Antimicrobial resistance detection methods in water environments: a scoping review

Antimicrobial resistance (AMR) in water environments poses a significant threat to public health, ecosystem stability, and the effectiveness of antimicrobial treatments. This review aims to provide a comprehensive overview of the methods used to detect AMR in various water environments. A literature search was conducted following the PRISMA guidelines. Original articles published in English relating to AMR in water environments were included. Reviews, protocols, and abstracts were excluded. A total of 115 publications were selected for full-text evaluation. Overall, river water samples were the most commonly assessed samples across all of the reviewed studies (49/115 studies, 42%). The top 3 countries investigating AMR genes in water samples were the USA (19 studies, 17%), China (11 studies, 10%), and Brazil (10 studies, 9%). The review revealed that polymerase chain reaction and metagenomic methods are increasingly preferred for their high sensitivity, specificity, and comprehensive detection capabilities, appearing in 65/115 (57%) and 31/115 (27%) studies, respectively. Despite higher costs and technical complexity, these methods provide valuable insights into the resistome of water environments. Culture-dependent methods, while most cost effective and straightforward, are limited by their time-consuming nature and inability to detect non-viable resistant organisms, reducing their effectiveness in comprehensive AMR surveillance. The review addresses the challenges and limitations of current detection methods and proposes directions for future research to develop more robust, cost-effective, and user-friendly detection methods. The review highlights the urgent need for integrated approaches to monitor and mitigate AMR in water environments, ensuring better public health and environmental protection.