Molecular characterization of colistin-resistant Klebsiella pneumoniae in a tertiary care hospital: First report of the mcr-1.32 gene in Tunisia

Background Colistin resistance mediated by mcr genes poses a critical threat to antimicrobial therapy, particularly in multidrug-resistant Klebsiella pneumoniae . To date, no human clinical isolate carrying mcr-1 has been reported in Tunisia. Objectives This study aims to assess colistin resistance rates in carbapenemase-resistant clinical K. pneumoniae isolates, characterize genetic resistance determinants in resistant strains, and screen for the occurrence of the mcr-1 gene. Methods A cross-sectional study was conducted from January to December 2024 at Habib Thameur Hospital, Tunis. Colistin resistance was assessed via broth microdilution (EUCAST criteria). Resistance genes were detected via multiplex PCR and confirmed via Sanger sequencing. Sequence identity was analysed with BLASTn and the CARD database. Results Among the 143 carbapenem-resistant K. pneumoniae isolates, 16 [11.2% (95% CI: 6.5–17.5%)] were colistin resistant. All the isolates were multidrug resistant, with a high prevalence of the blaOXA-48 (87.5%) and blaNDM (68.8%) carbapenemase genes and the ESBL genes blaCTX-M (87.5%) and blaSHV (68.8%). Additional resistance determinants included the qnrS (93.8%), qnrB (75%), and 16S rRNA methylase genes ( rmtF , rmtC , and armA ). One isolate (0.2%) carried the mcr-1.32 gene with 100% sequence identity, displaying moderate colistin resistance (MIC: 8 mg/L) and harboring multiple resistance genes. Conclusion This study reports the first detection of the plasmid-mediated colistin resistance gene mcr-1 in a clinical K. pneumoniae isolate in Tunisia. These findings highlight the potential for horizontal gene transfer and underscore the need for enhanced genomic surveillance, strict antibiotic stewardship, and One Health strategies to mitigate the spread of mcr -mediated resistance in North Africa.