Dissemination of resistance genes in aquaculture environments exposed to veterinary drugs: a metagenomic study in experimental microcosms

• Grant number: 25/12305-8
• Support Opportunities: Scholarships in Brazil - Post-Doctoral
• Start date: November 01, 2025
• End date: October 31, 2028
• Field of knowledge: Agronomical Sciences - Fishery Resources and Fishery Engineering - Aquaculture
• Principal Investigator: Jonas Augusto Rizzato Paschoal
• Grantee: Lucas David Rodrigues dos Santos
• Host Institution: Faculdade de Ciências Farmacêuticas de Ribeirão Preto (FCFRP). Universidade de São Paulo (USP). Ribeirão Preto , SP, Brazil
• Associated research grant: 21/08152-0 - Challenge of the use of drugs in fish farming in the context of One Health: evaluation of efficacy, safety and risk analysis., AP.TEM

Abstract

The intensification of aquaculture production systems, characterized by high population densities, promotes the emergence and spread of infectious diseases, leading to the frequent use of veterinary drugs, such as antibacterial and antiparasitics. However, residues of these compounds in aquatic environments can disrupt local microbiota and promote the dissemination of antimicrobial resistance genes (ARGs). Although Brazil is one of the world's largest animal protein producers, it lacks specific regulations for drug use in fish farming. This regulatory gap has resulted in the indiscriminate use of veterinary pharmaceuticals, including the simultaneous administration of different drug classes and inappropriate dosages. This project aims to evaluate the impacts of antibacterials and antiparasitics use on fish microbiota and the environmental compartments (such as water and sediment) through controlled experiments in microcosms simulating subtropical aquaculture systems. Fish will be exposed to different treatment regimes, both individually and in combination, followed by a systematic analysis of tissues and environmental matrices. DNA will be extracted from biological (fish tissues) and environmental (water and sediment) samples and subjected to high-throughput shotgun metagenomic sequencing, allowing detailed characterization of microbial diversity, with a specific focus on the detection and quantification of ARGs. The study will also investigate the potential for co-selection resulting from simultaneous exposure to multiple drugs, as well as the effects of subtherapeutic concentrations of antibacterials on microbiomes. The findings will support the development of safer and more sustainable strategies for veterinary drug use in aquaculture within a One Health approach.