Comparison of conventional molecular and whole-genome sequencing methods for subtypingSalmonella entericaserovar Enteritidis strains from Tunisia

We sought to determine the relative value of conventional molecular methods and whole-genome sequencing (WGS) for subtypingSalmonella entericaserovar Enteritidis recovered from 2000 to 2015 in Tunisia and to investigate the genetic diversity of this serotype. A total of 175SalmonellaEnteritidis isolates were recovered from human, animal, and foodborne outbreak samples. Pulsed-field gel electrophoresis (PFGE), multiple locus variable-number tandem repeat analysis (MLVA), and whole-genome sequencing were performed. Eight pulsotypes were detected for all isolates with PFGE (DI = 0.518). Forty-fiveSalmonellaEnteritidis isolates were selected for the MLVA and WGS techniques. Eighteen MLVA profiles were identified and classified into two major clusters (DI = 0.889). Core genome multilocus typing (cgMLST) analysis revealed 16 profiles (DI = 0.785). Whole-genome analysis indicated 660 single-nucleotide polymorphism (SNP) divergences dividing these isolates into 43 haplotypes (DI = 0.997). The phylogenetic tree supported the classification ofSalmonellaEnteritidis isolates into two distinct lineages subdivided into five clades and seven subclades. Pairwise SNP differences between the isolates ranged between 302 and 350. We observed about 311 SNP differences between the two foodborne outbreaks, while only less or equal to 4 SNP differences within each outbreak. SNP-based WGS typing showed an excellent discriminatory power comparing with the conventional methods such as PFGE and MLVA. Besides, we demonstrate the added value of WGS as a complementary subtyping method to discriminate outbreak from non-outbreak isolates belonging to common subtypes. It is important to continue the survey ofSalmonellaEnteritidis lineages in Tunisia using WGS.

Automated summary

The study compared the relative value of conventional molecular methods and whole-genome sequencing in subtyping Salmonella enterica serovar Enteritidis in Tunisia from 2000 to 2015, and investigated the genetic diversity of this serotype. WGS showed excellent discriminatory power and demonstrated added value as a complementary subtyping method for discriminating outbreak from non-outbreak isolates belonging to common subtypes. Continuing the survey of Salmonella Enteritidis lineages using WGS in Tunisia is important.