A new core-genome multi-locus sequence typing (cgMLST) scheme for V. cholerae is now publicly available on pubmlst.org/vcholerae. New genomes can now be submitted and analyzed on PubMLST within minutes. Tools such as GrapeTree, Interactive Tree of Life, and PHYLOViZ are all integrated within the website to allow for quick follow-up analyses. This cgMLST scheme, containing 2,443 core genes, has been used to analyze over 1,000 V. cholerae genomes from both private collections and publicly available databases. This dataset includes representative isolates from known outbreaks and endemic countries. Along with epidemiological data, it is possible to use this cgMLST scheme to monitor V. cholerae diversity at both the local and global levels. A 1:1 mapping with a previously established V. cholerae MLST scheme from our lab has been carried out to demonstrate backwards compatibility with prior MLST studies.
The full manuscript entitled "A Vibrio cholerae core genome multilocus sequence typing scheme to facilitate the epidemiological study of cholera," published in the Journal of Bacteriology, details the application of this cgMLST scheme to study cholera outbreaks. This work was done in collaboration with Dr. Cheryl Tarr from the Centers of Disease Control and Prevention and Dr. Munirul Alam from the International Centre for Diarrhoeal Disease Research, Bangladesh.
cgMLST minimum spanning tree of all Yemen isolates and representative 7th pandemic El Tor strains (from Liang et al., 2020)