Draft genome sequence of a co-harbouring bla_NDM-5 and mcr-1.1 Escherichia coli phylogroup A isolate associated with patient colonisation in Ireland

Objectives: While Escherichia coli phylogroup-A is typically associated with commensal strains, some isolates can harbour virulence and exhibit multidrug-resistant (MDR) phenotypes. We report the draft genome of a rare instance of carbapenem, fosfomycin and colistin resistant E. coli phylogroup-A, isolated as part of routine screening of a human patient in a clinical setting in Ireland.

Methods: E. coli E230738 was identified using MALDI-ToF/MS. Antibiotic susceptibility testing was performed using the Sensitire-EUMDRXXF plate. Whole-genome-sequencing was conducted with NextSeq1000, and genomic analysis identified antibiotic-resistance-genes (ARGs) and virulence-factors (VFs). Phylogenetic analysis was performed using whole-genome-multilocus-sequence-typing (wgMLST).

Results: E. coli E230738 genome was identified to belong to phylogroup-A/ST10 complex and to harbour 63 ARGs (17 acquired). Resistance to beta-lactams, including carbapenems and cephalosporins was likely due to predicted chromosomal bla_NDM-5. Colistin resistance appeared associated with acquired mcr-1.1. Despite lacking fosfomycin-inactivating-enzymes, fosfomycin resistance was observed, possibly due to efflux pumps. 47 chromosomal VFs were identified, involved in adhesion and iron acquisition amongst others. Plasmid replicons associated with the spread of MDR genes such as IncHI2/HI2A were detected. Phylogenetic analysis showed the closest relative being a strain from the UK differing by 851 genes.

Conclusion: This is a first detected instance of a bla_NDM-5 and mcr-1.1 co-occurring in E. coli in Ireland. The MDR profile of E. coli E230738 highlights the growing public health threat posed by the dissemination of MDR E. coli lineages with limited treatment options and underscores the need for clinical screening coupled with genomic surveillance to better understand evolving MDR patterns in E. coli.