Objectives: With conventional microbiological methods significant proportion of middle ear effusion (MEE) proves to be sterile. Accurate molecular biological techniques have been used to identify only pathogen bacteria. Matrix assisted laser desorption and ionization time-of-flight mass spectrometry (MALDI-TOF MS) is an adequate tool to examine samples precisely for wide range of bacterial species simultaneously. The aim of this study is to investigate the frequency and complexity of bacterial flora in MEE in Otitis media with effusion (OME) by MALDI-TOF MS.

Methods: MEE from 40 children with chronic otitis media with effusion were examined for 2000 pathogen, facultative pathogen and non-pathogen bacterial species using MALDI-TOF MS. Two MEE samples from children who underwent cochlear implantation with healthy middle ear were also examined by the same way.

Results: No bacteria were found in healthy control samples and 92.2% of OME samples were positive for at least one bacterium. In 52.5% of samples more than one bacterium was identified. In total 42 bacterial species were found in the middle ear samples. 18.75% of positive samples contained otopathogen bacterium.

Conclusion: MALDI-TOF MS is a suitable tool to identify a wide range of bacterial species in MEE. Results show that bacterial flora of MEE in OME is more diverse and abundant than it was formerly thought. This previously unreported bacterial invasion may help to get closer to the proper understanding and therapy of OME.