Draft genome sequence of a co-harbouring blaNDM-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, i...
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Elsevier
2025-01-01
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| Series: | Journal of Global Antimicrobial Resistance |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S2213716524004594 |
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| author | Anna Tumeo Francesca McDonagh Aneta Kovarova Kate Ryan Christina Clarke Georgios Miliotis |
| author_facet | Anna Tumeo Francesca McDonagh Aneta Kovarova Kate Ryan Christina Clarke Georgios Miliotis |
| author_sort | Anna Tumeo |
| collection | DOAJ |
| description | 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 blaNDM-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 blaNDM-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. |
| format | Article |
| id | doaj-art-ea5019b797af4d74a3868866d8299abc |
| institution | Kabale University |
| issn | 2213-7165 |
| language | English |
| publishDate | 2025-01-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Journal of Global Antimicrobial Resistance |
| spelling | doaj-art-ea5019b797af4d74a3868866d8299abc2025-02-08T05:00:27ZengElsevierJournal of Global Antimicrobial Resistance2213-71652025-01-01406265Draft genome sequence of a co-harbouring blaNDM-5 and mcr-1.1 Escherichia coli phylogroup A isolate associated with patient colonisation in IrelandAnna Tumeo0Francesca McDonagh1Aneta Kovarova2Kate Ryan3Christina Clarke4Georgios Miliotis5Antimicrobial Resistance and Microbial Ecology Group, School of Medicine, University of Galway, Galway, IrelandAntimicrobial Resistance and Microbial Ecology Group, School of Medicine, University of Galway, Galway, IrelandAntimicrobial Resistance and Microbial Ecology Group, School of Medicine, University of Galway, Galway, IrelandAntimicrobial Resistance and Microbial Ecology Group, School of Medicine, University of Galway, Galway, IrelandDepartment of Medical Microbiology, Health Services Executive, Galway University Hospital, Galway, IrelandAntimicrobial Resistance and Microbial Ecology Group, School of Medicine, University of Galway, Galway, Ireland; Centre for One Health, Ryan Institute, University of Galway, Galway, Ireland; Corresponding author. Mailing address: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 blaNDM-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 blaNDM-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.http://www.sciencedirect.com/science/article/pii/S2213716524004594E. coliPhylogroup Amcr-1.1blaNDM-5Ireland |
| spellingShingle | Anna Tumeo Francesca McDonagh Aneta Kovarova Kate Ryan Christina Clarke Georgios Miliotis Draft genome sequence of a co-harbouring blaNDM-5 and mcr-1.1 Escherichia coli phylogroup A isolate associated with patient colonisation in Ireland Journal of Global Antimicrobial Resistance E. coli Phylogroup A mcr-1.1 blaNDM-5 Ireland |
| title | Draft genome sequence of a co-harbouring blaNDM-5 and mcr-1.1 Escherichia coli phylogroup A isolate associated with patient colonisation in Ireland |
| title_full | Draft genome sequence of a co-harbouring blaNDM-5 and mcr-1.1 Escherichia coli phylogroup A isolate associated with patient colonisation in Ireland |
| title_fullStr | Draft genome sequence of a co-harbouring blaNDM-5 and mcr-1.1 Escherichia coli phylogroup A isolate associated with patient colonisation in Ireland |
| title_full_unstemmed | Draft genome sequence of a co-harbouring blaNDM-5 and mcr-1.1 Escherichia coli phylogroup A isolate associated with patient colonisation in Ireland |
| title_short | Draft genome sequence of a co-harbouring blaNDM-5 and mcr-1.1 Escherichia coli phylogroup A isolate associated with patient colonisation in Ireland |
| title_sort | draft genome sequence of a co harbouring blandm 5 and mcr 1 1 escherichia coli phylogroup a isolate associated with patient colonisation in ireland |
| topic | E. coli Phylogroup A mcr-1.1 blaNDM-5 Ireland |
| url | http://www.sciencedirect.com/science/article/pii/S2213716524004594 |
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