title: How recent advances in molecular tests could impact the diagnosis of pneumonia.
abstract: Molecular diagnostic tests have been the single major development in pneumonia diagnostics over recent years. Nucleic acid detection tests (NATs) have greatly improved the ability to detect respiratory viruses and bacterial pathogens that do not normally colonize the respiratory tract. In contrast, NATs do not yet have an established role for diagnosing pneumonia caused by bacteria that commonly colonize the nasopharynx due to difficulties discriminating between pathogens and coincidental carriage strains. New approaches are needed to distinguish infection from colonization, such as through use of quantitative methods and identification of discriminating cut-off levels. The recent realization that the lung microbiome exists has provided new insights into the pathogenesis of pneumonia involving the interaction between multiple microorganisms. New developments in molecular diagnostics must account for this new paradigm.
authors.affiliation: a Department of Pathology , University of Otago, Christchurch, and Microbiology Unit, Canterbury Health Laboratories , Christchurch , New Zealand.
authors.forename: David R
authors.initials: DR
authors.lastname: Murdoch
mesh_terms: D000071997:Blood Culture; D003955:Diagnostic Tests, Routine / Q000295:instrumentation / Q000379:methods*; D017408:Guidelines as Topic; D006801:Humans; D008168:Lung / Q000382:microbiology / Q000821:virology; D064307:Microbiota / Q000235:genetics; D025202:Molecular Diagnostic Techniques / Q000295:instrumentation / Q000379:methods*; D009305:Nasopharynx / Q000382:microbiology / Q000821:virology; D018410:Pneumonia, Bacterial / Q000175:diagnosis* / Q000382:microbiology; D011024:Pneumonia, Viral / Q000175:diagnosis* / Q000821:virology; D011933:Reagent Kits, Diagnostic / Q000706:statistics & numerical data
chemical_list: D011933:Reagent Kits, Diagnostic
keywords: PCR; Pneumonia; diagnostics; etiology; microbiome; molecular tests