title: Molecular genetic methods in the diagnosis of lower respiratory tract infections.
abstract: Molecular diagnostic techniques, such as PCR, have become useful tools for the rapid etiological diagnosis of lower respiratory tract infections. Nucleic acid amplification tests (NAATs) have been evaluated for detecting most respiratory pathogens, and commercial assays are available for some pathogens. However, standardized protocols are needed before these assays are introduced into routine diagnostic use. For pneumonia, NAATs offer advantages over conventional tests for the detection of Mycoplasma pneumoniae, Legionella spp. and Chlamydia pneumoniae. For pneumococcal pneumonia in adults, PCR adds little to existing diagnostic tests, and is unable to distinguish pneumococcal colonization from infection when testing respiratory samples. Although less sensitive than culture-based methods, several commercial molecular diagnostic assays have been developed for tuberculosis and are useful rapid tests for selected patients. PCR can now be considered the rapid diagnostic test of choice for pertussis and some respiratory virus infections. Further work is required to better characterize the role of molecular diagnostic tests for diagnosing lower respiratory tract infections, and to develop standard assays that can be readily adopted by routine diagnostic laboratories.
authors.affiliation: Department of Pathology, Christchurch School of Medicine and Health Sciences, and Microbiology Unit, Canterbury Health Laboratories, Christchurch, New Zealand. david.murdoch@cdhb.govt.nz
authors.forename: David R
authors.initials: DR
authors.lastname: Murdoch
mesh_terms: D001424:Bacterial Infections / Q000175:diagnosis / Q000382:microbiology; D001886:Bordetella pertussis / Q000235:genetics / Q000302:isolation & purification; D002689:Chlamydia / Q000235:genetics / Q000302:isolation & purification; D006193:Haemophilus influenzae / Q000235:genetics / Q000302:isolation & purification; D006801:Humans; D007875:Legionella / Q000235:genetics / Q000302:isolation & purification; D008967:Molecular Biology / Q000379:methods*; D009161:Mycobacterium / Q000235:genetics / Q000302:isolation & purification; D009177:Mycoplasma pneumoniae / Q000235:genetics / Q000302:isolation & purification; D021141:Nucleic Acid Amplification Techniques; D045363:Pneumocystis carinii / Q000235:genetics / Q000302:isolation & purification; D011020:Pneumonia, Pneumocystis / Q000175:diagnosis / Q000382:microbiology; D016133:Polymerase Chain Reaction; D012141:Respiratory Tract Infections / Q000175:diagnosis* / Q000382:microbiology*; D045473:Severe acute respiratory syndrome-related coronavirus / Q000235:genetics / Q000302:isolation & purification; D013296:Streptococcus pneumoniae / Q000235:genetics / Q000302:isolation & purification; D014777:Virus Diseases / Q000175:diagnosis / Q000821:virology