Microbiology for dentists theme 1 Flashcards
1
Q
What are examples of microorgansims ?
A
bacteria viruses archaea fungi protozoa
2
Q
What are the origins of life ?
A
4 bn years ago cellular life came into being
2 bn years ago modern eukaryotes existed
0.5 bn years ago multicellular life evolved
3
Q
What is evolution ?
A
the process of change over time which results in new species
4
Q
What is phylogeny ?
A
evolutionary relationships between organisms
5
Q
How is phylogeny determined ?
A
genetic relationhips- looking at the rRNA gene
6
Q
Why is the rRNA gene used ?
A
present in all organisns
shows a high degree of variability
7
Q
What is the process for determining phylogeny ?
A
isolate DNA
Make copies of the rRNA gene
sequence the DNA
analyse and compare
8
Q
Which microorganisms dominate the tree of life ?
A
bacteria
arachaea
eukarya
9
Q
What are example of eukarya ?
A
protozoa
animals
fungi
plants
10
Q
What are archaea ?
A
they diverged from bacteria
they have some similarities to eukarya - similar DNA replication
correlation with periodontal disease
11
Q
What are protozoa ?
A
single celled eukaryotes
found in aquatic environments- dental unit waterlines
graze on bacteria
12
Q
What is an example of protozoa ?
A
plasmodium- malaria
13
Q
What are fungi ?
A
simple eukaryotes
make multicellular structures
grow as branched tubes
14
Q
What is the fungi cell wall made of ?
A
chitin
15
Q
What are viruses ?
A
obligate intracellular parasites
acellular
nucleic acid in a protein coat
evovle rapidly
16
Q
What are prions ?
A
proteinaceous infectious agents
proteins that have changed conformation from an alpha helix to a beta pleated sheet
they are autocatalytic- can cause further conformational changes
leads to degeneration in brain function
extremely resistant to heat
17
Q
How can prions be transmitted ?
A
contamianted food
hormone treatments
surgical instruments
18
Q
How is a prion formed ?
A
normal protein adopts a misfolded protein shape
prion binds to normal proteins
leads to the conversion of more protesins
19
Q
What do prions aggregate to form ?
A
amyloid fibrils
20
Q
How are amyloid fibrils made ?
A
from the stacking of beta pleated sheets
21
Q
What do amyloid fibrils do ?
A
disrupt cell function
cause neuro-degenerative disorders
22
Q
What type of neuro-degenerative disorders do prions cause ?
A
transmissable spongiform encephalopathies
23
Q
What are prions resistant to ?
A
heat resistant
protease resistant
24
Q
What are the 3 categories of prion disease ?
A
spontaneous
acquired
inherited
25
What is an example of a spontaneous prion disease ?
sporadic CJD
26
What is an example of inherited prion disease ?
familial CJD
27
What is an example of acquired prion disease ?
Kuru
28
Why do prions have long incubation periods ?
they replicate slowly
29
What property of prions allows them to form plaques ?
theyre insoluble
30
How is neuronal tissue death via prions visible ?
spongiform pathology
31
What is the relevance of prions to dentistry ?
dental tissues are considered low risk
could be iatrogenic transmission
difficult to destroy- essential to autoclave instruments and use single-use instruments
32
What is a major problem with prions ?
they cant be detected as they have no assay
33
What is the basic structure of a virus ?
a nucleic acid and a protein capsid coat
34
What are the 2 types of proteins ?
enveloped and non-enveloped
35
What are enveloped viruses ?
they consist of the nucleic acid and the protein capsid and the lipid layer which is embedded with glycoproteins
36
What are the 3 types of viral genome shapes ?
linear
circular
segmented
37
What are the 2 types of nucleic acid ?
DNA and RNA
| single stranded or double stranded
38
What is the purpose of the viral genome ?
to encode for proteins- structural, proteases and enzymes
39
Which enzymes do viruses need ?
reverse transcriptase
DNA polymerase
RNA polymerase
40
What is the mode of action for a virus ?
1. genome codes for proagation proteins
2. Infection of the host
3. Genome replication
4. Invasion of immune system
41
Which types of virues are most likely to cause disease ?
Single stranded RNA
| Double stranded DNA
42
What is the life cycle of a DNA virus ?
```
phagocyte brings virus
virus infects epithelial cell
harnesses replication machinery
trasncribe into RNA
RNA is translated into viral proteins
lysis - pathology
```
43
What is the life cycle of an RNA virus ?
viruses contain reverse transcriptase- convert viral RNA into DNA
Replicate DNA
Integration into the genome
transcribed and translated
more RT Made, capsid proteins and envelope proteins to assemble new viruses
44
What is persistence ?
some proviruses will insert into the viral chromosome and remain there- evade the immune system - latent
45
What is an example of an RNA enveloped virus ?
HIV
46
What is an example of an RNA non-enveloped virus ?
Rhino
47
What is an example of a DNA enveloped virus ?
Herpes
48
What is an example of a DNA non-enveloped virus ?
HPV
49
What are some viruses that are systematic but cna have oral effects ?
MMR
50
What are the oral signs of measles ?
rash-kopliks spots
51
What are the oral signs of mumps ?
salivary gland inflammation
52
What are the oral signs of rubella ?
Rash
53
What are some viral infections of the mouth ?
hand, foot and mouth disease
Herpes
HIV
54
What is hand, foot and mouth disease ?
enterovirus that causes oral blisters
55
What is Herpes ?
Large class of structurally similar viruses
56
What is HPV ?
linked to oral cancer
| causes papillomas of the oral mucosa and the genitals
57
Which HPV are associated with HPV ?
16 and 18
58
Which HPV are restricted to the oral cavity ?
13 and 32
59
What does HIV cause ?
AIDS
60
What is HIV Associated with ?
oral candidosis
| NUG
61
Which cells does HSV 1 infect ?
mucosal epithelial cells
| neuronal cells
62
How is HSV 1 latent ?
hides in the immune system until reactivated
63
What does reactivated HSV1 cause ?
stomatitis
64
How is HSV1 transmitted ?
through saliva
65
What are the factors that lead to NUG ?
stress
smoking
HPV
66
What plaque control methods are used for NUG ?
ultrasonic
chlorohexidine
metronidiazole
OHI
67
What are the symptoms of HSV1 ?
cold sores
68
What are the symptoms of Varicella-zoster ?
child- chicken pox
| adult-shingles
69
What are the symptoms of epstein barr ?
Glandular fever
70
What are the symptoms of cytomegalovirus ?
congential defects
71
What are the symptoms of HHV8?
Kaposis sarcoma-affects AIDS patients
72
How is varicella - zoster virus trasnmitted ?
aerosols and direct contact
73
How do shingles appear ?
in the facial nerve tract
74
Why arent kids vaccinated against chicken pox ?
because its mild
| also vaccinating kids reduced the boosting of immunity ex-chicken pox adults get from being exposed to chicken pox kids
75
How is Hepatitis B transmitted ?
blood saliva STI
76
What are the severe effects of Hepatitis B ?
hepatocellular carcinoma
77
Is Hep B present in the mouth ?
it is present in the mouth but does not cause oral disease
78
How can you look for viral infection ?
clinical apperance
lab tests- ELISA and sero conversion to look for antibodies
viral culture
histology from a biopsy
79
How can we prevent viral infections ?
cross infection control
| vaccines
80
Which drugs are used in anti-viral healthcare ?
acyclovis
81
What are the characteristics of prokaryotes ?
no membrane bound organelles
haploid
no fusion of gametes
82
Why are fungi described as chemoorganotrophs ?
secrete extracellular enzymes which digest organic material
83
What are hyphae ?
network of filaments of fungi
84
What are mycelium ?
they grow over surfaces in a network
85
What is the fungi cell wall made of ?
chitin
86
What is different about fungi cell membranes ?
they contain ergestrol rather than cholesterol
87
What colour is the gram stain in GP bacteria and why ?
Purple
| thick peptidoglycan layer able to retain the crystal-iodide complex
88
What are flagella ?
rotating protein motors that allow motility
| made of flagellin sub units
89
What is rotation in flagella couple to ?
flow of protons across the membrane
90
What is the method for the gram stain ?
```
create a heat fixed smear
flood with crystal violet
add iodide complex
decolourise with alcohol
counterstain with safarnin
```
91
What are acid-fast bacterial cell walls ?
very high lipid/wax content
contain mycolic acids
found in mycobacterium TB
92
What is the method for detecting acid fast bacterial cell walls ?
detected with carbol fuschin
driven in with heat
destain with 3% alcohol
93
What are the cytoplasmic membranes of gram positive and gram negative cell walls ?
phospholipid bilayer
94
What is the structure of gram negative outer membranes ?
LPS
| asymmetrical
95
What are fimbriae ?
protein filamentous structures
enable cells to adhere to surfaces
aid in biofilm production
96
What are pili ?
used in conjugation- DNA transfer
used in adhesion
found in streptococus pyogenes
type 4 have a twitching motility
97
What are capsules made of ?
polysaccharides and the proteins
98
What is the purpose of the capsule ?
aid adherence - biofilm production
evade phagocytosis
stop desiccation (protect against drying out )
99
What are cell inclusions ?
packets of energy resources
100
What is the purpose of cell inclusions ?
safe way to store energy and avoid osmotic stress
101
What are some examples of cell inclusions ?
glycogen
| poly-B-hydroxybutyric acid
102
What are endospores ?
certain bacteria can only form them
| highly differentiated cells that are very resistant
103
How are endospores destroyed ?
by autoclaving
104
What is an examples of endospores ?
clostridium dificil
| arent killed by antibiotics
105
What do bacteria require to grow ?
they consume and produce energy-
they require macronutrients and micronutrients
water
trace elements
106
What are heterotrophs ?
obtain carbon from organic material
107
What are autotrophs ?
obtain carbon from C02
108
What are auxotrophs ?
cant synthesis organic compounds like amino acids
109
What is fermentation ?
an anaerobic process
| organic compound used as the electron acceptor and donor
110
What is respiration ?
aerobic process
| electron donor is oxidised with oxygen
111
Where do fermentation and respiration happen ?
in both humans and bacteria
112
What is homolactic fermentation ?
fermentation of hexose sugars leads to 2 lactate and 2 H+
113
What is the relevance of lactic acid ?
major product found in dental caries
114
Which bacteria in plaque ferment to produce lactic acid ?
streptococus mutans
115
What is the first step in both respiration and fermentation ?
glycolysis
116
How is ATP produced in fermentation ?
substrate level phosphorylation
117
How is ATP produced in respiration ?
oxidative phosphorylation
| electron transport chain
118
How much ATP is made in aerobic respiration ?
38 ATP
| included glycolysis and the citric acid cycle
119
What is the purpose of the citric acid cycle ?
to produce reducing agents
120
What protein is needed for ATP synthesis in respiration ?
FOFI ATPase
121
What is FOFI ATPase ?
A highly abundant proten growing in bacterial cell walls
122
How does FOFI ATPase generate ATP ?
flow of protons into cells
123
How do Oral bacteria use FOFI ATPase ?
streptococus mutans uses ATPase to pump protons out of cells when conditions are too acidic to reduce the acidity
124
What is the definition of bacterial growth ?
irreversible increase in biomass and usually numbers of bacteria
125
How can we measure bacterial growth ?
microscopy
colony forming units
absorbance
growth curves
126
What is the process of bacterial cell division ?
```
binary fission
DNA replication
cell elongation
septum formation
distinct cells
cell separation
distinct cells
```
127
How is bacterial growth described ?
exponential
| number of cells doubles during a constant time
128
What is the risk of such a high increase in a short time ?
increases the risk of pathogenic bacteria
129
What are the phases of bacterial growth ?
exponential
ststionary
death
130
What are the 3 methods used for measuring bacterial growth ?
microscopic counts
viable and serial dilutions
tubidimetric methods
131
Why is e.coli used as a lab model organism ?
more is known about it than any organism
grows rapidly and has simple nutritional requirements
established genetics and genome
132
What is the e.coli genome like ?
circular chromosome made of 4.6 million base pairs
| encodes around 4400 base pairs
133
What is an operon ?
genes encoding enzymes in a single biochemical pathway
134
What are plasmids ?
small circular pieces of DNA found in varying numbers in the cell
135
What types of genes do chromosomes carry ?
genes that are useful but arent essential for survival
| eg. antibiotic resistance
136
How can genetic information be exchanged by plasmids ?
bacteria die and release plasmids that can be absorbed by bacteria
137
What are the 3 types of horizontal gene transfer ?
conjugation
transformation
transduction
138
What does horizontal gene transfer have the ability to do ?
ability to change the genotype and the phenotype of an organism
make the bacteria "fitter"- multiply faster or give resistance
139
What is DNA transformation ?
DNA uptake freely from the environment
140
What is transduction ?
bacteriophage mediated
bacteriophage will infect a bacterial cell and take up the host DNA
it will then inject the DNA into another cell and then integrate it into the chromosome - donor DNA will take up new functions
141
What is conjugation ?
pilus mediated
pilus extends from the donor to the recipient and adheres
plasmids are transported down the pillus
142
How is DNA incorporated into the chromosome of the recipient ?
Homologous recombination
143
Give an example of transformation using tryptophan ?
e.coli strains that lacka a tryptophan pathway grow on an a tryptophan lacking agar- no growth
take DNA from tryptophan from tryptophan positive cells - cells will uptake DNA
grow on tryptophan agar- see visible growth
144
What are the goals of genetic manipulation ?
knock out genes
change individual amino acids in a protein
FISH
produce recombinant proteins like insulin
145
What are the steps in Recombinant DNA technology ?
Creation of the recombinant DNA
Cloning of the DNA in an organism
Using the DNA - express the gene
146
How can we clone recombinant DNA ?
amplify the DNA by introducing it into a living cell which will produce many identical copies
147
What are the tools for Recombinant DNA technology and why ?
enzymes- to cut DNA and RNA
vectors - act as a vehicle to transport the DNA into host cell for replication
cells- Amplify and express the DNA
DNA and RNA - Raw genetic material
148
Which enzymes are needed in recombinant DNA technology ?
Restriction enzymes
SNA Ligase
Taq polymerase
Reverse transcriptase
149
What do restriction enzymes do and give an example ?
cleave and cut DNA at very specific sequences- molecular scissors
eg. Restriction endonuclease
150
What does DNA ligase do ?
stick DNA fragments together
151
What does Taq polymerase do ?
used in PCR- creates multiple copies of the DNA fragment
152
What does reverse transcriptase do ?
convert RNA into DNA
153
How are restriction enzymes produced and whyn ?
naturally produced by bacteria to cleave bacteriophage DNA
154
Which sequences do restriction enzymes recognise and what do they produce ?
recognise 4-8 base pairs in a palindromic sequence
| produce either sticky or blunt ends
155
What are sticky ends ?
they are overhanging at either the 5' or 3' end
| compatible overhangings are annealed with DNA ligase
156
What do vectorrs contain that allows the insertion of the new recombinant DNA ?
restriction sites so DNA can be efficiently introduced into host DNA
157
How can we check which cells have taken up the DNA ?
the plasmid will have an antibiotic resistance gene - if the cell has taken up the plasmid the gene will be expressed and the cells will be able to be grown on agar containing penicillin
158
What do vectors contain to allow for expression of the inserted gene ?
regulatory sequences
159
How do plasmids replicate ?
independent of the bacterial chromosome
160
What do plasmids have that allows recognition by the host replication machinery ?
origin of repication
161
What is the polylinker ?
a piece of synthetic DNA that allows the insertion of new gene
162
What does the polylinker contain ?
lacZ gene which codes for the B-galactosidase enzyme
which turns a dye from blue to white
If the polylinker is disrupted - gene is successfully added- blue colonies
163
What are other example of vectors beside plasmids ?
phagemids
cosmids
bacteriophages
164
What are cosmids and phagemids ?
genetically engineered hybrids which replicate as a plasmid but can be packaged as a bacteriophage
165
How is the recombinant plasmid inserted into the cells ?
via transformation- either by electroporation or using Calcium chloride heat shock, 42 degrees for 3 mins
166
Where does each cell in a colony arise from ?
a single e.coli cell
| each cell in the colony will contain copies of the same plasmid - clones
167
What were the disadvantages of using amimal insulin ?
side effects
difficult to purify
autoimmune reactions
168
How is recombinant insulin made ?
the gene for proinsulin has 2 introns - DNA is first converted to mRNA
then reverse transcribed into DNA to get rid of introns
the gene is inserted into a plasmid
plasmid inserted into cell and cloned in E.coli
169
Examples of other proteins made using recombinant technology ?
Erythropoietin
| Tpa
170
How can recombinant DNA be applied dentally ?
recombinant DNA can be used to manipulate genes
| create a genetically altered strain of S.mutans that doesnt produce lactic acid
171
What is a planktonic solution ?
a solution of cells that are homogenous , single species and nutrient rich
172
What is a surface associated collection ?
they have limited hetrogeneity
single species
nutrient rich
173
What are natural collections of bacteria ?
in the from of a structured community with organic matter and active microbes
heterogenous
mixed species
nutrient limited (gradient of nutrients)
174
What is a biofilm ?
a functioning and growing community of microbial cells encased within a matrix polymers and associated with a surface
175
In nature how are most bacteria found ?
associated at a surface
176
How are biofilms produced ?
attachment of planktonic cells
| sticky matrix develops
177
What is the difference in growth rates between biofilms and planktonic solutions ?
biofilms have mixed growth rates
| planktonic cells have uniform growth rates
178
What is the difference in the distribution of oxygen and nutrients between planktonic cells and biofilms ?
even distribution of nutrients and oxygen in planktonuc solutions
uneven distribution in biofilms
179
What is the contact between cells like in biofilms and planktonic solutions ?
biofilms- cells in close contact
| planktonic- cells separated
180
Is there an ECM in biofilms ?
yes
| not in planktonic solutions
181
What are emergent properties ?
properties that emerge as a result of putting things together
bacteria behave differently in cultures and biofilms
182
What is the difference in antibiotic resistance between a biofilm and a solution of cells ?
biofilm is 1000 x more resistant to antibiotics than planktonic cells
183
Are biofilms likely to be more or less pathogenic than planktonic cells ?
more pathogenic
184
What can biofilms do with the immune system ?
biofilms can hide from host immunity
185
What type of niches can biofilms produce ?
strictly anaerobic bacteria can be found at interfaces if the bacteria surrounding them suck oxygen away
186
Where are biofilms found ?
anywhere there is an interface
moisture
nutrients and energy source
187
What is the biofilm structure ?
3D
Open
water channels permeate the matrix
heterogeneous distribution with microcolonies found
unequal distribution of waste and nutrients as the marix impedes mass transfer
oxygen and nutrient gradients
188
What is the matrix a mixture of ?
polysaccharides
proteins
nucleic acids
189
What is the purpose of the matrix ?
bind cells together
trap nutrients for microbial growth
prevent cell detachment
190
Which smaller molecules may also be trapped in the matrix ?
nutrients
metals
signalling molecules
191
What is pseudomonas aeruginosa ?
model bacterium used for biofilm development
makes mushroom shaped biofilms
opportunistic pathogen
present in water and lungs of those with CF
catheter infections
192
What are diagnostic criteria for biofilm infections ?
pathogenic
associated with a surface
aggregated cells in clusters with a matric
resistant to antibiotics
193
Why are bacteria resistant to antibiotics ?
```
poor penetration
slow growing
persister cells
sequestration from the immune system
elevated expression of efflux pumps
```
194
How does slow growing cells lead to antibiotic resistance ?
antibiotics work by virtue or targeting fast bacterial growth processes such as cell wall synthesis .
Biofilm bacteria are slow growing - no processes to target
195
Is growth a major factor to consider when determining antibiotic resistance ?
no growth is a minor factor because evidence has showed that antibiotics are just as effective at targeting mRNA synthesis in planktonic and biofilm bacteria
196
What are persister cells ?
populations of bacteria contain a small proportion of inactive dormant cells
difficult to kill dormant cells with antibiotics
they are significant proportion of biofilm bacteria
responsible for hip joint replacements 15-20 years later
197
How do biofilm bacteria evade the immune system ?
resitant to phagocytosis- inflammatory cells cant penetrate matrix
antibodies penetrate poorly
adaptive responses
198
How does pseudomonar Spp evade the immune system ?
produces rhamndlipids which kill neutrophils
| interactions with oral stretococci produces a complement evading protein
199
Which bacteria upregulate efflux pumps ?
e.coli
Pseudomans aeurigonosa
candida albacans
efflux pumps are not effective against all antibiotics
200
What is mass transfer ?
movement in and out
201
How can we measure mass transfer ?
using fluorescently labelled latex beads
202
Is diffusion impeded by the matrix ?
it can be but not for small molecules
water molecules can be carried through water channels
large molecules are also only weakly limited
203
Is the matrix charged ?
yes the matrix is anionic
204
What is the significance of the matrix being charged ?
metal cations can become trapped in an anionic matrix
| reactive molecules such as peroxide can be ianctivated by the matrix
205
What is the structure of the matrix ?
it is thought to be a 3D web.
206
What is the pan genome ?
all gene present in a whole species
207
What is the size of the genome of Haemophilus Influenzae ?
1.8 million base pairs
208
What is the smallest naturally occuring genome ?
Cassoerella mdii
209
What is the largest bacterial genome ?
Soragrium Cellulosom
210
When was the first human genome draft published ?
2001
211
How are microbial genomes represented ?
open reading frames on the outside
| genes colour coded by function
212
What does an ORF consist of ?
ribosomal binding site
starting codon
coding sequence
213
How do computers determine if ORFs are genuine ?
find possible start/stop codons
count codons between to see if it could be a protein- need 300 amino acids
find a possible ribosome binding site
214
What is the core genome ?
shared by all strains of the same species
| for basic functions like DNA Replication
215
What is the pan genome ?
includes optional extras-present in some strains of the species but not all eg.genes for virulence
pan=core+accessory
216
What are chromosomal islands ?
regions of the bacterial chromosome that are foreign origin
contain clustered genes for extra properties
found by comparison of the core and pan genome
217
What are pathogenicity islands ?
chromosomal islands that encode genes for virulence factors
218
Why are chromosomal islands assumed to be foreign ?
come about via horizontal gene transfer
come about via transposition
codon bias that differs from the norm
found in some strains but not others
219
What is the mircobiome ?
total complement of microorganims in an environment (including those associated with a higher organism)
220
What does metagenomic sequencing do ?
obtains information about all DNA present
221
Which gene can be specfically sequenced ?
16S rRNA gene
222
Which organisms do not have the 16S rRNA gene ?
viruses- lack rRNA gene
| fungi-18s rRNA gene
223
What technique should you use to identify which microbes are present ?
SSU rRNA approaches
224
Which techniques should you use to observe microbial activity ?
look at
RNA- metatranscriptomics
Proteins- Metaproteomics
Metabolites- Metabonomics
225
What techniques should you use to assess the genetic potential of a microorganism ?
Metagenomics
226
What is beta diversity ?
diversity between individuals at a single body site
227
What is alpha diversity ?
Diversity between individuals at different body sites
228
Which is generally lower beta or alpha diversity ?
beta diversity
229
What can the core microbiome influence ?
```
lifestyle
genotype
physiology
immune system
pathobiology
```
230
What does mothers milk contain ?
antibodies that lead to protection against pathogens and sugars that good bacteria feed on
231
What diseases does the human microbiome have a role in determining ?
obesity
IBD
liver development
DM
232
What is the link between mouthwashes and blood pressure ?
normally oral bacteria convert nitrates to nitrites
in saliva that we swallow
reduced to nitric oxide
widens blood vessels
mouthwashes get rid of the bacteria that do this- leads to increase in BP
233
What is disease aetiology ?
study of the causation of diseases
234
What is the germ theory of disease ?
states that microorganisms lead to disease
235
What is anthrax ?
a disease of cattle and sometimes humans
| caused by bacillus anthracis
236
What did koch establish regarding anthrax ?
bacteria were always present in blood of animal with disease
took samples and cultured in virtreous humour
injected blood into mouse
injected into mouse- got anthrax
237
What is bacillus anthracis ?
endospore forming
gram positive soil bacterium
3 forms
238
What are the criteria that form Kochs Postulates ?
1. Organism must be present in all cases of disease and not in healthy individuals
2. Must be able to be isolated in pure culture
3. Isolated cells must cause disease in a suitable animal
4. the organism must be reisolated from the infected animal
239
Where are Legionnaires bacteria found ?
in the environment - usually warm water environments
240
How do legionella bacteria grow ?
grow with amoebae - allows them to survive in harsh environments.
241
From 2011 what must all dental practices have ?
a legionnaires risk assessment
242
Under what circumstances is it not possible to fulfil Kochs postulates ?
Asymptomatic carriers- carry organism and not have disease
viruses- could not be cultured in 1900s as well as prions
some infections are polymicrobial
might not be suitable animal organisms
might be the level of the bacterium rather than its presence that leads to disease
243
How do organisms cause disease ? 6 Is
```
implantation
in-utero
ingestion
inhalation
injection
inunction (rubbing)
```
244
What is the advantage of using DNA analysis to identify infectious agents ?
circumvents the isolation of the infectious agents
very sensitive
quantitative
245
What does commensal mean ?
an organism that lives in harmless association with its host ?
246
What is colonisation ?
sustained presence of an organism at a body site
247
What is a pathogen ?
an organism that can cause disease in otherwise healthy individuals
248
What is a carriage ?
When the host acts as a source of infection but shows no symptoms themselves
249
What is an opportunistic pathogen ?
an organism which requires the host to have a pre-existing deficit before it causes disease
250
What is an infection ?
growth of a non native microorganism at a body site without damage to the host
251
What is virulence ?
a measure of the capacity of microorganism to cause disease
252
What are virulence factors ?
genes which express proteins or other molecules which contribute to virulence
253
What are endogenous infections ?
caused by infectious agents that are already present in the body but have dormant and inactive for some time.
254
What are exogenous infections ?
acquired from sources outside the patient
255
What are examples of virulence factors that pathogens can possess ?
adhesins
invasins
toxins
extracellular enzymes
256
What do virulence factors enable pathogens to do ?
survive and replicate in the host
257
What does bordotella pertussis cause ?
whooping cough
258
What does yeninia pestis cause ?
plague
259
What are some examples of opportunistic pathogens ?
staphyloccus epidermis - catheters develops biofilms
Pseudomonas aeuriginosa- burns can break down skin allowing the bacteria to penetrate.
E.coli
260
What are the stages of an infection ?
```
exposure to pathogens
adherence to skin and mucosa
invasion through epithelium
infection
growth and production of virulence factors
toxicity and invasiveness
```
261
What is adherence ?
initial attachment and interaction between bacterial surface and tissue
262
Which bacterial structures allow adherence ?
pilli
fimbriae
surface proteins
263
What does E.coli do with its pili ?
it has type 1 pilli that adhere to epithelial cells in the urinary tract and stop the bacteria from being flushed out
264
What does vibrio cholerae do ?
it is highly motile in bodily fluids and mucosa of intestinal epihelium
make contact with cells and causes disease
265
How does the skin act as defence ?
natural barrier
| antimicrobial fatty acids and antibacterial peptides
266
How does the stomach act as a defence ?
it has a very high acidity of around 2
lots of bacteria needed to vause infection however in the case of proton pump inhibitor medicine a lower number of bacteria are needed to infect
267
What do tears contain ?
lysozymes that degrade bacterial cell walls
268
What do epithelial cells have that can protect against infection ?
tight junctions - inhibit pathogen invasion and infection
269
What are the bodys adaptive host defences ?
phagocytosis
inflammation
antibodies
270
How can bacteria overcome skin defences ?
they have keratinases that degrade the junctions between epithelial cells and penetrate skin
271
How do bacteria overcome flushing ?
flagella and fimbriae carry out adherence - attach to mucosa to stop flushing out
272
How can bacteria overcome mucus ?
they can swim and degrade mucin
273
How can bacteria evade phagocytosis ?
they have VI capsules that prevent against complement fixation
274
How can bacteria overcome antibodies ?
have proteases that break down antibodies
kill host defence host cells
antigenic variation
275
What is antigenic variation ?
infectious agents able to change their surface proteins and carbohydrates expressed leading to evasion from the immune system
this leads to a cycling of fever
276
What is bacteraemia ?
invasion of bacteria into the blood stream
277
What is septicaemia ?
infection in the blood stream
278
How can septicaemia be detected ?
cytokine storm- increased levels of cytokines
279
What are the ways in which bacteria can invade ?
```
lungs
gut
UT
nerve pathways
cell to cell
```
280
What are examples of tissue degrading enzymes and what do they do ?
collagenase- breaks down collagen
hyaluronidase - breaks down junctions between cell walls
haemolysin- lyses erythrocytes
281
What do siderophores do ?
take up iron
282
What are some exmaples of microbial virulence factors ?
O-antigen inhibits phagocyte killing
| VI capsule stops complement binding
283
What is an example of an endotoxin ?
LPS in gram negative outer membrane
| causes fever, septic shock and inflammation
284
What are exotoxins ?
they are secreted by bacteria
285
What is the problem with exotoxins ?
the dont require the bacterium to cause infection
| antibiotics are now useless so better to vaccinate against
286
What are some examples of exotoxins ?
tetanus toxin
| diptheria toxin
287
Where can you find tetanus toxin ?
soil - it attacks the CNS
288
What does the diptheria toxin do ?
stops cell protein synthesis
289
What is clostridium tetani ?
gram postive, spore forming rod
secretes a neurotoxin that stops neurotransmitter release from inhibitory synapses
leads to lockjaw
290
What is clostridium botulinim ?
bacterium found in soil, water and food
| tinned food undergoes botulinum cook
291
What is the clostridium botulinum toxin used for ?
treat muscle conditions
| botox
292
What does diptheria do ?
inhibits protein synthesis
| causes a pseudomembrane that can block the airways
293
What is necrotising fascitis ?
tissue destruction by toxins initiate an overactive immune response
flesh eating
294
What are some pathogens involved in necrotising fascitis ?
S.pyogenes and MRSA
295
What is an acute infection ?
short duration
296
What is a chronic infection ?
long duration
297
What are some factors that increase susceptibility to disease ?
trauma
age
nutrition
hormones
298
How has their been a shift in the way that we now view the way disease is caused ?
Kochs gave us the idea that the presence of a pathogen was enough to cause disease but now we think it might be the level rather than the presence that can cause disease.
299
What is dysbiosis ?
a shift in the balance of bacteria towards an unhealthy number of bacteria
300
Sequencing the 16srRNA gene tells us what ?
it can help us identify the pathogen but it is not exact- OTU- operational taxonomic unit
301
What do we need to be careful about when we find pathogens in disease ?
correlation is not causation
302
What is metagenomic sequencing ?
sequencing all the DNA present including non bacterial and then suing bioinformatics to predict function of DNA
303
Identifying bacteria from different body sites led to what conclusion ?
different body sites are dominated with certain bacteria
| core taxa at every site
304
What is the commensal gut microbiota essential for ?
the development of an immune system
305
Which diseases are associated with differences in the gut microbiota ?
Obesity
Colorectal cancer
IBD
306
What can antibiotics potentially do ?
control pathogens but also lead to dysbiosis
307
What is important about microbial function when it comes to disease ?
disease isnt just about the pathogens being present- changes in the function of the community can also be a driver for disease.
eg. Crohns disease- reduced expression of amino acid metabolism
308
What is associated with inflammatory bowel disease ?
genetics
change in the microbial microbiotia - composition and function - decrease in amino acid synthesis
decrease in alpha diversity
309
What do we need to consider when treating the microbiome with antibiotics ?
careful selection of antibiotics to minimise shifts in microbiota
avoid repeated use of single antibiotics
repopulate the gut with good bacteria
310
What are prebiotics ?
designed to feed good bacteria
encourage good bacteria to take over
eg. amino acids
311
What are probiotics ?
deliver microorganims to the gut
| not very regulated
312
What is a foecal microbiotia transplantation ?
take good bacteria and insert into infected people
| results arent long lasting
313
What are the major dental plaque related diseases ?
periodontitis
| dental caries
314
What is the specific plaque hypothesis ?
diseases are caused by a single microorganism
315
What is the non specific plaque hypothesis ?
diseases are caused by the amount of plaque
316
What is the ecological plaque hypothesis ?
diseases are caused by the interactions of specific microorganisms in the microbial community
317
What is the process of dental caries ?
health
subsurface demineralisation
white spot lesion
cavitation
318
What does the ecological plaque hypothesis state about dental caries aetiology ?
```
stress
excess sugar
acid production
low pH
leads to environmental and ecological change
demineralisation
```
319
What are keystone species ?
disproprptionately large effects on the population given their abundance
320
What does a keystone pathogen do ?
supports and stabilises the dysbiotic state
| triggering an immune response that is overactive and unhelpful
321
What are keystone species associated with ?
periodontitis
322
What type of microbiotia is periodontitis initiated by ?
synergistic and dysbiotic
323
What does polymicrobial synergy say about periodontitis ?
different members of the community have different gene combinations that fulfil roles that allow shaping and survival of a disease provoking microbiotia
324
What is clinical microbiology ?
in vitro diagnosis and management of diseases caused my microorganisms
325
What is the role of the clinical microbiology lab ?
provide accurate info about the presence or absence of microbes in a patient sample
aid in management
provide info about antimicrobial susceptibility
testing in a clinically relevant time frame
326
What makes a good diagnostic test in microbiology ?
specific
sensitive
time is relevant
easy to use
327
What does specificity mean with clinical testing ?
no false positives
| provides high level of confidence with results
328
What does sensitivity mean ?
detect low levels of cells and viral particles
329
What can we use direct microscopy for ?
visualise microorganisms
lacks sensitivity and specificity
requires large amount of pathogen
use gram stain and morphology
330
How can we identify bacteria based on isolation techniques ?
bacteria have different growth requirements like oxygen/temperature
use specialised media
331
How can we use antibodies to test for pathogens ?
detect antigens using latex particles coated in antibod, leads to agglutination, useful if patient has already had antibiotics
take blood samples and look for evidenc eof antibodies to certain diseases- eg.MMR
332
How does PCR happen ?
heat DNA to denature it
separate strands
anneal primers at lower temp
taq polymerase binds and amplifies DNA
333
What are the advantages of PCR based testing ?
rapid
detect different pathogens in the same tube
increased sensitivity
specific
334
For which disease is PCR testing standard ?
whooping cough
| bordetella pertusis
335
How do you carry out the gram stain ?
apply crystal violet
Add iodine
wash with alcohol
counter stain with safranin
336
What is the oxidase test ?
oxidase positive bacteria contain cytochrome C oxidase
this uses oxygen for energy production in the etc
test for the presence of cytochrome C oxidase
337
Which bacteria are usually OX+ ?
gram negative
| helicobacter pylori etc
338
What are the limitations of culture based methods ?
some organisms grow slowly, difficult to grow or dont grow at all
not helpful if patient has already taken antibiotics
339
What is syndromic testing ?
testing for multiple pathogens at the same time
340
How do you carry out the urease test ?
mix bacteria with urease broth (urea and phenol red)
broth is mix of urea and indicator
if bacteria have the enzyme urease they will break down the urea into ammonia - colour change to yellow
341
What is the catalase test ?
place hydrogen peroxide on slide
add loopful of bacteria
if the bacteria have catalase they will break the hydrogen peroxide down into oxygen and water
342
How is urease relevant to dental plaque ?
having urease means that bacteria can convert urea toa ammonia and raise the pH - this can protect against caries
343
How do helicobacter pylori use urease ?
ammonia produced neutralises the stomach acid and allows the bacterium to survive ad cause stomach ulcers
344
What is the DNase test ?
degradation of DNA releases free nucleotides
| this turns toludine blue pink
345
What is the coagulase test ?
latex particles are coated with fibrinogen if the bacteria have coagulase - bind the fibrinogen into a clot. Visible as agglutination of the blue particles
346
What is the appearance of Staphylococus Aureus ?
appears a bunch of grapes - cocci shaped
347
Is S.Aureus gram positive or negative ?
gram positive- stains purple due to thick peptidoglycan layer
348
Where can you find S.aureus ?
anterior nares, nasopharynx and skin
349
Is S.aureus catalase positive or negative ?
Catalase positive- can liberate oxygen from hydrogen peroxide
350
Is S.aureus commensal ?
it can be commensal but is associated with infection so can be opportunistic
351
Is S.aureus coagulase positive ?
coagulase positive
352
Is S.aureus DNase positive ?
yes- helps it escape from host DNA released to trap pathogens
353
What is a major problem with S.aureus ?
MRSA
354
What are some diseases S.aureus can cause ?
food poisoning, toxic shock syndrome
355
What are streptococcus salivarius ?
oral streptoccoci that are potentially pathogenic - can cause infective endocarditits
356
How is S.salivarius importnat in dental caries ?
it can produce acid from sugar and has increased numbers at carious lesions
357
is S.salivarius urease positive ?
yes- urease converts urea to ammonia which can protect against dental caries
358
Is S.Salivarius gram positive ?
yes gram positive-stains purple
359
What is the shape of S.salivarius ?
cocci shaped but forms strips of streps
360
Why does S.salivarius produce a greenish tinge on blood agar ?
they produce hydrogen peroxide and lack catalase
361
Where can you mainly find e.coli ?
enteric
362
Is e.coli harmful ?
it is commonly used as a lab model organism
| some strains are pathogenic
363
Which strains of e.coli are pathogenic ?
those that possess the 157 version of the O antigen- part of the LPS
364
What common diseases does e.coli cause ?
diarrhoea and vomiting
| UTIs
365
Are e.coli gram negative or positive ?
gram negative
366
What is the shape of e.coli ?
rod shaped bacillus
367
Is e.coli motile ?
yes and it has fimrbriae
368
Does e.coli ferment lactose ?
yes
369
Is e.coli catalase postive ?
yes - gives it protection against hydrogen peroxide
370
What is selective media ?
designed to allow the growth of selected bacteria whilst inhibiting most
371
What is indicator media ?
chromogenic tests that allow us to identify particular media
372
How can we use carbohydrate profiles to detect bacteria ?
bacteria ferment sugars into acids
| overnight incubation turns a red indicator to yellow in presence of acid
373
What are the advantages of broth culture ?
```
easy
large amounts of cells can be cultured
economic
in broth culture all cells are growing whilst in agar only cells at the edges are growing
use for total viable counts
```
374
What are the disadvantages of broth culture ?
distinguish between different bacteria
| difficult to get a colony of one type
375
What is XLD agar ?
used for the identification of enteric bacteria because it contains sodium desoxycholate - inhibits gram positive bacteria
376
What is CLED agar used for ?
non selective and used for culture of bacteria from urine specimens
377
What is blood agar ?
uses haemolysis to idnetify different bacteria from alpha, beta or gamma haemolysis
378
What is staph agar ?
a selective medium based on a high salt concentration
| staphyloccoci are resistant to salt
379
Which stains can you use to make bacteria visible under a microscope ?
gram stain
| ziehl neelson
380
Which samples is microsocopy useful for ?
samples that otherwise wouldnt contain bacteria
381
What is the structure of LPS ?
consists of a lipid, core polysaccharide and O-polysaccharide
382
How is it better to detect diseases ?
by tracking antigens in pathogens rather thatn identiying the pathogen
383
How can we use latex agglutination to detect antigens ?
coloured latex beads have antibody specific for an antigen attached
mix suspension of bacterial cells with beads and antibody will bind to antigen if present casing agglutination
384
Is N.Gonnorhoeae gram positive or negative ?
gram negative- stains pink
385
What is the advantage of N.gonorrhoaeae being encapsulated ?
the polysaccharide layer limits the ability of phagocytes to engulf it
386
Is N.gonoorhoaea DNase positive ?
yes it can break down host bacteria and trap the pathogen
387
What is the shape of N.Gonorrhoae ?
diploccocus
388
Is N.Gonorrhoaeae catalase positive ?
yes
389
What does it mean if N.gonorrhoeae is fastidious ?
has complex nutrtitional requirement that requires blood and amino acids to groq
390
Is Gonoorhoaea an STI ?
yes- 2nd most common after chlamidya
391
Which areas does N.gonorrhoeae affect ?
genitals
rectum
eyes
mucous membranes
392
What is the mechanism of action of N.gonorrhoeae ?
bacteria adheres to cells via pilli
proteases are produced to digest epithelial cells
trigger inflammatory response- leads to damage in the fallopian tubes and leads to infertility.
393
What are the virulence factors of S.Aureus ?
potent exotoxins- TSSt1 leading to toxic sock syndrome
394
What are the virulence factors in N. gonorrhoae ?
outer membrane porin that protects against phagocytes
395
What are the transmission and symptoms of N.gonorrhoeae ?
green discharge, lower abdomen pain and burning when urinating
transmitted by unprotected sex and childborth
396
Is L.pneumophilia gram negative or positive ?
gram negative- stains pink
397
What is the shape of L.pneumophilia ?
small short rod with flagella
398
Where can you find L.pneumophilia ?
water environments
aerosols
dental water lines- run water though every morning to get rid of stagnant water
399
What are the virulence factors of L.pneumophilia ?
secretes molecules that protect it against phagocytes
400
What are the diseases that L.pneumophilia causes ?
Legionnaires disease- lethal pneumonia
| pontiac fever
401
How can L.pneumophilia lead to lung damage ?
results in lysis of the macrophage- immune system unable to clear- leading to lung damage
402
How can we diagnose infection with L.Pneumophilia ?
Rapid diagnosis with PCR
403
Is C.diificile gram positive or negative ?
gram positive- stains purple
404
What does C.dificile do ?
colonises intestinal epithelium leading to diarrhoea, abdominal pain
pseudomembrane formation in the pharynx
releases toxins
405
What are the virulence factors of C.difficile ?
toxins that have enterotoxic and cytotoxic activity
toxins A and B
proinflammatory interluekins and TNF
406
Where can you find C.difficile ?
digestive system
elderly
immunosupressed
407
Is N.Gonnorhoeae gram positive or negative ?
gram negative- stains pink
408
What is the advantage of N.gonorrhoaeae being encapsulated ?
the polysaccharide layer limits the ability of phagocytes to engulf it
409
Is N.gonoorhoaea DNase positive ?
yes it can break down host bacteria and trap the pathogen
410
What is the shape of N.Gonorrhoae ?
diploccocus
411
Is N.Gonorrhoaeae catalase positive ?
yes
412
What does it mean if N.gonorrhoeae is fastidious ?
has complex nutrtitional requirement that requires blood and amino acids to groq
413
Is Gonoorhoaea an STI ?
yes- 2nd most common after chlamidya
414
Which areas does N.gonorrhoeae affect ?
genitals
rectum
eyes
mucous membranes
415
What is the mechanism of action of N.gonorrhoeae ?
bacteria adheres to cells via pilli
proteases are produced to digest epithelial cells
trigger inflammatory response- leads to damage in the fallopian tubes and leads to infertility.
416
What are the virulence factors of S.Aureus ?
potent exotoxins- TSSt1 leading to toxic sock syndrome
417
What are the virulence factors in N. gonorrhoae ?
outer membrane porin that protects against phagocytes
418
What are the transmission and symptoms of N.gonorrhoeae ?
green discharge, lower abdomen pain and burning when urinating
transmitted by unprotected sex and childborth
419
Is L.pneumophilia gram negative or positive ?
gram negative- stains pink
420
What is the shape of L.pneumophilia ?
small short rod with flagella
421
Where can you find L.pneumophilia ?
water environments
aerosols
dental water lines- run water though every morning to get rid of stagnant water
422
What are the virulence factors of L.pneumophilia ?
secretes molecules that protect it against phagocytes
423
What are the diseases that L.pneumophilia causes ?
Legionnaires disease- lethal pneumonia
| pontiac fever
424
How can L.pneumophilia lead to lung damage ?
results in lysis of the macrophage- immune system unable to clear- leading to lung damage
425
How can we diagnose infection with L.Pneumophilia ?
Rapid diagnosis with PCR
426
Is C.diificile gram positive or negative ?
gram positive- stains purple
427
What does C.dificile do ?
colonises intestinal epithelium leading to diarrhoea, abdominal pain
pseudomembrane formation in the pharynx
releases toxins
428
What are the virulence factors of C.difficile ?
toxins that have enterotoxic and cytotoxic activity
toxins A and B
proinflammatory interluekins and TNF
429
Where can you find C.difficile ?
digestive system
elderly
immunosupressed
430
Which factor of S.Aureus is responsible for food poisoning ?
enterotoxin- a preformed toxin so symptoms occur faster
431
Name 3 different characteristics of bacterial cells that allow us to identify them by microscopy ?
shape
colour
motility- flagella
432
What type of substance is the target of diagnostic tests for clostridium difficile ?
clostridium toxin- use antobody based detection for toxin in faeces
433
Is brillialnce candida agar selective or indicative ?
both
434
What changes occur following the growth of beta haemolytic bacteria ?
lysis of red blood cells
| bleaching of agar- becomes straw coloured and translucent
