Open Access Highly Accessed Research article

Genome sequencing reveals diversification of virulence factor content and possible host adaptation in distinct subpopulations of Salmonella enterica

Henk C den Bakker1*, Andrea I Moreno Switt1, Gregory Govoni23, Craig A Cummings2, Matthew L Ranieri1, Lovorka Degoricija2, Karin Hoelzer1, Lorraine D Rodriguez-Rivera1, Stephanie Brown1, Elena Bolchacova2, Manohar R Furtado2 and Martin Wiedmann1

  • * Corresponding author: Henk C den Bakker

  • † Equal contributors

Author affiliations

1 Department of Food Science, Cornell University, Ithaca NY, 14853, USA

2 Life Technologies Corporation, 850 Lincoln Centre Drive, Foster City CA, 94404, USA

3 AvidBiotics Corp., 300 Utah Ave., Suite 150, South San Francisco, CA, 94080, USA

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Citation and License

BMC Genomics 2011, 12:425  doi:10.1186/1471-2164-12-425

Published: 22 August 2011



Divergence of bacterial populations into distinct subpopulations is often the result of ecological isolation. While some studies have suggested the existence of Salmonella enterica subsp. enterica subclades, evidence for these subdivisions has been ambiguous. Here we used a comparative genomics approach to define the population structure of Salmonella enterica subsp. enterica, and identify clade-specific genes that may be the result of ecological specialization.


Multi-locus sequence analysis (MLSA) and single nucleotide polymorphisms (SNPs) data for 16 newly sequenced and 30 publicly available genomes showed an unambiguous subdivision of S. enterica subsp. enterica into at least two subpopulations, which we refer to as clade A and clade B. Clade B strains contain several clade-specific genes or operons, including a β-glucuronidase operon, a S-fimbrial operon, and cell surface related genes, which strongly suggests niche specialization of this subpopulation. An additional set of 123 isolates was assigned to clades A and B by using qPCR assays targeting subpopulation-specific SNPs and genes of interest. Among 98 serovars examined, approximately 20% belonged to clade B. All clade B isolates contained two pathogenicity related genomic islands, SPI-18 and a cytolethal distending toxin islet; a combination of these two islands was previously thought to be exclusive to serovars Typhi and Paratyphi A. Presence of β-glucuronidase in clade B isolates specifically suggests an adaptation of this clade to the vertebrate gastrointestinal environment.


S. enterica subsp. enterica consists of at least two subpopulations that differ specifically in genes involved in host and tissue tropism, utilization of host specific carbon and nitrogen sources and are therefore likely to differ in ecology and transmission characteristics.