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

本研究对2001年至2011年美国境内16起主要暴发疫情与3起散发病例对应的52株肠炎沙门氏菌（Salmonella enterica subsp. enterica serovar Enteritidis, SE）分离株完成全基因组测序，并联合4种分子分型方法开展回顾性调查。全基因组单核苷酸多态性分型（Whole Genome Single Nucleotide Polymorphism Typing, WGST）可清晰区分所有暴发聚类，并通过稳健的系统发育推断提供了极具参考价值的流行病学信息。尽管多位点可变数目串联重复序列分型（MLVA）与CRISPR-MVLST的分辨能力均高于脉冲场凝胶电泳（PFGE），但MLVA在划分暴发聚类方面表现更优，而CRISPR-MVLST则具备追踪SE主要进化谱系与生态起源的潜力。本研究结果表明，全基因组测序（WGS）可作为评估与基准比对分子分型方法的可靠平台。