Genome-wide host-associated population structure of Sarcoptes scabiei: One Health implications

Scabies, caused by the mite Sarcoptes scabiei, affects more than 200 million people at any one time and can be complicated by severe secondary bacterial disease. The same mite causes sarcoptic mange in companion animals, livestock and wildlife. Population-scale nuclear genomic data spanning diverse hosts and geographical regions remain limited.

We generated whole-genome sequence data for 106 S. scabiei samples and incorporated 19 publicly available datasets from humans, companion animals, livestock and wildlife. After quality filtering, 83 of 125 sample-level datasets were retained. We assessed ancestry, phylogenetic relationships, nucleotide diversity, genetic differentiation, gene-level variation and candidate selection signals.

We identified 1,568,031 filter-passing nuclear variants, including 698,136 single-nucleotide polymorphisms; sample-level heterozygosity estimates ranged from 0.27% to 11%. ADMIXTURE, principal component and phylogenetic analyses supported seven ancestry clusters broadly corresponding to host-associated groups, with pairwise fixation-index estimates ranging from 0.22 to 0.92. Multi-metric analysis identified 1600 candidate selection blocks - eight hard-sweep, 486 soft-sweep and 1106 ancient-adaptation blocks - and six conserved low-diversity blocks. Variable genes showed nominal enrichment for DNA repair, cell adhesion and signalling, whereas invariable genes showed nominal enrichment for ribosomal function, oxidative phosphorylation and mitochondrial processes.

This expanded multi-host analysis reinforces and extends evidence that host association is a prominent correlate of genome-wide population structure in S. scabiei. The findings provide a population-genomic resource for future host-stratified One Health surveillance and investigations of transmission, adaptation and acaricide resistance in scabies and sarcoptic mange.