Microorganisms in respiratory tract of patients diagnosed with atypical pneumonia: results of a research based on the use of reverse transcription polymerase chain reaction (RT-PCR) DNA microarray method and enzyme-linked immunosorbent assay.

Tokman, Hrisi Bahar; Aslan, Mustafa; Ortaköylü, Gönenç; Algingil, Reyhan Calişkan; Yüksel, Pelin; Karakullukçu, Asiye; Kalayci, Fatma; Saribaş, Suat; Cakan, Hüseyin; Demir, Tuncalp; Kocazeybek, Bekir S

BACKGROUND Numerous molecular-based tests were applied for the laboratory-based diagnosis of viruses. In this cross-sectional case control study, in addition to bacteria, we aimed to determine respiratory viruses using, for the first time in our country, the Reverse Transcription PCR DNA Microarray method, and we also aimed to evaluate its diagnostic performance. METHODS Respiratory viruses were investigated from nasopharyngeal swabs of 76 patients diagnosed with atypical pneumonia and 64 healthy controls using the CLART Pneumovir (Genomica, Spain) kit and from 10 mL blood samples of the same subjects. M. pneumoniae IgM was detected by ELISA and L. pneumophila IgM and C. pneumoniae IgM by indirect immunofluorescence. Person's chi-square test was used for statistical analysis. RESULTS Our results showed that the specificity (100%) and the positive predictive value (100%) of the CLART Pneumovir kit were high, but its sensitivity (53%), its negative predictive value (64%), and its kappa value (50%) were low. Parainfluenza Virus type 3 and M. pneumoniae were found alone or together as the most common microorganisms while no cases of human bocavirus, adenovirus, rhinovirus, or coronavirus were detected. CONCLUSIONS Our results demonstrated that, during the study period, most of our patients had atypical pneumonia due to Parainfluenza Virus type 3 and M. pneumoniae co-infection.