Advanced Techniques in Diagnostic Microbiology

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viii Contributors Jacques Schrenzel Department of Internal Medicine Clinical Microbiology Laboratory Geneva University Hospital 21 rue Micheli-du-Crest Geneva 14, 1211, Switzerland Susan Sefers Molecular Infectious Diseases Laboratory Departments of Pathology Vanderbilt University School of Medicine 1161 21st Avenue South Nashville, TN 37232-5310, USA Charles W. Stratton Departments of Pathology and Medicine Vanderbilt University School of Medicine 1161 21st Avenue South Nashville, TN 37232-5310, USA Yi-Wei Tang Departments of Medicine and Pathology Vanderbilt University School of Medicine 1161 21st Avenue South Nashville, TN 37232-5310, USA Sihe Wang Northwestern University The Feinberg School of Medicine Children’s Memorial Hospital 2300 Children’s Plaza Chicago, IL 60614, USA Yun F. (Wayne) Wang Department of Pathology Emory University School of Medicine Grady Memorial Hospital 80 Jesse Hill Dr., S.E. Atlanta, GA 30303, USA Donna M. Wolk Department of Clinical Pathology and Medicine University of Arizona Department of Pathology and Laboratory Medicine South Arizona VA Health Care System 3601 South 6th Ave. Tucson, AZ 85723, USA Fann Wu Clinical Microbiology Services Department of Pathology Columbia University Medical Center New York Presbyterian Hospital 622 West 168th Street New York, NY 10032, USA Josephine Wu Molecular Pathology Laboratory Department of Pathology Mount Sinai School of Medicine, Box 1122 One Gustave Levy Place New York, NY 10029, USA S. Steve Yan Food and Drug Administration Rockville, MD 20855, USA Fei Ye Molecular Pathology Laboratory Department of Pathology Mount Sinai School of Medicine, Box 1122 One Gustave Levy Place New York, NY 10029, USA Bingjiao Yin Molecular Pathology Laboratory Department of Pathology Mount Sinai School of Medicine, Box 1122 One Gustave Levy Place New York, NY 10029, USA
Page 2: Advanced Techniques in Diagnostic M
Page 6: Yi-Wei Tang Molecular Infectious Di
Page 10: vi Contributors Wonder Drake Depart
Page 16: Contributors ix David Zhang Molecul
Page 20: xii Preface advantages and disadvan
Page 24: xiv Contents 11 PCR and Its Variati
Page 28: Part I Techniques
Page 32: 4 X.Y.Han and microbial factors det
Page 36: 6 X.Y.Han TABLE 1.1. Commercial con
Page 40: 8 X.Y.Han However, the two CMBCSs d
Page 44: 10 X. Y. Han Reimer, L. G., Wilson,
Page 48: 12 S. Wang and X. Zheng therapy wit
Page 52: 14 S. Wang and X. Zheng of H. pylor
Page 56: 16 S. Wang and X. Zheng A further m
Page 60: 18 S. Wang and X. Zheng tubes for G
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20 S. Wang and X. Zheng Graham, D.
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22 S. Wang and X. Zheng two test me
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24 S. Campbell and M. L. Landry Pri
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26 S. Campbell and M. L. Landry opp
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28 S. Campbell and M. L. Landry dir
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TABLE 3.1. Characteristics of the t
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TABLE 3.2. Application of technique
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TABLE 3.2 (Continued) Pathogen Meth
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TABLE 3.2 (Continued) Pathogen Meth
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38 S. Campbell and M. L. Landry Rap
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40 S. Campbell and M. L. Landry Ger
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4 Advanced Antibody Detection YUN F
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44 Y. F. Wang grouped into several
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46 Y. F. Wang variety of substrates
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48 Y. F. Wang One reason accounting
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50 Y. F. Wang by a carbodiimide con
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52 Y. F. Wang TABLE 4.2. Type of co
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54 Y. F. Wang small-volume samples
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56 Y. F. Wang Multiplexed Bead Assa
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58 Y. F. Wang the reliability of th
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60 Y. F. Wang Hemmila, I., Dakubu,
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62 Y. F. Wang (2002). Specific, sen
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64 C. Qi, C. W. Stratton, and X. Zh
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6 Biochemical Profile-Based Microbi
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86 J. Aslanzadeh + beta hemolytic +
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88 J. Aslanzadeh Gram Negative Cocc
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90 J. Aslanzadeh Preliminary Identi
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92 J. Aslanzadeh tryptophane result
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94 J. Aslanzadeh β-naphthylamine p
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96 J. Aslanzadeh Reading the test b
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98 J. Aslanzadeh TABLE 6.1. Commonl
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100 J. Aslanzadeh Do not incubate t
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102 J. Aslanzadeh Using a sterile i
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104 J. Aslanzadeh Voges-Proskaure (
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106 J. Aslanzadeh The strip is exam
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108 J. Aslanzadeh ferrous sulfate i
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110 J. Aslanzadeh TABLE 6.2. Commer
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112 J. Aslanzadeh substrates. It is
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114 J. Aslanzadeh The reagents will
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116 J. Aslanzadeh Killian, M. (1974
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118 D. Dare Furthermore, the amount
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120 D. Dare be required. Currently,
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122 D. Dare TABLE 7.1. Comparison o
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124 D. Dare Search results Combined
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126 D. Dare (a) No. genera 4123 No.
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128 D. Dare that similarity of the
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130 D. Dare Dare, D., Sutton, H., K
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132 D. Dare McKenna, T., Lunt, M.,
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8 Probe-Based Microbial Detection a
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136 T. Hong Hybridization and Detec
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138 T. Hong Candida species can det
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140 T. Hong and 100%, respectively.
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142 T. Hong Wagner, M., Schmid, M.,
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144 F. Wu and P. Della-Latta migrat
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146 F. Wu and P. Della-Latta TABLE
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148 F. Wu and P. Della-Latta DNA d
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150 F. Wu and P. Della-Latta TABLE
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152 F. Wu and P. Della-Latta λ 1 2
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154 F. Wu and P. Della-Latta Summar
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156 F. Wu and P. Della-Latta pneumo
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10 In Vitro Nucleic Acid Amplificat
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160 H. Li and Y-W. Tang of these me
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162 H. Li and Y-W. Tang Currently,
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164 H. Li and Y-W. Tang La Rocco, M
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11 PCR and Its Variations MICHAEL L
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168 M. Loeffelholz and H. Deng to o
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170 M. Loeffelholz and H. Deng FIGU
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172 M. Loeffelholz and H. Deng be i
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174 M. Loeffelholz and H. Deng the
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176 M. Loeffelholz and H. Deng RT-P
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178 M. Loeffelholz and H. Deng Dete
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180 M. Loeffelholz and H. Deng buff
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182 M. Loeffelholz and H. Deng Grat
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12 Non-Polymerase Chain Reaction Me
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186 M.L. Pendrak and S.S. Yan TMA (
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188 M.L. Pendrak and S.S. Yan dsDNA
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190 M.L. Pendrak and S.S. Yan (van
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192 M.L. Pendrak and S.S. Yan ampli
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194 M.L. Pendrak and S.S. Yan FIGUR
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196 M.L. Pendrak and S.S. Yan RCA m
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202 M.L. Pendrak and S.S. Yan TABLE
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204 M.L. Pendrak and S.S. Yan of hu
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206 M.L. Pendrak and S.S. Yan Kwoh,
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208 M.L. Pendrak and S.S. Yan Smirn
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13 Recent Advances in Probe Amplifi
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212 D. Zhang et al. TABLE 13.1. Com
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214 D. Zhang et al. scanner after h
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216 D. Zhang et al. FIGURE 13.3. Sc
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218 D. Zhang et al. FIGURE 13.4. Sc
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220 D. Zhang et al. A. B. Invasive
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222 D. Zhang et al. FIGURE 13.6. Pr
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224 D. Zhang et al. The mecA probe
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226 D. Zhang et al. Landegren, U.,
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14 Signal Amplification Techniques:
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230 Y. F. Wang Virus (3)* (2) (4)*
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232 Y. F. Wang 1. Denaturation 2. H
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234 Y. F. Wang Application of the T
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236 Y. F. Wang specimen. A study (K
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238 Y. F. Wang amplification techno
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240 Y. F. Wang Cuzick, J., Szarewsk
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242 Y. F. Wang Qian, X., & Lloyd, R
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244 R. P. Podzorski, M. Loeffelholz
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16 Direct Nucleotide Sequencing for
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266 Tao Hong approximately 10 min (
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268 Tao Hong frequently caused prob
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270 Tao Hong for the use of the 16S
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272 Tao Hong of MRSA. The coagulase
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274 Tao Hong Gürtler, V., & Barrie
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17 Microarray-Based Microbial Ident
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278 T.J. Gentry and J. Zhou These a
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280 T.J. Gentry and J. Zhou the des
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282 T.J. Gentry and J. Zhou Communi
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284 T.J. Gentry and J. Zhou PCR-bas
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286 T.J. Gentry and J. Zhou Althoug
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288 T.J. Gentry and J. Zhou Korczak
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290 T.J. Gentry and J. Zhou Willse,
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292 X. Qin allow real-time monitori
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294 X. Qin which the observed fluor
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296 X. Qin that there would be no G
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298 X. Qin 2005). Furthermore, the
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300 X. Qin Cattoli, G., Drago, A.,
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302 X. Qin Kostrikis, L.G., Touloum
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304 X. Qin Ririe, K.M., Rasmussen,
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19 Amplification Product Inactivati
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308 S. Sefers and Y-W. Tang Most de
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310 S. Sefers and Y-W. Tang UNG Pro
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312 S. Sefers and Y-W. Tang 4' Psor
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314 S. Sefers and Y-W. Tang Isopsor
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316 S. Sefers and Y-W. Tang used is
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318 S. Sefers and Y-W. Tang Conclus
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Part II Applications
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324 X.Y. Han TABLE 20.1. The number
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326 X.Y. Han Homology Search and Re
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328 X.Y. Han TABLE 20.2. Examples o
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330 X.Y. Han Conclusion In summary,
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332 X.Y. Han Shimizu, T., Ohtani, K
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TABLE 21.1. Licensed / Approved Cli
Page 692:
TABLE 21.1. (Continued) Tradename(s
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TABLE 21.1. (Continued) Tradename(s
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340 Y. Hu and I. Hirshfield gel ele
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342 Y. Hu and I. Hirshfield Since 1
Page 708:
344 Y. Hu and I. Hirshfield they ar
Page 712:
346 Y. Hu and I. Hirshfield Antibod
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348 Y. Hu and I. Hirshfield all ove
Page 720:
350 Y. Hu and I. Hirshfield chances
Page 724:
352 Y. Hu and I. Hirshfield Tang, Y
Page 728:
354 A. C. T. Lo and K. M. Kam in tu
Page 732:
356 A. C. T. Lo and K. M. Kam is no
Page 736:
358 A. C. T. Lo and K. M. Kam stabl
Page 740:
360 A. C. T. Lo and K. M. Kam Stran
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362 A. C. T. Lo and K. M. Kam organ
Page 748:
364 A. C. T. Lo and K. M. Kam probe
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366 A. C. T. Lo and K. M. Kam major
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368 A. C. T. Lo and K. M. Kam Molec
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370 A. C. T. Lo and K. M. Kam a sec
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372 A. C. T. Lo and K. M. Kam cervi
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374 A. C. T. Lo and K. M. Kam E6 an
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376 A. C. T. Lo and K. M. Kam M. (2
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378 A. C. T. Lo and K. M. Kam Hippe
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380 A. C. T. Lo and K. M. Kam Larse
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382 A. C. T. Lo and K. M. Kam Nobbe
Page 788:
384 A. C. T. Lo and K. M. Kam chlam
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386 A. C. T. Lo and K. M. Kam ureal
Page 796:
388 A. Kilic and W. Drake Lipids wi
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390 A. Kilic and W. Drake America,
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392 A. Kilic and W. Drake MTB from
Page 808:
394 A. Kilic and W. Drake with anti
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396 A. Kilic and W. Drake Molecular
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398 A. Kilic and W. Drake and monit
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400 A. Kilic and W. Drake system; t
Page 824:
402 A. Kilic and W. Drake transillu
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404 A. Kilic and W. Drake Real-Time
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406 A. Kilic and W. Drake Caws, M.,
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408 A. Kilic and W. Drake Marttila,
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410 A. Kilic and W. Drake Torres, M
Page 844:
412 P. Francois and J. Schrenzel an
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414 P. Francois and J. Schrenzel th
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416 P. Francois and J. Schrenzel A
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418 P. Francois and J. Schrenzel St
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420 P. Francois and J. Schrenzel Ac
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422 P. Francois and J. Schrenzel or
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424 P. Francois and J. Schrenzel Lo
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426 P. Francois and J. Schrenzel Va
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428 D. Ernst et al. several microme
Page 880:
430 D. Ernst et al. reanalysis to d
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432 D. Ernst et al. Neisseria menin
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434 D. Ernst et al. A. B. SEB-beads
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436 D. Ernst et al. IL-6, IL-8, and
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pg/ml 120 100 80 60 40 20 0 120 100
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440 D. Ernst et al. Although interf
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442 D. Ernst et al. Lal, G., Balmer
Page 908:
26 Molecular Strain Typing Using Re
Page 912:
446 S. R. Frye and M. Healy FIGURE
Page 916:
448 S. R. Frye and M. Healy Automat
Page 920:
450 S. R. Frye and M. Healy TABLE 2
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452 S. R. Frye and M. Healy Noncomm
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454 S. R. Frye and M. Healy 2001).
Page 932:
456 S. R. Frye and M. Healy (Stempe
Page 936:
458 S. R. Frye and M. Healy isolate
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460 S. R. Frye and M. Healy molecul
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462 S. R. Frye and M. Healy Boerlin
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464 S. R. Frye and M. Healy Fey, P.
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466 S. R. Frye and M. Healy Kwara,
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468 S. R. Frye and M. Healy Pfaller
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470 S. R. Frye and M. Healy Tang, Y
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27 Molecular Differential Diagnoses
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474 J. Han The technology advanceme
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476 J. Han Targets Optimal Conditio
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478 J. Han TABLE 27.1. Comparison o
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480 J. Han TABLE 27.3. Comparison o
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482 J. Han suspension hybridization
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484 J. Han fluorescent dye is remov
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486 J. Han TABLE 27.5. List of path
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TABLE 27.8. Detection results of th
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490 J. Han common in HAI. In additi
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492 J. Han TABLE 27.12. Detection r
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494 J. Han TABLE 27.14. List of pat
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496 J. Han TABLE 27.18. Detectable
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TABLE 27.20. List of gene targets i
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500 J. Han Benefits and Impact: Del
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502 J. Han significantly increasing
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504 J. Han Hindiyeh, M., Hillyard D
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506 E. M. Marlowe and D. M. Wolk Al
Page 1036:
TABLE 28.1. Automated specimen proc
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510 E. M. Marlowe and D. M. Wolk Au
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512 E. M. Marlowe and D. M. Wolk La
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514 E. M. Marlowe and D. M. Wolk me
Page 1052:
516 E. M. Marlowe and D. M. Wolk mo
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518 E. M. Marlowe and D. M. Wolk Mo
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520 E. M. Marlowe and D. M. Wolk Ha
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522 E. M. Marlowe and D. M. Wolk Sa
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Index A acetate utilization, 100 Ac
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Index 527 rapid antigen tests, 27-2
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Index 529 flow cytometric immunoass
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Index 531 Human T-Lymphotropic Viru
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Index 533 MLEE. See multilocus enzy
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Index 535 PNA. See peptide-nucleic
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Index 537 Roseomonas, 328-329 rotav
Page 1096:
Index 539 T TaqMan probes, 293-296
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