Whole-genome sequence analysis of clinically isolated carbapenem resistant Escherichia coli from Iran

Abstract

Background The emergence of carbapenem-resistant Enterobacterales (CRE) continues to threaten public health due to limited therapeutic options. In the current study the incidence of carbapenem resistance among the 104 clinical isolates of Escherichia coli and the genomic features of carbapenem resistant isolates were investigated. Methods The susceptibility to imipenem, tigecycline and colistin was tested by broth dilution method. Susceptibility to other classes of antimicrobials was examined by disk diffusion test. The presence of blaOXA-48, blaKPC, blaNDM, and blaVIM carbapenemase genes was examined by PCR. Molecular characteristics of carbapenem resistant isolates were further investigated by whole-genome sequencing (WGS) using Illumina and Nanopore platforms. Results Four isolates (3.8%) revealed imipenem MIC of ≥32 mg/L and positive results for modified carbapenem inactivation method and categorized as carbapenem resistant E. coli (CREC). Colistin, nitrofurantoin, fosfomycin, and tigecycline were the most active agents against all isolates (total susceptibility rate of 99, 99, 96 and 95.2% respectively) with the last three compounds being found as the most active antimicrobials for carbapenem resistant isolates (susceptibility rate of 100%). According to Multilocus Sequence Type (MLST) analysis the 4 CREC isolates belonged to ST167 (n = 2), ST361 (n = 1) and ST648 (n = 1). NDM was detected in all CREC isolates (NDM-1 (n = 1) and NMD-5 (n = 3)) among which one isolate co-harbored NDM-5 and OXA-181 carbapenemases. WGS further detected blaCTX-M-15, blaCMY-145, blaCMY-42 and blaTEM-1 (with different frequencies) among CREC isolates. Co-occurrence of NDM-type carbapenemase and 16S rRNA methyltransferase RmtB and RmtC was found in two isolates belonging to ST167 and ST648. A colistin-carbapenem resistant isolate which was mcr-negative, revealed various amino acid substitutions in PmrB, PmrD and PhoPQ proteins. Conclusion About 1.9% of E. coli isolates studied here were resistant to imipenem, colistin and/or amikacin which raises the concern about the outbreaks of difficult-to-treat infection by these emerging superbugs in the future.

High prevalence of OXA-48-like and NDM carbapenemases among carbapenem resistant Klebsiella pneumoniae of clinical origin from Iran

“…The PCR products were electrophoresed in a 1.5 % agarose with 1× TAE (Tris/Acetate/EDTA) buffer and DNA safe stain (Yekta Tajhiz Azma, Iran) and visualized under UV light using a Uvitec Gel Documentation system (Cambridge, UK). K. pneumoniae and Escherichia coli carrying the studied genes (identified during previous studies and confirmed for carrying the genes by sanger sequencing or whole genome sequencing ( 15 ) were used as positive controls.…”

Carbapenem resistance in <i>Enterobacterales</i> from agricultural, environmental and clinical origins: South Africa in a global context

“…Although NDM and OXA-48 β-lactamases are more common to E. coli ST131, less common VIM, KPC and IMP β-lactamases were also reported in this species in some studies [68] . E. coli ST648, a high-risk pandemic clone, was reported in studies, each containing bla NDM–5 [78] , [79] . Other researchers looking at prevalence of STs among clinical E. coli reported ST131, ST405, ST648, ST410 and ST167, with ST167 most significantly associated with carbapenem resistance [80] .…”