PDF(Pubmed)
Abstract：
Yersinia enterocolitica (Y. enterocolitica) is the most frequent etiological agent of yersiniosis and has been responsible for several national outbreaks in Norway and elsewhere. A standardized high-resolution method, such as core genome Multilocus Sequence Typing (cgMLST), is needed for pathogen traceability at the national and international levels. In this study, we developed and implemented a cgMLST scheme for Y. enterocolitica. We designed a cgMLST scheme in SeqSphere + using high-quality genomes from different Y. enterocolitica biotype sublineages. The scheme was validated if more than 95% of targets were found across all tested Y. enterocolitica: 563 Norwegian genomes collected between 2012 and 2022 and 327 genomes from public data sets. We applied the scheme to known outbreaks to establish a threshold for identifying major complex types (CTs) based on the number of allelic differences. The final cgMLST scheme included 2,582 genes with a median of 97.9% (interquartile range 97.6%-98.8%) targets found across all tested genomes. Analysis of outbreaks identified all outbreak strains using single linkage clustering at four allelic differences. This threshold identified 311 unique CTs in Norway, of which CT18, CT12, and CT5 were identified as the most frequently associated with outbreaks. The cgMLST scheme showed a very good performance in typing Y. enterocolitica using diverse data sources and was able to identify outbreak clusters. We recommend the implementation of this scheme nationally and internationally to facilitate Y. enterocolitica surveillance and improve outbreak response in national and cross-border outbreaks.
摘要：
小肠结肠炎耶尔森氏菌（Y.小肠结肠炎）是耶尔森氏菌病最常见的病因，并在挪威和其他地方引起了几次全国性的暴发。一种标准化的高分辨率方法，如核心基因组多位点序列分型（cgMLST），在国家和国际层面上需要病原体的可追溯性。在这项研究中,我们为小肠结肠炎Y开发并实施了cgMLST方案。我们在SeqSphere中设计了一个cgMLST方案，使用来自不同小肠结肠炎Y生物型亚谱系的高质量基因组。如果在所有测试的小肠结肠炎Y中发现了超过95％的目标，则该方案得到了验证：2012年至2022年之间收集的563个挪威基因组和来自公共数据集的327个基因组。我们将该方案应用于已知的爆发，以根据等位基因差异的数量建立识别主要复杂类型（CT）的阈值。最终的cgMLST方案包括2,582个基因，在所有测试的基因组中发现的目标中位数为97.9％（四分位距97.6％-98.8％）。爆发分析使用四个等位基因差异的单连锁聚类确定了所有爆发菌株。这个阈值确定了挪威的311个独特的CT，其中CT18,CT12和CT5被确定为最常见的与疾病暴发相关.cgMLST方案在使用不同的数据源键入小肠结肠炎Y方面表现出非常好的性能，并且能够识别爆发集群。我们建议在国内和国际上实施该计划，以促进小肠结肠炎的监测，并改善国家和跨境疫情的疫情应对。
