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

Abstract

BackgroundDivergence 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.ResultsMulti-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.ConclusionsS. 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.

Comparison of Typing Methods with a New Procedure Based on Sequence Characterization for Salmonella Serovar Prediction

“…The design of better PCR primers and approaches that use PCR and subsequent sequencing of target genes that contribute to O-antigen expression should, in the future, be able to address this issue. Specifically, as full-genome sequences for isolates representing additional O groups become available (54,55), the design of primers capable of detecting all 46 Salmonella serogroups should be feasible. Without full-genome sequences and the ability to compare rfb clusters, the ability to design new robust O-antigen primers for serogroup determination is limited.…”

Immunoproteomic Analysis of Antibody in Lymphocyte Supernatant in Patients with Typhoid Fever in Bangladesh

“…HlyE shares Ͼ90% amino acid identity with ClyA in E. coli K-12 (29), and in S. Typhi, it has been shown to be expressed under the control of the PhoP regulon (27,30) that regulates gene expression important in intracellular survival of S. enterica. Within the genus Salmonella, HlyE was originally found only in the typhoidal serotypes S. Typhi and S. Paratyphi A (29), but an analysis of a larger spectrum of salmonellae (by genome sequencing, comparative genomic hybridization, and PCR analysis) recently revealed that the hlyE gene has a wider distribution and that it is also present in some of the nontyphoidal Salmonella serotypes (including, but not limited to, invasive isolates of Salmonella serotypes Schwarzengrund, Montevideo, Bredeney, and others) (28,31,32).…”

Integrative Analysis of Salmonellosis in Israel Reveals Association of Salmonella enterica Serovar 9,12:l,v:− with Extraintestinal Infections, Dissemination of Endemic S. enterica Serovar Typhimurium DT104 Biotypes, and Severe Underreporting of Outbreaks

“…This analysis showed that the newly sequenced S. 9,12:l,v:Ϫ serovar is a member of the S. enterica subsp. enterica clade B (26).…”

“…Genome sequence analysis also showed an interesting composition of virulence genes present in various clade B genomes (26,27). These include three usher-chaperone fimbrial systems, one of which is the Tcf (Typhi colonization factor), a fimbrial cluster encoded between STM0182-STM0183 homologs and an additional fimbrial operon downstream of the ISSod13 transposase.…”