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

Tropical Medicine and Health

Research

Tetsu Yamashiro¹  Ken-Ichiro Kuninobu²  Futoshi Hasebe³  Yu Takizawa⁴  Taichiro Takemura⁴ 

[1] Department of Bacteriology, Graduate School of Medicine, University of the Ryukyus, 207 Uehara Nishihara, 903-0215, Okinawa, Japan;Graduate School of Biomedical Sciences, Nagasaki University, 1-12-4 Sakamoto Nagasaki city, 852-8523, Nagasaki, Japan;Graduate School of Biomedical Sciences, Nagasaki University, 1-12-4 Sakamoto Nagasaki city, 852-8523, Nagasaki, Japan;Vietnam Research Station, Institute of Tropical Medicine, Nagasaki University, 1-12-4 Sakamoto Nagasaki city, 852-8523, Nagasaki, Japan;Vietnam Research Station, Institute of Tropical Medicine, Nagasaki University, 1-12-4 Sakamoto Nagasaki city, 852-8523, Nagasaki, Japan;

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

DOI  :  10.1186/s41182-023-00500-4

 received in 2022-11-14, accepted in 2023-01-17,  发布年份 2023

来源: Springer

【 摘 要 】

BackgroundCholera 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.MethodsPacBio 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.ResultsThe 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 “CTXcla” and a stretch of “truncated CTXcla-CTXcla” 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.ConclusionsMan9 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.

【 授权许可】

CC BY   
© The Author(s) 2023

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