碳青霉烯耐药大肠埃希菌的基因组学特点分析  

Analysis on the genomic characterization of carbapenem resistant Escherichia coli

作　　者：曹小利[1] 张葵[1] 周辉[1] 郑洁[1] 周万青[1] 张之烽[1] 沈瀚[1] CAO Xiaoli;ZHANG Kui;ZHOU Hui;ZHENG Jie;ZHOU Wanqing;ZHANG Zhifeng;SHEN Han(Department of Laboratory Medicine, Nanjing Drum Tower Hospital, Nanjing 210008, Jiangsu, China)

机构地区：[1]南京大学附属鼓楼医院检验科,南京210008

出　　处：《临床检验杂志》2021年第11期810-816,共7页Chinese Journal of Clinical Laboratory Science

基　　金：国家自然科学基金(81902124);南京市医学科技发展基金-南京市卫生青年人才培养工程(QRX17059)。

摘　　要：目的分析碳青霉烯耐药大肠埃希菌(CREC)的基因组流行病学特征,调查共携带blaNDM和blaKPC的大肠埃希菌在南京鼓楼医院的流行情况,并分析该类细菌的播散特点。方法对2015年从南京6家医院收集的11株CREC菌株,进行全基因组测序组装后,分析耐药基因、毒力因子、多位点序列分型(MLST)、血清型和FimH型的分布并构建系统发育树。对于从南京鼓楼医院2013—2017年收集的CREC菌,使用PCR和DNA测序法筛选共携带blaNDM和blaKPC的菌株,脉冲场凝胶电泳技术(PFGE)进行遗传相关性分析;接合试验分析基因的可转移性。结果所有的CREC都携带了至少1种碳青霉烯酶编码基因,其中,9株CREC细菌携带blaNDM-5,3株携带blaKPC-2,2株携带blaNDM-1,3株同时携带blaNDM-5和blaKPC-2。MLST分析发现7种不同的序列分型(ST),2株细菌为ST410,其余的6种ST型依次为ST3489、ST156、ST683、ST297、ST167和ST361;其次,11株细菌中鉴定出6种不同的血清型和8种Fim型;11株细菌的质粒图谱虽然呈多样性,但每株细菌都含有质粒复制子IncX3。系统发育分析表明,11个CREC分离株之间有很大的遗传多样性;PFGE显示6株共携带blaNDM和blaKPC的分离株之间也存在较大的遗传多样性。接合试验表明blaNDM可转移,但与blaKPC基因不在同一质粒。结论blaNDM是CREC中主要的碳青霉烯酶基因,blaNDM-5是主要的blaNDM基因,可能通过IncX3质粒水平传播。MLST、Fim分型、血清分型和进化树发育表明CREC呈遗传多样性。Objective To characterize the genomic epidemiology of carbapenem resistant Escherichia coli(CREC)strains and investigate the prevalence of E.coli isolates co-carrying blaNDM and blaKPC in Nanjing Drum Tower Hospital and further analyze the spread characteristics.Methods A total of 11 CREC isolates were collected in 2015 from 6 hospitals in Nanjing and analyzed using whole genome sequencing.The distribution of resistance determinants,virulence elements,multi-locus sequence type(MLST),serotypes and FimH types were determined,and their phylogeny was also analyzed.PCR and DNA sequencing were used to screen the E.coli isolates co-carrying blaNDM and blaKPC from the CREC in Nanjing Drum Tower Hospital during 2013 to 2017.Pulsed field gel electrophoresis(PFGE)was preformed to analyze the genetic relatedness,and conjugation assay was used to assay the transferability of the blaNDM and blaKPC genes.Results All the CREC carried at least one carbapenemase.Among them,NDM-5(n=9)was the most frequent carbapenemase,followed by blaKPC-2(n=3)and blaNDM-1(n=2).Three isolates produced blaNDM-5 and blaKPC-2.MLST analysis found 7 distinct STs,including ST410(n=2),ST3489(n=1),ST156(n=1),ST683(n=1),ST297(n=1),ST167(n=1)and ST361(n=1).Six distinct serotypes and 8 Fim types were identified.A great diversity of plasmid profiles was observed with plasmid replicon IncX3 being the most frequent(n=11).Phylogenetic analysis showed great diversity among the 11 CREC isolates and the 6 additional isolates co-carrying blaNDM and blaKPC which were selected for comparison from the strains collected in Nanjing Drum Tower Hospital.Conjugation assays demonstrated that blaNDM could be co-transferable in different plasmid of blaKPC.Conclusion blaNDM should be the major gene of carbapenemase among CREC and blaNDM-5 should be the main variant which might be horizontally disseminated by IncX3 plasmids.These isolates displayed genetic diversity by MLST,Fim typing and serotyping.

关 键 词：大肠埃希菌 碳青霉烯耐药 NDM-5 IncX3 KPC-2 

分 类 号：R446.5[医药卫生—诊断学]