Genomic diversity of Salmonella enterica -The UoWUCC 10K genomes project

Authors

Mark Achtman, Warwick Medical School
Zhemin Zhou, Warwick Medical School
Nabil Fareed Alikhan, Warwick Medical School
William Tyne, Warwick Medical School
Julian Parkhill, University of Cambridge
Martin Cormican, National Salmonella
Chien Shun Chiou, Center for Disease Control Taiwan
Mia Torpdahl, Statens Serum Institut
Eva Litrup, Statens Serum Institut
Deirdre M. Prendergast, Celbridge, Co. Kildare
John E. Moore, Belfast City Hospital
Sam Strain, Animal Health and Welfare Northern Ireland
Christian Kornschober, Austrian Agency for Health and Food Safety
Richard Meinersmann, USDA REE Agricultural Research Service
Alexandra Uesbeck, University of Cologne
François Xavier Weill, Institut Pasteur, Paris
Aidan Coffey, Department of Biological Sciences, Munster Technological University, Bishopstown, Cork, IrelandFollow
Helene Andrews-Polymenis, Texas A&M University
Roy Curtiss, University of Florida
Séamus Fanning, University College Dublin

Document Type

Article

Creative Commons License

This work is licensed under a Creative Commons Attribution 4.0 International License.

Disciplines

Biology

Publication Details

Wellcome Open Research

© 2021 Achtman M et al.

Abstract

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.

Recommended Citation

Achtman M, Zhou Z, Alikhan NF et al. Genomic diversity of Salmonella enterica -The UoWUCC 10K genomes project [version 2; peer review: 2 approved]. Wellcome Open Res 2021, 5:223 (https://doi.org/10.12688/wellcomeopenres.16291.2)