Epidemic clones, oceanic gene pools and eco-LD in the free living marine pathogen Vibrio parahaemolyticus

TL;DR

This study analyzes the global genetic diversity and structure of Vibrio parahaemolyticus, revealing oceanic gene pools, stable ecotypes, and key genetic interactions influencing its population dynamics.

Contribution

It uncovers the existence of distinct oceanic gene pools, proposes ecotype subdivision based on population structure, and identifies specific epistatic interactions and functional systems in the bacterium.

Findings

Identified two main oceanic gene pools in Vibrio parahaemolyticus.

Discovered a thirty-fold difference in effective population size estimates.

Found a single strong epistatic interaction between distant genome regions.

Abstract

We investigated global patterns of variation in 157 whole genome sequences of Vibrio parahaemolyticus, a free-living and seafood associated marine bacterium. Pandemic clones, responsible for recent outbreaks of gastroenteritis in humans have spread globally. However, there are oceanic gene pools, one located in the oceans surrounding Asia and another in the Mexican Gulf. Frequent recombination means that most isolates have acquired the genetic profile of their current location. We investigated the genetic structure in the Asian gene pool by calculating the effective population size in two different ways. Under standard neutral models, the two estimates should give similar answers but we found a thirty fold difference. We propose that this discrepancy is caused by the subdivision of the species into a hundred or more ecotypes which are maintained stably in the population. To investigate the genetic factors involved, we used 51 unrelated isolates to conduct a genome-wide scan for epistatically interacting loci. We found a single example of strong epistasis between distant genome regions. A majority of strains had a type VI secretion system associated with bacterial killing. The remaining strains had genes associated with biofilm formation and regulated by c-di-GMP signaling. All strains had one or other of the two systems and none of isolate had complete complements of both systems, although several strains had remnants. Further top-down analysis of patterns of linkage disequilibrium within frequently recombining species will allow a detailed understanding of how selection acts to structure the pattern of variation within natural bacterial populations.