Value of molecular biology tests in community-acquired acute pneumonia

Abstract

For patients hospitalized with community-acquired acute pneumonia (CAP), molecular tools (especially multiplex PCR syndromic panels) are associated with a significant improvement of microbiological diagnosis yield, compared with conventional methods. Two main families of tests are currently available: targeted viral PCR tests (influenza, SARS-CoV-2, RSV) performed on nasopharyngeal swabs and adapted to epidemic situations; and "upper respiratory tract" (nasopharyngeal) or "lower respiratory tract" (deep swabs) syndromic panels to detect a broad spectrum of viral and bacterial agents, sometimes including resistance genes. These tests are not recommended for routine use in CAP patients treated in ambulatory settings. In hospitalized CAP patients, their use must be guided by severity, epidemic context, and therapeutic implications. "Upper respiratory tract" panels can be useful when an atypical agent or a virus undetected by targeted PCR tests is suspected. "Lower respiratory tract" panels must only be used in case of severe forms or complex situations. Clinical trials showed real diagnostic value but variable clinical impact, which is often limited in the absence of an optimization strategy for the antibiotic therapy. Multiplex PCR syndromic panels represent a promising step forward in the management of patients hospitalized with CAP, but their clinical value still depends on several factors: type of panel and swab, quick results, presence of mobile teams of infectious diseases specialists, and capacity to correctly interpret results to guide treatment decisions.

Keywords: Community-acquired acute pneumonia; Molecular biology; Multiplex PCR; Syndromic panel.