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

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 bla _OXA-48, bla _KPC, bla _NDM, and bla _VIM 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 bla _CTX-M-15, bla _CMY-145, bla _CMY-42 and bla _TEM-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.