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

BMC Microbiology

Research

Samaneh Barmudeh¹  Mehri Haeili¹  Narges Zeinalzadeh¹  Hossein Samadi Kafil²  Virginia Batignani³  Arash Ghodousi⁴  Daniela Maria Cirillo⁴  Maryam Omrani⁵ 

[1] Department of Animal Biology, Faculty of Natural Sciences, University of Tabriz, Tabriz, Iran;Drug Applied Research Center, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran;Emerging Bacterial Pathogens Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy;Emerging Bacterial Pathogens Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy;Vita-Salute San Raffaele University, Milan, Italy;IRCCS San Raffaele Scientific Institute, Milan, Italy;

关键词: Carbapenem resistance;    Escherichia coli;    NDM-1;    NDM-5;    Whole genome sequencing;    Epidemiology;   

DOI  :  10.1186/s12866-023-02796-y

 received in 2022-09-29, accepted in 2023-02-16,  发布年份 2023

来源: Springer

【 摘 要 】

BackgroundThe 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.MethodsThe 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.ResultsFour 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.ConclusionAbout 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.

【 授权许可】

CC BY   
© The Author(s) 2023

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