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Laboratory Techniques Used to Maintain and Differentiate Biotypes of Vibrio cholerae Clinical and Environmental Isolates
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VicPred: A Vibrio cholerae Genotype Prediction Tool.

Imchang Lee1,2, Sung-Min Ha1, Min-Gyung Baek3,4

  • 1School of Biological Sciences, Seoul National University, Seoul, South Korea.

Frontiers in Microbiology
|September 27, 2021
PubMed
Summary

A new web tool, VicPred, analyzes Vibrio cholerae genomes to predict pathogenic traits and antibiotic resistance without lab work. This tool aids in understanding cholera"s spread and developing targeted interventions.

Keywords:
7th pandemicsCTXφO serogroupSXTVPIVSPVibrio choleracholera

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Area of Science:

  • Microbiology
  • Genomics
  • Bioinformatics

Background:

  • Genomic data offers a pathway to predict pathogen traits, reducing reliance on laboratory experiments.
  • Currently, no genome-based tools exist for identifying Vibrio cholerae pathogenic traits.

Purpose of the Study:

  • To develop a web-based prediction tool for identifying Vibrio pathogenic traits.
  • To utilize 796 whole-genome sequences of V. cholerae for trait identification.

Main Methods:

  • Development of a web-based application named VicPred.
  • Analysis of 796 V. cholerae whole-genome sequences.
  • Classification of O-antigen gene clusters and identification of gene composition.
  • Mapping of CTX prophage and related elements in pandemic strains.
  • Analysis of SXTs (sulfamethoxazole/trimethoprim resistance elements) and genomic islands (GIs).

Main Results:

  • Successfully classified 68 O-antigen gene clusters from 49 V. cholerae serogroups.
  • Identified gene composition within O-antigen clusters for each serogroup.
  • Revealed the arrangement and location of CTX prophage in seventh pandemic strains.
  • Analyzed SXTs and GIs, highlighting increasing antibiotic resistance trends in V. cholerae strains.
  • Demonstrated high resistance of V. cholerae strains to specific antibiotics.

Conclusions:

  • VicPred enables analysis of pathogenic traits in newly sequenced V. cholerae strains.
  • The tool aids in understanding the genomic basis of V. cholerae pathogenicity and drug resistance.
  • Further genome data integration will enhance the precision of genome-based pathogenic trait analysis.