VCGIDB: A Database and Web Resource for the Genomic Islands from Vibrio Cholerae.

Youngjae Hur,Inwoo Baek,Jongsik Chun,Sung-Min Ha,Mauricio Chalita

doi:10.3390/pathogens8040261

Abstract

Vibrio cholerae is the causative agent of cholera, which is a severe, life-threatening diarrheal disease. The current seventh pandemic has not been eradicated and the outbreak is still ongoing around the world. The evolution of the pandemic-causing strain has been greatly influenced by lateral gene transfer, and the mechanisms of acquisition of pathogenicity in V. cholerae are mainly involved with genomic islands (GIs). Thus, detecting GIs and their comprehensive information is necessary to understand the continuing resurgence and newly emerging pathogenic V. cholerae strains. In this study, 798 V. cholerae strains were tested using the GI-Scanner algorithm, which was developed to detect candidate GIs and identify them in a comparative genomics approach. The algorithm predicted 435 highly possible genomic islands, and we built a database, called Vibrio cholerae Genomic Island Database (VCGIDB). This database shows advanced results that were acquired from a large genome set using phylogeny-based predictions. Moreover, VCGIDB is a highly expendable database that does not require intensive computation, which enables us to update it with a greater number of genomes using a novel genomic island prediction method. The VCGIDB website allows the user to browse the data and presents the results in a visual manner.

Highlights

IntroductionThe causative agent of cholera, remains a global public health threat
Vibrio cholerae, the causative agent of cholera, remains a global public health threat
From 798 V. cholerae strains, GI-Scanner algorithm predicted 435 highly possible genomic islands, including 67 genomic islands already found in a previous study [6]

Summary

Introduction

The causative agent of cholera, remains a global public health threat. The disease causes severe and acute diarrhea, which is potentially followed by shock, acidosis, and death [1]. There have been seven pandemics of cholera since 1817, with the seventh pandemic beginning in 1961 in Makassar, Sulawesi, Indonesia. V. cholerae strains are classified into serogroups based on the somatic. O antigen, and there are over 200 serogroups [2] of V. cholerae. The seventh pandemic of cholera was caused by O1 strains of the El Tor biotype, whereas the sixth pandemic was caused by O1 strains of the classical biotype. The evolution of the seventh-pandemic strains has been greatly influenced by lateral gene transfer (LGT) [4]

Methods

Results

Discussion

Conclusion