Effective Surveillance Using Multilocus Variable-Number Tandem-Repeat Analysis and Whole-Genome Sequencing for Enterohemorrhagic Escherichia coli O157
Effective Surveillance Using Multilocus Variable-Number Tandem-Repeat Analysis and Whole-Genome Sequencing for Enterohemorrhagic Escherichia coli O157
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DOI：
10.1128/aem.00728-19
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发表时间：
2019-09-01
影响因子：
4.4
通讯作者：
Yoshino, Shuji
中科院分区：
文献类型：
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作者：
Lee, Kenichi;Izumiya, Hidemasa;Yoshino, Shuji
由于肠出血性大肠杆菌（EHEC）血清群O 157可能引起大规模食源性疫情，因此有必要进行国家和国际监测。为了开发一种有效的分子监测方法，比较了传统的方法，多位点可变数目串联重复序列分析（MLVA），全基因组测序（WGS）分析。对7个MLVA型的369株EHEC O 157及其近缘种的WGS进行了综合电子分型、核心基因组单核苷酸多态性（cg-SNP）和核心基因组多位点序列分型（cgMLST）分析。cgSNP分析的分型分辨率最高。然而，错配修复蛋白基因mutS的序列的测定是必要的，因为该基因的自发缺失可能导致超变表型。MLVA具有足够的分型分辨率用于短期暴发调查，并具有快速和高通量的优势。cgMLST显示出比cgSNP更低的分型分辨率，但它耗时更少，并且不需要那么多的计算机能力。因此，cgMLST适用于使用大数据集（例如，使用公共数据库进行国际比较）。总之，筛查MLVA其次是cgMLST和cgSNP分析将提供最高的分型分辨率，提高准确性和成本效益的肠出血性大肠杆菌O 157 surveillance.IMPORTANCE肠出血性大肠杆菌（EHEC）血清群O 157的密集监测是很重要的，以检测爆发，并防止细菌的传播。测序技术的最新进展使得使用全基因组序列（WGS）进行分子监测成为现实。为了开发快速、高通量和经济有效的分型方法用于实时监测，对WGS和传统分型方法多位点可变数目串联重复分析（MLVA）的分型分辨率进行了评估。MLVA、核心基因组单核苷酸多态性（cgSNP）和核心基因组多位点序列分型（cgMLST）的国家级系统比较表明，WGS和MLVA的组合是提高EHEC O 157监测的一种现实方法。
Due to the potential of enterohemorrhagic Escherichia coli (EHEC) serogroup O157 to cause large food borne outbreaks, national and international surveillance is necessary. For developing an effective method of molecular surveillance, a conventional method, multilocus variable-number tandem-repeat analysis (MLVA), and whole-genome sequencing (WGS) analysis were compared. WGS of 369 isolates of EHEC O157 belonging to 7 major MLVA types and their relatives were subjected to comprehensive in silico typing, core genome single nucleotide polymorphism (cg-SNP), and core genome multilocus sequence typing (cgMLST) analyses. The typing resolution was the highest in cgSNP analysis. However, determination of the sequence of the mismatch repair protein gene mutS is necessary because spontaneous deletion of the gene could lead to a hypermutator phenotype. MLVA had sufficient typing resolution for a short-term outbreak investigation and had advantages in rapidity and high throughput. cgMLST showed less typing resolution than cgSNP, but it is less time-consuming and does not require as much computer power. Therefore, cgMLST is suitable for comparisons using large data sets (e.g., international comparison using public databases). In conclusion, screening using MLVA followed by cgMLST and cgSNP analyses would provide the highest typing resolution and improve the accuracy and cost-effectiveness of EHEC O157 surveillance.IMPORTANCE Intensive surveillance for enterohemorrhagic Escherichia coli (EHEC) serogroup O157 is important to detect outbreaks and to prevent the spread of the bacterium. Recent advances in sequencing technology made molecular surveillance using whole-genome sequence (WGS) realistic. To develop rapid, high-throughput, and cost-effective typing methods for real-time surveillance, typing resolution of WGS and a conventional typing method, multilocus variable-number tandem-repeat analysis (MLVA), was evaluated. Nation-level systematic comparison of MLVA, core genome single nucleotide polymorphism (cgSNP), and core genome multilocus sequence typing (cgMLST) indicated that a combination of WGS and MLVA is a realistic approach to improve EHEC O157 surveillance.