全基因组测序分析北京地区人源结肠弯曲菌基因组特征和耐药性

Analysis of genomic characteristics and antimicrobial resistance of Campylobacter coli from humans in Beijing through whole genome sequencing

目的 了解北京地区人源结肠弯曲菌的耐药特征、毒力特征及多位点序列分型等遗传进化关系。方法 对2019-2021年北京市肠道门诊腹泻病例中分离到的36株结肠弯曲菌,采用琼脂稀释法进行抗生素敏感性检测;基于全基因组测序结果分析其耐药基因、毒力基因、多位点序列分型及全基因组单核苷酸多态性(whole genome single nucleotide polymorphisms, wgSNPs)遗传进化分析。结果 36株结肠弯曲菌对萘啶酸和四环素的耐药率为100.0%,对环丙沙星的耐药率为97.2%,对红霉素和阿奇霉素的耐药率为38.9%;36株菌均为多重耐药株,有10种耐药模式。基于全基因组测序结果,36株结肠弯曲菌分为21种ST型,优势克隆群为CC828;携带大环内脂类、喹诺酮类、氨基糖苷类、酰胺醇类、四环素类等多种类型耐药基因;携带6类38种毒力基因。wgSNPs遗传进化分析显示克隆群CC1150与优势克隆群CC828相距较远,处于独立的分枝,CC828克隆群内菌株聚集成3簇,呈现多样性分布。结论 北京市人源结肠弯曲菌分离株耐药严重,多重耐药谱广泛;耐药基因与耐药表型有一定的关联;克隆复合体以CC828为主,具有较高的遗传多样性。

This study was aimed at investigating the characteristics of drug resistance,virulence,and multi locus sequence typing(MLST)of Campylobacter coli strains isolated from humans in Beijing.Antibiotic susceptibility testing was performedwith the agar dilution method on 36 C.coli strains isolated from outpatients with diarrhea between 2019 and 2021 in Beijing.Whole genome sequencing was applied to analyze the drug resistance genes and virulence genes;MLST and whole genome single nucleotide polymorphisms(wgSNPs)were used to determine genetic evolutionary relationships.The 36 C.coli strains showed drug resistance rates of 100.0%to nalidixic acid and tetracycline,97.2%to ciprofloxacin,and 38.9%to erythromycin and azithromycin.All 36 strains were multidrug resistant,and showed ten drug resistance patterns.According to WGS,21 STs were identified among the 36 C.coli isolates,and the dominant clonal complex(CC)was CC828.Antibiotic resistance genes associated with macrolides,quinolones,aminoglycosides,amide alcohols and tetracycline were found.Thirty-eight genes in six classes associated with virulence were detected.The wgSNP phylogenetic analysis indicated that CC1150 was in an independent branch far from the dominant CC828.The strains of CC828 grouped into three clusters with high diversity.The antibiotic resistance of these C.coli isolates from patients with diarrheain Beijing was relatively severe,and a wide multidrug resistance pattern was observed.A correlation between resistance genotypes and phenotypes was found.CC828 was the main clone complex with high genetic diversity.