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.

A key strength of our study was the availability of quantitative bacterial load outputs in addition to qualitative detection results. Quantification of bacterial DNA load may be important in distinguishing infection from oropharyngeal contamination in sputum. Most molecular work done to date has focused on S. pneumoniae, and a cutoff of 10 4 -10 5 gene copies/mL is typically described as a significance threshold [20, 21, 29, 44] . A cutoff of 10 5 CFU/mL is also generally agreed upon for sputum culture as determined through years of experience. Based on these data, we applied a significance threshold of ≥10 5 CFU/ mL for all bacterial loads, and this did not significantly decrease overall pathogen detection. However, it remains unclear whether a single molecular cutoff is relevant for all bacterial species and whether cutoffs for sputum culture are relevant to sputum PCR. Quantitative molecular tools for many bacterial species are new [32, 33] , and there is a clear need for further exploration of their role. Determination of thresholds for significant and nonsignificant detection are key targets for future work.