title: Epidemic Clones, Oceanic Gene Pools, and Eco-LD in the Free Living Marine Pathogen Vibrio parahaemolyticus.
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 27-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 cyclic dimeric 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.
authors.affiliation: State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China BGI-Shenzhen, Shenzhen, China dongshengzhou1977@gmail.com danielfalush@gmail.com ruifuyang@gmail.com.
authors.forename: Yujun
authors.initials: Y
authors.lastname: Cui
authors.affiliation: State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China BGI-Shenzhen, Shenzhen, China dongshengzhou1977@gmail.com danielfalush@gmail.com ruifuyang@gmail.com.
authors.forename: Xianwei
authors.initials: X
authors.lastname: Yang
authors.affiliation: Department of Infectious Disease Epidemiology, Imperial College, London, United Kingdom.
authors.forename: Xavier
authors.initials: X
authors.lastname: Didelot
authors.affiliation: State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China.
authors.forename: Chenyi
authors.initials: C
authors.lastname: Guo
authors.affiliation: BGI-Shenzhen, Shenzhen, China.
authors.forename: Dongfang
authors.initials: D
authors.lastname: Li
authors.affiliation: State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China.
authors.forename: Yanfeng
authors.initials: Y
authors.lastname: Yan
authors.affiliation: State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China.
authors.forename: Yiquan
authors.initials: Y
authors.lastname: Zhang
authors.affiliation: BGI-Shenzhen, Shenzhen, China.
authors.forename: Yanting
authors.initials: Y
authors.lastname: Yuan
authors.affiliation: BGI-Shenzhen, Shenzhen, China.
authors.forename: Huanming
authors.initials: H
authors.lastname: Yang
authors.affiliation: BGI-Shenzhen, Shenzhen, China.
authors.forename: Jian
authors.initials: J
authors.lastname: Wang
authors.affiliation: BGI-Shenzhen, Shenzhen, China.
authors.forename: Jun
authors.initials: J
authors.lastname: Wang
authors.affiliation: State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China.
authors.forename: Yajun
authors.initials: Y
authors.lastname: Song
authors.affiliation: State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China dongshengzhou1977@gmail.com danielfalush@gmail.com ruifuyang@gmail.com.
authors.forename: Dongsheng
authors.initials: D
authors.lastname: Zhou
authors.affiliation: Medical Microbiology and Infectious Diseases, College of Medicine, Institute of Life Science, Swansea University, Swansea, Wales, United Kingdom dongshengzhou1977@gmail.com danielfalush@gmail.com ruifuyang@gmail.com.
authors.forename: Daniel
authors.initials: D
authors.lastname: Falush
authors.affiliation: State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China BGI-Shenzhen, Shenzhen, China dongshengzhou1977@gmail.com danielfalush@gmail.com ruifuyang@gmail.com.
authors.forename: Ruifu
authors.initials: R
authors.lastname: Yang
mesh_terms: D001208:Asia; D018441:Biofilms; D002876:Chromosomes, Bacterial / Q000235:genetics; D004843:Epistasis, Genetic; D005788:Gene Pool; D056426:Genetic Loci; D005828:Genetics, Population; D016680:Genome, Bacterial; D008800:Mexico; D009792:Oceans and Seas; D010802:Phylogeny; D058974:Phylogeography; D020641:Polymorphism, Single Nucleotide; D011995:Recombination, Genetic; D012623:Seawater / Q000382:microbiology; D017422:Sequence Analysis, DNA; D014736:Vibrio parahaemolyticus / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification*
keywords: coalescent theory; molecular epidemiology; population genetics; population structure; whole-genome sequencing