Population analysis of clinical and environmental Vibrio parahaemolyticus isolated from eastern provinces in China by removing the recombinant SNPs in the MLST loci.
Vibrio parahaemolyticus is a common seafood-borne pathogenic bacterium which causes gastroenteritis in humans. Continuous surveillance on the molecular characters of the clinical and environmental V. parahaemolyticus strains needs to be conducted for the epidemiological and genetic purposes. To generate a picture of the population distribution of V. parahaemolyticus in eastern China isolated from clinical cases of gastroenteritis and environmental samples, we investigated the genetic and evolutionary relationships of the strains using the commonly used multi-locus sequence typing (MLST, in which seven house-keeping genes are used in the protocol). A highly genetic diversity within the V. parahaemolyticus population was observed but ST3 was still dominant in the clinical strains, and 103 new sequence types (ST) were found in the clinical strains by searching in the global V. parahaemolyticus MLST database. With these genetically diverse strains, we estimated the recombination rates of the loci in MLST analysis. The locus recA was found to be subject to exceptionally high rate of recombination, and the recombinant single nucleotide polymorphisms (SNPs) were also identified within the seven loci. The phylogenetic tree of the strains was re-constructed using the maximum likelihood method by removing the recombination SNPs of the seven loci, and the minimum spanning tree was re-constructed with the six loci without recA. Some changes were observed in comparison with the previously used methods, suggesting that the homologous recombination has roles in shaping the clonal structure of V. parahaemolyticus. We propose the recombination-free SNPs strategy in the clonality analysis of V. parahaemolyticus, especially when using the maximum likelihood method.
State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou 310003, China.
Xin
X
Lu
State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou 310003, China.
Haijian
H
Zhou
State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou 310003, China.
Xiaoli
X
Du
State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou 310003, China.
Sha
S
Liu
State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China; School of Food and Chemical Engineering, Beijing Technology and Business University, Beijing 100048, China.
Jialiang
J
Xu
State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou 310003, China.
Zhigang
Z
Cui
State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou 310003, China. Electronic address: pangbo@icdc.cn.
Bo
B
Pang
State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou 310003, China. Electronic address: kanbiao@icdc.cn.
Biao
B
Kan
D002681:China; D005828:Genetics, Population; D006801:Humans; D058885:Multilocus Sequence Typing; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*; D011995:Recombination, Genetic; D014735:Vibrio Infections / Q000382:microbiology; D014736:Vibrio parahaemolyticus / Q000145:classification / Q000235:genetics*; D014764:Viral Proteins / Q000235:genetics*
D014764:Viral Proteins
MLST; Population structure; Recombination; SNP; V. parahaemolyticus; recA