Use of the BIOFIRE® FILMARRAY® Pneumonia plus Panel to characterize the etiology of lower respiratory tract infections among hospitalized patients in Southern Province, Sri Lanka.

Abstract

Background: Lower respiratory tract infections (LRTIs) account for a heavy burden of illness in low- and middle-income country settings, but the etiology of these infections is often unknown. In this study, we applied the BIOFIRE^® FILMARRAY^® Pneumonia plus Panel, a multiplex polymerase chain reaction assay with bacterial, viral, and antibacterial resistance gene targets, on sputum samples to evaluate the etiology of community-acquired LRTI among hospitalized patients in southern Sri Lanka.

Methods: We enrolled children and adults hospitalized with LRTIs at a public tertiary care hospital in southern Sri Lanka from 2019 to 2021. Demographic and clinical data were collected, and a sputum sample for each patient was tested using the Pneumonia plus Panel. Assay results were compared with sputum culture results. Fisher's exact test was applied to identify association between the presence of viruses, bacteria, or antimicrobial resistant genes and the findings of the chest radiographs during hospitalization as well as associations between the genomic concentration identified through the panel and the bacteria known to cause typical pneumonia infection included in the panel.

Results: In 267 patients tested, the most detected bacteria by the Pneumonia plus Panel were the Klebsiella pneumoniae group (41.9%), Staphylococcus aureus (34.5%), and the Acinetobacter calcoaceticus-baumannii complex (32.6%). The most detected viruses were the human rhinovirus/enterovirus (19.5%) and influenza A (10.9%). In total, 211 patients (79.0%) had at least one gram-negative bacterium and 139 patients (52.1%) had at least one gram-positive bacteria. As for Antimicrobial Resistance, 96 patients (40.0%) had at least one carbapenem resistant gene, 56 patients (21.0%) had an extended spectrum beta-lactamase related gene, and 42 patients (15.7%) had a methicillin resistant gene. Only 15 patients (5.6%) were identified to have Pneumonia plus Panel results matching with sputum culture results.

Conclusions: Our findings suggest that patients with LRTI in Southern Province, Sri Lanka have a high prevalence of gram-negative bacteria and antibacterial resistance in their sputum samples. However, it remains difficult to differentiate isolates that are colonizers not leading to disease versus the true cause of infection via the use of the BIOFIRE^® FILMARRAY^® Pneumonia plus Panel on sputum samples.