microbiology Flashcards
pathogen
organism that causes or is capable of causing disease
commensal
organism which colonises the host but causes no disease in normal circumstance
opportunistic
microbe that only causes disease if host defences are compromised
pathogenicity
the degree to which a given organism is pathogenic
asymptomatic carriage
when a pathogen is carried harmlessly to a tissue site where it causes no disease
bacterial nomenclature
consists of genus and species
e.g. staphylococcus (genus) aureus (species)
areas that are colonised
most mucosal surfaces
digestive tracr, nasal cavity, skin, urethra, vagina
sterile areas
lungs
gallbladder
kidneys
upper urinary tract
bacterial morphology
divided into coccus (round) and bacillus (rod)
further divided into gram positive or negative
structures in bacteria
inner and outer membrane capsule chromosome of circular DNA pili flagella
differences between gram positive and negative
different cell envelope
negative have 2 membranes and lipopolysaccharides
positive have much more peptidoglycan
bacterial environment
temp= -800 degrees to +80 degrees pH= 4-9
growth of bacteria
lag phase
exponential phase
stationary phase- number of viable bacteria decreases
endotoxin
component of outer membrane of bacteria
exotoxin
secreted proteins
gene mutation
base substitution
deletion
insertion
gene transfer
transformation e.g. via plasmid
transduction e.g. via phage
conjugation e.g. via sex pilus
plasmids
proteins can be synthesised using plasmid DNA
tend to be spread during bacterial conjugation
gram stain steps
- apply primary crystal violet (purple)stain to fixed, heated bacteria
- add iodide which binds to stain and fixes it to cell wall
- decolourise with ethanol or acetone
- counter stain with safranin (pink)
- negative lipids interact with decolouriser and lose their other lipopolysaccharides and crystal violet- iodide (CV-I) so appear pink with counterstain
- positive are dehydrated by decolouriser and the cell wall and CV-I are trapped in the multilayered peptidoglycan so are purple
gram stain of neisseria gonorrhoea
similar appearance to kidney beans with concave sides facing each other
staphylococci gram stain
appear in clusters
catalase test
flavoproteins reduce O2 using superoxide dismutase- producing H2O2
2H2O2 -> 2H20 +O2
staph are catalase + but strep aren’t
coagulase test
distinguishes s.aureus (positive) from other staphylococci (negative)
it activates prothrombin to convert fibrinogen to fibrin
a positive test- clot forms
latex test for staph. aureus
positive= agglutination occurring
haemolysis
ability of a bacteria to breakdown red blood cells in blood agar
requires expression of haemolysin
optochin sensitivity
strep. pneumoniae are optochin sensitive
other strep are resistant
oxacillin disc
the oxacillin disc tests for penicillin sensitivity
resistant strains should have a MIC performed to penicillin to ascertain level of resistance
selective indicator medial for fram negactive bacilli
MacConkey agar
cysteine lactose electrolyte deficient (CLED) media
MacConkey agar
o Bile salts inhibit Gram-positive bacteria and inhibits swarming of a Gram negative
bacterium Proteus spp.
o Crystal violet also inhibits some Gram-positive bacteria
o Neutral red acts as a pH indicator so that bacteria that ferment lactose (Lac+) and
release H+ appear pink or red
o Lactose is available for Lac+ micro-organisms
o Peptone is used by Lac- micro-organisms, resulting in production of NH3 and a rise in pH
cysteine lactose electrolyte deficient (CLED) media
o Electrolyte deficient media prevents swarming of Proteus mirbilis
o Bromothymol blue is indictor, lactose ferementation causes blue to yellow change,
decarboxylation of L-cyteine results in blue colour
o Used as media for urinary pathogens
lactose fermenter on CLED agar
A simple but important method of classifying members of the Enterobacteriaceae is based
upon lactose fermentation. Classically lactose fermenting organisms are E. coli, Klebsiella, Enterobacter and Citrobacter species.
non-lactose fermenter on CLED agar
The non-lactose fermenting organisms usually belong to the genera other than those
mentioned in slide ‘Lactose fermenter on CLED agar’. However, some lactose fermenting organisms, because they are late lactose fermenters, may appear as a non-lactose
fermenter. Late lactose fermenters are recognised by a positive ONPG test.
motility
distinguishes bacteria
flagella staining patterns
swarming motility patterns on agar
oxidase test
-Tests if micro-organism contains a cytochrome oxidase or indophenol oxidase
-Utilises a redox indicator such as N,N,N’,N’-tetramethyl-p-phenylenediamine (TMPD)
-In oxidised state indicator dark blue or maroon
-Implies organism able to use oxygen as the terminal
electron acceptor
3 main types of gram positive bacteria
streptococcus
staphylococcus
corynebacterium
coagulase
enzyme produced by bacteria that clots blood plasma
fibrin clot formation around bacteria protects it from phagocytosis
staphylococcus
coagulase +ve or -ve
s.aureus is most important (coag +ve)
coag -ve are important in opportunistic infections
staphylococcus habitat
nose
skin
MRSA
resistant to: beta-lactams genatmicin erythromycin tetacycline
staph. aureus virulence factors
pore forming toxins
proteases
toxic shock syndrome toxin
protein A
staph. aureus associated conditions
pyogenic- wound infections, pneumonia, endocarditis
toxic mediated- toxic shock syndrome, food poisoning
coag -ve - infected implants, septicaemia
coagulase- negative staphylococci
s. epidermidis
s. saprophticus
s. epidermidis
infections in debilitated, prostheses - opportunistic
main virulence factor is ability to form persistent biofilms
s. saprophticus
acute cystitis
haemagglutinin for adhesion
urease
streptococci classification
haemolysis
lancefield typing
biochemical properties
alpha haemolysis
partial
greening
H2O2 reacts with Hb
e.g. s.intermedius
beta haemolysis
complete lysis
haemolysins O and S
e.g. s.pyogenes
gamma haemolysis
no lysis
some s. mutans
sero-grouping
method of grouping catalase negative, coagulase negative bacteria based on bacterial carbohydrate cell surface antigens
infections caused by S. pyogenes
wound infections tonsillitis otitis media impetigo scarlet fever
S. pyogenes virulence factors
capsule- hyaluronic acid
M surface protein- encourages complement degradation
enzymes
toxins
s. pneumoniae
normally commensal in oropharynx in 30% of people
causes - pneumonia, otitis media, sinusitis, meningitis
s. pneumoniae predisposing factors
impaired mucus trapping
hypogammaglobulinaemia
asplenia
s. pneumoniae virulence factors
capsule
inflammatory wall constituents
cytotoxin
viridans streptococci
collective name for oral streptococci
alpha or gamma haemolytic
some cause dental abscesses
important in infective endocarditis
C. diphtheriae
droplet spread
can grow in the presence of potassium tellurite
C. diphtheriae toxin
inhibits protein synthesis
C. diphtheriae prevention
vaccination with toxoid
most relevant gram negative bacteria
proteobacteria
chlamydiae
spirochaeta
bacteroidetes
proteobacteria
family of enterobacteriacaeae
rods
motile
facultatively anaerobic
e. coli infections
wounds infections UTIs gastroenteritis travellers diarrhoea bacteraemia meningitis
why are some e.coli strains pathogenic
have additional DNA that causes them to be pathogenic
several pathovars, many serotypes or strains
shigella
closely related to e. coli
four species- dysenteriae, flexneri, boydii, sonnei
severe bloody diarrhoea
pathogenesis of shigella
acid- tolerant
person-person or contaminated water and food transmission
invasion of shigella
moves form cell to cell in colonic mucosa
cause damage to mucosa which results in diarrhoea
shigella virulence determinant
shiga toxin- causes cell death by blocking protein
salmonella
two species= enterica and bongori (rare)
salmonella infections
gastroenteritis
enteric fever
bacteraemia
salmonella pathogenesis
- ingestion of contaminated food/water
- invades gut epithelium of small intestine
- intestinal secretory response
- does not produce toxins
- enters submucosa
- intracellular survival/replication
vibrio cholerae
facultative anaerobe
curved rods with single polar flagellum
cholera= most severe diarrhoeal disease
vibrio cholerae pathogenesis
faceal-oral route incubation voluminous watery stools no blood, pus or fever 60% mortality
vibrio cholerae virulence determinants
TCP pili required for colonisation
cholera toxin
pseudomonas aeruginosa
single polar flagellum
opportunistic
antibiotic resistant
pseudomonas aeruginosa acute infections
localised- burns, UTI, keratitis
systemic
ICU patients
pseudomonas aeruginosa chronic infections
cystic fibrosis patients
pseudomonas aeruginosa virulence determinants
twitching motility
multiple toxins
legionella pneumophila
immunocompromised
severe 15-20% mortality
fastidious- charcoal agar
legionella pneumophila pathogenesis
modulates trafficking of phagosome
avoids phagosome-lysosome fusion
differentiate to replicative phase
bordetella pertussis
whooping cough
short rods- coccobacilli
fastidious
non-invasive
bordetella pertussis toxins
pertussis toxin
adenylate cyclase- haemolysin toxin (increases cAMP)
neisseria
non-flagellated diplococci
fastidious
2 species= meningitidis and gonorrhoeae
n. meningitidis
asymptomatic in nasopharynx of 5-10% rises to 20-90% during outbreaks aerosal transmission (person to person)
n. meningitidis pathogenesis
crosses nasopharyngeal epithelium and enters blood stream
enters subarachnoid space after crossing blood brain barrier
n. meningitidis virulence determinants
capsule is major determinant
n. gonorrhoeae
asymptomatic in 30% of females
person-person sexually transmitted
proctitis, gingivitis, pharyngitis
n. gonorrhoeae virulence determinants
twitching motility
non-capsulated
campylobacter
spiral rods
unipolar or bipolar flagella
most common cause of food poisoning
bacteroides
non-motile rods
strict anaerobes
commensal flora of the large intestine is most abundant (30-40%)
most common cause of anaerobic infections
chlamydia
small and non motile
obligate intracellular parasites
many live asymptomatically as endosymbionts
growth cycle of chlamydia
2 developmental stages-
elementary bodies= infectious, enter cell through endocytosis, prevent phagolysosome fusion
reticulate bodies= replicative, non-infectious, possess tubular projections
life cycle of chlamydia
- entry as elementary bodies
- prevent phagolysosome fusion
- conversion into reticulate body
- multiplication
- convert back to elementary body
- cell lysis and release
chlamydia. trachomatis
most common std
can spread to uterus and ovaries
usually asymptomatic
can also cause conjunctivitis- hand to eye
Chlamydophila. pneumoniae
respiratory tract
infects other mammals
Chlamydophila. psittaci
mainly birds
spirochetes
long, slender, helical, flexible
free living and non-pathogenic
modified outer membrane
B. burgdoferi
lyme disease tick borne bull's eye rash spreads through ECM culture in medium containing rabbit serum
T. pallidum
syphilis
primary stage- localised infection, days to weeks
secondary stage- systemic, 1 to 3 months
tertiary stage- gummas in bone and soft tissue, neurosyphilis, several years
Gram-negative pathogens in the respiratory tract
o Bordetella pertussis o Haemophilus influenzae o Pseudomonas aeruginosa o Legionella pneumophila o Chlamydia pneumoniae
Gram-negative pathogens in the GI tract
o Vibrio cholerae o Shigella dysenteriae/S. flexneri o S. enterica sv enteritidis/typhimurium o Some Escherichia coli serotypes o Campylobacter jejuni/C. coli o Helicobacter pylori o Bacteroides fragilis
Gram-negative pathogens and meningitis
o Neisseria meningitidis
o Some E. coli serotypes
o Haemophilus influenzae
Gram-negative pathogens in the urinary tract
o Some E. coli serotypes
o Proteus mirabilis
o Klebsiella pneumoniae
Gram-negative pathogens- STIs
o Neisseria gonorrhoeae
o Chlamydia trachomatis
o Treponema pallidum
Gram-negative pathogens in wound infections
o Some E. coli serotypes
o Bacteroides fragilis
o Pseudomonas aeruginosa
3 groups of worms
nematodes
trematodes
cestodes
nematodes
round worms
intestinal, larva migrans, tissue
trematodes
flatworms, flukes
blood, liver, lung, intestinal
cestodes
tapeworms
non-invasive, invasive
features of helminths
cannot usually reproduce without a period of development outside the body
although they usually produce a large number of larvae or eggs, they cannot increase the burden without re-exposure
pre-patent period
interval between infection and appearance of eggs in the stool
intestinal nematodes
transmitted from human to human via egg or larvae
the egg or larva is not usually infectious when first passed and has to undergo a period of development in the soil
Ascaris lumbricoides: the large roundworm
cream coloured
15-30cm long
lives a year or more
pre-patent period is 60-75 days
loeffler’s syndrome
associated with larval migration through lungs
10-14 days after infection
cough, fever, wheeze, eosinophilia
Ascaris lumbricoides effects of adult
often asymptomatic
can be mechanical e.g. intestinal obstruction or malnutrition
Ascaris lumbricoides odd presentation
emerging from nose
perforated eardrum
The Hookworm
white worm
1cm in length
life expectancy 1-5 years
The Hookworm 2 species
ancylostoma duodenale
necator americanus
The Hookworm clinical features
ground itch- papules at site of entry of the larvae
pulmonary symptoms- mild due to pulmonary migration
most common cause of iron deficiency
The Hookworm diagnosis
stool microscopy for eggs
The Hookworm treatment
iron supplements
pyrantel
mebendazole
Enterobius vermicularis: the pinworm or threadworm
most common helminth infection in the uk
Enterobius vermicularis life cycle
adult is resident in large bowel
female adult emerges from anus at night to lay eggs on the perineum
the eggs are infectious after 4 hours are ingested by next host
Enterobius vermicularis clinical features
pruritus ani
appendicitis
vaginal penetration- endometritis, infertility
affects whole families
Enterobius vermicularis diagnosis
microscopy of sellotape strip from perianal region
Enterobius vermicularis treatment
mebendazole
piperazine
pyrantel
Trichuris trichiura: the whipworm
2-5cm long
live 1 year
pre-patent period is 70-90 days
partially buried in the mucosa of large bowel
Trichuris trichiura clinical features
resident of large bowel
asymptomatic
co exists with ascaris lumbricoides
Trichuris trichiura diagnosis
stool microscopy for eggs
Trichuris trichiura treatment
mebendazole
albendazole
Strongyloides stercoralis
causes strongloidiasis
2mm long
lies buried in small intestinal mucosa
pre-patent period is 17-28 days
Strongyloides stercoralis clinical features
pruritus at site of entry
malabsorption
eosinophilia
hyperinfection syndrome
visceral larva migrans
caused by toxocara canis and t.cati (dog and cat roundworm)
mainly a disease of children
diagnose with eosinophilia and serology
treat with mebendazole
ocular toxocariasis
larvae trapped in retina see a granulomatous reaction blindness diagnose with serology and biopsy treat with mebendazole
cutaneous larva migrans
creeping itchy skin eruption
dog hookworms
lesions at site where larvae penetrate
treat with topical or systemic thiabendazole
Dracunculus medinensis: The Guinea worm
100cm long
lives one year subcutaneously
incubation period is one year
worm emerges from skin
Dracunculus medinensis clinical
localised pain
blister bursting
tetanus or sepsis
Dracunculus medinensis diagnosis
drop water on ulcer promotes egg release
Dracunculus medinensis treatment
local- wind out worm
mebendazole
Dracunculus medinensis prevention
sieving of water