Original Article

Multiplex PCR for lower respiratory tract infection diagnosis in ICU and non-ICU settings: enhancing diagnostic stewardship in Indian tertiary care

Abstract

Background and Objectives: Lower respiratory tract infections (LRTIs) are a leading cause of morbidity and mortality in both ICU and non-ICU patients. Timely identification of causative pathogens and antimicrobial resistance (AMR) genes is critical for optimizing therapy. This study evaluated the diagnostic performance of the BioFire FilmArray Pneumonia Panel (BFPP), a multiplex PCR assay, for pathogen and AMR detection in LRTI cases at a tertiary care hospital in India.
Materials and Methods: A retrospective study was conducted over 29 months (October 2022–February 2025) on 251 respiratory specimens from clinically suspected LRTIs. BFPP was performed for bacterial, viral, and AMR gene detection, with results compared to conventional aerobic bacterial culture. Diagnostic yield, co-infection rates, and concordance were assessed using kappa statistics.
Results: BFPP detected at least one pathogen in 81.7% of samples versus 44.2% by culture, with 55.8% showing polymicrobial infections. Sensitivity was 94.6%, with moderate agreement with culture (κ = 0.428). Among 251 cases, predominant bacteria included Acinetobacter baumannii (29.5%), Klebsiella pneumoniae (24.7%), and Pseudomonas aeruginosa (19.9%). Major viral agents were human rhinovirus/enterovirus (15.1%) and influenza A virus (13.1%). Among 174 AMR-positive cases, blaCTX-M (59.2%), bla-NDM (56.9%), and blaOXA-48 (46.6%) were the most frequently detected resistance genes.
Conclusion: The BioFire FilmArray Pneumonia Panel (BFPP) demonstrated high diagnostic sensitivity of 94.6% and detected pathogens in 81.7% of suspected LRTI cases, compared to 44.2% positivity by conventional culture. BFPP identified 69 additional pathogens missed by culture, enabling earlier targeted therapy and improved diagnostic stewardship in ICU and non-ICU settings.

1. GBD 2016 Lower Respiratory Infections Collaborators. Estimates of the global, regional, and national morbidity, mortality, and aetiologies of lower respiratory infections in 195 countries, 1990-2016: a systematic analysis for the Global Burden of Disease Study 2016. Lancet Infect Dis 2018; 18: 1191-1210.
2. Kumar R, Dar L, Amarchand R, Saha S, Lafond KE, Purakayastha DR, et al. Incidence, risk factors, and viral etiology of community-acquired acute lower respiratory tract infection among older adults in rural north India. J Glob Health 2021; 11: 04027.
3. Satav A, Crow R, Potdar V, Dani V, Satav S, Chadha M, et al. The burden of respiratory syncytial virus in children under 2 years of age in a rural community in Maharashtra, India. Clin Infect Dis 2021; 73(Suppl_3): S238-S247.
4. Webber DM, Wallace MA, Burnham CA, Anderson NW. Evaluation of the BioFire FilmArray Pneumonia Panel for detection of viral and bacterial pathogens in lower respiratory tract specimens in the setting of a tertiary care academic medical center. J Clin Microbiol 2020; 58(7): e00343-20.
5. Enne VI, Aydin A, Baldan R, Owen DR, Richardson H, Ricciardi F, et al. Multicentre evaluation of two multiplex PCR platforms for the rapid microbiological investigation of nosocomial pneumonia in UK ICUs: the INHALE WP1 study. Thorax 2022; 77: 1220-1228.
6. Ginocchio CC, Garcia-Mondragon C, Mauerhofer B, Rindlisbacher C; and the EME Evaluation Program Collaborative. Multinational evaluation of the BioFire FilmArray Pneumonia plus Panel as compared to standard of care testing. Eur J Clin Microbiol Infect Dis 2021; 40: 1609-1622.
7. Wu P, Ling KH. Comparison of FilmArray Pneumonia Panel to routine diagnostic methods and its potential impact in an adult intensive care unit in Hong Kong and the potential role of emergency departments. Hong Kong J Emerg Med 2024; 31: 159-164.
8. Kamel NA, Alshahrani MY, Aboshanab KM, El Borhamy MI. Evaluation of the BioFire FilmArray Pneumonia Panel Plus to the conventional diagnostic methods in determining the microbiological etiology of hospital-acquired pneumonia. Biology (Basel) 2022; 11: 377.
9. Lim YK, Kweon OJ, Kim HR, Kim TH, Lee MK. Impact of bacterial and viral coinfection in community-acquired pneumonia in adults. Diagn Microbiol Infect Dis 2019; 94: 50-54.
10. Zelus CS, Blaha MA, Samson KK, Kalil AC, Van Schooneveld TC, Marcelin JR, et al. Lower respiratory tract coinfection in the ICU: prevalence and clinical significance of coinfection detected via microbiological analysis of bronchoalveolar lavage fluid with a comparison of invasive methodologies. Crit Care Explor 2022; 4(6): e0708.
11. Li M, Wang J, Yao Z, Liao H, Su S, Yang X, et al. Metagenomic-based pathogen surveillance for children with severe pneumonia in pediatric intensive care unit. Front Public Health 2023; 11: 1177069.
12. Shen X, Feng B, Shi W, Cheng W, Zhang T. Concomitant viral and bacterial pneumonia among patients in ICU with mechanical respiratory support. J Infect Dev Ctries 2022; 16: 1482-1489.
13. Heitz M, Levrat A, Lazarevic V, Barraud O, Bland S, Santiago-Allexant E, et al. Metagenomics for the microbiological diagnosis of hospital-acquired pneumonia and ventilator-associated pneumonia (HAP/VAP) in intensive care unit (ICU): a proof-of-concept study. Respir Res 2023; 24: 285.
14. Santella B, Serretiello E, De Filippis A, Folliero V, Iervolino D, Dell’Annunziata F, et al. Lower respiratory tract pathogens and their antimicrobial susceptibility pattern: A 5-year study. Antibiotics (Basel) 2021; 10: 851.
15. Gong J, Yang J, Liu L, Chen X, Yang G, He Y, et al. Correction: Evaluation and clinical practice of pathogens and antimicrobial resistance genes of BioFire FilmArray Pneumonia panel in lower respiratory tract infections. Infection 2024; 52: 705.
16. Lee SH, Ruan SY, Pan SC, Lee TF, Chien JY, Hsueh PR. Performance of a multiplex PCR pneumonia panel for the identification of respiratory pathogens and the main determinants of resistance from the lower respiratory tract specimens of adult patients in intensive care units. J Microbiol Immunol Infect 2019; 52: 920-928.
17. Kakati B, Singh R, Mittal G, Koul N. Comparative performance of BioFire Pneumonia Panel and standard culture-based methods for diagnosing pneumonia in critically ill patients: impact on antibiotic stewardship. Indian J Med Microbiol 2024; 49: 100568.
18. Chambe E, Bortolotti P, Diesnis R, Laurans C, Héquette-Ruz R, Panaget S, et al. Performance and impact on antibiotic prescriptions of a multiplex PCR in a real-life cohort of critically ill patients with suspected ventilated pneumonia: a retrospective monocentric observational study. Antibiotics (Basel) 2023; 12: 1646.
19. Matsuura H, Arimoto K, Takahashi Y, Kishimoto M. Combination of a multiplex pneumonia panel and Gram staining for antimicrobial selection to treat lower respiratory tract infection. Pneumonia (Nathan) 2024; 16: 4.
20. Szymankiewicz MT, Szczepanska A, Stefaniuk E. Evaluation of the BioFire FilmArray Pneumonia plus Panel for detecting bacterial etiological agents of lower respiratory tract infections in an oncologic hospital: comparison with conventional culture method. Pol J Microbiol 2023; 72: 391-398.
21. Escudero D, Fernández-Suárez J, Forcelledo L, Balboa S, Fernández J, Astola I, et al. Evaluation and clinical impact of Biofire FilmArray Pneumonia Panel Plus in ICU-hospitalized COVID-19 patients. Diagnostics (Basel) 2022; 12: 3134.
22. Cojuc-Konigsberg G, Moscona-Nissan A, Guijosa A, Mireles Dávalos CD, Martínez MEJ, Mújica Sánchez MA, et al. Diagnostic accuracy of the BioFire FilmArray Pneumonia Panel in COVID-19 patients with ventilator-associated pneumonia. BMC Infect Dis 2023; 23: 524.
23. Cremet L, Gaborit B, Bouras M, Drumel T, Guillotin F, Poulain C, et al. Evaluation of the FilmArray Pneumonia Plus Panel for rapid diagnosis of hospital-acquired pneumonia in intensive care unit patients. Front Microbiol 2020; 11: 2080.
24. García-Martínez A, Rojo-Gutiérrez L, Llanes-Somellera S, Aguilar-Zapata D. Diagnostic accuracy comparison of the BioFire FilmArray Pneumonia Panel versus routine diagnostic methods for diagnosis of ventilator-associated pneumonia: a real life study. Open Forum Infect Dis 2023; 10(Suppl_2): ofad500.631.
Files
IssueVol 17 No 6 (2025) QRcode
SectionOriginal Article(s)
DOI https://doi.org/10.18502/ijm.v17i6.20360
Keywords
Multiplex polymerase chain reaction Lower respiratory tract infection Antimicrobial resistance Diagnostic stewardship BioFire film array
Rights and permissions
Creative Commons License This work is licensed under a Creative Commons Attribution-NonCommercial 4.0 International License.
How to Cite
1.
Singh R, Kakati B. Multiplex PCR for lower respiratory tract infection diagnosis in ICU and non-ICU settings: enhancing diagnostic stewardship in Indian tertiary care. Iran J Microbiol. 2025;17(6):929-935.