Comparative genomic analysis for monitoring Salmonella Enteritidis outbreaks in poultry

Salmonella is a common zoonotic pathogen found in domestic birds. Salmonella Enteritidis (SE) is the most virulent serovar for humans. During 2015-2016, an unusual increase in SE diagnosis in human has been reported in Israel. Since, the main source of SE is table eggs, we have tested the presence of SE in various poultry houses, egg sorting stations, and imported eggs. In total 23 SE isolates were collected. The objective of this study was to identify the source of SE using next generation sequencing technology. Genomic DNA of all SE isolates as well as from two commercial vaccine strains and a laboratory reference strain was sequenced and assembled.

Whole genome sequences (WGS) were analyzed by Multi-Locus Sequence Type analysis (MLST) comparing 7 conserved genes, ribosomal gene MLST (rMLST) analysis, and whole genome MLST (wgMLST) analysis. Seven-genes MLST failed to separate the isolates; however rMLST analysis was able to divide them into 4 groups, while wgMLST analysis separated the isolates into 14 distinct groups. In most cases, a high similarity has been observed between isolates derived from the same, suggesting the persistence of a single clone. It can be concluded that several outbreaks from different sources of SE occurred in Israel during 2015-2016.

This study has demonstrated the usefulness of WGS in monitoring and tracing outbreaks of SE in poultry and can be applied for control of human outbreaks.