Bacterial pathogens in chronic and recurrent tonsillitis: surface vs. core tonsillar microbiota assessed by MALDI-TOF mass spectrometry

The aetiology of chronic tonsillitis (CT) remains incompletely characterised, and surface tonsillar swab culture may not accurately reflect the microbiota of deeper tonsillar tissue. We aimed to identify bacterial pathogens in CT by three-site intraoperative sampling, compare surface and core microbiological findings, evaluate the diagnostic utility of antistreptolysin O (ASO) and anti-DNase B titres, and characterise antibiotic susceptibility profiles. A prospective observational study enrolled 110 CT patients undergoing tonsillectomy. Samples were collected from the tonsillar surface and core under aerobic conditions, and from the core under anaerobic conditions. Organisms were identified by MALDI-TOF mass spectrometry. Paired comparisons (surface vs. core) were performed using McNemar’s test with Bonferroni correction. Antibiotic susceptibility was interpreted according to EUCAST 2025 breakpoints. Among 106 cultured bacterial species, 14 were classified as potentially pathogenic; at least one pathogen was confirmed in 108 patients (98.2%). Staphylococcus aureus was the most frequently isolated organism (60.0%), followed by Streptococcus pneumoniae (58.2%) and Streptococcus anginosus (44.5%); Streptococcus pyogenes was detected in only 9.1% of patients. Combined-core prevalence was significantly higher than surface prevalence for S. aureus , S. pneumoniae , S. anginosus , and H. influenzae (all p < 0.001 after Bonferroni correction); surface and combined-core findings were discordant in 82.7% of patients, with pathogens recovered exclusively from the combined core in 21.8%. Erythromycin resistance was observed in 30.8% of S. aureus , 33.3% of S. anginosus , and 20.0% of S. pneumoniae isolates. Neither ASO nor anti-DNase B predicted fulfilment of the Paradise criteria on logistic regression; anti-DNase B positivity was associated with S. pyogenes recovery from the tonsillar surface. Surface swab culture substantially underestimates the bacteriological complexity of CT. Core sampling with anaerobic culture conditions provides a more complete microbiological assessment. The observed macrolide resistance supports susceptibility-guided use of erythromycin, particularly when it is considered as an alternative in patients with beta-lactam allergy. ASO and anti-DNase B should be interpreted in the context of clinical suspicion for recent streptococcal infection rather than as universal CT markers.