Antimicrobial resistance in environment and wastewaters of a swine slaughterhouse – tracking ESKAPE bacteria and ESBL-/carbapenemase-producing Escherichia coli

Introduction This study investigated the occurrence, antimicrobial resistance (AMR) profiles, and genomic features of selected ESKAPE bacteria and ESBL-/carbapenemase-producing Escherichia coli isolated from wastewater and floor swabs in a swine slaughterhouse in Central Italy. Methods By integrating microbiological and genomic analyses across different operational phases, the study observed persistence and dissemination of antimicrobial resistant bacteria (ARB) within the abattoir environment. Results E. coli was the most prevalent species (39.6%) across all matrices, confirming its role as an indicator of fecal and environmental contamination. Despite cleaning and depuration, few ARB and antimicrobial resistance genes (ARGs) persisted, particularly in wastewater, reflecting the partial efficacy of conventional sanitation and treatment measures. The antimicrobial susceptibility tests revealed high resistance against ampicillin (47.2%), tetracycline (41.2%), and trimethoprim (34.0%), with multidrug resistant isolates occurring in nearly one-third of samples. Whole-genome sequencing identified the resistome, e.g., bla TEM , bla CTX-M , and bla OXA-48 genes. The detection of bla NDM in treated wastewater underscores the potential for environmental dissemination of carbapenemase producers. Phylogenetic analyses revealed clonal persistence of OXA- and ESBL-producing E. coli and Acinetobacter baumannii across samples, while livestock-associated MRSA ST398 indicated localized contamination events. Discussion These findings demonstrate that slaughterhouse ecosystems can function as active reservoirs and transmission nodes for AMR.