Microbiology KP notes Flashcards
what is the procedure for the Gram stain?
- apply a primary stain such as crystal violet (purple) to heat fixed bacteria
- add iodine which binds to crystal violet and helps fix it to the cell wall
- decolorise with ethanol or acetone
- counterstain with safranin (pink)
what are the results of the Gram stain?
- in gram-negative bacteria, the decoloriser interacts with the lipids and cells lose their outer lipopolysaccharide membrane
and the crystal violet-iodide (CV-I) complexes, thus they appear pink with counterstain - in gram-positive bacteria, the decoloriser dehydrates the cell
wall and the CV-I gets trapped in the multi-layered peptidoglycan resulting in a purple appearance with counterstain
Gram positive = purple
Gram negative = pink
what is the Ziehl-Neelsen stain? what are the results?
- Gram stain can differentiate most bacteria
- but mycobacteria e.g. TB are acid-fast bacilli that do not take up the gram stain
- instead they take up a stain called Ziehl-Neelsen
acid-fast bacilli = red e.g. Mycobacterium
non acid-fast bacilli = blue e.g. E.coli
what is the catalase test? what are the results?
• essentially add H2O2 to bacteria and see for bubbling reaction (positive reaction)
• used to differentiate between staphylococci
and streptococci
• Staphylococci are catalase positive
• Streptococci are catalase negative
• many Gram negative bacteria e.g. E.coli and fungi (aspergillus spp.) are catalase positive
what is the coagulase test? what are the results?
- coagulase is an enzyme produced by Staphylococcus. aureus that converts (soluble) fibrinogen in plasma to (insoluble) fibrin
- other staphylococci do not produce coagulase, e.g. S. epidermis
- thus this test distinguishes S. aureus (coagulase positive) from other staphylococci (coagulase negative)
- S. aureus is coagulase positive = clumping
- other staphylococci are coagulase negative = no clumping
what is the haemolysis test?
- haemolysis is the ability of bacteria to break down red blood cells in blood agar
- it requires the expression of haemolysin
- very useful for classifying streptococci
what is alpha haemolysis?
an indistinct zone of partial destruction of red blood cells (RBCs) appears around the colony, often accompanied by a greenish to brownish discolouration of the medium (opaque)
what are examples of alpha haemolytic organisms?
- Streptococcus pneumoniae (can cause lobar pneumonia & meningitis) is alpha haemolytic
- S. oralis
- S. milleri
- S. sanguis
- many oral streptococci are alpha haemolytic
- some alpha haemolytic species can cause serious pathology such as infective endocarditis - caused by viridans streptococci
- S. intermedius is also alpha haemolytic
what is beta haemolysis?
a clear, colourless zone appears around the colonies, in which the red blood cells have undergone complete lysis
what are examples of beta haemolytic organisms?
- Streptococci pyogenes, Streptococci agalactiae and many other streptococci are beta haemolytic
- many other bacteria besides streptococci can be beta
haemolytic including S. aureus and listeria monocytogenes
how can S. aureus be differentiated from other beta haemolytic organisms?
it’s important to differentiate staphylococcus aureus and this can be done by:
• looking at appearance on blood agar - will be creamy
yellow
• also will have a positive coagulase test
how can you differentiate between different beta haemolytic bacteria?
by using Lancefield grouping (detecting surface antigens)
what is Lancefield grouping?
- used to differentiate between beta haemolytic bacteria
- detects surface antigens
- A, C, G = tonsillitis and skin infection
- B = neonatal sepsis and meningitis
- D = UTI/enterococci
what is gamma haemolyis?
no haemolysis of RBCs
what are examples of organisms showing gamma haemolysis?
- enterococcus faecalis
- Staphylococcus saprophyticus
- Staphylococcus epidermidis
- S. bovis
- S. mutans
- S. milleri
what is the optochin test?
- place optochin soaked disc on agar and watch bacterial growth
- test to differentiate between streptococcus pneumoniae (causes lobar pneumonia and meningitis - sensitive to optochin so will be a clear zone around the disc
- Viridans streptococci (infective endocarditis) and other alpha haemolytic streptococci are resistant to it so there will be growth around the disc
what are results of the optochin test?
sensitive = Streptococci pneumoniae; clear zone of no growth around disc
resistant = Viridans streptococci; growth around disc
what is the oxidase test?
- tests if micro-organism contains a cytochrome oxidase - an enzyme of the bacterial electron transport chain
- all bacteria that are oxidase positive are aerobic
- bacteria that are oxidase negative may be either aerobic or anaerobic
what are some oxidase positive bacteria?
- P. aeruginosa
- V. cholerae
- Campylobacter e.g. C. jejuni
- Helicobacter
what are the results of the oxidase test?
- oxidase positive = blue - bacteria is aerobic e.g. V. cholerae
- oxidase negative = no colour change - bacteria may be aerobic or anaerobic
what does MacConkey agar grow? what are its uses?
- only grows Gram negative bacilli
- good at differentiating between lactose-fermenting and non-lactose fermenting Gram negative bacilli such as enterobacteria (gut coliforms)
- bile salts present on this agar inhibit Gram positive bacteria and inhibit the swarming of a Gram negative bacterium Proteus spp.
how does MacConkey agar show lactose/non-lactose fermenting bacteria?
has a pH indicator on it so bacteria that ferment lactose and thus produce acid will make the agar appear pink/red
what are some lactose fermenting bacteria that can be identified on MacConkey agar?
- E. coli
- Klebsiella pneumonia
- Enterobacter spp.
what are some non-lactose fermenting bacteria that can be identified on MacConkey agar?
- Salmonella spp.
- Shigella spp.
what is the use of XLD agar?
used to differentiate Salmonella and Shigella mainly
what are the results of MacConkey agar?
- Gram negative bacilli only
- will turn pink/red if lactose fermenting bacteria e.g. E. coli
- will turn white/transparent if non-lactose fermenting e.g. Salmonella
what are the results of XLD agar?
Salmonella = red/pink colonies some with black spots
Shigella = red/pink colonies
what are some Gram positive cocci?
- Staphylococci
- Streptococci
- Enterococci
- anaerobic Streptococci e.g. peptostreptococci
what are some Gram negative cocci?
- Neisseria
- Moraxella
- anaerobic cocci e.g. Veillonella spp.
what are some Gram positive bacilli?
- Bacillus e.g. B. anthracis
- Clostridia
- Corynebacteria e.g. C. diptheriae
- Listeria monocytogenes
- anaerobic bacilli e.g. Clostridia
- Propionibacteria
what are some Gram negative bacilli?
- E. coli
- Campylobacter
- Pseudomonas
- Salmonella
- Shigella
- Proteus
give some examples of aerobic Gram positive cocci?
staphylococcus and streptococcus
give some examples of Staphylococcus?
S. aureus and S. epidermidis
give some examples of anaerobic Gram positive cocci?
peptostreptococcus
give some examples of anaerobic Gram negative bacilli?
Bacteroides (e.g. B. fragilis)
what are some examples of aerobic Gram negative bacilli?
- coliforms
- pseudomonads
- vibrio
- parvobacteria
what areas of the body are sterile and non-sterile?
non-sterile: nasal cavity, larynx, stomach, colon
sterile: lungs, gall bladder, kidneys, eye, CSF
what is the growth rate of bacteria?
- you measure bacterial growth by shining light on bacteria and measuring absorption
- bacteria divide by binary fission
- the growth lag is due to the fact the bacteria are taking in the nutrients needed to divide and grow
- then there is exponential growth until the nutrient runs out
- viable = death phase
what is transformation in bacteria?
the genetic alteration of a bacterial cell via the uptake of an exogenous substance e.g. via plasmid
what is transduction in bacteria?
process by which foreign DNA is introduced into a bacteria via vector or virus e.g. via a bacteriophage (virus)
what is conjugation in bacteria?
the transfer of genetic material between bacterial cells by direct cell-cell contact e.g. via sex pilus
what is the normal habitat of Staphylococcus? how many species are there?
- normal habitat is on the nose and skin
- at least 40 species
- can be coagulase positive (clumping) or negative (no clumping)
- coagulase converts fibrinogen to fibrin i.e. clot - some bacteria produce it
to protect against white blood cells e.g. S. aureus
what is the common clinical presentation of S. aureus?
- pain in shoulder
- elevated temperature
- MRI scan - disc injection and osteomyelitis (bone infection) C6 and C7
- blood cultures show staphylococcus aureus
- treat with flucloxacillin (antibiotic) for 3 months
- Staph. aureus is responsible for around 90% of osteomyelitis
how is S. aureus spread?
aerosol and touch e.g. coughing and breathing
what is MRSA resistant to?
- Beta-lactams antibiotics
- gentamicin
- erythromycin
- tetracycline
what is the virulence/pathogenic factors of S. aureus?
- pore-forming toxins (some produce these) e.g:
• PVL toxin which is prodcued by many MRSA strains and causes haemorrhagic pneumonia
• alpha-haemolysin which can induce apoptosis (at low
levels) or cause widespread necrosis (at high levels) - proteases e.g:
• exfoliatin which causes scalded skin syndrome - toxic shock syndrome toxin (TSST) which stimulates cytokine release
- protein A which is a surface protein which binds
immunoglobulins in wrong orientation
what are the pore-forming toxins of S. aureus? what are their actions?
• PVL toxin which is prodcued by many MRSA strains and causes haemorrhagic pneumonia
• alpha-haemolysin which can induce apoptosis (at low
levels) or cause widespread necrosis (at high levels)
what are associated conditions of S. aureus?
- wound infections (staph. aureus is very good at colonising these)
- abscesses
- osteomyelitis
- scalded skin syndrome
- toxic shock syndrome
- food poisoning
what are some coagulase negative bacteria?
S. epidermis and S. saprophyticus
what are features of S. epidermis?
- opportunistic infections in prosthetic limbs and catheters
- its main virulence factor is its ability to form persistent biofilms
what can S. saprophyticus cause?
acute cystitis
in what ways can streptococci be classified?
- haemolysis
- Lancefield typing
- biochemical properties
what is Lancefield typing?
a method of grouping catalase negative and coagulase negative bacteria based on the bacterial carbohydrate cell surface antigens
what are important groupings in Lancefield typing?
Group A - Strep. pyogenes
Group B - Strep. agalactiae; neonatal infections
what are some infections that are caused by Strep. pyogenes?
- wound infections such as cellulitis
- tonsillitis and pharyngitis
- otitis media
- scarlet fever (caused by erythrogenic toxin)
what are complications of Strep. pyogenes?
- rheumatic fever
- glomerulonephritis
- some strains produce erythrogenic toxin which is responsible for scarlet fever, this toxin is a super-antigen meaning it gives rise to an exaggerated immunological response and increased
circulating cytokine levels - infection with any strain of Strep pyogenes can give rise to complications that are immunologically mediated, so prompt treatment is required to reduce risks
- assessment of risk can be estimated from the anti-streptolysin O titre
what can be used to assess risk for complications of Strep. pyogenes?
anti-streptolysin O titre
what are the secreted virulence/pathogenic factors of Strep. pyogenes?
- hyaluronidase - spreading
- streptokinase - breaks down clots
- C5a peptidase - reduces chemotaxis
- streptolysins O & S toxin - binds cholesterol
- erythrogenic toxin - exaggerated response
what is the action of hyaluronidase in Strep. pyogenes?
speading
what is the action of streptokinase in Strep. pyogenes?
breaks down clots
what is the action of C5a peptidase in Strep. pyogenes?
reduces chemotaxis
what is the action of streptolysins O and S toxin in Strep. pyogenes?
binds cholesterol
what is the action of erythrogenic toxin in Strep. pyogenes?
exaggerated response
what are surface virulence/pathogenic factors of Strep pyogenes?
- hyaluronic acid capsule - protection
* M protein - surface protein that encourages complement degradation
what is the action of hyaluronic acid capsule in Strep. pyogenes?
protection
what is the action of M protein in Strep. pyogenes?
surface protein that encourages complement degradation
what is the common presentation of Strep. pneumoniae?
- heavy smoker with nasal congestion and fever
- 2 days later gets cough and severe chest pain
- rust-coloured sputum
- chest X-ray shows consolidation (lung filled with liquid)
- blood and sputum culture show Strep. pneumoniae (draughtsman colonies)
what infections does Strep. pneumoniae cause?
- pneumonia
- otitis media (middle ear infection)
- sinusitis
- meningitis
what are pre-disposing factors for Strep. pneumoniae?
- impaired mucus trapping e.g. viral infection
- hypogammaglobulinemia - low levels of serum immunoglobulins which are required for efficient phagocytosis
- asplenia - since spleen produces protein called tuftsin which acts to enhance phagocytosis so with no spleen then no tuftsin and this impairs phagocytosis and thus risk of infection
- diabetes
- renal disease
- sickle cell disease
- very young (younger than 2) since immune response to
polysaccharide antigens is very poor
what are the virulence/pathogenic factors of Strep. pneumoniae?
- polysaccharide capsule (84 types) - is antiphagocytic - there is a polyvalent vaccine available for those under 2 but this only protects against 23/84 types
- teichoic acid binds to choline receptors
- peptidoglycan helps protect bacteria
- pneumolysin cytotoxin is a pore-forming toxin
what is the action of the polysaccharide capsule in Strep. pneumoniae?
(84 types) - is antiphagocytic - there is a polyvalent vaccine available for those under 2 but this only protects against 23/84 types
what is the action of teichoic acid in Strep. pneumoniae?
binds to choline receptors
what is the action of peptidoglycan in Strep. pneumoniae?
helps protect bacteria
what is the action of pneumolysin cytotoxin in Strep. pneumoniae?
pore-forming toxin
what are viridans streptococci?
- collective name for oral streptococci
- alpha or non-haemolytic
- some cause dental caries and abscesses
what viridans streptococci cause infective endocarditis?
S. sanguis and S. oralis
what viridans streptococci are the most pathogenic?
most pathogenic are the milleri group:
- S. intermedius
- S. anginosis
- S. constellatus
- causing deep organ abscesses e.g. in brain & liver
what is the common presentation of Corynebacterium diphtheriae?
- child with severe sore throat
- fever and malaise for 2 days
- lymphadenopathy (swollen) in neck
- rapid breathing
- thick greyish membrane on tonsils
what does the swab show in Corynebacterium diptheriae?
gram positive rods/bacilli
what is the treatment of Corynebacterium diptheriae?
treated with anti-toxin (pre-formed antibody to toxin) and erythromycin (antibiotic helps remove symptoms and stop carriage and spread but
does not destroy pathogen)
how is Corynebacterium diptheriae spread?
droplet spread
what is the virulence factor in Corynebacterium diptheriae?
caused by the production of a toxin which inhibits protein synthesis (inactivates elongation factor-2 in host cells by adding ADP-ribosyl group to aa dipthamide)
how can Corynebacterium diptheriae be prevented?
- prevention by vaccination with toxoid (inactivated toxin)
- can grow in the presence of potassium tellurite - selective method for isolating this bacteria from throats of patients
what is LPS?
lipopolysaccharide is an endotoxin and forms the outer leaflet of the outer membrane of gram-negative bacteria and comprises:
- Lipid A - the toxic portion of LPS that is anchored in the outer leaflet of the outer membrane
- core (R) antigen - short chain of sugars, some are unique to LPS
- somatic (O) antigen - a highly antigenic repeating chain of
oligosaccharides
what is lipid A?
the toxic portion of LPS that is anchored in the outer leaflet of the outer membrane
what is the core (R) antigen?
short chain of sugars, some are unique to LPS
what is somatic (O) antigen?
a highly antigenic repeating chain of oligosaccharides
why do gram negative bacteria find secreting a toxin more difficult than gram positive bacteria?
the toxin/effector (protein) needs to travel past two membranes rather than just one
what are the cell surface antigens of gram negative bacteria?
- K antigen (EPS capsule)
- H antigen (flagellum)
- O (somatic) antigen (LPS)
what are examples of bacteria that do and don’t have a H antigen?
- Shigella has no H antigen since it does not have flagellum
- Salmonella does have a H antigen since it does have a flagellum
what are features of Enterobacteria (coliforms)? what is used to differentiate between lactose fermenting and non-lactose fermenting forms?
- rods/bacilli
- most are motile i.e. have flagella
- some are intestinal parasites
- are able to grow in anaerobic conditions
- MacConkey agar is used to differentiate between lactose and non-lactose fermenting
what are features of Escherichia coli?
• commensals - most abundant facultative anaerobe (facultative means
is able to i.e. is able to respire anaerobic, but not only anaerobically, can respire aerobically too)
• they have flagella
• there are many serotypes/strains
• they all share a common ‘core’ genome
what are some infections that are caused by pathogenic E. coli strains?
- wound infections (surgical)
- Urinary Tract Infections (UTIs) - also known as cystitis,
75%-80% female UTIs are from catheterisation - gastroenteritis in children and adults
- travellers’ diarrhoea
- bacteraemia - the presence of bacteria in the blood
- meningitis in infants - rare in the UK
what are the differences between pathogenic and commensal E. coli?
- pathogenic E.coli contains blocks of genes that are not present in commensal E.coli (that live in the gut)
- many pathogenic E.coli have ‘acquired’ pathogenicity from other bacteria by ‘mating’ and acquiring pathogenic blocks of genes
what is the virulence/pathogenicity factor for E. coli causing travellers diarrhoea? what is its mechanism of action?
- strain is called enterotoxigenic (ET) E.coli (ETEC)
- has pilli which enable it to adhere to the tissue of the small intestine
- when it binds to the tissue it releases a labile toxin that alters the role of the Gs protein on the GI cell surface meaning it can no longer stimulate adenyl cyclase resulting in more Cl- being released into the GI lumen
- this results in water following, resulting in diarrhoea
what are the four species of Shigella?
- S. dysenteriae
- S. flexneri
- S. boydii
- S. sonnei (commonest cause)
what is the action of the shigella species?
all four species cause damage to the intestinal mucosa that result in:
- acute infection of the large intestine
- painful diarrhoea often with blood and mucus in the stools
what is the infective dose of Shigella?
the infective dose is just 100 bacteria thus extremely easy to be infected
how is Shigella spread?
spread from person-to-person or via contaminated water or food
what are microfold (M) cells?
• these are found in the gut-associated lymphoid tissue
(GALT) of the Peyer’s patches and in the mucosa-
associated lymphoid tissue (MALT)
• these cells initiate mucosal immunity responses and allow for the transport of microbes across the epithelial cell layer from the gut lumen where interactions with immune cells can take place
what is the pathogenesis of Shigella infection?
- bacteria are acid-tolerant so can survive and pass through the stomach
- bacteria target microfold (M) cells
- shigella induce their own uptake by M-cells, they then cross the epithelial cell layer where they are engulfed by macrophages
- however, once engulfed they induce the apoptosis of the macrophages resulting in the release of damaging free radicals resulting in an inflammatory response and cell damage
- eventually the bacteria will be destroyed by neutrophils
what toxin might Shigella release?
shiga toxin
what is the action of the shiga toxin released by Shigella?
some shigella bacteria also release a shiga toxin which disrupts protein synthesis resulting in necrosis:
• this toxin targets the kidney resulting in haemolytic uraemic syndrome which can lead to death
• shiga toxin is also produced by some E.coli e.g. EHEC
what are the two species of Salmonella?
- S.enterica - responsible for salmonellosis (any infection caused with salmonella)
- S.bongori - rare, results from reptile contact
what are some infections caused by Salmonella?
- gastroenteritis
- enteric fever; typhoid
- bacteraemia
what are features of gastroenteritis caused by Salmonella?
- frequent cause of food poisoning from milk and poultry
- 6-36 hour incubation
- resolves in a week
- localised infection
what are features of enteric fever caused by Salmonella?
- systemic disease
- caused by Salmonella typhi and Salmonella paratyphi
- spread is faecal-oral
- results in fever, headache, dry cough
- splenomegaly and hepatomegaly
- diarrhoea may develop
what is the cause of enteric/typhoid fever?
Salmonella typhi and Salmonella paratyphi
what is the spread of enteric/typhoid fever?
faecal-oral
what are features of bacteraemia caused by Salmonella?
presence of bacteria in the blood - uncommon
what is the pathogenesis of salmonellosis?
- ingestion of contaminated food/water
- has a high infective dose - need to ingest a significant amount for infection
- Salmonella mediates its endocytosis across the gut lumen
what is the pathogenesis of gastroenteritis caused by Salmonella?
• bacteria presence results in chemokine release and
neutrophil recruitment
• this results in neutrophil-induced tissue injury due to the inflammatory response
• there is fluid and electrolyte loss due to cell damage
resulting in diarrhoea
• eventual inflammation/necrosis of gut mucose
what is the pathogenesis of enteric fever caused by Salmonella?
• migrates to the basolateral membrane of cells in the
intestinal lumen - Peyers patch where it results in
inflammation and ulceration - diarrhoea
• however, initially there is little damage to the gut mucosa
• bacteria is then engulfed and survives then spreads
systemically via the lymph nodes
• then enters bloodstream via the thoracic duct and then
multiplies in the macrophages of the liver, spleen and bone marrow resulting in septicaemia which results in massive
fever
• then spreads to the gall bladder from the liver where person can be in a carrier state from 1 year to the rest of their life
what are features of Klebsiella pneumoniae? what infections can it cause?
- opportunistic
- causes different nosocomial (hospital acquired) infections:
• pneumonia
• bloodstream infections
• wound or surgical site infections
• meningitis
what are features of Vibrio cholerae?
- facultative anaerobe
- curved rods/bacilli with single polar flagellum
- results in cholera - the most severe diarrhoeal disease
how is Vibrio cholerae transmitted?
faecal-oral route - faecal contaminated water and uncooked shellfish
what is the infective dose of Vibrio cholerae?
high infective dose is required since its sensitive to acid i.e. acid in stomach - requires many to get past the stomach
what is the incubation period of Vibrio cholerae?
5 hours (multiplies in small intestine)
what is the clinical presentation of Vibrio cholerae?
- results in voluminous watery (rice-water) stools i.e. secretory diarrhoea
- can lose 20 litre/day plus electrolytes, this results in:
• dehydration and subsequent death
• 60% mortality - there is no blood or fever since there is no invasion or damage to mucosa
what is the treatment of Virbio cholerae?
80% treated with oral rehydration
what are the virulence determinants of Vibrio cholerae?
- pilli - required for colonisation
* Cholera toxin - acts in same way as E.coli labile toxin
what is the action of the Cholera toxin in Vibrio cholerae?
- results in uncontrolled cyclic AMP production
- which results in the activation of protein kinases
- which causes the modification of ion transporter activity causing the loss of Cl- & Na+ resulting in massive H2O loss
what are features of Pseudomonas aeruginosa?
- motile - single polar flagellum
- opportunistic (serious cause of nosocomial infections)
- multiple antibiotic resistance
where can Pseudomonas aeruginosa cause localised acute infections?
- burn/surgical wounds
- UTIs (catheters)
- keratitis (inflammation of cornea)
where can Pseudomonas aeruginosa cause systemic (bacteraemic) acute infections?
neutropenic (low on neutrophils) patients (leukaemia, chemotherapy, AIDS)
what can Pseudomonas aeruginosa cause in ICU patients?
nosocomial pneumonia
what can Pseudomonas aeruginosa cause chronically?
cystic fibrosis
what is the effect of Pseudomonas aeruginosa on CF patients?
- have poor functioning Cl- transporters meaning they have dehydrated lung mucus which is the perfect environment for bacteria to grow
- virtually impossible to remove pseudomonas in cystic fibrosis patient since antibiotic resistant
what are features of Haemophilus influenzae?
- exclusively human parasite
- nasopharyngeal carriage in 25-80% population
- fastidious (specific requirement for survival)
- non-motile
where are Haemophilus influenzae infections mainly seen?
young children and adult smokers
what can Haemophilus influenzae cause in young children and adult smokers?
- important cause of meningitis, when it crosses the blood-brain barrier (less than 5yrs) and bronchopneumonia
- epiglottitis, sinusitis, otitis media (ear infection)
- bacteraemia
- cystic fibrosis and COPD lung infections
how is Haemophilus influenzae fastidious?
- specific requirement for survival
• will not grow on blood agar which supports growth of many other fastidious bacteria - since it cannot access haem in this form
• will only grow on chocolate agar: - blood agar which has been heated to 80 degrees to allow the release of haem by red blood cells
what is chocolate agar?
blood agar which has been heated to 80 degrees to allow the release of haem by red blood cells
what are the virulence determinants of Haemophilus influenzae? what do each of them cause?
• pilli: adherence to epithelial cells and mucin
• capsule:
- commensals and respiratory tract pathogens are non-capsulate
- invasive strains are capsulate (can penetrate the
nasopharyngeal epithelium)
• lipopolysaccharide (LPS) endotoxin - results in inflammation
what is Bordatella pertussis? how infectious is it?
- pertussis is whooping cough
- short (sometimes oval) rods/bacilli
- highly contagious with a low infect dose
what is the transmission of Bordatella pertussis?
aerosol transmission
what is the pathophysiology of Bordatella pertussis infection? what is the clinical presentation?
• adhere to the ciliated epithelia of the upper respiratory tract/trachea
• non-specific flu-like symptoms followed by paroxysmal coughing
(cough followed by inhalation resulting in whooping sound)
• can lead to sub-conjunctival haemorrhage
what is Neisseria? where does it present?
• non-flagellated diplococci (go around in pairs)
• present in polymorphonuclear lymphocytes of CSF or urethral
discharge during infection
what are the two species of Neisseria?
N. meningitidis
N. gonorrhoeae
what are features of N. meningitidis? what is the transmission?
- present in the nasopharynx of 5-10% of the population
(asymptomatic) - person-person aerosol transmission (university or barracks)
what is the pathogenesis of N. meningitidis infection?
crosses the nasopharyngeal epithelium and enters the
bloodstream in a small proportion of colonised individuals:
- asymptomatic bacteraemia (if low numbers of bacteria) or septicaemia if high
- meningitis - the colonisation of the subarachnoid space after crossing the blood-brain barrier
- there is a very high risk of mortality in the septicaemic form if not treated
what are the virulence determinants of N. meningitidis? what do they each do?
• capsule is major virulence determinant:
- non-capsulated is only found in the nasopharynx
- capsule is anti-phagocytic
• pilli on bacteria promote colonisation and cell invasion
• lipopolysaccharide results in cytokine cascade and
inflammatory response which can lead to sepsis
what is the role of the capsule as a virulence determinant in N. meningitidis? where is the non-capsulated form found?
capsule is major virulence determinant:
- non-capsulated is only found in the nasopharynx
- capsule is anti-phagocytic
what is the role of pili as a virulence determinant in N. meningitidis?
pilli on bacteria promote colonisation and cell invasion
what is the role of LPS as a virulence determinant in N. meningitidis?
LPS results in cytokine cascade and inflammatory response which can lead to sepsis
what are features of N. gonorrhoea? how is it spread?
- not a commensal but can be asymptomatic (30% of infected females)
- person to person only
- non-capsulated unlike N.meningitis
what is the clinical presentation of N. gonorrhoea infection?
it’s an STD resulting in:
• urethritis with additional infection of female genitalia
• can lead to infection of the fallopian tubes if infection
ascends
what are types of Campylobacter?
C. jejuni and C. coli
what are features of Campylobacter?
• spiral rods/bacilli • most common cause of food poisoning in UK and US: - undercooked poultry e.g. BBQ - unpasteurised milk • has a low infective dose
what is the most common cause of food poisoning in the UK and US?
Campylobacter
- undercooked poultry e.g. BBQ
- unpasteurised milk
what is the clinical presentation of Campylobacter infection?
- results in mild-sever diarrhoea often with blood - usually self-limiting within a week
- Campylobacter shed in faeces for around 3 weeks
what are the virulence factors of Campylobacter?
invasins and cytolethal distending toxin (CDT)
what is the role of invasins as a virulence factor of Campylobacter?
- invades ileal and colonic epithelial cells
* resulting in local acute inflammatory response i.e. tissue damage
what is the role of cytolethal distending toxin as a virulence factor of Campylobacter?
arrests the cell cycle meaning target cells swell and lyse
what are features of Helicobacter pylori?
- require CO2 (microaerophilic)
* spiral shaped
how much of the population does Helicobacter pylori affect?
present in 50% of global population but only a fraction will develop the disease
what diseases is Helicobacter pylori associated with?
- major role in gastritis and peptic ulcer disease
* implicated in gastric adenocarcinoma
what is the virulence factor of H. pylori? what does it do?
urease - hydrolyses urea to generate ammonia to act as a buffer to gastric acid
what are features of Chlamydia?
very small and non-motile
what are the two developmental stages in the growth cycle of Chlamydia?
- elementary bodies; dormant
- reticulate bodies; metabolically active and fragile
what are features of elementary bodies of Chlamydia?
- infectious
- enter cell through endocytosis
- prevent phagosome fusion
- dormant
what are features of reticulate bodies of Chlamydia?
- replicative
- non-infectious
- metabolically active
- fragile
what is the most common STD?
Chlamydia trachomatis
where can Chlamydia trachomatis spread to? is it symptomatic?
- can spread to the uterus and ovaries resulting in pelvic inflammatory disease
- usually asymptomatic
what is the clinical presentation of Chlamydia trachomatis?
- can cause conjunctivitis (STD)
* can cause trachoma - blindness that is spread via flies
what are the most common sites/modes of infection caused by Gram-negative pathogens?
- respiratory tract
- urinary tract
- GI tract
- meningitis
- STIs
- wound infections
what Gram-negative pathogens can infect the respiratory tract?
- Bordetella pertussis
* Haemophilus influenzae
what Gram-negative pathogens can infect the urinary tract?
- some E.coli strains
* Klebsiella pneumoniae
what Gram-negative pathogens can infect the GI tract?
- Vibrio cholera
- Shigella dysenteriae
- some E.coli strains
- Campylobacter jejuni
- Helicobacter pylori
what Gram-negative pathogens can cause meningitis?
- Neisseria meningitidis
* Haemophilus influenzae
what Gram-negative pathogens can cause STIs?
- Klebsiella pneumoniae
* Chlamydia trachomatis
what Gram-negative pathogens can cause wound infections?
- Pseudomonas aeruginosa
* some E.coli strains
what are features of fungi?
- eukaryotic - have a nuclear membrane
- chitinous cell wall
- heterotrophic: get nutrients from what they are living on
- move by means of growth or spore release
what are yeasts?
type of fungi that is a small single celled organisms that divide by budding
what are moulds?
type of fungi that form multicellular hyphae and spores
what are dimorphic fungi?
some fungi exist as both yeasts and moulds switching between the two when
conditions suit - these are dimorphic fungi
what is an example of a dimorphic fungi?
Coccidioides immitis
how does Coccidioides immitis act as a dimorphic fungi?
- grow as mould at ambient temperature
* convert to yeast form at body temperature after inhalation
what is the effect of fungi on humans?
- only a few fungal forms can actually infect humans
- fungi have an inability to grow at 37 degrees (body temperature)
- fungi also cannot evade the adaptive/innate immune response
what is the burden of fungal disease?
- enormous since most will have had at least one in lifetime e.g nappy rash,
tinea pedis (athletes foot) and fungal asthma - however life-threatening fungal infection is rare in healthy hosts
what are invasive/life threatening fungal diseases in immunocompromised hosts?
- Candida line infections
- Pneumocystis
- invasive aspergillosis
what are invasive/life threatening fungal diseases in post-surgical patients?
intra-abdominal infections
what are invasive/life threatening fungal disease in healthy hosts?
- fungal asthma
- travel associated fungal infections e.g. dimorphic fungi
what is the aim of antimicrobial drug therapy?
to achieve inhibitory levels of the agent at the site of the infection without host cell toxicity
what does treating fungal disease rely on?
relies on identifying molecules with selective toxicity for organism targets
what is the target of fungal disease treatments?
- target does not exist in humans
- target is significantly different to human analogue
- drug is concentrated in organism cell with respect to humans
- organism has an increased permeability to the compound
- human cells are ‘rescued’ from toxicity by alternative metabolic pathways
why is selective toxicity harder to achieve for fungi?
in general the concept of selective toxicity is much harder to achieved for fungi as opposed to bacteria due to the fact that fungi are eukaryotic, and so are human cells thus they are more similar and thus harder to differentiate
what is the nucleus like in fungi? what are drugs that target this?
- DNA/RNA synthesis and protein synthesis
- similar to mammalian
- drugs targeting these: Flucytosine
what does the fungal cell wall contain? what are drugs that target this?
- mannoproteins
- B1,3 glucan
- B1,6 glucan
- chitin
- does not exist in humans
- drugs targeting these: Echinocandins
what does the fungal plasma membrane contain? what are drugs that target this?
- containing ergosterol
- human cell membrane contains cholesterol NOT ergosterol
- drugs targeting these: Amphotericin, Azoles and Terbinafine
what is the equivalent to cholesterol in fungi?
ergosterol
what is an amphoteric compound?
a compound that is able to act as a base and an acid
what is an example of a polyene?
amphotericin B
what are polyenes? what are their mechanism of actions?
- drugs used to treat fungal infections
- e.g. Amphotericin B
- cause pore formation in ergosterol containing membranes
- fungicidal
what is the affinity of amphotericin B for cholesterol in mammalian membranes?
it has 10 times lower affinity for cholesterol in mammalian
membranes
what toxicity can amphotericin B/polyenes cause?
- nephrotoxicity - dose dependent; usually reversible
- distal renal tubular acidosis (hypokalaemia)
- can cause hyperkalaemia if infused rapidly resulting in cellular damage
- also causes infusion related; chills/rigors/hypotension and
acute anaphylactoid reactions
what is the mechanism of action of allylamines?
- causes the reversible inhibition of squalene epoxidase (an enzyme required for growth of the fungi)
- it’s a fungicidal
what is an example of an allylamine?
Terbinafine
what is the metabolism of allylamines/terbafine? what are they primarily used against?
- it is well absorbed but undergoes extensive first pass metabolism resulting in a bioavailability of only 45%
- distributes extensively to poorly perfused sites such as the skin and nail beds (common sites of fungal infection)
- primarily used against Candida and Aspergillus
what are the side effects of allylamines/terbafine?
- well tolerated and only results in taste disturbance and deranged liver function tests (LFT)
- it does result in increased CYP450 metabolism but this is by multiple enzymes and is minimally inhibitory
what is the mechanism of action of azoles?
- dose-dependent inhibitors of 14a-sterol demethylase - an important intermediate in the pathway of cholesterol (human) and ergosterol (fungi) production
- it’s a fungistatic
what azoles are active against different fungal infections?
• clotrimazole and ketoconazole is active against Candida
• fluconazole is active against Cryptococcus
• itraconazole is active against Aspergillus and dimorphics such as
Coccidiodes and Sporothrix
what azoles work against Candida?
clotrimazole and ketoconazole
what azoles work against Cryptococcus?
fluconazole
what azoles work against Aspergillus and dimorphics e.g. Coccidiodes and Sporothrix?
itraconazole
what are adverse events caused by azoles?
- relatively safe
- all associated with transaminitis (elevated transaminases in liver) and GI side effects
- rare to cause severe hepatitis
- alopecia with long term fluconazole
- GI symptoms are more pronounced with itraconazole:
• nausea, abdominal pain and diarrhoea
• rare life threatening liver failure
what are drug interactions of fluconazole? how is it metabolised?
- hydrophilic and excreted unchanged
* less significant interactions with: warfarin, anxiolytics and calcineurin inhibitors
what are drug interactions of itraconazole? how is it metabolised?
• a potent CYP3A4 inhibitor • interactions with: - less significant interactions with: warfarin, anxiolytics and calcineurin inhibitors - steroids - statins
what are features of azole resistance? what drugs are most affected?
- multiple mechanism in Candida
- fluconazole and voriconazole most affected
what is the mechanism of action of echinocandins?
- inhibit 1,3 B glucan synthase - interferes with fungal cell wall synthesis
- is fungicidal to susceptible yeasts
- is fungistatic to moulds
- has activity against mould but not yeast forms of dimorphics
what fungi are intrinsically resistant to echinocandins?
some fungi genera that do not have large amounts of 1,3 B glucan in their cell wall are intrinsically resistant to this drug class:
- Crytococcus
- Zygomycetes
- Trichosporon
- limited activity against Scedosporium
what is the bioavailability, penetration and drug interactions of echinocandins?
- has poor oral bioavailability thus IV only
- has poor penetration into the CSF, eye and urine
- few drug interactions
what drug toxicity can echinocandins cause?
- rare type-1 hypersensitivity
- hepatotoxicity
- hypokalaemia
what are the drug compounds, mechanism of action and uses of polyenes?
- Amphotericin B, Nystatin
- binds to sterols and destabilises cell membrane
- used in systemic and topical disease
what are the drug compounds, mechanism of action and uses of azoles?
- clotrimazole, miconazole, ketoconazole, fluconazole, itraconazole, voriconazole, posaconazole
- inhibits ergosterol biosynthesis
- used in topical and systemic disease
what are the drug compounds, mechanism of action and uses of allylamines?
- terbinafine
- inhibit ergosterol biosynthesis
- used in superficial infections, including onychomycosis
what are the drug compounds, mechanism of action and uses of echinocandins?
- caspofungin, anidulafungin, micafungin
- inhibit the formation of cell wall glucan
- used in systemic disease
what are the drug compounds, mechanism of action and uses of pyrimidines?
- 5-fluorocytosine
- inhibit DNA and RNA synthesis
- used in systemic disease
what are the drug compounds, mechanism of action and uses of grisan?
- griseofulvin
- inhibits microtubule assembly
- used in topical disease
how is Candida cultured?
- blood cultures are only half as sensitive for fungi as for bacteria
- it’s better to pick-up from tissue/fluids:
• if cultured properly
• if these samples can be obtained
what drugs are Candida sensitive to?
- pretty much all Candida are sensitive to Echinocandins
- pretty much all Candida are sensitive to Amphotericin B
what is 1,3 B-D glucan?
- the cell wall component of many fungi including common ascomycetous pathogens and pneumocystis
- released into serum during invasive infection
what is onychomycosis?
fungal nail infection; very common
what is onychomycosis caused by?
- caused by dermatophyte moulds:
• grow best at about 30 degrees - Trichophyton rubrum is the most common cause
what is the most specific test for onychomycosis?
microscopy is most specific, but 30% of the culture is negative
what are broad differential diagnoses of onychomycosis?
- psoriasis
- lichen planus
- trauma
- eczema
- malignant melanoma
what are the treatment options of onychomycosis? what are features of treatment?
- results of sampling can be confusing
- limited treatment options:
• topical amorolfine
• systemic itraconazole or terbinafine - treatment takes ages
- high failure rate with all therapies
what are features of Pneumocystis infection?
- infection/colonisation of health people is frequent and occurs early in life
- disease develops only with moderate-severe immunocompromised
especially in HIV, transplant and steroids - think pneumocystis when a patient has hypoxia that is more severe than the chest x-ray would suggest - especially with gradual onset or risk
factors
what is treatment of Pneumocystis?
- Co-trimoxazole
- Clindamycin
- Pentamidine
- Trimetrexate
what are the Mycobacteria of medical importance? what diseases do they each cause?
- M. tuberculosis; tuberculosis
- M. leprae; leprosy
- M.avium complex (MAC); disseminated infections in AIDS, infections in patients with chronic lung disease
- M. kansasii - chronic lung infection
- M. marinum - fish tank granuloma
- M. ulcerans - Buruli ulcer
what organism causes TB?
Mycobacterium tuberculosis
what organism causes leprosy?
M. leprae
what organism causes disseminated infections in AIDS?
M. avium complex
what organism causes chronic lung infection?
M. kansasii
what organism causes fish tank granuloma?
M. marinum
what organism causes a Buruli ulcer?
M. ulcerans
what are microbiological features of Mycobacteria? what is its growth, spore formation, motility, cell wall content like?
- aerobic
- have resistance to destaining by acid and alcohol
- may cause meningitis - tuberculosis meningitis
- can withstand phagolysosomal killing
- non-spore formin
- non-motile bacillus/rods
- high cell wall content of high molecular weight lipids
- slow growing
- cell wall key components
are Mycobacteria aerobic or anaerobic?
aerobic
can Mycobacteria withstand phagolysosomal killing?
yes
what is the cell wall content of Mycobacteria? what are the key components of the cell wall?
- weakly gram-positive or colourless - it difficult to stain mycobacteria since they have a thick cell wall that doesn’t take up stain easily
- cell wall contains lipoarabinomannan
- survives inside macrophages, even in low pH environments
- mycolic acids and liporabinomannan - make up strong waxy cell wall that is hard for the immune system to target/damage
what is the growth of Mycobacteria? what does this mean for treatment?
- M. tuberculosis generation time 15-20 hours compared to 1 hour for common bacterial pathogens
- slow growth means its difficult for antibiotics to target the division phase of the mycobacteria
what are Koch postulates?
- bacteria should be found in all people with disease
- bacteria should be isolated from the infected lesions in people with the disease
- a pure culture inoculated into a susceptible person should produce symptoms of the disease
- the same bacteria should be isolated from the intentionally infected individual
what are features of acid-fast bacilli/rods? what makes it resistant to Gram stain?
- high lipid content with mycolic acids in cell wall makes Mycobacteria resistant to Gram stain
- slightly curved, beaded bacilli/rods
what is the result of acid-fast bacilli on the Ziehl-Neelsen stain?
red/pink (positive for acid-fast)
how can nucleic acid be detected in Mycobacteria?
- nucleic acid amplification using PCR
- produces rapid result for mycobacterium tuberculosis
- highly sensitive and specific test
- recommended for the rapid diagnosis in TB endemic countries
how are Mycobacteria processed in the body?
- Mycobacteria are acid fast bacilli that are phagocytosed by macrophages and are placed in a phagolysosome within the macrophage
- the bacteria has adapted to the intracellular environment and aims to withstand phagolysosomal killing and escape to the cytosol - primarily through the presence of their thick waxy cell wall
- the host aims to kill the mycobacterium using microbicidal molecules
- acidification aids digestion and degradation by proteases of the mycobacteria which results in the generation of antigens for presentation
to T-cells
what is the immunity of Mycobacterial infection?
- effective immunity requires CD4 T-cells which generate interferon gamma and this helps activate intracellular killing by macrophages
- IL-12 release by macrophages further stimulates the generation of T helper cells and interferon gamma release
- genetic defects in interferon gamma or IL-12 receptors or elements of their signalling pathways result in susceptibility to mycobacterial infection
what are features of granuloma in Mycobacterial infection?
granuloma are lesions the arise in a response that tries to contain mycobacteria (but also occur in other infections and non-infectious
processes):
• highly stimulated macrophages become epithelioid cells
• some macrophages fuse with each other to form giant multinucleate cells “Langhans giant cells”
• T cells including cytotoxic CD8 T-cells infiltrate the granuloma
how does a granuloma affect Mycobacteria?
a granuloma prevents nutrients from entering - thereby starving the mycobacteria:
• TB will go into a dormant state when inside the granuloma
• can reactivate at some point in the future when conditions are better
what is the response time of the immune system to Mycobacteria?
the highly immunogenic nature of mycobacterial lipids stimulate T-cell responses 3-9 weeks after exposure to M. tuberculosis
what are positive effects of the highly immunogenic nature of mycobacterial lipids?
macrophage killing of mycobacteria, containment of
infection, formation of a tissue granuloma
what are negative effects of the highly immunogenic nature of mycobacterial lipids?
hypersensitivity reactions (type 4) with skin lesions, eye lesions and swelling of joints
how can the reactivity of mycobacteria be measured?
- this reactivity can be measured in the tuberculin skin test where intradermal injection of purified protein derivatives induce skin swelling and redness
- it can also be measured in interferon gamma release assays
how are interferon gamma release assays used to detect mycobacteria?
- use antigens specific to M. tuberculosis e.g. ESAT-60 and CFP10 to distinguish between this and BCG vaccine or environmental mycobacteria
- IGRAs demonstrate exposure to M.tuberculosis but not active infection
what are principles of mycobacteria treatment?
- slowly replicating bacteria so need prolonged treatment - 6 months of antimicrobials
- there are different populations of mycobacteria in particular locations
intracellularly and extracellularly or in environments of differing pH - resistance may emerge on treatment so use multi-drug combinations to ensure target all populations and mutants
- compliance is essential; directly observed treatment used for many patient groups to ensure success
what is the standard therapy for tuberculosis?
- Isoniazid (INH), Rifampicin (RIF), Pyrazinamide (PZA), Ethambutol (ETH) for two months
- Isoniazid and rifampicin for further 4 months
what is given if resistance develops to anti-tuberculosis drugs?
- fluroquinolones
- injectable agents such as; streptomycin, cyclosporine and capreomycin
- prothionamide
what are the side effects of anti-tuberculosis drugs?
- hepatotoxicity - Isoniazid, rifampicin, pyrazinamide
- peripheral neuropathy with isoniazid - give vitamin B6 to protect against this
- optic neuritis - ethambutol
what is the pathophysiology of primary tuberculosis?
- bacilli settle in apex (top part near shoulders) and granuloma forms
- bacilli taken in lymphatics to hilar lymph nodes
- in apex of lungs there is more air and less blood supply thus fewer defending white cells to fight off infection
what is a primary complex of tuberculosis?
granuloma + lymphatics + lymph nodes
what is the pathophsyiology of latent tuberculosis?
- cell mediated immune (CMI) response from T-cells
* primary infection is contained but CMI persists
what is the clinical presentation and diagnosis of latent tuberculosis?
- no clinical disease (normal chest x-ray)
* detectable CMI to TB on tuberculin skin test of IGRA
what is the pathophysiology of pulmonary tuberculosis?
- could occur immediately following primary disease (post-primary) or after latent reactivation
- cell mediated immune (CMI) response from T-cells
- necrosis in lesion
- caseous material coughed up leaving cavity
- TB may spread in lung causing other lesions
- CMI and caseation in lesion results in cavity
where do tuberculosis bacilli spread?
bacilli can spread from apex to hilar lymph nodes and then elsewhere
what can TB spread beyond the lungs cause?
- TB meningitis
- miliary TB (widespread dissemination and tiny spotted lesions all over lungs and elsewhere)
- pleural TB
- bone and joint TB
- genitourinary TB
what are the three groups of worms/helminths?
- nematodes (roundworms)
- trematodes (flatworms, flukes)
- cestodes (tapeworms)
what are types of nematodes (roundworms)?
- intestinal
- Larva migrans
- tissue (filaria)
what are types of trematodes (flatworms, flukes)?
- blood
- liver
- lung
- intestinal
what are types of cestodes (tapeworms)?
- non-invasive
* invasive
what are features of helminths/worm-related diseases?
- rare in UK - most cases are imported
- adult worms cannot usually reproduce without a period of development outside the body - worm cannot replicate inside body, so if it cannot get out it will eventually die
- thus, although they usually produce innumerable larvae or eggs (which may themselves cause disease), the total worm burden cannot increase without constant re-exposure to infection
what is the pre-patent period in helminth disease?
the interval between infection and the appearance of eggs in the stool
what are protozoa?
- single-celled eukaryotic organisms with a definitive nucleus
- eaten by invertebrates
- important parasitic and symbiotic relationships
what is the main biological role of protozoa?
consumers of bacteria, algae and microfungi
how do protozoa eat food?
all eat food by phagocytosis and then digest it in intracellular vacuoles
in what environment do protozoa exist?
in aqueous environments and the soil
what are mastigophora (flagellates)?
- type of protozoa
- flagellum as main locomotory organelle
- usually reproduce by binary fission
what are examples of mastigophora?
- intestinal flagellates
- haemoflagellates
- other body sites
what is an example of an intestinal flagellate?
Giardia lamblia
what is the presentation of Giardia lamblia?
- 7-day business trip to Delhi 2 months ago
- loose stools on last day of stay in India
- ongoing offensive diarrhoea daily since return to UK
- flatulence, abdominal cramps
what is an example of a haemoflagellate?
Trypanosoma spp.
what is the presentation of African Trypanosomiasis?
- also known as ‘sleeping sickness’
- bitten on arm by insect; lesion developed 2 weeks
later > self-resolved - 2 years later he gets fever, lethargy and myalgia
- excessive weight loss
- personality change
- irritability
- increasing daytime tiredness
- coma
- the West African strain is more severe compared to
the more endemic East African strain
what are sarcodina? how do they move?
- amoebae
- move by means of flowing cytoplasm and production of pseudopodia
what is an example of sarcodina?
Entanomoeba histolytica
what is the presentation of amoebiasis?
- 2-month visit to rural Botswana
- bloody diarrhoea
- on return to UK, increasing right upper quadrant pain
- CT shows liver abscess
what are apicomplexa?
- sporozoans
- no locomotory extensions
- all species are parasitic
- most are intracellular parasites
- reproduce by multiple fission
what are examples of apicomplexa?
- malaria: Plasmodium spp.
- other: Cryptosporidium spp. and Toxoplasma gondii
what is the presentation of toxoplasmosis?
- recent HIV positive diagnosis: CD4 count: 70 (below 450 = low and below 100 = high risk of AIDs)
- 2-week history of progressive left sided weakness
- headaches and visual disturbances
- commonly presents when people are
immunosuppressed e.g. HIV/AIDs or cancer on chemotherapy
what are ciliophora?
- ciliates
- very large group
- have cilia that beat rhythmically at some stage in lifecycle
- two types of nuclei (macronucleus and micronucleus)
what is an example of ciliophora? what does it cause?
Balantidium coli - presents mainly in those who are
immunocompromised
- causes severe diarrhoea and/or ulceration of colon
what are microsporidia? what can they cause?
- very small
- production of resistant spores
- causes diarrhoea in immunocompromised