Comparative genomics of Salmonella enterica serovar Enteritidis ST-11 isolated in Uruguay reveals lineages associated with particular epidemiological traits

Salmonella enterica serovar Enteritidis is a major cause of foodborne disease in Uruguay since 1995. We used a genomic approach to study a set of isolates from different sources and years. Whole genome phylogeny showed that most of the strains are distributed in two major lineages (E1 and E2), both belonging to MLST sequence type 11 the major ST among serovar Enteritidis. Strikingly, E2 isolates are over-represented in periods of outbreak abundance in Uruguay, while E1 span all epidemic periods. Both lineages circulate in neighbor countries at the same timescale as in Uruguay, and are present in minor numbers in distant countries. We identified allelic variants associated with each lineage. Three genes, ycdX, pduD and hsdM, have distinctive variants in E1 that may result in defective products. Another four genes (ybiO, yiaN, aas, aceA) present variants specific for the E2 lineage. Overall this work shows that S. enterica serovar Enteritidis strains circulating in Uruguay have the same phylogenetic profile than strains circulating in the region, as well as in more distant countries. Based on these results we hypothesize that the E2 lineage, which is more prevalent during epidemics, exhibits a combination of allelic variants that could be associated with its epidemic ability

PCR typing of representative blood isolates from Lima hospitals using different gene markers.

<p>A) The <i>gyrA-</i>IS200-<i>rcsC</i> amplification distinguishes serovar Typhi from other serovars. B) and C) The <i>spvC</i> and <i>spvRA</i> markers detect the virulence plasmid (pSV). D) <i>traC</i> is a marker for the megaplasmid of Infantis (pESI). E) Plasmid profiles of the same strains. The asterisks below the bands in the plasmid profiles indicate the plasmid suspected to be the pSV. Tm, Typhimurium; E, Enteritidis; Ch, Choleraesuis; Ty, Typhi; PA, Paratyphi A; PB, Paratyphi B; and I, Infantis.</p

Characterization of <i>Salmonella enterica</i> isolates causing bacteremia in Lima, Peru.

<p>Characterization of <i>Salmonella enterica</i> isolates causing bacteremia in Lima, Peru.</p

Characterization of <i>Salmonella enterica</i> isolates causing bacteremia in Lima, Peru, using multiple typing methods

<div><p>In this study, different molecular typing tools were applied to characterize 95 <i>Salmonella enterica</i> blood isolates collected between 2008 and 2013 from patients at nine public hospitals in Lima, Peru. Combined results of multiplex PCR serotyping, two- and seven-loci multilocus sequence typing (MLST) schemes, serotyping, IS200 amplification and RAPD fingerprints, showed that these infections were caused by eight different serovars: Enteritidis, Typhimurium, Typhi, Choleraesuis, Dublin, Paratyphi A, Paratyphi B and Infantis. Among these, Enteritidis, Typhimurium and Typhi were the most prevalent, representing 45, 36 and 11% of the isolates, respectively. Most isolates (74%) were not resistant to ten primarily used antimicrobial drugs; however, 37% of the strains showed intermediate susceptibility to ciprofloxacin (ISC). Antimicrobial resistance integrons were carried by one Dublin (<i>dfra1</i> and <i>aadA1</i>) and two Infantis (<i>aadA1</i>) isolates. The two Infantis isolates were multidrug resistant and harbored a large megaplasmid. Amplification of <i>spvC</i> and <i>spvRA</i> regions showed that all Enteritidis (n = 42), Typhimurium (n = 34), Choleraesuis (n = 3) and Dublin (n = 1) isolates carried the <i>Salmonella</i> virulence plasmid (pSV). We conclude that the classic serotyping method can be substituted by the multiplex PCR and, when necessary, sequencing of only one or two loci of the MLST scheme is a valuable tool to confirm the results. The effectiveness and feasibility of different typing tools is discussed.</p></div

Multilocus sequence typing of 18 selected <i>Salmonella</i> isolates from Lima, Peru^*.

<p>Multilocus sequence typing of 18 selected <i>Salmonella</i> isolates from Lima, Peru^{<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0189946#t002fn001" target="_blank">*</a>}.</p