Molecular evidence of hybridization between pig and human Ascaris indicates an interbred species complex infecting humans

Abstract

Human ascariasis is a major neglected tropical disease caused by the nematode <i>Ascaris lumbricoides</i>. We report a 296 megabase (Mb) reference-quality genome comprised of 17,902 protein-coding genes derived from a single, representative <i>Ascaris</i> worm. An additional 68 worms were collected from 60 human hosts in Kenyan villages where pig husbandry is rare. Notably, the majority of these worms (63/68) possessed mitochondrial genomes that clustered closer to the pig parasite <i>Ascaris suum</i> than to <i>A. lumbricoides</i>. Comparative phylogenomic analyses identified over 11 million nuclear-encoded SNPs but just two distinct genetic types that had recombined across the genomes analyzed. The nuclear genomes had extensive heterozygosity, and all samples existed as genetic mosaics with either <i>A. suum</i>-like or <i>A. lumbricoides</i>-like inheritance patterns supporting a highly interbred <i>Ascaris</i> species genetic complex. As no barriers appear to exist for anthroponotic transmission of these 'hybrid' worms, a one-health approach to control the spread of human ascariasis will be necessary.