Comparative Approaches to Microbial Profiling in Odontogenic Sinusitis with Periapical Lesions

Background Odontogenic sinusitis (ODS) is a common cause of unilateral maxillary sinusitis, and it arises from periapical lesions (PAL) or other odontogenic foci. This infection is polymicrobial and anaerobe-rich, thus standard culture methods often underestimate its diversity. Molecular techniques such as quantitative polymerase chain reaction (QPCR) and next-generation sequencing (NGS) may better characterize the microbial burden and composition. Methods Paired sinus mucosal biopsy (SIN) and the tissue scrapings from periapical lesion (PAL) specimens were collected from 28 patients with ODS. Bacterial detection was performed using conventional culture, and QPCR targeting ten clinically relevant taxa. For paired sampled from three randomly selected patients 16S rRNA amplicon sequencing was performed. Microbial load, taxa richness, and the similarity of bacterial communities between the two anatomically connected sites were compared across the molecular methods. Statistical analysis included the Wilcoxon signed-rank, McNemar, and Bray–Curtis dissimilarity testing. Results Culture yielded low detection rates, identifying only a limited set of pathogens ( Staphylococcus aureus , Streptococcus anginosus , and Fusobacterium nucleatum ) in a minority of samples. In contrast, QPCR demonstrated significantly higher detection frequencies, particularly in PAL specimens. Porphyromonas gingivalis (96.8%), F. nucleatum (90.3%), and the S. anginosus group (90.3%) were highly prevalent in PAL, while SIN samples showed lower but overlapping positivity (89.3%, 67.9%, and 50.0%, respectively). Overall, PAL samples harbored significantly higher bacterial loads and taxa richness than SIN specimens (Wilcoxon p = 0.0004). 16S rRNA amplicon sequencing confirmed the presence of polymicrobial communities in both sites and revealed additional taxa beyond those included in the QPCR panel. Jaccard distance and Bray–Curtis analyses revealed patient-specific overlap: some PAL and SIN pairs shared nearly identical microbiota, while others exhibited marked divergence. Conclusions PALs represent a reservoir of mostly anaerobic bacterial species that may translocate into the maxillary sinus, establishing ODS. While there is overlap in bacterial communities, sinus samples exhibit a lower burden and site-specific shifts in taxa composition. Culture alone underestimates ODS microbial complexity, whereas QPCR and 16S rRNA amplicon sequencing provide much deeper insights. Combined molecular approaches are essential for accurate pathogen detection and for guiding effective management of ODS.