Epidemiological studies indicated a link between the epidermal infestation with Sarcoptes scabiei and impetigo, particularly in tropical settings. Scabies mites are known to promote Group A Spreptococcal (GAS) and S. aureus 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 and their micro-environments were isolated from two patients (A, B) in northern Australia. Two ~80M paired-end reads Illumina libraries were generated of which ~2M (2.54%) and 0.4M (0.62%) microbial reads were filtered out by mapping to human genome (hg19) and the recently available draft mite genomes. Taxonomic profiling revealed a microbial community dominated by the phylum Firmicutes (A: 79% and B: 59%). Actinobacteria (A: 11% and B: 1.8%) - which are most prevalent in normal skin samples- were underrepresented. The most abundant genera comprise Streptococcus (mostly group A and G), Staphylococcus (mostly S. aureus and S. argenteus), Acinetobacter (mostly A. baumannii) and Corynebacterium. The microbiome community associated with scabies was enriched in metabolic functions such as carbohydrates and fatty acid metabolisms. Major streptococcal virulence factors were identified.
This study confirmed the association of GAS and S. aureus with scabies, identified further associated pathogens such as non-group A streptococci or A. Baumannii. Based on these crucial fundamental findings a larger amplicon-based study including patients from five different countries has commenced.