一株分离自鸡肉样品的多重耐药大肠埃希菌的全基因组测序及耐药性研究

以分离自宁波市市售鸡肉中的一株大肠埃希菌ECCNB12-2为研究对象,使用微量肉汤稀释法进行最小抑菌浓度(MIC)测定,结果显示,该菌株对氨苄西林、庆大霉素、大观霉素、四环素、氟苯尼考、磺胺异恶唑、复方新诺明、头孢噻夫、恩诺沙星、氧氟沙星等10种抗生素耐药。采用第三代高通量测序技术对该菌株进行全基因组测序,随后对基因组完成图进行获得性耐药基因、毒力因子、质粒水平转移元件预测。菌株ECCNB12-2染色体基因组大小为5 539 489 bp,GC含量为50.37%,同时携带有4个质粒,大小分别为147 451 bp(pTB-nb1)、139 752 bp(pTB-nb2)、82 252 bp(pTB-nb3)、253 793 bp(pTB-nb4)。获得性耐药基因预测结果显示,染色体基因组、质粒pTB-nb1及质粒pTB-nb4上共携带有40个获得性耐药基因,同时菌株基因组检测出12个毒力因子。质粒水平转移元件预测结果显示,pTB-nb4质粒包含完整的水平转移系统,理论上具有高度的自主接合转移潜力。以上研究表明,分离自市售鸡肉样品的ECCNB12-2菌株是一株高风险的多重耐药菌株,反映了市售鸡肉中细菌耐药状况的严重性,相关研究结果为食源性细菌耐药安全风险评估提供了参考。

Whole-genome sequencing and antibiotic resistance study of a multi-drug resistant Escherichia coli isolated from chicken

An Escherichia coli called ECCNB12-2 isolated from chicken in Ningbo city was studied. The MICs to antibiotic were determined using mircrobroth dilution assay. The results indicated that ECCNB12-2 showed resistance to 10 kinds of antibiotics including ampicillin, gentamicin, spectinomycin, tetracycline, florfenicol, sulfisoxazole, trimethoprim/sulfamethoxazole, ceftiofur, enrofloxacin and ofloxacin. Whole genome sequencing of strain ECCNB12-2 with the third generation of high-throughput sequencing technology was performed. The prediction of acquired antimicrobial resistance genes, virulence factors and mobile genetic elements was carried out based on the whole-genome sequence. The whole genome size of strain ECCNB12-2 was 5 539 489 bp with GC content of 50.37%. At the same time, four plasmids were carried, which had the size of 147 451 bp (pTB-nb1), 139 752 bp (pTB-nb2), 82 252 bp (pTB-nb3) and 253 793 bp (pTB-nb4), respectively. A total of 40 acquired antimicrobial resistance genes were detected on the chromosome, pTB-nb1 and pTB-nb4. And 12 virulence factors were found on the whole-genome sequence. The prediction results of mobile genetic elements showed that the pTB-nb4 had high potential for self-transferability. The study indicated that the ECCNB12-2 isolated from chicken was a multi-drug resistant strain which had a serious risk. It also reflected the severity of antibiotic resistance in commercial chickens. These results provided basic information for risk assessment of antibiotic resistance of foodborne bacterial.