Show simple item record

dc.contributor.authorHealth Service Executive (HSE)
dc.contributor.authorAchtman, Mark
dc.contributor.authorZhou, Zhemin
dc.contributor.authorAlikhan, Nabil-Fareed
dc.contributor.authorTyne, William
dc.contributor.authorParkhill, Julian
dc.contributor.authorCormican, Martin
dc.contributor.authorChiou, Chien-Shun
dc.contributor.authorTorpdahl, Mia
dc.contributor.authorLitrup, Eva
dc.contributor.authorPrendergast, Deirdre M
dc.contributor.authorMoore, John E
dc.contributor.authorStrain, Sam
dc.contributor.authorKornschober, Christian
dc.contributor.authorMeinersmann, Richard
dc.contributor.authorUesbeck, Alexandra
dc.contributor.authorWeill, François-Xavier
dc.contributor.authorCoffey, Aidan
dc.contributor.authorAndrews-Polymenis, Helene
dc.contributor.authorCurtiss Rd, Roy
dc.contributor.authorFanning, Séamus
dc.date.accessioned2022-02-01T16:09:55Z
dc.date.available2022-02-01T16:09:55Z
dc.date.issued2021-02-01
dc.identifier.issn2398-502X
dc.identifier.pmid33614977
dc.identifier.doi10.12688/wellcomeopenres.16291.2
dc.identifier.urihttp://hdl.handle.net/10147/631260
dc.descriptionBackground: 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.en_US
dc.description.abstractBackground: 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.
dc.language.isoenen_US
dc.rightsCopyright: © 2021 Achtman M et al.
dc.subjectINFECTION CONTROLen_US
dc.subjectHEALTH NEEDS ASSESSMENTen_US
dc.subjectIMMUNISATIONen_US
dc.subjectHigh throughput sequencingen_US
dc.subjectLarge scale genomic databaseen_US
dc.subjectPopulation genomicsen_US
dc.subjectSalmonellaen_US
dc.subject.otherINFECTIOUS DISEASESen_US
dc.subject.otherPUBLIC HEALTH DEPARTMENTen_US
dc.subject.otherENVIRONMENT AND HEALTHen_US
dc.subject.otherNEWSLETTERen_US
dc.subject.otherDRINKING WATERen_US
dc.subject.otherHEALTH PROTECTIONen_US
dc.subject.otherHEALTH IMPROVEMENTen_US
dc.subject.otherHEALTH SERVICE PLANNINGen_US
dc.subject.otherHEALTH STATUSen_US
dc.subject.otherPUBLIC INFORMATIONen_US
dc.titleGenomic diversity of The UoWUCC 10K genomes project.en_US
dc.typeArticleen_US
dc.identifier.journalWellcome open researchen_US
dc.source.journaltitleWellcome open research
dc.source.volume5
dc.source.beginpage223
dc.source.endpage
refterms.dateFOA2022-02-01T16:09:56Z
dc.source.countryUnited Kingdom
dc.source.countryEngland


Files in this item

Thumbnail
Name:
wellcomeopenres-5-18280.pdf
Size:
4.961Mb
Format:
PDF

This item appears in the following Collection(s)

Show simple item record