Comprehensive resistome and antibiotic profiling in wastewater and biosolids: a case study

Wastewater treatment plants (WWTPs) are widely recognized as hotspots for the accumulation of antimicrobial resistance determinants (AMR). This study analyses the presence of antibiotic resistance genes (ARGs), mobile genetic elements (MGEs), and antibiotic residues in influent and effluent wastewater, as well as in dehydrated and composted sludge from a municipal WWTP including a composting facility in southern Spain. Influent wastewater exhibited different ARG profiles, including macrolide-lincosamide-streptogramin (MLSB), aminoglycoside, tetracycline, quinolone, and multidrug resistance related genes, alongside MGEs such as intI1, IS26, and qepA. Although treatment processes reduced microbial loads and the relative abundance of ARGs, several ARGs and MGEs persisted in effluent water. Dehydrated Sludge matrices showed the presence of tetracycline and macrolide antibiotics (e.g., doxycycline and azithromycin), consistent with their physicochemical properties related with their environmental persistence. Composting treatment led to an effective decreasing in the global ARG load, however, key MGEs, including integrons, insertion sequences, and transposons, remained detectable, indicating the persistence of residual genetic reservoirs, which can be justified by the presence of antibiotics at low concentration and/or co-occurring stressors. The application of resistance metrics, such as the Antibiotic Resistance Gene Index (ARGI) and the Standard Resistance Gene Index (SRGI), enabled comparison with European benchmark data, revealing that ARG loads detected in wastewater and sludge matrices were consistent with previously reported regional data. The detection of clinically relevant genes (e.g., mcr-1, qacEΔ1, and merA) indicates that these matrices may act as reservoirs of resistance determinants of public health concern. Overall, these findings highlight the value of molecular surveillance and resistance indices and the need for longer-term studies of AMR in wastewater and sludge systems.