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Tables of Contents for DNA Methods in Clinical Microbiology
Chapter/Section Title
Page #
Page Count
Preface
vii
 
DNA-based technology: an introduction
1
11
The scope of DNA-based methods
1
2
Old versus new technology
3
1
Parameters of DNA-based methods
4
2
DNA-based diagnostic tests
6
3
`Resolved results'
9
3
Nucleic acids: the essentials
12
32
Nucleic acids (RNA and DNA)
12
12
Target sequences
24
3
Specimens
27
3
Extraction of nucleic acids
30
14
Probe-based (hybridization) methods
44
12
Labelling of probes
44
5
Preparation of samples
49
1
Hybridization (probe-target annealing)
49
1
In situ hybridization
50
1
Examples of probe-based tests
50
3
Sensitivity and specificity
53
1
False-positive and false-negative results
54
2
Nucleic acid amplification I: polymerase chain reaction
56
70
The principle of PCR
56
1
PCR: some practical details
56
4
PCR instrumentation: thermal cyclers
60
1
PCR products: detection and quantification
61
6
PCR inhibitors
67
2
False-positive and false-negative results; controls
69
2
Contamination with extraneous DNA
71
2
Types of PCR
73
10
PCR-based studies in clinical microbiology
83
1
Reports from the literature I: detection of pathogens
84
22
Reports from the literature II: detection of genes
106
4
Reports from the literature III: detection of uncultivable pathogens
110
1
Reports from the literature IV: PCR vs other diagnostic methods
111
7
Reports from the literature V: evaluation of PCR
118
8
Nucleic acid amplification II: NASBA, TMA, SDA
126
26
NASBA and TMA
126
5
SDA
131
7
Reports from the literature
138
14
Nucleic acid amplification III: ligase chain reaction
152
16
Thermal cycling
152
1
Extent of amplification
152
2
Detection of products
154
1
The Abbott LCx® Chlamydia trachomatis assay
154
3
The Abbott LCx® Mycobacterium tuberculosis assay
157
1
Anticontamination measures in the LCx assays
158
1
Reports from the literature (Abbott LCx® assays)
159
9
Nucleic-acid-based typing
168
35
Typing: some applications
168
2
Typing systems: some general characteristics
170
1
Typing: conventional methodology
171
1
Typing: nucleic-acid-based methodology
172
31
DNA-based (`genotypic') antibiotic susceptibility testing
203
26
Origins of antibiotic resistance
203
2
Antimicrobial susceptibility testing in Chalmydia trachomatis
205
1
Antimicrobial susceptibility testing in Helicobacter pylori
206
1
Antimicrobial susceptibility testing of HIV-1
207
3
Antimicrobial susceptibility testing of hepatitis B virus
210
2
Antimicrobial susceptibility testing of Staphylococcus aureus
212
5
Antimicrobial susceptibility testing of Mycobacterium tuberculosis
217
12
Quantification of pathogens
229
8
bDNA
230
2
PCR-based quantification
232
2
NASBA-based quantification
234
1
Cross-linking quantitative assay
234
3
Appendix I The future: chip technology
237
2
Appendix II Commercial products, systems and sources
239
6
Index
245