Population Structure And Virulence Factors Of Vibrio Vulnificus Based On Whole Genome Sequence

Vibrio vulnificus is a Gram-negative halophilic bacterium with obvious seasonal and regional growth characteristics,which is suitable for living in estuarial,coastal and marine environments with surface temperature higher than 13? from May to October every year.This bacterium can cause human infection from consumption of seafood as well as wound contact with marine waters.Infection is very rapid,with an average incubation period of only 16 hours for wound infection and 26 hours for septicaemia.The pathogen affects male patients(85%),elderly patients(> 40 years old),and people with basic diseases such as liver disease,diabetes,and immune diseases in particularly.V.vulnificus is the pathogen with the highest mortality of food-borne diseases in Vibrio genus.Nevertheless,there is insufficient knowledge of virulence-associated factors across the whole genome wide for this species at present.The study on population genomics of V.vulnificus can advance our understanding on its evolution and transmission,which provides a new reference for the source tracking and prevention of this pathogen.In this study,we use V.vulnificus as a model to solve two major challenges in the evolutionary study of frequently recombining bacteria: genetic diversity and pathogenicity.We analyzed the whole genome sequences of 260 V.vulnificus strains.The strains were isolated from 1977 to 2018 and collected from 10 countries in Asia,Europe,North America and South America,among which 182 strains were from environment sources and 78 strains were from clinical sources.Therefore,we perform the study with three sections:1.Population structure and geographical distribution of V.vulnificusIn this study,we analyzed 260 V.vulnificus genomes,including 139 newly sequenced by high-throughput sequencing technology in this study and 121 published genomes. 229462 SNPs were identified,including 103117 in the intergenic region,124999 synonymous SNPs,40165 non-synonymous SNPs,and 1255 non-sense SNPs.Further phylogenetic analysis divided V.vulnificus into five branches.The distribution of the pedigree showed obvious geographical aggregation.L1 mainly gathered Chinese strains with a high proportion of clinical strains,while L2 mainly gathered American strains with a high proportion of environmental strains.2.Correlation analysis between known virulence factors and isolation sources of V.vulnificusWe found 226 virulence factors in the core database of VFDB.In addition,we found 56 other virulence factors through literature search.Only two known virulence factors(pld A,vgr G)were significantly correlated with the isolation sources of V.vulnificus by chi-square test.In conclusion,most of the known virulence factors cannot explain the differences between clinical and environmental isolates of V.vulnificus.3.Identification of virulence-associated factors by BGWASWe used software pyseer to manifest the associations between sources of isolates and SNPs,genes,and Kmers,respectively.We found that 11 genes to be crucial correlated with clinical isolates of V.vulnificus,among which 9 were first identified in this study.Conclusion: By using methods of population genomics and statistical genetics,We deeply analyzed the population structure and virulence-associated factors of V.vulnificus across the whole genome.Our findings offered new targets on vaccine designing and drug development,so that we can have some insight on pathogenic mechanism of this pathogen.