Quantitative PCR-Based Analysis of Bacterial Profiles in Periapical Lesions and Maxillary Sinus in Odontogenic Sinusitis

Odontogenic sinusitis (ODS) is a common cause of unilateral maxillary sinusitis arising from periapical lesions (PALs) or other dental sources. The infection is typically polymicrobial and dominated by anaerobic bacteria, which are often under detected by routine culture. Molecular approaches such as quantitative polymerase chain reaction (QPCR) and next-generation sequencing (NGS) may provide improved characterization of the microbial burden and community structure. This study aimed to compare culture-based methods, targeted quantitative PCR, and 16S rRNA sequencing in paired samples to characterize microbial composition of ODS and evaluate diagnostic performance. Paired sinus mucosal biopsy (SIN) and periapical lesion (PAL) samples were collected from 28 patients with clinically confirmed ODS. Bacterial detection was performed using conventional culture and targeted QPCR assays for ten clinically relevant taxa. In three randomly selected patients, paired samples were additionally analyzed by 16S rRNA gene amplicon sequencing. Microbial load, taxa richness, and similarity between the two anatomically connected sites were assessed using Wilcoxon signed-rank, McNemar, Jaccard distance, and Bray–Curtis dissimilarity analyses. Results: Culture showed low sensitivity, identifying a limited number of pathogens, primarily Staphylococcus aureus, Streptococcus anginosus, and Fusobacterium nucleatum, in a minority of samples. In contrast, QPCR demonstrated substantially higher detection rates, particularly in PAL samples. Porphyromonas gingivalis (96.8%), Fusobacterium spp. (100.0%), and the S. anginosus group (90.3%) were highly prevalent in PAL specimens, with overlapping but lower detection in SIN samples. PAL samples exhibited significantly higher bacterial loads and taxa richness than paired SIN samples (Wilcoxon p = 0.0004). 16S rRNA sequencing confirmed polymicrobial communities at both sites and identified additional taxa not included in the QPCR panel. Similarity analyses revealed pronounced interindividual variability, ranging from near-identical to highly divergent paired microbiota. Periapical lesions act as reservoirs of predominantly anaerobic bacteria that may seed the maxillary sinus in ODS. Although microbial overlap exists, sinus communities display lower burden and site-specific compositional shifts. Culture-based diagnostics underestimate ODS microbial complexity, whereas combined molecular approaches provide a more comprehensive and clinically informative assessment.