Microbes in acute otitis media in Finnish children

Saara Sillanpää Microbes in acute otitis media in Finnish children Department of otorhinolaryngology, University of Tampere Department of Virology, Faculty of Medicine and Life Sciences, University of Tampere Background: Viruses and bacteria contribute to the pathogenesis of acute otitis media (AOM). The prevalence of different bacteria and their antibiotic resistance profile influence the treatment of AOM in clinical practice. The present study addresses the role of different microbes in the pathogenesis of AOM by focusing on the possible role of one virus group, human parechoviruses (HPeV), as well as bacterial pathogens using modern DNA -based diagnostic methods. In addition, the antibiotic resistance of cultivable bacteria was characterised. Methods: Middle ear fluid (MEF) samples, nasal swab samples and stool samples were collected from 87 children (aged 5-42 months) during 100 AOM episodes. HPeV was analysed from all sample types using the sensitive RT-PCR method. Bacterial pathogens from MEF samples were also studied with PCR assays and the whole bacteriome was characterised using modern mass sequencing technologies. Bacterial culture and antibiotic resistance testing were performed for the MEF samples. Results: HPeV was detected in 4/91 (4%) of the MEF samples, 3/98 (3%) of the nasal swab samples and 6/92 (7%) of the stool samples during AOM episodes. In MEF samples, bacterial culture was positive in 41/91 (45%) and the most common cultivated pathogens included H. influenzae in 17/91 (19%), S. pneumoniae in 15/91 (16%) and M. catarrhalis in 8/91 (9%). PCR increased markedly the proportion of samples positive for H. influenzae 30/90 (33%), S. pneumoniae 27/90 (30%) and M. catarrhalis 42/90 (47%). In addition, A. otitidis was detected in 6/90 (7%), S. aureus in 5/90 (6%) and P. aerigunosa in 1/90 (1%) of samples. Next generation sequencing detected bacteria in 76/90 (84%) of samples, but did not reveal new important bacteria. Beta-lactamase production was seen in 4/17 (24%) of the cultivated H. influenzae strains and in 8/8 (100%) of the cultivated M. catarrhalis strains. In addition, 3/15 (20%) of S. pneumoniae strains were intermediately resistant to penicillin. Erythromycin non-susceptibility was seen in 7/15 (47%) of S. pneumoniae and in 8/17 (47%) of H. influenzae strains. Altogether, 4/15 (27%) of S. pneumoniae strains and 6/17 (35%) of H. influenzae strains we non-susceptible to trimethoprim-sulfamethoxazole. Conclusions: HPeVs were associated in the minority of AOM cases. This study showed, for the first time using unbiased analyses of the MEF bacteriome, that the previously reported bacteria H. influenzae, S. pneumoniae and M. catarrhalis are the most prevalent in AOM. Previously unknown bacteria were not detected with mass sequencing. M. catarrhalis was the most common bacteria in MEF according to PCR and mass sequencing results, but often detected in minute quantities, and the clinical importance of this finding has to be answered in further studies. From the clinical point of view, multiresistant or otherwise problematic resistant strains of bacteria were relatively rare in this study population.