Molecular Epidemiology Of Carbapenem-resistant Escherichia Coli Strains Isolated From Patients With Urinary Tract Infection

Objective:To investigate the homology,phenotypes,drug-resistant genes of carbapenem-resistant Escherichia coli strains isolated from patients with urinary tract infection so as to provide guidance for clinical treatment and prevention as well as control of nosocomial infection.Methods:Twenty-four carbapenem-resistant Escherichia coli strains were collected from inpatients with urinary tract infection in the Affiliated hospital of QINGDAO University from January 2019 to December 2020.Meriere Vite K-2 Compact system was used for the identification and antimicrobial susceptibility testing of these strains.The next-generation sequencing technology platform was conducted to obtain the whole genome sequencing data of all strains.Then,the drug resistance genes,multi-locus sequences（MLST）and plasmid replicon types of the strains were obtained by using Res Finder and Plasmid Finder software.Homology between strains was analyzed by pulsed-field gel electrophoresis（PFGE）and Bio Numberic（7.6）software.S1 nuclease digestion electrophoresis（S1-PFGE）and liquid phase conjugation test of plasmid were used to detect the plasmids carried by E.coli.Results:（1）Drug sensitivity results showed that all of twenty-four Escherichia coli strains were resistant to penicillins,enzyme inhibitors,third-generation cephalosporins and ertapenem.In addition,the resistance rates of these Escherichia coli strains to fosfomycin and polycolistin were 16.7%（4/24）and 4.1%（1/24）,respectively.（2）Out of the 24 carbapenem-resistant Escherichia coli strains,22 carried the bla_NDMgene,and the other two strains（QD08 and QD21）did not carry any carbapenemase-resistance gene,but the two strains harboring carried the bla_CTX-M-3and bla_CTX-M-14genes,respectively.The bla_NDMgene subtypes carried by 22 Escherichia coli strains were bla_NDM-1（18.3%,4/22）,bla_NDM-5（68.2%,15/22）,bla_NDM-7（4.5%,1/22）,bla_NDM-9（4.5%,9/22）and bla_NDM-13（4.5%,1/22）,respectively.The QD24 strain of Escherichia coli carried both the bla_NDM-13and polymyxin resistance gene mcr-1.1,and it was resistant to polymyxin（MIC 8.0mg/L）.In addition,among the 15 Escherichia coli strains carrying bla_NDM-5gene,4 strains carried fosfomycin resistance genes fos A3（3/15）or fos A7（1/15）.The 24 strains also carried quinolone,aminoglycoside and other resistant genes.（3）There were 11 ST types in 24Escherichia coli strains,mainly ST167,ST410,ST69,ST617 and ST224,accounting for33.3%（8/24）,12.5%（3/24）,12.5%（3/24）,8.3%（2/24）and 8.3%（2/24）,respectively.ST167 and ST617 were predominant in the Escherichia coli carrying bla_NDM-5（68.2%,15/22）.（4）Based on Tenover rule and Bio Numerics（7.6）software analysis,the PFGE electrophoretic band types of the 24 Escherichia coli strains were divided into 9 groups（A～I）,and the similarity ratio of Dice coefficient among them was 67.7%～100%.In addition,the 24 strains of Escherichia coli S1-PFGE showed that each strain carried one or five plasmids,ranging in size from 10kb to 260kb.Two strains of ST69 E.coli（QD14and QD18）had three plasmids in the same size,and the Dice coefficient ratio of PFGE band digested by Xba I was 100%.In addition,Plasmid Finder（2.1）software was used to analyze the sequencing data of 24 Escherichia coli strains.It was found that each strain had 1-6 replicon,and the bla_NDMgene was mainly located on the Inc X3-type plasmid,accounting for 45.5%（10/22）.Conclusions:（1）In this study,the resistance of Escherichia coli isolates to carbapenems was mainly related to their bla_NDMgene,and these strains also carried a variety of drug resistance genes,which was consistent with the multidrug resistance phenotypes.（2）The bla_NDMgene carried by Escherichia coli strains was mainly bla_NDM-5subtype,and there were also multiple subtype distribution,indicating the diversity of the evolution of the drug resistance genes.（3）To the best our knowledge,it was firstly reported that Escherichia coli strain harbored both bla_NDM-13and mcr-1.1 genes in the worldwide,which should attract the attention of clinicians.