Integrated qPCR and Shotgun Metagenomics for Surveillance of Antimicrobial Resistance in Municipal Wastewater from Central Italy
The extensive use of antibiotics in human medicine, veterinary practice, and agriculture has accelerated the emergence and spread of antibiotic-resistant bacteria and antibiotic resistance genes. In particular, urban wastewater constitutes a significant reservoir of antimicrobial resistance (AMR) that requires monitoring and surveillance. By integrating targeted quantitative PCR and untargeted shotgun metagenomics applied to municipal wastewater in central Italy (April 2025 – March 2026), the authors demonstrated the ubiquitous presence of all clinically relevant markers (qnrS, blaKPC, blaCTX-M, and intI1), which exhibited significant seasonal dynamics. Metagenomic analysis revealed high levels of resistance to macrolide-lincosamide-streptogramin (MLS), aminoglycoside, and beta-lactam antibiotic classes. It is crucial to study the epidemiology of drug-resistant microorganisms in wastewater and to conduct environmental surveillance using a “One Health” approach.
Suggested by Dr.ssa Federica Di Timoteo