Table_1_Isolate-Based Surveillance of Listeria monocytogenes by Whole Genome Sequencing in Austria.DOCX

Listeria monocytogenes (L. monocytogenes) is a ubiquitous organism that can easily enter the food chain. Infection with L. monocytogenes can cause invasive listeriosis. Since 2014, in Austria, L. monocytogenes isolates from human and food/food-associated samples have been provided on a mandatory basis by food producers and laboratories to the National Reference Laboratory. Since 2017, isolates undergo routinely whole genome sequencing (WGS) and core genome Multilocus Sequence Typing (cgMLST) for cluster analyses. Aims of this study were to characterize isolates and clusters of 2017 by using WGS data and to assess the usefulness of this isolate-based surveillance for generating hypotheses on sources of invasive listeriosis in real-time. WGS data from 31 human and 1744 non-human isolates originating from 2017, were eligible for the study. A cgMLST-cluster was defined as two or more isolates differing by ≤10 alleles. We extracted the sequence types (STs) from the WGS data and analyzed the food subcategories meat, fish, vegetable and diary for associations with the ten most prevalent STs among food, through calculating prevalence ratios (PR) with 95% confidence intervals (CI). The three most frequent STs among the human isolates were ST1 (7/31; 22.6%), ST155 (4/31; 12.9%) and ST451 (3/31; 9.7%) and among the non-human isolates ST451 (614/1744; 35.2%), ST8 (173/1744, 10.0%) and ST9 (117/1744; 6.7%). We found ST21 associated with vegetables (PR: 11.39, 95% CI: 8.32–15.59), ST121 and ST155 with fish (PR: 7.05, 95% CI: 4.88–10.17, PR: 3.29, 95% CI: 1.86–5.82), and ST511, ST7 and ST451 with dairy products (PR: 8.55, 95% CI: 6.65–10.99; PR: 5.05, 95% CI: 3.83–6.66, PR: 3.03, 95% CI: 2.02–4.55). We identified 132 cgMLST-clusters. Six clusters contained human isolates (ST155, ST1, ST101, ST177, ST37 and ST7) and for five of those cgMLST-based cluster analyses solely was able to hypothesize the source: an Austrian meat processing company, two Austrian cheese manufacturers and two vegetable processing companies, one based in Austria and the other in Belgium. Determining routinely STs in food isolates by WGS allows to associate STs with food products. Real-time WGS of L. monocytogenes isolates provided mandatorily, proved to be useful in promptly generating hypotheses on sources of invasive listeriosis.

Listeria monocytogenes（单核细胞增生李斯特菌，简称L. monocytogenes）是一种广泛分布的微生物，其易于进入食物链。感染L. monocytogenes可导致侵袭性李斯特菌病。自2014年起，在奥地利，食品生产者和实验室有义务将来自人类和食品/食品相关样本的L. monocytogenes分离株提交至国家参考实验室。自2017年起，分离株将接受常规的全基因组测序（WGS）和核心基因组多位点序列分型（cgMLST）以进行聚类分析。本研究的目的是利用WGS数据对2017年的分离株和聚类进行特征描述，并评估基于分离株的监测在实时生成侵袭性李斯特菌病来源假设方面的有效性。2017年来自31个人类和1744个非人类分离株的WGS数据符合研究要求。cgMLST聚类被定义为两个或更多个分离株之间差异不超过≤10个等位基因。我们从WGS数据中提取了序列类型（STs），并通过计算流行比（PR）及其95%置信区间（CI），分析了食品子类别（肉类、鱼类、蔬菜和乳制品）与食物中十种最常见STs之间的关联。在人类分离株中，最常见的三个STs分别为ST1（7/31；22.6%）、ST155（4/31；12.9%）和ST451（3/31；9.7%），而在非人类分离株中则为ST451（614/1744；35.2%）、ST8（173/1744；10.0%）和ST9（117/1744；6.7%）。我们发现ST21与蔬菜相关（PR：11.39，95% CI：8.32–15.59），ST121和ST155与鱼类相关（PR：7.05，95% CI：4.88–10.17；PR：3.29，95% CI：1.86–5.82），ST511、ST7和ST451与乳制品相关（PR：8.55，95% CI：6.65–10.99；PR：5.05，95% CI：3.83–6.66；PR：3.03，95% CI：2.02–4.55）。我们识别了132个cgMLST聚类。其中六个聚类包含人类分离株（ST155、ST1、ST101、ST177、ST37和ST7），针对这五个聚类，基于cgMLST的聚类分析仅能推测出来源：一家奥地利肉类加工公司、两家奥地利奶酪制造商以及两家蔬菜加工公司，一家位于奥地利，另一家位于比利时。通过WGS常规确定食品分离株的STs，可以将其与食品产品关联起来。对强制提交的L. monocytogenes分离株进行实时WGS，已被证明在迅速生成侵袭性李斯特菌病来源假设方面具有实用性。