RT Journal Article SR Electronic T1 Origins of pandemic clones from environmental gene pools JF bioRxiv FD Cold Spring Harbor Laboratory SP 063115 DO 10.1101/063115 A1 B. Jesse Shapiro A1 Inès Levade A1 Gabriela Kovacikova A1 Ronald K. Taylor A1 Salvador Almagro-Moreno YR 2016 UL http://biorxiv.org/content/early/2016/07/10/063115.abstract AB Some microbes can transition from an environmental lifestyle to a pathogenic one1–3. This ecological switch typically occurs through the acquisition of horizontally acquired virulence genes4–7. 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 one of them reduced the ability of clinical strains to colonize a mammalian host, whereas two other alleles conferred efficient 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.