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

Didrik H Grevskott; Francisco Salvà-Serra; Edward R B Moore; Nachiket P Marathe

doi:10.1016/j.jgar.2023.04.005

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

J Glob Antimicrob Resist. 2023 Jun:33:291-293. doi: 10.1016/j.jgar.2023.04.005. Epub 2023 Apr 21.

Authors

Didrik H Grevskott¹, Francisco Salvà-Serra², Edward R B Moore³, Nachiket P Marathe⁴

Affiliations

¹ Department of Contaminants and Biohazards, Institute of Marine Research (IMR), Bergen, Norway.
² Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden; Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Gothenburg, Sweden; Culture Collection University of Gothenburg (CCUG), Department of Clinical Microbiology, Sahlgrenska University Hospital, Region Västra Götaland and Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden; Microbiology, Department of Biology, University of the Balearic Islands, Palma de Mallorca, Spain.
³ Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden; Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Gothenburg, Sweden; Culture Collection University of Gothenburg (CCUG), Department of Clinical Microbiology, Sahlgrenska University Hospital, Region Västra Götaland and Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.
⁴ Department of Contaminants and Biohazards, Institute of Marine Research (IMR), Bergen, Norway. Electronic address: nachiket.marathe@hi.no.

PMID: 37086893
DOI: 10.1016/j.jgar.2023.04.005

Abstract

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), bla_TEM-1, rmtB1, bla_NDM-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.

Keywords: Antibiotic resistance genes; Escherichia coli; NDM-6 carbapenemase; Norway; ST167; Sewage-based surveillance.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Anti-Bacterial Agents / pharmacology
Escherichia coli Infections*
Escherichia coli*
Humans
Plasmids / genetics
Sewage
beta-Lactamases / metabolism

Substances

Sewage
beta-Lactamases
Anti-Bacterial Agents