Abstract
Genomic information can be used to predict major pathogenic traits of pathogens without the need for laboratory experimentation. However, no Vibrio cholerae genome-based trait identification tools currently exist. The aim of this study was to develop a web-based prediction tool to identify Vibrio pathogenic traits using publicly available 796 whole-genome sequences of V. cholerae. Using this application, 68 structural O-antigen gene clusters belonging to 49 serogroups of V. cholerae 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 V. cholerae, and the increasing trend in drug-resistance revealing high resistance of the V. cholerae strains to certain antibiotics. The pathogenic traits of newly sequenced V. cholerae 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.
Highlights
The seventh pandemic of Vibrio cholerae is distinct from previous pandemics owing to the emergence of new serotypes and biotypes
A single O-antigen gene cluster (OAGC) should be allocated to O1 and O139 serogroups, 19 and two variations in OAGC were identified among the genomes of O1 and O139 serogroups, respectively
The results of the O serogrouping and prediction of CTX prophagerelated elements are summarized in Supplementary Table 4 and Supplementary Figure 1
Summary
The seventh pandemic of Vibrio cholerae is distinct from previous pandemics owing to the emergence of new serotypes and biotypes El Tor and V. cholerae O139), which spread rapidly over a wider area and cause new disease patterns with relatively moderate symptoms lasting longer These strains, the causative agents of the seventh pandemic, had different traits than the former strain that caused the last pandemic. Researches on new mutant strains have shown that the integration of cholera toxinrelated phages is dynamic and variable in combination (Ramamurthy et al, 1993; Bik et al, 1996; Dalsgaard et al, 2001; Lee et al, 2009; Kim et al, 2014b, 2015) These pioneering studies have broadened our knowledge and understanding of cholera, the number of O serogroups to be analyzed increases, and more investigations are needed to determine the exact type of cholera
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