【摘要】 目的 对2018—2023年福州市分离的霍乱弧菌进行全基因组测序，预测毒力基因、耐药基因和序列位点信息，分析不同菌株间遗传关系，为防治霍乱提供依据。方法 对60株霍乱弧菌进行全基因组序列测定，运用生物信息学软件对测序数据进行质控、基因组装和预测，采用PubMLST、ResFinder、VFDB等数据库预测不同菌株的多位点序列分型、耐药基因和毒力基因情况，结合NCBI数据库，经核心基因组单核苷酸多态性（core genes Single Nucleotide Polymorphism,cgSNP）系统发育分析和去重组分析，采取最大似然法构建系统发育树。结果 60株霍乱弧菌基于7个管家基因分型，获得16种已知序列型（sequence type, ST）和38种新分配的ST,O₁群临床分离株H339为ST75,O1群食品分离株H13、H363和H381均为ST175，非O₁/非O139群霍乱弧菌（non-O₁/non-O139 Vibrio cholerae,NOVC）分离株H263、H357均为ST1218,H293、H306均为ST1700,H311、H314、H316均为ST1699，其余分离株存在多样性。共预测29种耐药基因，包括喹诺酮类、叶酸通路拮抗剂类、氨基糖苷类和β-内酰胺等，大部分菌株携带喹诺酮类耐药基因。经过VFDB数据库预测，所有病原菌株均含有rtx、hlyA毒力因子，96.7%（58/60）菌株携带tlh基因，O₁群分离株均携带tcp、zot、ace基因，O₁群临床分离株携带ctxA基因。全基因组系统发育树进化分析将全部菌株分为20个分支，基因组高度分歧。结论 新发现38种STs。O₁群食品分离株之间存在遗传相关性，O₁群临床分离株与O₁群食品分离株之间、O₁群与NOVC菌株之间亲缘关系较远，分离菌株存在多样性。此项研究能够为食源性疾病溯源提供数据支持。更多还原

【Abstract】 ObjectivesTo sequence the whole genome of Vibrio cholerae strains isolated from Fuzhou between 2018 and2023, predict virulence genes, antimicrobial resistance genes, and sequence loci information, analyze the genetic relationships among different strains, and provide evidence for cholera prevention and control.MethodsWhole genome sequencing was performed on 60 strains of Vibrio cholerae, and bioinformatics software was used for quality control, gene assembly, and prediction of the sequencing data. PubMLST, ResFinder, and VFDB databases were used to predict the multilocus sequence typing, antimicrobial resistance genes, and virulence genes of different strains. Combined with the NCBI database, the phylogenetic tree was constructed by the maximum likelihood method through the core cgSNP phylogenetic analysis and derecombination analysis.ResultsBased on the typing of 7 housekeeping genes, 60 Vibrio cholerae strains can be categorized into 16 known STs and 38 newly assigned STs. The clinical isolate H339 of serogroup O₁ was identified as ST75. Serogroup O₁ food isolates H13, H363, and H381 were all ST175. H263 and H357, the NOVC isolates, were both ST1218. H293 and H306were ST1700. H311, H314, and H316 were all ST1699, with the remaining isolates displaying diversity. A total of 29antimicrobial resistance genes were predicted, including aminoglycosides, β-lactams, quinolones, and folate pathway antagonists, with the majority of the strains carrying quinolones antimicrobial resistance genes. According to the VFDB prediction, all isolates had the virulence factors rtx and hlyA, 96.7%（58/60） of the strains carried the tlh genes, all serogroup O₁ isolates carried tcp, zot, and ace genes, and all serogroup O₁ clinical isolates carried ctxA genes. Phylogenetic tree analysis of the whole genome divided all strains into 20 branches, indicating high genomic divergence.ConclusionsThirty-eight new STs were identified. Genetic correlations were found among serogroup O₁ food isolates, whereas serogroup O₁clinical isolates and serogroup O₁ food isolates, as well as between serogroup O₁ and NOVC strains, show distant phylogenetic relationships.There was diversity among the isolates. This study provides data support for the traceability of foodborne diseases.更多还原