Antimicrobial resistance genes in the aquaculture sector: global reports and research gaps.

Aquaculture has been one of the fastest-growing food production systems over the last decade and increased intensification of production has created conditions that favour disease outbreaks. Antibiotics are commonly applied in the animal food sector to fight against antibacterial infections, however their inappropriate use contributes to the emergence of antibiotic-resistant bacteria. Investment in research and capacity-strengthening, in parallel to enforcing existing regulations around antimicrobial use, are potentially powerful tools in tackling the threat of antimicrobial resistance (AMR) emanating from animal producing systems such as aquaculture. However, directing investment effectively is challenging due to the limited data available that hinders the identification of risk areas for current and future AMR emergence. Here, we aim to partially fulfill this gap by analyzing the current peer-reviewed literature reporting AMR genes in aquaculture food production systems and combining the data in a systematic map. Systematic searches of three bibliographic databases, a search engine, and 120 reviews returned 10 699 articles which were screened at title and abstract and then by full text (n = 1100). 218 articles, spanning 39 countries and 6 continents, met all inclusion criteria and were coded to retrieve bibliographic, methodology and study outcome data. AMR gene detections were associated with 44 families of fish and crustaceans and 75 genera of bacteria, with most studies employing primer-based methods to detect ARGs. A narrative synthesis explores implications for future research and policy as well as limitations of the systematic mapping methodology.The accepted manuscript in pdf format is listed with the files at the bottom of this page. The presentation of the authors' names and (or) special characters in the title of the manuscript may differ slightly between what is listed on this page and what is listed in the pdf file of the accepted manuscript; that in the pdf file of the accepted manuscript is what was submitted by the author