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

作者：Xiangyu Deng, Shaoting Li, Tongzhou Xu, Zhemin Zhou, Michelle Moore, Ruth Timme, Shaohua Zhao, Charlotte Lane, Blake A. Dinsmore, François‐Xavier Weill, Patricia I. Fields · 发表于：Applied and Environmental Microbiology · 年份：2025 · DOI：10.1128/aem.02600-24 · 被引用次数：10 · 研究领域：Salmonella and Campylobacter epidemiology、Vibrio bacteria research studies、Plant Pathogenic Bacteria Studies

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. IMPORTANCE The utility of Salmonella serotyping has evolved from a primary subtyping method, where the need for strain discrimination justified its complexity, to a supplemental subtyping scheme and nomenclature convention, where clarity and simplicity in communication have become important for it...