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

Authors: ACHTMAN, MARK - Warwick Medical School; ZHOUA, ZHEMIN - Warwick Medical School; ALIKHAN, NABIL-FAREED - Warwick Medical School; TYNE, WILLIAM - Warwick Medical School; PARKHILL, JULIAN - University Of Cambridge; CORMICAN, MARTIN - National Salmonella, Shigella & Listeria Reference Laboratory; CHIOU, CHIEN-SHUN - Taiwan Centers For Disease Control; TORPDAHL, MIA - Staten Serum Institute; LITRUP, EVA - Staten Serum Institute; Meinersmann, Richard - Rick; PRENDERGAST, DEIRDRE - Department Of Agriculture, Food, And The Marine; MOORE, JOHN - Belfast City Hospital; STRAIN, SAM - Animal Health And Welfare Ni; KORNSCHOBER, CHRISTIAN - Austrian Agency For Health And Food Safety Ltd (AGES); UESBECK, ALEXANDRA - University Of Cologne; WEILL, FRANCOIS-XAVIER - Institut Pasteur - France; COFFEY, AIDAN - Cork Institute Of Technology; ANDREWS-POLYMENIS, HELENE - Texas A&M University; CURTISS, ROY - University Of Florida; FANNING, SEAMUS - University College Dublin

Submitted to: Wellcome Open Research
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 2/1/2021
Publication Date: 2/1/2021
Citation: Achtman, M., Zhoua, Z., Alikhan, N., Tyne, W., Parkhill, J., Cormican, M., Chiou, C., Torpdahl, M., Litrup, E., Meinersmann, R.J., Prendergast, D.M., Moore, J.E., Strain, S., Kornschober, C., Uesbeck, A., Weill, F., Coffey, A., Andrews-Polymenis, H., Curtiss, R., Fanning, S. 2021. The UoWUCC 10K Salmonella genomes project. Wellcome Open Research. 5:223. https://doi.org/10.12688/wellcomeopenres.16291.2.
DOI: https://doi.org/10.12688/wellcomeopenres.16291.2

Interpretive Summary: High throughput sequencing has made many bacterial genomic sequences available but the population of sequenced cells has been highly biased toward human clinical isolates. Such biases make it difficult to reconstruct accurate histories of the organisms that results in errors in conclusions on the timing of when new clones appear. The first objective of this study was to put together a broadly representative reference population of Salmonella enterica, a major cause of human disease from foods. To that end, 10,000 isolates were collected from a variety of sources in 73 different countries. The genomes of 9769 isolates were sequenced. The second objective of the study was to demonstrate the utility of the data in analyzing S. enterica. The total number of genes that were analyzed was 3002 genes. It was found that clusters of that differed at less than 900 genes were correlated with single serotypes and were called HC900 clusters, thus giving the sequence classification scheme context with known clinical syndromes for serotypes. With some notable exceptions, clones of Salmonella tended to be geographically limited. This data set will help international research give context to their Salmonella genomic analyses.

Technical Abstract: Publicly available genomes of Salmonella enterica have a strong bias to isolates from human disease in the United States and the UK, and from domesticated animals in the United States. Here we describe a historical collection of 10,000 strains isolated between 1891-2010 from 73 distinct countries. They were obtained from 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. We also report that 9769 of their annotated genomic sequences are now publicly available, together with their metadata. These genomes dramatically extend the breadth of diversity for S. enterica that is available in public databases, as demonstrated by an overview of their entire core genomic diversity as well as more detailed examinations of exemplar Lineages including serovars Typhimurium, Enteritidis and Mbandaka.