The Salmonella In Silico Typing Resource (SISTR): an open web-accessible tool for rapidly typing and subtyping draft Salmonella genome assemblies

For nearly 100 years serotyping has been the gold standard for the identification of Salmonella serovars. Despite the increasing adoption of DNA-based subtyping approaches, serotype information remains a cornerstone in food safety and public health activities aimed at reducing the burden of salmonellosis. At the same time, recent advances in whole-genome sequencing (WGS) promise to revolutionize our ability to perform advanced pathogen characterization in support of improved source attribution and outbreak analysis. We present the Salmonella In Silico Typing Resource (SISTR), a bioinformatics platform for rapidly performing simultaneous in silico analyses for several leading subtyping methods on draft Salmonella genome assemblies. In addition to performing serovar prediction by genoserotyping, this resource integrates sequence-based typing analyses for: Multi-Locus Sequence Typing (MLST), ribosomal MLST (rMLST), and core genome MLST (cgMLST). We show how phylogenetic context from cgMLST...

近百年来，血清分型一直是沙门氏菌血清型鉴定的金标准。尽管基于DNA的亚型分析方法日益普及，但血清型信息仍是食品安全和公共卫生领域旨在减轻沙门氏菌病负担的核心依据。与此同时，全基因组测序（whole-genome sequencing, WGS）的最新进展有望彻底革新我们开展高级病原体特征分析的能力，从而为更精准的来源溯源和暴发分析提供支持。我们在此介绍沙门氏菌虚拟分型资源库（Salmonella In Silico Typing Resource, SISTR）——一个可针对沙门氏菌基因组草图快速同步执行多种主流亚型分析方法的生物信息学平台。除通过基因血清分型预测血清型外，该资源库还整合了基于序列的分型分析功能，包括多位点序列分型（Multi-Locus Sequence Typing, MLST）、核糖体多位点序列分型（ribosomal MLST, rMLST）及核心基因组多位点序列分型（core genome MLST, cgMLST）。我们将展示如何利用cgMLST提供的系统发育背景...