title: Diagnostic Molecular Mycobacteriology in Regions With Low Tuberculosis Endemicity: Combining Real-time PCR Assays for Detection of Multiple Mycobacterial Pathogens With Line Probe Assays for Identification of Resistance Mutations.
abstract: Molecular assays have not yet been able to replace time-consuming culture-based methods in clinical mycobacteriology. Using 6875 clinical samples and a study period of 35months we evaluated the use of PCR-based assays to establish a diagnostic workflow with a fast time-to-result of 1-2days, for 1. detection of Mycobacterium tuberculosis complex (MTB), 2. detection and identification of nontuberculous mycobacteria (NTM), and 3. identification of drug susceptible MTB. MTB molecular-based detection and culture gave concordant results for 97.7% of the specimens. NTM PCR-based detection and culture gave concordant results for 97.0% of the specimens. Defining specimens on the basis of combined laboratory data as true positives or negatives with discrepant results resolved by clinical chart reviews, we calculated sensitivity, specificity, PPV and NPV for PCR-based MTB detection as 84.7%, 100%, 100%, and 98.7%; the corresponding values for culture-based MTB detection were 86.3%, 100%, 100%, and 98.8%. PCR-based detection of NTM had a sensitivity of 84.7% compared to 78.0% of that of culture-based NTM detection. Molecular drug susceptibility testing (DST) by line-probe assay was found to predict phenotypic DST results in MTB with excellent accuracy. Our findings suggest a diagnostic algorithm to largely replace lengthy culture-based techniques by rapid molecular-based methods.
authors.affiliation: Institut für Medizinische Mikrobiologie, Universität Zürich, Gloriastrasse 30/32, 8006 Zürich, Switzerland.
authors.forename: Vanessa
authors.initials: V
authors.lastname: Deggim-Messmer
authors.affiliation: Institut für Medizinische Mikrobiologie, Universität Zürich, Gloriastrasse 30/32, 8006 Zürich, Switzerland.
authors.forename: Guido V
authors.initials: GV
authors.lastname: Bloemberg
authors.affiliation: Institut für Medizinische Mikrobiologie, Universität Zürich, Gloriastrasse 30/32, 8006 Zürich, Switzerland; Nationales Zentrum für Mykobakterien, Gloriastrasse 30/32, 8006 Zürich, Switzerland.
authors.forename: Claudia
authors.initials: C
authors.lastname: Ritter
authors.affiliation: Institut für Medizinische Mikrobiologie, Universität Zürich, Gloriastrasse 30/32, 8006 Zürich, Switzerland.
authors.forename: Antje
authors.initials: A
authors.lastname: Voit
authors.affiliation: Institut für Medizinische Mikrobiologie, Universität Zürich, Gloriastrasse 30/32, 8006 Zürich, Switzerland; Nationales Zentrum für Mykobakterien, Gloriastrasse 30/32, 8006 Zürich, Switzerland.
authors.forename: Rico
authors.initials: R
authors.lastname: Hömke
authors.affiliation: Institut für Medizinische Mikrobiologie, Universität Zürich, Gloriastrasse 30/32, 8006 Zürich, Switzerland; Nationales Zentrum für Mykobakterien, Gloriastrasse 30/32, 8006 Zürich, Switzerland. Electronic address: pkeller@imm.uzh.ch.
authors.forename: Peter M
authors.initials: PM
authors.lastname: Keller
authors.affiliation: Institut für Medizinische Mikrobiologie, Universität Zürich, Gloriastrasse 30/32, 8006 Zürich, Switzerland; Nationales Zentrum für Mykobakterien, Gloriastrasse 30/32, 8006 Zürich, Switzerland.
authors.forename: Erik C
authors.initials: EC
authors.lastname: Böttger
mesh_terms: D000900:Anti-Bacterial Agents / Q000494:pharmacology; D001426:Bacterial Proteins / Q000235:genetics; D015342:DNA Probes / Q000378:metabolism; D024881:Drug Resistance, Bacterial / Q000187:drug effects / Q000235:genetics*; D006801:Humans; D009169:Mycobacterium tuberculosis / Q000187:drug effects / Q000235:genetics* / Q000302:isolation & purification; D009170:Nontuberculous Mycobacteria / Q000187:drug effects / Q000235:genetics* / Q000302:isolation & purification; D009693:Nucleic Acid Hybridization; D010641:Phenotype; D012336:RNA, Ribosomal, 16S / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D060888:Real-Time Polymerase Chain Reaction; D017422:Sequence Analysis, DNA; D014376:Tuberculosis / Q000175:diagnosis* / Q000382:microbiology
chemical_list: D000900:Anti-Bacterial Agents; D001426:Bacterial Proteins; D015342:DNA Probes; D012336:RNA, Ribosomal, 16S
keywords: Drug susceptibility; Line probe assay; Mycobacterium tuberculosis; Nontuberculous mycobacteria; Real-time PCR