Microbiology Flashcards
Extremophiles
Live under extreme conditions
Halophiles
Need high salt conditions
Thermophiles
Can thrive at temperatures betwen 60-120
Cryophiles
Grow better at tempartures of 15 or lower
Acidophile
Optimum pH level at or below 3
Alkaliphile
Optimal growth at pH levels of 9 or above
Xerophile
Grow in extremely dry, desiccating conditions
Brightfield Microscopy
0.2um resolving power, 1000x,
Mostly used gram staining
Darkfield
0.2um, 1000x
Examination of very thing organisms against dark background (spirochetes)
Phase constrast
0.2um, 1000x
To observe unstained live organisms
Fluorescence
0.2u, 1000x
Mainly for immunodiagnostic fluorescent dye attached to organism
Scanning Electron
20nm, 10,000x
Examination of surface feature of cells and viruses, gives illusion of depth (3D)
Transmission electron
0.2nm, 200,000x
Examination of cellular and viral ultra structure, reveals internal features
Gram positive vs Gram negative
Gram positive = 1 membrane and cell wall is thick
Gram negative = 2 membrane and cell wall is thin
Taxonomic catergories
Kingdom, Phylum, Class, Order, Family, Genus, Species
Endospores
Endospores are resistant to heat, cold, drying and many chemicals and can survive for many years in soil or dust. The spores germinate after landing on moist, nutrient-rich surface and develop into vegetative state. Important for survival, but not for reproduction (dormant, metabolically active)
Flagella
Provide motility, powered by proton-motif force
Fimbriae (pili)
Hair-like structures, not associated with motility. Pili often contain an adhesin at tip which is used to bind to host cells (colonisation). Some produce sex pilli for conjugation (exchange of genetic material)
Slime layers
Gelatinous material secreted from cells used for gliding and aggregation. Formation of biofilms (dental plaque )
Capsules
Firmly attached to the cell surface and usually composed of polysaccharide. Provides protection from desiccation and immune system. Immune evasion factor
Strain
Genetic variant of a species (subtype)
Serotype
subtype that can defined by using specific antibodes
Pathovar
subtype with tissue/host specificity
Isolate
Pure microbial sample obtained from an infected individual
Coagulase Test
Used for identification of Staph Aureus. Mediates fibrin polymerisation that can be seen as clot in plasma
Oxidase test
Some obligate aerobic bacteria produce cytochrome C oxidase as part of the respiratory chain. Incubation of bacteria with oxidase reagent results in dark blue stain. Only use results <20 seconds
Catalase test
Use to differentiate between Staph and Strep, both gram positive. Staph will produce catalase producing bubbles.
Microbact strips
Reactions are assessed by change of colour, either by the product of pH indicator. Test produces code, which compares to analysis sheet
Antiobiotic Susceptibilty test
Differentiate between species with different resistance. Test conducted on lawn agar plates with antibiotic discs.
Selective Agar
Contains inhibitors to discourage growth of certain organsism
Differential Agar
Contains indicators to differentiate organisms.
Mannitol Salt Agar
use to identify Staph aureus. Salt inhibits non-haloduric bacteria, mannitol can be used as a carbon source by Staph aureus, but not by an other Staphylococci. Fermentation of mannitol results in a pH decrease, which is detected by a pH indicator changed from red to yellow
Sabourand agar
selective for fungi, as low pH suppresses growth of most bacteria. Non -differential
Eosin-methylene blue agar (EMB)
selective for gram-negative bacteria as aniline dyes are toxic for gram positive bacteria. Differential for lactose fermenter. Appearance fo pink colonies indicates lactose fermentation (white = negative)
Blood Agar plate
Growth of many fastidious bacteria. Differentiates for haemolytic reactions. alpha = some, beta = all, gamma = none
Cytine-lactose-electrolyte deficient (CLED) agar
used for growth of urinary pathogens. Lack of electrolytes inhibits movement of motile organisms. Differentiates lactose fermenters (yellow), blue = negative
Bile-Esculine agar:
selective for Enterococci (Group D streptococci). Oxgall inhibits non-enteric bacteria. Esculine hydrolysis results in a dark brown color. Some members of the Enterobacteriaceae family also hydrolyse esculine
Cell aggulination
Antibodies recognise component on cell surface resulting in visible clumping (agglutination). Basis of serotyping, where serum is used to distinguish between different types of a given species based on specific antibodies to a variable surface molecule
Latex bead agglutination
Antibodies (or antigen) can be bound to latex beads. A positive reaction leads to visible clumping of the latex beads. Used for e.g Lancefield group typing of Streptococci
Western-blot
For identification of proteins or antibodes. Proteins are separated on a gel according to their molecular weight and then immobilized by blotting onto a nitrocellulose membrane. Antibodies are added to the membrane and specific binding to protein occurs. A second antibody labeled with an enzyme and with specificity to the Fc region of the first antibody is added. Binding is monitored by adding a substrate that is converted by an enzyme resulting in a detectable protein band
Anti-streptolysin O assay
antibodies against steptolysin O are a marker for a recent S. pyogenes infection and important for diagnosis of poststreptococcal diseases such as acute rheumatic fever. Red blood cells are mixed with streptolysin O and patient serum. Lysis of RBC leads to a red solution. If lysis is inhibited by neutralizing ab in the serum. RBC sediment and the solution remians clear
Restriction fragment length polymorphism (RFLP)
small mutations on the genome can leda to destruction (or generation) of a recognition sequence for a restriction enzyme (a DNase that cleaves at short specific DNA sequences). This leads to changes in the length of DNA fragments after treatment with the DNase and can be detected after separating the DNA fragments on an agarose gel. Mainly used to epidemiological studies
PCR
Uses specific oligo DNA primers and a heat-stable DNA-polymerase to amplify very small amounts of DNA. Important method to identify organisms that cannot be easily grown in culture. Also used to amplify small amounts of DNA.
Fluorescene in situ hybridisation
Cytogenetic method that uses fluorescent probes specific to certain DNA or RNA sequences
Organic antibiotics
isolated from bacteria or fungi
Semi-synthetic antibiotic
further derivisation of organic compound for greater efficacy, ampicilin, methicillin, oxacillin
Synthetic
generated in the lab
Antibacterial spectrum
gives the range of activity against bacteria. e.g broad or narrow. A narrow antibiotic is only effective against a limited variety of bacteria. A broad-spectrum antibiotic works against a larger variety of bacteria
Bacteriostatic activity
is the level of antimicrobial activity that inhibits growth of an organism
Bactericidal activity
is the level of antimicrobial activity that kills the organism
Antibiotic combination
different antibiotics are sometimes combined to broaden the antimicrobial spectrum, to treat polymicrobial infections
Antibiotic synergism
enhanced antimicrobial activity of combined drugs compared to activity of each individual antibiotics
Antibiotic antagonism
activity of one antibiotic interferes with activity of other, so the sum of activity is less than most active individual drug
Minimum inhibitory concentration
minimum concentration of an antibiotic to inhibit growth of a given bacterium
Minimum Bactericidal concentration
minimum concentration of an antibiotic to kill a given bacterium. MBC is reached when colony forming units (CFU) are reduced by 99.9% below control
Antibiogram
this shows the sensitiviy of an isolated strain to a certain antibiotic. The semi-quantative method is based on diffusion of the antibiotic from a filter disc on an agar plate producing a concentration gradient around the disc. the MIC can be calculated from the diameter
Drugs that block cell water synthesis: B-lactam antibiotics
inhibit peptidoglycan synthesis by irreversible inhibition of transpeptidase (=penicillin binding protein PBP), the enzyme that catalyse the peptide-cross links. Eg. penicillin. These antibiotics are bactericidal
B-lactams include penicillin, cephalosporins, carbapenems
Gram negative bacteria are resistant to penicllin, does not pass through outer membrane porins, however extended spectrum penicillins (amoxicillin, ampicillin) can
Drugs that block cell wall synthesis: Glycopeptides
which inhibits PG synthesis by binding to the petides of the peptidoglycan monomers. Drug of last resort for MRSA. eg vancomysin
Inhibitors of RNA transcription: Rifamycins
inhibit bacterical RNA polymerase. typically used against Myobacteria. Rifamysins are bactericidal.
Inhibitors of nucleic acid synthesis: Quinolones and Fluoroquinones
bind DNA topoisomerases and prevent DNA replication. They are broad spectrum, bactericidal and coomnly used against urinnary tract infection. They can enter host cells, which makes them useful against intracellular bacteria. Due to increased resistance, quinolones have been replaced with fluroquinolones which are more active.
Antimetabolites: Sulfonamides and diaminopyrimidines
prevent the synthesis of tetrahydrofolic acid from PABA. Tetrrahydrofolic acid is a cofactor needed to synthesise nucleic acids and methionine. Mammalian cells depends on external folate. These antibiotics are bacteriostatic and useuful against urinary tract infection and Shigellosis
Antibiotics: Inhibition of protein synthesis
Antibiotics that can bind to the 2 different subunits of the ribosomes, some targeted to the 50s and others to the 80s.
Binding to the 30s subunit: Aminoglycosides
freeze the 30s initiation complex resulting in misreading (induce frameshift) of DNA. They are mostly effective against aerobic, gram negative bacteria and are bactericidal and synergistic with penicillin.
Binding to the 30s subunit: Tetracyclines
inhibit binding of aminoacyl-t-RNA to the acceptor site on the ribosome. They have broad-spectrum activity, are bacteriostatic and used against many different bacterial infections.
Binding to the 50s subunit: Macrolides
inhibit translocation of the peptidyl transferase activity. from the A to the P site. They are bacteriostatic and active against Gram-positives and Mycoplasma
Binding to the 50s subunit: Lincosamides
inhibit peptidyl transferase activity. They have broad-spectrum activity and are bacteriostatic
Binding to the 50s subunit: Chloramphenicol
is a broad-spectrum, bacteriostatic antibiotic. Only used in certain cases such as bacterial meningitis, due to strong side-effects
Antibiotic resistance mechanisms
Exclusion of antibiotic from site of action - outer membrane of Gram-negatives often impermeable
New or modified antibiotic insensitive target - MRSA produces PBP2a (altered transpeptidase) with reduced affinity for penicillin
Efflux pump for the antibiotic removal from site of action - specific transport out of the cell e.g tetracylclin, macrolides, fluroquinolones
Enzymatic modification or degradation of the antibiotic - some bacteria produce B-lactamase, which breaks the B-lactam ring. Some B-lactamases are specific for certain B-lactams, while others inactivate a wide range of B-lactams.
Antibiotic resistance (genetic vs non-genetic)
Non-genetic (intrinsic drug resistance
- metabolic inactivity
- lack of target structure, mycoplasmas (lack cell wall)
- exclusion, antibiotic can’t enter cell
Genetic resistance
- Chromosomal resistance- spontaneous mutation n a gene encoding a target receptor
- Acquired resistance - conjugation (plasmid transmid)
- Transformation (transfer of free DNA)
- Transduction (Transfer by viral DNA)
MRSA
Methicillin resistant S-aureus, carry Staph cassette chromosome mec (SCCmec)
integrated in bacterial genome
SCCmecII: mainly in hospital MRSA strains, also encodes resistance
SCCmecIV: mainly in community acquired MRSA
Staph aureus: general info
Gram postiive-spherical cocci, found in irregular grape-like cluters. Non-motile. Halodurent
Staph aureus: location
mosit skin folds, oropharynx, GI tract and urogentical tract. 15%
of people are persistant nasopharyngeal carriers.
Staph aureus: resistance
has b-lactamase gene. MRSA and vancoymcin resistnat strains have emerged too
S.aureus: catalase test
Postive
S.aureus: coagulase test
Positive
S.aureus: Adhesins
MSCRAMMS (Microbial surface components recognizing adhesive matrix molecules) - cell wall atttached proteins found in gram positive bacteria. They specifcally bind to host extracellular matrix proteins, fibronectin, elastin, laminin, vitronectin and collage. Important for tissue colonisation
S.aureus: factors that damage host cell
Cytolysins - alpha toxin form membrane pores. Beta toxin hydrolyses membrane phospholipids. Gamma tozin are pore forming toxins. Toxic to leukocytes, erythrocytes and tissue cells
Exfoliative toxins - serine proteases that split intercellular bridges (desmosomes) in stratum granulosum, resulting in peeling.
S.aureus: Spreading factors
Lipases: hydrolyse lipids for invasion of cutaneous tissues
Nucleases - hydrolyses DNA, decrease viscocity of pus
Hyaluronidase: hydrolyses hyaluronic acid in connective tissue
Proteases - serine protease, aureolysin
Staphylokinase (fibrolysin) - causes fibrolysis
S.aureus: Superantigens
Toxic shock syndrome toxin , Staphylococcal enterotoxins
The staphylococcal SAgs are struturally and functionally related to the streptococcal superantigens. SAgs trigger massive release of pro-inflammatory cytokins and over-stimulation of the host immune response, resulting in system inflamation. Some of them can also cause food poisoning.
S.aureus: Immune evasion factors
Capsule - a dense polysaccharide coast that prevents oponisation with ab and complement. It also contains water which protects bacteria against desiccaiton
Slime layer - loose-boudn water-soluble film (biofilm) made from polysaccharides, which protects from immune factors and antiobiotics
Catalase: detoxifies peroxide produced by macrophages and neutrophils. The catalase test is used to distinguish staphylococci from streptococci
Clumping factor (CIF-A) bound coagulase - binds fibrinogen and converts it to insoluble fibrin. Fibrin deposition of cell surface prevents oponisation and phagocytosis. CIF-A also promotes cell aggregation (clumping). The coagulase test is used to identify S.aureus, as it is not produced by any other staphylococci
Protein A: found on the surface of most S.aureus strains. It binds IgG in wrong orientation thereby preventing oponisation and phagocytosis
S.aureus - Superficial skin disease
Impetigo - localised cutaneous infection with pus-filled vesicles. Primarily young children
Folliculitis - impetigo involving hair follicles
Furuncles or boils: painful pus-filled cutaneous nodules
Carbuncles: coalescence of furnuncles, extenstions into subcutaneous tissue that can lead to bacteremia and systemic disease
S.aureus - Disease 2
Osteomyelitis - can occur after hematogenous dissemination of bacteria to bone or by a secondary infection from trauma. Usually involves metaphyseal area of long bones. The cure rate is good, if treated with appropriate antibiotics
Septic arthritis - mainly found in children and young adults receiving intra-articular injections or caused by hematogenous spread from a localised focus. Characterised by painful erythematous joint and purulent material (pus) in joint space
Staphylococcal Scaled Skin Syndrome (SSSS) - cutaneous blisters followed by desquamation of epithelum caused by action of exfoliative toxins. affects mainly neonates and young children. Mortaility usually low
Bacteremia and endocarditis - spread of bacteria into the blood from a focus on infection (bacteremia). More than 50% of cases are hospital acquired (surgery, contaminated catheters). Bacteria can then spread to other organs, particular the heart leading to endocarditis S.aureus endocarditis has a mortality rate of nearly 50%. Bacterial endocarditis results in damage to the endothelial lining of the heart. The infected heart valaved is often coated with bacteria, platelets and cellular debris. Perofration of heart valve can occur mainly by secreted enzymes. Flushing of the debris into the blood can lead to septic emboli.
S.aureus - Disease 3
Pneumonia - can occur after aspiration of oral secretion or by hematgenous spread resulting in consolidation and abscess formation in lung. Cytolytic toxins are believed to play a role
Staphylococcal food poisoning - contamination of food by human carrier and improper food handling. Not infection. Mediated by heat stable enterotoxins (SEA and SEB..) that cause sever vomiting, diarrhea, abdominal pain, nausea, sweating headache. It has a rapid onset (hours), and generally doesn’t last long
TSS - caused by superantigen producing strains.
Menstrual TSS - growth of TSST-producing strain in vagina (TSST is the only superantigen that can penetrate mucosal bacteria) caused by prolonged use of expandable tampons.
Non-menstrual - grwoth of superantigen producing strain in wound. Toxins are released into the bblood and can cause systemic disease with fever, hypotension, erythematous rash and multiple organ failure. 30-40% mortality rate.
S.aureus - susceptible patientsq
infants
children with poor hygiene
mentruating women
patient with intravascular catheers
patients with compromised pulmonary function
immunocompromised patients
diabetes
Streptococci: general info
Gram positive cocci, grow in chains. Susceptible to penicillin
Streptococcus: Classification
A: S.pyogenes
B: S.agalactiae
C: S.disgalactiae, S.equi
D: S.bovis, Enterococcus spp
Group F: S.intermedius
No lancefield antigen: S.pneumoniae, viridan group
(write down on sheet)
S.aureus - risk factors
presence of foreign body
previous surgical procedure
poor hygiene of hospital staff
lack of antibodies
use of antibiotics that supress microbial flora
Streptococcus: where and how is it transmitted
Upper respiratory tract and respiratory droplets
Streptococcus Virulence Factors: Adhesins
MSCRAMMS: same as Staph.aureus
Pilli:
Streptococcus: Factors that damage the host cell
Cytolysins:
Streptolysin O (SLO): oxygen-labile cytolysin that forms pores in host cell membrane
Streptolysin S: (SLS): oxygen stable cytolysin that lyses leucocytes,erys and platelets
Completely lyses red blood cells
Streptococcus: spreading factors
Lipases: hydrolyse lipids, for invasion of cutaneous tissues
Nucleases: hydrolyses DNA, decrease viscosity of pus
Hyaluronidase: hydrolyses hyaluronic acid in connective tissue
Proteases: streptococcal cysteine protease (SCP) with wide substrate spectrum
Streptokinase (fibrolysin): causes fibrinolysis (dissolves clots)
Streptococcus: Superantigens
Streptococcal pyogenic exotosins, Streptococcal mitogenic exotoxin Z (SMEZ) :
Structurally and functionally related to the Staph superantigens, but they don’t cause food poisoning. trigger massive release of pro-inflammatory cytokines and over stimulation of the host immune response, resulting in system inflammation
Streptococcus: Immune evasion factors
Capsule: a dense hylauronic acid coat that prevents oponisation with ab and complement (inhibits phagocytosis). Only is some strains. Camoflauge effect.
M-protein: in addiotn to its function as an adhesin, M protein prevents complement factor C3b from oponising
C5a peptidase: a proteae that cleaves complement factor C5a prevent neutrophil migration to the site of infection
S.pyogenes non invasive diseases
Impetigo - same as Staph aureus
Pharyngitis: develops 2-4 days after exposure to S.pyogenes. Symptoms includes sore throat, fever, reddened pharynx, tonsillitis
Scarlet fever: a complication of pharyngitis that can develop into serious systemic disease. Epidemic outbreaks with high mortality rates in the 19th century. Caused by strains that produce the superantigen pyrogenic exotoxin A (SPE-A) = “scarlet fever toxin”
Cellulitis: infection of skin that involves subcutaneous tissue. An acute and rapidly spreading infection
S.pyogenes invasive diseases
Necrotising fasciitis: a deep infection of the skin that involves destruction of muscles. S.pyogenes is introduced through e.g minor cuts, trauma, burn, surgery or vesicular viral infection. The deep tissue infection is supported by spreading factors, such as DNAses, proteases and hyaluronidase. NF often develops into sever systemic disease with high mortaility (TSS)
Streptococcal toxic shock syndrome (STSS): often follows necrotising facsciitis and sepsis. STSS, mortality rate 30-70% (more severe than staphylococcal TS). Massive release of pro-inflammatory cytokines occurs in response to superantigen secretion. Systemic inflammation, symptoms includes fever, headache, multiorgan failure and shock.
Rheumatic fever and rheumatic heart disease - connected to pharyngitis and tonsilitis. Develops after untreated/chronic sore throats due to S.pyogenes. Inflammation of endocardium, myocardium, pericardium results in thickened and deformed heart valves and granulomas in myocardium. The disease often starts with inflammatory changes in joints.
ARF (acute renal failure) is an autoimmune disease, NOT an infection. It is triggered by molecular mimcry an antibody cross infection where antibodies generated against the M protein also bind to host proteins (cardiac myosin, collagen). Triggers a type 2 hypersensitivity immune response
S.agalactiae
Gram positive, long chains, either B or non haemolytic, lancefield B group carbohydrate. Resides in upper respiratory and genitourinary tract.
Neonatal disease: pneumonia, bacteremia, sepsis, meningitis
Infections in pregnant women: UTI, bacteremia
Viridans Streptococci
Alpha haemolytic
Oropharynx, gastrointestinal tract and genitourinary tract. Commensales of mouth flora.
Virulance factors: some carry adhesins/pilli for binding to teeth, biofilm
Disease: dental caries, bacterial endocarditis, septic shock in immunocompromised patients
Streptococcus pneumoniae
Diplococci or short chains, most strains have outer capsule.
Pharynx -> lungs -> sinuses, ears
conditions that interfere with bacterial interference at risk
capsule, and pneumolysin - destroys ciliated epithelial cells
Disease: pneumonia, menigitis, bacteremia, sinusitis and otitis media
Alpha haemolysis
Infiltration of neutrophils and macrophages
Symptoms: Fever, yellowish sputum, chest pain
Cholera: vibrio cholerae
general info
Gram negative: comma shaped rod
Cholera: Source
Source: contaminated water, contaminated by faeces
Reservoir = shellfish in coastal water
Cholera: Route of transmission
Route of transmission: drinking water contaminated by faeces of infected individuals. Other contact with faeces of infected.
Cholera: risk factors for infection
Risk factors for infection: poor hygiene and sanitation
Cholera: key virulence factors
Key virulence factors:
Colonisation: Flagellum, Type 4 pilus
Damage: Cholera Toxin
Cholera: progression of symptoms
Progression of symtoms: Vomiting then profuse watery diarrhoea
Cholera: Identification and diagnosis
Sample tested: stool
Microscopy: Gram negative comma shaped rod
Culture: yellow coloured (sucrose fermenting) colonies of Thiosulfate-citrate bile salts sucrose (TCBS) agar
Cholera: treatment options
Oral rehydration (salt,sugar water) or IV fluids if serious
Antibiotics: Doxycycline (cheap), reduces shedding. Not a huge effect on symptoms and duration of disease
Cholera: prevention options
Provide clean water and effective sanitation. Antiobiotics may reduce bacterial shedding. There is a vaccine, variants of the inactivated oral vaccine are currently in use. live attenuated vaccine also approved
Campylobacteriosis: causative agent
Campylobacter jejuni
Campylobacteriosis: source
Gut bacteria found in faeces from farm animals and birds. Most commonly attributed source is chicken
Campylobacteriosis: route of transmission
faecal/oral route
Campylobacteriosis: Risk factors for infection
eating undercooked chicken and other contaminated food or water. Immune deficiencies for more serious invasive diseases.
Campylobacteriosis: key virulence factors
Colonisiation: flagellae, outer membrane adhesins
Immune evasion: Lipooligosaccharide mimicking our molecules
Damage: cytolethal distending toxin increases water secretion, cholera-like toxin leads to cell death
Campylobacteriosis: progression of symptoms
Intestinal colonisation, leading to diarrhoea, inflammation and abdominal pain.
Sequellae: molecular mimicry can lead to immune cross-reactivity at joints (reactive arthritis) and nerves (Guillain Barre syndrome)
Campylobacteriosis: sample tested
Stool, blood in rare cases of invasive diseases
Campylobacteriosis: microscopy
Gram-negative rod, seagull shape
Campylobacteriosis: Culture
CAMPY agar, blood agar base with antiobiotics to inhibit other faecal bacteria. Incubate in microaerophilic conditions
tCampylobacteriosis: Treatment options
Keep hydrated, pain relief
Antiobiotics: yes , severe ,azithromycin, erythormyin especially if prolonged or at risk of invasive disease
Campylobacteriosis: prevention options
Cook food properly, control carriage in farm animals. No vaccine
Clostridioides difficile: causative agent
Clostridium difficile
Clostridioides difficile: general info
endospore forming, anaerobic, gram positive rod. Primarily problem in hospital patients
Clostridioides difficile: source
Human gut flora
Clostridioides difficile: route of transmission
Faecal/oral route between people
Clostridioides difficile: risk factors for infection
Broad spectrum antibiotics and other treatments that disrupt the gut flora
Clostridioides difficile: virulence factors
Colonisation: endospores
Damage: two similar c.difficile toxins
Clostridioides difficile: progression of symptoms
Watery diarrhoea, pseudomembranous colitis, then toxic megacolon in worst cases
Clostridioides difficile: sample tested
stool
Clostridioides difficile: microscopy and culture
Not useful as people can be colonised without infection
Clostridioides difficile: toxin testing
Immunodiffusion test for toxin in stool, sometimes immunodiffusion for cell antigens and PCR for toxin genes
Clostridioides difficile: treatment options
Rehydration and pain relief
Antiobiotics: discontinue precipitating antiobiotics. Treat Cd with metronidazole or vancomycin.
If very severe, may need surgery to remove colon
Clostridioides difficile: prevention options
Good hygiene, especially patient toilets, restrict risk antiobiotics. No vaccine
Clostridioides difficile: why relapse
endospores not killed by antibiotics, can lie dormant.
Prevented by restoring normal gut flora. e.g using transplant of gut bacteria from healthy individuals
Most common cause of microbial cause of diarrhoea in NZ
Camplybacteriosis
Clostridioides difficile: mutation
Europe, australia. Resistant to fluoroquionlones, produces more toxins A and B because of a mutation in a toxin repressor gene and exhibits a higher rate of sporulation
Major causes of community acquired UTIs
E.coli most common. Proteus mirabilis, Klebsiella pneumoniae and Staphlococcus saprophyticus
Major causes of hospital acquired UTIs
E.coli, Enteric bacteria (Klebsiella) , Proteus, Staphylococci, Pseudomonas, Enterococci
UPEC: general info
Uropathogenic Escherichia coli (UPEC). Oxidase negative, gram negative rod.
UPEC: source
Colonic flora of patient
UPEC: route of transmission
Faecal matter to vagina/urethra
UPEC: risk factors for infection
Being female, (shorter route), previous UTI, antibiotics that deplete competitive vaginal flora, poor hygiene, anatomical conditions
UPEC: virulence factors
Colonisation: pilli, type 1, for colonisation of bladder, pap pilli for kidneys
Immune evasion: invasion of bladder mucosa
Proliferation: Siderophores for iron acquisition
Damage: LPS for inflammation, toxins, (Cytolysins, contribute to immune cell killing)
Progression of symptoms: Cystitis (urinary bladder infection, urgerncy, frequency, hesitation, dysuria), maybe blood in urine. Pyelonephritis (more serious kideny infection) key new symptom of flank pain (pain higher up)
UPEC: identification and diagnosis of cystitis
sample tested
urine
UPEC: identification and diagnosis of cystitis
Microscopy
G-rods, neutrophils
UPEC: identification and diagnosis of cystitis
Culture:
CLED agar (yellow colonies); MacConkey agar red colonies with zone of precipitations > 105 CFU/ml
UPEC: identification and diagnosis of cystitis
Further tests:
MALDI-TOF (biochemical tests to distinguish from other lactose fermenters). Urine dipstick Nitrite (bacteria in urine). Leukocyte esterase (WBC in urine)
UPEC: cystits
How can we treat the symptoms
Fluids, pain relief
UPEC: Cystitis
Antibiotics:
Probably, but if mild may not be needed. Trimethoprim, Sulfamethoxazole and Trimethoproim, fluroquinolones
UPEC: Cystitis
Options in most severe cases
Fluids, pain relief, antibiotics
UPEC: cystitis
Prevention options
Fluids, go to toilet, good hygiene, various remedies that work some people
UPEC: pyelonephritis
Sample tested:
Add blood to samples tested
UPEC: pyelonephritis
Microscopy: Culture: Further tests:
As cystitis
UPEC: pyelonephritis
Antibiotics
Yes, need to kill infecting bacteria before do damage to kidenys
UPEC: pyelonephritis
Prevention options
Effective treatment of cystitis
Hospital acquired UPEC
Source:
Patients colonic flora
Hospital acquired UPEC
Route of transmission
Bacteria from faecal matter travels via catheter to bladder
Hospital acquired UPEC: Risk factors for infection
Urinary catheter, with risk increasing each day
Hospital acquired UPEC: key virulence factors
As cystitis
colonisation: biofilm forms on catheter
Hospital acquired UPEC:
Progression of symptoms
As cystitis, but patient may be less likely to notice as not going to toilet. Bad and urine collected will be cloudy
Hospital acquired UPEC: sample tested
Urine collected, catheter tip, blood
Hospital acquired UPEC: Treatment options
Remove catheter, fluids, pain relief
Hospital acquired UPEC: antibiotics
Yes
Hospital acquired UPEC: Prevention options
Remove catheter when not needed
Mutations: E. coli UTI
E.coli and other members of the enterobacteriaciae carry plasmids with antibiotic resistance specifically to penicllin, cephalosporin and in some carbapenemases. Some hospitals have a large problem with these bacteria, and screen patients on admision so colonised patients, can be segregated from uncolonised patients. Treat with polymyxin B or E.
Monitor renal toxicitiy to polymyxin.
How does Ebola work?
- Attachment of glycoprotein to TIM-1 receptor on epithelial cells lining respiratory tract, conjuctiva around eyes, skin or body.
- Pentration: Viral envelope fuses with host cell, passes into cytoplasm
- Uncoating: Viral envelope releases nucleic acid. Polymerase protein turns negative-sense RNA into postive sense mRNA template.
- Translation: mRNA uses host-cell systems to replciate viral RNA
Ebola: source
From bats to animals to humans
Ebola: symptoms
Fever, headache, weakness, sore throat, joint and muscle pains
followed by vomiting, diarrhoea, stomach pain, impaired kidney and liver function
sometimes: both internaly and external bleeding, sometimes rash, red eyes and hiccups.
Ebola: mortality rate
25-100%
Ebola treatment:
Monoclonal antibodies, fluids and electrolytes, support other infections and symptoms
Vaccination but not that effective
Main cellular properties of yeasts
Germ tube, pseudohypa, hypa
Germ tube forms in less that 2hrs in serum broth for candida albicans
Main cellular properties of moulds
Conidia used in asexual reproduction
Ascophore used in sexual reproduction
Skin infections associated with yeasts and moulds
Ringworm and tinea
Dermatophytes: microsporum, trichophyton, epidermophyton
Mucosal infections associated with yeasts and moulds
Thrush
Candida albicans
Invasive infections associated with yeasts and moulds
Sepsis, meningitis, pneuomonia
(SiMP)
Candida, Cryptococcus, Aspergillus
Yeasts and moulds associated with exacerbation of asthma
Penicllium, Aspergillus, Cladosporium
Mechanism of the antifungal drug Azole
FLU inhibits ergosterol biosynthesis resulting in depletion of this sterol in the cell membrane
Mechanism of the antifungal Polyene
Pore/channel fomred in Arn8 results in cell death
Mechanism of the antifungal Candins
Candin inhibits fungal glucan synthase
Mechanism of antifungal 5-Fluorocytosine
Inhibition of protein and DNA synthesis
Cutaneous mycoses (Fungal): source
Humans (trichophyton and epidermophyton) and Animals, esp Pets (Microsporum)
Cutaneous mycoses (Fungal): route of transmision
direct contact, sometimes via fomties
Cutaneous mycoses (Fungal): risk factors
small abrasions, humidity, diabetes
Cutaneous mycoses (Fungal): symptoms
Itchiness, distinctive appearance
Cutaneous mycoses (Fungal): identification and diagnosis
Microscopy and agar growth. May fluorescence under black light (UV-A)
Cutaneous mycoses (Fungal): sample tested
hairs, skin scraping from infected areas
Cutaneous mycoses (Fungal): treatment options
Antifungal creams and systemic treatment for severe cases or onychomycosis (nail infection). Imidazoles and synthetic allyamines
Cutaneous mycoses (Fungal): prevention options
Infection can be avoided by lifestyle and hygiene modifications such as avoiding walking barefoot on damp floors particularly in communal areas. Avoid contact. Dry between toes. Treat ringworm in pets and avoid contact. Avoid or prevent chaffing.
Candidiasis/thrush (Fungal mucosal infection): source
mucosal flora
Candidiasis/thrush (Fungal mucosal infection): route of transmission
contact with carrier (overgrowth, a dysbiosis)
Candidiasis/thrush (Fungal mucosal infection): risk factors
antibiotic use depleting competitive flora, immunosupression
Candidiasis/thrush (Fungal mucosal infection): identification and diagnosis
microscopy (germ tube/ hypae); selective agars, e.g CHROMagar Candida (green/blue colonies)
Candidiasis/thrush (Fungal mucosal infection): sample tested
Swab/scrape
Candidiasis/thrush (Fungal mucosal infection): Treatment options
Nystatin (oral suspension); Imidazole (lozenge, suppository, pessary); fluconzaole (DiFlucan)
Candidiasis/thrush (Fungal mucosal infection): prevention options
Prophylactic drug, espeically if in risk group/recurrent
Invasive aspergillosis (Fungal systemic): source
soil, compost, built environment growth of mould
Invasive aspergillosis (Fungal systemic): route of transmission
airborne conidia
Invasive aspergillosis (Fungal systemic): Risk factors
Previous lung infection, immunosuppression (transplant, HIV cancer treatment)
Invasive aspergillosis (Fungal systemic): symptoms
lung infection, possible spread to other organs (pain and loss function effects)
Invasive aspergillosis (Fungal systemic): identification and diagnosis
Microscopy, culture, PCR, Galactomannan EIA
Invasive aspergillosis (Fungal systemic): Sample tested
Biopsy
Invasive aspergillosis (Fungal systemic): Treatment options
IV imidazoles (voriconazole)
Invasive Candida (Fungal systemic): source
mucosal infection, injected drugs
Invasive Candida (Fungal systemic): Route of transmission
penetrate weakened mucosal defences, injected
Invasive Candida (Fungal systemic): Risk factors
Immunosuppresion, IV drug use (can also cause damage for yeast to easily colonise)
Invasive Candida (Fungal systemic): symptoms
Sepsis
Invasive Candida (Fungal systemic): Sample tested
Blood/biopsy
Invasive Candida (Fungal systemic): Treatment options
Fluconazole, alternative is echinocandin
Invasive Candida (Fungal systemic): Prevention options
Treat mucosal infection, discourage drug use
Crytococcal meningitits (Fungal systemic): source
basidospores in bird (pigeon) faeces
Crytococcal meningitits (Fungal systemic): Route of transmission
aerolised basidospores
Crytococcal meningitits (Fungal systemic): Risk factors
contact with source, immunosuppresion
Crytococcal meningitits (Fungal systemic): Identification and diagnosis
microscopy (encapsulated yeast), culture, crypotococcal antigen test (EIA)
Crytococcal meningitits (Fungal systemic): Sample tested
Sputum for lung colonisation, CSF (meningitis)
Crytococcal meningitits (Fungal systemic): Treatment options
Amphotericin B (intrathecal), 5-flurocytosine (IV or oral) but may be toxicity issues
Crytococcal meningitits (Fungal systemic): Prevention options
avoid contact with source
Exacerbation of conditions Asthma: Source, aeitology, prevention options
Growth in homes, allergic reaction to inhaled conidia, good quality housing
General STI transmission
Require intimiate contact for transmission
Require persistent infection to allow for occasional opportunites for transmission
May remain as local infection or may disseminate
May be an important cause of neonatal disease
Important bacterial STIs
Chlamydia, Gonorrhoea, Syphillis
Important Viral STIs
Human papilloma virus, Herpes simplex, HIV
Important fungal STIs
Candidiasis
Important Protozoal STIs
Trichomonas
Urethritis
Inflammation of urethra, can be purulent
Cervicitis
Inflammation of cervix, can be purulent
Epididymis complications
Inflammation of epididymis, chronic pain, infertility, hypogonadism, defective hormone production
Pelvic inflammatory disease
Inflammation of uterus, fallopian tubes, ovaries
Chronic pelvic pain, ectopic pregnancy, infertility
Gonorrhoea: causative agent
Neisseria gonorrhoeae, second most prevalent bacterial STI
Gonorrhoea: transmission
Transmitted during vagina, oral and anal sex
Female to male = 20% / episode
Male to female = 50% episode
Can be passed to baby during childbirth
Gonorrhoea: asymptomatic
>50% woman
~5% men
Gonorrhoea: symptoms
Pain and inflammation/burning during urination
If untreated can lead to systemic dissemination
Skin pustules
Septic arthritis
Meningitis
Endocarditis
Pelvic inflammatory disease
Septic abortion
Infertility
Gonorrhoea: is it notifiable?
Yes, rates higher than UK and Australia
Gonorrhoea: treatment
Penicillin initially very effective (MIC < 0.01mg/L)
Accumulation of mutations in porins, acquisition of gene for new transpeptidase made it resistant
Plasmid with gene for beta lactamase too
Ciprofloxacin treatment initally very effective
Recommended treatmnet = Intramuscular ceftriaxone with oral azithromycin
Gonorrhoea: coinfection
20% of heterosexual men also have chlamydia
40% of heterosexual women also have chlamydia
Syphilis: causative agent
Treponema pallidum
Syphilis: is it notifiable
Yes
Syphilis: initial infection
Chancre (painless ulcer that heals spontaneously)
Syphilis: secondary disease
If untreated develop secondary disease in 2-8 weeks. Bacteraemic dissemination = widespread rash
Rash, fever, malaise, aseptic meningitis, hepatitis, etc
Relapses then “recovery” over 1-4 years
If untreated 1/3 develop tertiary disease years later, small vessel vasculitis = inflammation of blood vessels affecting brain and aorta
Syphillis: pregnancy
Untreated syphilis during pregnancy always results in foetal infection. Half of pregnancies will end in miscarriage or stillbirth
Syphilis: treatment
Penicillin - no resistance
Effective blood level required for at least 7 days
Intramuscular benzathine penicillin
Penicillin G IV for 10 days
Chlamydia: causative agent
Chlamydia trachomatis
Chlamydia: two diffferent classification
A-K serovars classified by prominent outer membrane protein ompA
Occulogenital strains infect epithelial cells of either genital tract or inner eyelids
Chlamydia: LGV
Lymphgranuloma venereum (LGV) - infect macrophages, spread through lymph nodes. Predominantly gay sex, buboes in groin. Protocolitis (inflammation) of colon and rectum
Chlamydia: Genital serovars
Transmitted through vaginal, oral and anal sex. Can be passed during childbirth.
>70% of women asymptomatic
~25% of men asymptomatic
Chlamydia: treatment
Single dose of azithromycin, or doxycycline 100mg twice daily for 7 days
Chlamydia: untreated women
If untreated can lead to pelvic inflammatory disease in ~50% of asymptomatic women. = infection of uterus, fallopian tubes, ovaries, chronic pelvic pain, ectopic pregnancy, infertility
Chlamydia: untreated neonates
Conjunctivitis and potentially blindness and pneumonia in babies born vaginally to infected women
Chlamydia: untreated men
Pain, swelling, inflammation of epididymis and testes, urethritis, reactive arthritis and infertility
Chlamydia: elementary body
metabolically inactive but highly infectious
Chlamydia: reticulate body
metabolically active and replicative form
Chlamydia: cycle of bodies
Reticulate body begins to divide, T3SS needles penetrate inclusion membrane to secrete effectors. Infectious elemenary boides escape by cell lysis or extrusion to initiate new infection. Reticulate bodies diffrentiate back into elementary bodies
Tuberculosis: causative agent
Mycobacterium tuberculosis
Tuberculosis: most commonly presents
Most commonly presents as a lung disease but can become disseminiated throughout the body
Tuberculosis: General information
Complex lipid-rich cell wall
Acid fast bacilli (AFBs)
Grows very slowly
Resistant to common antibiotics
Lives inside macrophges
Tuberculosis: transmission
Bacilli inhaled as droplets
droplets survive for hours
Infectious dose is <5 bacilli
Droplets settle in alveolus
Tuberculosis: Granulomas
Bacilli are engulfed by alveolar macrophges. Infected macrophages recruit additional macrophages and other immune cells to form organised structures called granulomas. Believed to require adaptive immunity.
Tuberculosis: Why are granulomas important?
For restricting bacterial expansion
Tuberculosis: what happens?
Most infections are asymptomatic
10% lead to active disease
Actove disease is when bacteria are infectious
If untreated death rate is 50%
Tuberculosis: Symptoms
Quartet of symptoms: weight loss, night sweats, fever, malaise
(We never fuck mums)
Tuberculosis: Who gets the disease?
2 billion people infected
>10 million active cases
>9 million new cases/year
>1.3million deaths/year
Tuberculosis: HIV
20x more likely to get TB, 10% of TB cases are HIV+.
Major benefits of Anti Retroviral Therapy (ART) in terms of TB risk and mortality
Tuberculosis: Risk factors
Born outside NZ, reside with someone who was born outside NZ
Tuberculosis: Vaccination
M. bovis Bacille Calmette Guerin (BCG)
Derived from virulent isolate of bovine tuberculosis
Lost important virulence factors
Efficacy ranges 0-80%,
only effective during childhood
Risk of disseminated infection in HIV+ infants (BCGosis)
Tuberculosis: Diagnosis, Chest x-ray
Cloudiness (granulomas) and caving formation seen
Cheap but can’t tell if they’re infectious
Tuberculosis: Diagnosis, microscopy
Ziehl-Neelsen sputum stain
Tuberculosis: Diagnosis, Gene Xpert
PCR based, Detects organism in sputum, detects resistance markers
Tuberculois: interferon testing
Detect release of interferon by lymphocytes in reponse to mycobacterial antigens. Can’t distinguish between latent infection and disease
Tuberculosis: Mantoux test
Tuberculin, purified protein derivative, cell wall extract of Mtb
Lymphocytes in person previously exposed will migrate causing lump.
>5mm = +
Can’t distinguish between vaccination and infection
Tuberculosis: Quantiferon Gold testing
Tube with Mtb specific antigen, add patient blood, lymphocytes previously exposed to Mtb will release interferon. Can’t distinguish between latent and old infection
Tuberculosis: Treatment
Multidrug regiments for 6 months to stop resistance emerging
Two month intensive phase:
Isoniazid, Rifampicin, Pyrazinamide, Ethambutol
(I really pluck eggs)
Four month continuation phase:
Insoniazid, Rifampicin
Tuberculosis: MDR
Resistant to isoniazid and rifampicin, mainly from India, China and Russia
Tuberculosis: MDR treatments
Group A first, then B, then C
Tuberculosis: XDR TB
Pre-XDR-TB = resistant to rifampicin and any fluroquinolone
XDR-TB = resistant to rifampicin, any fluroquinolone, and at least one of bedaquiline or linezolid
Tuberculosis: Control
Eliminate poverty, control animal TB, isolation of infectious patients, Better diagnosis, faster drug treatment with more tolerable drugs
Tuberculosis: COVID
TB decreased since COVID pandemic
Louis Pasteur
Pasteur was able to show that air contained spores of living organims
When placed into nutrient broth the organisms reproduced
When he now boiled the broth in a special swan necked contained that allowed air but kept dust out the broth remained free of organisms
This simple experiment helped disproved the theory of spontaneous generation
Bacterial growth Kinetics
Check image on desktop
Obligate aerobes
Required O2, no fermentation, e.g mycobacterium tuberculosis
Obligate anaerobes
cannt survive in presence of oxygen (e.g clostridium tetani)
Facultative anaerobes
can metabolise energy aerobically (respiration) or anaerobically (fermentation). Prefer O2 as more ATP is produced, e.g E.coli
Microaerophiles
Require oxygen (no fermentation), but cannot survive in higher concentrations of O2 (e.g Helicobacter pylori)
Aerotolerant bacteria
cannot ulilise O2 (fermentation only) but are not harmed
Cell wall morphology
Check images
Indigenous microflora
All micobes (bacteria, fungi, protozoa) that reside on or within a person
A fetus has no indigenous microflora
Bacteria on our skin
1 trillion
most common: Staphylococcus, Streptococcus and Corynebacterium
Metabolise sweat to produce body odor
Oral streptococci
Biofilms of bacteria 300 to 500 cells thick on surface teeth
Dental plaque (mostly Streptococcus sanguis and S.mutans)
Firmicutes and Bacteroidetes in the gut
>>500 species of bacteria, weighing about 3.3 pounds
They break down carbohydrates, make essential nutrients like
vitamins K & B12 and crowd out harmful bacteria
Vaginal flora
beneficial bacteria (Lactobacillus family)
Secrete lactic acid (protect against hostile invaders like the pathogenic yeast Candida albicans (vaginal thrush)
HPV
Persistent (latent) virus infections
virus lies dormant within the cell
>100 types can infect humans, causing a variety of warts
other viruses, herpes virus, chickenpox virus
Fossil viruses
about 1/12 of our genome consists of stretches of DNA from viruses that infected our ancestors millions of years ago
Symbiosis
organsims in live together in close association
Mutualism
beneficial to both symbionts
Neutralism
neither symbiont is affected by relationship
Commensalism
beneficial to only one symbiont
Parasitism
harmful to one symbiont (host), beneficial to other symbiont (parasite)
Synergism
two or more microorganisms “team up” to cause disease. Synergisitic or polymicrobial infection
Pathogen
Microorganism that cause disease <3%
Opportunistic pathogen
has the potential to cause disease
Bacterial portals of entry
See folder
Koch’s postulates
The microorganism must always be found in similarly diseased animals but not in healthy ones
The microorganism must be isolated from a diseased animal and grown in pure culture
The isolated microorganism must cause the original disease when inoculated in a susceptible host
The microorganisms must be re-isolated from the experimentally infected animals
Koch’s postulate - revised
Original postulates were based on cholera and TB
P1: should be abandoned, as some organisms can be carried asymptomatically
P2: some organisms cannot be grown in culture
P3: ‘must’ is replaced by ‘should’ as infection by certain organism does not always cause disease
Incubation period
time between infection and onset of symptoms
Prodomal period
Patient feels out of sorts, but no disease symptoms
Illness
Experience of symptoms associated with disease
Convalescent period:
time during which patient recovers
Passive carrier
Never had the disease
Incubatory carrier
during incubation period
Convalescent carrier
recovering from disease
Active carrier
completely recovered
Localised infection:
pathogens are contained at site of infection (e.g abscess)
Systemic infection:
pathogen spreads throughout the body
Acute infection
rapid onset and rapid recovery
Chronic infection
slow onset and slow recovery
Latent infection:
Pathogen not completely eradicated after recovery and can cause symptoms in future
(ex. herpes, chickenpox, tuberculosis,…)
Secondary infection:
Disease that follows primary infection (ex pneumonia after mild respiratory infection)
Infectious disease vs microbial intoxication
Check folder
Staphylococcus aureus: Treatment
Penicillin/amoxicillin - work well against Streptococcus pyogenes, but most S.aureus are resistant
Augmentin - amoxicillin plus B-lactamase inhibitor
Flucloxacillin - B lactamase resistant penicillin, works well against S.pyogenes and S.aureus except MRSA
Vancomysin: used against MRSA (avoid use against MSSA to prevent development of resistant strains (‘last resort drug’)
Invasin
intracellular growth
resistance to antiobiotics
protection from immune system
Cytolysins
Destroy ery, leukocytes and tissue cells
access to nutrients
immune evasion
bacterial spreading
B-lactamase resistant penicillins
Methicillin, oxacillin, flucoxacillin
Cluvanic acid: B-lactamase inhibitor
Augementin = amoxicillin + clavulanic acid
S.aureus: Corneal ulcer
Deep infection of the cornea
Usually after abrasion e.g contact lenses
Can be caused by S.aureus, but also several other bacteria, viruses and fungi
Outbreak
sudden increase in occurence
Pandemic
Outbreak that has spread across a wide region
Endemic
Cases at a baseline level in a geographic area
R0
Infectiousness, determined by organism, dose, route of tranmission
Reff
Effective R, take into account public health measures like vaccination
Infection fatality rate
Estimated deaths as a proportion of all infected
Case fatality rate
Death as a proportion of confirmed cases
How is Ebola spread?
Bodily fluids of a person who is sick or has died from Ebola
Objects contaminated with the virus
Infected animals
