Comparative metagenomics reveals poultry and swine farming are hotspots for multidrug and tetracycline resistance

Antibiotic misuse in livestock is a major threat to human health, as bacteria are quickly developing resistance to them. We performed a comparative analysis of 25 faecal metagenomes from swine, poultry, cattle, and humans to investigate their resistance profiles. Our analysis revealed that all genes conferring resistance to antibiotic classes assessed except tetracyclines were more prevalent in poultry manure than in the remaining species. We detected clinically relevant antibiotic resistance genes, such as mcr-1 which confers resistance to polymyxins. Among them, extended-spectrum β-lactamase blaCTX-M genes were particularly abundant in all species. Poultry manure was identified as a hotspot for multidrug resistance, which may compromise medical treatment options. Urgent actions in the livestock industry are imperative to hamper the emergence and spread of antibiotic resistance. [Display omitted] •A comparative analysis performed on 25 fecal metagenomes from livestock and humans.•Resistance profiles revealed the prevalence of resistance in poultry manure.•Clinically relevant antibiotic resistant genes were detected in livestock manure.•Poultry manure as a hotspot for multidrug-resistant bacteria threatens human health.•AcTions in livestock industry are urgent to hamper antibiotic resistance spread.