Comparative genome analysis of extended-spectrum-β-lactamase-producing Escherichia coli sequence type 131 strains from Nepal and Japan

Tohru Miyoshi-Akiyama, Jatan Bahadur Sherchan, Yohei Doi, Maki Nagamatsu, Jeevan B. Sherchand, Sarmila Tandukar, Norio Ohmagari, Teruo Kirikae, Hiroshi Ohara, Kayoko Hayakawa

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Abstract

The global spread of extended-spectrum-β-lactamase (ESBL)-producing Escherichia coli (ESBL-E. coli) has largely been driven by the pandemic sequence type 131 (ST131). This study aimed to determine the molecular epidemiology of their spread in two Asian countries with contrasting prevalence. We conducted wholegenome sequencing (WGS) of ESBL-E. coli ST131 strains collected prospectively from Nepal and Japan, two countries in Asia with a high and low prevalence of ESBL-E. coli, respectively. We also systematically compared these genomes with those reported from other regions using publicly available WGS data for E. coli ST131 strains. Further, we conducted phylogenetic analysis of these isolates and all genome sequence data for ST131 strains to determine sequence diversity. One hundred five unique ESBL-E. coli isolates from Nepal (February 2013 to July 2013) and 76 isolates from Japan (October 2013 to September 2014) were included. Of these isolates, 54 (51%) isolates from Nepal and 11 (14%) isolates from Japan were identified as ST131 by WGS. Phylogenetic analysis based on WGS suggested that the majority of ESBL-E. coli ST131 isolates from Nepal clustered together, whereas those from Japan were more diverse. Half of the ESBL-E. coli ST131 isolates from Japan belonged to virotype C, whereas half of the isolates from Nepal belonged to a virotype other than virotype A, B, C, D, or E (A/B/C/D/E). The dominant sublineage of E. coli ST131 was H30Rx, which was most prominent in ESBL-E. coli ST131 isolates from Nepal. Our results revealed distinct phylogenetic characteristics of ESBL-E. coli ST131 spread in the two geographical areas of Asia, indicating the involvement of multiple factors in its local spread in each region.

Original languageEnglish
Article numbere00289-16
JournalmSphere
Volume1
Issue number5
DOIs
Publication statusPublished - 01-09-2016

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Nepal
Spectrum Analysis
Japan
Genome
Escherichia coli
Molecular Epidemiology
Pandemics

All Science Journal Classification (ASJC) codes

  • Microbiology
  • Molecular Biology

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Miyoshi-Akiyama, T., Sherchan, J. B., Doi, Y., Nagamatsu, M., Sherchand, J. B., Tandukar, S., ... Hayakawa, K. (2016). Comparative genome analysis of extended-spectrum-β-lactamase-producing Escherichia coli sequence type 131 strains from Nepal and Japan. mSphere, 1(5), [e00289-16]. https://doi.org/10.1128/mSphere.00289-16
Miyoshi-Akiyama, Tohru ; Sherchan, Jatan Bahadur ; Doi, Yohei ; Nagamatsu, Maki ; Sherchand, Jeevan B. ; Tandukar, Sarmila ; Ohmagari, Norio ; Kirikae, Teruo ; Ohara, Hiroshi ; Hayakawa, Kayoko. / Comparative genome analysis of extended-spectrum-β-lactamase-producing Escherichia coli sequence type 131 strains from Nepal and Japan. In: mSphere. 2016 ; Vol. 1, No. 5.
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abstract = "The global spread of extended-spectrum-β-lactamase (ESBL)-producing Escherichia coli (ESBL-E. coli) has largely been driven by the pandemic sequence type 131 (ST131). This study aimed to determine the molecular epidemiology of their spread in two Asian countries with contrasting prevalence. We conducted wholegenome sequencing (WGS) of ESBL-E. coli ST131 strains collected prospectively from Nepal and Japan, two countries in Asia with a high and low prevalence of ESBL-E. coli, respectively. We also systematically compared these genomes with those reported from other regions using publicly available WGS data for E. coli ST131 strains. Further, we conducted phylogenetic analysis of these isolates and all genome sequence data for ST131 strains to determine sequence diversity. One hundred five unique ESBL-E. coli isolates from Nepal (February 2013 to July 2013) and 76 isolates from Japan (October 2013 to September 2014) were included. Of these isolates, 54 (51{\%}) isolates from Nepal and 11 (14{\%}) isolates from Japan were identified as ST131 by WGS. Phylogenetic analysis based on WGS suggested that the majority of ESBL-E. coli ST131 isolates from Nepal clustered together, whereas those from Japan were more diverse. Half of the ESBL-E. coli ST131 isolates from Japan belonged to virotype C, whereas half of the isolates from Nepal belonged to a virotype other than virotype A, B, C, D, or E (A/B/C/D/E). The dominant sublineage of E. coli ST131 was H30Rx, which was most prominent in ESBL-E. coli ST131 isolates from Nepal. Our results revealed distinct phylogenetic characteristics of ESBL-E. coli ST131 spread in the two geographical areas of Asia, indicating the involvement of multiple factors in its local spread in each region.",
author = "Tohru Miyoshi-Akiyama and Sherchan, {Jatan Bahadur} and Yohei Doi and Maki Nagamatsu and Sherchand, {Jeevan B.} and Sarmila Tandukar and Norio Ohmagari and Teruo Kirikae and Hiroshi Ohara and Kayoko Hayakawa",
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Miyoshi-Akiyama, T, Sherchan, JB, Doi, Y, Nagamatsu, M, Sherchand, JB, Tandukar, S, Ohmagari, N, Kirikae, T, Ohara, H & Hayakawa, K 2016, 'Comparative genome analysis of extended-spectrum-β-lactamase-producing Escherichia coli sequence type 131 strains from Nepal and Japan', mSphere, vol. 1, no. 5, e00289-16. https://doi.org/10.1128/mSphere.00289-16

Comparative genome analysis of extended-spectrum-β-lactamase-producing Escherichia coli sequence type 131 strains from Nepal and Japan. / Miyoshi-Akiyama, Tohru; Sherchan, Jatan Bahadur; Doi, Yohei; Nagamatsu, Maki; Sherchand, Jeevan B.; Tandukar, Sarmila; Ohmagari, Norio; Kirikae, Teruo; Ohara, Hiroshi; Hayakawa, Kayoko.

In: mSphere, Vol. 1, No. 5, e00289-16, 01.09.2016.

Research output: Contribution to journalArticle

TY - JOUR

T1 - Comparative genome analysis of extended-spectrum-β-lactamase-producing Escherichia coli sequence type 131 strains from Nepal and Japan

AU - Miyoshi-Akiyama, Tohru

AU - Sherchan, Jatan Bahadur

AU - Doi, Yohei

AU - Nagamatsu, Maki

AU - Sherchand, Jeevan B.

AU - Tandukar, Sarmila

AU - Ohmagari, Norio

AU - Kirikae, Teruo

AU - Ohara, Hiroshi

AU - Hayakawa, Kayoko

PY - 2016/9/1

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N2 - The global spread of extended-spectrum-β-lactamase (ESBL)-producing Escherichia coli (ESBL-E. coli) has largely been driven by the pandemic sequence type 131 (ST131). This study aimed to determine the molecular epidemiology of their spread in two Asian countries with contrasting prevalence. We conducted wholegenome sequencing (WGS) of ESBL-E. coli ST131 strains collected prospectively from Nepal and Japan, two countries in Asia with a high and low prevalence of ESBL-E. coli, respectively. We also systematically compared these genomes with those reported from other regions using publicly available WGS data for E. coli ST131 strains. Further, we conducted phylogenetic analysis of these isolates and all genome sequence data for ST131 strains to determine sequence diversity. One hundred five unique ESBL-E. coli isolates from Nepal (February 2013 to July 2013) and 76 isolates from Japan (October 2013 to September 2014) were included. Of these isolates, 54 (51%) isolates from Nepal and 11 (14%) isolates from Japan were identified as ST131 by WGS. Phylogenetic analysis based on WGS suggested that the majority of ESBL-E. coli ST131 isolates from Nepal clustered together, whereas those from Japan were more diverse. Half of the ESBL-E. coli ST131 isolates from Japan belonged to virotype C, whereas half of the isolates from Nepal belonged to a virotype other than virotype A, B, C, D, or E (A/B/C/D/E). The dominant sublineage of E. coli ST131 was H30Rx, which was most prominent in ESBL-E. coli ST131 isolates from Nepal. Our results revealed distinct phylogenetic characteristics of ESBL-E. coli ST131 spread in the two geographical areas of Asia, indicating the involvement of multiple factors in its local spread in each region.

AB - The global spread of extended-spectrum-β-lactamase (ESBL)-producing Escherichia coli (ESBL-E. coli) has largely been driven by the pandemic sequence type 131 (ST131). This study aimed to determine the molecular epidemiology of their spread in two Asian countries with contrasting prevalence. We conducted wholegenome sequencing (WGS) of ESBL-E. coli ST131 strains collected prospectively from Nepal and Japan, two countries in Asia with a high and low prevalence of ESBL-E. coli, respectively. We also systematically compared these genomes with those reported from other regions using publicly available WGS data for E. coli ST131 strains. Further, we conducted phylogenetic analysis of these isolates and all genome sequence data for ST131 strains to determine sequence diversity. One hundred five unique ESBL-E. coli isolates from Nepal (February 2013 to July 2013) and 76 isolates from Japan (October 2013 to September 2014) were included. Of these isolates, 54 (51%) isolates from Nepal and 11 (14%) isolates from Japan were identified as ST131 by WGS. Phylogenetic analysis based on WGS suggested that the majority of ESBL-E. coli ST131 isolates from Nepal clustered together, whereas those from Japan were more diverse. Half of the ESBL-E. coli ST131 isolates from Japan belonged to virotype C, whereas half of the isolates from Nepal belonged to a virotype other than virotype A, B, C, D, or E (A/B/C/D/E). The dominant sublineage of E. coli ST131 was H30Rx, which was most prominent in ESBL-E. coli ST131 isolates from Nepal. Our results revealed distinct phylogenetic characteristics of ESBL-E. coli ST131 spread in the two geographical areas of Asia, indicating the involvement of multiple factors in its local spread in each region.

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