Comparison of subtyping methods for Salmonella enterica serotype Enteritidis strains isolated from outbreaks in Sichuan, 2008–2018

Objective  To compare the molecular typing methods for the Salmonella Enteritidis strains isolated from the outbreaks in Sichuan province and provide evidence for the rapid and reliable source tracing of the outbreaks. Methods  Pulse-field gel electrophoresis (PFGE), multilocus variable-number of tanden-repeat analysis (MLVA), clustered regularly interspaced short palindromic repeats (CRISPR), multilocus sequence typing (MLST) and whole genome sequencing-based Single Nucleotide Polymorphism (WGS-SNP) were used for the subtyping of S. Enteritidis strains isolated from the outbreaks in Sichuan from 2008 to 2018. Simpson Diversity Index (DI) was used as an indicator to compare the subtyping power of a single method and a combination of methods. Results  When PFGE, MLVA, CRISPR, and MLST were used alone, the DI values were all lower than 0.9. The DI value of PFGE_XbaI and MLVA increased to above 0.9 when PFGE_XbaI and MLVA were used together. WGS-SNP had the highest DI value (0.971). Conclusion  The most suitable method for the molecular subtyping of S. Enteritidis strains isolated from the outbreaks in Sichuan was WGS-SNP. In the absence of genome analysis capability, the PFGE_XbaI+MLVA method is recommended.