Antimicrobial resistance genes in wild coyotes (Canis latrans) from Guanacaste and Central conservation areas of Costa Rica

Effective antimicrobial resistance (AMR) surveillance and mitigation efforts require locally adapted approaches that consider both ecological and public health dimensions. The coyote ( Canis latrans ) is widely distributed in Costa Rica, especially in buffer zones between conserved ecosystems and human settlements, and frequently interacts with local communities and domestic animals. In this study, we investigated the potential of C. latrans as a sentinel species for environmental AMR monitoring in Costa Rica. Fecal samples were opportunistically collected from two conservation areas, Guanacaste (ACG) and Central (ACC), between March and August 2022. Species confirmation was achieved through mitochondrial D-loop sequencing. We evaluated the prevalence and spatial distribution of nine antimicrobial resistance genes (ARGs) in microbial DNA extracted from coyote scat deposition. Multidrug-resistant microbiomes were detected in 74% of the samples (26/35). ARG prevalence was higher in regions with greater human population density, with detection rates of 23% in the ACC compared to 13% in the ACG. Analysis of the most frequently detected genes ( sul II, tet Q, tet Y, and cat AI) revealed significant differences in gene abundance and distribution between conservation areas (PERMANOVA, F = 3.944, p = 0.0084). Additionally, host genetic analysis using coyote mtDNA provided the first preliminary insight into population genetics in Costa Rica, revealing low haplotype ( n = 3), haplotype diversity (Hd = 0.606), and nucleotide diversity (π = 0.0099). This study contributes baseline data to guide conservation and public health policy in the region, providing valuable information for controlling AMR in Costa Rica.