Complete sequence of a new conjugative multidrug-resistance encoding IncFII/IncFIA/IncFIB plasmid carrying NDM-6 metallo-β-lactamase from pathogenic Escherichia coli sequence type 167 isolated from sewage in Norway

Abstract

[eng] Objectives The aim of the current study was to determine the genomic map of resistance genes and to understand the potential for mobility of a new NDM-6-carrying plasmid from a pathogenic Escherichia coli strain. A complete and closed genome sequence of the E. coli strain was obtained by applying a combination of short-read Illumina and long-read Nanopore-based sequencing. Methods Isolation of E. coli was performed, using ECC CHROMagar , and antibiotic sensitivity patterns were determined, using Sensititre EUVSEC3 plates. Whole-genome sequencing was performed, using Illumina MiSeq- and Oxford Nanopore MinION-based sequencing. Conjugation experiments were performed, using filter-mating and a green fluorescent protein (GFP)-tagged E. coli strain. Results Two carbapenem-resistant E. coli strains were isolated from sewage. These strains (2-331 and 2-333) belonged to sequence type (ST) 167 and carried an NDM-6 carbapenemase. The complete genome of strain 2-331 (GenBank accession no.: CP110117-22.1) was assembled into six contigs, representing a complete circular chromosome of 4 947 178 bp and five plasmids, ranging from 143 596 bp to 1549 bp. Plasmid p2-331_1 (∼144 kb), belonging to the IncFII/IncFIA/IncFIB group, carried multiple antibiotic resistance genes, including mph(A), mrx(A), blaTEM-1, rmtB1, blaNDM-6, ble, sul1, qacEΔ1, aadAΔ, dfrA12, and tet(A). Plasmid p2-331_1 was transferred from strain 2-331, via conjugation, conferring resistance against eight different classes of antibiotics to a GFP-tagged E. coli strain. Conclusions Our study showed the emergence of a new conjugative plasmid-carrying NDM-6 carbapenemase from pathogenic E. coli ST167 for the first time in Norway. The importance of population-based sewage-surveillance for understanding the antimicrobial resistance situation within the community is highlighted.