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Category: Clinical Microbiology
Molecular Methods for Direct Detection of Microorganisms in Clinical Specimens, Page 1 of 2
< Previous page | Next page > /docserver/preview/fulltext/10.1128/9781555817435/9781555815271_Chap12_2-1.gif /docserver/preview/fulltext/10.1128/9781555817435/9781555815271_Chap12_2-2.gifAbstract:
The detection of pathogenic microorganisms directly in clinical specimens by molecular methods has been investigated extensively using a variety of nucleic acid probe hybridization, target amplification, and signal-generating formats. Commercial product development has focused on direct diagnosis of blood-borne and sexually transmitted diseases and respiratory pathogens using solid-and solution-phase hybridization with nonisotopic nucleic acid probes and several different target amplification methods, including conventional PCR, strand displacement amplification, transcription-mediated amplification, and, more recently, real-time PCR. Many laboratories are developing their own “home brew” assays for pathogen detection using real-time PCR for organisms not addressed by commercial kits (Table 12.1-4).
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GeneXpert cartridge. S, sample; 1, reagent 1; 2, reagent 2.
GeneXpert cartridge. S, sample; 1, reagent 1; 2, reagent 2.
Melting peaks corresponding to B. parapertussis and B. pertussis
Melting peaks corresponding to B. parapertussis and B. pertussis
Commercially available, FDA-cleared Chlamydia trachomatis and Neisseria gonorrhoeae tests a
a This table contains examples of FDA-cleared or -approved nucleic acid amplification tests that are commercially available in the United States. It is not intended to be all-inclusive. Websites of the manufacturers are useful sources of the most up-to-date information.
b FCU, first-catch urine.
c SDA, strand displacement amplification.
d Inhibition control is optional with manual assay performance but cannot be run on Viper platform.
e ThinPrep PreservCyt Liquid PAP medium for collection of cervical cells.
f Roche PCR is not cleared for Neisseria gonorrhoeae testing on female urine.
g Clearance granted to Cytyc Corporation, Boxborough, MA, not Roche Molecular Systems, Inc.
Commercially available, FDA-cleared Chlamydia trachomatis and Neisseria gonorrhoeae tests a
a This table contains examples of FDA-cleared or -approved nucleic acid amplification tests that are commercially available in the United States. It is not intended to be all-inclusive. Websites of the manufacturers are useful sources of the most up-to-date information.
b FCU, first-catch urine.
c SDA, strand displacement amplification.
d Inhibition control is optional with manual assay performance but cannot be run on Viper platform.
e ThinPrep PreservCyt Liquid PAP medium for collection of cervical cells.
f Roche PCR is not cleared for Neisseria gonorrhoeae testing on female urine.
g Clearance granted to Cytyc Corporation, Boxborough, MA, not Roche Molecular Systems, Inc.
Commercially available, FDA-cleared HIV-1 quantitative tests a
a This table contains examples of FDA-cleared or -approved nucleic acid tests that are commercially available in the United States. It is not intended to be all-inclusive and does not contain tests used for screening of blood products. Websites of the manufacturer are useful sources of the most up-to-date information. Abbreviations: NASBA, nucleic acid sequence-based amplification; bDNA, branched-chain DNA; PPT, plasma preparation tube.
Commercially available, FDA-cleared HIV-1 quantitative tests a
a This table contains examples of FDA-cleared or -approved nucleic acid tests that are commercially available in the United States. It is not intended to be all-inclusive and does not contain tests used for screening of blood products. Websites of the manufacturer are useful sources of the most up-to-date information. Abbreviations: NASBA, nucleic acid sequence-based amplification; bDNA, branched-chain DNA; PPT, plasma preparation tube.
PCR primers and probes for the detection of HSV-1 and HSV-2
a 6-FAM and QUASAR 670 represent the 5' reporter fluorophores for the HSV-1 and the HSV-2 probes, respectively. BHQ-1 and BHQ-2 are the quencher molecules for the HSV-1 and the HSV-2 probes, respectively. These reporter and quencher molecules are covalently linked to the oligonucleotides.
PCR primers and probes for the detection of HSV-1 and HSV-2
a 6-FAM and QUASAR 670 represent the 5' reporter fluorophores for the HSV-1 and the HSV-2 probes, respectively. BHQ-1 and BHQ-2 are the quencher molecules for the HSV-1 and the HSV-2 probes, respectively. These reporter and quencher molecules are covalently linked to the oligonucleotides.
Primer-probe mix formulations a
a IPC, internal positive control; Rx, reaction.
Primer-probe mix formulations a
a IPC, internal positive control; Rx, reaction.
PCR primers and probe for detection of Mycoplasma pneumoniae in respiratory specimens
a Label probe 5′ end with biotin.
PCR primers and probe for detection of Mycoplasma pneumoniae in respiratory specimens
a Label probe 5′ end with biotin.
Thermal cycler parameters for B. pertussis/B. parapertussis real-time PCR
a Cont., continuous.
Thermal cycler parameters for B. pertussis/B. parapertussis real-time PCR
a Cont., continuous.
PCR primers and probe for quantitation of human CMV
a 6-FAM and TAMRA represent the 5′ reporter fluorophore and the 3′ quencher, respectively. These molecules are covalently linked to the oligonucleotide.
PCR primers and probe for quantitation of human CMV
a 6-FAM and TAMRA represent the 5′ reporter fluorophore and the 3′ quencher, respectively. These molecules are covalently linked to the oligonucleotide.
Primer-probe mix formulation a
a IPC, internal positive control; Rx, reaction.
Primer-probe mix formulation a
a IPC, internal positive control; Rx, reaction.