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Chapter 6 studies may solve some of the questions surrounding this topic. Whole genome sequencing of the SAGOXB.0066 strain and other S. Agona strains was undertaken during this research by collaborators (Professor Mark Achtman et al. University College Cork [185]). All S. Agona strains involved in this research were referred to the whole genome research group at UCC. However, due to time constrains the project did not assess the sequences generated specifically for biofilm related genes. It would have been of interest to investigate if there were any important differences in genes up/down regulated that differentiated the density of biofilm formed by particular strains over an extended period of time. For example, the two S. Agona strains had notable different biofilm density levels after 168 hours biofilm formation. RNA samples were isolated from each biofilm run using Total RNA freeze and archived at -80°C following the recommended conditions. Due to time constrains, the achieved samples were not used for microarray studies, as initially desired. Moreover, it would have been of use to identify the main biofilm properties that lead to resistance to the disinfectant agents, such as particular proteins contained in the EPS and if the EPS was dependent on the biofilm substratum. Most food processing environments, a biofilm may consist of multiple species of organisms. As a result it may be of interest to consider the inclusion of multiple organisms in laboratory based biofilm studies. Examining S. enterica biofilm density when developed in a mixed biofilm was also discussed for inclusion in this project. However, due to time constraints, it was determined that it may be more appropriate to undertake mixed species biofilm after single species biofilm studies are Page 219
Chapter 6 better understood. The research presented in this thesis provides comprehensive investigation into the density of S. enterica biofilm formed on contact surfaces, the density of biofilm formed after an extensive period of time and the efficacy of disinfectant agents against an established S. enterica biofilm. Moreover, the research presented in this thesis provides a clearer description on the level of repeatability using biofilm development models and the caution needed when suggesting significant differences between strains based on a limited number of strains, biofilm substrata or repeated measures. Page 220
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Salmonella enterica - biofilm forma
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Table of Contents Page Number 1.16.
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Table of Contents Page Number 4.1.2
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Table of Contents Page Number 6.8.4
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List of Abbreviations Table Page Nu
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List of Abbreviations List of Abbre
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Summary of Content Summary of Conte
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“To show your true ability is alw
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Acknowledgements ever met, Fiona th
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Acknowledgements This Ph.D. thesis
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Chapter 1 1.1. Salmonella Salmonell
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Chapter 1 may impose enormous costs
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Chapter 1 cracks or penetration of
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Chapter 1 detected by agglutination
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Chapter 1 become colonized with >10
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Chapter 1 antigens [z27],[z45] [1].
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Chapter 1 S. Agona has also been im
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Chapter 1 isolated from undercooked
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Chapter 1 The S. Typhimurium strain
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Chapter 1 ecosystem with the use of
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Chapter 1 [82]. Previous research h
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Chapter 1 to genes involved in flag
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Chapter 1 observation has also been
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Chapter 1 [119] and flow cell react
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Chapter 1 based disinfectant) the s
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Chapter 1 formation of two strains
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Chapter 1 shield the S. Agona cells
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Chapter 1 Key Objectives of this st
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Chapter 2 2. Abstract Food-borne pa
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Chapter 2 indicated that there may
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Chapter 2 taken from industrial set
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Chapter 2 2.1.4. CDC Biofilm Reacto
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Chapter 2 can be performed without
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Chapter 2 To summarise, previous au
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Chapter 2 2.3. Methods for examinin
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Chapter 2 and the biofilm formed th
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Chapter 2 2.4. Statistical Analysis
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Chapter 2 Table 2.1: Strain charact
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Chapter 2 XII. The gas port and med
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Chapter 2 II. Primary fixative cons
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Chapter 2 IX. Once the conditions w
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Chapter 2 Figure 2.1: Image of CBR
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Chapter 2 2.6. Results 2.6.1. Asses
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Chapter 2 2.6.3. SEM Analysis of su
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Chapter 2 Figure 2.6: Complete remo
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Chapter 2 2.6.5. Mean log 10 densit
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Chapter 2 2.6.6. Mean log 10 densit
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Chapter 2 Table 2.5: Mean log 10 de
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Chapter 2 The results displayed in
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Chapter 2 Table 2.7: Difference bet
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Chapter 2 Table 2.8: The mean log 1
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Chapter 2 Figure 2.7: Graph of the
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Chapter 2 also used “high” soni
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Chapter 2 2.8. Summary All 13 strai
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Chapter 3 3. Abstract It has been e
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Chapter 3 classified as persistent
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Chapter 3 was plated onto TSA for e
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Chapter 3 Figure 3.1: The mean log
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Chapter 3 Figure 3.3: SEM image of
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Chapter 3 Table 3.2: Difference bet
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Chapter 3 3.4.3. Intra-serovar vari
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Chapter 3 3.4.4. Strain variation i
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Chapter 3 3.4.5. The density of bio
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Chapter 3 3.5. Discussion As illust
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Chapter 3 As discussed in section 3
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Chapter 3 increased biofilm appeare
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Chapter 4 Examining the efficacy of
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Chapter 4 through laboratory based
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Chapter 4 acid and quaternary ammon
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Chapter 4 the surface the temperatu
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Chapter 4 availability of multiple
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Chapter 4 peracetic acid (100, 200,
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Chapter 4 As discussed previously,
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Chapter 4 Dey/Engley (Difco) neutra
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Chapter 4 sterilisation was achieve
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Chapter 4 IX. Aliquots of 100µl of
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Chapter 4 XV. XVI. XVII. XVIII. XIX
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Chapter 4 4.3. Results 4.3.1. Suspe
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Chapter 4 Table 4.3: Mean log 10 de
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Chapter 4 Benzalkonium chloride was
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Chapter 4 4.4. Discussion Suspensio
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Chapter 4 effective at eliminating
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Chapter 4 Surprisingly, Nguyen et a
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Chapter 4 though a contact time of
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Chapter 4 provide a more standardis
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Chapter 4 hours instead of the stan
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Chapter 5 5. Abstract Examining bio
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Chapter 5 dry and rough (bdar) morp
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Chapter 5 absence of curli and cell
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Chapter 5 studies such as the micro
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Chapter 5 discussed in chapter 4. T
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Chapter 5 5.2. Methods 5.2.1. Colon
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Chapter 5 XIII. XIV. XV. XVI. XVII.
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Chapter 5 XVI. XVII. XVIII. XIX. XX
Page 190 and 191: Chapter 5 5.3.2. Repeatability of m
Page 192 and 193: Chapter 5 Figure 5.2: Stained biofi
Page 194 and 195: Chapter 5 was formed at room temper
Page 196 and 197: Chapter 5 Table 5.3: The density of
Page 198 and 199: Chapter 5 5.3.4. The density of bio
Page 200 and 201: Chapter 5 Table 5.6: The difference
Page 202 and 203: Chapter 5 Table 5.7: The difference
Page 204 and 205: Chapter 5 Table 5.8: Summary of ass
Page 206 and 207: Chapter 5 interpretation therefore
Page 208 and 209: Chapter 5 measures of S. enterica b
Page 210 and 211: Chapter 5 cells peaks [165, 191]. D
Page 212 and 213: Chapter 5 5.5. Limitations of the s
Page 214 and 215: Chapter 6 Discussion of S. enterica
Page 216 and 217: Chapter 6 However, a number of auth
Page 218 and 219: Chapter 6 It is of interest to exam
Page 220 and 221: Chapter 6 were similar at 48 hours.
Page 222 and 223: Chapter 6 attributable to a small n
Page 224 and 225: Chapter 6 chosen as an appropriate
Page 226 and 227: Chapter 6 undetermined. However, th
Page 228 and 229: Chapter 6 reason for this may be du
Page 230 and 231: Chapter 6 Moreover, based on the re
Page 232 and 233: Chapter 6 responsible for increased
Page 234 and 235: Chapter 6 not fully capture the ran
Page 236 and 237: Chapter 6 However, the extent of bi
Page 238 and 239: Chapter 6 6.10. Conclusions and rec
Page 242 and 243: Bibliography Bibliography Page 221
Page 244 and 245: Bibliography 12. T. Takata, J.L., H
Page 246 and 247: Bibliography 29. Barker, J., M. Nae
Page 248 and 249: Bibliography 47. Threlfall, E.J., H
Page 250 and 251: Bibliography 65. CDC. Investigation
Page 252 and 253: Bibliography 83. Ledeboer, N., Frye
Page 254 and 255: Bibliography 100. Chia, T., Goulter
Page 256 and 257: Bibliography 117. Buckingham-Meyer,
Page 258 and 259: Bibliography 133. European Committe
Page 260 and 261: Bibliography Supernatant of a Hafni
Page 262 and 263: Bibliography 165. Díez-García, M.
Page 264 and 265: Bibliography cultivation of Staphyl
Page 266 and 267: Bibliography Compounds. 2012. Appli
Page 268 and 269: Bibliography 215. Buck, et al., A q
Page 270 and 271: Bibliography Canadian Journal of Ps
Page 272 and 273: Appendix 1 Appendix 1— List of Re
Page 274 and 275: Appendix 1 Appendix 1 - List of Equ
Page 276 and 277: Appendix 2 Colour index High outlie
Page 286 and 287: Appendix 3 Appendix 3-Figure 2: PFG
Page 288 and 289: Appendix 4 Poster Presentation Envi
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