Title : Characterization of respiratory viral infections in immunocompromised cancer and bone marrow transplant patients by multiplex syndromic PCR: A retrospective analysis from a comprehensive cancer centre in Western India
Abstract:
Background: Respiratory viral infections are a significant cause of morbidity and mortality in immunocompromised cancer and bone marrow transplant patients. Infections in this population are often more severe, atypical, and rapidly progressive. As different microbial pathogens can cause similar clinical symptoms, identifying the causative agent based on symptoms alone is challenging. This often leads to empiric antibiotic use and contributes to the development of antibiotic resistance. Rapid diagnostic tests for pathogen identification are therefore crucial for guiding appropriate treatment. The BioFire Film Array Multiplex PCR Respiratory Panel is one such diagnostic tool for rapid detection of respiratory pathogens. This study aimed to characterize the common respiratory viruses causing infections in cancer and bone marrow transplant patients.
Methods: This was a retrospective, laboratory-based observational study conducted from January 2024 to December 2025. Nasopharyngeal/oropharyngeal swabs in viral transport medium, collected from patients with suspected upper respiratory tract infections, were received in the Microbiology laboratory. Samples were processed on the BioFire film Array Multiplex Syndromic PCR Respiratory Panel as per the manufacturer’s instructions. The panel detects 15 respiratory viruses and 5 bacterial pathogens with a turnaround time of approximately 1 hour.
Results: A total of 805 samples were analysed. Respiratory pathogens were detected in 674 samples, while 151 samples were negative. Of the 674 positive samples, 670 were viruses and 4 were bacterial pathogens: Mycoplasma pneumoniae (n=3) and Chlamydia pneumoniae (n=1). The most common viruses were Human rhinovirus/Enterovirus (238), respiratory Syncytial Virus (99), Parainfluenza virus type 3 (92), severe acute respiratory syndrome coronavirus 2 (42) Influenza A H1-2009 (26), Corona virus OC43 (26), Adenovirus (23) and 101 others like Influenza A H1-2010, Corona virus NL63, Influenza B, Influenza AH3, Parainfluenza virus 1, Coronavirus 229E, Coronavirus HKU 1, Parainfluenza virus 2 and Parainfluenza virus 4.The top 7 viruses accounted for ∼70% of all pathogens detected. Bacterial pathogens constituted only 0.59% of detections.
Conclusion: Respiratory viruses were detected in 83.7% of all samples tested. Human Rhinovirus/Enterovirus, RSV, and Parainfluenza virus type 3 were the most common pathogens in this immunocompromised cohort. Bacterial co-infections were rare. The BioFire Multiplex PCR panel enables rapid identification of 15 respiratory viruses within ∼1 hour, facilitating timely clinical decision-making and helping to reduce unnecessary antibiotic prescriptions. "Characterizing viral epidemiology in this cohort can guide infection control and prophylaxis strategies."
