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使用全基因组测序对2016年食源性疾病暴发中的呕吐和腹泻菌株进行特征分析:应对微生物学、流行病学和生物信息学挑战

Characterization of Emetic and Diarrheal Strains From a 2016 Foodborne Outbreak Using Whole-Genome Sequencing: Addressing the Microbiological, Epidemiological, and Bioinformatic Challenges.

作者信息

Carroll Laura M, Wiedmann Martin, Mukherjee Manjari, Nicholas David C, Mingle Lisa A, Dumas Nellie B, Cole Jocelyn A, Kovac Jasna

机构信息

Department of Food Science, Cornell University, Ithaca, NY, United States.

Department of Food Science, The Pennsylvania State University, University Park, PA, United States.

出版信息

Front Microbiol. 2019 Feb 12;10:144. doi: 10.3389/fmicb.2019.00144. eCollection 2019.

Abstract

The Bacillus cereus group comprises multiple species capable of causing emetic or diarrheal foodborne illness. Despite being responsible for tens of thousands of illnesses each year in the U.S. alone, whole-genome sequencing (WGS) is not yet routinely employed to characterize group isolates from foodborne outbreaks. Here, we describe the first WGS-based characterization of isolates linked to an outbreak caused by members of the group. In conjunction with a 2016 outbreak traced to a supplier of refried beans served by a fast food restaurant chain in upstate New York, a total of 33 group isolates were obtained from human cases ( = 7) and food samples ( = 26). Emetic ( = 30) and diarrheal ( = 3) isolates were most closely related to (group III) and (group IV), respectively. WGS indicated that the 30 emetic isolates (24 and 6 from food and humans, respectively) were closely related and formed a well-supported clade distinct from publicly available emetic group III genomes with an identical sequence type (ST 26). The 30 emetic group III isolates from this outbreak differed from each other by a mean of 8.3 to 11.9 core single nucleotide polymorphisms (SNPs), while differing from publicly available emetic group III ST 26 group genomes by a mean of 301.7-528.0 core SNPs, depending on the SNP calling methodology used. Using a WST-1 cell proliferation assay, the strains isolated from this outbreak had only mild detrimental effects on HeLa cell metabolic activity compared to reference diarrheal strain ATCC 14579. We hypothesize that the outbreak was a single source outbreak caused by emetic group III belonging to the species, although food samples were not tested for presence of the emetic toxin cereulide. In addition to showcasing how WGS can be used to characterize group strains linked to a foodborne outbreak, we also discuss potential microbiological and epidemiological challenges presented by group outbreaks, and we offer recommendations for analyzing WGS data from the isolates associated with them.

摘要

蜡样芽孢杆菌群包含多种能够引起呕吐型或腹泻型食源性疾病的菌种。仅在美国,每年就有数万起此类疾病,但全基因组测序(WGS)尚未常规用于对食源性疾病暴发中的该菌群分离株进行特征描述。在此,我们描述了首例基于WGS对与该菌群成员引起的一次暴发相关的分离株进行的特征分析。结合2016年一起追溯到纽约州北部一家快餐连锁餐厅供应的炒豆供应商的暴发事件,共从人类病例(n = 7)和食品样本(n = 26)中获得了33株该菌群分离株。呕吐型(n = 30)和腹泻型(n = 3)分离株分别与蜡样芽孢杆菌(Ⅲ群)和苏云金芽孢杆菌(Ⅳ群)关系最为密切。WGS表明,30株呕吐型分离株(分别有24株和6株来自食品和人类)关系密切,形成了一个得到充分支持的进化枝,与公开可得的具有相同序列型(ST 26)的呕吐型Ⅲ群基因组不同。此次暴发的30株呕吐型Ⅲ群分离株彼此之间平均有8.3至11.9个核心单核苷酸多态性(SNP)差异,而与公开可得的呕吐型Ⅲ群ST 26蜡样芽孢杆菌群基因组平均有301.7 - 528.0个核心SNP差异,具体取决于所使用的SNP检测方法。使用WST - 1细胞增殖试验,与参考腹泻型菌株苏云金芽孢杆菌ATCC 14579相比,此次暴发中分离出的菌株对HeLa细胞代谢活性只有轻微的有害影响。我们推测此次暴发是由属于蜡样芽孢杆菌种的呕吐型Ⅲ群单一来源引起的,尽管食品样本未检测呕吐毒素cereulide的存在。除了展示WGS如何用于对与食源性疾病暴发相关的蜡样芽孢杆菌群菌株进行特征描述外,我们还讨论了蜡样芽孢杆菌群暴发带来的潜在微生物学和流行病学挑战,并提供了分析与之相关的分离株WGS数据的建议。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/c7b6/6379260/b11d05b1288b/fmicb-10-00144-g0002.jpg

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