Molecular characterization of ESBL and carbapenemase producing Uropathogenic Escherichia coli in hospitalized patients, Tehran, Iran

Abstract Background Uropathogenic Escherichia coli (UPEC) with antibiotic resistance and virulence factors can cause urinary tract infections (UTIs). The aim of this survey was to evaluate the genetic characteristic of extended-spectrum beta-lactamases (ESBLs) and carbapenemase producing UPEC (CP-UPEC) isolates.Methods In this cross-sectional study, 300 UPEC isolates were collected from the urine samples of patients hospitalized between January 2019 and December 2020. The antibiotic susceptibility of the isolates was evaluated by disk diffusion method. The minimum inhibitory concentration (MIC) of meropenem and CAZ/AVI were determined by E-test, and that of colistin was determined by micro broth dilution method. Biofilm formation was assessed by microtiter plate assay. Antibiotic-resistant genes, virulence factors, phylogroups, and serogroups were detected by polymerase chain reaction (PCR) technique. The relationship between the isolates was evaluated by pulsed-field gel electrophoresis (PFGE) typing. Sequence type 131 (ST131) isolates were identified by PCR and confirmed by multilocus sequence typing.Results A total of 100 isolates were collected from UTI patients which 36% (n = 36) of isolates were ESBL producing E. coli (EP-E.coli). Among 36 EP-E.coli isolates, 14 (38.8%), 33.3% (n = 12), 25% (n = 9), and 16.6% (n = 6) were temocillin, carbapenem, CAZ/AVI, and colistin resistant. 33.5% (n = 11/36) of EP-E.coli were carbapnememase producing E.coli (CP-E.coli). Also, of these 36 isolates, 29 (80.5%) harbored blaCTX−M gene and 7 (19.4%) were detected to be ST131. In addition, blaOXA−48 and blaNDM carbapenemase genes existed in CP-E.coli isolates. Virulence genes were mostly fimH (97.2%; n = 35), iutA (86.1%; n = 31), and fuA (80.5%; n = 29). O1 (36.1%), and O25 (22.2%) were predominant serogroups. Phylogroup typing showed that 52.7% of isolates belonged to B2 phylogroup, and PFGE typing showed 32 singletons and 2 clusters.Conclusions Our findings revealed the high prevalence of antibiotic resistant in EP-E.coli isolates, likely due to the excess clinical use of antibiotics. In addition CP-E.coli isolates belonging to ST131-O25-B2 could carry blaNDM and blaOXA−48 genes and transferred between different ward of our hospital, since there are limited options to treat the infection caused by these isolates, surveillance is needed to control the spread of such multidrug-resistant strains of E. coli.