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

Abstract

Salmonella enterica is the leading etiologic agent of bacterial food-borne outbreaks worldwide. This ubiquitous species contains more than 2,600 serovars that may differ in their host specificity, clinical manifestations, and epidemiology. To characterize salmonellosis epidemiology in Israel and to study the association of nontyphoidal Salmonella (NTS) serovars with invasive infections, 48,345 Salmonella cases reported and serotyped at the National Salmonella Reference Center between 1995 and 2012 were analyzed. A quasi-Poisson regression was used to identify irregular clusters of illness, and pulsed-field gel electrophoresis in conjunction with whole-genome sequencing was applied to molecularly characterize strains of interest. Three hundred twenty-nine human salmonellosis clusters were identified, representing an annual average of 23 (95% confidence interval [CI], 20 to 26) potential outbreaks. We show that the previously unsequenced S. enterica serovar 9,12:l,v:- belongs to the B clade of Salmonella enterica subspecies enterica, and we show its frequent association with extraintestinal infections, compared to other NTS serovars. Furthermore, we identified the dissemination of two prevalent Salmonella enterica serovar Typhimurium DT104 clones in Israel, which are genetically distinct from other global DT104 isolates. Accumulatively, these findings indicate a severe underreporting of Salmonella outbreaks in Israel and provide insights into the epidemiology and genomics of prevalent serovars, responsible for recurring illness.

FIG 1

(A) Annual incidence of reported NTS, invasive NTS infections, and predicted salmonellosis clusters in Israel, 1999 to 2012. The annual incidence of NTS Salmonella cases (circles and solid line) and the number of invasive NTS infections (triangles and dotted line) are shown per 100,000 population and were inferred from the laboratory-confirmed Salmonella cases received at the National Salmonella Reference Center. The yearly number of clusters (squares and broken line) was predicted by the Farrington statistical surveillance model as described in Materials and Methods. (B) Seasonal distribution of salmonellosis clusters, 1999 to 2012, and invasive and stool infections with reported NTS Salmonella in Israel, 1995 to 2012.

FIG 2

S. 9,12:l,v:− is a member of S. enterica subsp. enterica clade B. The maximum likelihood cladogram of 385 Salmonella strains and S. 9,12:l,v:− was constructed by FastTree using 3,384 orthologous Salmonella genes. Internal nodes show local support values based on the Shimodaira-Hasegawa test. Distances on the tree represent substitutions per variable site.

FIG 3

Prevalence of endemic MDR S. Typhimurium DT104 pulsotype. The PFGE profile of three S. Typhimurium DT104 isolates responsible for three clusters that occurred in 2001, 2005, and 2011 (red) was compared to the pulsotypes of S. Typhimurium DT104 NCTC 13348 (green) and 57 sporadic isolates (blue) of S. Typhimurium isolated in the past decade. DNA from all isolates was digested with XbaI, and the degree of genetic similarity is shown by the dendrogram at the left.

FIG 4

Phylogenetic relationship of identified Israeli DT104 isolates with global S. Typhimurium DT104. Maximum clade credibility tree of 335 S. Typhimurium DT104 isolates and six Israeli DT104 isolates (95799, 98346, 104772, 108402, 116045, and 138736, in red) was constructed based on 2,353 SNPs using BEAST v1.80. The tree was calibrated using isolation dates of the strains. The distances represent time, and internal nodes show clade support (bootstrap values) as posterior probabilities.