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

The aim of the current study was to determine the genomic map of resistance genes and to understand the potential for mobility by a NDM-6-carrying 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. 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. Two carbapenem-resistant E. coli strains were isolated from sewage. These strains (2-331 and 2-333) belonged to the sequence type (ST) 167 and carried an NDM-6 carbapenemase. The complete genome of isolate 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 1,549 bp. Plasmid p2-331_1 (∼144 kb), belonging to the IncFII/IncFIA/IncFIB group, carries 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 nine different classes of antibiotics to a GFP-tagged E. coli strain. Our study shows 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.