Genomic Analysis of a mcr-9.1-Harbouring IncHI2-ST1 Plasmid from Enterobacter ludwigii Isolated in Fish Farming

Vera Manageiro; Vanessa Salgueiro; Tânia Rosado; Narcisa M Bandarra; Eugénia Ferreira; Terry Smith; Elsa Dias; Manuela Caniça

doi:10.3390/antibiotics11091232

Genomic Analysis of a mcr-9.1-Harbouring IncHI2-ST1 Plasmid from Enterobacter ludwigii Isolated in Fish Farming

Antibiotics (Basel). 2022 Sep 10;11(9):1232. doi: 10.3390/antibiotics11091232.

Authors

Vera Manageiro^{1

2

3}, Vanessa Salgueiro^{1

2

3}, Tânia Rosado⁴, Narcisa M Bandarra^{5

6}, Eugénia Ferreira^{1

2

3}, Terry Smith^{7

8}, Elsa Dias^{2

3

4}, Manuela Caniça^{1

2

3

9}

Affiliations

¹ National Reference Laboratory of Antibiotic Resistances and Healthcare Associated Infections, Department of Infectious Diseases, National Institute of Health Dr. Ricardo Jorge, 1649-016 Lisbon, Portugal.
² Centre for the Studies of Animal Science, Institute of Agrarian and Agri-Food Sciences and Technologies, University of Porto, 4051-401 Porto, Portugal.
³ AL4AnimalS, Associate Laboratory for Animal and Veterinary Sciences, 1300-477 Lisboa, Portugal.
⁴ Laboratory of Biology and Ecotoxicology, Department of Environmental Health, National Institute of Health Dr. Ricardo Jorge, 1649-016 Lisbon, Portugal.
⁵ Division of Aquaculture, Upgrading and Bioprospecting, Portuguese Institute for the Sea and Atmosphere, IPMA, 1749-077 Lisbon, Portugal.
⁶ CIIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto, Av. General Norton de Matos s/n, 4450-208 Matosinhos, Portugal.
⁷ Molecular Diagnostics Research Group, School of Biological and Chemical Sciences, National University of Ireland, H91 DK59 Galway, Ireland.
⁸ Centre for One Health, Ryan Institute, National University of Ireland, H91 TK33 Galway, Ireland.
⁹ CIISA, Center for Interdisciplinary Research in Animal Health, Faculty of Veterinary Medicine, University of Lisbon, 1300-477 Lisbon, Portugal.

Abstract

This study analyzed the resistome, virulome and mobilome of an MCR-9-producing Enterobacter sp. identified in a muscle sample of seabream (Sparus aurata), collected in a land tank from multitrophic fish farming production. Average Nucleotide Identity analysis identified INSAq77 at the species level as an Enterobacter ludwigii INSAq77 strain that was resistant to chloramphenicol, florfenicol and fosfomycin and was susceptible to all other antibiotics tested. In silico antimicrobial resistance analyses revealed genes conferring in silico resistance to β-lactams (bla_ACT-88), chloramphenicol (catA4-type), fosfomycin (fosA2-type) and colistin (mcr-9.1), as well as several efflux pumps (e.g., oqxAB-type and mar operon). Further bioinformatics analysis revealed five plasmid replicon types, including the IncHI2/HI2A, which are linked to the worldwide dissemination of the mcr-9 gene in different antibiotic resistance reservoirs. The conserved nickel/copper operon rcnR-rcnA-pcoE-ISSgsp1-pcoS-IS903-mcr-9-wbuC was present, which may play a key role in copper tolerance under anaerobic growth and nickel homeostasis. These results highlight that antibiotic resistance in aquaculture are spreading through food, the environment and humans, which places this research in a One Health context. In fact, colistin is used as a last resort for the treatment of serious infections in clinical settings, thus mcr genes may represent a serious threat to human health.

Keywords: One Health; aquaculture; mcr-9 gene; seabream.

Abstract

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