Hypervirulent clade 2, ribotype 019/sequence type 67 Clostridioides difficile strain from Japan

Ryoichi Saito,Isaac Prah,Yoko Nukui,Alafate Ayibieke,Ryuji Koike,Yasuhiro Itsui,Kazunari Sonobe,Yukino Usui,Shuji Tohda,Shiori Ito,Jun Nakajima,Yoshibumi Aiso,Yoshiro Hadano

doi:10.1186/s13099-019-0336-3

Ryoichi Saito, Isaac Prah + Show 11 more

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https://doi.org/10.1186/s13099-019-0336-3

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Abstract

BackgroundClostridioides difficile ribotype (RT) 019/sequence type (ST) 67 strains belong to a hypervirulent lineage closely related to RT027/ST1; however, limited data are available for hypervirulent clade 2 lineages in Japan. Herein, we report the draft genome of a C. difficile strain B18-123 belonging to clade 2, RT019/ST67 for the first time in Japan.ResultsThe pathogenicity locus carried by B18-123 (19.6 kb) showed higher homology (97.29% nucleotide identity) with strain R20291 (RT027/ST1) than the reference strain 630 (RT012/ST54), and B18-123 harbored 8-nucleotide substitutions in tcdC. However, it did not contain an 18-base pair (bp) deletion or a single-bp deletion at position 117 in tcdC, which was identified in the previous strain R20291. A cytotoxicity assay revealed similar cytotoxicity levels between strains B18-123 and ATCC BAA-1870 (RT027/ST1). The B18-123 strain was found to be susceptible to metronidazole and vancomycin.ConclusionOur findings contribute to the further understanding of the characteristics of hypervirulent clade 2 including RT019/ST67 lineages.

Highlights

Clostridioides difficile infection (CDI) is a well-known cause of healthcare-associated infections, ranging from mild diarrhea to severe pseudomembranous colitis and even death
We reported the detection of a C. difficile strain B18-123 belonging to hypervirulent clade 2, RT019/ ST67, in Japan isolated from a patient with multiple recurrent episodes of severe diarrhea
In Japan, only two ST67 strains without ribotype data have been deposited in the GenBank in 2019, no report of CDI incidences with RT019/ST67 in Japan has been published so far in English literature

Summary

Introduction

Clostridioides difficile infection (CDI) is a well-known cause of healthcare-associated infections, ranging from mild diarrhea to severe pseudomembranous colitis and even death. Limited data, including genome sequences, are available for hypervirulent clade 2 because of its extremely low prevalence among CDI incidences in Japan [15]. We reported the detection of a C. difficile strain B18-123 belonging to hypervirulent clade 2, RT019/ ST67, in Japan isolated from a patient with multiple recurrent episodes of severe diarrhea. Clostridioides difficile ribotype (RT) 019/sequence type (ST) 67 strains belong to a hypervirulent lineage closely related to RT027/ST1; limited data are available for hypervirulent clade 2 lineages in Japan. We report the draft genome of a C. difficile strain B18-123 belonging to clade 2, RT019/ST67 for the first time in Japan

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