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

Rajender Singh; Barnali Kakati

doi:10.18502/ijm.v17i6.20360

Rajender Singh Department of Microbiology, Himalayan Institute of Medical Sciences, Swami Rama Himalayan University, Jolly Grant, Dehradun, India
Barnali Kakati Department of Microbiology, All India Institute of Medical Sciences, Rishikesh, India

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

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-positivecases, 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 de-tected pathogens in 81.7% of suspected LRTI cases, compared to 44.2% positivity by conventional culture. BFPP identified69 additional pathogens missed by culture, enabling earlier targeted therapy and improved diagnostic stewardship in ICUand non-ICU settings.