Microbiology Flashcards
Define pathogen.
Organism that causes or is capable of causing a disease.
Define commensal.
Organism that colonises the host without causing a disease, in normal circumstances.
List 5 locations commensals are found.
1) skin
2) mouth
3) mucosal surfaces
4) urethra
5) vagina
List 7 locations commensals are not found, i.e. sterile.
1) blood
2) cerebrospinal fluid
3) pleural cavity
4) peritoneal cavity
5) lower respiratory tract
6) urinary tract
7) joints
Define virulence.
The degree to which a pathogen is pathogenic.
What is a synonym of virulence?
Pathogenicity.
Define virulence factor. (5)
Molecules produced by pathogens that enable them to:
1) colonise host
2) obtain host nutrients
3) immunoevade
4) immunosuppress
5) enter and exit cells (intracellular pathogen)
Define asymptomatic carriage.
Pathogen in a tissue site without causing a disease.
List Koch’s postulates of disease. (4)
1) microbe must be found in all diseased individuals
2) microbe must be isolated from diseased individual and grown into a pure culture
3) individual inoculated with pure microbe culture should develop disease
4) microbe must be reisolated from inoculated diseased individual
Define coccus.
Round bacteria.
Define bacillus.
Rod-shaped bacteria.
Define diplococcus.
Paired round bacteria.
Define vibrio.
Curved rod-shaped bacteria.
Define spirochaete.
Spiral rod-shaped bacteria
Define spore.
Dormant form of bacteria that is highly resistive to physical and chemical influences.
Define opportunistic pathogen.
Organism that causes disease only in immunocompromised individuals.
Define desiccation.
A state of extreme dryness.
What temperature is the bacterial environment?
-80C to +80C.
What pH is the bacterial environment?
pH 4 to pH 9.
List 3 forms of mutation that lead to genetic variations in bacteria.
1) substitution
2) deletion
3) insertion
List 3 forms of gene transfer that lead to genetic variation in bacteria.
1) transformation, e.g. plasmid
2) transduction, e.g. phage
3) conjugation, e.g. sex pilus
How long can spores be desiccated?
> 50 years.
How long can bacteria be desiccated?
2 hours to 3 months.
Define endotoxin.
Lipopolysaccharide (LPS), found on outer membrame of Gram negative bacteria.
Define exotoxin.
Proteins secreted by bacteria.
Which has a specific action, exotoxin or endotoxin?
Exotoxin.
List the 3 components of LPS of Gram negative bacteria.
1) lipid A - toxic
2) core antigen (R) - short sugar chain
3) somatic antigen (O) - repeating oligosaccharide chain
Which is stable in high temperatures, exotoxin or endotoxin?
Endotoxin.
What is Gram staining?
Staining method used to separate bacteria into two groups, Gram positive and Gram negative.
Which doesn’t bind well to immune cell receptors, exotoxin or endotoxin?
Endotoxin.
What property does the Gram stain use to differentiate bacteria? (2)
Peptidoglycan in cell walls.
1) Gram positive bacteria have a single membrane cell wall with large amounts of peptidoglycan.
2) Gram negative bacteria have a double membrane cell wall with small amounts of peptidoglycan.
List the steps of Gram staining. (4)
1) crystal violet stain - purple primary stain
2) iodide - fixes crystal violet to peptidoglycan
3) ethanol/acetone - decolorisation
4) safranin/carbyfuscin - pink counter stain
Why do Gram negative bacteria find secreting proteins harder?
Protein has to pass through two membranes.
How do you differentiate Gram positive cocci into Staphylococci and Streptococci?
Catalase testing.
What are the results of catalase testing? (2)
1) Staphylococcus, catalase positive.
2) Streptococcus, catalase negative.
Define Staphylococcus.
Clusters of Gram positive cocci.
How do you differentiate Staphylococci?
Coagulase test.
What is the coagulase test?
Test for the enzyme coagulase.
What is coagulase?
A virulence factor that clots blood plasma, forming a fibrin clot around the bacteria protecting it from phagocytosis.
What are coagulase negative bacteria generally?
Opportunistic.
How do you differentiate Staphylococci aureus? (5)
1) cocci
2) clustered
3) Gram positive
4) coagulase test positive
5) golden colour
How do you differentiate Staphylococcus saprophyticus? (4)
1) cocci
2) clustered
3) Gram positive
4) coagulase negative
Define Streptococcus.
Chains of Gram positive cocci.
List 3 ways of differentiating Streptococci.
1) haemolytic testing
2) Lancefield grouping
3) optochin disc testing
List the 3 outcomes of haemolytic testing.
1) α - partial lysis —> greening
2) β - complete lysis —> clearing
3) γ - no lysis —> red
List 5 α haemolytic Streptococci.
1) Streptococci pneumoniae
2) viridans Streptococci
3) Streptococci oralis
4) Streptococci milleri
5) Streptococci sanguis
List 2 β haemolytic Streptococci.
1) Streptococci pyogenes
2) Streptococci agalactiae
Name a γ haemolytic Streptococci.
Streptococci bovis.
How do you differentiate Staphylococcus epidermidis? (4)
1) cocci
2) clustered
3) Gram positive
4) coagulase negative
What is Lancefield grouping.
Using antibodies to test for carbohydrate cell surface antigens.
What is a positive result in Lancefield grouping?
Suspension of bacteria, agglutination.
What are the Lancefield types.
A-H and K-V, but A and B are most important.
What Streptococci is Lancefield group A postive?
Streptococci pyogenes.
What Streptococci is Lancefield group B positive?
Streptococci agalactiae.
Describe optochin disc testing. (3)
1) disc is placed on agar
2) if growth is inhibited around the disc, positive
3) if growth is normal around disc, negative
What is optochin testing used to differentiate?
Streptococci pneumoniae.
How do you differentiate Streptococci pneumoniae? (5)
1) cocci
2) chained
3) Gram positive
4) α haemolytic
5) optochin disc sensitive
How do you differentiate viridans Streptococci? (5)
1) cocci
2) chained
3) Gram positive
4) α haemolytic
5) optochin disc resistant
Where do viridans Streptococci generally infect?
Orally.
How do you differentiate Streptococci pyogenes? (5)
1) cocci
2) chained
3) Gram positive
4) β haemolytic
5) Lancefield group A
How do you differentiate Streptococci agalactiae? (5)
1) cocci
2) chained
3) Gram positive
4) β haemolytic
5) Lancefield group B
How do you differentiate Streptococcus bovis? (4)
1) cocci
2) chained
3) Gram positive
4) γ haemolytic
What are the 2 groups of Gram positive bacilli?
1) aerobic
2) anaerobic
List the 3 types of aerobic Gram positive bacilli.
1) Cornybacterium, e.g. C. diphtheria
2) Listeria, e.g. L. monocytogenes
3) Bacillus, e.g. B. anthracis
Name a type of anaerobic Gram positive bacilli.
Clostridium.
List 4 examples of Clostridium.
1) Clostridium perfringens
2) Clostridium tetani
3) Clostridium botulinium
4) Clostridium dificile
List 3 types of Gram negative cocci.
1) Neisseria
2) Moraxella
3) Veillonella
How do you differentiate Gram negative bacilli?
Whether they ferment in lactose.
List 3 agar plates containing lactose that differentiate Gram negative bacilli.
1) MacConkey
2) CLED
3) XLD
List 2 lactose fermenting Gram negative bacilli.
1) Escherichia coli
2) Klebsiella
List 3 non lactose fermenting Gram negative bacilli.
1) Shigella
2) Salmonella
3) Pseudomonas
How do you differentiate lactose fermenting Gram negative bacilli? (2)
1) biochemical identification, e.g. API strips
2) sensitivity tests
What is the colour change in MacConkey agar with the presence of a lactose fermenting Gram negative bacilli?
Yellow —> Red.
What type of bacteria does the Gram stain not differentiate?
Mycobacteria.
What test is used to differentiate Mycobacteria?
Ziehl-Neelsen staining. Stains red.
List 7 Mycobacterium and an associated medical condition.
1) Mycobacterium tuberculosis - tuberculosis
2) Mycobacterium leprae - leprosy
3) Mycobacterium avium - chronic lung infection
4) Mycobacterium kansasii - chronic lung infection
5) Mycobacterium marinum - fish tank granuloma
6) Mycobacterium ulcerans - Buruli ulcer
7) Mycobacterium fortuitum - skin and soft tissue infections
List 7 features of Mycobacterium.
1) aerobic
2) bacillus
3) Gram neutral (colourless) to weakly Gram positive
4) non spore forming
5) non motile
6) high molecular weight lipid cell wall
7) slow growing
Describe the immunology of Mycobacterium, and the formation of granulomas. (10)
1) Mycobacterium phagocytosed by macrophages
2) Mycobacterium is trafficked into a phagolysosome
3) Mycobacterium adapted to withstand phagolysosome
4) Mycobacterium escapes to cytosol
5) unable to kill the Mycobacterium, macrophages activate into epithelioid histiocytes
6) epithelioid histiocytes fuse forming Langerhan giant cells
7) granuloma forms
8) T cells infiltrate the granuloma
9) fibroblasts surround the granuloma to ‘wall it off’
10) central tissue of granuloma may necrose
How long do memory cells take to generate in primary tuberculosis?
4-8 weeks.
List 2 outcomes of primary tuberculosis.
1) latent tuberculosis (90%)
2) pulmonary tuberculosis (5%)
Where do tuberculosis granulomas tend to form?
Lung apexes.
Why do tuberculosis granulomas tend to form in lung apexes? (2)
1) more air supply
2) less blood supply —> fewer leukocytes
List 2 things Mycobacterium high molecular weight lipid cell wall results in.
1) surviving in harsh environments, e.g. macrophage lysosomes
2) resistant to Gram stain
List 4 features that is a result of Mycobacterium’s slow growth.
1) slow reproduction
2) slow growth in humans
3) slow growth in culture —> hard to culture
4) slow response to treatment —> 6 months minimum
How do you differentiate non lactose fermenting Gram negative bacilli?
Oxidase test.
What is the result of Oxidase testing?
Oxidase positive —> Pseudomonas.
Define helminths.
Parasitic worms.
List the 3 groups of helminth.
1) nematodes - roundworms
2) trematodes - flatworms (flukes)
3) cestodes - tapeworms
List 2 locations of nematodes (roundworms).
1) intestines
2) skin
List 4 locations of trematodes (flatworms).
1) intestines
2) liver
3) lung
4) blood
List 2 types of cestodes.
1) non-invasive - remains in intestines
2) invasive - leaves intestines
List 4 features of helminth related diseases.
1) one of the commonest diseases in world
2) rare in UK
3) helminths reproduce only after developing outside of host
4) helminths produce countless larvae/eggs
Define pre-patent period.
Interval between helminth infection and appearance of larvae/eggs in stool.
List 6 methods to control helminth related disease.
1) treatment of carriers
2) mass chemotherapy e.g. everyone
3) targeted chemotherapy e.g. haematuric individuals
4) water contamination prevention
5) toilet provisions
6) health education
List 7 common viral infections.
1) respiratory
2) herpes group
3) hepatitis group
4) enterovirus
5) diarrhoea causing
6) rash causing
7) HIV
List 2 unusual principles of viruses.
1) same virus can cause different diseases, e.g. enteroviruses
2) different viruses can cause same disease, e.g. hepatitis group
List 5 basic properties of viruses.
1) inert outside host cell
2) function inside host cell
3) possess only one type of nucleic acid (RNA or DNA)
4) no cell wall —> outer protein coat
5) surface protein receptors —> allows attachment onto host cell
List 3 features of viruses that suggest they are living.
1) nucleic acid core
2) outer protein capsid
3) replicate (inside host cell)
List 4 features that suggest viruses are non-living.
1) only one type of nucleic acid
2) no cell wall
3) no organelles
4) cannot replicate by themselves
List 6 stages of viral replication.
1) attachment
2) cell entry
3) host cell interaction
4) replication
5) assembly
6) release
What happens during viral attachment?
Viral surface protein receptors attach to specific cells, e.g. HIV gp120 to CD4 T cells.
What happens during viral cell entry?
Central viral core containing nucleic acid and associated proteins enter host cell.
What happens during viral host cell interaction.
Virus evades host cell defence mechanisms.
What happens during viral replication? (3)
1) virus localises in nucleus, cytoplasm or both
2) virus uses host cell materials (enzymes, amino acids, nucleotides)
3) virus produces progeny viral nucleic acids and proteins
What happens during viral assembly?
Progeny viral nucleic acids and proteins are assembled at nucleus, cytoplasm or cell membrane.
What happens during viral release?
Virus leaves host cell by either lysis or exocytosis.
List 4 methods viruses cause disease.
1) direct destruction of host cells, e.g. HIV
2) modification of host cell structure or function, e.g. rotavirus
3) host overreaction, e.g. hepatitis B
4) cell proliferation/immortalisation, e.g. human papillomavirus
List 3 ways viruses evade host defences.
1) persistence
2) variability
3) modulation of host defences
What type of cell are fungi?
Eukaryotes.
List 4 components of fungal cell walls.
1) chitin
2) mannoproteins
3) B1,3 glucan
4) B1,6 glucan
What drugs target fungal cell walls?
Echinocandins.
List 3 drugs targeting fungal cell membranes.
1) Amphotericin
2) Azoles
3) Terbinafine
What do fungal cell membranes contain instead of cholesterol?
Ergosterol.
Is fungal DNA, RNA and protein synthesis similar to mammals?
Yes.
Describe fungal nutritional intake.
Heterotrophic.
Define heterotrophic.
Inability to produce organic substances from inorganic substances. Rely on outside nutrients.
List the 2 forms of fungi.
1) yeast - <1%
2) mould - >99%
What form are yeasts found in?
Single cells.
List 2 forms moulds are found in.
1) multicellular hyphae
2) multicellular spores
Define dimorphic fungi.
Fungi able to switch between yeasts and moulds depending on conditions.
List 2 reasons why fungi are generally not pathogenic.
1) inability to grow at 37ºC - non cell invasive
2) no method to combat immune response
List 5 common fungal infections.
1) nappy rash
2) vulvovaginal candidiasis - ‘yeast infection’
3) onychomycosis - nail infection
4) otitis externa - swimmer’s ear
5) fungal asthma
List 3 instances when fungal infections are life threatening.
1) immunocompromised
2) post-surgical
3) fungal asthma
List 3 reasons why is treating fungal infections difficult.
1) fungi are eukaryotic
2) similar to host cells
3) difficult to treat without host cell toxicity
What drugs target fungal DNA, RNA and protein synthesis? (1)
Flucytosine.
Define Protozoa.
Single-called eukaryotes.
List 2 environments Protozoa are found.
1) aqueous environments
2) soil
List the 5 major classifications of Protozoa.
1) flagellates
2) amoebae
3) sporozoa
4) microsporidia
5) cilliates
Give an example of a Protozoa.
Malaria.
List the 5 species of malaria that infect human.
1) Plasmodium falciparum
2) Plasmodium ovale
3) Plasmodium vivas
4) Plasmodium malariae
5) Plasmodium knowlesi
List 4 signs of malaria.
1) anaemia
2) jaundice
3) heptosplenomegaly
4) black water fever - dark urine
List 8 symptoms of malaria.
1) fever*
2) chills
3) headache
4) myalgia
5) fatigue
6) abdominal pain
7) diarrhoea
8) vomiting
What type of malaria causes complicated symptoms.
Plasmodium falciparum.
List 5 symptoms of complicated malaria.
1) cerebral
2) acute respiratory distress syndrome (ARDS)
3) renal failure
4) sepsis
5) bleeding/anaemia
Define antibiotic.
Molecules that bind to a target site on a bacteria, causing either growth inhibition or direct death.
Define target sites.
Points of biochemical reactions, crucial to survival of the bacterium.
List the 5 functional classes of antibiotics.
1) inhibitors of cell wall synthesis
2) inhibitors of nucleic acid synthesis
3) inhibitors of protein synthesis
4) inhibitors of cell membrane function
5) anti-metabolites
Define anti-metabolites.
Molecules that inhibit the use of a metabolite, e.g. anti-folates.
List 3 groups of antibiotics that inhibit cell wall synthesis.
1) beta lactams, e.g. penicillin
2) vancomycin
3) bacitracin
How does penicillin inhibit cell wall synthesis?
Disrupts peptidoglycan production.
What process must bacteria be undergoing for penicillin to be effective?
Replication.
What type of bacteria are penicillin more effective against, and why?
Gram positive. Gram negative bacteria have an extra lipopolysaccharide layer that decreases penetration to peptidoglycan.
List 2 ways that antibiotics inhibit nucleic acid synthesis.
1) affect DNA replication, e.g. rifampicin (RNA polymerase)
2) affect DNA folding, e.g. fluoroquinolone (DNA gyrase)
List 4 types of antibiotics that inhibit protein synthesis.
1) aminoglycosides, e.g. gentromycin
2) tetracyclines
3) lincosamides
4) macrolides, e.g. erthyromycin
What are bacteriostatic antibiotics?
Antibiotics that prevent bacteria growth.
Describe bacteriostatic antibiotic’s efficacy.
Kill >90% in 18-24 hours.
List 3 ways bacteriostatic antibiotics work.
1) inhibit nucleic acid synthesis
2) inhibit protein synthesis
3) anti-metabolite
List 2 beneficial effects of bacteriostatic antibiotics.
1) reduce exotoxin production
2) reduce endotoxin surge likeliness
What are bactericidal antibiotics?
Antibiotics that kill bacteria.
Describe bactericidal antibiotic’s efficacy.
Kill 99.9% in 18-24 hours.
List 2 ways bactericidal antibiotics work.
1) inhibit cell wall synthesis
2) inhibit cell membrane function
Can antibiotics be both bacteriostatic and bactericidal?
Yes.
List 3 things that affect whether a antibiotic is bacteriostatic or bactericidal.
1) conditions
2) pathogen
3) concentration
List 3 instances when bactericidal antibiotics are useful.
1) poor tissue penetration, e.g. endocarditis
2) difficult to treat infections, e.g. tuberculosis
3) need to eradicate infection quickly, e.g. meningitis
List 2 things an antibiotic must do to be effective.
1) occupy an adequate number of binding sites - concentration
2) occupy binding sites for an adequate period of time - time
List the 2 types of antibiotic killing.
1) concentration dependant killing
2) time dependant killing
What is the key parameter of concentration dependant killing?
How high antibiotic concentration is above MIC.
Peak Concentration/MIC ratio
List 2 types of antibiotics that are concentration dependant killers.
1) aminoglycosides
2) quinolone
What is the key parameter of time dependant killing?
How long antibiotic concentration remains above MIC between doses.
t>MIC
List 3 types of antibiotics that are time dependant killers.
1) beta lactams, e.g. penicillin
2) macrolides, e.g. erythromycin
3) oxazolidiones
Define minimum inhibitory concentration (MIC).
Minimum concentration of antibiotic required to stop bacterial growth.
List 8 considerations before prescribing antibiotics.
1) side effects
2) drug interactions
3) intolerance, allergy, anaphylaxis
4) age
5) kidney function
6) liver function
7) pregnancy and breast feeding
8) risk of Clostridium difficile
List 3 ways bacteria develop resistance to antibiotics.
Intrinsic 1) naturally resistant Acquired 2) spontaneous gene mutation 3) horizontal gene transfer
List 3 methods of horizontal gene transfer.
1) conjugation - plasmid transfer via sex pilli
2) transduction - DNA insertion by bacteriophages
3) transformation - picking up naked DNA
List 2 important antibiotic resistant bacteria.
1) methicillin resistant Staphylococcus aureus (MRSA)
2) vancomycin resistant Enterococci (VRE)
Define minimum bactericidal concentration (MBC).
Minimum concentration of antibiotics required to kill all bacterium.
List the 3 groups of HIV.
1) main (M)
2) outlying (O)
3) new (N)
List the clades of main group.
1) A-D
2) F-H
3) J-K
Where is clade A found?
West and Central Africa.
Where is clade B found?
Europe and USA.
Where is clade C found?
Southern Africa.
List the 9 steps of HIV replication.
1) attachment
2) entry
3) uncoating
4) reverse transcription
5) genome integration
6) transcription
7) translation
8) assembly
9) budding
How many genes does HIV contain?
9.
List 7 cells HIV can infect.
1) helper T cells*
2) macrophages
3) dendritic cells
4) bone marrow progenitors (CD34+)
5) renal epithelial cells
6) brain micro vascular endothelial cells
7) astrocytes
List 3 reasons why is immune response to HIV poor.
1) antibodies to gp120 are slow to develop
2) antibodies to gp120 are ineffective as gp120 is not immunogenic
3) HIV escapes killer T cells through antigen mutations
List 5 ways HIV depletes helper T cell numbers.
1) induces apoptosis*
2) cytotoxicity of infected cells
3) decreased production
4) redistribution (peripheries —> lymphoid)
5) bystander cell killing (infected cells kill uninfected cells)
Define sanctuary site.
Areas poorly penetrated by drugs, allowing tumours and pathogens evade effects of the drug.
List 4 sanctuary sites of HIV.
1) bone marrow
2) central nervous system
3) gastrointestinal tract
4) genital tract
List 2 factors used to monitor HIV infection.
1) helper T cell count
2) HIV viral load
List 3 symptoms that should prompt asking about sexual history.
1) fever
2) rash
3) non-specific symptoms
When should you think about doing a HIV test?
No clear reasons for symptoms or recurring infection in unexpected patient.
What is the most common opportunistic infection associated with HIV?
Pneumocystis pneumonia (PCP).
What is HAART?
Highly active antiretroviral therapy. 3 or more antiretroviral drugs that act on different points of HIV’s replication.
What is another name for Lancefield D positive gram negative cocci
Enterococci.
