Long-read metagenomics reveals stable resistome and microbiome in treated Italian slaughterhouse wastewater: a preliminary study

Antimicrobial resistance (AMR) poses a major threat to global health, and food production environments are increasingly recognized as potential reservoirs and dissemination points for resistant bacteria and antimicrobial resistance genes (ARGs). Slaughterhouse wastewater contains complex microbial communities originating from multiple animal sources and processing activities, yet the effectiveness of current treatment processes in mitigating microbiological and resistome-associated risks remains poorly understood. In this study, we applied high-throughput long-read metagenomic sequencing to characterize microbial community composition and resistome profiles in wastewater samples collected before and after physicochemical treatment from four Italian slaughterhouses. Taxonomic profiling revealed a diverse microbiome dominated by Bacillota and Pseudomonadota , along with DNA assigned to potentially clinically relevant taxa, including members of the ESKAPE group. Resistome analysis identified 96 ARGs conferring resistance to 16 antimicrobial classes. Comparative analyses of pre- and post-treatment samples showed no significant changes in microbial community structure, alpha- and beta-diversity metrics, or ARG profiles. These findings indicate that the applied coagulation–flocculation-based treatment has limited effects on the relative composition of the wastewater microbiome and resistome, as detected by shotgun metagenomics. Our results suggest that slaughterhouse wastewater may act as a persistent environmental reservoir of antimicrobial resistance determinants and highlight the need for enhanced treatment strategies and resistome-oriented surveillance within a One Health framework. Given the limited sample size and the preliminary nature of this investigation, these findings should be interpreted as exploratory and hypothesis-generating, rather than broadly generalizable.