Authors
Health Service Executive (HSE)Achtman, Mark
Zhou, Zhemin
Alikhan, Nabil-Fareed
Tyne, William
Parkhill, Julian
Cormican, Martin
Chiou, Chien-Shun
Torpdahl, Mia
Litrup, Eva
Prendergast, Deirdre M
Moore, John E
Strain, Sam
Kornschober, Christian
Meinersmann, Richard
Uesbeck, Alexandra
Weill, François-Xavier
Coffey, Aidan
Andrews-Polymenis, Helene
Curtiss Rd, Roy
Fanning, Séamus
Issue Date
01/02/2021Keywords
INFECTION CONTROLHEALTH NEEDS ASSESSMENT
IMMUNISATION
High throughput sequencing
Large scale genomic database
Population genomics
Salmonella
Local subject classification
INFECTIOUS DISEASESPUBLIC HEALTH DEPARTMENT
ENVIRONMENT AND HEALTH
NEWSLETTER
DRINKING WATER
HEALTH PROTECTION
HEALTH IMPROVEMENT
HEALTH SERVICE PLANNING
HEALTH STATUS
PUBLIC INFORMATION
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Wellcome open researchDOI
10.12688/wellcomeopenres.16291.2PubMed ID
33614977Abstract
Background: Most publicly available genomes of Salmonella enterica are from human disease in the US and the UK, or from domesticated animals in the US. Methods: 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. Results: 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. Conclusions: 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.Item Type
ArticleLanguage
enISSN
2398-502Xae974a485f413a2113503eed53cd6c53
10.12688/wellcomeopenres.16291.2
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Except where otherwise noted, this item's license is described as https://creativecommons.org/licenses/by/4.0/
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