Characterisation of Citrobacter freundii and Enterobacter cloacae complex isolates co-carrying blaNDM-1 and mcr-9 from three hospitals

Abstract

Objectives: Antimicrobial resistance (AMR) is a global health concern related to antimicrobial use and the subsequent emergence of resistant organisms, including carbapenemase-producing Enterobacterales (CPE). CPE isolate co-carrying blaNDM-1 and mcr-9.1 have been scarcely reported internationally. The identification of 20 such isolates, including 16 of one species, within a group of three hospitals in one region indicated potential dissemination within and between healthcare facilities. Methods: Twenty isolates were pseudo-anonymised and identified via MALDI-ToF MS. Antimicrobial susceptibility testing was performed by disc diffusion, and Minimal Inhibition Concentration for colistin was carried out using the UMIC system. Short-read sequencing was conducted using the Illumina MiSeq platform, and genomic analysis identified antimicrobial resistance genes, virulence factors and plasmid contigs. Taxonomic classification of draft genomes was bioinformatically assessed using Kraken2. Results: This collection comprised of Enterobacter hormaechei (n = 16), Citrobacter freundii (n = 3) and Enterobacter cloacae (n = 1) sourced from patient rectal swabs collected during routine screening (n = 13) or from healthcare-associated environmental sites (n = 7). The E. hormaechei isolates included four different ST types with one unassigned ST. Contig-based plasmid analysis identified 17 plasmid replicon types among the isolates. IncHI2A, IncHI2, and pKPCCAV1321_1 were detected in all isolates. Linked blaNDM-1 and mcr-9.1 gene spread in hospitals likely occurred via plasmid-mediated transfer rather than spread of E. hormaechei. Conclusions: This study represents the first documented instance of blaNDM-1/mcr-9.1 co-occurrence in Europe to date. It highlights the increasing public health threat posed by antimicrobial resistance and underscores the importance of genomic surveillance and clinical screening.

Keywords

• Carbapenemase producing
• Enterobacterales
• Hospital
• Ireland
• CPE
• Mobile genetic elements