Effective Surveillance Using Multilocus Variable-Number Tandem-Repeat Analysis and Whole-Genome Sequencing for Enterohemorrhagic Escherichia coli O157

被引：13

作者：

Lee, Kenichi ^{[1
]}

Izumiya, Hidemasa ^{[1
]}

Iyoda, Sunao ^{[1
]}

Ohnishi, Makoto ^{[1
]}

Morimoto, Yo ^{[2
]}

Ogawa, Keiko ^{[2
]}

Konno, Takayuki ^{[3
]}

Kumagai, Yuko ^{[3
]}

Seto, Junji ^{[4
]}

Kikuchi, Rie ^{[5
]}

Unno, Yuri ^{[6
]}

Nakamoto, Arimi ^{[6
]}

Kawai, Yuko ^{[7
]}

Hirai, Shinichiro ^{[8
]}

Yokoyama, Eiji ^{[8
]}

Obata, Hiromi ^{[9
]}

Konishi, Noriko ^{[9
]}

Homma, Sachiko ^{[10
]}

Kubomura, Akiko ^{[10
]}

Sasaki, Kuniharu ^{[10
]}

Anzawa, Youko ^{[10
]}

Ogawa, Atsuko ^{[11
]}

Matsumoto, Yuko ^{[11
]}

Aoki, Junko ^{[12
]}

Kimata, Keiko ^{[13
]}

Isobe, Junko ^{[13
]}

Kimura, Eriko ^{[14
]}

Noda, Makiko ^{[15
,16
,17
]}

Kadokura, Yukiko ^{[15
,16
,17
]}

Kameyama, Yoshihiko ^{[15
,16
,17
]}

Ohishi, Takeshi ^{[18
]}

Nakajima, Satoko ^{[18
]}

Konaka, Kenji ^{[18
]}

Takeda, Naoki ^{[18
]}

Fujimoto, Naoki ^{[18
]}

Wakabayashi, Yuki ^{[19
,20
,21
]}

Nomoto, Ryohei ^{[22
,23
]}

Hama, Natsuki ^{[22
,23
]}

Kawai, Hisahiro ^{[24
]}

Naka, Atsushi ^{[24
]}

Nakajima, Hiroshi ^{[24
]}

Kariya, Hideaki ^{[24
]}

Hiratsuka, Takahiro ^{[25
]}

Aota, Tatsuaki ^{[26
]}

Sasaki, Mari ^{[27
,28
,29
]}

Yoshino, Shuji ^{[30
]}

机构：

[1] Natl Inst Infect Dis, Dept Bacteriol 1, Tokyo, Japan

[2] Hokkaido Inst Publ Hlth, Sapporo, Hokkaido, Japan

[3] Akita Prefectural Res Ctr Publ Hlth & Environm, Hlth & Hyg Div, Akita, Japan

[4] Yamagata Prefectural Inst Publ Hlth, Yamagata, Japan

[5] Fukushima Prefectural Inst Publ Hlth, Sukagawa, Fukushima, Japan

[6] Ibaraki Prefectural Inst Publ Hlth, Ami, Ibaraki, Japan

[7] Chiba City Inst Hlth & Environm, Gunma Prefectural Inst Publ Hlth & Environm Sci, Chiba, Japan

[8] Chiba Prefectural Inst Publ Hlth, Chiba, Japan

[9] Tokyo Metropolitan Inst Publ Hlth, Tokyo, Japan

[10] Kawasaki City Inst Publ Hlth, Kawasaki, Kanagawa, Japan

[11] Yokohama City Inst Publ Hlth, Yokohama, Kanagawa, Japan

[12] Niigata Prefectural Inst Publ Hlth & Environm Sci, Niigata, Japan

[13] Toyama Inst Hlth, Dept Bacteriol, Toyama, Japan

[14] Ishikawa Prefectural Inst Publ Hlth & Environm Sc, Fukui Prefectural Inst Publ Hlth & Environm Sci, Nonoichi, Ishikawa, Japan

[15] Gifu Prefectural Res Inst Hlth & Environm Sci, Gifu, Japan

[16] Shizuoka City Inst Environm Sci & Publ Hlth, Shizuoka, Japan

[17] Kyoto City Inst Hlth & Environm Sci, Kyoto, Japan

[18] Kyoto Prefectural Inst Publ Hlth & Environm, Kyoto, Japan

[19] Osaka Inst Publ Hlth, Osaka, Japan

[20] Sakai City Inst Publ Hlth, Sakai, Osaka, Japan

[21] Hyogo Prefectural Inst Publ Hlth Sci, Kobe, Hyogo, Japan

[22] Kobe Inst Hlth, Kobe, Hyogo, Japan

[23] Nara Prefectural Inst Hlth, Kashihara, Nara, Japan

[24] Okayama Prefectural Inst Environm Sci & Publ Hlth, Okayama, Japan

[25] Hiroshima Prefectural Technol Res Inst, Hlth & Environm Ctr, Hiroshima, Japan

[26] Hiroshima City Inst Publ Hlth, Hiroshima, Japan

[27] Kagawa Prefectural Res Inst Environm Sci & Publ H, Takamatsu, Kagawa, Japan

[28] Kitakyushu City Inst Hlth & Environm Sci, Kitakyushu, Fukuoka, Japan

[29] Oita Prefectural Inst Hlth & Environm, Oita, Japan

[30] Miyazaki Prefectural Inst Publ Hlth & Environm, Miyazaki, Japan

来源：

APPLIED AND ENVIRONMENTAL MICROBIOLOGY | 2019年 / 85卷 / 17期

关键词：

core genome SNP analysis; core genome multilocus sequence typing; enterohemorrhagic Escherichia coli; multilocus variable-number tandem-repeat analysis; whole-genome sequencing; NATIONAL SURVEILLANCE; OUTBREAK DETECTION; TYPING SCHEME; COPY NUMBER; PREVALENCE; MUTATION; CATTLE; ASSOCIATION; DISCOVERY; SYSTEM;

D O I：

10.1128/AEM.00728-19

中图分类号：

Q81 [生物工程学（生物技术）]; Q93 [微生物学];

学科分类号：

071005 ; 0836 ; 090102 ; 100705 ;

摘要：

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.

引用

页数：12

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