Rapid Molecular Diagnostics for Lower Respiratory Tract Infections

Barbara D. Alexander, MD, MHS; Kimberly E. Hanson, MD, MHS; Adriana E. Rosato, PhD; David B. Nash, MD; Maren S. Fragala, PhD; Steven E. Goldberg, MD, MBA • Published: April 28, 2025 • Last Reviewed: March, 2026

A new manuscript published in Journal of Urgent Care Medicine, co-authored by esteemed experts and advisory board members, describes how molecular diagnostics for lower respiratory tract infections fills a selective gap in urgent care medicine.

Authors include Barbara D. Alexander, MD, MHS; Kimberly E. Hanson, MD, MHS; Adriana E. Rosato, PhD; David B. Nash, MD; Maren S. Fragala, PhD; Steve Goldberg, MD, MBA

Lower respiratory tract infections (LRTIs), including community-acquired pneumonia, are a leading cause of hospitalization and mortality in the United States.

In many clinical settings—especially urgent care—diagnosis is often based on empiric treatment, meaning providers treat based on the most likely pathogen rather than confirmed identification. This approach can lead to:

• Diagnostic uncertainty
• Inappropriate treatment
• Unnecessary antibiotic use

Rapid molecular diagnostics help address this gap by enabling earlier and more accurate pathogen identification, supporting more targeted and effective care.

• Lower respiratory tract infections are a major cause of hospitalization and death
• Empiric treatment can lead to diagnostic uncertainty and inappropriate antibiotic use
• Multiplex PCR testing can detect viral and bacterial pathogens simultaneously
• Molecular diagnostics offer >90% sensitivity and specificity for many pathogens
• Faster, accurate diagnosis supports antibiotic stewardship and better outcomes
• Early pathogen identification can reduce hospital length of stay

Community-acquired pneumonia is a leading cause of infectious disease-related hospitalization and death in the United States. While current guidelines recommend treatment with ‘empiric’ therapy based on the most likely pathogen, diagnostic uncertainty and error can lead to inappropriate treatments and unnecessary antibiotic prescribing. Non-specific treatment of community acquired pneumonia presents a clinical challenge for urgent care physicians where reduced diagnostic uncertainty could lead to more targeted care.

Diagnostic uncertainty can be reduced through innovations in molecular diagnostics.  This has been shown in inpatient and emergency department settings with syndromic multiplex polymerase chain reaction-based testing.  Syndromic multiplex panels enable physicians to order tests by ‘syndrome’ (for example, upper or lower respiratory tract symptoms) in patients for whom empiric decision-making or available point-of-care testing have proved insufficient.  These tests offer high diagnostic accuracy for detecting both viral and bacterial respiratory pathogens with sensitivity and specificity above 90% for most pathogens.  The detection of multiple pathogens simultaneously facilitates early pathogen-directed treatment, reducing unnecessary use of antibiotics, and shortening the length of pneumonia-related hospitalization.

Use of syndromic multiplex polymerase chain reaction-based testing in urgent care settings could also improve community-acquired pneumonia treatment through early and accurate identification of the infecting pathogen. Patients with potential lower respiratory tract infections who could benefit may include those with worsening symptoms, recent antibiotic treatment, comorbidities, risk for polymicrobial pathogens, or severity in clinical presentation. In these cases, early and accurate detection of the infecting pathogen could inform treatment and help reduce unnecessary or inappropriate antibiotic use. To prevent overtreatment, testing is most appropriate for patients with infectious signs and symptoms with panels aligned to those presenting clinical symptoms in order to increase the likelihood that the organisms detected are pathogenic.