TABLE 10.

Real-time PCR methods for mycobacteriologya

Method or speciesSpecimenTechnologyTargetStatusConventional methodClinical sensitivity vs. conventional methodTurnaround time vs. conventional methodReference(s)Comments
Genus screenCultureLightCycler FRET HP16S rRNAHBCultureNAFaster 243 3 primer/probe sets to detect Mycobacterium spp., Mycobacterium avium, Mycobacterium tuberculosis
Genus screenCultureABI 7700 molecular beacons16S rRNAHBCultureNAFaster 449 Also differentiation of Mycobacterium tuberculosis and comparison w/Amplicor PCR
Genus screenRespiratory and nonrespiratoryABI 7700 molecular beaconsIS6110, senX3, regX3HBCultureGreaterFaster 50 Genus screen and Mycobacterium tuberculosis detection and quantitation
Genus screenRespiratoryABI 7700 molecular beacons16S rRNAHBCultureLowerFaster 136 Genus screen and Mycobacterium tuberculosis detection
Genus screenFine-needle aspirates, tissueiCycler TaqManITSHBCultureGreaterFaster 51 1 primer set/3 probes to detect Mycobacterium spp., Mycobacterium avium, Mycobacterium tuberculosis
Mycobacterium abscessus CultureLightCycler FRET HP hsp65, 16S rRNAHBCulture, biochemicals or hsp65 RFLPNAFaster 443 Multiplex assay to differentiate Mycobacterium abscessus and Mycobacterium chelonae
Mycobacterium avium complexCultureLightCycler FRET HP16S rRNAHBCultureNAFaster 243 3 primer/probe sets to detect Mycobacterium spp., Mycobacterium avium, Mycobacterium tuberculosis
Fine-needle aspirates, tissueiCycler molecular beaconsITSHBCulture, nucleic acid probeGreaterFaster 51 1 primer set/3 probes to detect Mycobacterium spp., Mycobacterium avium, Mycobacterium tuberculosis
TissueABI 7700 TaqMan hsp65 ExpmtlCulture, nucleic acid probeLowerFaster 481 Research in birds
Mycobacterium avium subsp. paratuberculosisCultureLightCycler SYBRIS900HBCultureNAFaster 353
Fixed tissueGeneAmp 5700 TaqManIS900HBCultureNAFaster 107 Investigation of sarcoid etiology
Mycobacterium bovis CultureLightCycler FRET HP oxyR, narG, RD1HBCulture, biochemicalsNAFaster 462 Differentiation of Mycobacterium tuberculosis, Mycobacterium bovis, Mycobacterium bovis BCG
Mycobacterium bovis TissueLightCycler FRET HPIS6110ExpmtlCulture, histopathologyLowerFaster 478 Research in cattle
Mycobacterium bovis BCGCultureLightCycler FRET HP oxyR, narG, RD1HBCulture, biochemicalsNAFaster 462 Differentiation of Mycobacterium tuberculosis, Mycobacterium bovis, Mycobacterium bovis BCG
Mycobacterium chelonae CultureLightCycler FRET HP hsp65, 16S rRNAHBCulture, biochemicals, or hsp65 RFLPNAFaster 443 Multiplex assay to differentiate Mycobacterium abscessus and Mycobacterium chelonae
Mycobacterium genavense TissueABI 7700 TaqMan hsp65 ExpmtlCulture/nucleic acid probeLowerFaster 481 Research in birds
Mycobacterium leprae TissueLightCycler FRET HP pra HBMicroscopyLowerEqual 235
Mycobacterium tuberculosis CultureLightCycler FRET HP oxyR, narG, RD1HBCulture, biochemicalsNAFaster 463 Differentiation of Mycobacterium tuberculosis, Mycobacterium bovis, Mycobacterium bovis BCG
Mycobacterium tuberculosis complexCultureLightCycler FRET HP16S rRNAHBCultureNAFaster 243 3 primer/probe sets to detect Mycobacterium spp., Mycobacterium avium, Mycobacterium tuberculosis
CultureLightCycler FRET HPITSHBCultureNAFaster 236
Culture, sputumLightCycler FRET HPIS6110HBCultureLowerFaster 169 Idaho Technology LightCycler
Culture, respiratoryLightCycler FRET HPITSHBCultureLowerFaster 315 Also compared with Amplicor PCR test
Culture, respiratory and nonrespiratoryABI 7700 molecular beacons16S rRNAHBCultureLowerFaster 449 Differentiation of Mycobacterium tuberculosis from NTMs; comparison w/Amplicor PCR
Respiratory and nonrespiratoryABI 7700 molecular beaconsIS6110, senX3, regX3HBCultureGreaterFaster 50 Genus screen and Mycobacterium tuberculosis detection and quantitation
RespiratorySmartCycler TaqManIS6110HBCultureEqualFaster 70 Also compared with Amplicor PCR test
Respiratory and nonrespiratoryABI 7700 molecular beacons16S rRNAHBCultureLowerFaster 136 Genus screen and Mycobacterium tuberculosis detection
Respiratory and nonrespiratoryABI 7000 TaqManIS6110HBCultureNRFaster 260 Comparison with AMTD PCR test
SputumABI 7700 molecular beaconsIS6110HBMicroscopy and cultureNAFaster 94 Mycobacterium tuberculosis quantitation
Fine-needle aspirates, tissueiCycler TaqManITSHBCultureGreaterFaster 51 1 primer set/3 probes to detect Mycobacterium spp., Mycobacterium avium, Mycobacterium tuberculosis
Fixed tissueABI 7700 molecular beaconsGM-CSF, IFN-γ, etc.ExpmtlConventional PCRNAFaster 562 Gene expression in mouse granulomas
Mycobacterium tuberculosis complex genotypingCultureABI 7700 molecular beacons gyrA, katGLDIS6110 RFLPNAFaster 412 Genotyping of Mycobacterium tuberculosis complex
Mycobacterium tuberculosis complex susceptibilityCultureLightCycler FRET HP katG, rpoBLDBroth dilutionNAFaster135, 300, 495, 496INH and RIF resistance
CultureLightCycler FRET HP rpoB LDBroth dilutionNAFaster 106 RIF resistance
CultureLightCycler SYBR16S rRNALDBroth dilutionNAFaster 416 RIF resistance; 2 clinical specimens
CultureABI 7700 molecular beacons ahpC, oxyR, inhA, kasALDBroth dilutionNAFaster 378 INH and RIF resistance
Culture, sputumABI 7700 molecular beacons rpoB LDBroth dilutionEqualFaster 110, 379RIF resistance
Culture, sputumiCycler TaqMan katG LDBroth dilutionLowerFaster 505 INH resistance
Culture, smear-positive clinical specimensiCycler molecular beacons katG, inhA, rpoBLDBroth dilutionEqualFaster 274 INH and RIF resistance
RespiratoryABI 7700 TaqMan rpoB, katG, embBLDBroth dilutionEqualFaster 523 8 probes to detect INH, RIF, EMB resistance
Mycobacterium ulcerans TissueABI 7700 TaqManIS2404LDCulture, conventional PCRGreaterFaster 417
  • a Abbreviations: EMB, ethambutol; Expmtl, experimental; HP, hybridization probe; INH, isoniazid; LD, laboratory developed; NA, not applicable; NR, not reported; RIF, rifampin; RFLP, restriction fragment length polymorphism; NTM, nontypeable mycobacteria; GM-CSF, granulocyte-macrophage colony-stimulating factor; IFN, interferon; HB, home brew; AMTD, amplified Mycobacterium tuberculosis direct test.