Department of Food Science, Cornell University, Ithaca, New York 14853, USA.
Nestlé Institute of Food Safety and Analytical Sciences, Nestlé Research Center, Case Postale 44, Vers-chez-les-Blanc, CH-1000 Lausanne 26, Switzerland.
J Food Prot. 2021 Jul 1;84(7):1104-1113. doi: 10.4315/JFP-20-417.
Public health and regulatory agencies worldwide sequence all Listeria monocytogenes isolates obtained as part of routine surveillance and outbreak investigations. Many of these entities submit the sequences to the National Center for Biotechnology Information Pathogen Detection (NCBI PD) database, which groups the L. monocytogenes isolates into single nucleotide polymorphism (SNP) clusters based on a pairwise SNP difference threshold of 50 SNPs. Our goal was to assess whether isolates with metadata that suggest different sources or locations could show evidence for close genetic relatedness indicating a recent common ancestor and a possible unknown common source. We compared the whole genome sequencing (WGS) data of 249 L. monocytogenes isolates sequenced here, which have detailed metadata, with WGS data of nonclinical isolates on NCBI PD. The 249 L. monocytogenes isolates originated from natural environments (n = 91) as well as from smoked fish (n = 62), dairy (n = 56), and deli meat (n = 40) operations in the United States. Using a combination of subtyping by core genome multilocus sequence typing and high-quality SNP, we observed five SNP clusters in which study isolates and SNP cluster isolates seemed to be closely related and either (i) shared the same geolocation but showed different source types (one SNP cluster); (ii) shared the same source type but showed different geolocations (two SNP clusters); or (iii) shared neither source type nor geolocation (two SNP clusters). For one of the two clusters under (iii), there was, however, no strong bootstrap support for a common ancestor shared between the study isolates and SNP cluster isolates, indicating the value of in-depth evolutionary analyses when WGS data are used for traceback and epidemiological investigations. Overall, our results demonstrate that some L. monocytogenes subtypes may be associated with specific locations or commodities; these associations can help in investigations involving multi-ingredient foods such as sandwiches. However, at least some L. monocytogenes subtypes can be widespread geographically and can be associated with different sources, which may present a challenge to traceback investigations involving these subtypes.
世界各地的公共卫生和监管机构对从常规监测和暴发调查中获得的所有李斯特菌分离株进行测序。这些实体中的许多将序列提交给国家生物技术信息中心病原体检测（NCBI PD）数据库，该数据库根据 50 个 SNP 的成对 SNP 差异阈值将李斯特菌分离株分为单核苷酸多态性（SNP）簇。我们的目标是评估是否具有表明不同来源或地点的元数据的分离株是否可以显示出密切遗传关系的证据，表明存在最近的共同祖先和可能未知的共同来源。我们比较了 249 株李斯特菌分离株的全基因组测序（WGS）数据，这些分离株具有详细的元数据，以及 NCBI PD 上非临床分离株的 WGS 数据。这 249 株李斯特菌分离株来自美国的自然环境（n=91）以及熏鱼（n=62）、乳制品（n=56）和熟食肉（n=40）操作。使用核心基因组多位点序列分型和高质量 SNP 的组合进行分型，我们观察到五个 SNP 簇，研究分离株和 SNP 簇分离株似乎密切相关，并且（i）具有相同的地理位置，但具有不同的来源类型（一个 SNP 簇）；（ii）具有相同的来源类型，但具有不同的地理位置（两个 SNP 簇）；或（iii）既不共享来源类型也不共享地理位置（两个 SNP 簇）。然而，对于（iii）下的两个簇之一，研究分离株和 SNP 簇分离株之间的共同祖先没有很强的自举支持，这表明在使用 WGS 数据进行溯源和流行病学调查时进行深入进化分析的价值。总体而言，我们的结果表明，一些李斯特菌亚型可能与特定地点或商品有关；这些关联有助于调查涉及三明治等多成分食品的暴发。然而，至少一些李斯特菌亚型在地理上可能分布广泛，并与不同的来源有关，这可能对涉及这些亚型的溯源调查构成挑战。
