Official Journal of the European Union. Council Directive 2006/88/EC on animal health requirements for aquaculture animal products thereof, and on the prevention and control of certain diseases in aquaculture. Official Journal of the European Union. 2006: 14–56. https://eur-lex.europa.eu/LexUriServ/LexUriServ.do?uri=OJ:L:2006:328:0014:0056:en:PDF.

FAO. Climate change: unpacking the burden on food safety. Rome: Food and safety series; 2020.

Google Scholar 

OECD/FAO. OECD-FAO Agricultural Outlook 2020–2029. OECD Publishing Paris, /Food and Agriculture Organization of the United Nations, Rome. 2020.

Schar D, Klein EY, Laxminarayan R, Gilbert M, Van Boeckel TP. Global trends in antimicrobial use in aquaculture. Sci Rep. 2020;10:1–9.

Article  Google Scholar 

Bergheim A, Schumann M, Brinker A. Water pollution from fish farms. Encycl Water. 2019. https://doi.org/10.1002/9781119300762.wsts0101.

Article  Google Scholar 

Departamento de Salud Animal, Acuicultura S de. Informe sobre uso de antimicrobianos en la salmonicultura nacional - primer semestre año 2023. 2023. https://www.sernapesca.cl/app/uploads/2023/12/informe_sobre_el_uso_am_en_la_salmonicultura_nacional_-_1er_semestre_-_2023.pdf

Turnbull J, Bell A, Adams C, Bron J, Huntingford F. Stocking density and welfare of cage farmed Atlantic salmon: application of a multivariate analysis. Aquaculture. 2005;243:121–32.

Article  Google Scholar 

Quesada SP, Paschoal JAR, Reyes FGR. Considerations on the aquaculture development and on the use of veterinary drugs: special issue for fluoroquinolones-a review. J Food Sci. 2013;78:1321–33.

Article  Google Scholar 

Lim SJ, Jang E, Lee SH, Yoo BH, Kim SK, Kim TH. Antibiotic resistance in bacteria isolated from freshwater aquacultures and prediction of the persistence and toxicity of antimicrobials in the aquatic environment. J Environ Sci Health B. 2013;48:495–504.

Article  PubMed  CAS  Google Scholar 

Burridge L, Weis JS, Cabello F, Pizarro J, Bostick K. Chemical use in salmon aquaculture: a review of current practices and possible environmental effects. Aquaculture. 2010;306:7–23.

Article  CAS  Google Scholar 

Cabello FC, Godfrey HP, Tomova A, Ivanova L, Dölz H, Millanao A, et al. Antimicrobial use in aquaculture re-examined: its relevance to antimicrobial resistance and to animal and human health. Environ Microbiol. 2013;15:1917–42.

Article  PubMed  Google Scholar 

Chen J, McIlroy SE, Archana A, Baker DM, Panagiotou G. A pollution gradient contributes to the taxonomic, functional, and resistome diversity of microbial communities in marine sediments. Microbiome. 2019;7:1–12.

Article  Google Scholar 

Lu J, Zhang X, Wang C, Li M, Chen J, Xiong J. Responses of sediment resistome, virulence factors and potential pathogens to decades of antibiotics pollution in a shrimp aquafarm. Sci Total Environ. 2021;794:148760.

Article  PubMed  CAS  Google Scholar 

Wang JH, Lu J, Zhang YX, Wu J, Luo Y, Liu H. Metagenomic analysis of antibiotic resistance genes in coastal industrial mariculture systems. Bioresour Technol. 2018;253:235–43.

Article  PubMed  CAS  Google Scholar 

Chen B, Yang Y, Liang X, Yu K, Zhang T, Li X. Metagenomic profiles of antibiotic resistance genes (ARGs) between human impacted estuary and deep ocean sediments. Environ Sci Technol. 2013;47:12753–60.

Article  PubMed  CAS  Google Scholar 

Chen B, Lin L, Fang L, Yang Y, Chen E, Yuan K, et al. Complex pollution of antibiotic resistance genes due to beta-lactam and aminoglycoside use in aquaculture farming. Water Res. 2018;134:200–8.

Article  PubMed  CAS  Google Scholar 

Tomova A, Ivanova L, Buschmann AH, Rioseco ML, Kalsi RK, Godfrey HP, et al. Antimicrobial resistance genes in marine bacteria and human uropathogenic Escherichia coli from a region of intensive aquaculture. Environ Microbiol Rep. 2015;7:803–9.

Article  PubMed  CAS  Google Scholar 

Birnstiel S, Sebastián M, Romera-Castillo C. Structure and activity of marine bacterial communities responding to plastic leachates. Sci Total Environ. 2022. https://doi.org/10.1016/j.scitotenv.2022.155264.

Article  PubMed  Google Scholar 

Kemper N. Veterinary antibiotics in the aquatic and terrestrial environment. Ecol Indic. 2008;8:1–13.

Article  CAS  Google Scholar 

Topp E, Larsson DGJ, Miller DN, Van den Eede C, Virta MPJ. Antimicrobial resistance and the environment: assessment of advances, gaps and recommendations for agriculture, aquaculture and pharmaceutical manufacturing. FEMS Microbiol Ecol. 2018. https://doi.org/10.1093/femsec/fix185.

Article  PubMed  Google Scholar 

Food and Agriculture Organization of the United Nations FAO. The state of World Fisheries and Aquaculture. The state of world fisheries and aquaculture 2018 - Meeting the sustainable development goals. Rome; 2018.

Berglund B. Environmental dissemination of antibiotic resistance genes and correlation to anthropogenic contamination with antibiotics. Infect Ecol Epidemiol. 2015;5:28564.

PubMed  Google Scholar 

Bhattacharyya A, Haldar A, Bhattacharyya M, Ghosh A. Anthropogenic influence shapes the distribution of antibiotic resistant bacteria (ARB) in the sediment of Sundarban estuary in India. Sci Total Environ. 2019;647:1626–39.

Article  PubMed  CAS  Google Scholar 

Shah SQAA, Cabello FC, L’Abée-Lund TM, Tomova A, Godfrey HP, Buschmann AH, et al. Antimicrobial resistance and antimicrobial resistance genes in marine bacteria from salmon aquaculture and non-aquaculture sites. Environ Microbiol. 2014;16:1310–20.

Article  PubMed  CAS  Google Scholar 

Miranda CD, Rojas R. Occurrence of florfenicol resistance in bacteria associated with two Chilean salmon farms with different history of antibacterial usage. Aquaculture. 2007;266:39–46.

Article  CAS  Google Scholar 

Bodor A, Bounedjoum N, Vincze GE, Erdeiné Kis Á, Laczi K, Bende G, et al. Challenges of unculturable bacteria: environmental perspectives. Rev Environ Sci Biotechnol. 2020;19:1–22.

Article  CAS  Google Scholar 

Alain K, Querellou J. Cultivating the uncultured: Limits, advances and future challenges. Extremophiles. 2009;13:583–94.

Article  PubMed  Google Scholar 

Rodrigues CJC, de Carvalho CCCR. Cultivating marine bacteria under laboratory conditions: overcoming the “unculturable” dogma. Front Bioeng Biotechnol. 2022;10:1–14.

Article  Google Scholar 

Miller RA, Carson J, Dalsgaard I, Gaunt PS, Gieseker C, Hawke JP, et al. VET04-A2. Methods for Broth Dilution Susceptibility Testing of Bacteria Isolated from Aquatic Animals; Approved Guideline—Second Edition. 2nd ed. Clinical and Laboratory Standards Institute (CLSI); 2014.

CLSI National Committee for Clinical Laboratory Standards. M45. Methods for Antimicrobial Dilution and Disk Susceptibility Testing of Infrequently Isolated or Fastidious Bacteria; Proposed Guideline. Guidelines CLSI. 2015.

Murray AK, Zhang L, Yin X, Zhang T, Buckling A, Snape J, et al. Novel insights into selection for antibiotic resistance in complex microbial communities. mBio. 2018. https://doi.org/10.1128/mBio.00969-18.

Article  PubMed  PubMed Central  Google Scholar 

Lundström SV, Östman M, Bengtsson-Palme J, Rutgersson C, Thoudal M, Sircar T, et al. Minimal selective concentrations of tetracycline in complex aquatic bacterial biofilms. Sci Total Environ. 2016;553:587–95.

Article  PubMed  Google Scholar 

Feng Y, Sun JW, Shi WW, Duan JL, Sun XD, Feng LJ, et al. Microplastics exhibit accumulation and horizontal transfer of antibiotic resistance genes. J Environ Manage. 2023;336:117632.

Article  PubMed  CAS  Google Scholar 

Tillett D, Neilan BA. Xanthogenate nucleic acid isolation from cultured and environmental cyanobacteria. J Phycol. 2000;36:251–8.

Article  CAS  Google Scholar 

Love MI, Huber W, Anders S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 2014;15:1–21.

Article  Google Scholar 

Katoh K, Misawa K, Kuma KI, Miyata T. MAFFT: a novel method for rapid multiple sequence alignment based on fast fourier transform. Nucleic Acids Res. 2002;30:3059–66.

Article  PubMed  PubMed Central  CAS  Google Scholar 

Capella-Gutiérrez S, Silla-Martínez JM, Gabaldón T. trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics. 2009;25:1972–3.

Article  PubMed  PubMed Central  Google Scholar 

Price MN, Dehal PS, Arkin AP. FastTree 2—approximately maximum-likelihood trees for large alignments. PLoS ONE. 2010. https://doi.org/10.1371/journal.pone.0009490.

Article  PubMed  PubMed Central  Google Scholar 

Alcock BP, Raphenya AR, Lau TTY, Tsang KK, Bouchard M, Edalatmand A, et al. CARD 2020: antibiotic resistome surveillance with the comprehensive antibiotic resistance database. Nucleic Acids Res. 2020;48:D517–25.

PubMed  CAS