Whole-genome sequencing of Staphylococcus spp. isolated from antibiotics treated healthy human subjects Raw sequence reads. Staphylococcus

While systemic antibiotics are critical in controlling infections and reducing morbidity and mortality, overuse of antibiotics is presumed to contribute to negative repercussions such as selection of antimicrobial-resistant organisms and collateral damage to commensal microbes. In a prospective, randomized study of four clinically relevant antibiotic regimens [doxycycline (20mg or 100mg), cephalexin, or trimethoprim/sulfamethoxazole], we investigated microbial alterations on skin following administration of systemic antibiotics to healthy human volunteers. Samples from different skin and oral sites and stool were collected before, during, and up to 1 year after antibiotic use, and shotgun metagenomic sequencing was performed. Taxonomic analysis showed that subjects receiving doxycycline 100mg and TMP/SMX exhibited significantly greater changes to their skin microbial communities, as compared to those receiving other regimens, or untreated controls. Oral and stool microbiota also demonstrated fluctuations after antibiotics. Bacterial culturing in combination with whole-genome sequencing revealed specific emergence, expansion, and persistence of antibiotic-resistant staphylococci, harboring tetK or tetL and dfrC or dfrG genes, in all subjects who received doxycycline 100mg and TMP/SMX, respectively. Finally, analysis of metagenomic data revealed an increase of genes involved in gene mobilization, indicating stress responses of microbes to antibiotics. Collectively, these findings demonstrate direct, long-lasting effects of antibiotics on skin microbial communities, highlighting the skin microbiome as a site for the development and persistence of antibiotic resistance and the risks of overprescribing.