Genome skimming of dog faecal samples reveals mitogenomes indistinguishable from those of red fox-derived Uncinaria stenocephala

Abstract The northern hookworm, Uncinaria stenocephala , is the primary hookworm infecting dogs in temperate regions, but red foxes ( Vulpes vulpes ) are also frequent hosts. The extent to which fox-derived U. stenocephala contributes to canine transmission remains unclear. In this study, we assembled complete mitochondrial genomes (mitogenomes) from two adult U. stenocephala worms collected from red fox and two mitogenomes recovered via genome skimming from dog faecal egg isolates. Comparative analysis revealed >99% identity across all U. stenocephala mitogenomes with no discernible genetic differences for dog- and fox-derived U. stenocephala , supporting their conspecificity. Phylogenetic analysis confirmed paraphyly of the genus Uncinaria and clear distinction of U. stenocephala from the badger hookworm U. criniformis , resolving historical taxonomic ambiguity. We applied a 3% nucleotide divergence threshold to assess species boundaries across hookworm mitogenomes, confirming potential cryptic diversity in Necator americanus, U. sanguinis and A. caninum . Our findings demonstrate the utility of genome skimming for recovering hookworm mitogenomes from faecal samples and highlight the need for broader mitogenomic characterization across hookworm taxa to refine taxonomy and understand host associations.