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.

One limitation of our study was that it was restricted to CAP patients who could produce a sputum specimen. Also, we did not include blood culture or urinary antigen tests. Sputum is a pragmatic, although imperfect, choice of specimen type for the microbiological investigation of CAP. Microscopy for sputum quality is not routinely carried out locally; however, only mucopurulent material was tested, and the cellular content was quantified by human GAPDH gene PCR to rule out salivary specimens. However, sputum that is expectorated from the lower airways will always be at risk of oropharyngeal flora contamination. Despite the limitations, national CAP guidelines [1, 5] recommend sputum investigation for patients admitted to the hospital with moderate to severe CAP, both to aid microbiological diagnosis in order to guide therapy as well as for surveillance. Alternative lower respiratory specimen types such as bronchoalveolar lavage fluids may be expected to be less at risk of contamination, but these require a semi-invasive procedure that is certainly not routine in nonintubated patients.