| Summary: | Epidemiological studies link <i>Sarcoptes scabiei</i> infection and impetigo. Scabies mites can promote <i>Streptococcus pyogenes</i> (Group A <i>Streptococcus</i>) and <i>Staphylococcus aureus</i> infections by breaching the skin barrier and excreting molecules that inhibit host innate immune responses. However, little is known about the composition and the function of the scabies-associated microbiota. Here, high-throughput whole-metagenome sequencing was used to explore the scabies-associated microbiome. Scabies mites including their immediate microenvironments were isolated from two patients with severe scabies in Northern Australia. Two ~45–50 million paired-end reads Illumina libraries were generated of which ~2 (5.1%) and 0.7 million (1.3%) microbial reads were filtered out by mapping to human (hg19) and mite draft genomes. Taxonomic profiling revealed a microbial community dominated by the phylum Firmicutes (A: 79% and B: 59%) and genera that comprise <i>Streptococcus</i>, <i>Staphylococcus</i>, <i>Acinetobacter,</i> and <i>Corynebacterium</i>. Assembly of the metagenome reads resulted in genome bins representing reference genomes of <i>Acinetobacter baumannii</i>, <i>Streptococcus dysgalactiae</i> (Group C/G), <i>Proteus mirablis</i> and <i>Staphylococcus aureus</i>. The contigs contained genes relevant to pathogenicity and antibiotics resistance. Confocal microscopy of a patient skin sample confirmed <i>A. baumannii</i>, Streptococci and <i>S. aureus</i> in scabies mite gut and faeces and the surrounding skin. The study provides fundamental evidence for the association of opportunistic pathogens with scabies infection.
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