201. Longitudinal sinonasal microbiome profiling for identification of bacterial acute exacerbations of chronic rhinosinusitis

Joanna Szaleniec, MD, PhD (otolaryngologist) Jagiellonian University Medical College, Krakow, PL & Sano
Sylwia Bożek, Junior Research Specialist, Structural and Functional Genomics Team, Sano, Krakow, PL

Abstract:

Introduction: The aim of our study was to characterize the poorly explored temporal dynamics of the sinonasal microbiome, particularly during acute rhinosinusitis (ARS) and exacerbations of chronic rhinosinusitis (AECRS). While current literature provides guidelines for the clinical diagnosis of bacterial versus non-bacterial ARS, there is no evidence for differentiating between bacterial and non-bacterial AECRS, and most episodes are treated with antibiotics. 

Material and Methods: In this longitudinal observational study, samples of the sinonasal microbiome were obtained from 55 subjects (36 patients with CRS and 19 healthy volunteers) at regular intervals at baseline, as well as during episodes of ARS, AECRS, and after antibiotic treatment. A total of 293 samples were collected. Microbiological analyses included bacterial culture and full-length 16S rRNA sequencing. To our knowledge, this is the largest longitudinal study of the sinonasal microbiome to date utilizing third-generation sequencing, which enables species-level identification of bacteria. 

Results: Bacterial ARS was characterized by “blooms” (marked dominance) of a single pathogen. Infections with a clinical presentation of viral or post-viral ARS were usually not associated with significant microbiome shifts; however, “blooms” of M. catarrhalis and H. influenzae were sometimes observed. Similar “blooms” were noted in 25% of AECRS cases, while in the remaining 75% no apparent shifts were observed. Interestingly, expansion of pathogens, including S. aureus, was frequently clinically silent. 

Conclusions: Active bacterial infection in the sinuses is characterized by a significant expansion of a single pathogenic species. Some episodes of clinically “viral” or “post-viral” ARS follow the microbiological pattern of bacterial infection but remain self-limiting and do not require antibiotics. Sequencing may provide a valuable tool for differentiating between bacterial and non-bacterial AECRS and reducing the overuse of antibiotics in AECRS. 

About the authors:

Joanna Szaleniec is a specialist in otorhinolaryngology and an endoscopic sinus surgeon, as well as the author and co-author of 57 scientific publications. Since 2007, she has been affiliated with the Jagiellonian University Medical College and the University Hospital in Krakow. Her research on the sinonasal microbiome is conducted in collaboration with Sano Centre for Personalized Computational Medicine.

su.krakow.pl

otolaryngologia.cm-uj.krakow.pl


Sylwia Bożek is a junior research specialist at Structural and Functional Genomics Group at Sano Centre for Personalized Computational Medicine. Her main research interests are human microbiome and its impact on health and disease.

References:

  1. Burdon IA, Psaltis AJ. Changes in the sinus microbiome in health and chronic rhinosinusitis. Curr Opin Otolaryngol Head Neck Surg. 2026 Feb 1;34(1):8-15. doi: 10.1097/MOO.0000000000001087. Epub 2025 Oct 3. PMID: 41076729.
  2. Wagner Mackenzie, B., Chang, K., Zoing, M. et al. Longitudinal study of the bacterial and fungal microbiota in the human sinuses reveals seasonal and annual changes in diversity. Sci Rep 9, 17416 (2019). https://doi.org/10.1038/s41598-019-53975-9
  3. Paramasivan S, Bassiouni A, Shiffer A, Dillon MR, Cope EK, Cooksley C, Ramezanpour M, Moraitis S, Ali MJ, Bleier B, Callejas C, Cornet ME, Douglas RG, Dutra D, Georgalas C, Harvey RJ, Hwang PH, Luong AU, Schlosser RJ, Tantilipikorn P, Tewfik MA, Vreugde S, Wormald PJ, Caporaso JG, Psaltis AJ. The international sinonasal microbiome study: A multicentre, multinational characterization of sinonasal bacterial ecology. Allergy. 2020 Aug;75(8):2037-2049. doi: 10.1111/all.14276. Epub 2020 Mar 30. PMID: 32167574.
  4. Cunningham-Oakes E, Carlisle D, Booth J et al. Implementing portable, real-time 16S rRNA sequencing in the healthcare sector enhances antimicrobial stewardship eBioMedicine, 2026; 129
  5. Szaleniec J, Bezshapkin V, Krawczyk A, Kopera K, Zapala B, Gosiewski T, Kosciolek T. Determinants of the microbiome spatial variability in chronic rhinosinusitis. Rhinology. 2024 Feb 1;62(1):119-126. doi: 10.4193/Rhin22.423. PMID: 38009901.