Respiratory pathogens in children with acute lower respiratory infection detected through multiplex real-time PCR

Abstract

Introduction: Acute respiratory infection in children has a high burden of disease. Detection of multiple microorganisms through molecular testing of nasopharyngeal swab samples could change the paradigm of a single pathogen being the cause of respiratory disease in children and prove its usefulness in clinical practice. Objective: To characterize the pathogens identified in nasopharyngeal swab samples by means of multiplex real-time polymerase chain reaction (RT-PCR), as well as clinical variables and laboratory findings in children <5 years diagnosed with acute lower respiratory tract infection (ALRTI) and hospitalized in Bogotá D.C., Colombia. Materials and methods: Cross-sectional study conducted in 81 children hospitalized between September 2019 and March 2020 at the Clínica Cafam and in whom nasopharyngeal swab samples were collected for microbiological identification using the Allplex™ multiplex RT-PCR assay. Correlations between the number of pathogens and blood cells and C-reactive protein levels were determined by Spearman's rank correlation coefficient. Results: Patients’ mean age was 17.23 months (±14.44), 54.32% were males, and 51.85% were young infants. A total of 149 microorganisms (60.40% viruses) were identified in 63 children (77.78%). Mixed infection and coinfection were reported in 48.15% and 11.11% of children, respectively. Regarding clinical findings, shortness of breath, upper airway obstruction, cough, fever and pharyngitis were the most common clinical signs and/or symptoms in patients with mixed infection (32.97%), coinfection (64.40%), mixed infection (29.78%), and absence of microorganism (22.00%), respectively. A negative correlation was observed between the number of leukocytes and the number of neutrophils and the number of microorganisms detected in the preschoolers group (r=-0.46; p=0.058 and r=-0.51; p=0.033, respectively). Furthermore, a positive correlation was found between monocyte count and the number of microorganisms detected (r=0.53; p=0.0096). Conclusion: Multiplex RT-PCR assay allowed the identification of microorganisms in most children, as well as cases of mixed infection and coinfection in more than half of the sample. In addition, clinical findings in these children were highly heterogeneous as per the assay result.