Abstract

Antimicrobial resistance (AMR) is an ancient and natural phenomenon, yet it now poses a critical threat to global health. Human activities, particularly animal husbandry, have shaped microbial evolution by creating manure-rich environments that promote interactions between environmental and host-associated bacteria and facilitate horizontal gene transfer. Here, we investigated dormant, potential antibiotic-producing bacteria, microbial communities, and their AMR genes and mobile genetic elements in 18th-century preindustrial slaughterhouse surroundings excavated in Turku, Finland. By combining cultivation, genomic analyses, metagenomic sequencing, and ancient DNA authentication methods, we reconstructed preindustrial microbiomes and resistomes to better understand the early ecology and evolution of AMR, and to explore the role of antibiotic-producing bacteria in the emergence of AMR. Our results reveal putative ancestral forms of resistance mechanisms only recently characterized, such as fosfomycin thiol transferase fosI, plasmid-associated tmexCD-toprJ efflux pumps conferring resistance to last-resource antibiotic tigecycline, as well as sequences related to mobility of AMR genes. These findings demonstrate that key AMR elements were already present prior to widespread antibiotic use, reflecting their long-term environmental origins.