Advanced Techniques in Diagnostic Microbiology

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Index 533 MLEE. See multilocus enzyme electrophoresis MLST. See multilocus sequence typing molecular amplification techniques common sources of errors, 298 contamination, 298 degradation control, 298 extraction as rate-limiting, 298 product detection-characterization, 243–263 molecular beacons, 189, 199, 293, 296–297 molecular differential diagnostics (MDD), 472–502 benefits-impact, 500–502 diarrheal diseases, 492–494 encephalitis, 490–492 food-borne diseases, 492–494 health care associated infections, 487–490 human papillomavirus typing, 490 MRSA, 495–499 optimal features, 473 respiratory infections, 485–487 tuberculosis, 494–495 See also technology integration Moraxella spp., 88, 100, 328 Morganella, 97 motility indole lysine (MILS) medium, 96–97 MR. See methyl red test mucosa-associated lymphoid tissue (MALT) lympohoma, 11 Mueller-Hinton agar (MHA), 64, 71, 78 multianalytic profile (xMAP), 42, 45, 48–50, 52 automation, 57 ELISA assays, 56 multiple infectious agents, 430 multilocus enzyme electrophoresis (MLEE), 271 multilocus sequence typing (MLST), 271, 513 MRSA, 453 organism specific applications, 450 strain typing, 451 multiplex bead-based flow cytometric immunoassays, 427–443 multiplex flow cytometry. See multianalytic profile multiplex PCR, 474–477 primer set incompatibilities, 475 trial-error method, 485 multiplexed bead-based assays assessment of biomarkers using, 435–440 cytokine measurements, 435–436 microbes-toxins simultaneous measurement, 433–435 SARS, 436–440 sepsis, 435–436 xMAP, 56–57 multiplexed indirect immunofluorescnece assay. See multianalytic profile multiplexed particle-based flow cytometric assays. See multianalytic profile multiplexing challenges, 474 definition, 473 multplex flow cytometric immunoassays measurement of microbial agents, 432–433 mycobacterial interspersed repetitive unit-variable-number tandem repeat (MIRU-VNTR), 454 Mycobacterium 16S rRNA, 327 ITS regions, 269 pyrosequencing, 272 real-time PCR, 297 sequencing of hsp65, 267–270 See also specific types Mycobacterium avium blood cultures, 7–8 probes, 136 RFLP, 459 Mycobacterium avium complex (MAC), 459 DNA sequencing, 266 probes, 136 Mycobacterium gordonae probes, 136 Mycobacterium inracellulare probes, 136 Mycobacterium kansasii probes, 136 Mycobacterium mucogenicum blood cultures, 7 Mycobacterium tuberculosis AIDS, 8 BACTEC systems, 392–393 biochemical tests, 392 blood cultures, 8 cell walls, 387–388 cerebral spinal fluid, 390 co-infection with HIV, 388 contamination, 393 conventional methods for identification, 391–392 direct tests, 395–396 DNA sequencing, 266 drug resistance, 293, 387–410, 402 enhanced amplified direct test, 395 environmental monitoring, 457
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Advanced Techniques in Diagnostic M
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Yi-Wei Tang Molecular Infectious Di
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vi Contributors Wonder Drake Depart
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viii Contributors Jacques Schrenzel
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Preface Clinical microbiologists ar
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Contents Part I Techniques 1 Automa
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Contents xv 22 Review of Molecular
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1 Automated Blood Cultures XIANG Y.
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Interpretation of Significance 1. A
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1. Automated Blood Cultures 7 conta
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1. Automated Blood Cultures 9 Crump
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2 Urea Breath Tests for Detection o
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2. Urea Breath Tests 13 and point o
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2. Urea Breath Tests 15 Other detec
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TABLE 2.1. Comparison of 13 C-urea
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2. Urea Breath Tests 19 Bazzoli, F.
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2. Urea Breath Tests 21 Logan, R. (
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3 Rapid Antigen Tests SHELDON CAMPB
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3. Rapid Antigen Tests 25 antigen i
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3. Rapid Antigen Tests 27 either on
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3. Rapid Antigen Tests 29 and moves
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3. Rapid Antigen Tests 31 Applicati
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Fungi Cryptococcus Agglutination, E
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Adenovirus, enteric types 40,41 EIA
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3. Rapid Antigen Tests 37 Antigen t
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3. Rapid Antigen Tests 39 retains a
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3. Rapid Antigen Tests 41 Wilhelmi,
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4. Advanced Antibody Detection 43 D
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TABLE 4.1. Types of antibody detect
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4. Advanced Antibody Detection 47 c
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4. Advanced Antibody Detection 49 U
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4. Advanced Antibody Detection 51 a
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4. Advanced Antibody Detection 53 a
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4. Advanced Antibody Detection 55 H
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4. Advanced Antibody Detection 57 r
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4. Advanced Antibody Detection 59 A
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4. Advanced Antibody Detection 61 M
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5 Phenotypic Testing of Bacterial A
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5. Antimicrobial Susceptibility Tes
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Susceptibility Tests for Fastidious
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References 5. Antimicrobial Suscept
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6. Biochemical Profile-Based Microb
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7 Rapid Bacterial Characterization
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7. MALDI-TOF MS 119 photons followe
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7. MALDI-TOF MS 121 for analysis by
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7. MALDI-TOF MS 123 Sample wells Ca
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7. MALDI-TOF MS 125 also given. Thi
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7. MALDI-TOF MS 127 characteristics
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References 7. MALDI-TOF MS 129 Ande
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7. MALDI-TOF MS 131 Hindre, T., Did
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7. MALDI-TOF MS 133 von Wintzingero
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8. Probe-Based Microbial Detection
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9 Pulsed-Field Gel Electrophoresis
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9. Pulsed-Field Gel Electrophoresis
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PFGE Performance Characteristics 9.
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TABLE 10.1. Nucleic acid amplificat
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10. In Vitro Nucleic Acid Amplifica
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11. PCR and Its Variations 167 Prin
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11. PCR and Its Variations 169 Exte
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11. PCR and Its Variations 171 targ
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11. PCR and Its Variations 173 bind
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11. PCR and Its Variations 175 Reve
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11. PCR and Its Variations 177 ampl
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11. PCR and Its Variations 179 pres
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11. PCR and Its Variations 181 Soft
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11. PCR and Its Variations 183 Saik
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12. Non-PCR Amplification 185 1989;
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12. Non-PCR Amplification 187 FIGUR
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12. Non-PCR Amplification 189 This
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12. Non-PCR Amplification 191 FIGUR
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12. Non-PCR Amplification 193 and c
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12. Non-PCR Amplification 195 used
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12. Non-PCR Amplification 197 do no
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Application of the SDA Technique Re
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12. Non-PCR Amplification 201 Ancho
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12. Non-PCR Amplification 203 Baner
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12. Non-PCR Amplification 205 Guilf
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12. Non-PCR Amplification 207 Nilss
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12. Non-PCR Amplification 209 Wang,
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13. Recent Advances in Probe Amplif
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14. Signal Amplification Techniques
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TABLE 14.1. Comparison of bDNA and
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References 14. Signal Amplification
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15 Detection and Characterization o
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15. Agarose Gel Electrophoresis, So
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16. Direct Nucleotide Sequencing 26
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17. Microarrays for Microbial Chara
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18 Diagnostic Microbiology Using Re
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TABLE 18.1. Comparison of four fluo
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18. Real-Time PCR Based on FRET 295
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19. Amplification Product Inactivat
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TABLE 19.1. Comparison of inactivat
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20 Bacterial Identification Based o
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20. Analysis of 16S rRNA Gene Seque
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21 Molecular Techniques for Blood a
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Hepatitis B Surface Antigen (Anti-H
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Vironostika HIV-1 Microelisa System
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21. Blood and Blood Product Screeni
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22 Review of Molecular Techniques f
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22. Molecular Techniques for STDs D
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Traditional Diagnostic Methods 22.
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References 22. Molecular Techniques
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23 Advances in the Diagnosis of Myc
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23. Diagnosis of Mycobacterium tube
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Immunodiagnostic Methods 23. Diagno
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24 Rapid Screening and Identificati
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24. Rapid Screening and Identificat
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25 Bead-Based Flow Cytometric Assay
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A. Test 488-635 nm 680 nm Analyte o
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25. Bead-Based Flow Cytometric Assa
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26. Molecular Strain Typing 445 tha
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26. Molecular Strain Typing 447 FIG
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TABLE 26.1. Comparison of strain-ty
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26. Molecular Strain Typing 451 Som
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26. Molecular Strain Typing 453 and
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26. Molecular Strain Typing 455 pat
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Surveillance for Potential Infectio
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26. Molecular Strain Typing 459 the
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26. Molecular Strain Typing 461 of
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26. Molecular Strain Typing 463 Cow
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26. Molecular Strain Typing 465 Hea
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26. Molecular Strain Typing 467 May
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26. Molecular Strain Typing 469 Shu
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26. Molecular Strain Typing 471 Ver
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27. Molecular Differential Diagnose
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TABLE 27.11. Detection results of t
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TABLE 27.13. Detection of 25 HPV ty
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TABLE 27.16. List of pathogens iden
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TABLE 27.19. Results of the TB drug
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TABLE 27.21. Example data for the G
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28 Pathogen Detection in the Genomi
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Page 1038: Cephid Smart Cycler 1600 16/run www
Page 1070: 526 Index B Babesia, 16S rRNA, 328
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Page 1082: 532 Index LCR. See ligase chain rea
Page 1088: Index 535 PNA. See peptide-nucleic
Page 1092: Index 537 Roseomonas, 328-329 rotav
Page 1096: Index 539 T TaqMan probes, 293-296
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