Salmonella serotypes in the genomic era: simplified Salmonella serotype interpretation from DNA sequence data

Abstract

In the era of genomic characterization of strains for public health microbiology, whole genome sequencing (WGS)-enabled subtyping of Salmonella provides superior discrimination of strains compared to traditional methods such as serotyping. Nonetheless, serotypes are still very useful; they maintain historical continuity and facilitate clear communication. Genetic determination of serotypes from WGS data is now routine. Genetic determination of rarer serotypes can be problematic due to a lack of sequences for rare antigen types and alleles, a lack of understanding of the genetic basis for some antigens, or some inconsistencies in the White-Kauffmann-Le Minor (WKL) Scheme for Salmonella serotype designation. Here, we present a simplified interpretation of serotypes to address the shortcomings of genetic methods, which will allow the streamlined integration of serotype determination into the WGS workflow. The simplification represents a consensus perspective among major U.S. public health agencies and serves as a WGS-oriented interpretation of the WKL Scheme. We also present SeqSero2S, a bioinformatics tool for WGS-based serotype prediction using the simplified interpretation.