Extended-Spectrum and Last-Resort β-Lactams Exert Increasing Impacts on Chicken Manure-Derived Copiotrophic Microbiomes and Resistomes

Understanding the environmental dissemination of antimicrobial resistance (AMR) is crucial for mitigating its spread and for reducing the clinical burden of resistant infections. Within a One Health framework, animal husbandry systems, and particularly animal gut microbiomes, are widely used as models for agricultural environments, because their high densities and recurrent antibiotic exposure create strong selective pressures that can impact both environmental and human resistomes. In a previous study, we demonstrated that copiotrophic enrichment in medium that stimulates growth of gut-associated bacteria, can reveal clinically associated bacterial populations and associated antibiotic resistance genes (ARGs) that are not detected by direct environmental sampling. In the present study, we applied this enrichment approach to poultry manure to examine how {beta}-lactamase-resistant antibiotics (cefotaxime and meropenem) shape copiotrophic gut-like microbial community composition and resistance profiles relative to an earlier {beta}-lactam (ampicillin) and to antibiotic-free controls. Our results show that {beta}-lactamase-resistant antibiotics induced more pronounced shifts in both microbial diversity and ARG profiles than the early {beta}-lactam. When focusing on specific taxa, differential responses were observed correlating to antimicrobial range of action. Together, these findings underline how the diversity of pathogen and AMR indicators in gut microbiomes may be shaped by different selective pressures imposed by {beta}-lactamase-resistant antibiotics.