Comparative analysis of core genome MLST and SNP typing within a European Salmonella serovar Enteritidis outbreak.
Comparative analysis of core genome MLST and SNP typing within a European Salmonella serovar Enteritidis outbreak.
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DOI：
10.1016/j.ijfoodmicro.2018.02.023
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发表时间：
2018-06-02
影响因子：
5.4
通讯作者：
Maiden MCJ
中科院分区：
文献类型：
--
作者：
Pearce ME;Alikhan NF;Dallman TJ;Zhou Z;Grant K;Maiden MCJ
食源性细菌性疾病的多国爆发在其检测，跟踪和通知方面提出了挑战。随着食品越来越多地跨境分发，此类疫情变得越来越普遍。这增加了对高分辨率、可访问和可复制的分离株分型方案的需求。在这里，我们评估了一个核心基因组多位点分型（cgMLST）计划的高分辨率可重复分型肠道沙门氏菌（S。enterica）分离株，通过将其应用于欧洲大爆发的S.肠道血清型使用基于单核苷酸多态性（SNP）的方法对这次爆发进行了广泛的表征。cgMLST分析与原始的基于SNP的分析、流行病学数据和全基因组MLST（wgMLST）分析一致。结合cgMLST和流行病学数据证实，分离株之间的遗传多样性早于爆发，并可能存在于感染源。因此，隔离和遗传多样性的国家之间没有联系，但cgMLST集群是一致的隔离日期。此外，与公开可用的肠杆菌分离株数据的比较表明，所提出的cgMLST方案具有高度可扩展性，能够在沙门氏菌属内对暴发进行情境化。因此，cgMLST方案被证明是一种标准化和可扩展的分型方法，可以在实验室和司法管辖区之间分析和比较沙门氏菌疫情。cgMLST被提议作为沙门氏菌的通用分型方案。cgMLST与SNP分析一致，更容易在实验室间实施。基因组数据与疫情流行病学一致。
Multi-country outbreaks of foodborne bacterial disease present challenges in their detection, tracking, and notification. As food is increasingly distributed across borders, such outbreaks are becoming more common. This increases the need for high-resolution, accessible, and replicable isolate typing schemes. Here we evaluate a core genome multilocus typing (cgMLST) scheme for the high-resolution reproducible typing of Salmonella enterica (S. enterica) isolates, by its application to a large European outbreak of S. enterica serovar Enteritidis. This outbreak had been extensively characterised using single nucleotide polymorphism (SNP)-based approaches. The cgMLST analysis was congruent with the original SNP-based analysis, the epidemiological data, and whole genome MLST (wgMLST) analysis. Combination of the cgMLST and epidemiological data confirmed that the genetic diversity among the isolates predated the outbreak, and was likely present at the infection source. There was consequently no link between country of isolation and genetic diversity, but the cgMLST clusters were congruent with date of isolation. Furthermore, comparison with publicly available Enteritidis isolate data demonstrated that the cgMLST scheme presented is highly scalable, enabling outbreaks to be contextualised within the Salmonella genus. The cgMLST scheme is therefore shown to be a standardised and scalable typing method, which allows Salmonella outbreaks to be analysed and compared across laboratories and jurisdictions. cgMLST is proposed as a universal typing scheme for Salmonella. cgMLST is congruent with SNP analyses and easier to implement across laboratories. Genomic data are consistent with the epidemiology of the outbreak.
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影响因子：
3.3
作者：
Hoffmann M;Zhao S;Pettengill J;Luo Y;Monday SR;Abbott J;Ayers SL;Cinar HN;Muruvanda T;Li C;Allard MW;Whichard J;Meng J;Brown EW;McDermott PF
通讯作者：
McDermott PF
影响因子：
2.8
作者：
Hendriksen, Rene S.;Vieira, Antonio R.;Aarestrup, Frank M.
通讯作者：
Aarestrup, Frank M.
影响因子：
1.7
作者：
Bankevich, Anton;Nurk, Sergey;Pevzner, Pavel A.
通讯作者：
Pevzner, Pavel A.
影响因子：
11.8
作者：
Galanis, E;Wong, DMALF;WHO Global Salm Surv
通讯作者：
WHO Global Salm Surv
DOI：
10.2307/2412448
发表时间：
1970-01-01
期刊：
SYSTEMATIC ZOOLOGY
影响因子：
--
作者：
FITCH, WM
通讯作者：
FITCH, WM