A geographically widespread outbreak investigation and development of a rapid screening method using whole genome sequences of enterohemorrhagic Escherichia coli O121

Ken Ichi Lee; Tomoko Morita-Ishihara; Sunao Iyoda; Yoshitoshi Ogura; Tetsuya Hayashi; Tsuyoshi Sekizuka; Makoto Kuroda; Makoto Ohnishi; Hiroko Takenuma; Junji Seto; Yu Suzuki; Kyoko Mashiko; Shigenori Matsui; Shinichiro Hirai; Eiji Yokoyama; Noriko Konishi; Hiromi Obata; Akemi Kai; Atsuko Ogawa; Yuko Matsumoto; Ayako Kikuchi; Emiko Kitagawa; Hitomi Kasahara; Maki Sekiguchi; Yuji Tsuchiya; Hiromi Nakamura; Kazuko Seto; Junko Tanabe; Mayumi Tsujimoto; Hisahiro Kawai; Hiroko Dannnoue; Ritsuko Ohata; Hiroshi Nakajima; Hiroko Yamada; Kanako Masuda; Fuyuki Okamoto; Shuji Yoshino; Kazuyoshi Hozumi; Working Group in Japan EHEC Working Group in Japan

doi:10.3389/fmicb.2017.00701

A geographically widespread outbreak investigation and development of a rapid screening method using whole genome sequences of enterohemorrhagic Escherichia coli O121

Ken Ichi Lee, Tomoko Morita-Ishihara, Sunao Iyoda, Yoshitoshi Ogura, Tetsuya Hayashi, Tsuyoshi Sekizuka, Makoto Kuroda, Makoto Ohnishi, Hiroko Takenuma, Junji Seto, Yu Suzuki, Kyoko Mashiko, Shigenori Matsui, Shinichiro Hirai, Eiji Yokoyama, Noriko Konishi, Hiromi Obata, Akemi Kai, Atsuko Ogawa, Yuko MatsumotoAyako Kikuchi, Emiko Kitagawa, Hitomi Kasahara, Maki Sekiguchi, Yuji Tsuchiya, Hiromi Nakamura, Kazuko Seto, Junko Tanabe, Mayumi Tsujimoto, Hisahiro Kawai, Hiroko Dannnoue, Ritsuko Ohata, Hiroshi Nakajima, Hiroko Yamada, Kanako Masuda, Fuyuki Okamoto, Shuji Yoshino, Kazuyoshi Hozumi, Working Group in Japan EHEC Working Group in Japan

Pathobiology

Research output: Contribution to journal › Article › peer-review

15 Citations (Scopus)

Abstract

From 2014 to 2015, we investigated a suspected nationwide outbreak of enterohemorrhagic Escherichia coli serogroup O121. However, similar pulsed field gel electrophoresis (PFGE) profiles and the lack of epidemiological links between the isolates made detection of the outbreak difficult. To elucidate a more precise genetic distance among the isolates, whole genome sequence (WGS) analyses were implemented in the investigation. The WGS-based single nucleotide polymorphism (SNP) analysis showed that 23 out of 44 isolates formed a distinct cluster (the number of intra-cluster SNPs was ≤8). Specific genomic regions in the clustered isolates were used to develop a specific PCR analysis. The PCR analysis detected all the clustered isolates and was suitable for rapid screening during the outbreak investigation. Our results showed that WGS analyses were useful for the detection of a geographically widespread outbreak, especially for isolates showing similar PFGE profiles and for the development of a rapid and cost-effective screening method.

Original language	English
Article number	701
Journal	Frontiers in Microbiology
Volume	8
Issue number	APR
DOIs	https://doi.org/10.3389/fmicb.2017.00701
Publication status	Published - Apr 20 2017

All Science Journal Classification (ASJC) codes

Microbiology
Microbiology (medical)

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10.3389/fmicb.2017.00701

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Lee, K. I., Morita-Ishihara, T., Iyoda, S., Ogura, Y., Hayashi, T., Sekizuka, T., Kuroda, M., Ohnishi, M., Takenuma, H., Seto, J., Suzuki, Y., Mashiko, K., Matsui, S., Hirai, S., Yokoyama, E., Konishi, N., Obata, H., Kai, A., Ogawa, A., ... EHEC Working Group in Japan, W. G. I. J. (2017). A geographically widespread outbreak investigation and development of a rapid screening method using whole genome sequences of enterohemorrhagic Escherichia coli O121. Frontiers in Microbiology, 8(APR), Article 701. https://doi.org/10.3389/fmicb.2017.00701

Lee, KI, Morita-Ishihara, T, Iyoda, S, Ogura, Y, Hayashi, T, Sekizuka, T, Kuroda, M, Ohnishi, M, Takenuma, H, Seto, J, Suzuki, Y, Mashiko, K, Matsui, S, Hirai, S, Yokoyama, E, Konishi, N, Obata, H, Kai, A, Ogawa, A, Matsumoto, Y, Kikuchi, A, Kitagawa, E, Kasahara, H, Sekiguchi, M, Tsuchiya, Y, Nakamura, H, Seto, K, Tanabe, J, Tsujimoto, M, Kawai, H, Dannnoue, H, Ohata, R, Nakajima, H, Yamada, H, Masuda, K, Okamoto, F, Yoshino, S, Hozumi, K & EHEC Working Group in Japan, WGIJ 2017, 'A geographically widespread outbreak investigation and development of a rapid screening method using whole genome sequences of enterohemorrhagic Escherichia coli O121', Frontiers in Microbiology, vol. 8, no. APR, 701. https://doi.org/10.3389/fmicb.2017.00701

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title = "A geographically widespread outbreak investigation and development of a rapid screening method using whole genome sequences of enterohemorrhagic Escherichia coli O121",

abstract = "From 2014 to 2015, we investigated a suspected nationwide outbreak of enterohemorrhagic Escherichia coli serogroup O121. However, similar pulsed field gel electrophoresis (PFGE) profiles and the lack of epidemiological links between the isolates made detection of the outbreak difficult. To elucidate a more precise genetic distance among the isolates, whole genome sequence (WGS) analyses were implemented in the investigation. The WGS-based single nucleotide polymorphism (SNP) analysis showed that 23 out of 44 isolates formed a distinct cluster (the number of intra-cluster SNPs was ≤8). Specific genomic regions in the clustered isolates were used to develop a specific PCR analysis. The PCR analysis detected all the clustered isolates and was suitable for rapid screening during the outbreak investigation. Our results showed that WGS analyses were useful for the detection of a geographically widespread outbreak, especially for isolates showing similar PFGE profiles and for the development of a rapid and cost-effective screening method.",

author = "Lee, {Ken Ichi} and Tomoko Morita-Ishihara and Sunao Iyoda and Yoshitoshi Ogura and Tetsuya Hayashi and Tsuyoshi Sekizuka and Makoto Kuroda and Makoto Ohnishi and Hiroko Takenuma and Junji Seto and Yu Suzuki and Kyoko Mashiko and Shigenori Matsui and Shinichiro Hirai and Eiji Yokoyama and Noriko Konishi and Hiromi Obata and Akemi Kai and Atsuko Ogawa and Yuko Matsumoto and Ayako Kikuchi and Emiko Kitagawa and Hitomi Kasahara and Maki Sekiguchi and Yuji Tsuchiya and Hiromi Nakamura and Kazuko Seto and Junko Tanabe and Mayumi Tsujimoto and Hisahiro Kawai and Hiroko Dannnoue and Ritsuko Ohata and Hiroshi Nakajima and Hiroko Yamada and Kanako Masuda and Fuyuki Okamoto and Shuji Yoshino and Kazuyoshi Hozumi and {EHEC Working Group in Japan}, {Working Group in Japan}",

note = "Publisher Copyright: {\textcopyright} 2017 Lee, Morita-Ishihara, Iyoda, Ogura, Hayashi, Sekizuka, Kuroda, Ohnishi and EHEC Working Group in Japan.",

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T1 - A geographically widespread outbreak investigation and development of a rapid screening method using whole genome sequences of enterohemorrhagic Escherichia coli O121

AU - Lee, Ken Ichi

AU - Morita-Ishihara, Tomoko

AU - Iyoda, Sunao

AU - Ogura, Yoshitoshi

AU - Hayashi, Tetsuya

AU - Sekizuka, Tsuyoshi

AU - Kuroda, Makoto

AU - Ohnishi, Makoto

AU - Takenuma, Hiroko

AU - Seto, Junji

AU - Suzuki, Yu

AU - Mashiko, Kyoko

AU - Matsui, Shigenori

AU - Hirai, Shinichiro

AU - Yokoyama, Eiji

AU - Konishi, Noriko

AU - Obata, Hiromi

AU - Kai, Akemi

AU - Ogawa, Atsuko

AU - Matsumoto, Yuko

AU - Kikuchi, Ayako

AU - Kitagawa, Emiko

AU - Kasahara, Hitomi

AU - Sekiguchi, Maki

AU - Tsuchiya, Yuji

AU - Nakamura, Hiromi

AU - Seto, Kazuko

AU - Tanabe, Junko

AU - Tsujimoto, Mayumi

AU - Kawai, Hisahiro

AU - Dannnoue, Hiroko

AU - Ohata, Ritsuko

AU - Nakajima, Hiroshi

AU - Yamada, Hiroko

AU - Masuda, Kanako

AU - Okamoto, Fuyuki

AU - Yoshino, Shuji

AU - Hozumi, Kazuyoshi

AU - EHEC Working Group in Japan, Working Group in Japan

PY - 2017/4/20

Y1 - 2017/4/20

N2 - From 2014 to 2015, we investigated a suspected nationwide outbreak of enterohemorrhagic Escherichia coli serogroup O121. However, similar pulsed field gel electrophoresis (PFGE) profiles and the lack of epidemiological links between the isolates made detection of the outbreak difficult. To elucidate a more precise genetic distance among the isolates, whole genome sequence (WGS) analyses were implemented in the investigation. The WGS-based single nucleotide polymorphism (SNP) analysis showed that 23 out of 44 isolates formed a distinct cluster (the number of intra-cluster SNPs was ≤8). Specific genomic regions in the clustered isolates were used to develop a specific PCR analysis. The PCR analysis detected all the clustered isolates and was suitable for rapid screening during the outbreak investigation. Our results showed that WGS analyses were useful for the detection of a geographically widespread outbreak, especially for isolates showing similar PFGE profiles and for the development of a rapid and cost-effective screening method.

AB - From 2014 to 2015, we investigated a suspected nationwide outbreak of enterohemorrhagic Escherichia coli serogroup O121. However, similar pulsed field gel electrophoresis (PFGE) profiles and the lack of epidemiological links between the isolates made detection of the outbreak difficult. To elucidate a more precise genetic distance among the isolates, whole genome sequence (WGS) analyses were implemented in the investigation. The WGS-based single nucleotide polymorphism (SNP) analysis showed that 23 out of 44 isolates formed a distinct cluster (the number of intra-cluster SNPs was ≤8). Specific genomic regions in the clustered isolates were used to develop a specific PCR analysis. The PCR analysis detected all the clustered isolates and was suitable for rapid screening during the outbreak investigation. Our results showed that WGS analyses were useful for the detection of a geographically widespread outbreak, especially for isolates showing similar PFGE profiles and for the development of a rapid and cost-effective screening method.

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VL - 8

JO - Frontiers in Microbiology

JF - Frontiers in Microbiology

IS - APR

M1 - 701

ER -

A geographically widespread outbreak investigation and development of a rapid screening method using whole genome sequences of enterohemorrhagic Escherichia coli O121

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