title: Molecular methods for pathogen and microbial community detection and characterization: current and potential application in diagnostic microbiology.
abstract: Clinical microbiology laboratories worldwide have historically relied on phenotypic methods (i.e., culture and biochemical tests) for detection, identification and characterization of virulence traits (e.g., antibiotic resistance genes, toxins) of human pathogens. However, limitations to implementation of molecular methods for human infectious diseases testing are being rapidly overcome allowing for the clinical evaluation and implementation of diverse technologies with expanding diagnostic capabilities. The advantages and limitation of molecular techniques including real-time polymerase chain reaction, partial or whole genome sequencing, molecular typing, microarrays, broad-range PCR and multiplexing will be discussed. Finally, terminal restriction fragment length polymorphism (T-RFLP) and deep sequencing are introduced as technologies at the clinical interface with the potential to dramatically enhance our ability to diagnose infectious diseases and better define the epidemiology and microbial ecology of a wide range of complex infections.
authors.affiliation: Department of Microbiology, Immunology & Infectious Diseases, University of Calgary, Calgary, Alta, Canada.
authors.forename: Christopher D
authors.initials: CD
authors.lastname: Sibley
authors.forename: Gisele
authors.initials: G
authors.lastname: Peirano
authors.forename: Deirdre L
authors.initials: DL
authors.lastname: Church
mesh_terms: D001419:Bacteria / Q000235:genetics / Q000302:isolation & purification / Q000472:pathogenicity; D003141:Communicable Diseases / Q000175:diagnosis* / Q000453:epidemiology / Q000382:microbiology; D019295:Computational Biology; D005658:Fungi / Q000235:genetics / Q000302:isolation & purification / Q000472:pathogenicity; D016680:Genome, Bacterial; D016681:Genome, Fungal; D060005:Genotyping Techniques; D006801:Humans; D046228:Microarray Analysis / Q000379:methods; D008828:Microbiological Techniques / Q000379:methods* / Q000592:standards; D058889:Molecular Typing / Q000379:methods*; D016133:Polymerase Chain Reaction / Q000379:methods; D012150:Polymorphism, Restriction Fragment Length; D011933:Reagent Kits, Diagnostic
chemical_list: D011933:Reagent Kits, Diagnostic