溶藻弧菌群体基因组学研究

溶藻弧菌(Vibrio alginolyticus)是一种能够对人类以及鱼、虾、贝类等水产品致病的弧菌,给人类健康带来威胁,也给水产养殖业造成巨大的经济损失.目前该物种基于全基因组的遗传多样性和重要遗传元件研究报道较少.本研究对采集自全国4个省份的68株溶藻弧菌进行高通量测序,获得全基因组序列,并结合113株公开发表的...

Population genomics study of Vibrio alginolyticus

Vibrio alginolyticus is a Gram-negative bacillus that causes vibriosis to human and aquatic products,including fish,shrimp and shellfish.It poses a threat to public health and causes enormous economic losses to the aquaculture industry.However,research on genetic diversity and pathogenicity-related genetic elements based on whole genome is still lacking.In this study,sixty-eight strains of V.alginolyticus were collected from four provinces of China and the whole genome sequences were obtained.Combined with 113 publicly available genome sequences downloaded from NCBI,we inferred the population structure of V.alginolyticus by using fineSTRUCTURE software,and identified the virulence and antibiotic resistance factors using the VFDB,CARD and ResFinder database.The results indicated that V.alginolyticus included two main lineages,named Lineage 1 and Lineage 2.Both lineages distributed in America and Asia,but all the European genomes were classified into Lineage 1.A single cross-ocean transmission event was inferred from one of the 12 identified clonal groups in our dataset.V.alginolyticus genome contains a variety of virulence factors,such as tlh,OmpU,and IlpA,etc.The distribution of virulence factors revealed no lineage-specificity,but some of which revealed differences in their geographical distribution.A lower frequency of VP1611,vcrD,vopD,fleR/flrC and a higher frequency of IlpA were observed in genomes of Europe than other continents.In China,a lower frequency of fleR/flrC,and no IlpA were observed in genomes from Guangxi province.Among the identified antibiotic resistance genes,TxR and fos are significantly enriched in Lineage 2.In addition,TxR is more common in genomes from Asia,compared with the American and European genomes.But in China,the frequency of TxR in Sichuan genomes is much lower than in other provinces.We also found that large fragments of plasmids or ICEs that carried multiple drug resistance genes were present in five V.alginolyticus genomes(VA24,VA28,2014V-1011,ZJ-T and Vb1833).Based on population genomics analysis,our study delineated the population structure,distribution of virulence and antibiotic resistance related factors of V.alginolyticus,which lays a foundation for future study of genetic characters and pathogenesis mechanism of this pathogen and will improve the works on monitoring,prevention and control of this pathogen.