Rapid multiplex polymerase chain reaction for the detection of respiratory pathogens in pediatric patients under 5 years of age: a single center study
DOI:
https://doi.org/10.18203/2349-3291.ijcp20262946Keywords:
Acute respiratory tract infections, FilmArray respiratory panel, Real-time RT-PCR, Respiratory pathogens, Nasopharyngeal swabAbstract
Background: Acute respiratory tract infections (ARTIs) are leading causes of morbidity and mortality in children under 5 years, with similar clinical presentations making pathogen identification challenging. The objective of this study is to rapidly detect the causative organism of acute upper respiratory tract infection using the FilmArray respiratory panel 2.1 plus (FARP).
Methods: A cross-sectional prospective study was conducted at the Bangladesh Institute of Tropical and Infectious Diseases from September 2024 to February 2025. Nasopharyngeal swab specimens were collected from 60 pediatric patients (≤5 years) presenting with ARTI symptoms within 7 days of onset. Samples were analyzed using FARP 2.1 plus, capable of detecting 19 viruses and 4 atypical bacteria within 45 minutes.
Results: The cohort comprised 35 males (58.33%) and 25 females (41.67%) with a mean age of 20±17 months. The diagnostic yield was 95% (57/60). Human rhinovirus/enterovirus was most prevalent (53.3%), followed by respiratory syncytial virus (43.3%) and adenovirus (33.3%). mixed infections predominated, occurring in 55% of cases, with rhinovirus/enterovirus and RSV being the most common combination (21.2%). Age-stratified analysis revealed higher rhinovirus/enterovirus prevalence in infants <1 year (68.1%) compared to children 1-5 years (44.7%).
Conclusions: FilmArray demonstrated excellent diagnostic performance with high pathogen detection rates and revealed complex coinfection patterns in pediatric ARTI. The predominance of mixed infections and age-specific pathogen distributions emphasizes the importance of comprehensive molecular diagnostics for optimal clinical management and infection control strategies in pediatric respiratory medicine.
References
World Health Organization. World Health Statistics 2010. 2010. Available at: https://www.who.int/ publications/i/item/9789241563987. Accessed on 15 May 2026.
GBD 2019 Chronic Respiratory Diseases Collaborators. Global burden of chronic respiratory diseases and risk factors, 1990-2019: an update from the Global Burden of Disease Study 2019. EClinicalMedicine. 2023;59:101936.
Foulongne V, Guyon G, Rodière M, Segondy M. Human metapneumovirus infection in young children hospitalized with respiratory tract disease. Pediatr Infect Dis J. 2006;25(4):3549.
Wolf DG, Greenberg D, Kalkstein D, Shemer-Avni Y, Givon-Lavi N, Saleh N, et al. Comparison of human metapneumovirus, respiratory syncytial virus and influenza A virus lower respiratory tract infections in hospitalized young children. Pediatr Infect Dis J. 2006;25(4):3204.
Liu WK, Liu Q, Chen DH, Liang HX, Chen XK, Chen MX, et al. Epidemiology of acute respiratory infections in children in Guangzhou: a three-year study. PLoS One. 2014;9(5):e96674.
Bhuyan GS, Hossain MA, Sarker SK, Rahat A, Islam MT, Haque TN, et al. Bacterial and viral pathogen spectra of acute respiratory infections in under-5 children in hospital settings in Dhaka city. PloS One. 2017;12(3):e0174488.
Cillo´niz C, Dominedò C, Torres A. Multidrug resistant gram-negative bacteria in community-acquired pneumonia. Annual Update in Intensive Care and Emergency Medicine 2019. 2019;p.459-75.
Barenfanger J, Drake C, Leon N, Mueller T, Troutt T. Clinical and financial benefits of rapid detection of respiratory viruses: an outcomes study. J Clin Microbiol. 2000;38(8):2824-8.
Mahony JB, Blackhouse G, Babwah J, Smieja M, Buracond S, Chong S, et al. Cost analysis of multiplex PCR testing for diagnosing respiratory virus infections. J Clin Microbiol. 2009;47(9):2812-7.
Tsuchiya LR, Costa LM, Raboni SM, Nogueira MB, Pereira LA, Rotta I, et al. Viral respiratory infection in Curitiba, Southern Brazil. J Infect. 2005;51:401-7.
Leland DS, Ginocchio CC. Role of cell culture for virus detection in the age of technology. Clin Microbiol Rev. 2007;20:49-78.
Zumla A, Al-Tawfiq JA, Enne VI, Kidd M, Drosten C, Breuer J, et al. Rapid point of care diagnostic tests for viral and bacterial respiratory tract infections-needs, advances, and future prospects. Lancet Infect Dis. 2014;14:1123.
Liao RS, Tomalty LL, Majury A, Zoutman DE. Comparison of viral isolation and multiplex real-time reverse transcription-PCR for confirmation of respiratory syncytial virus and influenza virus detection by antigen immunoassays. J Clin Microbiol. 2009;47:527-32.
Nolte FS, Marshall DJ, Rasberry C, Schievelbein S, Banks GG, Storch GA, et al. MultiCodePLx system for multiplexed detection of seventeen respiratory viruses. J Clin Microbiol. 2007;45:2779-86.
Huang HS, Tsai CL, Chang J, Hsu TC, Lin S, Lee CC. Multiplex PCR system for the rapid diagnosis of respiratory virus infection: systematic review and meta-analysis. Clin Microbiol Infect. 2018;24:1055-63.
Yang S, Rothman RE. PCR-based diagnostics for infectious diseases: uses limitations, and future applications in acute-care settings. Lancet Infect Dis. 2004;4:337-48.
Poritz MA, Blaschke AJ, Byington CL, Meyers L, Nilsson K, Jones DE, et al. FilmArray, an automated nested multiplex PCR system for multi-pathogen detection: development and application to respiratory tract infection. PLoS One. 2011;6(10):e26047.
Biomerieux. BioFire® Respiratory Panel 2.1-EZ (RP2.1-EZ). Available at: https://www.biomerieux. com/us/en/our-offer/clinical-products/biofire-respiratory-panels.html. Accessed on 15 May 2026.
Mahony JB. Detection of respiratory viruses by molecular methods. Clin Microbiol Rev. 2008;21(4):716-47.
Brendish NJ, Malachira AK, Armstrong L, Houghton R, Aitken S, Nyimbili E, et al. Routine molecular point-of-care testing for respiratory viruses in adults presenting to hospital with acute respiratory illness (ResPOC): a pragmatic, open-label, randomised controlled trial. Lancet Respir Med. 2017;5(5):401-11.
Rhedin S, Lindstrand A, Rotzén-Östlund M, Tolfvenstam T, Ohrmalm L, Rinder MR, et al. Clinical utility of PCR for common viruses in acute respiratory illness. Pediatrics. 2014;133(3):e538-45.
Popowitch EB, O'Neill SS, Miller MB. Comparison of the Biofire FilmArray RP, Genmark eSensor RVP, Luminex xTAG RVPv1, and Luminex xTAG RVP fast multiplex assays for detection of respiratory viruses. J Clin Microbiol. 2013;51(5):1528-33.
Jain S, Williams DJ, Arnold SR, Ampofo K, Bramley AM, Reed C, et al. Community-acquired pneumonia requiring hospitalization among U.S. children. N Engl J Med. 2015;372(9):835-45.
Shi T, McAllister DA, O'Brien KL, Simoes EAF, Madhi SA, Gessner BD, et al. Global, regional, and national disease burden estimates of acute lower respiratory infections due to respiratory syncytial virus in young children in 2015: a systematic review and modelling study. Lancet. 2017;390(10098):946-58.
Jartti T, Lehtinen P, Vuorinen T, Osterback R, van den Hoogen B, Osterhaus AD, et al. Respiratory picornaviruses and respiratory syncytial virus as causative agents of acute expiratory wheezing in children. Emerg Infect Dis. 2004;10(6):1095-101.
Peltola V, Waris M, Österback R, Susi P, Ruuskanen O, Hyypiä T. Rhinovirus transmission within families with children: incidence of symptomatic and asymptomatic infections. J Infect Dis. 2008;197(3):382-9.
Asner SA, Science ME, Tran D, Smieja M, Merglen A, Mertz D. Clinical disease severity of respiratory viral co-infection versus single viral infection: a systematic review and meta-analysis. PLoS One. 2014;9(6):e99392.
Goka EA, Vallely PJ, Mutton KJ, Klapper PE. Single, dual and multiple respiratory virus infections and risk of hospitalization and mortality. Epidemiol Infect. 2015;143(1):37-47.
Martin ET, Kuypers J, Wald A, Englund JA. Multiple versus single virus respiratory infections: viral load and clinical disease severity in hospitalized children. Influenza Other Respir Viruses. 2012;6(1):71-7.
Scotta MC, Chakr VC, de Moura A, Becker RG, de Souza AP, Jones MH, et al. Respiratory viral coinfection and disease severity in children: A systematic review and meta-analysis. J Clin Virol. 2016;80:45-56.
Harada Y, Kinoshita F, Yoshida LM, Minh le N, Suzuki M, Morimoto K, et al. Does respiratory virus coinfection increases the clinical severity of acute respiratory infection among children infected with respiratory syncytial virus? Pediatr Infect Dis J. 2013;32(5):441-5.
Varela FH, Sartor ITS, Polese-Bonatto M, Azevedo TR, Kern LB, Fazolo T, et al. Rhinovirus as the main co-circulating virus during the COVID-19 pandemic in children. J Pediatr (Rio J). 2022;98(6):579-86.
Pierangeli A, Gentile M, Di Marco P, Pagnotti P, Scagnolari C, Trombetti S, et al. Detection and typing by molecular techniques of respiratory viruses in children hospitalized for acute respiratory infection in Rome, Italy. J Med Virol. 2007;79(4):463-8.
Kusel MM, de Klerk NH, Kebadze T, Vohma V, Holt PG, Johnston SL, et al. Early-life respiratory viral infections, atopic sensitization, and risk of subsequent development of persistent asthma. J Allergy Clin Immunol. 2007;119(5):1105-10.
Nair H, Nokes DJ, Gessner BD, Dherani M, Madhi SA, Singleton RJ, et al. Global burden of acute lower respiratory infections due to respiratory syncytial virus in young children: a systematic review and meta-analysis. Lancet. 2010;375(9725):1545-55.
Lynch JP 3rd, Kajon AE. Adenovirus: Epidemiology, Global Spread of Novel Serotypes, and Advances in Treatment and Prevention. Semin Respir Crit Care Med. 2016;37(4):586-602.
Williams JV, Harris PA, Tollefson SJ, Halburnt-Rush LL, Pingsterhaus JM, Edwards KM, et al. Human metapneumovirus and lower respiratory tract disease in otherwise healthy infants and children. N Engl J Med. 2004;350(5):443-50.
Michelow IC, Olsen K, Lozano J, Rollins NK, Duffy LB, Ziegler T, et al. Epidemiology and clinical characteristics of community-acquired pneumonia in hospitalized children. Pediatrics. 2004;113(4):701-7.
Downloads
Published
How to Cite
Issue
Section
