Whole-genome analysis of a Vibrio cholerae O1 biotype classical strain isolated in 1946 in Sasebo city, Nagasaki prefecture, from a returnee from the northeast part of China

Ken-Ichiro Kuninobu; Taichiro Takemura; Yu Takizawa; Futoshi Hasebe; Tetsu Yamashiro

doi:10.1186/s41182-023-00500-4

Whole-genome analysis of a Vibrio cholerae O1 biotype classical strain isolated in 1946 in Sasebo city, Nagasaki prefecture, from a returnee from the northeast part of China

Trop Med Health. 2023 Feb 2;51(1):5. doi: 10.1186/s41182-023-00500-4.

Authors

Ken-Ichiro Kuninobu¹, Taichiro Takemura², Yu Takizawa³, Futoshi Hasebe^{1

3}, Tetsu Yamashiro⁴

Affiliations

¹ Graduate School of Biomedical Sciences, Nagasaki University, 1-12-4 Sakamoto Nagasaki city, Nagasaki, 852-8523, Japan.
² Vietnam Research Station, Institute of Tropical Medicine, Nagasaki University, 1-12-4 Sakamoto Nagasaki city, Nagasaki, 852-8523, Japan. t.takemura@iaea.org.
³ Vietnam Research Station, Institute of Tropical Medicine, Nagasaki University, 1-12-4 Sakamoto Nagasaki city, Nagasaki, 852-8523, Japan.
⁴ Department of Bacteriology, Graduate School of Medicine, University of the Ryukyus, 207 Uehara Nishihara, Okinawa, 903-0215, Japan. tyamashi@med.u-ryukyu.ac.jp.

Abstract

Background: Cholera is a water-borne disease caused by toxigenic Vibrio cholerae serogroups O1 and O139. Not a few studies on the whole-genome analyses of V. cholerae O1 biotype El Tor have been published; however, the number of analyses for biotype classical is limited. The whole-genome analysis was made on a V. cholerae biotype classical strain, Man9, isolated in 1946 in Sasebo city, Nagasaki prefecture, from a returnee from the northeast part of China.

Methods: PacBio RSII was used to determine the whole-genome of Man9. De novo assemblies were made with CLC Genomics Workbench 8.5.1 and Canu. 2.0 and annotated by Prokka version 1.12. Upon determining the configuration of the CTX prophage region, combined procedures of PCR, RFLP with Southern blotting, and Sanger sequencing method were used. The phylogenetic tree was constructed by RaxML and visualized by Phandango. The identification of Cas genes and spacer sequences was made by CRISPR-finder and NCBI Blast search. These data were compared with those of V. cholerae serogroup O1 biotype classical O395.

Results: The Man9 carried the 2.9 Mb (Chr1) and 1.1 Mb (Chr2) chromosomes with 2683 and 1198 CDSs, respectively. The genome similarity between Man9 and O395 was 97.0% when the total genomes were compared. Man9 carried a 380-kb inversion on the Chr1, and 95-kb and 35-kb fragments were not present on the Chr1 and on the Chr2, respectively. Man9 monophyletically clustered with 23 other biotype classical strains on the core gene phylogenetic tree analyses. Man9 carries "CTX^cla" and a stretch of "truncated CTX^cla-CTX^cla" on the Chr1 and the Chr2, respectively, which is the opposite arrangement of O395. Man9 carries CRISPR-Cas system subtype I-E with 33 spacers, 64% of which were identical to those of O395.

Conclusions: Man9 differs from O395 by 3% on the total genome comparison; however, genomic analysis of a strain having circulated in the interpandemic period between the 6th and the 7th cholera pandemic is valuable and contributes to understanding the evolution of pathogenic V. cholerae.

Keywords: Biotype classical; CTX prophage region; De novo assembly; Interpandemic between the 6th and the 7th cholera pandemic; Nagasaki prefecture; Phylogenetic tree; Sasebo city; Vibrio cholerae O1; Whole-genome analysis.

Grants and funding

JP16H02775/MEXT