TY - JOUR T1 - Origins of pandemic clones from environmental gene pools JF - bioRxiv DO - 10.1101/063115 SP - 063115 AU - B. Jesse Shapiro AU - Inès Levade AU - Gabriela Kovacikova AU - Ronald K. Taylor AU - Salvador Almagro-Moreno Y1 - 2016/01/01 UR - http://biorxiv.org/content/early/2016/09/12/063115.abstract N2 - Some microbes can transition from an environmental lifestyle to a pathogenic one1–4. This ecological switch typically occurs through the acquisition of horizontally acquired virulence genes5–8. However, the genomic features that must be present in a population prior to the acquisition of virulence genes and emergence of pathogenic clones remain unknown. We hypothesized that virulence adaptive polymorphisms (VAPs) circulate in environmental populations and are required for this transition. We developed a comparative genomic framework for identifying VAPs, using Vibrio cholerae as a model. We then characterized several environmental VAP alleles to show that, while some of them reduced the ability of clinical strains to colonize a mammalian host, other alleles conferred efficient host colonization. These results show that VAPs are present in environmental bacterial populations prior to the emergence of virulent clones. We propose a scenario in which VAPs circulate in the environment, they become selected and enriched under certain ecological conditions, and finally a genomic background containing several VAPs acquires virulence factors that allows for its emergence as a pathogenic clone.PGPandemic genome;EGEnvironmental genome;SNPSingle nucleotide polymorphism;VAPVirulence adaptive polymorphism;NSNonsynonymous;SSynonymous. ER -