Microbiology Flashcards
Define prokaryotic cell and provide examples of prokaryotic organisms
Prokaryotic cell – a cell that do not contain a nucleus or membrane bound organelles.
Examples:
- Bacteria
- Archaea
Describe the two basic forms of prokaryotic cell
Two basic forms of prokaryotic cell:
- Bacteria:
- Peptidoglycan cell wall for rigidity and shape
- Cell membrane
- Lack of organized nucleus but may have plasmids
- May be parasites
- Archaea:
- Similar morphology to bacteria but no peptidoglycan
- Similar metabolism and genetics to eukaryotes
- No known archaea pathogens or parasites
No internal membranes or organelles
Recall the basic prokaryotic (bacterial) cell structure (8 points)
Define eukaryotic cell and provide examples of eukaryotic organisms
Eukaryotic cell – a cell which contains a nucleus and membrane bound organelles.
Examples:
- Animals
- Plants
- Fungi
- Protazoa (single-celled)
Describe the 4 basic forms of eukaryotic cell
Four basic forms of eukaryotic cell:
Eukaryote cell structure – animal:
- Typically smaller than plant cells (10-30 micrometres in length)
- Phospholipid bilayer cell membrane with no cell wall
- Various shapes: cuboidal, columnar, squamous, dendritic, etc.
- Highly differentiated: nerve cell, muscle cell, epithelial cell, blood cells, etc.
Eukaryote cell structure – plant:
- Typically larger than animal cells (10-100 micrometres in length) and cuboid in shape
- Extra components of plant cell:
- Plasmodesmata (communicating pores), chloroplasts, vacuole, cellulose cell wall.
Eukaryotic cell structure – fungal:
- Yeast cells – unicellular
- Key differences to animal cell and bacterial cell:
- Chitin cell wall
- Vacuole
- Nucleus
- Moulds – multiple hyphae
Eukaryotic cell structure – protozoa:
- Single-celled eukaryote
- Free living or parasite (not classified as animal, but exhibits animal-like behaviours: predation, motility)
- Example: amoeba
Recall the basic eukaryotic (animal) cell structure (12 points):
Eukaryote (animal) cell structure:
- Nucleus (contains genetic material)
- Nucleolus (synthesis of RNA/assembly of ribosome)
- Cell membrane (lipid bilayer with proteins and sugars)
- Cytoplasm (80% water, suspends organelles)
- Mitochondria (double membrane, supplies ATP for cell)
- Golgi apparatus (processes and packages proteins into vesicles)
- Smooth ER (lipid synthesis and metabolism)
- Rough ER (studded with ribosomes, protein metabolism)
- Ribosome (site of protein synthesis)
- Lysosome (contains enzymes, breakdown of waste products of cell)
- Peroxisome (contains catalase to reduce 2H2O2 → 2H2O + O2)
- Cytoskeleton (to give cell shape and mechanical resistance).
Compare bacteria, archaea, and eukarya with reference to the following 5 features:
- Cell membrane
- Gene structure
- Internal cell structure
- Metabolism
- Reproduction
Compare Gram-positive cell wall vs Gram-negative cell wall
Define virus and provide examples
Virus – obligate intracellular parasite:
- Not cellular
- Viruses contain DNA or RNA
- Virus replicate only within living cells – use the cells ‘machinery’ to replicate
- Some viruses (bacteriophages) directly infect bacterial cells
Examples:
- HIV
- Coronavirus
- Influenza
- Herpes
Describe the basic structure of a virus
Virus structure:
- Nucleocapsid:
- Protein and genome complex – DNA or RNA
- Three shapes:
- Icosahedral e.g. Herpes
- Helical e.g. Ebola
- Complex e.g. HIV
- May have a lipoprotein envelope
Define prion and provide a key example
Prions – proteinaceous infection particles:
- Not cellular
- Do not contain DNA or RNA
- Promotes refolding of native (host) proteins → pathology
- Infect nerve cells
Key example – Ceutzfeldt-Jakob disease:
- Transmissible spongiform encephalopathy
- Humans who develop this disease will slowly lose the ability to think and to move properly and will suffer from memory loss and progressive brain damage until they can no longer see, speak or feed themselves.
- Very difficult to destroy (even by standard sterilization techniques)
List the main oral habitats for microbes (7 points)
Oral habitats:
- Teeth
- Gingival sulcus
- Tongue
- Cheeks
- Hard palate
- Soft palate
- Tonsils.
Changes occur over time – deciduous teeth exfoliation, orthodontic appliances, prostheses.
Stagnation areas – occlusal fissures, poor restorations, misaligned teeth, orthodontic appliances, prostheses.
Summarize the oral microbiome (4 points)
Oral microbiome (4 points):
- Bacteria – mostly bacterial (500-700 common species); ~50% culturable
- Fungi – yeasts (Candida albicans – esp. associated with dentures); filamentous and dimorphic fungi
- Viruses – Herpesviruses, Adenoviruses, Rhinoviruses, Papovaviruses, Orthomyxoviridae (influenza)
- Protozoa – Entamoeba gingivalis (amoeba prevalent in 95% patients with gingivitis).
Describe the flora of the oral cavity
Gram-positive cocci:
- Aerobic streptococci:
- Streptococcus mutans, S. salivarius, S. anginosus, S. mitis
- Anaerobic streptococci
Gram-positive rods and filaments:
- Lactobacilli, Propionibacterium
- Actinomyces
Gram-negative cocci:
- Neisseria, Veillonella
Gram-negative rods – facultative anaerobes:
- Haemophilus, Aggregatibacter, Eikenella, Capnocytophaga
Gram-negative Rods – obligate anaerobes:
- Porphyromonas, Prevotella, Fusobacteria, Leptotrichia, Wolinella, Selenomonas, Treponema
Explain the 4 main factors affecting the growth of microorganisms in the oral cavity
Modulating factors affecting growth of oral microbiome – “SLAM”:
-
Saliva and gingival crevicular fluid:
- Flushing microbes
- Complex mix of organic and inorganic components
- Source of microbial nutrients (e.g. carbohydrates and proteins)
- Growth inhibitions (e.g. lysozyme, lactoferrin, IgA)
- Buffering capacity maintaining pH (acidic saliva favours cariogenic bacteria)
-
Local environment
- Moisture (i.e. mouth breathing in athletic population)
- Local pH
- Antimicrobial therapy
- Diet (i.e. sugars)
- Fluoride
-
Anatomy – hard to clean areas:
- Shape and alignment of teeth
- Quality of restorations
- Periodontal condition may favour proteolytic bacteria
- Microbial factors – composition of microbial flora and competition between commensal and pathogenic organisms (i.e. colonization resistance)
Describe colonization resistance within the oral microbiome
Colonization resistance:
- Commensal oral flora inhibits non-oral organisms
- Competition for receptors for adhesion (e.g. to hard tissues)
- Production of toxins - Streptococcus salivarius produce enocin which inhibits Streptococcus pyogenes
- Production of metabolic products (e.g. acids which lower pH)
- Use of metabolic products (e.g. Veillonella spp. - use acids produced by Streptococcus mutans)
- Plaque biofilm
List some common bacterial, viral, and fungal infections of the oral cavity
Bacterial:
- Caries, gingivitis, periodontitis, strep throat
Viral:
- Herpes simplex type I
Fungal
- Oral candidiasis
Explain the process of microbiological sampling and provide examples of specimens
Microbiological sampling
Aim: to assist the clinician in reaching a definitive diagnosis
Process (4 key steps):
- Clinical request
- Collection and transport of specimens
- Laboratory analysis
- Interpretation of the microbiology report
Outcome: clinician assisted in making treatment decision.
Avoid contamination of samples - difficult for oral specimens.
Examples of specimens:
- Aspirate of pus from purulent infection
- Deep gingival smear for acute ulcerative gingivitis
- Rinse for quantifying oral Candida
- Paper point samples for periodontal pockets for molecular identification (gene probing using PCR)
Describe the 3 main types of lab analysis of microbiological samples
Lab analysis of microbiological samples:
- Non-cultural methods:
- Microscopy
- Gene probing
- Cultural methods – not all microbes will grow in the lab:
- Solid or liquid media to grow bacteria and fungi
- Identify bacteria using biochemical tests or genotyping
- Cultured cells to grow viruses (obligate intracellular parasites)
- Solid or liquid media to grow bacteria and fungi
- Immunological methods:
- Identify organisations using antibodies
- Detect antibodies in serum – important if microbes hard to grow.
Describe the qualitative and quantitative susceptibility testing methods
Qualitative susceptibility test method (zones of inhibition):
- Agar plate with paper discs impregnated with antibiotic on the plate
- After incubation, growth of bacteria is observed
- Areas around the antibiotic disc where no bacterial growth can be seen are known as ‘zones of inhibition’.
Quantitative susceptibility test method (minimum inhibitory concentration)
- Tests minimum inhibitory concentration (MIC) of antimicrobial agent needed to inhibit growth of microorganism (e.g. MIC50 ⇒ conc. for 50% inhibition)
- Microorgansms are cultured in a 96-well plate with a concentration gradient of antimicrobial agent
- Where wells do not turn cloudy, this indicates inhibition of microorganism growth and the specific minimum concentration of antimicrobial agent can be determined quantitatively
Recall the classification of Gram-positive bactera
Recall the classification of Gram-negative bactera
Describe aerobic, facultative, and anaerobic growth of bacteria
Aerobic, facultative, and anaerobic growth:
- Obligate aerobe – oxygen essential for growth: Mycobacterium tuberculosis
- Facultative anaerobe - grows in the presence or absence of oxygen: mutans streptococci
- Obligate anaerobe - grows only in the absence of oxygen: Porphyromonas gingivalis
Explain bacterial spore formation
Bacterial spore formation – hard to kill (contains DNA, cell membrane, some cytoplasm, water, keratin coat):
Occurs in response to adverse conditions e.g. scarce nutrients: Bacillus and Clostridium
Describe the properties of biofilm (4 points)
Properties of biofilm:
- Bacteria growing in biofilms have different properties to the same bacteria growing planktonically (i.e. free-floating in bodily fluids)
- Biofilms are more resistant to antibiotics and chemotherapeutic agents
-
Mechanical cleansing effective at removing biofilm:
- Subgingival cleansing – ultrasonic debridement
- Supragingival cleansing – toothbrushing
- Disruption of biofilm not always clinically appropriate:
- Pseudomonas aeruginosa in cystic fibrosis
- Legionella in stagnant water pipes
- Removal of a central venous catheter with suspected colonization of S. epidermidis (removal from vein can result in shear force which breaks off biofilm adhered to the plastic → venous bacterial shower in veins)
Define oral biofilm (9 points)
Oral biofilm (i.e. dental plaque) is an adherent mass of diverse micro-organisms in a muco-polysaccharide matrix. It cannot be rinsed off but can be removed by brushing.
Biofilms are made up of symbiotic communities of different micro-organisms.
They develop in a structured way and are spatially and functionally organized.
The species within communicate with each other (i.e. quorum sensing).
They are less susceptible to host defences and antimicrobial agents than planktonic bacteria.
Resident bacteria can dampen the immune response via communication with host mucosal cells
If this balanced coexistence breaks down disease can occur (e.g. caries, gingivitis, periodontitis).
It forms in 5 key stages
List the key consequences of oral biofilm formation (3 points)
Consequences of oral biofilm depends on niche site – 3 key dental plaque-mediated diseases:
- Caries
- Gingivitis
- Periodontitis
Describe the risk factors for oral biofilm formation
Risk factors for oral biofilm formation:
- Poor oral hygiene (↓mechanical disturbance, ↓Fl- load)
- Anatomical areas protected from host defences and where mechanical action fails to remove bacteria (i.e. niche sites):
- Occlusal fissure (leading to occlusal caries)
- Interproximal space (leading to interproximal cares)
- Cervical surface (esp. if root exposed, leading to root caries)
- Gingival sulcus (leading to acute gingivitis)
- Periodontal pockets (progressing from gingivitis to periodontitis)
- Increased risk of oral biofilm formation where there is reduced oral function:
- ↓Salivary flow rate
- ↓Muscular movement
- ↓Immune mechanisms
- ↓Commensal microflora competition
- Reduced function may be as a result of increased age, disease, drug-induced, congenital abnormality, trauma.
List the key stages of oral biofilm formation (5 points)
Key stages of oral biofilm formation:
“Adhesive Colonies Are Created Dynamically”
- Adhesion – conditioning film
- Colonization – linking film
- Accumulation – co-aggregation and re-conditioning film
- Complex community – further accumulation and maturation film
- Dispersal – remodelling and shedding film
Key stages of oral biofilm formation – stage 1
Describe the following oral biofilm formation stage:
Adhesion – conditioning film(3 points)
Adhesion – conditioning film:
- Salivary glycoproteins selectively adhere to naked tooth surface to form acquired pellicle – helps to protect teeth from acids
- Planktonic microbial cells reversibly adhere to acquired pellicle via a balance of electrostatic attraction (i.e. van der Waals forces) and electrostatic repulsion
Key stages of oral biofilm formation – stage 2
Describe the following oral biofilm formation stage:
Colonization – linking film (4 points)
Colonization – linking film:
- Irreversible adhesion and linking up (polymer bridging) between pioneer species and acquired pellicle to form microcolonies on acquired pellicle
- Key pioneer species of microcolonies: S. oralis group – S. sanguinis, S. oralis, S. mitis.
Key stages of oral biofilm formation – stage 3
Describe the following oral biofilm formation stage:
Accumulation – co-aggregation and re-conditioning film (4 points)
Accumulation – co-aggregation and re-conditioning film:
- Additional early colonizers co-aggregate to the pioneer species to increase diversity and re-condition biofilm (microbial composition varies between niches)
- Bacteria communicate with each other (via quorum sensing) and multiply in ecological succession → further reconditioning to reflect the local changes of niche environment
- Quorum-sensing molecules:
- Secretion of extra polysaccharide matrix
- Modulation of bacterial metabolism deep in the biofilm
- Production of virulence factors e.g. drug-destroying genes.
Key stages of oral biofilm formation – stage 4
Describe the following oral biofilm formation stage:
Complex community – further accumulation and maturation film (4 points)
Complex community – further accumulation and maturation film:
- If left undisturbed, there is continued accumulation (microbial succession, growth and an increased species diversity by late colonizers) resulting in a ‘mature’ or climax type of biofilm within a week
- Overall composition of biofilm complex depends on the niche:
- Occlusal fissure
- Interproximal space
- Cervical surface (esp. if root exposed)
- Gingival sulcus
- Periodontal pocket.
Key stages of oral biofilm formation – stage 5
Describe the following oral biofilm formation stage:
Dispersal – remodelling and shedding film (6 points)
Dispersal – remodelling and shedding film:
- The ‘mature’ (climax) biofilm is susceptible to hydrodynamic shearing and mechanical disturbance from masticatory forces – results in passive dispersal
- Limited access to nutrients at the core of the biofilm leads to dispersal signalling and biofilm structure remodelling to maintain an optimal surface area/volume ratio to facilitate diffusion of nutrients and removal of metabolic end-products – results in active dispersal
- Bacteria may disperse as microcolonies or become planktonic again – cyclic nature.
List the microbial species in oral biofilm linked to dental caries (4 points)
Organisms in biofilm linked to dental caries:
- Mutans streptococci – initiating organism of caries
- Lactobacillus spp. – involved in deeper lesions; pioneer organism in advancing front of caries
- Actinomyces spp. – associated with root caries.
Lactic acid bacteria include Streptococci spp. and Lactobacilli spp.
Compare the microbial species in oral biofilm linked to gingivitis vs. periodontitis
Biofilm ecological shift from gingivitis → periodontitis
Microbial species in oral biofilm linked to gingivitis:
- ~55% Gram-positive with occasional spirochetes and motile rods
- Examples of bacteria:
- Streptococcus sanguinis
- Fusobacterium nucleatum
- Veillonella spp.
Micobiral species in oral biofilm liked to periodontitis:
- ~75% Gram negative of which 90% anaerobic motile rods and spirochaetes
- Examples of bacteria:
- P. gingivalis
- P. intermedia
- F. nucleatum
- T. forsythia
- Aggregatibacter spp.
What is the main source of nutrients of the oral biofilm?
Saliva is the main source of nutrients of oral bacteria – formation of glucose to lactate by lactic acid bacteria
Increased sucrose load in the oral environment (i.e. when eating) correlates with a net formation and metabolism of glucose to lactic acid (reduced pH)
The lactic acid is produced because the micro-organisms wish to survive
Excess sugar can kill bacteria (sugar kill) and to avoid this they have to metabolize the fermentable carbohydrates as rapidly as possible
Describe the overall process of dental caries and the associated microorganisms (6 points)
Overall process of dental caries:
- Localized destruction of tooth tissue by bacterial fermentation of dietary carbohydrates (i.e. sucrose) which produces acids
- Caused by normal oral commensal flora
- Dynamic process of cyclic mineralization and demineralizaiton of tooth surface over time
- Considered pathological when there is an imbalance in favour of net demineralization of enamel and later dentine.
Protective factors vs pathological factors
Recall the ecological plaque hypothesis for dental caries
Describe the microbiology of normal periodontal health
Microbiology in normal periodontal health:
- Mainly Gram-positive cocci:
- S. oralis group – S. sanguinis, S. oralis, S. mitis.
- Actinomyces naeslundii
- Actinomyces viscosus
- Veillonella spp. (Gram –ve anaerobic cocci)
Describe periodontal disease and the associated micro-organisms
Spectrum of disease from acute (reversible) gingivitis → chronic (irreversible) periodontitis:
- Direct action of microbes
- Indirect action of host immune system
Microorganisms:
- Gingivitis (~55% Gram +ve bacteria):
- Periodontitis (~75% Gram -ve bacteria):
Recall the four principal phases of plaque-associated periodontal disease
Four principal phases of plaque-associated periodontal disease
Describe the inital lesion (2–4 days) of periodontal disease (3 points)
Initial lesion (2–4 days of initial plaque accumulation):
- No inflammation evident microscopically (gingivitis not clinically evident)
- Histologically clinically healthy gingival tissues
- Slightly elevated vascular permeability and vasodilatation:
- GCF flows out of gingival sulcus leading to flushing action
- Migration leukocytes (primarily neutrophils) in small numbers through gingival connective tissue into sulcus.
Four principal phases of plaque-associated periodontal disease
Describe the early lesion (4–7 days) of periodontal disease (6 points):
Early lesion (4–7 days of continued plaque accumulation):
- Gingivitis that is now clinically evident
- Increased vascular permeability, vasodilatation, and GCF flushing
- Proliferation of JE cells
- Large numbers of infiltrating leukocytes (neutrophils and also lymphocytes)
- Degeneration of fibroblasts (fibroblasts play a key role in collagen formation and wound healing)
- Start of collagen destruction
Four principal phases of plaque-associated periodontal disease
Describe the established lesion (2–3 weeks) of periodontal disease (6 points):
Established lesion (2–3 weeks of continued plaque accumulation – chronic gingivitis):
- Dense inflammatory cell infiltrate – plasma cells (antibody response), lymphocytes, neutrophils
- Elevated release of matrix metalloproteinases which degrade extracellular matrix components, including collagens which make up connective tissues (i.e. periodontal ligament, gingival fibres)
- Elevated release of lysosomal contents of neutrophils → further hydrolytic activity of enzymes in ECM
- Significant collagen depletion → increased mobility and drifting of tooth
- Proliferation of epithelium → formation of pocket epithelium containing large numbers of neutrophils
- Results in ‘false pocketing’ on basic periodontal examination (BPE).
Four principal phases of plaque-associated periodontal disease
Describe the advanced lesion (transition from gingivitis to periodontitis) of periodontal disease (6 points):
Advanced lesion (marks the transition from gingivitis to periodontitis):
- Determined by bacterial challenge, host inflammatory response and other susceptibility factors
- Further destruction of collagen subjacent to the JE, with fibrosis at distant sites
- Predominance of inflammatory cells in connective tissues
- Predominant immune cells are plasma cells (antibody-mediated response, IgA)
- Extension of the lesion into the periodontal ligament and supportive alveolar bone (visible on radiograph), exhibited as clinical attachment loss and pocket formation (periodontal defects).
- Considered periodontitis from this point onward
Recall the ecological plaque hypothesis for periodontal disease
Describe necrotizing ulcerative gingivitis (5 points)
Necrotizing ulcerative gingivitis:
- Acutely inflamed, red, shiny, and bleeding gingivae
- Irregularly shaped ulcers on the interdental papillae
- Painful condition – pseudomembranous slough (offensive smell)
- Linked to poor OH, stress, smoking, malnutrition, immunosuppression
- Anaerobic, polymicrobial infection (fusospirochaetal complex):
- Fusobacterium nucleatum
- Spirochaetes spp.
Describe leprosy
Leprosy:
- Mycobacterium leprae
- Atrophy of the anterior nasal spine, saddle nose
List 9 infections associated with Streptococcus pyogenes (group A)
Streptococcus pyogenes causes a number of spreading infections with minimal local suppuration; the most notable are:
- Tonsillitis
- Pharyngitis
- Necrotizing fasciitis (streptococcal gangrene; ‘flesh eating bacteria’)
- Scarlet fever
- Mastoiditis
- Sinusitis
- Otitis media (middle-ear infection)
- Wound infections leading to cellulitis and lymphangitis
- Impetigo and erysipelas (a brawny, massive skin infection)
List the complications associated with Streptococcus pyogenes (group A) infection
Complications associated with Streptococcus pyogenes (group A) infection
After an episode of infection, some patients develop complications which may have long-lasting effects:
- Rheumatic fever
- Glomerulonephritis
- Erythema nodosum
Virulence factors:
- In cellulitis, hyaluronidase (spreading factor) mediates the subcutaneous spread of infection
- Erythrogenic toxin causes the rash of scarlet fever
- Post-streptococcal infection:
- Rheumatic fever ⇒ immunological cross-reaction between bacterial antigen and human heart tissue (type 2 ‘cytotoxic’ hypersensitivity)
- Acute glomerulonephritis ⇒ immune complexes bound to glomeruli (type 3 ‘immune complex deposition’ hypersensitivity)