Genetic characterization of Vibrio cholerae strains genome in Fuzhou City from 2018 to 2023
- Author:
LIN Wenzhen
;
LIU Xiufeng
;
CHEN Fanbing
- Publication Type:Journal Article
- Keywords:
Vibrio cholerae;
whole genome sequencing;
MLST typing;
antimicrobial resistance genes;
virulence genes;
phylogenetic tree
- From:
China Tropical Medicine
2024;24(6):727-
- CountryChina
- Language:Chinese
-
Abstract:
Abstract: Objectives To sequence the whole genome of Vibrio cholerae strains isolated from Fuzhou between 2018 and 2023, predict virulence genes, antimicrobial resistance genes, and sequence loci information, analyze the genetic relationships among different strains, and provide evidence for cholera prevention and control. Methods Whole genome sequencing was performed on 60 strains of Vibrio cholerae, and bioinformatics software was used for quality control, gene assembly, and prediction of the sequencing data. PubMLST, ResFinder, and VFDB databases were used to predict the multilocus sequence typing, antimicrobial resistance genes, and virulence genes of different strains. Combined with the NCBI database, the phylogenetic tree was constructed by the maximum likelihood method through the core cgSNP phylogenetic analysis and de-recombination analysis. Results Based on the typing of 7 housekeeping genes, 60 Vibrio cholerae strains can be categorized into 16 known STs and 38 newly assigned STs. The clinical isolate H339 of serogroup O1 was identified as ST75. Serogroup O1 food isolates H13, H363, and H381 were all ST175. H263 and H357, the NOVC isolates, were both ST1218. H293 and H306 were ST1700. H311, H314, and H316 were all ST1699, with the remaining isolates displaying diversity. A total of 29 antimicrobial resistance genes were predicted, including aminoglycosides, β-lactams, quinolones, and folate pathway antagonists, with the majority of the strains carrying quinolones antimicrobial resistance genes. According to the VFDB prediction, all isolates had the virulence factors rtx and hlyA, 96.7% (58/60) of the strains carried the tlh genes, all serogroup O1 isolates carried tcp, zot, and ace genes, and all serogroup O1 clinical isolates carried ctxA genes. Phylogenetic tree analysis of the whole genome divided all strains into 20 branches, indicating high genomic divergence. Conclusions Thirty-eight new STs were identified. Genetic correlations were found among serogroup O1 food isolates, whereas serogroup O1 clinical isolates and serogroup O1 food isolates, as well as between serogroup O1 and NOVC strains, show distant phylogenetic relationships. There was diversity among the isolates. This study provides data support for the traceability of foodborne diseases.
- Full text:20250618102649761316.Genetic characterization of Vibrio cholerae strains genome in Fuzhou City from 2018 to 2023.pdf
