Sinonasal and gastrointestinal bacterial composition and abundance are stable after 1 week of once‐daily oral antibiotic treatment for chronic rhinosinusitis

Abstract Background Despite the widespread prescription of antibiotics for the treatment of chronic rhinosinusitis (CRS), their efficacy remains uncertain. Limited penetration of systemic antibiotics into the sinonasal mucosa has been reported previously by this group. This study aimed to investigate the short‐term effects of antibiotics on the sinus and gut microbiota as well as any relationships these had with drug distribution. Methods Thirty subjects undergoing functional endoscopic sinus surgery for CRS were randomized to one of three groups: (1) doxycycline (100 mg daily for 7 days); (2) roxithromycin (300 mg daily for 7 days); and (3) control (no antibiotics given). Sinonasal and stool samples collected before and after treatment were analyzed using 16S ribosomal RNA (rRNA) gene‐targeted amplicon sequencing and Droplet Digital polymerase chain reaction (PCR) for bacterial community composition and the quantification of bacterial DNA, respectively. Results There were no significant major bacterial community shifts or changes to bacterial diversity and load following the treatment period in all patient groups. Non‐significant trend reductions were observed in gut microbial diversity with antibiotics. For the roxithromycin group, sinonasal bacterial diversity was negatively correlated with serum drug levels and reduced overall compared to controls ( p < 0.05). The relative abundance of Staphylococcus ASV129 in sinonasal samples reduced with increasing mucus doxycycline levels ( p = 0.01). Conclusion Antibiotic prescription for CRS should be further investigated because of preliminary evidence of poor sinonasal drug penetration, unproven efficacy, and the potential impact of dysbiosis in the sinuses and off‐target sites. Further studies should consider distinguishing the presence of DNA from viable and nonviable bacteria.