Human depopulation reshapes antimicrobial resistance dynamics in wildlife through ecological and transmission processes.

Antimicrobial resistance (AMR) in wildlife is often interpreted as a spillover consequence of anthropogenic contamination, but the effects of long-term human depopulation remain poorly understood. We investigated quinolone-resistant Escherichia coli (QRE) and third-generation cephalosporin-resistant E. coli (3CRE) in wildlife and environmental samples from the Difficult-to-Return zones (DRZ), where human activity has been restricted since the 2011 Fukushima Daiichi Nuclear Power Plant accident, and from areas outside the DRZ (OUTSIDE), where human activity is present. Samples were collected from wild boar (n = 326), raccoons (n = 177), masked palm civets (n = 51), other wildlife (n = 39), wallows (n = 5), rivers (n = 9), and ponds (n = 9). Generalized additive models (GAMs) evaluated QRE occurrence using camera-trap-derived wildlife density, land-use variables, and livestock indices; core genome single-nucleotide polymorphism (cgSNP) analysis assessed genomic relatedness and transmission. QRE detection in wild boar was significantly higher in the DRZ, and cgSNP analysis indicated extensive clonal sharing among DRZ wild boar. GAM analysis further showed that QRE carriage increased with local wild boar density, supporting density-associated clonal expansion. In raccoons and masked palm civets, QRE carriage was associated with agricultural land, suggesting an influence of human-modified landscapes. Additionally, bla CTX-M-15 was disseminated across host species via a conserved mobile genetic element, suggesting horizontal gene transfer alongside clonal spread. These findings show that long-term human depopulation can reshape wildlife AMR dynamics and highlight the importance of integrating wildlife population management into One Health-based AMR risk assessments for human reinhabitation.