TABLE 22.

Real-time PCR methods for fungia

GenusSpecimenTechnologyTargetStatusConventional methodClinical sensitivity vs. conventional methodTurnaround time vs. conventional methodReference(s)Comments
Aspergillus BAL fluidiCycler TaqMan18S rRNAHBCulture, histopathologyGreaterFaster 428 Compared with antigen detection
BAL fluid, bloodLightCycler FRET HP18S rRNAHBNANAFaster 287 MagNA Pure vs. manual extraction
BAL fluid, lung tissueLightCycler FRET HPITSExpmt1Culture, histopathologyGreaterFaster 358 Research in rabbits
BAL fluid, tissueLightCycler FRET HPmito. tRNAHBCulture, histopathologyGreaterFaster 397
BAL fluid, bloodLightCycler FRET HPcyto. bHBCulture, histopathologyNRFaster 459 Quantitative; nested PCR was more sensitive
Blood, serumABI 7700 TaqMan5.8S rRNAHBCulture, histopathologyLowerFaster 376 Quantitative
Blood, plasmaABI 7700 TaqMan18S rRNAHBCulture, histopathologyGreaterFaster 206, 210Compared with antigen detection
Blood, serumABI 7700 TaqMan28S rRNAHBCulture, histopathologyGreaterFaster 61 Compared with antigen detection
Serum, plasma, cell pelletABI 7700 TaqMan fks HBCulture, histopathologyNRFaster 81 Evaluation of serum, white cell pellet, plasma
BloodLightCycler FRET HP18S rRNAHBCulture, histopathologyNRFaster 285, 385Quantitative
Blood, tissueLightCycler FRET HP18S rRNAExpmt1Culture, histopathologyGreaterFaster 286 Research in mice and rabbits
SerumLightCycler FRET HPmito. rRNAHBCultureGreaterFaster 80 Comparison with antigen detection
CultureABI 7700 TaqMan atr HBConventional PCRNAFaster 445 Monitoring of efflux pump transcript levels
CultureABI 7700 Molecular Beacons mdr HBConventional PCRNAFaster 331 Monitoring of expression levels
TissueABI 7700 TaqMan18S rRNAExpmt1CFU quantitationNAFaster 41 Caspofungin efficacy monitoring in mice
TissueLightCycler FRET HP18S rRNAHBCulture, histopathologyEqualFaster 194 3 clinical specimens
Candida BloodABI 5700 TaqManITS2HBCultureGreaterFaster 290-292Quantitative
BloodLightCycler FRET HP18S rRNAHBCultureNRFaster 285, 385Quantitative
BloodLightCycler FRET HP18S rRNAHBCultureGreaterFaster 543 Detects seven species with one probe set
BloodLightCycler FRET HPITSHBCultureEqualFaster 444 Detects/differentiates six species with four probe sets
CultureABI 7700 TaqManITS2HBCultureNAFaster 157 Detects/differentiates six species with three probe sets
CultureABI 7700 TaqMan erg11 HBBroth dilutionNAFaster 65, 144Fluconazole resistance genotyping
CultureABI 7700 molecular beaconsITS2HBCulture, phenotypic assaysNAFaster 368 C. dubliniensis identification
CultureLightCycler FRET HP erg11 HBBroth dilutionNAFaster 284 Fluconazole resistance genotyping
CultureLightCycler FRET HP erg11, cdr, mdr HBBroth dilutionNAFaster 129, 256Fluconazole resistance genotyping
CultureLightCycler FRET HP act Expmt1CultureNAFaster 351 Cutaneous C. albicans viability model
CultureLightCycler SYBR5.8S rRNAHBCulture, biochemicalsNAFaster 188 Detects/differentiates six species with six primer sets
Oral rinseLightCycler SYBR18S rRNAHBCultureLowerFaster 543
TissueLightCycler FRET HP18S rRNAHBCultureGreaterFaster 194 1 clinical specimen
Coccidioides CultureLightCycler FRET HPAg2/PRAHBCulture, nucleic acid probeNAFaster 31 Extraction procedure safety evaluated
Conidiobolus TissueLightCycler FRET HP18S rRNAHBCulture, microscopyEqualFaster 194 1 clinical specimen
Cryptococcus CultureLightCycler SYBR5.8S rRNAHBCulture, biochemicalsNAFaster 188
TissueLightCycler FRET HP18S rRNAExpmt1CultureLowerFaster 32 Research in mice; quantitative
Histoplasma Culture, BAL fluid, tissue, bone marrowLightCycler FRET HPITSLDCulture, nucleic acid probeEqual except for bone marrowFaster 303 3 clinical specimens
TissueLightCycler FRET HP18S rRNALDCulture, nucleic acid probeEqualFaster 194 1 clinical specimen
Paracoccidioides CultureABI 7700 TaqMan20 genesLDConventional PCRNRFaster 301 Yeast and hyphal phases differential gene expression
Pneumocystis Oral swabs, tissueiCycler SYBRmt LSUExpmt1Stains, microscopyNAEqual 276 Quantitative monitoring of levels in rats
TissueLightCycler FRET HP dhfr Expmt1Stains, microscopyNREqual 250 Quantitative; research in rats
BAL fluidABI 7700 TaqManmt LSULDStains, microscopyGreaterEqual 308 Quantitative
BAL fluid, oral washes, sputumLightCycler FRET HP msg LDStains, microscopyEqualEqual 128, 251Quantitative
Pneumocystis BAL fluidLightCycler SYBRmt SSULDStains, microscopyNREqual 204 Quantitative
Nasopharyngeal aspirateABI 7700 TaqManmt LSULDStains, microscopyNREqual 497 Comparison with nested PCR, noninvasive
PlasmidABI 7700 SYBR dhps LDConventional PCR, sequencingNAFaster 334 Genotyping of dhps gene
Oral washLightCycler FRET HP msg HBStains, microscopyLowerEqual 249 Quantitative, noninvasive
Sputum, bronchial washLightCycler SYBR5S rRNALDStains, microscopyNREqual 360 Comparison with conventional PCR
Stachybotrys CultureABI 7700 TaqMan18S rRNALDCulture, microscopyNAFaster 85 Quantitative
  • a Abbreviations: ASR, analyte-specific reagent; LD, laboratory developed; NA, not applicable; NR, not reported; cyto., cytochrome; Expmtl, experimental; HP, hybridization probe; Mito. or mt, mitochondrial; BAL, bronchoalveolar lavage; HB, home brew; ITS, internal transcribed spacer; LSU, large subunit; SSU, small subunit.