Microbiology and cell injury Flashcards
What are differences between viruses and bacteria?
Virus - obligate intracellular parasites, no ribosomes, DNA or RNA not both, 10-100s genes
Bacteria - usually free living, ribosomes, DNA and RNA, can be seen by light microscopy, 100-1000s genes
What are differences between bacterial and human cells?
Bacterial cells - no nucleus, no intracellular organelles except ribosomes, no introns
Human cells - nucleus, intracellular organelles, introns, larger volume
What are fungi?
Eukaryotes, so have a nucleus
Cell wall contains chitin (different from plant and bacterial cell walls)
What is the difference between Protozoa and metazoa?
Protozoa: single celled eukaryotes
Live in or out of host cells
Metazoa: multicellular organisms including arthropods, worms
What are prions?
Proteinaceous infectious particles
BSE, CJD, Kuru, Scrapie, nv-CJD
Very difficult to destroy
What is a commensal organism?
Organism that is found normally on external surfaces (includes lumina) Collection of commensals = microbiota
What commensal organisms are found on the skin?
Staphylococci, Streptococci, Propionobacteria (acne)
What commensal bacteria are found in the upper respiratory tract?
Haemophilus, pneumococcus, respiratory viruses, Streptococci
What commensal bacteria are found in the gut?
Bacteroides, “gut bacteria” e.g. E. coli, Klebsiella, viruses
What commensal organisms are found in the genital tract?
Streptococci, Haemophilus, Anaerobes, Lactobacilli
What is colonisation?
Presence of commensal or opportunistically pathogenic organisms not causing harm
What is colonisation resistance?
Resident microbes compete for space and nutrients with pathogens thereby protecting the host: “friendly bacteria”
What can be a treatment for antibiotic resistant c dif infection?
Faecal transplant
What is an infection?
Situation in which a microbe is established and growing in a host, whether or not the host is harmed
What is a pathogen? And what is the difference between an obligate and opportunistic pathogen?
Micro-organisms that can cause disease
Obligate pathogens e.g. Salmonella Typhi, Shigella (dysentery) cause disease to survive and spread
Opportunistic pathogens: cause disease only in individuals with abnormal host defences e.g Pseudomonas aeruginosa
Give an example of an obligate infection with 100% virulence
Rabies
What are Kochs postulates for linking a pathogen to a disease?
Pathogen must be present in every case of the disease
It must be isolated from the diseased host & grown in pure culture
Specific disease must be reproduced when a pure culture of
the pathogen is inoculated into a healthy susceptible host
Pathogen must be recoverable from the experimentally infected host
What colour do gram positive bacteria stain?
Purple because of peptidoglycan
What shape are staphylococci?
Round clumps
What shape are streptococci?
Round chains
What cellular adaptations occur as a result of increased demand or increased stimulation by growth factors/hormones?
Hyperplasia, hypertrophy
What cellular adaptations occur as a result of decreased nutrients or stimulation?
Atrophy
What cellular adaptations occur as a result of chronic irritation?
Metaplasia
What are features of irreversible damage?
Severe mitochondrial damage
Rupture of lysosomal and plasma membranes
What are the 7 causes of cell injury?
Oxygen deprivation Physical agents Chemicals and drugs Infectious agents Immune reactions Generic derangements Nutritional imbalances
Name 4 causes of hypoxia
Local - embolus
Systemic - cardiac failure
Oxygen problems - altitude
Haemoglobin problems - anaemia
What type of necrosis is formed by extreme heat or cold?
Coagulative
What are differences between apoptosis and necrosis?
Necrosis - cell swelling, nuclear dissolution, disrupted plasma membrane, enzymatic digestion of cell contents, adjacent inflammation, pathological
Apoptosis - cell shrinkage, nuclear fragmentation, membrane intact, apoptotic bodies, no inflammation, physiological
What cellular changes can result in cellular injury?
Decrease in ATP Mitochondrial damage Entry of Ca Increase in reactive oxygen species Membrane damage Protein misfolding DNA damage
What effects does a depletion of ATP have on a cell?
Cellular swelling, blebs
Loss of microvilli
ER swelling
Clumping of nuclear chromatin - decrease in pH due to anaerobic respiration
Decreased protein synthesis, lipid deposition
What are consequences of mitochondrial damage?
Membrane permeability transition pore - loss of membrane potential
Mitochondrial membrane proteins released into cytosol - cytochrome c, pro apoptotic proteins
What effects can calcium excitotoxicity have on a cell?
Membrane damage
Nuclear damage
Decrease in ATP - mitochondrial damage
How does oxidative stress cause cell injury?
Free radicals are unstable
They initiate auto catalytic reactions in other molecules - formation of lipid peroxidases, abnormal protein folding, DNA mutations
By what 3 mechanisms can free radicals be formed?
Absorption of irradiation
Endogenous and normal metabolic reactions
Transition metals
What mechanisms can remove free radicals?
Spontaneous decay
Anti-oxidants - vit A, vit E, ascorbic acid, glutathione
Storage proteins - ferritin, transferrin
Enzymes - SOD, glutathione peroxidase
Which key membranes can have defects during cell injury?
Mitochondrial
Plasma
Lysosomal
What are the 6 patterns of necrosis?
Coagulative - ischemia, architecture maintained
Liquefactive - infection, pus
Caseous - cheesy, TB
Gangrenous - ischemia, can be wet or dry, wet if infected
Fat - digestion of tissue by enzymes, white chalky deposits
Fibrinoid - leaky
What is an infarction?
Area of ischaemic necrosis in tissue or organ
White - arterial occlusion
Red - venous occlusion, loose tissues, dual blood supply
What are the phases of apoptosis?
Induction - DNA damage, withdrawal of stimulatory signals, death promoting signals
Commitment - cell death signals
Degradation - endonucleases, destroy lamin and actin
What disorders are associated with defective apoptosis and increased survival?
Neoplastic cells - no apoptosis
Autoimmune cells - apoptosis targeted to wrong cells
What disorders are associated with defective apoptosis and decreased survival?
Neurodegenerative disorders - ER stress
Ischaemic injury
Death of virus infected cells
What are 3 important factors when requesting laboratory investigations?
Accuracy
Relevance
Interpreted in clinical context
What are 5 reasons for ordering laboratory investigations?
Diagnosis Screening Monitoring of treatment Prognosis Suitability for treatment
What relevant information is required when ordering lab tests?
Patient demographics Type of specimen Tests required Clinical diagnosis Relevant treatments
What is a problem with the reference range when interpreting results?
5% of healthy individuals will lie outside the reference range
Abnormal is not necessarily pathological
Normal result does not rule out pathology
Results should be interpreted in the clinical context
Give examples of some gram positive bacteria
Cocci - Staphylococcus aureus (incl.MRSA) - Streptococcus pneumoniae - Streptococcus pyogenes (group A strep, necrotising fasciitis) Bacilli - Bacillus anthracis (anthrax) - Bacillus cereus (rice food poisoning) - Listeria - Propionobacterium acnes
Give examples of some gram negative bacteria
Rods - E. coli - Klebsiella - Pseudomonas - Haemophilus Cocci - Neisseria (gonorrhoeaand meningococcus)
What shape are campylobacter?
Seagull shaped
Which pathogens can pose a high risk to lab staff when culturing them?
Brucella
TB
Listeria
Shigella
What are 2 methods of sensitivity testing?
Disc diffusion
Broth dilution
Give 4 examples of labile cells
Squamous epithelium: Skin, mouth, oesophagus
Glandular epithelium: Gut
Transitional Epithelium: Urinary tract
Blood-forming Cells: Bone Marrow
Give 4 examples of stable cells
Liver (Hepatocytes)
Endocrine Glands
Bone (Osteocytes)
Fibrous Tissue (fibrocytes)
Give 3 examples of permanent cells
Neurons Cardiac Muscle (practically) Skeletal Muscle (practically)
Give examples of stem cells found in adults
Skin: Basal cells hair follicle bulb GIT: Crypts of Lieberkühn Lung: Type 2 pneumocytes Blood: Haemopoietic stem cells Liver: Terminal bile ducts Cornea: Limbal arcade
What regulates Growth of cells?
Rate of population growth depends on whether cells Divide, Differentiate (cessation of division) or Die (apoptosis)
Growth is proportionate to cell gain/cell loss
What are some signalling molecules required for cells to survive?
Cell Surface Receptors: Epidermal Growth Factor
Small Hydrophobic Molecules: Pass through plasma membrane, Cytoplasmic or nuclear receptors, Cortisol, Oestrogen
When do cells proliferate?
When stimulated by growth factors
What is the M phase of the cell cycle?
Mitosis and cytokinesis - nuclear and cytoplasmic division
At what point in the cell cycle does DNA replicate?
S phase
What controls the cell cycle?
Positive: Signals from outside the cell (e.g. GF), Phosphorylation Reactions, Cyclin Dependent Kinases/Cyclin Complexes
Negative: Cyclin Kinase Inhibitors, Checkpoints
What is p53?
Senses DNA damage, Induces p21 (Cyclin dependent kinase inhibitor) stops progression
What is hyperplasia?
Increase in the number of cells within a tissue which may then be increased in size
Physiological Hyperplasia: Hormonal e.g. endometrium
Compensatory: Partial hepatectomy
What is atrophy?
Shrinkage in cell size by loss of cell substance
Reduction in organ size through cell loss – involution
Cellular atrophy involves self digestion of organelles - autophagy
What are causes of atrophy?
Reduced workload Loss of nerve supply Reduced blood supply Inadequate nutrition Loss of endocrine stimulation Ageing
What is metaplasia?
Reversible change from one adult cell type to another adult cell type Adaptive response to various stimuli
New cell type better adapted to the stimulus
Fertile ground for the later development of cancer
Can occur in connective tissues
Give examples of pathological metaplasia
Glandular to squamous epithelium in the bronchus of smokers
Squamous to glandular in reflux oesophagitis i.e. Barrett’s
What is dysplasia?
Premalignant condition
Increased cell growth
Cellular atypia
Altered differentiation
What is neoplasia?
Abnormal growth of cells which persists after initiating stimulus has been removed
Cell growth has escaped from normal regulatory mechanisms
Benign/ Malignant – invasion and metastases
List host risk factors for infection
Compromised Host: resistance mechanisms inactive so probability of infection is increased
Extremes of Age: Very young and very old more susceptible
Stress and starvation
Disruption of normal physiological and anatomical barriers to infection Congenital and acquired immunodeficiency: Cancer and transplant treatments; AIDS
Describe how bacteria cause disease
Access: can they get to the site of infection
Adherence: can they stick
Growth: can they multiply
Invasion
Protection from killing by immune system
Protection from killing by antibiotics
What virulence factors do bacteria posses?
Adherence mechanisms: pili, flagella, adhesins
Growth: access to essential nutrients e.g iron
Tissue destruction: toxins, byproducts of metabolism
Evade phagocytosis: capsule, antigen variation, intracellular infection
Evasion of killing
Walling off site of infection e.g coagulase
What are risk factors for urinary tract infections?
Being female Abnormal urinary tract Stones Congenital abnormality Prostatism Pregnancy Catheterisation Diabetes
Which common pathogen commonly causes urinary tract infections? And describe its virulence factors
E.coli the single commonest cause, Carried in large intestine
Uropathogenic strains
Adhesins (pili) improve adhesion to urethral and bladder mucosa
Haemolysin increases invasion
Siderophores scavenge iron for growth
Complement resistance: capsule
Antibiotic resistance common
What are common causes of urinary tract infections?
Escherichia coli 75-90% UTI in otherwise healthy people
Other gram negative “gut bacteria”/ coliforms: Proteus (stones), Klebsiella
Staphylococcus saprophyticus: common in young women
Faecal streps: Enterococci
Almost anything can stick to a catheter, Pseudomonas especially
What are upper and lower urinary tract infections?
Upper: pyelonephritis
Lower: cystitis
What is sterile pyuria?
White cells in urine but no microbes
Usually if antibiotics given before sample is taken
In Interpreting urine microbiology results, what cell count is suggestive of infection?
> 10^5 WBC/ ml
How do you avoid high contamination rates from perineal flora in urine samples?
Mid stream urine
Describe Catheter-associated UTI
Any patient with a urinary catheter will experience colonisation of the urinary tract by a mixed flora within a few days
Asymptomatic colonisation does not warrant treatment
Treat only if symptomatic (e.g. bladder or loin pain, fever, septicaemia)
Treatment will work best if catheter removed for a few days
Biofilm formation (bacteria and secretions), resistant to antibiotics
Manipulation or removal of a catheter in presence of infection can cause septicaemia
Give prophylactic antibiotics
List 5 targets of antimicrobial drugs
Cell wall Nucleic acid synthesis Cell membrane Nucleic acid precursor synthesis - folate Protein synthesis
List the categories of antimicrobials in common clinical use
Penicillins: target cell wall
Vancomycin: target cell wall
Floxacin, rifampicin: target nucleic acid synthesis
Daptomycin, target cell membrane
Trimethoprim: target folate, first line in UTIs
Erythromycin, gentamicin: target protein synthesis
Define the terms empirical, prophylactic and targeted therapy
Empirical antibiotics: used before causative pathogen known, choice determined by likely diagnosis and local epidemiology
Prophylactic: given to prevent infection. Proven efficacy in preventing surgical infections and post-splenectomy infection
Targeted: therapy informed by definitive diagnosis (clinical and or microbiological)
Give an example of a broad spectrum and narrow spectrum antibiotic
Broad: cephalosporins
Narrow: flucloxacillin
List the principal mechanisms of resistance to antibiotics
Eject the drug from the cell: efflux
Use a different metabolic process: bypass
Alter the binding site or target
Break the drug down: enzyme inactivation
Why give focussed antibiotics rather than general ones once the specific organism is known?
Minimise side-effects in individual patient
Minimise resistance in individual patient
Minimise resistance in community (public health)
What are common side effects of antibiotics?
Gastric upset
Allergy (especially penicillins, trimethoprim)
Microbiome disruption: thrush is common, Antibiotic-associated colitis (Clostridium difficile), may be fatal
Antimicrobial resistance
What is a tumour?
A swelling
inflammatory – abscess
neoplasm - growth
What is a neoplasm?
Abnormal growth of cells which persists after initiating stimulus has been removed
Cell growth has escaped from normal regulatory mechanisms
Benign/Malignant – invasion and metastases
What is a benign neoplasm?
Cells grow as a compact mass and remain at their site of origin
What is a malignant neoplasm?
Growth of cells is uncontrolled
Cells can spread into surrounding tissue and spread to distant sites Cancer = a malignant growth
What are behavioural differences between benign and malignant tumours?
Benign: No invasion, No metastasis, Retain function, Variable growth rate, often low
Malignant: Invade, Metastasise, Lose function, Variable growth rate, maybe high
What do benign and malignant tumours look like Macroscopically?
Benign: Capsule? Well defined edge
Malignant: Ill-defined margin, Haemorrhage, Necrosis
What do benign and malignant tumours look like microscopically?
Benign: Nuclear variation in size, chromasia and shape minimal, Low mitotic count, normal mitoses, Retention of specialisation, Structural differentiation retained, Organised, Expansile cohesive growth
Malignant: Nuclear variation in size, chromasia and shape minimal to marked, often variable, Low to high mitotic count, abnormal mitoses, Loss of specialisation, Structural differentiationshows wide range of
changes, Not organised, Local invasion beyond normal boundaries
What changes underly a transformation of cells to Cancer?
A change to DNA or gene expression permitting them to form tumours
Change must be non-lethal and passed onto daughter cells
What is clonality in relation to Cancer?
Tumours develop from a single cell – form a monoclonal population
If clonality can be proved, this is strong evidence for neoplasia
Further mutations lead to neoplasia
Describe plasma cell tumours
Plasma cells make antibody
Each bears either kappa or lambda light chain
Tumours will have either all kappa or all lambda - clonal
What is a retinoblastoma?
Tumour of retina in children
40% of cases familial, 60% sporadic
Familial cases occur younger (1yr age) and can be bilateral
Inherited: defect of Rb gene on one allele
How do tumours develop?
Alteration is to more than one gene, can also be epigenetic
Genes concerned are oncogenes/tumour suppressor genes
Inheritance and environment key factors
What is displasia?
Premalignant condition Increased cell growth Cellular atypia Altered differentiation Can range from mild to severe Sites: Cervix, Bladder, Stomach/oesophagus
What is in situ malignancy?
Epithelial neoplasm with features of malignancy
Altered cell growth
Cytological atypia
Altered differentiation
No invasion through basement membrane
In most tissues Severe dysplasia = carcinoma in situ
Which genes are involved in Cancer formation?
Positive (accelerator) (Oncogenes): Signals from outside the cell (e.g. growth factors), Receptors – EGFR/HER2, Coupling molecules – RAS, BRAF, Phosphorylation Reactions, Cyclin Dependent Kinases/Cyclin Complexes
Negative (brakes) (Tumour Suppressor Genes): Signals from outside the cell (e.g. GI), Cyclin Kinase Inhibitors, Checkpoints
What are the hallmarks of cancer?
Sustaining proliferative signalling Evading growth suppressors Activating invasion and metastasis Enabling replicative immortality Inducing angiogenesis Resisting cell death
What are emerging characteristics of cancer?
Avoiding immune destruction
Tumour promoting inflammation
Genome instability and mutation
Deregulating cellular energetics
What defines growth rate?
Growth = mitosis/(death + differentiation)
What factors allow Self Sufficiency in Growth Signals in cancers?
Oncogenes/Proto-oncogenes Growth Factors Receptors Signal Transduction Transcription Factors Cell Cycle Entry
Which Tumour Suppressor Genes do we see a loss of function in in cancers?
p53
What is the Warburg effect?
Deregulation of cellular metabolism in cancer cells
Switch to glycolytic pathway
What cell combinations may be found in a tumour?
Cancer cells Cancer stem cells Immune inflammatory cells Invasive cancer cells Cancer associated fibroblasts Endothelial cells Pericytes
How do cancer cells avoid immune destruction?
Secreting immune suppressant cytokines: Transforming Growth Factor beta (TGFb) Interleukin 10 Fas ligand – kill invading Fas+ lymphocytes Inhibit dendritic cell maturation
How do cancer cells Induce tumour-promoting inflammation?
Secrete chemokines to attract macrophages and other cells
Necrosis releases pro-inflammatory cytokines
Why is angiogenesis a cardinal feature of tumours?
Required for tumour growth
1-2 mm maximum size without new vessels
Provides nutrients
Route for metastasis
