infectious diseases
Nucleic Acid–Based Identification Methods for Infectious Disease
Introduction
Nucleic acid–based methods detect organism-specific DNA or RNA sequences extracted from the microorganism. Sequences may or may not be amplified in vitro. Nucleic acid–based (molecular) identification has become commonplace in clinical settings; the resulting rapid identification allows the patient to be placed on specific antimicrobial therapy and avoid prolonged management on empiric, potentially inappropriate drugs. Nucleic acid–based methods are generally specific and highly sensitive and can be used for all categories of microbes. Results can be provided rapidly. Because each test typically is specific to a single organism, the clinician must know the diagnostic possibilities and request tests accordingly. For example, if a patient has symptoms suggesting influenza but the influenza season is over, doing a more general viral diagnostic test (eg, viral culture) rather than a specific flu test is better because another virus (eg, parainfluenza, adenovirus) may be the cause. Recent advances have led to the development of multiplex assays, in which a single nucleic acid–based test can detect and differentiate between ≥ 2 causative microorganisms. Multiplex assays are currently available for detecting biological warfare agents, SARS-CoV-2 variants, and certain respiratory tract pathogens (ie, multiplex assays encompassing a panel of respiratory viruses such RSV [respiratory syncytial virus], adenovirus, influenza, parainfluenza, as well as non-viral pathogens such as pneumococci, mycoplasmas, and chlamydiae). Multiplex assays have similar sensitivity and specificity as single target assays but are mostly qualitative and may be more difficult to interpret in a given patient. Nucleic acid–based tests are qualitative, but quantification methods exist for a limited but increasing number of infections (eg, Hepatitis B, Acute , 