The shared microbiota of humans and companion animals as evaluated from Staphylococcus carriage sites

Staphylococcus aureus and other coagulase-positive staphylococci (CPS) may colonize skin and mucous membrane sites and cause skin and soft tissue infections (SSTI) in humans and animals. Factors that modulate colonization and infection by methicillin-resistant S. aureus (MRSA) in humans remain unclear, including the role of the greater microbial community and environmental factors such as contact with companion animals. In the context of a parent study evaluating the households of outpatients with community MRSA SSTI, the objectives of this study were: 1) to characterize the microbiota that colonizes typical coagulase-positive Staphylococcus spp. (CPS) carriage sites in humans and their companion pets; 2) to analyze associations between Staphylococcus infection/carriage and the composition and diversity of microbial communities; and 3) to analyze factors that influence sharing of microbiota between pets and humans. We enrolled 25 households containing 56 pets and 30 humans. Sampling locations were matched to anatomical sites cultured by the parent study for MRSA (people) or CPS (pets). Microbiota were characterized using culture-independent sequencing of bacterial 16S ribosomal RNA (rRNA) genes. Pets were colonized with a greater relative abundance of Proteobacteria, whereas people were colonized with greater relative abundances of Firmicutes and Actinobacteria. MRSA carriage in the human nares as determined by cultures was associated with microbiota of the inguinal crease/axilla, but not the nares. Household membership was strongly associated with microbial communities, in both humans and pets, and humans in houses with no pets were more similar to each other than humans in pet-owning households.