Medical Microbiology Flashcards
What is the reporting triangle?
How many people does ARI’s diagnostic bacteriology lab serve? How many specimens per year?
530000 people, 700k specimens per year
What do medical microbiologists do?
Advice on diagnosis of infection, supervision and review of lab tests, advice on test result interpretation, advice on treatment/management, infection control/prevention advice, antibiotic policy
What are possible infecting agents? [5]
Bacteria, viruses, fungi, parasites, prions
Taking specimens: what are sterile and non-sterile sites?
What’s the difference?
Sterile: blood, CSF, lung, bladder, Non-sterile: skin, nasopharynx, urethra, gut
Sterile: shouldn’t be any organisms in these sites, Non-sterile: commensal flora abounds (and can even cause problem)
Microscopy: what can you do?
What can you definitely not see?
Unstained (see pus cells, parasites, etc), gram stain (see bacteria, yeast/fungi), ZN or auramine stain (see mycobacteria and other strains)
Can’t see viruses (only x1000 magnification)
Bacterial culture: types of media?
How else could you identify bacteria?
Non-selective (eg: blood, chocolate), selective (eg: MacConkey - enteric gram negative microbes)
Genetic typing (Should be: Transferable, Reliable, Able to discriminate different strains, Cheap, Effort required low, Standardized lab methods/interpretation)
Typing Methods Picture: What methods are there (phenotypic and genotypic)?
Biochemical sugar fermentation strip: how does it work?
What about enzyme reaction plates?
Strip containing various kinds of sugar in separate compartments. Innoculate strip with microorganism. If it can use sugars, it will, and the colour will change from red to yellow/orange. Depending on the result, you get a different seven digit ID, which can then be used to ID strain.
Special plates where different microbes will grow with different appearance (eg: a chromogenic substrate which makes E coli grow purple, and other coliforms grow pink) [eg: to identify altered transgenic strains]
How does serotyping work?
What about phage typing?
Targets antigenic variations on the cell surface with specific antibodies (eg: salmonella strain testing kit - different spots with different antibodies, will attach and be visible in appropriate spots)
Innoculate bacteriophage onto lawn of bacteria, and look for areas of lysis (if you know which bacteria the phage virus will attack, you can ID it based on what gets attacked) [old fashioned]
How would you ID viruses nowadays?
Other methods?
real time PCR (RNA/DNA viruses)
Antigen detection, serology to determine immunity, cell/tissue culture, electron microscopy (not really anymore)
Big issues relating to healthcare acquired infections?
MRSA, clostridium difficile, organisms with extended spectrum beta-lactamases (ESBLs), noroviruses
What are the signs and symptoms of clinical infection? [7]
Inflammation, pain, pyrexia (raised temp), tachycardia (fast HR), rigors (cold shivering despite raised temp), increased white cell count, increased C Reactive Protein
What’s the difference between a pathogen and a commensal?
What were Koch’s postulates in relation to whether something is a pathogen?
What is pathogenicity?
Pathogen is organism that can cause disease, commensals are part of natural flora (but can become pathogenic)
Organism must be found in all cases of disease, must be culturable outside of body for several generations, and should reproduce disease on inoculation
Capacity of microorganism to cause infection
Pathogenicity = Capacity of microorganism to cause infection. What is needed for something to increase its pathogenicity?
Infectivity (ability to become established), virulence (ability to cause harmful effects once established)
Give examples of things that increase the infectivity (ability to become established) of a microorganism
Attachment (eg: E Coli w/fimbriae that attach to receptors on uroepithelial cells), acid resistance (eg: heliobacter pylori produce urease that converts urea to ammonia, which is basic)
Virulence (capacity to cause harm once established) is conferred by virulence factors. What are these? Give three examples
Genetically determined microbial components.
Invasiveness: streptococcus pyogenes causes necrotising fascitis, cellulitis, connective tissue breakdown, and fibrinolysis (helps microbe invade other tissues)
Toxins [exotoxins released by microorganism, called enterotoxins if they act on GI tract, endotoxin is part of gram negative cell wall]: vibrio cholerae causes cholera (increases cAMP, inhibits Na/Cl uptake, upregulates Cl/HCO secretion, causes loss of water in poops)
Evasion of immune system: exotoxins of strep pyogenes and staph aureus stimulate division of T cells -> overwhelming cytokine production causes toxic shock
Gram positive: two important kinds? Different appearance?
Staphylococci (clusters of grapes), streptococci (chains of grapes)
Staphylococci: what test is used to identify staph aureus in particular? What if it is negative (and can they also be a problem)?
Why is staph aureus commonly penicillin resistant? Does this also provide resistance to methicillin?
Coagulase test (Positive = MRSA/MSSA)(Negative = many species inc. skin commensals, can be pathogenic in presence of foreign bodies [eg: valves/wires piercing skin, implants, etc] or when immunocompromised
Has beta-lactamase enzyme (that cuts beta-lactam ring). No - resistance to methicillin is provided by a different mechanism
How do you differentiate streptococci (3 possible types)?
Alpha-haemolytic (partial haemolysis - turns blood agar green), beta-haemolytic (complete haemolysis - turns blood agar clear), non-haemolytic (no change)
Give some examples of alpha-haemolytic streptococci
Streptococcus pneumoniae (causes pneumonia, meningitis, septicaemia), viridans streptococci (many species, normal oral flora, cause of infective endocarditis [heart valves])
How are beta-haemolytic (complete haemolysis - blood agar clear) streptococci further identified? Give examples from most clinically relevant groups.
Lancefield groupings (based on surface antigens): A-G (A, B, and D most clinically relevant)
A: strep pyogenes (sore throat, cellulitis, necrotising fasciitis)
B: strep agalactiae (neonatal sepsis, commonly (25%) carried in genital tract)
D: Enterococcus spp - e faecalis/faecium (gut commensal - causes UTIs)
Gram positive bacilli can be _______ or _________
Give three clostridium species names, and details
aerobic, anaerobic
C. Perfringens (soil/gut commensal, can cause food poisoning/gangrene of wounds)
C. Difficile (can be carried asymptomatically, can also cause squits and toxin production, often invades after antibiotic use)
C. tetani (toxins cause tetanus [uncontrolled muscle spasm due to loss of inhibition at neuromuscular junction])
What strains (gram positive bacilli) have been used for biological warfare?
Clostridium botulinum (also for botox), bacillus anthracis (anthrax- can also catch via exposure to infected animals/animal products)
