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Acknowledgements ever met, Fiona the Duracell bunny in a white coat, you both have set such a high standard I can only aspire to achieve the same. Sandra it’s great to have you back in Galway and thanks for all the coffee breaks to keep me sane on my breaks away from the reading room. To Catherine, my “little sister” in the lab, you have always made work so much fun and I am really going to miss out chats by the kettle. You’re a great worker and you will be at this stage before you know it! Thanks to all the NSSLRL staff - Niall thanks for all your advice on Salmonella and on achieving “domestic success”. Jean, the horse whisperer, thank-you for your advice and help over the years. Both of you kindly acted as a “Salmonella encyclopaedia” over the last four years. I would also like to thank Tori for all your help over the years. I would also like to thank Akke Vellinga for all her help. Despite not always agreeing with my approach you always worked hard on everything and you were always willing to give advice- you have certainly provided me with a more cautious approach to stats and I have learnt to look beyond the elusive “P values”. I would also like to thank Teck who the Meds’ aptly describe as “a living legend”. His friendly nature and wealth of knowledge has made him a great addition to the Bact family. Also our latest edition, Siobhan who is always willing to help anyone and is a great asset to the department. I would also like to thank Mary Whelan, for all your advice and chats over the years – you were scientist, councillor and comrade to so many staff and students over the years. We all still miss you but I am delighted that you are having so much fun in your retirement. I would also like to thank Benjamin Kanagaratnam for not only spss tutorials but also helping me to reflect on life. Your advice was not to look at how fast you get to the end of your road, but the journey you take in getting there. Those words ring true now as I can see how many friends I have made over the years. Also I would like to say thank-you to the staff in the microbiology laboratory in GUH. Belinda a truly inspirational scientist and a big thanks to all the girls over in the main lab who have always helped out when I xvii
Acknowledgements needed to call in a favour. Also to the team upstairs in Virology, especially for Collette who always went out of her way to accommodate me and allowed me to use their plate reader. I really appreciate all your help. I would also like to thank Professor Peter Dockery, Pierce Lalor and Dr. Eaodin Timmins for allowing me to drop over to look at my ‘bugs’ under your careful assistance. Professor Dockery, I really appreciate you taking time out of your busy schedule to go through the possible microscopy options. Also thank-you Pierce for all your advice on SEM and Gaelic football, maybe this is Mayo’s year. Lastly, I would like to thank my supervisors Dr. Dearbháile Morris and Professor Martin Cormican for their constant support and guidance over the years. Dearbháile your presence in the office has created a wonderful family environment that has allowed everybody who has worked there to thrive. Martin, thank-you for our weekly meeting towards the end I always entered with one eye closed in worried anticipation but always left with pride and an enthusiasm to write more. You certainly have perfected the art of supervision over the years! To say I have learnt a lot from you would be an understatement. At this stage I am indebted to you for the years you have provided guidance, knowledge, advice and most of all - you patience on guiding me through the challenges of a PhD. xviii
Page 1: Salmonella enterica - biofilm forma
Page 4 and 5: Table of Contents Page Number 1.16.
Page 6 and 7: Table of Contents Page Number 4.1.2
Page 8 and 9: Table of Contents Page Number 6.8.4
Page 10 and 11: List of Abbreviations Table Page Nu
Page 12 and 13: List of Abbreviations List of Abbre
Page 14 and 15: Summary of Content Summary of Conte
Page 16 and 17: “To show your true ability is alw
Page 20 and 21: Acknowledgements This Ph.D. thesis
Page 22 and 23: Chapter 1 1.1. Salmonella Salmonell
Page 24 and 25: Chapter 1 may impose enormous costs
Page 26 and 27: Chapter 1 cracks or penetration of
Page 28 and 29: Chapter 1 detected by agglutination
Page 30 and 31: Chapter 1 become colonized with >10
Page 32 and 33: Chapter 1 antigens [z27],[z45] [1].
Page 34 and 35: Chapter 1 S. Agona has also been im
Page 36 and 37: Chapter 1 isolated from undercooked
Page 38 and 39: Chapter 1 The S. Typhimurium strain
Page 40 and 41: Chapter 1 ecosystem with the use of
Page 42 and 43: Chapter 1 [82]. Previous research h
Page 44 and 45: Chapter 1 to genes involved in flag
Page 46 and 47: Chapter 1 observation has also been
Page 48 and 49: Chapter 1 [119] and flow cell react
Page 50 and 51: Chapter 1 based disinfectant) the s
Page 52 and 53: Chapter 1 formation of two strains
Page 54 and 55: Chapter 1 shield the S. Agona cells
Page 56 and 57: Chapter 1 Key Objectives of this st
Page 58 and 59: Chapter 2 2. Abstract Food-borne pa
Page 60 and 61: Chapter 2 indicated that there may
Page 62 and 63: Chapter 2 taken from industrial set
Page 64 and 65: Chapter 2 2.1.4. CDC Biofilm Reacto
Page 66 and 67: Chapter 2 can be performed without
Page 68 and 69:
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
Page 102 and 103:
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
Page 158 and 159:
Chapter 4 Table 4.3: Mean log 10 de
Page 160 and 161:
Chapter 4 Benzalkonium chloride was
Page 162 and 163:
Chapter 4 4.4. Discussion Suspensio
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Chapter 4 effective at eliminating
Page 166 and 167:
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
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Chapter 5 5.3.2. Repeatability of m
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Chapter 5 Figure 5.2: Stained biofi
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Chapter 5 was formed at room temper
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Chapter 5 Table 5.3: The density of
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Chapter 5 5.3.4. The density of bio
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Chapter 5 Table 5.6: The difference
Page 202 and 203:
Chapter 5 Table 5.7: The difference
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Chapter 5 Table 5.8: Summary of ass
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Chapter 5 interpretation therefore
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Chapter 5 measures of S. enterica b
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Chapter 5 cells peaks [165, 191]. D
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Chapter 5 5.5. Limitations of the s
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Chapter 6 Discussion of S. enterica
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Chapter 6 However, a number of auth
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Chapter 6 It is of interest to exam
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Chapter 6 were similar at 48 hours.
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Chapter 6 attributable to a small n
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Chapter 6 chosen as an appropriate
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Chapter 6 undetermined. However, th
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Chapter 6 reason for this may be du
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Chapter 6 Moreover, based on the re
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Chapter 6 responsible for increased
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Chapter 6 not fully capture the ran
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Chapter 6 However, the extent of bi
Page 238 and 239:
Chapter 6 6.10. Conclusions and rec
Page 240 and 241:
Chapter 6 studies may solve some of
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 278 and 279:
Page 280 and 281:
Page 282 and 283:
Page 284 and 285:
Page 286 and 287:
Appendix 3 Appendix 3-Figure 2: PFG
Page 288 and 289:
Appendix 4 Poster Presentation Envi
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