Nematode metabarcoding and dietary analysis uncover parasite sharing between wild and domestic canids in a tropical One Health system

Coyotes ( Canis latrans ) are highly adaptable mesopredators whose increasing overlap with domestic dogs and humans may facilitate parasite transmission at the wildlife–domestic interface. However, parasite diversity and transmission dynamics between wild and domestic canids remain poorly characterized in Central America. This study investigated gastrointestinal helminths infecting coyotes and domestic dogs in Costa Rica using an integrative molecular, morphological and ecological approach. Fecal samples were collected from coyotes and domestic dogs across protected, fragmented, and urban landscapes in Costa Rica. Host species identity was confirmed using cyt b RFLP and 12S metabarcoding, and individual coyotes were identified through SNP genotyping. Parasite communities were characterized using microscopy and deep amplicon sequencing of the nematode cytochrome oxidase 1 ( cox 1) gene. Phylogenetic and haplotype analyses were conducted for dominant parasites, and vertebrate 12S metabarcoding was used to evaluate coyote diet. Moreover, a reservoir capacity model was applied to estimate the potential contribution of coyotes to parasite transmission. Thirty-one individual coyotes and 149 domestic dogs were analyzed. Seven helminth groups were detected in metabarcoding, whereas microscopy identified four parasite species or groups. Ancylostoma caninum was the most prevalent nematode in both hosts, with 38.7% and 25.7% in coyotes and dogs, respectively. Metabarcoding detected higher parasite frequencies than microscopy and revealed additional taxa, including Toxocara canis and Spirocerca lupi DNA in dogs. Infection risk was significantly higher in fragmented and peri-urban environments than in protected areas (OR=16.000, 95% C.I. 1.381–185.405; and OR = 8.000, 95% C.I. 1.061–60.324, respectively). Moreover, phylogenetic and haplotype analyses revealed high genetic diversity but no host- or location-specific structuring of A. caninum , indicating recent parasite exchange among sympatric canids. Dietary metabarcoding showed frequent consumption of domesticated animals and small mammals, suggesting potential exposure to parasite paratenic or intermediate hosts. Our findings indicate that coyotes and domestic dogs share helminth communities across human-modified landscapes and that coyotes may function as potential reservoirs of zoonotic hookworms. These results highlight the importance of considering wildlife–domestic interfaces in parasite surveillance and support a One Health perspective for managing zoonotic parasite transmission.