The scabies mite, Sarcoptes scabiei, is a parasite of the skin that infects humans and other animal species, causing scabies, a disease that is characterised by rashes and extreme itching. It can also cause a severe form known as crusted scabies in individuals with impaired immunity. Scabies infections are a major health problem in remote indigenous communities in Australia, where co-infection of scabies wounds by Group A streptococci and Staphylococcus aureus is thought to be responsible for the high rate of rheumatic heart disease and chronic kidney disease.

As part of the scabies mite genome project, we have collected and sequenced mite DNA from several sources, including: pools of thousands of whole mites from a laboratory pig model, and 2 clinical isolate pools from human patients living in different regions of Northern Australia. This sequencing samples the metagenome of the mite, its gut flora and the wound micro-environment. We have applied a bait and assemble algorithm to this pooled sequence data to assemble the mitochondrial (Mt) genome. We have annotated the Mt genome and used SNP information to infer haplotypes. This provides insight for the first time into the genetic diversity of scabies infections.