PCR Detection of Microbial Pathogens PCR Detection of Microbial ...

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Pre-PCR Processing 45 In the future development of diagnostic PCR assays, research on pre-PCR processing is most likely to expand in response to the growing demand for rapid, robust and user-friendly PCR protocols. A future challenge for pre-PCR processing strategies is the design of PCR procedures integrating both sampling and DNA amplification as automated operations. Acknowledgments This work was supported by grants from VINNOVA, the Swedish Agency for Innovation Systems, and from the Commission of the European Community within the program “Quality of Life and Management of Living Resources,” QLRT-1999-00226. References 1. Lantz, P. G., Abu Al-Soud, W., Knutsson, R., Hahn-Hägerdal, B., and Rådström, P. (2000) Biotechnical use of the polymerase chain reaction for microbiological analysis of biological samples. Biotechnol. Annu. Rev. 5, 87–130. 2. Abu Al-Soud, W., and Rådström, P. (1998) Capacity of nine thermostable DNA polymerases to mediate DNA amplification in the presence of PCR-inhibiting samples. Appl. Environ. Microbiol. 64, 3748–3753. 3. Rossen, L., Nørskov, P., Holmstrøm, K., and Rasmussen, O. F. (1992) Inhibition of PCR by components of food samples, microbial diagnostic assays and DNAextraction solutions. Int. J. Food Microbiol. 17, 37–45. 4. Wilson, I. G. (1997) Inhibition and facilitation of nucleic acid amplification. Appl. Environ. Microbiol. 63, 3741–3751. 5. Abu Al-Soud, W., and Rådström, P. (2001) Purification and characterization of PCR-inhibitory components in blood cells. J. Clin. Microbiol. 39, 485–493. 6. Lantz, P. -G., Matsson, M., Wadström, T., and Rådström, P. (1997) Removal of PCR inhibitors from human faecal samples through the use of an aqueous twophase system for sample preparation prior to PCR. J. Microbiol. Methods 28, 159–167. 7. Monteiro, L., Bonnemaison, D., Vekris, A., et al. (1997) Complex polysaccharides as PCR inhibitors in feces: Helicobacter pylori model. J. Clin. Microbiol. 35, 995–998. 8. Kim, C. H., Khan, M., Morin, D. E., et al. (2001) Optimization of the PCR for detection of Staphylococcus aureus nuc gene in bovine milk. J. Dairy Sci. 84, 74–83. 9. Akane, A., Matsubara, K., Nakamura, H., Takahashi, S. and Kimura, K. (1994) Identification of the heme compound copurified with deoxyribonucleic acid (DNA) from bloodstains, a major inhibitor of polymerase chain reaction (PCR) amplification. J. Forensic Sci. 39, 362–372. 10. Tsai, Y. L., and Olson, B. H. (1992) Rapid method for separation of bacterial DNA from humic substances in sediments for polymerase chain reaction. Appl. Environ. Microbiol. 58, 2292–2295.
46 Rådström et al. 11. Powell, H. A., Gooding, C. M., Garret, S. D., Lund, B. M., and McKee, R.A. (1994) Proteinase inhibition of the detection of Listeria monocytogenes in milk using the polymerase chain reaction. J. Clin. Microbiol. 18, 59–61. 12. Khan, G., Kangro, H. O., Coates, P. J., and Heath, R. B. (1991) Inhibitory effects of urine on the polymerase chain reaction for cytomegalovirus DNA. J. Clin. Pathol. 44, 360–365. 13. Abu Al-Soud, W. A., Jönsson, L. J., and Rådström, P. (2000) Identification and characterization of immunoglobulin G in blood as a major inhibitor of diagnostic PCR. J. Clin. Microbiol. 38, 345–350. 14. Byrnes, J. J., Downey, K. M., Esserman, L., and So, A.G. (1975) Mechanism of hemin inhibition of erythroid cytoplasmic DNA polymerase. Biochemistry 14, 796–799. 15. Jaffe, R. I., Lane, J. D., and Bates, C.W. (2001) Real-time identification of Pseudomonas aeruginosa direct from clinical samples using a rapid extraction method and polymerase chain reaction (PCR). J. Clin. Lab. Anal. 15, 131–137. 16. Bailey, J. S. (1998) Detection of Salmonella cells within 24 to 26 hours in poultry samples with the polymerase chain reaction BAX system. J. Food Prot. 61, 792–795. 17. Dahlenborg, M., Borch, E., and Rådström, P. (2001) Development of a combined selection and enrichment PCR procedure for Clostridium botulinum types B, E and F and its use to determine prevalence in fecal samples from slaughter pigs. Appl. Environ. Microbiol. 67, 4781–4789. 18. Fahle, G. A., and Fischer, S. H. (2000) Comparison of six commercial DNA extraction kits for recovery of cytomegalovirus DNA from spiked human specimens. J. Clin. Microbiol. 38, 3860–3863. 19. Freise, J., Gerard, H. C., Bunke, T., et al. (2001) Optimised sample DNA preparation for detection of Chlamydia trachomatis in synovial tissue by polymerase chain reaction and ligase chain reaction. Ann. Rheum. Dis. 60, 140–145. 20. Lantz, P. G., Knutsson, R., Blixt, Y., Al Soud, W. A., Borch, E., and Rådström, P. (1998) Detection of pathogenic Yersinia enterocolitica in enrichment media and pork by a multiplex PCR: a study of sample preparation and PCR- inhibitory components. Int. J. Food Microbiol. 45, 93–105. 21. Shafer, R. W., Levee, D. J., Winters, M. A., Richmond, K. L., Huang, D. and Merigan, T. C. (1997) Comparison of QIAamp HCV kit spin columns, silica beads, and phenol- chloroform for recovering human immunodeficiency virus type 1 RNA from plasma. J. Clin. Microbiol. 35, 520–522. 22. Kramvis, A., Bukofzer, S., and Kew, M. C. (1996) Comparison of hepatitis B virus DNA extractions from serum by the QIAamp blood kit, GeneReleaser, and the phenol-chloroform method. J. Clin. Microbiol. 34, 2731–2733. 23. Hallier-Soulier, S., and Guillot, E. (1999) An immunomagnetic separation polymerase chain reaction assay for rapid and ultra-sensitive detection of Cryptosporidium parvum in drinking water. FEMS Microbiol. Lett. 176, 285–289. 24. Antognoli, M. C., Salman, M. D., Triantis, J., Hernandez, J., and Keefe, T. (2001) A one-tube nested polymerase chain reaction for the detection of Mycobacterium
Page 1 and 2: TM Methods in Molecular Biology VOL
Page 3 and 4: 4 Sachse 2. Selection of Target Seq
Page 5 and 6: Table 1 Target Sequences Used in PC
Page 7 and 8: 8 Sachse Fig. 1. Structural organiz
Page 9 and 10: 10 Sachse proteins (66-68), invasio
Page 11 and 12: 12 Sachse Since there appears to be
Page 13 and 14: 14 Sachse In the context of identif
Page 15 and 16: 16 Sachse to partially compensate t
Page 17 and 18: 18 Sachse nostic potential of PCR.
Page 19 and 20: 20 Sachse product has to be confirm
Page 21 and 22: 22 Sachse 7. van Camp, G., Fierens,
Page 23 and 24: 24 Sachse 33. Rappelli, P., Are, R.
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Page 27 and 28: 28 Sachse 89. Bloch, W. (1991) A bi
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Page 33 and 34: 34 Rådström et al. immunoglobulin
Page 35 and 36: 36 Rådström et al. and the captur
Page 37 and 38: Table 2 Comparison of the Performan
Page 39 and 40: 40 Rådström et al. explain these
Page 41 and 42: 42 Rådström et al. 5.1. Proteins
Page 43: 44 Rådström et al. neous. Consequ
Page 47 and 48: 48 Rådström et al. 39. Katcher, H
Page 49 and 50: 50 Rådström et al. 73. Nagai, M.,
Page 51 and 52: 52 Hoorfar and Cook 2. FOOD-PCR: A
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Page 85 and 86: 88 Frey Table 1 Presence of the Var
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98 Ewalt and Bricker (named for the
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100 Ewalt and Bricker 4. Ethidium b
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102 Ewalt and Bricker Primer Cockta
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104 Ewalt and Bricker Fig. 2. Typic
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106 Ewalt and Bricker with betaine
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108 Ewalt and Bricker unused ethidi
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110 Englen et al. which campylobact
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112 Englen et al. 18. Dehydrated cu
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114 Englen et al. 3.1.3. Fecal Samp
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116 Englen et al. respectively), an
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118 Englen et al. Fig. 1. Identific
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120 Englen et al. 3. Goossens, H.,
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122 Englen et al.
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124 Sachse and Hotzel Table 1 Compa
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126 Sachse and Hotzel Table 2 Prime
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128 Sachse and Hotzel 7. Phenol: sa
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130 Sachse and Hotzel 4. Vortex mix
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132 Sachse and Hotzel Fig. 2. Speci
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134 Sachse and Hotzel In the latter
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136 Sachse and Hotzel 17. Longbotto
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138 Popoff spastic paralysis. The g
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Table 3 Primers for Toxin Gene Dete
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142 Popoff 18. Agarose gel loading
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144 Popoff Taq reaction buffer 1X,
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146 Popoff almost all C. perfringen
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148 Popoff 2. Add to each PCR tube
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150 Popoff 7. Hielm, S., Hyyttia, E
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152 Popoff 35. Wieckowski, E., Bill
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154 Berri et al. 2. Materials 1. C.
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156 Berri et al. 3.3.2. Vaginal Swa
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158 Berri et al. Fig. 1. Trans-PCR.
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160 Berri et al. Fig. 3. Sensitivit
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162 Berri et al.
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164 Gallien The first description o
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166 Gallien
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168 Gallien 2. Materials 2.1. Bacte
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170 Gallien 10. Ethidium bromide: 1
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Table 2 Components (in µL) of 25-
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Table 4 Components (in µL) of 25-
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176 Gallien 3.3. Specific Isolation
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Table 6 PCR Conditions for Subtypin
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180 Gallien Fig. 3. Photographic im
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182 Gallien 3. Boyce, T. G., Swerdl
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184 Gallien enteropathogenic E. col
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186 O'Connor This chapter will desc
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188 O'Connor 2.2. PCR of Enriched F
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190 O'Connor 4. Notes 1. In enrichi
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192 O'Connor 4. O’Sullivan, N., F
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194 Lester and LeFebvre titers (4).
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196 Lester and LeFebvre 3.1.2. Samp
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Fig. 1. Sensitivity of the PCR assa
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200 Lester and LeFebvre 5. Swart, K
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202 Skuce et al. Table 1 Significan
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204 Skuce et al. commercial kits. E
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206 Skuce et al. Fig. 1. Schematic
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208 Skuce et al. 5. Disposable ster
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210 Skuce et al. 2.5.2. Sequence An
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212 Skuce et al. 2. Carefully trans
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Table 4 Recommended PCR Amplificati
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216 Skuce et al. Fig. 3. PCR produc
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218 Skuce et al. Fig. 5. Spoligotyp
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220 Skuce et al. 14. Aranaz, A., Li
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222 Skuce et al.
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224 Khan Simultaneous detection of
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226 Khan 10. Incubate for 20 min at
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228 Khan 5. Periodically, multiplex
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230 Khan
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232 Hotzel et al. tis (2). Particul
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234 Hotzel et al. 8. Sodium dodecyl
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236 Hotzel et al. 3. Methods 3.1. D
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238 Hotzel et al. 3.1.5. Semen (see
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240 Hotzel et al. Fig. 1 Detection
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242 Hotzel et al. 4. Notes 1. The u
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244 Hotzel et al. in Mycoplasma Pro
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246 Hotzel et al.
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248 Kobisch and Frey PCR assay to d
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250 Kobisch and Frey Table 1 Oligon
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252 Kobisch and Frey 3.2.1. Prepara
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254 Kobisch and Frey First round of
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256 Kobisch and Frey References 1.
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258 Christensen et al. thrombotic m
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260 Christensen et al. Table 1 Spec
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Table 2 Oligonucleotide Primers for
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264 Christensen et al. 3.2. Extract
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Table 3 PCR Protocols for the Patho
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268 Christensen et al. 2. Apply fra
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270 Christensen et al. 7. To reduce
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272 Christensen et al. 24. Fisher,
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274 Christensen et al. 54. Hunt, M.
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276 Malorny and Helmuth valent meta
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278 Malorny and Helmuth 12. Apparat
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280 Malorny and Helmuth 3.3. Amplif
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282 Malorny and Helmuth Table 2 Vol
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284 Malorny and Helmuth Table 4 PCR
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286 Malorny and Helmuth 3. Wallace,
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288 Malorny and Helmuth
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290 Wastling and Mattsson is an imp
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292 Wastling and Mattsson 2. Remove
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294 Wastling and Mattsson Fig. 1. B
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296 Wastling and Mattsson time PCR
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298 Wastling and Mattsson
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300 Pozio and La Rosa Table 1 Princ
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302 Pozio and La Rosa regions; spot
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304 Pozio and La Rosa 3. Proteinase
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306 Pozio and La Rosa Table 3 PCR-R
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308 Pozio and La Rosa 2. Pepsin sho
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310 Pozio and La Rosa
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312 Knutsson and Rådström The ref
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314 Knutsson and Rådström Fig. 1.
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316 Knutsson and Rådström 2.4. El
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318 Knutsson and Rådström the swa
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320 Knutsson and Rådström Fig. 3.
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322 Knutsson and Rådström 4. Alek
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324 Knutsson and Rådström 34. Hee
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