Denture acrylic biofilms

376 Pages·2017·29.84 MB·English

by  Daniel Morse

Denture acrylic biofilms:
microbial composition,
interactions and infection

Thesis submitted in the part-fulfilment of the requirements
of the degree of Doctor of Philosophy

Daniel James Morse
Oral and Biomedical Sciences
School of Dentistry
Cardiff University

2017
DECLARATION

This work has not been submitted in substance for any other degree or award
at this or any other university or place of learning, nor is being submitted
concurrently in candidature for any degree or other award.
Signed (candidate) Date 6th April 2018
STATEMENT 1
This thesis is being submitted in partial fulfilment of the requirements for the
degree of PhD.
Signed (candidate) Date 6th April 2018
STATEMENT 2
This thesis is the result of my own independent work/investigation, except
where otherwise stated, and the thesis has not been edited by a third party
beyond what is permitted by Cardiff University’s Policy on the Use of Third
Party Editors by Research Degree Students. Other sources are acknowledged
by explicit references. The views expressed are my own.
Signed (candidate) Date 6th April 2018
STATEMENT 3
I hereby give consent for my thesis, if accepted, to be available online in the
University’s Open Access repository and for inter-library loan, and for the title
and summary to be made available to outside organisations.
Signed (candidate) Date 6th April 2018
STATEMENT 4: PREVIOUSLY APPROVED BAR ON ACCESS
I hereby give consent for my thesis, if accepted, to be available online in the
University’s Open Access repository and for inter-library loans after expiry of
a bar on access previously approved by the Academic Standards &
Quality Committee.
Signed .......N/A........... (candidate) Date .............N/A.............

i
Acknowledgements
I would like to start by thanking my supervisory team; Prof. David Williams,
Dr. Melanie Wilson, Dr. Xiaoqing Wei, Prof. Mike Lewis and Dr. David Bradshaw.
There are no words to show my appreciation for giving me the opportunity to pursue
my dream of completing a PhD, and for the continued support and positivity for these
past four years. I am eternally grateful, and hope that I can someday begin to repay
my debt! I am extremely grateful for the support of the Engineering and Physical
Sciences Research Council, and GlaxoSmithKline Consumer Healthcare who funded
this PhD with an EPSRC-GSK Case Award studentship. This funding provided many
opportunities to pursue experimental ideas, and supported numerous trips to national
and international conferences to present my work.

Secondly, a PhD is a task of developing research independence, but so much
additional professional support happens behind the scenes. The PhD is a learning
process, and along the way I have gained invaluable knowledge and skills. It is difficult
to name everyone, but in particular I would like to thank Dr Yuri Cavalcanti, with whom
I worked alongside during his visiting research year, Ms Lucy Marsh for her academic
and personal support throughout my PhD journey, and Dr Rachael Jordan for taking
me under her wings when I first started and making the most difficult times that much
easier (and for answering my never-ending Candida questions). Dr Helen Rogers and
Dr Jeff Wilson for collection of the clinical samples and clinical advice, Dr Ann Smith
for support with the clinical study data analysis and interpretation. Dr Kirsty Sands, Dr
Paola Marino, Dr Josh Twigg; all part of the DW research group. Also, my sincere
gratitude for the support of Dr Craig Murdoch, Dr Helen Colley, Dr Lucie Hadley and
Mr Luke Jennings during my visit to University of Sheffield. Of course, the professional
and technical support from the ‘Tech Team’ at DENTL, and sorry to Dr Sarah Bamford
for my inability to ‘let go’ of my old agar plates in the culture fridge.

Thanks to all the friends I have made along this arduous journey; particularly
Jordanna (George), Elen, Rhiannon, Paul, Helen, Jabur, Daf, Hayley and Sue, and
everyone who has ever expressed an interest and spoken to me about my research
at conferences – I found inspiration in every conversation!

Finally, a massive thank you to my wife Lauren, without the support of whom I would
not have been in a position to follow my dream of completing a PhD; my two sons,
Ruben and Oliver who mean the absolute world to me, and give me a hundred
reasons to smile every day; my parents Lynda and Chris, Ian, Jen, and extended
families, and a special thank you to my mother in-law Shelley for her fantastic support
at home. Also, to my late grandmother, Joan, who always believed in me – I hope that
I have, and can continue to make you proud.

“If you think you can do it, you’re probably right!” Mr Alan Bootle
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Table of Contents
DECLARATION ..................................................................................................................................... i
Acknowledgements ............................................................................................................................ ii
List of tables ....................................................................................................................................... ix
List of figures .................................................................................................................................... xii
Preface ............................................................................................................................................... xx
Abstract ............................................................................................................................................. xxi
Chapter 1 .............................................................................................................................................. 1
Literature review ................................................................................................................................. 1
1.1 Biofilms ................................................................................................................................ 2
1.1.1 Introduction to biofilms and their ubiquitous prevalence ................................................. 2
1.1.1.1 The makeup and structure of biofilms .................................................................... 2
1.1.1.2 The role of extracellular DNA in biofilms ................................................................ 4
1.1.1.3 Biofilms in nature .................................................................................................... 5
1.1.1.4 Biofilms in medicine ................................................................................................ 5
1.1.2 Development of biofilms – a dynamic series of events ................................................... 7
1.1.2.1 Acquired surface pellicle, and subsequent microbial attachment and adherence of
primary colonisers to the surface ............................................................................................. 9
1.1.2.2 Biofilm maturation; arrival of secondary colonisers and development of 3D biofilm
architecture ............................................................................................................................ 10
1.1.2.3 The mature biofilm, microbial cell dispersal and subsequent implications ........... 12
1.1.3 Microbial interactions and responses to environmental factors .................................... 14
1.1.3.1 Quorum sensing ................................................................................................... 14
1.1.3.2 Inter-kingdom interactions .................................................................................... 15
1.1.4 Antimicrobials and their decreased efficacy against biofilms ........................................ 16
1.1.4.1 Physical mechanisms of biofilm protection ........................................................... 17
1.1.4.2 Active mechanisms of protection .......................................................................... 18
1.1.4.3 Persister cells ....................................................................................................... 19
1.2 The oral cavity ................................................................................................................... 20
1.2.1 The anatomy of the oral cavity ...................................................................................... 20
1.2.2 The oral microbiome ...................................................................................................... 23
1.2.2.1 The journey to characterise the oral microbiome ................................................. 23
1.2.2.2 Characterisation of microbial hierarchy and their relationships ............................ 24
1.2.3 Dysbiosis and development or progression of disease ................................................. 29
1.2.4 The role of saliva in the oral cavity, and changes with presence of oral prostheses .... 30
1.3 Candida .............................................................................................................................. 30
1.3.1 Taxonomical classification and characteristics of Candida species .............................. 30
1.3.2 Candida virulence factors .............................................................................................. 31
1.3.2.1 Candida polymorphism ......................................................................................... 31
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1.3.2.2 Mechanism and regulation of yeast to hyphae morphological transition .............. 32
1.3.2.3 Biofilm formation and important transcriptional regulators ................................... 34
1.3.2.4 Adhesion ............................................................................................................... 35
1.3.2.5 Hydrolytic enzymes ............................................................................................... 38
1.3.2.6 Candidal invasion of epithelium ............................................................................ 39
1.4 Candidoses ........................................................................................................................ 41
1.4.1 Candidoses as human infections .................................................................................. 42
1.4.1.1 Localised Candida infections ................................................................................ 42
1.4.1.2 Systemic Candida-associated infections .............................................................. 43
1.4.2 Oral candidoses............................................................................................................. 43
1.4.2.1 Chronic hyperplastic candidosis ........................................................................... 43
1.4.2.2 Pseudomembranous candidosis .......................................................................... 44
1.4.2.3 Erythematous candidosis...................................................................................... 46
1.4.2.4 Denture-associated stomatitis (DS) ...................................................................... 47
1.4.2.5 Microbial content of DS associated biofilms ......................................................... 49
1.4.3 Treatment of candidoses ............................................................................................... 51
1.5 Summary............................................................................................................................ 52
1.6 Project aims and objectives ............................................................................................... 53
Chapter 2 ............................................................................................................................................ 54
Denture-associated biofilm development and microbial interactions ........................................ 54
2.1 Introduction ........................................................................................................................ 55
2.2 Materials and Methods ...................................................................................................... 59
2.2.1 Microorganisms and culture conditions ......................................................................... 59
2.2.1.1 Overview of microorganisms used in this research .............................................. 59
2.2.2 Preparation of microorganisms, dental materials and experimental reagents .............. 59
2.2.2.1 Microbial culture conditions .................................................................................. 59
2.2.2.2 Standardisation of inocula .................................................................................... 60
2.2.2.3 Denture acrylic (poly(methyl-methacrylate), PMMA) coupon preparation ............ 60
2.2.2.4 Preparation of artificial saliva (AS) solution .......................................................... 61
2.2.2.5 Pre-conditioning PMMA coupons with AS ............................................................ 61
2.2.3 Adherence assay ........................................................................................................... 62
2.2.3.1 Aseptic transfer and inoculation of microorganisms to PMMA ............................. 62
2.2.3.2 Enumeration of adhered microorganisms ............................................................. 62
2.2.3.3 Fluorescence microscopy of adhered microorganisms ........................................ 63
2.2.4 Biofilm development and analysis ................................................................................. 63
2.2.4.1 Single- and mixed-species biofilm development on PMMA surface .................... 63
2.2.4.2 Culture enumeration of biofilms ............................................................................ 64
2.2.4.3 Confocal laser scanning microscopy (CLSM) ...................................................... 64
2.2.4.4 Quantification of C. albicans hyphae .................................................................... 65
2.2.4.5 Scanning electron microscopy (SEM) .................................................................. 67
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2.2.5 Quantitative PCR (qPCR) for C. albicans virulence genes ........................................... 67
2.2.5.1 Extraction of RNA ................................................................................................. 67
2.2.5.2 Reverse transcription of RNA to cDNA (RT) ........................................................ 68
2.2.5.3 qPCR analysis ...................................................................................................... 69
2.3 Results ............................................................................................................................... 71
2.3.1 Effect of preconditioning acrylic coupons with artificial saliva on microbial attachment
and biofilm formation .................................................................................................................. 71
2.3.1.1 Adherence of Candida albicans to PMMA ............................................................ 71
2.3.1.2 Adherence of Streptococcus species to PMMA ................................................... 71
2.3.2 Single and mixed-species biofilm formation on PMMA ................................................. 76
2.3.2.1 Effect of artificial saliva pre-conditioning of PMMA on C. albicans-only and
bacteria-only 72h biofilms ...................................................................................................... 76
2.3.2.2 Effect of artificial saliva pre-conditioning on mixed-species (C. albicans and
bacteria) biofilms .................................................................................................................... 80
2.3.3 Effect of oral bacteria within mixed species biofilms on expression of specific
C. albicans virulence factors ...................................................................................................... 81
2.3.3.1 Use of a standardised microbial inoculum to develop biofilms for in vitro
interactions ............................................................................................................................. 82
2.3.3.2 Morphological transition from yeast to hyphae ..................................................... 82
2.3.3.3 Expression of C. albicans virulence genes ........................................................... 89
2.4 Discussion.......................................................................................................................... 92
2.5 Conclusions ....................................................................................................................... 97
Chapter 3 ............................................................................................................................................ 99
In vitro 3D oral mucosal tissue model development ..................................................................... 99
3.1 Introduction ........................................................................................................................ 99
3.2 Materials and methods .................................................................................................... 104
3.2.1 Cell types and culture conditions................................................................................. 104
3.2.2 Type I collagen extraction ........................................................................................... 105
3.2.3 Development of an in vitro keratinocyte-only oral mucosal tissue model ................... 105
3.2.3.1 Cell preparation and seeding .............................................................................. 105
3.2.3.2 Establishing air-liquid interface and tissue model maintenance ......................... 108
3.2.4 Development of a full thickness in vitro oral mucosal tissue model ............................ 108
3.2.4.1 Establishment of the lamina propria ................................................................... 110
3.2.4.2 Keratinocyte seeding and establishment of epithelial layer................................ 111
3.2.4.3 Establishing the air-liquid interface to initiate tissue maturation in a 3D manner
and stratification ................................................................................................................... 111
3.2.5 Tissue processing and preparation for analysis .......................................................... 112
3.2.6 Histological staining ..................................................................................................... 112
3.2.7 Observational analysis of tissue models ..................................................................... 113
3.2.7.1 Keratinocyte-only tissue model analysis ............................................................. 113
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3.2.7.2 Full-thickness tissue model analysis .................................................................. 113
3.3 Results ............................................................................................................................. 115
3.3.1 Commercially available epithelial tissue model ........................................................... 115
3.3.2 In vitro development of epithelial tissue model ........................................................... 116
3.3.2.1 Effect of cell seeding density on tissue model development .............................. 116
3.3.2.2 Effect of culture period on tissue model development ........................................ 116
3.3.3 Development of full thickness tissue models .............................................................. 118
3.3.3.1 MatTek models as ‘gold standard’ ...................................................................... 118
3.3.3.2 Establishment of lamina propria ......................................................................... 119
3.3.4 Initial in vitro studies to develop full thickness tissue model ....................................... 124
3.3.5 Full thickness model culture ........................................................................................ 125
3.4 Discussion........................................................................................................................ 129
3.5 Conclusions ..................................................................................................................... 134
Chapter 4 .......................................................................................................................................... 135
Biofilm infection of oral mucosal tissue models and host immune responses ....................... 135
4.1 Introduction ...................................................................................................................... 136
4.2 Materials and Methods .................................................................................................... 141
4.2.1 Commercially available tissue models and culture conditions .................................... 141
4.2.1.1 EpiSkin SkinEthic Reconstituted Human Oral Epithelium (RHOE) .................... 141
4.2.1.2 MatTek EpiOral tissue model ............................................................................. 141
4.2.2 Tissue model preparation for biofilm infection ............................................................. 142
4.2.3 Post-infection processing of tissue models ................................................................. 143
4.2.3.1 Tissue model removal and preparation for analysis ........................................... 143
4.2.3.2 Histological preparation, analysis and fluorescence in situ hybridisation (FISH)
analysis via confocal microscopy ......................................................................................... 144
4.2.3.3 Biofilm-induced tissue model damage ................................................................ 145
4.2.4 Expression of human genes ........................................................................................ 146
4.2.4.1 Nucleic acid extraction and purification .............................................................. 146
4.2.4.2 Quantitative PCR ................................................................................................ 146
4.2.5 Monocyte cell responses to challenge with Candida .................................................. 149
4.2.5.1 Monocyte cell culture conditions and preparation .............................................. 149
4.2.5.2 Preparation of bacterial lipopolysaccharide (LPS) and heat killed Candida
albicans (HKC) ..................................................................................................................... 149
4.2.5.3 Monocyte priming and challenge with Candida .................................................. 149
4.2.5.4 Interleukin-23 cytokine ELISA ............................................................................ 150
4.2.6 Flow cytometry for monocyte Dectin-1 cell surface receptors .................................... 151
4.3 Results ............................................................................................................................. 152
4.3.1 Effect of bacteria in mixed-species biofilms on subsequent pathogenicity and tissue
damage in tissue model infections ........................................................................................... 152
4.3.2 Epithelial tissue model infection .................................................................................. 152
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4.3.2.1 Infection of SkinEthic Reconstituted Human Oral Epithelium .......................... 152
4.3.2.2 Infection of in vitro keratinocyte models ............................................................. 157
4.3.3 Full-thickness tissue model infections ......................................................................... 159
4.3.3.1 Infection of MatTek full-thickness tissue models ................................................ 159
4.3.3.2 Infection of in vitro full-thickness (FT) tissue models .......................................... 163
4.3.4 C. albicans virulence gene expression during tissue model infection ......................... 166
4.3.5 Immune cell responses to bacterial LPS and C. albicans ........................................... 169
4.3.5.1 THP-1 monocyte cell gene expression when stimulated with LPS .................... 169
4.3.5.2 IL-23 production when stimulated with LPS and heat killed C. albicans ............ 172
4.4 Discussion........................................................................................................................ 175
4.5 Conclusions ..................................................................................................................... 184
Chapter 5 .......................................................................................................................................... 185
Metataxonomic analyses of bacterial communities at sites within the oral cavity of denture-
wearing patients, presenting with and without denture-associated stomatitis ....................... 185
5.1 Introduction ...................................................................................................................... 186
5.2 Materials and Methods .................................................................................................... 191
5.2.1 Ethical approval and patient recruitment ..................................................................... 191
5.2.1.1 Research ethics approval ................................................................................... 191
5.2.2 Patient recruitment and sample collection .................................................................. 191
5.2.3 Clinical sampling.......................................................................................................... 192
5.2.4 Laboratory processing of swab samples ..................................................................... 193
5.2.4.1 Total microbial DNA extraction from clinical swab samples ............................... 193
5.2.5 Laboratory processing of imprint cultures ................................................................... 194
5.2.6 Identification of microorganisms from clinical samples by molecular methods ........... 195
5.2.6.1 Pre-amplification of pan-fungal DNA .................................................................. 195
5.2.6.2 Real-time PCR of pre-amplified DNA ................................................................. 195
5.2.7 Metataxonomic profiling of bacterial microbiome of clinical swab samples using the
Illumina MiSeq two stage amplification protocol ...................................................................... 196
5.2.7.1 Primary stage amplification................................................................................. 197
5.2.7.2 Second stage amplification ................................................................................. 197
5.2.7.3 Standardisation of PCR products for next-generation sequencing .................... 197
5.2.7.4 Preparation of sequence library .......................................................................... 198
5.2.7.5 Data analysis ...................................................................................................... 198
5.2.7.6 Community analysis of individual bacterial species ........................................... 199
5.3 Results ............................................................................................................................. 200
5.3.1 Patient demographics .................................................................................................. 200
5.3.2 Detection of Candida species in samples ................................................................... 200
5.3.3 Identification of detected Candida species .................................................................. 205
5.3.4 Metataxonomic profiling of bacterial species present in swab samples...................... 205
5.3.4.1 Primary analysis of sequence reads ................................................................... 205
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5.3.4.2 Analysis of OTUs between sample sites ............................................................ 206
5.3.4.3 Diversity of bacteria detected at each sample site ............................................. 207
5.3.4.4 Bacterial diversity by abundance and evenness of spread – Shannon index .... 208
5.3.4.5 Similarity of patient groups by grouping using non-metric multidimensional scaling
(NMDS) plots ........................................................................................................................ 212
5.3.4.6 Phylotypic distancing analysis demonstrated with Bray’s heatmap dendograms to
determine group similarities ................................................................................................. 212
5.3.5 Presence and differences in relative abundance of bacterial species detected at each
sample site ............................................................................................................................... 217
5.3.5.1 Bacterial species on the denture surface ........................................................... 217
5.3.5.2 Bacterial species on the palatal mucosa ............................................................ 221
5.3.5.3 Bacterial species on the tongue ......................................................................... 224
5.3.6 Sample size power calculation .................................................................................... 227
5.3.7 Effect of smoking status on bacterial microbiome ....................................................... 229
5.4 Discussion........................................................................................................................ 233
5.5 Conclusions ..................................................................................................................... 242
Chapter 6 .......................................................................................................................................... 243
General discussion ......................................................................................................................... 243
References ....................................................................................................................................... 260
Appendix I ........................................................................................................................................ 290
Appendix II ....................................................................................................................................... 298
Appendix III ...................................................................................................................................... 314
Appendix IV ..................................................................................................................................... 329
Appendix V....................................................................................................................................... 342

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List of tables

Chapter 1
Table 1.1 Typical components of biofilm matrices 3
Table 1.2 Biofilm related infections of the human body, and associated
with medical devices 7
Table 1.3 Categories and descriptions of relationships between
organisms 26
Table 1.4 Summary table of different roles of microorganisms within
polymicrobial communities and hosts 28
Table 1.5 Selected known virulence proteins and their associated roles in
candida virulence. 37
Table 1.6 Predisposing factors associated with development of oral
candidosis 45
Table 1.7 Summary of findings in a number of published studies to
investigate biofilms associated with denture stomatitis 50

Chapter 2
Table 2.1 List of microorganisms used in this research 59
Table 2.2 Fluorescent dyes used for confocal microscopy analysis of
biofilms 66
Table 2.3 Forward (F) and reverse (R) primers used for evaluation of C.
albicans virulence genes via quantitative polymerase chain reaction
(qPCR) 70
Table 2.4 Effect of artificial saliva pre-conditioning of acrylic coupons on
C. albicans adherence as measured by number of recovered viable C.
albicans. 73
Table 2.5 Effect of artificial saliva pre-conditioning of acrylic coupons on
S. sanguinis adherence as measured by number of recovered viable
S. sanguinis 75
Table 2.6 Effect of artificial saliva pre-conditioning of acrylic coupons on
formation of single-species 72h biofilms as measured by number of
recovered viable cells 77
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