Alterations of human skin microbiome and expansion of antimicrobial resistance after systemic antibiotics

Jay Hyun Jo, Catriona P. Harkins, Nicole H. Schwardt, Jessica A. Portillo, Matthew D. Zimmerman, Claire L. Carter, Md Amir Hossen, Cody J. Peer, Eric C. Polley, Véronique Dartois, William D. Figg, Niki M. Moutsopoulos, Julia A. Segre, Heidi H. Kong*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

35 Scopus citations


Although 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 (20 mg or 100 mg), cephalexin, or trimethoprim/sulfamethoxazole], we investigated microbial alterations on skin after administration of systemic antibiotics to healthy human volunteers. Samples from different skin and oral sites, as well as 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 100 mg and trimethoprim/sulfamethoxazole (TMP/SMX) exhibited 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 100 mg or TMP/SMX, respectively. Last, 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.

Original languageEnglish
Article numberabd8077
JournalScience Translational Medicine
Issue number625
StatePublished - 22 Dec 2021
Externally publishedYes


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