Recent mixing of Vibrio parahaemolyticus populations

Abstract

Humans have profoundly affected the ocean environment but little is known about anthropogenic effects on the distribution of microbes. Vibrio parahaemolyticus is found in warm coastal waters and causes gastroenteritis in humans and economically significant disease in shrimps. Based on data from 1103 genomes of environmental and clinical isolates, we show that V. parahaemolyticus is divided into four diverse populations, VppUS1, VppUS2, VppX and VppAsia. The first two are largely restricted to the US and Northern Europe, while the others are found worldwide, with VppAsia making up the great majority of isolates in the seas around Asia. Patterns of diversity within and between the populations are consistent with them having arisen by progressive divergence via genetic drift during geographical isolation. However, we find that there is substantial overlap in their current distribution. These observations can be reconciled without requiring genetic barriers to exchange between populations if long-range dispersal has increased dramatically in the recent past. We found that VppAsia isolates from the US have an average of 1.01% more shared ancestry with VppUS1 and VppUS2 isolates than VppAsia isolates from Asia itself. Based on time calibrated trees of divergence within epidemic lineages, we estimate that recombination affects about 0.017% of the genome per year, implying that the genetic mixture has taken place within the last few decades. These results suggest that human activity, such as shipping, aquatic products trade and increased human migration between continents, are responsible for the change of distribution pattern of this species.

Dynamics and Microevolution of Vibrio parahaemolyticus Populations in Shellfish Farms

“…Notably, some STs such as ST658 accounted for up to 4.59% of the total community, indicating that a few of the introduced V. parahaemolyticus populations had been established and fitted well in their new environment. This finding provides evidence supporting the hypothesis proposed by Yang et al that V. parahaemolyticus can multiply rapidly to constitute a substantial proportion of the bacteria in its new habitat ( 7 ). Thus, the transport of live aquatic animals deliberately delivered to distant farms in large quantities could have facilitated the transmission of bacteria among different regions or countries.…”

“…A previous study suggested that mixing of V. parahaemolyticus populations recently occurred ( 7 ). However, most investigated strains were collected from seafood or clinical samples and thus do not represent a defined epidemiological cohort.…”

“…Multiple transmission modes, including spreading by ocean currents, animal migration, and transportation of aquatic animals or trading of seafood products, might all play roles in the spread of this human pathogen ( 1 ). A previous study showed that V. parahaemolyticus could be divided into four diverse populations: VppUS1, VppUS2, VppX, and VppAsia ( 7 ). Moreover, the authors found that VppX and VppAsia are distributed worldwide, but the mixing of VppX and VppAsia populations occurred recently.…”

“…Previous studies suggested that both natural and human activities could contribute to the dissemination of V. parahaemolyticus ( 7 ). Ocean currents are one of the most widely recognized transmission routes for the spread of V. parahaemolyticus .…”

Genomic epidemiology of Vibrio cholerae reveals the regional and global spread of two epidemic non-toxigenic lineages

“…We used ClonalFrameML [38] to infer the recombination events in L3b and L9 lineages as previously described [39]. The input maximum likelihood trees were constructed using FastTree V2 [37] based on the whole genome alignments, non-core sites were ignored during the calculation.…”