Whole genome sequencing-based benchmarking of subtyping methods for Salmonella enterica serotype Enteritidis

A total of 52 Salmonella enterica subspecies enterica serotype Enteritidis (SE) isolates representing 16 major outbreaks and three sporadic cases in the United States between 2001 and 2011 were sequenced and subjected to a retrospective investigation with a combination of four subtyping methods. Whole genome single nucleotide polymorphism typing (WGST) resolved all outbreak clusters and provided useful epidemiological information with robust phylogenetic inference. While both MLVA and CRISPR-MVLST yielded higher discriminatory power than PFGE, MLVA outperformed in delineating outbreak clusters whereas CRISPR-MVLST showed the potential to trace major lineages and ecological origins of SE. Our results suggested that whole genome sequencing (WGS) makes a viable platform for the evaluation and benchmarking molecular subtyping methods.