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

Anna Tumeo; Francesca McDonagh; Aneta Kovarova; Kate Ryan; Christina Clarke; Georgios Miliotis

doi:10.1016/j.jgar.2024.11.018

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

J Glob Antimicrob Resist. 2024 Dec 5:40:62-65. doi: 10.1016/j.jgar.2024.11.018. Online ahead of print.

Authors

Anna Tumeo¹, Francesca McDonagh¹, Aneta Kovarova¹, Kate Ryan¹, Christina Clarke², Georgios Miliotis³

Affiliations

¹ Antimicrobial Resistance and Microbial Ecology Group, School of Medicine, University of Galway, Galway, Ireland.
² Department of Medical Microbiology, Health Services Executive, Galway University Hospital, Galway, Ireland.
³ Antimicrobial Resistance and Microbial Ecology Group, School of Medicine, University of Galway, Galway, Ireland; Centre for One Health, Ryan Institute, University of Galway, Galway, Ireland. Electronic address: [email protected].

PMID: 39644970
DOI: 10.1016/j.jgar.2024.11.018

Abstract

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 Sensititre-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 of which acquired. Resistance to beta-lactams, including carbapenems and cephalosporins was likely due to chromosomally identified 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. Forty-seven chromosomal VFs were identified, involved in adhesion and iron acquisition amongst other properties. Plasmid replicons associated with the spread of MDR genes such as IncHI2/HI2A were detected. wgMLST analysis showed the closest relative being a strain from the UK, exhibiting differences in the sequences of 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 concern 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.

Keywords: E. coli; Ireland; Phylogroup A; bla(NDM-5); mcr-1.1.