Multi-step genomic dissection of a suspected intra-hospital helicobacter cinaedi outbreak

Yasuhiro Gotoh, Takako Taniguchi, Dai Yoshimura, Keisuke Katsura, Yuji Saeki, Yasutoshi Hirabara, Mayumi Fukuda, Ichiro Takajo, Junko Tomida, Yoshiaki Kawamura, Yoshitoshi Ogura, Takehiko Itoh, Naoaki Misawa, Akihiko Okayama, Tetsuya Hayashi

Research output: Contribution to journalArticle

2 Citations (Scopus)

Abstract

Helicobacter cinaedi is an emerging pathogen causing bacteraemia and cellulitis. Nosocomial transmission of this microbe has been described, but detailed molecular-epidemiological analyses have not been performed. Here, we describe the results of a multi-step genome-wide phylogenetic analysis of a suspected intra-hospital outbreak of H. cinaedi that occurred in a hospital in Japan. The outbreak was recognized by the infectious control team (ICT) of the hospital as a sudden increase in H. cinaedi bacteraemia. ICT defined this outbreak case based on 16S rRNA sequence data and epidemiological information, but were unable to determine the source and route of the infections. We therefore re-investigated this case using whole-genome sequencing (WGS). We first performed a species-wide analysis using publicly available genome sequences to understand the level of genomic diversity of this under-studied species. The clusters identified were then separately analysed using the genome sequence of a representative strain in each cluster as a reference. These analyses provided a high-level phylogenetic resolution of each cluster, identified a confident set of outbreak isolates, and discriminated them from other closely related but distinct clones, which were locally circulating and invaded the hospital during the same period. By considering the epidemiological data, possible strain transmission chains were inferred, which highlighted the role of asymptomatic carriers or environmental contamination. The emergence of a subclone with increased resistance to fluoroquinolones in the outbreak was also recognized. Our results demonstrate the impact of the use of a closely related genome as a reference to maximize the power of WGS.

Original languageEnglish
Article number000236
JournalMicrobial Genomics
Volume5
Issue number1
DOIs
Publication statusPublished - Jan 1 2019

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Helicobacter
Disease Outbreaks
Dissection
Genome
Bacteremia
Cellulitis
Fluoroquinolones
Japan
Clone Cells
Infection

All Science Journal Classification (ASJC) codes

  • Epidemiology
  • Microbiology
  • Molecular Biology
  • Genetics

Cite this

Multi-step genomic dissection of a suspected intra-hospital helicobacter cinaedi outbreak. / Gotoh, Yasuhiro; Taniguchi, Takako; Yoshimura, Dai; Katsura, Keisuke; Saeki, Yuji; Hirabara, Yasutoshi; Fukuda, Mayumi; Takajo, Ichiro; Tomida, Junko; Kawamura, Yoshiaki; Ogura, Yoshitoshi; Itoh, Takehiko; Misawa, Naoaki; Okayama, Akihiko; Hayashi, Tetsuya.

In: Microbial Genomics, Vol. 5, No. 1, 000236, 01.01.2019.

Research output: Contribution to journalArticle

Gotoh, Y, Taniguchi, T, Yoshimura, D, Katsura, K, Saeki, Y, Hirabara, Y, Fukuda, M, Takajo, I, Tomida, J, Kawamura, Y, Ogura, Y, Itoh, T, Misawa, N, Okayama, A & Hayashi, T 2019, 'Multi-step genomic dissection of a suspected intra-hospital helicobacter cinaedi outbreak', Microbial Genomics, vol. 5, no. 1, 000236. https://doi.org/10.1099/mgen.0.000236
Gotoh, Yasuhiro ; Taniguchi, Takako ; Yoshimura, Dai ; Katsura, Keisuke ; Saeki, Yuji ; Hirabara, Yasutoshi ; Fukuda, Mayumi ; Takajo, Ichiro ; Tomida, Junko ; Kawamura, Yoshiaki ; Ogura, Yoshitoshi ; Itoh, Takehiko ; Misawa, Naoaki ; Okayama, Akihiko ; Hayashi, Tetsuya. / Multi-step genomic dissection of a suspected intra-hospital helicobacter cinaedi outbreak. In: Microbial Genomics. 2019 ; Vol. 5, No. 1.
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