基于全基因组测序的甲型副伤寒沙门菌暴发疫情分离株分子特征研究

Whole genome sequencing molecular characterization of Salmonella paratyphi A isolates from an outbreak

目的分析一起甲型副伤寒暴发疫情菌株的分子分型特征,为病原菌的确定和暴发疫情的防控提供科学依据。方法利用生化试验、血清学试验对病原菌进行鉴定,并将分离到的病原菌进行微量肉汤稀释法药物敏感性试验、PFGE分子分型分析、全基因组测序,利用全基因组数据与沙门菌MLST标准数据库比对获得序列型别(ST)、cgMLST序列号以及rMLST序列号并进行聚类分析,通过细菌基因组分析平台fIDBA分析病原菌的耐药、毒力相关基因。结果11株沙门菌血清型均为甲型副伤寒沙门菌,具有100%相似性的PFGE带型,MLST、cgMLST、rMLST的型别均分别为ST129型、cgST-2191型、rST3678型,表明此次暴发疫情菌株从分子特征角度可诊断为同一传染源导致。对萘啶酸100%耐药,对链霉素100%中介。发现本次疫情菌株基因组均携带29种耐药基因。通过毒力因子数据库比对,均携带21类250种已知毒力基因,其中以Ⅲ型分泌系统、粘附、鞭毛等最为常见。结论本次暴发疫情是由共同来源的、具有相同分子分型特征的甲型副伤寒沙门菌引起。在病原溯源研究中,应用全基因组数据可更精细分析菌株遗传进化特征、亲缘关系及毒力基因、耐药基因携带情况,可以作为替代PFGE、MLST的技术用于更精准的传染病分子流行病学调查分析研究。

This study analyzed the molecular typing characteristics of an outbreak strain of paratyphoid A,to provide a scientific basis for pathogen identification,outbreak prevention and control.Pathogenic bacteria were identified with biochemical and serological tests,and the isolates were subjected to microbroth dilution drug sensitivity testing,PFGE molecular typing analysis and whole genome sequencing.The sequence type(ST),cgMLST sequence number and rMLST sequence number were obtained by comparison of the whole genome data with the Salmonella MLST standard database,and cluster analysis was performed.The drug resistance genes,virulence genes and related genes in pathogenic bacteria were analyzed with the bacterial genome analysis platform fIDBA.The serotypes of 11 Salmonella strains were S.paratyphoid A,with highly similar PFGE bands.The types of MLST,cgMLST and rMLST were ST129,cgST-2191 and rST3678 respectively,thus suggesting that the outbreak strains arose from the same infectious source,on the basis of molecular characteristics.The strains were 100%resistant to naphthyridic acid and 100%sensitive to streptomycin.The genomes of the strains in this epidemic carried 29 drug resistance genes.Comparison with the virulence factor database indicated that all strains comprised 21 categories and 250 known virulence genes,among which the type III secretion system,adhesion and flagella were the most common.The outbreak was caused by S.paratyphoid A with molecular typing characteristics suggesting a common source.In pathogen traceability analysis,the application of whole genome data enables finer-grained analysis of genetic evolution characteristics,genetic relationships,virulence genes and drug resistance genes of strains,and can replace PFGE and MLST for more accurate molecular epidemiological investigation and analysis of infectious diseases.