First report of the mcr-1 gene in colistin-resistant Klebsiella pneumoniae in a tertiary care hospital in Tunisia

Colistin resistance mediated by mcr genes poses a critical threat to antimicrobial therapy, particularly in multidrug-resistant Klebsiella pneumoniae. While mcr-1 has been previously identified in clinical Escherichia coli in Tunisia, no human clinical K. pneumoniae isolate carrying this gene has been reported to date. This study aims to assess colistin resistance rates in carbapenem-resistant clinical K. pneumoniae isolates, characterize genetic resistance determinants in resistant strains, and screen for the occurrence of the mcr-1 gene. This study was conducted from January to December 2024 at Habib Thameur Hospital, Tunis and investigated colistin resistance among carbapenem-resistant K. pneumoniae isolates. 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 database. 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-like (14/16) and blaNDM (11/16) carbapenemase genes and the β-lactamases genes blaCTX-M (14/16) and blaSHV (11/16). Additional resistance determinants included the qnrS (14/16), qnrB (15/16), and 16 S rRNA methylase genes (rmtF, rmtC, and armA). One isolate carried the mcr-1 gene, displaying moderate colistin resistance (MIC: 4 mg/L) and harbouring multiple resistance genes. This study reports the first detection of the mobile colistin resistance gene mcr-1 in a clinical K. pneumoniae isolate in Tunisia. While chromosomal mechanisms remain predominant in colistin-resistant K. pneumoniae in the country, this finding underscores the urgent need for enhanced molecular surveillance and antibiotic stewardship to curb the potential risk for future dissemination of mcr-mediated resistance in North Africa.