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首页> 外文期刊>BMC Genomics >Evaluation of whole-genome sequencing for outbreak detection of Verotoxigenic Escherichia coli O157:H7 from the Canadian perspective
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Evaluation of whole-genome sequencing for outbreak detection of Verotoxigenic Escherichia coli O157:H7 from the Canadian perspective

机译：从加拿大的角度评估全基因组测序对暴发性大肠杆菌O157：H7的暴发检测

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Rapid and accurate identification of Verotoxigenic Escherichia coli (VTEC) O157:H7 is dependent on well-established, standardized and highly discriminatory typing methods. Currently, conventional subtyping tests for foodborne bacterial pathogen surveillance are rapidly being replaced with whole-genome sequencing (WGS) in public health laboratories. The capacity of WGS to revolutionize global foodborne disease surveillance has positioned this tool to become the new gold standard; however, to ensure evidence standards for public health decision making can still be achieved, the performance of WGS must be thoroughly validated against current gold standard methods prior to implementation. Here we aim to verify the performance of WGS in comparison to pulsed-field gel electrophoresis (PFGE) and multiple-locus variable-number tandem repeat analysis (MLVA) for eight retrospective outbreaks of VTEC O157:H7 from the Canadian perspective. Since real-time implementation and routine use of WGS in public health laboratories is highly reliant on standardized data analysis tools, we also provide a comparative analysis of two popular methodologies for WGS analyses; an in-house developed single nucleotide variant phylogenomics (SNVPhyl) pipeline and the BioNumerics whole genome multilocus sequence typing (wgMLST) tool. To provide a useful and consistent starting point for examining laboratory-based surveillance data for VTEC O157:H7 in Canada, we also aim to describe the number of genetic differences observed among outbreak-associated isolates. WGS provided enhanced resolution over traditional subtyping methods, and accurately distinguished outbreak-related isolates from non-outbreak related isolates with high epidemiological concordance. WGS also illuminated potential linkages between sporadic cases of illness and contaminated food, and isolates spanning multiple years. The topologies generated by SNVPhyl and wgMLST were highly congruent with strong statistical support. Few genetic differences were observed among outbreak-related isolates (≤5 SNVs/ ?10 wgMLST alleles) unless the outbreak was suspected to be multi-strain. This study validates the superiority of WGS and indicates the BioNumerics wgMLST schema is suitable for surveillance and cluster detection of VTEC O157:H7. These findings will provide a useful and consistent starting point for examining WGS data for prospective laboratory-based surveillance of VTEC O157:H7, but however, the data will continue to be interpreted according to context and in combination with epidemiological and food safety evidence to inform public-health decision making in Canada.
机译：快速，准确地鉴定维毒素性大肠杆菌（VTEC）O157：H7取决于成熟的，标准化的和高度歧视性的分型方法。当前，在公共卫生实验室中，用于食源性细菌病原体监测的常规子类型测试已被全基因组测序（WGS）迅速取代。 WGS革新全球食源性疾病监测的能力使该工具成为了新的金标准。但是，为了确保仍可以实现公共卫生决策的证据标准，在实施之前必须根据当前的金标准方法对WGS的性能进行全面验证。从加拿大的角度来看，我们旨在验证与8次回顾性爆发的VTEC O157：H7相比，脉冲场凝胶电泳（PFGE）和多位点可变数目串联重复重复分析（MLVA）的WGS性能。由于在公共卫生实验室中WGS的实时实施和常规使用高度依赖于标准化的数据分析工具，因此，我们还对WGS分析的两种流行方法进行了比较分析。内部开发的单核苷酸变异系统基因组学（SNVPhyl）管道和BioNumerics全基因组多基因座序列分型（wgMLST）工具。为了为检查加拿大的VTEC O157：H7的实验室监测数据提供有用且一致的起点，我们还旨在描述在暴发相关菌株中观察到的遗传差异数量。 WGS提供了比传统分型方法更高的分辨率，并在流行病学一致性高的情况下，准确区分了与暴发相关的分离株与非暴发相关的分离株。 WGS还阐明了零星的疾病病例和受污染的食物之间的潜在联系，以及跨越多年的隔离株。 SNVPhyl和wgMLST生成的拓扑与强大的统计支持高度一致。除非与爆发有关的分离株（≤5SNV / <？10 wgMLST等位基因），否则几乎没有遗传差异。这项研究证实了WGS的优越性，并表明BioNumerics wgMLST模式适用于VTEC O157：H7的监视和群集检测。这些发现将为检查WGS数据提供有用的和一致的起点，以便对基于VTEC O157：H7的实验室进行前瞻性监测，但是，将继续根据具体情况并结合流行病学和食品安全证据对数据进行解释加拿大的公共卫生决策。

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