Comprehensive genomic analysis of Vibrio cholerae from three outbreaks in Uganda, 2014 - 2016

Abstract Objective: This study aimed at providing a comprehensive genomic analysis of whole-genome sequence data obtained from V. cholerae isolates from different outbreaks in Uganda using bioinformatics approaches. Results :The ten sequenced strains of V. cholerae were found to carry virulence-associated genes MakA, ctxA, ctxB, carA, carB, trpB, clpB, ace, toxR, zot, rtxA, ompW, ompR, gmhA, fur, hlyA, rstR, Type IV secretion system genes, T6SS genes vasA-L, vgrG-2, vgrG-3, vipA/mglA, and vipB/mglB; alsD; alsR; the flagella-mediated cytotoxin gene, makA; Type IV pilus genes tcpA-F, tcpH-J, tcpN, tcpP-T, and icmF/vasK; adherence genes acfA-D, IlpA, and quorum sensing system genes luxS and cqsA. Pathogenicity islands identified were VSP-1, VSP-2, VPI-1, and VPI-2. Antimicrobial resistance genes identified in the strains included strA and B, APH(3'')-I, APH(3'')-Ib, APH(6)-Id, APH(6)-Ic, murA, pare, dfrA1, floR, catB, and catB9. The strains also contained genes of the VC1786 integrative and conjugative element. SNP-based phylogenetic analysis revealed 218 shared SNPs in the strains, of these, 98 were missense. Gene enrichment analysis of the 98 SNPs revealed enrichment in genes that mediate transmembrane-signaling activity, peptidyl-prolyl cis-trans isomerase activity, and phosphorelay response regulator activity.