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?
Microbe that only causes disease if host defences are compromised
What is meant by virulence/ pathogenicity?
The degree to which a given organism is pathogenic
What is asymptomatic carriage?
When a pathogen is carried harmlessly at a tissue site where it causes no disease
What is the resolving power of the eye?
100 micrometers
What is the resolving power of a light microscope?
0.2 micrometers
What is special about chlamydia?
Needs to grow in cells like a virus but is actually a bacteria
What are round bacteria called?
cocci
What are rod shaped bacteria called?
bacillus
What colour are the bacteria if theyre gram positive?
Purple
What colour are the bacteria if theyre gram negative?
Pink
What are the different types of cocci?
Diplococcus
Chain of cocci
Clusters of cocci
What are the different types of rods?
Chain of rods
Curved rod - vibrio
Spiral rod - spirochaete
What are the features of bacteria?
Capsule
Cell wall
Outer membrane
Inner membrane
Chromosome of circular double stranded DNA
pili
Sometime have extra sugar layer
What do motile bacteria have?
Flagella - these spin to allow movement
What stain needs to be done for bacteria that doesnt gram positive or negative stain?
Ziehl-Neelsen stain
What does the Ziehl-Neelsen stain do?
Detects acid- fast bacili
What are the features of a gram positive bacterial cell envelope?
Capsule
peptidoglycan
Lipoteichoic acid
Cytoplasmic membrane
What are the features of a gram negative bacterial cell envelope?
Capsule
Lipopolysaccharide (Endotoxin)
Outer membrane
Lipoprotein
Periplasmic space
Peptidoglycan
Inner membrane
What are the differences between gram positive and gram negative bacterial cell envelopes?
Positive – have phospholipid inner membrane – outside have large peptidoglycan – large peptidoglycan layer linked to phospholipid membrane
Gram negative – have 2 phospholipid membrane –
Lipopolysaccharide (Endotoxin) – can get endotoxic shock
Secreted effector
Protein secretion system
protein toxin or ‘effector’
What are the best areas for bacterial environemnt?
Temperature
<-800C to + 80C (1200C for spores)
pH
<4-9
Water/dessication
2 hours – 3 months (>50 years for spores)
Light
UV
What is the growth rate of bacteria?
Most viruses : Less than 1 hour
E.coli, S.Aureus: 20-30 min
Mycobacterium Tuberculosis: 24 HOURS
Fungi (Candida albicans): 30 min
Mycobacterium leprae: 2 weeks
What is an endotoxin?
Component of the outer membrane of bacteria, eg lipopolysaccharide in Gram negative bacteria
What is an exotoxin?
Secreted proteins of gram positive and gram negative bacteria
Exotoxin features
Composition: Protien
Action: Specific
Effect of heat: Labile
Antigenicity: Strong
Produced by :Gram positive/ Gram negative
Covertibility to toxoid: Yes
Endotoxin features
Composition: lipopolysaccharide
Action: non-specific
Effect of heat: stable
Antigenicity: weak
Produced by : LPS - gram negative
Covertibility to toxoid: No
What is a toxoid?
Toxoid is a toxin treated (usually with formaldehyde) so that it loses its toxicity but retains its antigenicity
What is a bacterial chromosome like?
Bacteria usually have one singular chromosome in a circle made up of DNA – have single RNA polymerase which makes messenger rna
Typically 2-4 10 to the power of 3 kilobases
What is a plasmid?
These can be transcribed and translated to make proteins
Have point mutation in chromosomes
Can be transferred around by different bacteria
What are some genetic variations in bacteria?
Mutation
-Base substitution
-Deletion
-Insertion
Gene transfer
-Transformation eg via plasmid
-Transduction eg via phage – bacterium infected by virus
-Conjugation eg via sex pilus
Classification of bacteria
Please look at slide 49 of ‘bacteria as a cause of disease’ REMEMBER THIS PLEASE
What are some examples of obligate intracellular bacteria?
Rickettsia
-R. rickettsii
-R. prowazekii
-R. conorii
Chlamydia
-C. trachomatis
-C. psittaci
-C. pneumoniae
Coxiella
-C. burnetii
These cannot be cultivated on media
What are some bacteria that may be cultured on artifical media with no cell wall?
Mollicutes
Mycoplasma pneumoniae
M. hominis
Ureaplasma urealyticum
What are the bacteria that can be cultured on artificial media with a cell wall split into?
Growing as filaments and growing as single cells
What are some examples of growing as filaments bacteria?
Actinomyces - A. israelii
Nocardia - N. asteroides
Streptomyces
What are the divisions of growing as single cells?
Rods
Cocci
Spirochaetes
What are spirochaetes eg?
Leptosira
L. . icterohaemorrhagiae
Treponema
T. pallidum
Borrelia
B. burghdorferi
B. recurrentis
What are some examples of gram negative cocci?
Anaerobic: VEILLONELLA
Aerobic: NEISSERIA
N. meningitidis
N. gonorrhoeae
What are some examples of gram positive cocci?
Aerobic: STAPHYLOCOCCUS - S. aureus, S. epidermidis
Streptococcus
Anaerobic: PEPTOSTREP-
TOCOCCUS
What are some examples of streptococcus?
BETA-HAEMOLYTIC
S. pyogenes (A)
S. agalactiae (B)
ALPHA-HAEMOLYTIC
S. pneumoniae
S. oralis
S. milleri
S. sanguis
NON-HAEMOLYTIC
S. bovis
ENTEROCOCCUS
E. faecalis (D)
What are some ZIEHL-NEELSEN
STAIN POSITIVE bacteria?
MYCOBACTERIA
M. tuberculosis
M. leprae
M. avium-intracellulare
M. ulcerans
M. kansasii
Examples of gram positive rods?
ANAEROBIC
CLOSTRIDIUM
C. perfringens
C. tetani
C. botulinum
C. difficile
PROPIONIBACTERIUM
P. acnes
Aerobic: AEROBIC
CORYNEBACTERIUM
C. diphtheriae
etc
LISTERIA
L. monocytogenes
etc
BACILLUS
B. anthracis
B. cereus
etc
If we do a gram film and get a gram + coccus with chains what do we have?
Streptococcus
If we do a gram film and get a gram + coccus with clusters what do we have?
Staphylococcus
What would happen if we did haemolysis on blood agar of streptococcus?
Alpha result: Alpha haemolytic strep ( viridans strep)
Beta result: Beta haemolytic strep Antigenic group (A,B,C,G)
What would happen if we did an optochin test of the alpha haemolytic strep?
If its resistant then its viridians strep
If its sensitive: S. penuomniae
What happens if you do a coagulase or DNAse test on staphylococcus?
Positive = S. aureus
Negative = Coagulase negative staphylococcus
What is coagulase?
Coagulase: enzyme produced
by bacteria that clots blood plasma.
What is the most important sstaphylococci?
S. Aureus
Staphylococci features
at least 40 species:
-‘Coagulase’ + ve or – ve
Fibrin clot formation around bacteria may protect
from phagocytosis.
-Coagulase -ve species, e.g. S. epidermidis only important as opportunistic infections
Normal habitat
-nose and skin
Staphylococcus aureus features?
Spread by aerosol and touch
-carriers & shedders
Virulence factors
-Pore-forming toxins (some strains)
-alpha - haemolysin
-Panton-Valentine Leucocidin ‘PVL’
Proteases
-Exfoliatin
Toxic Shock Syndrome toxin
-(stimulates cytokine release)
Protein A
-(surface protein which binds antibodies in wrong orientation)
MRSA features
resistant to major antibtiocis
Beta-lactams
gentamicin, erythromycin tetracycline
Why is SA a successful pathogen?
Due to a large range of virulence factors.
This includes pore forming toxins.
The PVL toxin is produced by many of the community MRSA strains and causes haemorrhagic pneumonia.
It is encoded by a pro-phage gene that is incorporated into the bacterial genome.
What is alpha haemolysin ?
Low concentration: induces apoptosis in cells by allowing exchange of monovalent ions across the cell membrane.
High concentration: it binds to the lipid membrane and causes massive necrosis
What are some coagulase negative staphylococci?
S.epidermidis:
-Infections are ‘opportunistic’
.immunocompromised,
.prostheses
-Main virulence factor - ability to form persistent biofilms
S.saprophyticus:
-Acute cystitis
.haemagglutinin for adhesion
.urease
What happens in alpha haemolysis on blood agar?
Alpha- haemolysis is due to the production of hydrogen peroxide, which reacts with haemoglobin to form the green compound met-haemoglobin. Get partial greening
S.penumoniae
What happens in beta haemolysis on blood agar?
Beta-haemolysis is due to the production of two pore-forming toxins – streptolysin O and S. Streptolysin O is oxygen sensitive and is very antigenic
e.g. S.pyogenes
What is antigenic sero grouping?
For Beta haemolytic strep only
Carbohydrate cell surface antigens
Lancefield Groups A-H and K-V
Group A - S.pyogenes
throat, skin, post partum
Group B - S.agalactiae neonatal infections
What is the lancefield microbead agglutination test?
Antiserum (antibodies) made that recognise each group
Tagged to tiny plastic beads
added to a suspension of bacteria
Antibodies bind bacteria and beads clump together
Visible to naked eye
What are the virulence factors (enzymes)
Hyaluronidase
- spreading
Streptokinase
- breaks down clots
C5a peptidase
- reduces chemotaxis
What are the virulence factors (Toxins)?
Toxins
Streptolysins O&S
-binds cholesterol
Erythrogenic toxin
-Streptococcal pyrogenic toxin e.g. SPeA – exaggerated response
What are the virulence factors (Surface)?
Capsule - hyaluronic acid
M protein – surface protein - M protein is an antiphagocytic protein and some strains carry a hyaluronic capsule layer, which is non-antigenic.
(encourages complement degradation)
What are some infections caused by S.pyogenes?
Respiratory
-Tonsillitis & pharyngitis - most common
Skin and Soft tissue
-Impetigo
-cellulitis
Scarlet fever
rheumatic fever
Features of S.pneumoniae?
Normal commensal in oro-pharynx ~ 30% of population
Causes - pneumonia, otitis media, sinusitis, meningitis
Predisposing factors
-impaired mucus trapping (e.g. viral infection)
-hypogammaglobulinaemia
-Asplenia
-HIV
What are the virulence factors of S.Pneumoniae?
Capsule
-polysaccharide (84 types), antiphagocytic
.polysaccharide vaccine ‘PPV’ 23 types
.conjugate vaccine ‘PCV’ 13 types
Inflammatory wall constituents
-teichoic acid (choline)
-peptidoglycan
Cytotoxin
-pneumolysin
What are some features of Viridans group streptococci?
alpha- haemolytic (or non-haemolytic)
Optochin resistant
Some cause dental caries & abscesses
Important in infective endocarditits
-S. sanguinis, S. oralis
Cause deep organ abscesses (e.g. brain, liver)
Most virulent are the “milleri group”
-S.intermedius, S.anginosus, S.constellatus
Viridans streptococci is a term used to describe collectively the oral streptococci.
What are some aerobic gram positive bacili?
Listeria monocytogenes
Bacillus anthracis (Anthrax) - spore forming
Corynebacterium diphtheriae
What are some anaerobic gram positive bacili?
Clostridia…: spore forming, survive in environment, produce toxins
C. tetani
Tetanus
C. botulinum
Botulism
C. difficile
antibiotic associated diarrhea
pseudomembranous colitis
Tetanus
From infected wounds
Toxin inhibit GABAs neurotransmission and cause muscle contractions and spasms progressing from head to body
‘Risus sardonicus ‘orrictusgrin
Botulism
From contaminated food (canned) or infected wounds - Botulinum toxin causes paralysis spreading from head to body
What is the model of the bacterial cell envelope in gram negative bacteria?
LPS (‘endotoxin’) forms the outer leaflet of the outer membrane of G-ves, and comprises:
1.Lipid A, the toxic portion of LPS - anchored in the outer leaflet of outer membrane.
2.Core (R) antigen, short chain of sugars, some are unique to LPS.
3.Somatic (O) antigen, a highly antigenic repeating chain of oligosaccharides.
What are some pathogenecity determinants/ virulence factors?
any product or strategy that contributes to pathogenicity/virulence
1.Colonisation factors: adhesins, invasins, nutrient acquisition, defence against the host
2.Toxins (‘effectors’): usually secreted proteins that cause damage, subversion
What are enterobacteria?
Family Enterobacteriaceae = more commonly termed “Enterobacteria”*
Rods, most are motile (peritrichous flagella) – flagella over entire surface of bacteria
Facultatively anaerobic
Some species colonise the intestinal tract (in a good or bad way!)
Family within proteobacteria
Rod shaped and gram negative: most gram negative are rod shaped
What are some cell surface antigens of Gram- negative bacteria?
H antigen (flagellum)
O (somatic) antigen (LPS)
K antigen (exopolysaccharide ‘capsule)
What is a serovar?
Antigenically distinct variants of a single species are referred to as ‘serovars’, i.e. E. coli O157:H7 (EHEC) and E. coli O45:K1:H7 (NMEC) are different serovars of E. coli.
What does amino acid/ carbohydrate sequence variation in cell surface structures cause?
Gives rise to antigenic variation among species AND between different strains of the same species.
What is Escherichia coli?
Commensals - most abundant facultative anaerobe (107-108/g faeces) Peritrichous flagella
What are the principal infections caused by pathogenic Escherichia coli strains?
Wound infections (surgical)
UTIs (cystitis; 75-80% ♀ UTIs - faecal source or sexual activity; catheterisation - most common type of nosocomial infection)
Gastroenteritis
Travellers’ diarrhoea
Bacteraemia (sometimes leading to sepsis syndrome)
Meningitis (infants) - rare in UK
Why are some E.coli strains pathogenic?
Several ‘pathovars’ (distinct pathogenic strategies)
Common ‘core genome’ (most genes are common to all strains/pathovars)
Acquisition of pathogenicity genes
‘lateral gene transfer’
What are Shigella?
Very closely related to Escherichia (= “E. coli + a virulence plasmid”) Four species:
S. dysenteriae, S. flexneri, S. boydii, S. sonnei
What is shigellosis and what does it cause?
Pathology like Enteroinvasive Escherichia coli (EIEC) but with the addition of Shiga toxin
Severe bloody diarrhoea (esp. S. dysenteriae) Frequent passage of stools (>30/d)
pus and blood, prostrating cramps, pain in straining, fever Self-limiting (in adults)
What is the pathogenesis of shigella infection?
Acid tolerant
Person-to-person or contaminated water and food
Entry through colonic M cells* (antigen sampling)
Induced uptake
M cells: overlie lymphoid follicles and deliver antigens to underlying immune cells.
How does invasion of the colonic mucosa occur by Shigella?
Look at slide 21 of gram negative bacteria powerpoint
Shigella bacteria enter M cell from apical surface of the lumen causing apoptotic macrophage to enter the cell and destroy M cell.
More shigella bacteria enter enterocyte (intestinal epithelial cell) from basolateral surface after which causes translocating polymorphonuclear leukocytes to be recruited to site of infection causing further damage to epithelium.
What is the major Shigella virulence determinant?
Shiga toxin (Stx)
What is the structure of Shiga toxin
Think of one big circle in the middle which is A and 5 smaller cirlces around it which is B
A is the catalytic subunit (glycosidase) and B is the receptor binding subunits
It cleaves N-glycosidic bond of adenosine residue in 28S rRNA of the 60S subunit of the ribosome (depurination)
> blocks EF-1 and EF-2 binding > protein synthesis inhibited > cell death
What are the complications of systemic absorption of Stx?
Targets kidney > microvascular thrombosis in kidneys > kidney failure
What are the 2 species of salmonella?
Two species:
S. enterica - responsible for salmonellosis
> 2,500 serovars*
S. bongori - rare (contact with reptiles)
What are some infections caused by S. Enterica?
1.Gastroenteritis/enterocolitis (serovars Enteritidis and Typhimurium)
Frequent cause of food poisoning (milk, poultry meat & eggs) Second highest no. of food-related hospitalisations/deaths (UK) 6-36 hr incubation, resolves (~7 days)
Localised infection, only occasionally systemic
2.Enteric fever - typhoid/paratyphoid fever (serovars Typhi and Paratyphi)
3.Poor quality drinking water/poor sanitation
Systemic disease
~20 million cases, ~200,000 deaths/yr (globally)
Bacteraemia (serovars Cholerasuis and Dublin) Uncommon
What is the pathogenesis of salmonellosis?
Ingestion of contaminated food/water - high I.D. (~106) unless in chocolate!
(‘faecal-oral route’)
1.Invasion of gut epithelium (small intestine)
2.Transcytosed to basolateral membrane
3.Enters submucosal macrophages
4.Intracellular survival/replication
What is the pathogenesis of gastroenteritis?
1.Bacterial-mediated endocytosis into M cell
2.Induction of interleukin-8 release from enterocyte>
3.Neutrophil recruitment and migration>
4.Neutrophil-induced tissue injury>
5.Fluid and electrolyte loss > diarrhoea
6.Inflammation/necrosis of gut mucosa
Look at slide 26 gram negative bacteria
What is the pathogenesis of enteric fever?
S. enterica and sv. Typhil
1.Bacterial-mediated endocytosis into enteric cell
2.Transcytosis to basolateral membrane of M cell
3.Survival in Macrophage >systemic spread
4. Migration to reticuloendothelial organs via lymphatics & blood
Look at slide 26 gram negative bacteria
What is the pathogenesis of typhoid (enteric fever)? (Small intestine)
- Ingestion of S.Typhi via bacterial endocytosis >
- Enters small intestine >
- Inflammation and ulceration of Peyer’s patches >
- Diarrhoea; haemorrhage or perforation (1-3% of
cases)#
What is the pathogenesis of typhoid (enteric fever)? (In general)
- Ingestion of S.Typhi via bacterial endocytosis >
- Enters small intestine >
- Travels from SI in lymphatic system within macrophages to Mesenteric lymph nodes
- From mesenteric lymph nodes enters bloodstream via thoracic duct >
- Goes to transient (primary) bacteraemia
- Multiplication in macrophage in liver, spleen and bone marrow
7a. CAN travel from liver to gall bladder where it stays in a carrier state for 1 year to rest of life
7b. Or bacteria is released into bloodstream (secondary bacteraemia) > Fever, kidney and other organs infected
Asymptomatic until bacteria released into bloodstream as secondary bactereamia
Proteus mirabalilis (pathogenic Enterobacteria)
can differentiate into an elongated hyperflagellated form > surface motility (‘swarming’)
Have swimmer and swarmer cells
catheter-associated UTIs (~30% cases) > pyelonephritis
produces urease (causes urine pH to increase) > calcium phosphate precipitation >
formation of bladder/kidney stones, catheter blockage
Klebsiella pneumoniae
environmental
opportunistic, nosocomial infections (neonates, elderly, compromised)
colonisation of GIT (normal) and oropharynx (less frequent) is benign but can lead to:
UTI, pneumonia (aspiration from oropharynx), surgical wound infections, bacteraemia > sepsis (high mortality).
multi-drug resistant (resistant to carbapenems)
Enterobacter (E. cloacae, E. aerogenes)
opportunistic, nosocomial (originating in hospital) outbreaks (including ICUs)
infections in lungs, urinary tract, abdominal cavity, intravascular devices, sepsis
spread from endogenous gut flora, can survive on skin, patient-to-patient transmission
cephalosporin-resistant forms
Yersinia spp - primary pathogen
Y. enterocolitica - localised to ileum: gastroenteritis
(diarrhoea with abdominal pain and fever)
Y. pestis - systemic: bubonic plague (zoonosis) = ‘black death’
Vibrio cholerae
Facultative anaerobe
Saline environments: commensal to planktonic crustaceans such as copepods
>ingestion by shellfish
> contamination of drinking water due to flooding of coastal areas or poor sanitation
Curved rods with single polar flagellum
What is the most severe diarrhoeal disease?
Cholera
Characterised by pandemics (7 since 1817)
1P-6P, Indian subcontinent;
7P began in Sulawesi (1961) > SE Asia (1963) >
Africa (1970) > Latin America (1991) > Caribbean (2010)
O1 serotype > epidemics (and occasionally O139 variant)
1.4-4.0 million cases/yr, 20,000-140,000 associated deaths
What is the pathogenesis of infection by V. cholerae?
Faecal-oral route (not person-to-person) - high infective dose required
(faecal contaminated water (poor sanitation) or undercooked shellfish from risk areas)
>
Incubation, few hours to 5 days (multiplies in small intestine)
>
Voluminous watery stools (‘secretory’ diarrhoea)
What are the effects of cholera?
Can lose 20 litres fluid/day plus electrolytes
> dehydration/death (hypovolaemic shock)
> 50-60% mortality if untreated
No blood, pus or fever (i.e. not dysenteric)
i.e. no invasion or damage to mucosa#
Most cases can be treated with ORT
What is the major virulence determinant of V. cholerae?
Cholera toxin (CT)
1.CT binds to a glycolipid receptor on epithelial cell (B subunits)
2. A subunit ADP-ribosylates G-protein (Gs) > locked in ‘ON’ state
3. Uncontrolled cAMP (cyclic AMP) production
4. Protein kinase activated
5. CFTR ion transporter activity modified (loss of Cl- & Na+ into gut lumen)
6. Leads to massive loss of H2O
CFTR: cystic fibrosis transmembrane conductance regulator (a Cl- ion transporter)
Pseudomonas aeruginosa
motile - single polar flagellum
ubiquitous, free-living, aerobe
opportunistic (serious cause of nosocomial infections)
resistant to multiple antibiotics (& disinfectants) - very difficult to treat
Infections caused by P. aeruginosa
Acute infections:
Localised:
burn/surgical wounds UTI (catheters) keratitis
Systemic:
(bacteraemic > sepsis)
neutropenic patients (leukaemia, chemotherapy, AIDS)
ICU patients:
(ventilators)
leading cause of nosocomial pneumonia
Chronic infections:
(i) Cystic fibrosis (CF) patients
Common denominator to all infections - compromised host defences
What are the virulence determinants of P. aeruginosa?
Multiple toxins - these are the main virulence determinants in acute infections:
Interferes with cell signalling:
ExoS (exoenzyme S)
ExoU (exoenzyme U)
Cell death/ damage:
ToxA (exotoxin A)
LasB (elastase)
PlcH (phospholipase)
HCN (cyanide)
pyocycanin (generates reactive oxygen species)
Haemophilus influenzae
Exclusively human parasite:
Nasopharyngeal carriage in 25-80% population
Opportunistic infections seen mainly in young children and adult smokers:
Meningitis* (age <5 yrs), 5-10% of adult cases
Bronchopneumonia
Epiglottitis, sinusitis, otitis media
Bacteraemia (often associated with pharyngitis)
Pneumonia in CF, COPD, HIV patients
What are the diagnostic characteristics of H.influenzae?
Fastidious
- requires ‘factor X’ (haem) and ‘factor Y’ (NAD)
therefore, cultured on chocolate agar
non - motile
What are the virulence determinants of H.influenzae?
Capsule -
invasive strains are capsulate (‘encapsulated’)
> can penetrate nasopharyngeal epithelium
>resistance to phagocytosis and complement system
- 6 different capsule serotypes (a-f)
(type b strains are the main cause of meningitis)
‘Hib’ vaccine has reduced the incidence
Commensals and upper respiratory tract pathogens are non-capsulate (‘unencapsulated’)
referred to as ‘non-typeable’ H. influenzae (NTHi)
(ii) LPS (‘endotoxin’) > inflammation
>complement resistance
Legionella pneumophila
Legionnaires’ disease - severe inflammatory pneumonia
Immunocompromised
Severe
Infection from man-made aquatic environments
Replicate within freshwater protozoa - intracellular parasite of amoeba
Can survive and replicate within alveolar macrophages
What is Bordetella pertussis?
pERTUSSIS - Whooping cough
B. parapertussis causes mild pharyngitis)
Short rods (‘coccobacilli’)
Fastidious
Humans - only known reservoir
Highly contagious (low I.D.) - aerosol transmission
Non-specific flu-like symptoms (~7 d), followed by paroxysmal coughing
Non-invasive
What are the toxins of B. pertussis?
Pertussis toxin (PT)
S1 subunit ADP-ribosylates G-protein (Gi) > locked in ‘OFF’ state
(in ON state, Gi inhibits adenylate cyclase)
Therefore, PT > cAMP levels rise
Adenylate cyclase-haemolysin toxin (CyaA) > cAMP levels rise
What is pertussis toxin composed of?
PT is composed of 6 protein subunits.
Subunit S1 has ADP-ribosylase activity.
What does the hypersynthesis of cAMP lead to?
suppression of innate immune functions, particularly phagocytosis by macrophages
What are the 2 species of Neisseria which are of medical importance?
N. meningitidis
N. gonorrhoeae
Non-flagellated diplococci
Fastidious
Two species of medical importance
Humans are the only known reservoir
Diplococci present in Polymorphonuclear leukocytes of CSF (meningitis) or urethral
discharge (gonorrhoea) during
infection
What are the features of N. meningitidis? (meningococcus)
Nasopharyngeal carriage in 5-10% population (asymptomatic)
Rises to 20-90% during outbreaks
Person-to-person (aerosol) transmission (universities, barracks, Haj)
What is the pathogenesis of N. meningitidis?
crosses nasopharyngeal epithelium and enters bloodstream
>low level bacteraemia (asymptomatic) or septicaemia (sepsis)
>meningitis: invasion of the meninges - bacteria enter CSF of subarachnoid space after crossing blood-brain barrier (second most frequent cause of meningitis in young children)
very high mortality of septicaemic form if not treated
> requires rapid diagnosis!
What are the virulent determinants of N. meningitidis?
Capsule serogroup B - 90% cases)
> anti-phagocytic
(noncapsulated N.m. only found in nasopharynx - not pathogenic)
(ii) LPS (membrane ‘blebs’)
>cytokine cascade
> sepsis
What are the features of N. gonorrhoeae?
Gonorrhoea - second most common STD worldwide
Person-to-person only
Infection can be asymptomatic (~10% men, ~50% women)
Usually characterised by urethritis with additional infection of female genitalia.
Serious complications in women - can lead to salpingitis and/or PID if infection ascends.
Features of Campylobacter?
C. jejuni, C. coli
Spiral rods
Unipolar (monotrichous) or bipolar (lophotrichous)
flagella
Most common cause of food poisoning in UK & USA
Mild to severe diarrhoea, often with blood - usually self-limiting (< 1 week)
Campylobacter shed in faeces for ~3 weeks
Features of Helicobacter pylori
Spiral shaped, tuft of polar flagella
Present in ~50% global population, but only a fraction develop disease
Major role in gastritis and peptic ulcer disease (80-90% of ulcers)
Implicated in ~10% cases of gastric adenocarcinoma & mucosa-associated lymphoid tissue lymphoma (linked to production of VacA and CagA toxins)
What are (Phylum) Bacteroidetes?
Non-motile rods
Strict anaerobes
Commensal flora (large intestine) - most abundant
Opportunistic - tissue injury (surgery, perforated appendix or ulcer)
> predominantly peritoneal cavity infections (peritonitis, intraabdominal abscesses are most common) can lead to bacteraemia
Most frequent cause of anaerobic infections, usually B. fragilis (although it is only 0.5-1.0% of total commensal Bacteroides)
Features of chlamydia and chlamydophila?
Very small, non-motile.
Obligate intracellular parasites.
Cannot culture in bacteriological media - detect by serum Abs* or PCR.
What is the life cycle of Chlamydia?
- Elementary bodies (EBs) - rigid, extracellular form, ~0.3 micrometres, dormant
infectious
enter cell through endocytosis
prevent phagosome-lysosome fusion
Differentiates into >
2. Reticulate bodies (RBs) - fragile, intracellular form, ~1.0 micrometres, metabolically active
replicative
non-infectious
acquire nutrients from host cell
Life cycle of chlamydia (part 2)
- Entry by Elementary bodies
2.Conversion of elementary
body to reticulate body - Prevention of phagosome-lysosome fusion
- Multiplication
- Conversion of reticulate body to elementary body
- Cell lysis and release of elementary bodies
(including DNA condensation)
How many biovars does C. trachomatis have?
3
What are the types of C. trachomatis biovars?
- trachoma biovar (serotypes A-C) >trachoma > blindness
(eye-to-eye transmission via hands, fomites or flies) - genital tract biovar (serotypes D-K)
most common STD - infects epithelial cells of mucous membranes of urethra (both sexes) and vagina
- can ascend to uterus and ovaries (PID, infertility)
- usually asymptomatic (i.e. 70-80% cases in women)
-conjunctivitis (STD), hand-to-eye transmission - lympho granuloma venereum (LGV) biovar (serotypes L1-L3)
-causes LGV (an STD) - invasive urogenital or anorectal infection
- endemic to the tropics, cases rising in Europe/N. America
What are features of C. pneuominiae?
respiratory tract (mild or “walking” pneumonia)
- ~10% community acquired pneumonias
What are the features of C. psitacci?
Mainly birds
psittacosis (zoonotic infection), severe pneumonia
Features of spirochaetes
Long, slender, helical, highly flexible
Most are free-living and non-pathogenic
Pathogenic varieties difficult to culture
Modified outer membrane (“outer sheath”)
(Treponema and Borrelia lack LPS, replaced by a different glycolipid)
What is the spirochaete endoflagellum?
Endoflagella located between
peptidoglycan and outer membrane.
Fixed at each end of the bacterium and confers shape.
Overlap in the centre of the bacterium.
Propels bacterium in a corkscrew motion
- swim faster in high viscosity medium
- hides” antigenic flagellum
What is Borrelia burgdorferi?
Lyme disease (zoonosis) (~300 cases in UK)
- bull’s eye rash, flu-like symptoms (fever, fatigue, headache)
- dissemination via lymphatics/blood to other organ (neurological problems in 10-15% patients, joints >arthritis)
What are the features of Leptospira interrogans?
contact of infected animal urine with mucous membrane or abraded skin
- flu-like symptoms
- severe form (Weil’s disease) in 10-15% infected individuals (jaundice, acute renal and hepatic failure, pulmonary distress,
haemorrhage)
What can treponema pallidum lead to?
Syphilis
1.primary stage - localised genital infection (ulcer (“chancre”))
days-weeks post-infection
(highly transmissible phase)
- secondary stage (~50% cases) - systemic
(skin (rash), swollen lymph nodes, joint pains,
muscle aches, headache, fever)
1-3 months post-infection
(still highly transmissible) - tertiary stage (~30% cases) - ‘gummas’ (granulomas) in bone and soft tissue,
cardiovascular syphilis (aorta),
neurosyphilis (brain and spinal cord).
Occurs several years post-infection
(non-infectious form)
What are the four major groups (phyla) of Gram- negative pathogens?
- Proteobacteria - all are rod-shaped (bacilli)* except Neisseria (diplococci)
and the Campylobacter/Helicobacter genera (spiral) - Bacteroidetes (Bacteroides) - rod-shaped (bacilli)
- Chlamydia - round (elementary bodies), pleiomorphic (reticulate bodies)
- Spirochaetae (Spirochaetes) - spiral/helical
*= some are curved, some are short (coccobacilli), but are bacilli nonetheless
What happens in bacterial respiration?
Gut pathogens must be able to survive in low oxygen environments and are
therefore usually facultative or obligate anaerobes.
For example, Bacteroides are obligate anaerobes, while members of the
Enterobacteriaceae and V. cholerae are facultative anaerobes.
Campylobacter/Helicobacter genera are microaerophiles.
Most of the other pathogenic species discussed are aerobic.
Define strain/ isolate
Refers to the name given to a bacterium that has been isolated from a patient to distinguish it from bacteria of the same species that were obtained from other patients.
Although the same species, the genome sequences are invariably different among strains due to random mutation/gene loss or acquisition of new genes. However, in an outbreak situation, for example in a hospital ward, you may expect bacteria isolated from different patients to have identical genome sequences
What is a serovar/ serotype?
are strains that have antigenic properties that differ from other strains of the same species.
What is a pathovar/ pathotype?
are strains that are distinguished by possession of particular pathogenic mechanisms rather than being based on antigenic differences between molecules on the bacterial cell surface (the serotype). However, different serovars may exist among members of each pathovar
What are biovars/ biotypes?
are variant bacterial strains that differ physiologically or biochemically from other strains in a particular species.
What does the M in M. tuberculosis stand for?
Mycobacterium
What is M. leprae?
Leprosy
Associated with deformity or loss of fingers
Tropical illness
Climate is warm
Illness of poverty and lack of medical infrastructure
Skin lesions causes issue – hypopigmented – can be destructive at the nose
Nervous lesions causes problems – damages transition of neural signals – causes loss of sensation – affects distal parts of body like hand and foot – don’t have pain response if you injure there
How many deaths have been caused by tuberculosis in the last 200 years?
1,000,000,000
How many deaths caused TB per year?
1.5m
How many new cases of TB do we get a year?
10.4m new cases per year
Mycobacteria doesnt stain well with what?
Gram staining
What does mycobacteria stain with?
Ziehl-Neelsen/ Acid fast positive
What are the features of Mycobacteria?
Slighly curved, beaded bacili
High lipid content with mycolic acids in cell wall makes Mycobacteria resistant to Gram stain
Ziehl-Neelsen stain
Need 10,000 bacili per ml sputum to diagnose
What is the microbiology of TB?
Aerobic, non spore forming, non motile bacillus
Cell wall: high molecular,weight lipids +++.
Slow growing – M tuberculosis generation time 15-20hr vs 1hr for common bacterial pathogens
Significant part of the 4.4 Mb genome of MTB encode genes involved in lipogensis and lipolysis.
Key components include:
- Mycolic acids
- Lipoarabinomannan
What are the challenges of mycobacterium tuberculosis?
Thick lipid rich cell wall making immune cell killing and penetration of drugs challenging
Slow growth
- Gradual onset of disease
– Takes much longer to diagnose
– Takes longer to treat
How can you catch TB?
Catch TB from someones lungs when theyre coughing?
What happens in primary tuberculosis?
-Initial ‘contact’ made by alveolar macrophages in lungs
- Bacilli taken in lymphatics to hilar lymph nodes
What happens in latent tuberculosis?
-Cell mediated immune response (CMI) from T cells
- Primary infection contained but CMI persists
- Latent TB;
. no clinical disease
* detectable CMI to TB on
tuberculin skin test
What happens in Pulmonary tuberculosis?
- Granulomas forms around bacilli that have settled in apex
- In apex of lungs there is more air and less blood suppy (fewer defending white cells to fight)
- Could occur immediately following
primary infection (post-primary)
or after later reactivation - necrosis results in abscess forming and
caseous material coughed up
What happens in Pulmonary tuberculosis?
- Granulomas forms around bacilli that have settled in apex
- In apex of lungs there is more air and less blood suppy (fewer defending white cells to fight)
- Could occur immediately following
primary infection (post-primary)
or after later reactivation - necrosis results in abscess forming and
caseous material coughed up - TB may spread in lung causing other lesions
- Granuloma + Lymphatics + Lymph nodes = Primary Complex
Causes cough, chest pain, fever
How can TB spread beyond the lungs?
TB meningitis
Miliary TB
Pleural TB
Bone and joint TB
Genito urinary TB
Bacili in lymph nodes
Bacili in lung
How does TB infect us?
- Aerosol transmission
- Primary TB in lung
- Latent TB can remain for decades
- Can spread beyond lungs
What is the immunology to mycobacteria?
- Mycobacteria are phagocytosed by macrophages and traffic to a phagolysosomes/ phagosome.
- The bacterium has adapted to the intracellular environment and aims to withstand phagolysosomal killing and escape to the cytosol
- M. tb eradication can happen by apoptosis mediated cell death, auto phagocytosome, by phagolysosome
- Effective immunity requires CD4 T-cells which generate interferon gamma and
this helps activate intracellular killing by macrophages.
What happens if a granuloma is formed?
Mycobacteria shut down metabolically in order to survive – dormancy
What happens if hallmark granuloma formation fails?
if it fails, e.g. in the lung, this can result in the formation of a cavity full of live
mycobacteria and eventual disseminated disease (consumption)
What does our body do to protect us?
- Primarily controlled by macrophages
- Requires a CD4 T cell response to be controlled
- Involves many cells of immunity - formulation of granulomas
- ## Granuloma stability controls reactivation of TB
How do we get a more rapid diagnosis of tuberculosis?
- GeneXpert MTB/RIF cartridge based test
- Nucleic acid amplification test using PCR
- Purifies and concentrates MTB, sonicates to
release genomic material and then performs
PCR - Rapid result for MTB and detects Rifampicin
resistance using fluorescence - Can detect 131 bacilli/ml
- Sensitivity 88%, Specificity 98%
- Recommended for rapid diagnosis in TB
endemic countries
What does the highly immunogenic nature of mycobacterial lipids do?
Stimulates T-cell responses in 3-9 weeks after exposure to M. tuberculosis
Positive effects: ²+ve effects; macrophage killing of mycobacteria
,containment of infection, formation of tissue
granulomata.
Negative effects: ; hypersensitivity reactions with skin lesions, eye lesions and swelling of joints
This reactivity is measured in the tuberculin skin test where intradermal injection of purified protein derivatives induces skin swelling and redness.
What are some standard therapy anti - TB drugs?
isoniazid (INH), rifampicin (RIF),
pyrazinamide (PZA) and ethambutol (ETH) x 2 months
followed by isoniazid and rifampicin for further 4 months
What are some second line treatments?
injectable agents (streptomycin,
cycloserine, capreomycin)
* Side effects are wide-ranging and severe, include liver
damage
What are some forms of resistance mechanisms?
Drug inactivation:
Mtb produces beta-lactamase
Drug titration:
Target overproduction
Alteration of a drug target:
- missense mutations
Altered cell envelope:
- Increased permeability and drug efflux
What are some multi drug reisistant TBs?
XDR-TB: resistant to four commonly used TB drugs. 6% of all TB cases
Resultant from inadequate TB therapy and failure to clear patients of bacteria
Treatment is lengthy and expensive
How can we treat XDR-TB?
BPaL regimen :
– Bedaquiline
– Pretomanid
– Linezolid
All oral treatments for 6 months
These can fail too with totally drug
resistant (TTR) TB. No known solution as
yet.
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
Why are viruses of global importance?
Lower respiratory infections, diarrheal diseases and HIV/AIDS are leading killers in lower income countries in 2016
40 MILLION with HIV - 8 MIL DONT know their status, 750 undiagnosed
What is MERS?
Middle Eastern Respiratory syndrome
MERS 2012-now
2578 cases
888 deaths (35%)
What viruses can cause miscarriage and birth defects?
Cytomegalovirus (CMV),Varicella Zoster Virus (VZV), Herpes Simplex Virus (HSV),
Rubella
What are some recent viral outbreaks?
. Influenza, Measles, Mumps, Norovirus, Covid
What are some cancer causing viruses?
Epstein Barr Virus (EBV) + lymphoma,
Hep B/C + hepatocellular carcinoma,
Human Papilloma Virus (HPV) + cervical/anal cancer,
HIV
What is a virus?
An infectious, obligate intracellular parasite comprising genetic material (DNA or RNA) surrounded by a protein coat/ and or membrane
All have a receptor binding protein to “dock” to cells
All contain genetic material
Virus has poisonous fluid
Comprises of genrtic materia (DNA or RNA) surround by protein coat and/ or membrane
What do we mean by obligate intracellular?
totally dependant on living cells for their replication and existance
What are the different shapes of viruses?
Helical
Icosahedral
Complex
Non-enveloped
-adenovirus, parvovirus
Enveloped
- influenza, HIV
When not in an infected cell what do viruses exist as?
Virions
Consist of:
Genetic material (DNA or RNA)
Protein coat (capsid)
What do human viruses range from?
Human viruses range in size from 20 to 260nm in diameter
What do bacteria have that viruses dont?
Cell walls
Organelles
DNA and RNA
How do viruses replicate?
- Attachment to specific receptors
- Cell entry - Uncoating of virion within cell
- HOST CELL INTERACTION + REPLICATION
- Migration of genome tocell nucleus
- Transcription to mRNA using host materials
- Use cell materials (enzymes, amino acids, nucleotides) for their replication; subvert host cell defence mechanisms.
- Translation of viral mRNA to produce:
- structural proteins, viral genome, non-structural proteins eg enzymes - Assembly of virion
- Release of new virus particles
a.Bursts out > cell death eg rhinovirus
b. budding/exocytosis
e.g. HIV, influenza
What is a virus completely dependent on?
A virus is completely dependent on its host cell’s machinery to exist and replicate, and enters a cell with only its genome +/- viral enzymes
How do viruses cause disease?
- Direct destruction of host cells
- Modification of host cells
- “Over-reactivity” of immune system
- Damage through cell proliferation
- Evasion of host defences
What happens in direct destruction of host cells?
host cell lysis and death after a viral replication period of 4 hours
e.g poliovirus
Polio affects neurons – gets into neurones – destroys neurones – causes weakness and paralysis
What happens in modification of host cell?
E.g. Rotavirus
>atrophies villi and flattens epithelial cells
>decreases small intestine surface area
>nutrients incl sugar not absorbed
>hyperosmotic state
>profuse diarrhoea
What happens in the over reactivity of the immune system?
e.g. Hep B
Infects liver cells and hepatocytes
T lymphocytes comes along and destroys stuff
What happens in damage through cell proliferation?
e.g Human papillovirus (HPV) > Cervical cancer
1. Acquisition through contact
2. Partial viral replication and expression of some HPV proteins
3. Viral DNA integrated into host chromosome
4. Continuous expression of oncoproteins causing cellular DNA mutations
5. Dysplasia and neoplasia >
6. Leads to Cell proliferation and local and metastatic spread
What happens in HPV (detailed)
1.HPV (types 16 or 18) infection of suprabasal layer in genital tract.
2.Partial viral replication including transcription and expression of several early
viral gene products (E1, E2, E4, E5).
3.Gradual movement of cells to mucosal surface through natural wear and tear.
4.At some point during this process the HPV genome may become integrated into
the host cell chromosome. Mutagenic agents (eg nicotine) may increase the
chance of integration.
5.Following integration, control of viral gene expression by the HPV E2 protein
is lost and the HPV E6 and E7 proteins may be expressed.
6.Two cell growth and proliferation suppressor proteins, Rb (retinoblastoma)
and p53 are prevented from operating.
7.Excessive cell growth and proliferation occurs and cervical cell carcinoma
results.
What happens in evasion of host defences?
After primary disease, virus not detectable but viral DNA lies latent and can reactivate, particularly at times of lower immune control (illness/immunosuppression/advancing age)
Can hide in nerve root ganglion, Lymphoid cells, Myeloid cells
Lymphoid cells - T cells, B cells, NK cells
Myeloid cells - monocytes, macrophages, neutrophils, basophils, eosinophils etc
What is Varicella Zoster Virus?
Primary - chickenpox
Reactivation - when immune system suppressed - Shingles
What is cell to cell spread in evasion of host defences?
E.g. Measles and HIV
Direct cell to cell spread has multiple advantages
Avoids random release into the environment
Increased speed of spread within tissues
Avoiding immune system
What happens in the evasion of host defences at the molecular level?
Antigenic variability eg influenza, HIV, rhinovirus
Ability to change the surface antigens in order to evade the host’s immune system
Explains:
- how a host can be re-infected with the same virus e.g. common cold
- why with influenza vaccination is required annually, as each season a different viral strain is circulating
What is prevention of host cell apoptosis?
In response to a viral infection, many cells undergo apoptosis, which reduces the amount of virus released from the cell
Prevention of host cell apoptosis allows the virus to continue replicating within it, so more virus is produced and then released. It also has an essential role into how some viruses are oncogenic (cancer causing).
Flu can recombine itself in different configurations
What is Downregulation of interferon and other intracellular host defence proteins ?
In normal cells:
Interferon synthesis stimulated > Antiviral state activated in neighbouring cells
In affected cells:
Interferon synthesis blocked > Neighbouring cell susceptible to infection
Why do viruses Viruses vary wildly in the range of clinical syndromes they can cause?
> Different host cells and tissues that they can infect
> Different methods of interaction with the host cell
What are the 5 types of immunoglobulins?
IgG
IgM
IgE
IgD
IgA
What happens in active immunity?
Cell-mediated immunity
Antibody-mediated immunity
Vaccination stimulates immune response and memory to a specific antigen/infection
Where IgA produced?
Breastmilk
What happens in Passive immunity?
Protection provided from the transfer of antibodies from immune individuals.
Most commonly cross-placental transfer of antibodies from mother to child (e.g. measles, pertussis)
Or, via transfusion of blood or blood products including immunoglobulin (e.g. Hep B)
Protection is temporary – usually only a few weeks or months.
#Immunity from someone else or a different source
First couple of months baby immunised using mothers breast milk antibodies
Antibodies degrade overtime
Active immunity is different
Active immunity gives you longer lasting immunity
What can vaccines be made from?
inactivated (killed) (e.g. pertussis, inactivated polio)
attenuated live organisms (e.g. yellow fever, MMR, polio, BCG)
secreted products (e.g. tetanus, diphtheria toxoids)
the constituents of cell walls/subunits (e.g. Hep B) or
recombinant components (experimental)
What is herd (population) immunity?
Get population immunity through vaccination or past infection
What is vaccine failure?
No vaccine offers 100% protection
Small proportion of individuals get infected despite vaccination.
Primary vaccine failure – person doesn’t develop immunity from vaccine.
Secondary vaccine failure – initially responds but protection wanes over time.
No such thing as perfect vaccine
Some people don’t have enough immune response
Vaccine expired, don’t get administered the proper way
What are examples of vaccine preventable diseases?
Diptheria
Tetany/ Tetanus
Pertussis/ Whooping cough
Polio
Haemophilus influenzae type B
Meningococcal disease
