Analysis of enterotoxigenic Bacillus cereus strains from dried foods using whole genome sequencing, multi-locus sequence analysis and toxin gene prevalence and distribution using endpoint PCR analysis
Analysis of enterotoxigenic Bacillus cereus strains from dried foods using whole genome sequencing, multi-locus sequence analysis and toxin gene prevalence and distribution using endpoint PCR analysis
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DOI：
10.1016/j.ijfoodmicro.2018.06.016
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发表时间：
2018-11-02
影响因子：
5.4
通讯作者：
Gopinath, Gopal R.
中科院分区：
文献类型：
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作者：
Carter, Laurenda;Chase, Hannah R.;Gopinath, Gopal R.
蜡样芽孢杆菌菌株是从干燥食品中分离出来的，这些食品包括从几家零售店购买的来自东南亚、墨西哥和印度的国际品牌香料、婴儿配方奶粉（PIF）样品、加药鱼饲料和膳食补充剂。采用多重终点PCR检测方法，确定了64株来自香料和PIF的菌株的遗传多样性，该方法旨在鉴定溶血素BL、非溶血性肠毒素、细胞毒素K和肠毒素FM毒素基因。十三个不同的B。在菌株中鉴定蜡样芽胞杆菌的致病基因模式或谱。随机选择B。对蜡状芽孢杆菌菌株进行测序，并使用生物信息学工具与来自国家生物技术信息中心的参考基因组进行比较。一个全面的多位点序列分析（MLSA）的设计使用等位基因从25个已知的MIST基因专门定制用于全基因组组装。来自一些FDA监管商品如干食品和加药鱼饲料的菌株的代表性基因组的队列用于证明25-MLSA方法用于快速聚类和鉴定基因组的实用性。该分析将来自含药鱼饲料、干食品和膳食补充剂的菌株聚类为遗传学相关的组。25-MLSA还指出B的多样性更大。蜡样芽胞杆菌菌株从食品和饲料比以前认识。我们的毒素基因PCR的综合方法，据我们所知，全基因组测序（WGS）为基础的序列分析，可能是第一个证明肠道致病潜力和基因组多样性并行。
Bacillus cereus strains were isolated from dried foods, which included international brands of spices from South East Asia, Mexico and India purchased from several retail stores, samples of powdered infant formula (PIF), medicated fish feed and dietary supplements. The genetic diversity of 64 strains from spices and PIF was determined using a multiplex endpoint PCR assay designed to identify hemolysin BL, nonhemolytic enterotoxin, cytotoxin K, and enterotoxin FM toxin genes. Thirteen different B. cereus toxigenic gene patterns or profiles were identified among the strains. Randomly selected B. cereus strains were sequenced and compared with reference Genomic Groups from National Center Biotechnology Information using bioinformatics tools. A comprehensive multi-loci sequence analysis (MLSA) was designed using alleles from 25 known MIST genes specifically tailored for use with whole genome assemblies. A cohort of representative genomes of strains from a few FDA regulated commodities like dry foods and medicated fish feed was used to demonstrate the utility of the 25-MLSA approach for rapid clustering and identification of Genome Groups. The analysis clustered the strains from medicated fish feed, dry foods, and dietary supplements into phylogenetically-related groups. 25-MLSA also pointed to a greater diversity of B. cereus strains from foods and feed than previously recognized. Our integrated approach of toxin gene PCR, and to our knowledge, whole genome sequencing (WGS) based sequence analysis, may be the first of its kind that demonstrates enterotoxigenic potential and genomic diversity in parallel.