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

Sep 29, 2026

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Lower respiratory tract infections are a major cause of morbidity and mortality in both ICU and non-ICU patients, making rapid pathogen identification and antimicrobial resistance (AMR) detection essential for optimizing therapy. This retrospective study evaluated the BioFire FilmArray Pneumonia Panel (BFPP) using 251 respiratory specimens collected over 29 months. BFPP performance was compared with conventional aerobic culture, assessing diagnostic yield, co-infection rates, and concordance to guide stewardship.

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Abstract

Introduction

Materials and Methods

| | RIGINAL ARTICLE | | --- | --- | | | O | Volume 17 Number 6 (December 2025) 929-935 DOI: [http://doi.org/10.18502/ijm.v17i6.20360](http://doi.org/10.18502/ijm.v17i6.20360) Multiplex PCR for lower respiratory tract infection diagnosis in ICU and non-ICU settings: enhancing diagnostic stewardship in Indian tertiary care Rajender Singh1*, Barnali Kakati2 1Department of Microbiology, Himalayan Institute of Medical Sciences, Swami Rama Himalayan University, Jolly Grant, Dehradun, India 2Department of Microbiology, All India Institute of Medical Sciences, Rishikesh, India Received: August 2025, Accepted: September 2025 showing cases, Pseudomonas 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% polymicrobial infections. Sensitivity was 94.6%, with moderate agreement with culture (κ = 0.428) . Among 251 predominant bacteria included Acinetobacter baumannii (29.5%), Klebsiella pneumoniae (24.7%), and 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. Keywords: Multiplex polymerase chain reaction; Lower respiratory tract infection; Antimicrobial resistance; Diagnostic stewardship; BioFire film array INTRODUCTION Lower respiratory tract infections (LRTIs) continue to be one of the most significant global health concerns, especially in low- and middle-income countries such as those in South Asia. (1). The Global Burden of Disease (GBD) 2019 report highlighted that India experiences an exceptionally high burden of LRTIs, with more than 2.7 million cases and over 600,000 deaths each year, ranking among the lead- *Corresponding author: Rajender Singh, MBBS, MD, Department of Microbiology, Himalayan Institute of Medical Sciences, Swami Rama Himalayan University, Jolly Grant, Dehradun, India. Tel: +91-9997358899 [Email: panwar.rajendra@gmail.com](Email: panwar.rajendra@gmail.com) Copyright © 2025 The Authors. Published by Tehran University of Medical Sciences. This work is licensed under a Creative Commons Attribution-Non Commercial 4.0 International license ([https://creativecommons.org/licenses/by-nc/4.0/](https://creativecommons.org/licenses/by-nc/4.0/)). Noncommercial uses of the work are permitted, provided the original work is properly cited. ing infectious causes of death in both children and adults (1). A community-based cohort study in rural north India reported an LRTI incidence of 248 per 1,000 person-years and LRTI-associated hospitalization rates of 12.7 per 1,000 person-years among older adults, underscoring

FAQs

What diagnostic approach did the study evaluate for LRTIs in ICU and non-ICU settings?

The study evaluated the BioFire FilmArray Pneumonia Panel (BFPP), a multiplex PCR assay, for detecting pathogens and AMR genes directly from respiratory specimens.

How did BFPP diagnostic yield compare with conventional aerobic culture?

BFPP detected at least one pathogen in 81.7% of samples, compared with 44.2% positivity by conventional culture.

Which AMR genes were most frequently detected among AMR-positive cases?

Among 174 AMR-positive cases, the most frequently detected resistance genes were blaCTX-M (59.2%), bla-NDM (56.9%), and blaOXA-48 (46.6%).

Sep 29, 2026

Uploaded by nayy☆