The frequency of detected pathogen genomes in children with acute respiratory infections

Due to the high prevalence of acute respiratory infections in children, it was of interest to determine the composition of bacterial and viral-bacterial associations for respiratory tract inhabiting microorganisms. To identify respiratory tract pathogens, especially viruses and unculturable bacteria, it is advisable to use molecular genetic research methods particularly PCR. The work was aimed at comparatively analyzing rate of genome detection for respiratory tract pathogens in children with acute respiratory infections and apparently healthy controls. Materials and methods. Children (97 people) were examined, of which 35 people — with acute respiratory infections of the upper respiratory tract (nasopharyngitis, pharyngitis, laryngitis) (ARI URT), 32 people — with acute respiratory infections of the lower respiratory tract (acute bronchitis, acute obstructive bronchitis) (ARI NDP) and 30 people — apparently healthy control at the time of examination. RNA and DNA of viral and bacterial pathogens were assessed in the oropharyngeal smears using PCR. Test systems produced by the Federal Budgetary Institution Central Research Institute of Epidemiology of Rospotrebnadzor and JSC Vector-Best were used. Results. An analysis of detection rate for DNA and RNA of bacterial and viral pathogens showed the presence of a wide range of them (20 different species/strains out of 27 identified) in oropharyngeal biomaterial from all examined children. The peak diversity and detection rate of pathogen genomes were found in apparently healthy subjects and children with ARI UDP (DNA of members from Herpesviridae family, S. pneumoniae, H. influaenzae, MSSA, MRCoNS). Associations of 4–6 pathogens prevailed in the microflora, and the “core” of both bacterial and viral-bacterial associations was the combination of S. pneumoniae and H. influenzae (in 93.3% and 60.0% of cases, respectively). In bacterial associations, staphylococci (MRSA and MRCoNS) and P. aeruginosa were also detected in healthy children, MSSA and other very rarely bacterial types were detected in children with ARI UDP. In children with NPD infections, the majority of whom (75.0±7.7%) were classified as long-term ill and had a complicated disease course, a noticeable depletion (decrease in taxonomic diversity) of the nasopharyngeal microbiota was found. Conclusion. The presented data indicate the presence in the biomaterial of the examined children of molecular genetic markers of a wide range of pathogens presented as viral-bacterial and bacterial associations, with varying composition being related to patient clinical status. Detection of pathogen genomes is important for choosing proper etiotropic therapy at early disease stages as well as prescribing probiotic drugs that can restore a balance in respiratory tract microflora.