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.

This study demonstrates that the use of a comprehensive multibacterial, multiviral molecular testing approach approximately doubles pathogen detection in patients with CAP from 39.3% to 86.7%, as well as provides valuable information about individual bacterial loads. Testing can be carried out within 1 working day to enable reporting of results in a clinically relevant time-frame, requires only a single LRT specimen, and is not negatively impacted by antibiotic administration prior to sampling. Only limited quantitative molecular bacterial testing has been carried out in a well-defined CAP setting [21, 25, 28, 29, 31] . As our study focused on testing sputum by molecular methods, our high level of pathogen detection for typical bacteria may not be directly comparable to results from other recent studies in hospitalized adult CAP. By combining several methodologies such as serology, culture, antigen detection, and PCR on multiple sample types, etiology was determined in 38%-76% of cases [4, 7, 21, 31, [36] [37] [38] [39] [40] [41] . Atypical bacteria were uncommon in our cohort (<5% patients), but it was not an epidemic period for M. pneumoniae [42] . Viruses were detected in approximately one third of patients, which is in agreement with the 13%-56% range reported in previous studies; influenza was also detected at comparable levels (<10%) [4, 7, 21, 31, 36, 38, 39, 43 ]. Although we were not able to test controls, viral detections by PCR from the upper respiratory tract have been found to be rare in asymptomatic adults compared with those with CAP in a recent study [43] .