全基因组测序分析2018年江西省临床分离非伤寒沙门菌耐药性研究

Analysis of nontyphoidal Salmonella clinical isolates antibiotic resistance based on whole genome sequencing in Jiangxi Province in 2018

目的掌握2018年江西省食源性疾病病例的非伤寒沙门菌分离株的耐药特征、耐药表型与耐药基因之间的对应关系,评价全基因组测序(whole genome sequencing,WGS)技术在耐药监测的应用前景。方法本研究以2018年江西省食源性疾病病例分离的58株非伤寒沙门菌为研究对象,用微量肉汤稀释法检测菌株对14种抗菌药物的耐药性,对58株非伤寒沙门菌进行WGS,拼接后的序列经过与ResFinder数据库比对,注释耐药基因。结果58株非伤寒沙门菌对四环素耐药率最高(77.59%,45/58),其次是氨苄西林(72.41%,42/58),对亚胺培南全部敏感。耐3类及3类以上抗生素的多重耐药菌株占56.90%(33/58),最高为6重耐药菌株占3.45%(2/58)。58株非伤寒沙门菌共筛选出47种11类耐药基因,喹诺酮耐药决定区(quinolone resistance-determining region,QRDR)存在gyrA、gyrB和parC基因突变。菌株对氨基糖苷类耐药基因携带率最高为100.00%(58/58),其次是四环素类耐药基因携带率为72.41%(42/58),大环内酯类耐药基因携带率最低为3.45%(2/58)。携带3类及3类以上耐药基因的菌株占77.59%(45/58),1.72%(1/58)菌株最高携带9类耐药基因。58株非伤寒沙门菌的药敏试验结果与检测出的已知耐药基因总体符合率达93.43%(611/654)。除喹诺酮类外,其他类别的抗生素耐药表型与耐药基因符合率均高于91%,部分种类的抗生素耐药表型与基因符合率达100%。结论非伤寒沙门菌耐药现象较为严重,其耐药表型与耐药基因有很高的一致性,WGS可作为预测沙门菌耐药性的有效手段。

Objective Understanding of bacterial antibiotic resistance is the basis for guiding clinical anti-infective therapy and monitoring antimicrobial resistance trends.The study was aimed to investigate the antibiotic resistance characteristics of nontyphoidal Salmonella isolates from foodborne disease cases in Jiangxi Province in 2018,study the correlations between resistance phenotypes and genotypes,and evaluate the application prospects of whole genome sequencing(WGS)in antimicrobial resistance surveillance.Methods In this study,58 nontyphoidal Salmonella strains were isolated from foodborne disease patients in Jiangxi Province in 2018 and were tested for susceptibility to 14 antimicrobials using broth microdilution.The 58 isolates were subjected to WGS,and resistance genes were identified from assembled sequences that compared with ResFinder database.Results 77.59%(45/58)of isolates were resistant to tetracycline,and 72.41%(42/58)were resistant to ampicillin.100.00%of isolates were susceptible to imipenem.56.90%(33/58)of isolates displayed resistance to at least 3 classes of antibiotics,and 3.45%(2/58)of isolates had resistance to at least 6 of 8 classes tested.A total of 47 unique resistance genes referred to 11 classes of antibiotics,plus mutations in gyrA,gyrB and parC structural of quinolone resistance-determining region(QRDR),were identified.100.00%(58/58)of isolates had aminoglycoside resistance genes,and 72.41%(42/58)of isolates harboured tetracycline resistance genes.Macrolide resistance genes were presented in 3.45%(2/58)of isolates.77.59%(45/58)of isolates were contained at least 3 classes of antibiotics resistance genes,and 1.72%(1/58)of isolates harboured at least 9 classes of resistance genes.The overall resistance genotypes and phenotypes were consistent in 93.43%(611/654)of cases.Except quinolones,the correlations were above 91%for tested antibiotics.Correlations were 100%for some classes of antibiotics.Conclusion The antibiotic resistance phenomenon of these isolates was serious.The resistance phenotypes were in good accordance with genotypes,and WGS can be used as an effective tool to predict the antibiotic resistance of nontyphoidal Salmonella.As more new antibiotic resistance genes were discovered,the consistency of resistance genotypes and phenotypes will be further improved.