Comprehensive Molecular Testing for Respiratory Pathogens in Community-Acquired Pneumonia

Gadsby, Naomi J.; Russell, Clark D.; McHugh, Martin P.; Mark, Harriet; Conway Morris, Andrew; Laurenson, Ian F.; Hill, Adam T.; Templeton, Kate E.

Bacteria were detected by molecular testing in specimens from 262 (81.1%) patients (Table 2) . When a cutoff of ≥10 5 CFU/mL was applied for assays where bacterial load was quantified, bacteria were detected in specimens from 231 (71.5%) patients. Including respiratory virus results, overall pathogen detection by molecular testing rose to 86.7% (n = 280; Table 2 ). H. influenzae and S. pneumoniae were the most frequently identified bacteria in patients with CAP, detected in 130 (40.2%) and 115 (35.6%) patients, respectively. Detection of more than 1 bacterial species occurred in 102 (31.6%) patients. H. influenzae or S. pneumoniae were present in 94 (92.2%) codetections. Viruses were detected in 98 (30.3%) patients (Table 2) ; rhinovirus was most commonly detected (12.7%, n = 41) followed by influenza A/B (7.1%, n = 23). However, viruses alone were found in only 18 (5.6%) of our patients, with 80 (81.6%) viruses codetected with bacteria ( Table 2 ). The most common combination was rhinovirus with H. influenzae and/or S. pneumoniae in 30 (37.5%) cases.