全基因组测序(WGS)是细菌亚型的首选方法,它正在迅速取代更传统的方法,如脉冲场凝胶电泳(PFGE)。在这里,我们使用高分辨率核心基因组单核苷酸变体(cgSNV)分型方法在来源归属的背景下表征了肠沙门氏菌血清型海德堡分离株的临床和食物。此外,包括成簇的规则间隔短回文重复(CRISPR)分析,以进一步支持该方法.我们的结果表明,cgSNV具有高度歧视性,并将爆发分离株分为不同的簇(0-4个SNV)。CRISPR分析还能够区分爆发菌株与流行病学无关的分离株。具体来说,我们的数据清楚地表明了这两种方法在确定2012年以流行病学为特征的海德堡S.使用0-10个SNV的分子截止值,在魁北克收集的246个海德堡临床和食品分离株的cgSNV分析,在爆发事件的同一年,据透露,零售和屠宰场鸡分离株可能是海德堡人感染的重要来源。有趣的是,与cgSNV遗传相关的分离株也具有与爆发分离株和集群相同的CRISPR.这表明CRISPR谱可作为确定食源性暴发中来源归因的补充方法。使用基因组分析还可以识别PFGE遗漏的大量病例,这表明大多数疫情可能被低估了。尽管流行病学信息仍必须支持基于WGS的结果,cgSNV方法是解决爆发事件并将这些事件归因于其各自来源的高度歧视性方法。CRISPR分型可以在源跟踪期间作为这种分析的补充工具。
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.