河南省人源和食源多重耐药致泻大肠埃希氏菌耐药特征与基因组分析

Antimicrobial resistance and genomic characteristics of multidrug resistant diarrheagenic Escherichia coli from human and food samples in Henan Province

目的了解河南省临床和食品来源中多重耐药的致泻大肠埃希氏菌的耐药性和基因组特征.方法对2017-2022年河南省分离的101株多重耐药致泻大肠埃希氏菌,通过微量肉汤稀释法进行抗生素敏感性实验.基于全基因组测序结果分析其耐药基因、多位点序列分型、质粒类型并基于核心基因组单核苷酸多态性位点(cgSNPs)构建系统发育树.结果101株多重耐药的致泻大肠埃希氏菌对氨苄西林、四环素、萘啶酸的耐药率最高,分别为87.1%、79.2%、64.4%;对头孢噻肟的耐药率为38.6%.全基因组测序数据表明:101株分离株可被分为60种ST型,其中ST10、ST1491、ST38是优势型别;101株分离株共预测出23种质粒类型,其中携带率最高的类型为IncFIB.分离株携带喹诺酮类、氨基糖苷类、βG内酰胺酶类、四环素类等多种耐药基因,其中超广谱βG内酰胺酶基因bla_(CTX-M-14)和bla_(CTX-M-55)上下游遗传环境中均存在插入序列(IS26、IS903B、ISECP1).结论河南省人源和食源多重耐药的致泻大肠埃希氏菌具有较高的遗传多样性,整体耐药水平较高,其bla_(CTX-M)基因的传播可能与插入序列(IS)有关.

This study was aimed at investigating the antimicrobial susceptibility and genomic characteristics of multidrug resistant diarrheagenic Escherichia coli isolated from human and food samples in Henan Province from 2017 to 2022.A total of 101 strains of multidrug resistant diarrheagenic E.coli were subjected to antimicrobial susceptibility testing with the broth dilution method.Whole genome sequencing was performed to analyze the antimicrobial resistance genes,multilocus sequence typing,and plasmid types.The sequencing data were used to construct a phylogenetic tree based on core genome single-nucleotide polymorphisms(cgSNPs).The isolates showed the highest resistance to ampicillin(87.1%),followed by tetracycline(79.2%)and nalidixic acid(64.4%).The resistance rate to cefotaxime was 38.6%.All 101 strains were classified into 60 STs,among which ST10,ST1491,and ST38 were dominant.Moreover,23 distinct plasmid replicons were identified,among which IncFIB was dominant.Diverse antimicrobial resistance genes(including quinolone,aminoglycoside,β-lactamase,and tetracycline)were identified.Insertion sequences(IS26,IS903B,and IS ECP1)were identified in upstream and downstream analysis of the gene context of the extended-spectrumβ-lactamase bla_(CTX-M-14) and bla_(CTX-M-55) genes.In conclusion,multidrug resistant diarrheagenic Escherichia coli isolated from clinical and food samples in Henan Province showed high genetic diversity and high antimicrobial resistance.The dissemination of bla_(CTX-M) carried by the strains was shown to be associated with the insertion sequence(IS).