Table_3_Source Tracking Based on Core Genome SNV and CRISPR Typing of Salmonella enterica Serovar Heidelberg Isolates Involved in Foodborne Outbreaks in Québec, 2012.xlsx

Whole-genome sequencing (WGS) is the method of choice for bacterial subtyping and it is rapidly replacing the more traditional methods such as pulsed-field gel electrophoresis (PFGE). Here we used the high-resolution core genome single nucleotide variant (cgSNV) typing method to characterize clinical and food from Salmonella enterica serovar Heidelberg isolates in the context of source attribution. Additionally, clustered regularly interspaced short palindromic repeats (CRISPR) analysis was included to further support this method. Our results revealed that cgSNV was highly discriminatory and separated the outbreak isolates into distinct clusters (0–4 SNVs). CRISPR analysis was also able to distinguish outbreak strains from epidemiologically unrelated isolates. Specifically, our data clearly demonstrated the strength of these two methods to determine the probable source(s) of a 2012 epidemiologically characterized outbreak of S. Heidelberg. Using molecular cut-off of 0–10 SNVs, the cgSNV analysis of 246 clinical and food isolates of S. Heidelberg collected in Québec, in the same year of the outbreak event, revealed that retail and abattoir chicken isolates likely represent an important source of human infection to S. Heidelberg. Interestingly, the isolates genetically related by cgSNV also harbored the same CRISPR as outbreak isolates and clusters. This indicates that CRISPR profiles can be useful as a complementary approach to determine source attribution in foodborne outbreaks. Use of the genomic analysis also allowed to identify a large number of cases that were missed by PFGE, indicating that most outbreaks are probably underestimated. Although epidemiological information must still support WGS-based results, cgSNV method is a highly discriminatory method for the resolution of outbreak events and the attribution of these events to their respective sources. CRISPR typing can serve as a complimentary tool to this analysis during source tracking.

全基因组测序（Whole-genome sequencing, WGS）是细菌分型的首选方法，正快速取代脉冲场凝胶电泳（pulsed-field gel electrophoresis, PFGE）等传统分型手段。本研究采用高分辨率核心基因组单核苷酸变异（core genome single nucleotide variant, cgSNV）分型方法，在来源溯源的研究框架下，对临床分离株与食品分离的肠炎沙门菌血清型海德堡（Salmonella enterica serovar Heidelberg）分离株进行特征分析。此外，本研究还纳入成簇规律间隔短回文重复序列（clustered regularly interspaced short palindromic repeats, CRISPR）分析，以进一步佐证该分型方法的有效性。
研究结果显示，cgSNV分型具有极高的分辨能力，可将暴发分离株划分为不同的聚类簇（单核苷酸变异差异为0~4个）。CRISPR分析同样能够区分暴发菌株与流行病学上无关联的分离株。具体而言，本研究数据清晰证明了这两种方法在确定2012年经流行病学表征的海德堡沙门菌暴发事件潜在传染源方面的优势。
以0~10个单核苷酸变异作为分子临界阈值，对暴发同年在魁北克地区收集的246株临床与食品来源的海德堡沙门菌分离株开展cgSNV分析后发现，零售与屠宰场来源的鸡源分离株可能是人类感染海德堡沙门菌的重要传染源。值得注意的是，经cgSNV鉴定为遗传相关的分离株，同时携带与暴发分离株及对应聚类簇一致的CRISPR型别。这表明CRISPR谱型可作为一种补充手段，用于食源性暴发事件的来源溯源分析。
本研究通过基因组分析还识别出大量被PFGE方法漏检的病例，这提示大多数暴发事件可能被低估。尽管基于WGS的分析结果仍需结合流行病学信息予以佐证，但cgSNV分型方法在暴发事件溯源及事件来源归因方面具有极高的分辨能力。CRISPR分型可作为该分析流程在传染源追踪过程中的补充工具。