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

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Yersinia PCR 323 20. Funk, J. A., Troutt, H. F., Isaacson, R. E., and Fossler, C .P. (1998) Prevalence of pathogenic Yersinia enterocolitica in groups of swine at slaughter. J. Food Prot. 61, 677–682. 21. de Boer, E. (1995) Isolation of Yersinia enterocolitica from foods, in Culture Media for Food Microbiology, vol. 34, Progress in Industrial Microbiology, (Corry, J. E. L., Curtis, G. D. W., and Baird, R. M., eds.), Elsevier Science B.V., Amsterdam, Netherlands, pp. 219–228. 22. Neubauer, H., Sprague, L. D., Scholz, H., and Hensel, A. (2001) The diagnostics of Yersinia enterocolitica infections: a review on classical identification techniques and new molecular biological methods. Berl. Münch. Tierärztl. Wochenschr. 114, 1–7. 23. Hill, W. E. (1996) The polymerase chain reaction: applications for the detection of foodborne pathogens. Crit Rev. Food Sci. Nutr. 36, 123–173. 24. Fredriksson-Ahomaa, M., Hielm, S. and Korkeala, H. (1999) High prevalence of yadA-positive Yersinia enterocolitica in pig tongues and minced meat at the retail level in Finland. J. Food. Prot. 62, 123–127. 25. Jourdan, A. D., Johnson, S. C., and Wesley, I. V. (2000) Development of a fluorogenic 5' nuclease PCR assay for detection of the ail gene of pathogenic Yersinia enterocolitica. Appl. Environ. Microbiol. 66, 3750–3755. 26. Bhaduri, S., and Cottrell, B. (1998) A simplified sample preparation method from various foods for PCR detection of pathogenic Yersinia enterocolitica: a possible model for other food pathogens. Mol. Cell. Probes 12, 79–83. 27. Vishnubhatla, A., Fung, D. Y., Oberst, R. D., Hays, M. P., Nagaraja, T. G., and Flood, S. J. (2000) Rapid 5' nuclease (Taq Man) assay for detection of virulent strains of Yersinia enterocolitica. Appl. Environ. Microbiol. 66, 4131–4135. 28. NMKL-163 (1998) Nordic committee on food analysis NMKL-163: Pathogenic Yersinia enterocolitica. PCR methods for detection in food. Esbo, Finland. 29. Lantz, P.G., Knutsson, R., Blixt, Y., Abu Al-Soud, W., 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. 30. Knutsson, R., Fontanesi, M., Grage, H. and Rådström, P. (2002) Development of a PCR-compatible enrichment medium for Yersinia enterocolitica: amplification precision and dynamic detection range during cultivation. Int. J. Food Microbiol. 72, 185–201. 31. ISO 3100–2 (1988) Meat and meat products—Sampling and preparation of test— Part 2: preparation of test samples for microbiological examination. International Organization for Standardization, Switzerland. 32. DIN 10113-1. (1997) Enumeration of viable aerobic bacteria of surfaces of utensils and equipment in contact with food. Deutsches Institut für Normung e.V. Berlin, Germany. 33. Knutsson, R., Blixt, Y., Grage, H., Borch, E., and Rådström, P. (2002) Evaluation of selective enrichment PCR procedures for Yersinia enterocolitica. Int. J. Food Microbiol. 73, 35–46.
324 Knutsson and Rådström 34. Heesemann, J., Keller, C., Morawa, R., Schmidt, N., Siemens, H. J., and Laufs, R. (1983) Plasmids of human strains of Yersinia enterocolitica: molecular relatedness and possible importance for pathogenesis. J. Infect. Dis. 147, 107–115. 35. Heesemann, J. and Grüter, L. (1987) Genetic evidence that outer membrane protein YOP1 of Yersinia enterocolitica mediates adherence and phagocytosis resistance to human epithelial cell. FEMS Microbiol. Lett. 40, 37–41. 36. Ruckdeschel, K., Roggenkamp, A., Schubert, S., and Heesemann, J. (1996) Differential contribution of Yersinia enterocolitica virulence factors to evasion of microbicidal action of neutrophils. Infect. Immun. 64, 724–733. 37. Gray, M. W., Sankoff, D., and Cedergren, R. J. (1984) On the evolutionary descent of organisms and organelles: a global phylogeny based on a highly conserved structural core in small subunit ribosomal RNA. Nucleic Acids Res. 12, 5837–5852. 38. Sambrook, J., Fritsch, E. F., and Maniatis, T. (1989) Molecular cloning: a laboratory manual, 2 nd ed., CSH Laboratory Press, Cold Spring Habor, New York, USA. 39. 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. 40. Abu Al-Soud, W., and Rådström, P. (2000) Effects of amplification facilitators on diagnostic PCR in the presence of blood, feces, and meat. J. Clin. Microbiol. 38, 4463–4470.
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TM Methods in Molecular Biology VOL
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4 Sachse 2. Selection of Target Seq
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Table 1 Target Sequences Used in PC
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8 Sachse Fig. 1. Structural organiz
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10 Sachse proteins (66-68), invasio
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12 Sachse Since there appears to be
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14 Sachse In the context of identif
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16 Sachse to partially compensate t
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18 Sachse nostic potential of PCR.
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20 Sachse product has to be confirm
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22 Sachse 7. van Camp, G., Fierens,
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24 Sachse 33. Rappelli, P., Are, R.
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26 Sachse 60. Furrer, B., Candrian,
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28 Sachse 89. Bloch, W. (1991) A bi
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30 Sachse
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32 Rådström et al. Fig. 1. Illust
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34 Rådström et al. immunoglobulin
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36 Rådström et al. and the captur
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Table 2 Comparison of the Performan
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40 Rådström et al. explain these
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42 Rådström et al. 5.1. Proteins
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44 Rådström et al. neous. Consequ
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46 Rådström et al. 11. Powell, H.
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48 Rådström et al. 39. Katcher, H
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50 Rådström et al. 73. Nagai, M.,
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52 Hoorfar and Cook 2. FOOD-PCR: A
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54 Hoorfar and Cook Fig. 2. Practic
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56 Hoorfar and Cook Fig. 4. The str
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Table 58 3 Hoorfar and Cook Test Co
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60 Hoorfar and Cook The choosing an
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62 Hoorfar and Cook 10. Demanding L
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64 Hoorfar and Cook 15. Anon. (1995
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66 Lübeck and Hoorfar ods for the
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68 Lübeck and Hoorfar amplificatio
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70 Lübeck and Hoorfar It may be ne
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72 Lübeck and Hoorfar specificity
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74 Lübeck and Hoorfar The latter i
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76 Lübeck and Hoorfar A simple che
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78 Lübeck and Hoorfar 13. Hanai, K
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80 Lübeck and Hoorfar 43. Mitchell
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82 Lübeck and Hoorfar 70. Lawrence
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84 Lübeck and Hoorfar 98. Lantz, P
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88 Frey Table 1 Presence of the Var
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90 Frey 13. Lysis buffer: 100 mM Tr
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92 Frey as template for PCR. In add
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94 Frey strains, including all sero
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96 Frey
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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
Page 269 and 270: 272 Christensen et al. 24. Fisher,
Page 271 and 272: 274 Christensen et al. 54. Hunt, M.
Page 273 and 274: 276 Malorny and Helmuth valent meta
Page 275 and 276: 278 Malorny and Helmuth 12. Apparat
Page 277 and 278: 280 Malorny and Helmuth 3.3. Amplif
Page 279 and 280: 282 Malorny and Helmuth Table 2 Vol
Page 281 and 282: 284 Malorny and Helmuth Table 4 PCR
Page 283 and 284: 286 Malorny and Helmuth 3. Wallace,
Page 285 and 286: 288 Malorny and Helmuth
Page 287 and 288: 290 Wastling and Mattsson is an imp
Page 289 and 290: 292 Wastling and Mattsson 2. Remove
Page 291 and 292: 294 Wastling and Mattsson Fig. 1. B
Page 293 and 294: 296 Wastling and Mattsson time PCR
Page 295 and 296: 298 Wastling and Mattsson
Page 297 and 298: 300 Pozio and La Rosa Table 1 Princ
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Page 301 and 302: 304 Pozio and La Rosa 3. Proteinase
Page 303 and 304: 306 Pozio and La Rosa Table 3 PCR-R
Page 305 and 306: 308 Pozio and La Rosa 2. Pepsin sho
Page 307 and 308: 310 Pozio and La Rosa
Page 309 and 310: 312 Knutsson and Rådström The ref
Page 311 and 312: 314 Knutsson and Rådström Fig. 1.
Page 313 and 314: 316 Knutsson and Rådström 2.4. El
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Page 319: 322 Knutsson and Rådström 4. Alek
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