Vibrio cholerae Genome sequencing. Vibrio cholerae

Pathogen emergence remains one of the most pressing public health concerns of our times. Here, using the agent of cholera, the Vibrio cholerae pandemic cholera group (PCG) as a model system, we investigate the evolutionary dynamics that lead to the emergence of human pathogens from environmental populations. Genomic comparison of over 1,100 V. cholerae genomes including novel isolates from this study, reveal a generalized cluster-driven phylogeny and evolution of the species. Emergence of PCG is largely based on modular acquisition of mobile genetic elements including small gene clusters and allelic variations, with distinct phylogenomic clusters acting as differential reservoirs of virulence factors. Surprisingly, PCG encodes few unique genes, which are mostly encoded within the super-integron, however, many genes within the group exhibit an aberrant degree of positive selection. Our analyses provide a compelling scenario for the emergence of pandemic clones in V. cholerae stablishing a blueprint for other bacterial pathogens.