AUTHOR=Lee Imchang , Ha Sung-Min , Baek Min-gyung , Kim Dong Wook , Yi Hana , Chun Jongsik 

TITLE=VicPred: A Vibrio cholerae Genotype Prediction Tool

JOURNAL=Frontiers in Microbiology

VOLUME=12

YEAR=2021

URL=https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2021.691895

DOI=10.3389/fmicb.2021.691895

ISSN=1664-302X

ABSTRACT=<p>Genomic information can be used to predict major pathogenic traits of pathogens without the need for laboratory experimentation. However, no <italic>Vibrio cholerae</italic> genome-based trait identification tools currently exist. The aim of this study was to develop a web-based prediction tool to identify <italic>Vibrio</italic> pathogenic traits using publicly available 796 whole-genome sequences of <italic>V. cholerae</italic>. Using this application, 68 structural O-antigen gene clusters belonging to 49 serogroups of <italic>V. cholerae</italic> were classified, and the composition of the genes within the O-antigen cluster of each serogroup was identified. The arrangement and location of the CTX prophage and related elements of the seventh cholera pandemic strains were also revealed. With the versatile tool, named VicPred, we analyzed the assemblage of various SXTs (sulfamethoxazole/trimethoprim resistance element) and major genomic islands (GIs) of <italic>V. cholerae</italic>, and the increasing trend in drug-resistance revealing high resistance of the <italic>V. cholerae</italic> strains to certain antibiotics. The pathogenic traits of newly sequenced <italic>V. cholerae</italic> strains could be analyzed based on these characteristics. The accumulation of further genome data will expedite the establishment of a more precise genome-based pathogenic traits analysis tool.</p>