-2 in {Symptomatic} and {Asymptomatic} {Individuals}},
	volume = {10},
	issn = {2165-0497},
	url = {https://journals.asm.org/doi/10.1128/spectrum.02229-22},
	doi = {10.1128/spectrum.02229-22},
	abstract = {The scale of the COVID-19 pandemic highlighted the need for viral diagnostic systems that are accurate and could be deployed at large population scales. Large-scale diagnostic or surveillance testing of large numbers of people requires collection of infected biological samples that is easy and rapid.
          , 
            ABSTRACT
            RT-PCR tests based on RNA extraction from nasopharyngeal swabs (NPS) are promoted as the “gold standard” for SARS-CoV-2 detection. However, the use of saliva samples offers noninvasive self-collection more suitable for high-throughput testing. This study evaluated performance of the TaqPath COVID-19 Fast PCR Combo kit 2.0 assay for detection of SARS-CoV-2 in raw saliva relative to a lab-developed direct RT-PCR test (SalivaDirect-based PCR, SDB-PCR) and an RT-PCR test based on RNA extraction from NPS. Saliva and NPS samples were collected from symptomatic and asymptomatic individuals (N = 615). Saliva samples were tested for SARS-CoV-2 using the TaqPath COVID-19 Fast PCR Combo kit 2.0 and the SDB-PCR, while NPS samples were tested by RT-PCR in RNA extracts according to the Irish national testing system. TaqPath COVID-19 Fast PCR Combo kit 2.0 detected SARS-CoV-2 in 52 saliva samples, of which 51 were also positive with the SDB-PCR. Compared to the NPS “gold standard” biospecimen method, 49 samples displayed concordant results, while three samples (35{\textless}Ct{\textless}37) were positive on raw saliva. Among the negative samples, 10 discordant cases were found with the TaqPath COVID-19 Fast PCR Combo kit 2.0 (PPA–83.05\%; NPA–99.44\%), compared to the RNA extraction-based NPS method, performing similarly to the SDB-PCR (PPA-84.75\%; NPA-99.63\%). The direct RT-PCR testing of saliva samples shows high concordance with the NPS extraction-based method for SARS-CoV-2 detection, and therefore provides a cost-effective and highly scalable system for high-throughput COVID-19 rapid-testing.
            
              IMPORTANCE
              The scale of the COVID-19 pandemic highlighted the need for viral diagnostic systems that are accurate and could be deployed at large population scales. Large-scale diagnostic or surveillance testing of large numbers of people requires collection of infected biological samples that is easy and rapid. Here, we demonstrate that raw saliva samples can be easily collected and tested by RT-PCR assays. Indeed, we find that direct testing of raw saliva by two different RT-PCR assays is as accurate (if not more accurate) than nasal swab-based RT-PCR testing. We present a cost-effective and highly scalable system for high-throughput COVID-19 rapid-testing.},
	language = {en},
	number = {6},
	urldate = {2023-03-14},
	journal = {Microbiology Spectrum},
	author = {Castillo-Bravo, Rosa and Lucca, Noel and Lai, Linyi and Marlborough, Killian and Brychkova, Galina and Sakhteh, Maryam Shideh and Lonergan, Charlie and O’Grady, Justin and Alikhan, Nabil-Fareed and Trotter, Alexander J. and Page, Andrew J. and Smyth, Breda and McKeown, Peter C. and Feenstra, Jelena D. M. and Ulekleiv, Camilla and Sorel, Oceane and Gandhi, Manoj and Spillane, Charles},
	editor = {Starolis, Meghan},
	month = dec,
	year = {2022},
	pages = {e02229--22},
	file = {Full Text:/usr/users/QIB_fr005/alikhan/Zotero/storage/HJPMM2WT/Castillo-Bravo et al. - 2022 - Clinical Performance of Direct RT-PCR Testing of R.pdf:application/pdf},
}