Abstract：
Enteric yersiniosis, the third most common food-borne zoonosis in Europe, is mainly caused by the pathogen Yersinia enterocolitica. In France, the yersiniosis microbiological surveillance is conducted at the Yersinia National Reference Laboratory (YNRL). Since 2017, isolates have been characterized by whole genome sequencing (WGS) followed by a 500-gene Yersinia-cgMLST. We report here the data of the WGS-based surveillance on Y. enterocolitica isolates for the 2017-2021 period. The YNRL characterized 7,642 Y. enterocolitica strains distributed in 2,497 non-pathogenic isolates from lineages 1Aa and 1Ab, and 5,145 specimens belonging to 8 pathogenic lineages. Among pathogenic isolates, lineage 4 was the most common (87.2%) followed by lineages 2/3-9b (10.6%), 2/3-5a (1.2%), 2/3-9a (0.6%), 3-3b, 3-3c, 1B, and 3-3d (0.1% per each). Importantly, we developed a routine surveillance system based on a new typing method consisting of a 1,727-genes core genome Multilocus Sequence Typing (cgMLST) specific to the species Y. enterocolitica followed by isolate clustering. Thresholds of allelic distances (AD) were determined and fixed for the clustering of isolates: AD ≤ 5 for lineages 4, 2/3-5a, and 2/3-9a, and AD ≤ 3 for lineage 2/3-9b. Clustering programs were implemented in 2019 in routine surveillance to detect genomic clusters of pathogenic isolates. In total, 419 clusters with at least 2 isolates were identified, representing 2,504 of the 3,503 isolates characterized between 2019 and 2021. Most clusters (n = 325) comprised 2 to 5 isolates. The new typing method proved to be useful for the molecular investigation of unusual grouping of cases as well as for the detection of genomic clusters in routine surveillance.
OBJECTIVE: We describe here the new typing method used for molecular surveillance of Yersinia enterocolitica infections in France based on a novel core genome Multilocus Sequence Typing (cgMLST) specific to Y. enterocolitica species. This method can reliably identify the pathogenic Y. enterocolitica subspecies and compare the isolates with a high discriminatory power. Between 2017 and 2021, 5,145 pathogenic isolates belonging to 8 lineages were characterized and lineage 4 was by far the most common followed by lineage 2/3-9b. A clustering program was implemented, and detection thresholds were cross-validated by the molecular and epidemiological investigation of three unusual groups of Y. enterocolitica infections. The routine molecular surveillance system has been able to detect genomic clusters, leading to epidemiological investigations.
OBJECTIVE: We describe here the new typing method used for molecular surveillance of Yersinia enterocolitica infections in France based on a novel core genome Multilocus Sequence Typing (cgMLST) specific to Y. enterocolitica species. This method can reliably identify the pathogenic Y. enterocolitica subspecies and compare the isolates with a high discriminatory power. Between 2017 and 2021, 5,145 pathogenic isolates belonging to 8 lineages were characterized and lineage 4 was by far the most common followed by lineage 2/3-9b. A clustering program was implemented, and detection thresholds were cross-validated by the molecular and epidemiological investigation of three unusual groups of Y. enterocolitica infections. The routine molecular surveillance system has been able to detect genomic clusters, leading to epidemiological investigations.
摘要：
肠孢子虫病,欧洲第三大最常见的食源性人畜共患病，主要由病原小肠结肠炎耶尔森氏菌引起。在法国,耶尔森氏菌病微生物监测在耶尔森氏菌国家参考实验室（YNRL）进行。自2017年以来，分离株的特征是全基因组测序（WGS），然后是500个基因的耶尔森氏菌-cgMLST。我们在这里报告了2017-2021年期间基于WGS的小肠结肠炎Y分离株监测数据。YNRL表征了7,642Y。小肠结肠炎菌株分布在来自谱系1Aa和1Ab的2,497个非致病性分离株中，和属于8个致病谱系的5145个标本。在病原分离物中，谱系4最常见(87.2%)，其次是谱系2/3-9b(10.6%)，2/3-5a（1.2%），2/3-9a（0.6%），3-3b,3-3c,1B,和3-3d（每个0.1%）。重要的是,我们基于一种新的分型方法开发了一种常规监测系统，该方法包括对小肠结肠炎Y种具有特异性的1,727个基因核心基因组多位点序列分型（cgMLST），然后进行分离聚类。确定并固定了分离株聚类的等位基因距离（AD）阈值：谱系4、2/3-5a的AD≤5，和2/3-9a，谱系2/3-9b的AD≤3。2019年在常规监测中实施了聚类计划，以检测致病性分离株的基因组聚类。总的来说,确定了至少2个分离株的419个簇，代表2019年至2021年间表征的3,503株分离株中的2,504株。大多数簇(n=325)包含2至5个分离物。新的分型方法被证明可用于异常病例分组的分子研究以及常规监测中基因组簇的检测。
目的：我们在这里描述了用于法国小肠结肠炎耶尔森氏菌感染的分子监测的新分型方法，该方法基于对小肠结肠炎耶尔森氏菌特异的新型核心基因组多位点序列分型（cgMLST）物种。该方法可以可靠地鉴定致病性小肠结肠炎耶氏亚种，并以较高的鉴别力比较分离株。在2017年至2021年之间，鉴定了属于8个谱系的5,145个致病性分离株，到目前为止，谱系4是最常见的，其次是谱系2/3-9b。实现了一个聚类程序，和检测阈值通过对三个不寻常的小肠结肠炎耶氏球菌感染组的分子和流行病学调查进行交叉验证。常规的分子监测系统已经能够检测基因组簇，导致流行病学调查。
目的：我们在这里描述了用于法国小肠结肠炎耶尔森氏菌感染的分子监测的新分型方法，该方法基于对小肠结肠炎耶尔森氏菌特异的新型核心基因组多位点序列分型（cgMLST）物种。该方法可以可靠地鉴定致病性小肠结肠炎耶氏亚种，并以较高的鉴别力比较分离株。在2017年至2021年之间，鉴定了属于8个谱系的5,145个致病性分离株，到目前为止，谱系4是最常见的，其次是谱系2/3-9b。实现了一个聚类程序，和检测阈值通过对三个不寻常的小肠结肠炎耶氏球菌感染组的分子和流行病学调查进行交叉验证。常规的分子监测系统已经能够检测基因组簇，导致流行病学调查。
