title: Mitochondrial Genome Sequence of the Scabies Mite Provides Insight into the Genetic Diversity of Individual Scabies Infections.
abstract: The scabies mite, Sarcoptes scabiei, is an obligate parasite of the skin that infects humans and other animal species, causing scabies, a contagious disease characterized by extreme itching. Scabies infections are a major health problem, particularly in remote Indigenous communities in Australia, where co-infection of epidermal scabies lesions by Group A Streptococci or Staphylococcus aureus is thought to be responsible for the high rate of rheumatic heart disease and chronic kidney disease. We collected and separately sequenced mite DNA from several pools of thousands of whole mites from a porcine model of scabies (S. scabiei var. suis) and two human patients (S. scabiei var. hominis) living in different regions of northern Australia. Our sequencing samples the mite and its metagenome, including the mite gut flora and the wound micro-environment. Here, we describe the mitochondrial genome of the scabies mite. We developed a new de novo assembly pipeline based on a bait-and-reassemble strategy, which produced a 14 kilobase mitochondrial genome sequence assembly. We also annotated 35 genes and have compared these to other Acari mites. We identified single nucleotide polymorphisms (SNPs) and used these to infer the presence of six haplogroups in our samples, Remarkably, these fall into two closely-related clades with one clade including both human and pig varieties. This supports earlier findings that only limited genetic differences may separate some human and animal varieties, and raises the possibility of cross-host infections. Finally, we used these mitochondrial haplotypes to show that the genetic diversity of individual infections is typically small with 1-3 distinct haplotypes per infestation.
authors.affiliation: Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia.|Department of Medical Biology, University of Melbourne, Melbourne, Victoria, Australia.
authors.forename: Ehtesham
authors.initials: E
authors.lastname: Mofiz
authors.affiliation: Victorian Life Sciences Computation Initiative, University of Melbourne, Melbourne, Victoria, Australia.
authors.forename: Torsten
authors.initials: T
authors.lastname: Seemann
authors.affiliation: Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia.|Department of Mathematics and Statistics, University of Melbourne, Victoria, Australia.
authors.forename: Melanie
authors.initials: M
authors.lastname: Bahlo
authors.affiliation: Menzies School of Health Research, Charles Darwin University, Casuarina, Northern Territory, Australia.
authors.forename: Deborah
authors.initials: D
authors.lastname: Holt
authors.affiliation: Menzies School of Health Research, Charles Darwin University, Casuarina, Northern Territory, Australia.
authors.forename: Bart J
authors.initials: BJ
authors.lastname: Currie
authors.affiliation: QIMR Berghofer Medical Research, Herston, Queensland, Australia.
authors.forename: Katja
authors.initials: K
authors.lastname: Fischer
authors.affiliation: Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia.|Department of Medical Biology, University of Melbourne, Melbourne, Victoria, Australia.|Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia.|Peter MacCallum Cancer Centre, East Melbourne, Australia.
authors.forename: Anthony T
authors.initials: AT
authors.lastname: Papenfuss
mesh_terms: D000818:Animals; D001315:Australia; D004272:DNA, Mitochondrial / Q000737:chemistry / Q000235:genetics*; D014644:Genetic Variation; D054629:Genome, Mitochondrial; D006239:Haplotypes; D006801:Humans; D058977:Molecular Sequence Annotation; D008969:Molecular Sequence Data; D020641:Polymorphism, Single Nucleotide; D012520:Sarcoptes scabiei / Q000145:classification / Q000235:genetics*; D012532:Scabies / Q000469:parasitology / Q000662:veterinary; D017422:Sequence Analysis, DNA; D013552:Swine; D013553:Swine Diseases / Q000469:parasitology
chemical_list: D004272:DNA, Mitochondrial