A Research Framework for Evaluating Next Generation Sequencing in Community-Acquired Pneumonia

Rapid diagnostic technologies are revolutionizing the clinical microbiology laboratory. Next generation sequencing (NGS) is poised to be the next powerful tool in standard clinical laboratories building on the widespread adoption of multiplex polymerase chain reaction (PCR) panels and matrix-assisted laser desorption/ionization-time of flight (MALDITOF) technology.[1] NGS can provide a quantitative analysis of all non-human DNA or RNA in a sample without requiring growth on a traditional medium. This improves the diagnostic yield of infections that are difficult to culture due to biofilm production, such as prosthetic joint infections.[2] As these technologies become faster and cheaper, research efforts are urgently needed to guide clinicians to wider applications of NGS, including use in non-sterile sites, such as lower and upper respiratory tract samples. The diagnostic utility of NGS of respiratory samples has already been noted in cases of pneumonia caused by pathogens that are difficult to identify through conventional testing.[3, 4] However, the use of NGS as a diagnostic tool in community-acquired pneumonia (CAP) remains to be elucidated. The characterization of the respiratory microbiome in clinical practice may improve the diagnosis and therefore the treatment of CAP. However, without adequate research, using NGS in patients with suspected CAP may unnecessarily accelerate antimicrobial prescribing simply by providing the names of all commensal organisms present in a respiratory sample.