Microbiology Flashcards
What is a pathogen?
Organism that causes or is capable of causing disease
What is a commensal?
Organism which colonises the host but causes no disease in normal circumstances
What is an opportunist pathogen?
A microbe that only causes disease if the host defences are compromised
What is asymptomatic carriage?
When a pathogen is carried harmlessly at a tissue site where it causes no disease
How are bacteria named?
Genus species
What colour does gram positive bacteria stain?
Purple
What colour does gram negative bacteria stain?
Pink
Describe the steps to gram staining?
- come in and stain
1. crystal violet
2. iodine
3. Acetate/alcohol
4. safranin counterstain
When is a Ziehl-Neelsen stain used?
On acid fast mycobacteria which have a high lipid and mycolic acid content (so gram staining doesn’t work)
What is the procedure for Ziehl-Neelsen staining?
- cells stained using carbol fuchsin
- washed using acid alcohol, mycobacteria remain purple
- slide then stained with methylene blue.
- purple mycobacteria can be identified
What is blood agar?
- a mix of sheep and horse blood
- medium for growing a wide range of bacteria
- non-selective
What is XLD agar?
- very selective growth medium used to isolate salmonella and shigella
- gut bacteria appear yellow
- shigella: red
- salmonella: red with black centres
What is MacConkey agar?
- designed to grow and differentiate gram negative bacilli
- contains red dye and lactose
- lactose fermenters: pink
- non-lactose fermenters: yellow/colourless
What is CLED agar?
- used in urine
- for gram -ve bacilli
- lactose fermenting: yellow
- non-lactose: blue
Which gram negative bacilli are lactose fermenting and which are non-lactose fermenting?
lactose fermenting: E.coli
non-lactose fermenting: salmonella, shigella
What is the catalase test?
- differentiates between staphylococcus and streptococcus genus
- bubbling = positive for staph
What are mycobacteria?
- slightly curved, beaded bacilli
- aerobic, non-spore forming, non motile bacillus
- gram positive
- slow growing
What challenges does TB present?
- Thick, lipid rich cell wall making immune cell killing and drug penetration challenging
- Slow growth: gradual onset, longer to diagnose, longer to treat. Can be months or years.
What are the 2 different shapes of bacteria?
Rods: bacilli (vibrio - curved and spirochaete)
Blobs: cocci (diplococci, chains, clusters)
In what environment can bacteria survive?
- From -80º to +80º
- pH 4-9
What are spores?
Spores are rounded forms of bacterial cells which are highly resistant to heat, chemicals and desiccation
What are endotoxins?
a component of the outer membrane of bacteria e.g. lipopolysaccharide in gram negative bacteria
- non-specific action
- stable in heat
- weak antigenicity
What are exotoxins?
Secreted proteins of Gram positive and Gram negative bacteria
- labile in heat
- strong antigenicity
What is gram positive bacteria?
Has a thick cell wall with a peptidoglycan layer
What is gram negative bacteria?
has a thick cell wall with liposaccharide and protein outer membrane
Describe the properties of S. aureus (coagulase, spread)?
- coagulase positive
- spread by air or touch
- people are either carriers or shedders
What is coagulase?
- An enzyme produced by bacteria that clots blood plasma.
- Fibrin clot formation around bacteria may protect from phagocytosis.
GIve examples of coagulase positive vs negative bacteria
- coagulase positive: staph aureus
- coagulase negative: staph epidermidis and saprophyticus
What virulence factors does S. aureus release that lead to its success?
- Pore-forming toxins (some strains) a - haemolysin and ‘PVL’
- Proteases
Exfoliatin - Toxic Shock Syndrome toxin (stimulates cytokine release)
- Protein A (surface protein which binds antibodies in wrong orientation)
What does MRSA stand for and which antibiotics is it resistant to?
- methicillin resistant staphylococcus aureus
- resistant to gentamicin (methicillin), erythromycin, tetracycline
What are coagulase negative forms of staph and what diseases do they cause?
- S. Epidermidis: opportunistic infections, forms persistent biofilms
- S. Saprophyticus: causes acute cystitis
What does streptococcus look like and how is it classified?
- Cocci in chains
- haemolytic, lancefield typing and biochemical properties
What is haemolysis?
- test performed where bacteria is grown on blood agar
- α: secretes hydrogen peroxide > partial haemolysis and greening
- β: 2 pore forming toxins > complete lysis, appears yellow/clear
- gamma: no lysis
How can β haemolytic strep be grouped?
- antigenic sero-grouping
- antibodies made that recognise each lancefield group (carb group in cell wall)
- tagged to white latex beads
- +ve result: antibodies bind bacteria and clump together
What are the most important Lancefield groupings?
- Group A: S.pyogenes
- Group B: S. agalacticae
How can α haemolytic strep be identified
- optochin test:
- resistant: viridans strep: no ring around filter paper disc
- sensitive: S. pneumoniae
What is an antibiotic?
Molecules that work by binding a target site on a bacteria - binding at points on the bacterium that are crucial to its survival
What are antimicrobials?
Agents that kill infectious pathogens including antifungals, antibacterials, antihelminithics, antiprotozoals and antiviral agents
What are β lactams?
Disrupt peptidoglycan production, through covenant bonding to the transpeptidase enzyme activity which interrupts cross linking and cell wall synthesis
What are examples of penicillins?
- Penicillin V
- Penicillin G
- Flucloxacillin
- Amoxicillin
- Pipericillin
What are examples of cephalosporins?
- Cefuroxime
- Cefotaxime
- Ceftriaxone
What are examples of glycopeptides?
- Vancomycin
- Teicoplanin
What are the layers of gram negative cell wall?
- capsule, lipopolysaccharide (endotoxin), outer membrane, lipoprotein, periplasmic space, peptidoglycan, inner membrane
What are the layers of gram positive cell walls?
- capsule, peptidoglycan, inner membrane
Which antibiotics affect protein synthesis by affecting ribosomes?
- gentamicin (aminoglycoside)
- doxycycline (tetracycline)
- clindamycin (lincosamide)
- clarithromycin (clarithromycin)
What are examples of sulphonamides?
- trimethoprim
- co-trimoxazole
- affect folic acid production
Which antibiotics affect nucleic acid synthesis?
- metronidazole
- ciprofloaxcin
How are bacteria pathogenic?
- Direct: destroy phagocytes + cells in which bacteria replicate
- indirect: inflammation, immune-pathology
- toxins: endo and exotoxins
What are we trying to achieve with antibiotics?
- give time and support for the immune system to deal with an infection
What is the action of antibiotics?
- Kill bacteria: inhibit cell wall synthesis (bacteriocidal)
- stop bacteria growing: inhibit protein synthesis, DNA replication or metabolism (bacteriostatic)
How much antibiotic is needed?
- drug must attach to its binding target and occupy an adequate number of binding sites
- antibiotic should remain at the binding site for a sufficient time period
Which drugs have their efficacy determined by time dependent killing?
t> minimum inhibitory concentration
- β lactams, clindamycin, macrolides
Which drugs have their efficacy determined by concentration dependent killing?
- aminoglycosides
- quinolones
How are fungal cells comparable to human cells?
- DNA/RNA/protein synthesis similar to mammalian cells
- cell wall doesn’t exist in humans
- plasma membrane contains ergosterol instead of cholesterol
How do bacteria resist antibiotics?
- change molecular configuration of antibiotic target
- destroy antibiotics using enzymes
- prevent antibiotic access
- remove antibiotic from bacteria
What is an example of antibiotic destruction?
- β lactam rings of penicillin are hydrolysed by bacterial enzyme β lactamase so it is no longer able to bind to the PBP
How can antibiotic access be prevented?
- bacterial membrane porin channel is modified e.g. the size, number, selectivity
How can the antibiotic be removed from the bacteria?
- proteins in bacterial membranes act as export/efflux pumps so the level of antibiotic is reduced.
What is intrinsic resistance?
- all subpopulations are equally resistant
- aerobic bacteria can’t reduce metronidazole to its active form
- vancomycin can’t penetrate the outer membrane of gram negative bacteria
What is MRSA?
- bacteriophage mediated
- resistance gene mecA is transferred
- encodes penicillin-binding protein 2a
- causes resistance to all β-lactam antibiotics
What factors must be considered when thinking about if an antibiotic is safe to prescribe?
- Intolerance, allergy and anaphylaxis
- Side effects
- Age
- Renal and Liver function
- Pregnancy and breast feeding
- Drug interactions
- Risk of Clostridium difficile
When are cephalosporins useful?
- Good for people with penicillin allergy
- Work against some resistant bacteria
- Get into different parts of the body e.g. meningitis
What are fungi?
- eukaryotic
- chitin cell wall
- heterotrophic
- move by growth of spores which are carried through air/water
What are some examples of fungal disease?
- Tinea pedis (athlete’s foot)
- onychomycosis (fungal nail infections)
- life threatening fungal infection is rare in healthy hosts
What are yeasts?
- small single celled organisms that divide by budding
- some fungi switch between yeasts and moulds
Why do fungi not tend to affect humans?
- inability to grow at 37 degrees
- innate and adaptive immune response
What methods can be used for fungal diagnostics?
- Radiology: aspergillus and zygomycetes
- microscopy: aspergillus, zygomycetes and yeasts
- culture
- PCR + antigen tests
How can fungal disease be treated?
- drugs that target the cell wall or plasma membrane
- it is difficult to identify molecules with selective toxicity for fungi because they are eukaryotic
What is the main form of treatment of fungal disease?
- azoles: broad class of drugs
How do moulds form and spread?
- form multicellular hyphae and spores
What are the types of gram positive cocci that can be cultured on artificial media?
staphylococcus and streptococcus
In what form do staph cocci appear and what are the 2 different types of staph?
- appear in clusters
- coagulase test > +ve = S. aureus and -ve = coagulase negative staph
Which sites in the body are sterile?
- blood
- CSF
- joints
- lower resp tract
- pleural fluid
- peritoneal cavity
- bladder
Which sites in the body are colonised by flora?
- GI tract
- skin
- oral cavity
- vagina
- urethra
What is a virus?
- An infectious, obligate intracellular parasite
- Comprises genetic material (DNA/RNA) surrounded by a protein coat/membrane
What is the typical size of a human virus?
20-60nm
How do viruses replicate?
- Attachment to specific receptor
- Cell entry: uncoating of virion within cell and transcription to mRNA using host materials
- Host cell interaction and replication: translation of viral mRNA to produce structural proteins, viral genome or non-structural proteins
- Assembly of virion: occurs in different locations depending on virus
- Release of new virus particles: bursts out > cell death/budding or exocytosis
How do viruses cause disease?
- Direct destruction of host cells
- Modification of host cell
- Over-reactivity of immune system
- Damage through cell proliferation
- Evasion of host defences
What are protozoa?
Unicellular eukaryotes with a nucleus
What are the 5 major classifications of protozoa?
- flagellates
- amobae
- cilliates
- sporozoa
- microsporidia
What is the host of malaria?
Humans and the female anopheles mosquito acts as a vector
What are the symptoms of malaria?
- fever
- chills
- headache
- myalgia
- fatigue
- diarrhoea and vomiting
What is the malaria cycle?
- parasites grow and multiply in liver cells
- parasites infect red blood cells, grow and cause them to burst.
How do we identify risks of infection?
- risk factors
- screening
- clinical diagnosis
- lab diagnosis
What are enterobacteriaceae?
- colonisers of large bowel, skin below waist and moist sites
- most common causes of UTI and intra abdominal infection
What is carbapenemase?
- inactivates carbapenem antibiotics
- previous one of the last resort antibiotics, now commonly used
- one of the broadest spectrum antibiotics available
What is MRSA resistant to?
- flucloxacillin and other β lactam antibiotics
When should hands be washed?
- before and after patient contact
- after handling bodily fluids
- after using the toilet
- before and after handling food
- before and after an aseptic procedure
- after removing PPE
What are the methods of HIV prevention?
- PREP: pre-exposure prophylaxis
- PEP: post-exposure prophylaxis (started within 72 hrs) not as effective as PREP.
- U=U: undetectable = untransmissible
What are the benefits to testing for HIV?
- Access to appropriate treatment and care
- Reduction in morbidity and mortality
- Reduction of vertical transmission
- Reduction of sexual transmission
- Public health /partner notification
- Cost-effective
What is involved in the 4th generation HIV test?
- venous blood sample
- includes p24 antigen and detects vast majority of infections at 4 weeks - repeated at 7 weeks if high index of suspicion
- high sensitivity and specificity
What is involved in a HIV point of care test?
- finger prick
- immediate result
- Lower sensitivity and specificity
- False positive and negative results
- Longer incubation period
How are HIV test results managed?
- Negative test:
Repeat if within “window period” - Positive result or result not clear
Phone Sexual Health for advice and appointment is arranged within 48 hours
Explain test “reactive” and needs further investigation
What type of virus is HIV?
- retrovirus
- uses reverse transcriptase to make a DNA copy which is integrated within DNA of affected cell.
What is the socio-economic impact of HIV in Africa?
- significant impact on life expectancy
- loss of economically productive adults
- inc and distorted spending on healthcare
- change in social structure: orphans cared for by grandparents
How does paediatric HIV infection occur?
- in utero: transplacental, during 3rd trimester
- intra partum: exposure to maternal blood/genital secretions during delivery
- breast milk
- risk is up to 45% of transmission
How can HIV transmission be prevented?
- condom use
- male circumcision
- treating STIs
- PreP/TasP/PeP
What are the key features of HIV pathogenesis?
- HIV is integrated into DNA of infected CD4- expressing cells
- HIV infects CD4+, helper T, Treg, T follicular, dendritic cells, macrophages
- HIV passes directly cell to cell so is inaccessible to antibodies
What are the acute non-specific symptoms of HIV?
- fever
- sore throat
- myalgia (muscle ache)
- rash
- occurs within 2-4 weeks of infection
Which bacteria commonly grows in reheated rice and is associated with takeaways?
- Bacillus cereus produces the toxin cereulide which causes vomiting
What indicates a bacterial infection?
- high neutrophil count
- raised CSF protein: dying bacteria + Abs
- reduced CSF glucose: neutrophils use as energy
What is a charcoal swab used for?
- allow for microscopy, culture and sensitivities
- used with Amies transport medium
- used for: ear, eye, skin and abscesses, throat, vaginal and wound swabs
- used for chlamydia
Which STIs and GU infections can a charcoal swab confirm?
- bacterial vaginosis
- candidiasis (thrush)
- gonorrhoeae
- trichomonas vaginalis
- group B strep
What type of bacteria is Neisseria gonorrhoeae and how is it treated?
- gram-negative diplococcus
- ciprofloxacin or azithromycin
What bacteria causes syphilis?
- Treponema pallidum
- spirochete
- incubation period: 21 days
What type of bacteria is Neisseria meningitidis?
- gram negative diplococci
What type of bacteria is Strep. pneumoniae?
- gram positive diplococci
- α haemolytic and optochin sensitive
How is S. pneumoniae treated?
- β lactam antibiotics: amoxicillin, cefuroxime and cefotaxime
- clarithromycin or ciprofloxacin in penicillin allergy
What type of bacteria is Haemophilus influenzae?
- gram negative cocobacilli
How is H. influenzae treated?
- β lactam antibiotics: co-amoxiclav
- tetracyclines: doxycycline
- NOT macrolides (-romycin)
What is Klebsiella pneumoniae and where is it found?
- gram negative bacilli
- found in flora of mouth and intestines
- homelessness, alcoholics, hospital
How is Klebsiella pneumoniae treated?
- β lactams: co-amoxiclav
- cephalosporins
What is Bordatella pertussis and how is it treated?
- gram negative bacillus
- causes whooping cough
- diagnosed by culture, PCR, ELISA for IgG against pertussis toxin
What is the treatment of Bordatella pertussis?
- clarithromycin
- vaccinated against as part of dTaP (diphtheria, tetanus and acellular Pertussis)
How is Corynebacterium diphtheriae treated?
- anti-toxin
- erythromycin/clarithromycin
