Investigation of infection Flashcards
How do you approach a patient with infection?
- history - tells you where to start focusing
- clinical examination
- general investigations - fbc, u+e, crp, lft etc
- microbiology investigations
All tests have false positives + false negatives, the predictive values depend on prior probability/prevalence - this was the case with C. Diff testing few years ago, over half of positives weren’t actually positives - be a “healthy sceptic”
What is the chain of investigation?
- Pick specimens - test with consent
- Transport to lab - urgent? bedside easier?
- Analysis in the lab
- Reporting from lab - telephone + electronic
- Guidance for clinician + patient - electronic + in person
- If you send test, you must check the result (or get someone else to do it for you)
If in doubt and you get stuck, ring up the microbiologist for advice
Give examples of microbiology investigations?
- Microscopy
- Culture
- Antigen detection
- Nucleic acid detection
- Antibody detection
What are the 5 microbes?
- Bacteria
- Viruses
- Fungi
- Protozoa
- Helminths
What 2 things do microbiology lab tests depend on when studying infection?
- The organism’s microbiology
- Lab methods available
What microbiological tests can be done for Staph aureus?
- Microscopy v good
- NAT/PCR good
- Culture v good
Sputum sample best for bacterial infections
What microbiological tests can be done for Treponema pallidum?
- Microscopy
- NAT/PCR
- Antibody (preferable)
What microbiological investigations are best for viruses, eg. Hep C?
- NAT/PCR
- Antibody testing
- Antigen testing to lesser extent
Blood sample best sent for viruses
How could you test for fungi microbiologically, eg. yeast (Cryptococcus)?
- Antigen
- Culture
- Microscopy
- NAT
What microbiological investigations are best for an abscess?
- Aspirate pus (not a swab)
- Gram directly
- Culture + sensitivity
What does this picture show?
- Blood agar haemolysis
- streak out bacteria to get to a single colony
- whatever this colony is, is lysing the red cells
- so haemolytic
- gram it -> can see it’s gram-positive cocci in chains
- must be streptococcus -> beta-haemolytic strep
- take organism, and stick it on another plate
What does this image show?
- previously identified bacteria stuck on another plate
- streak all across plate
- pluck on little discs, which have antibiotics in them
- over few hours, abx soak up into agar plate
- diffuse down gradient, the further away from disc the less abx conc
- can see which antibiotic is stopping bug from growing
- can identify whether sensitive or resistant
- this tends to be ~48hrs later (too long!), culture + sensitivity take time
What microbiological investigations would you do for suspected endocarditis?
- look at eyes, palms + toes
- look for bacteria (stuck on heart valve)
- 3 x blood cultures
- do ECHO
- follow Duke’s criteria (scoring system for endocarditis)
- antibody for culture negative
- look for Q fever + Bartonella
- if bad enough to need surgery, take valve out, then PCR vegetation -> find “valve 16s RNA” -> can get a species ID
What microbiological tests do you do for meningococcal meningitis?
- infection is in CNS, spread from blood
- send culture samples for: blood, CSF or throat
- microscopy of CSF (gram)
- NAD/PCR: blood, CSF
- Antigen detection: CSF
- Antibody detection
Describe the process of PCR
- Obtain target sequence from genomic DNA
- Denaturation: heat briefly to separate DNA strands
- Annealing: cool to allow primers to form H bond with ends of target sequence
- Extension: DNA polymerase adds nucleotides to the 3’ end of each primer
- Cycle 1 yields 2 molecules, cycle 2 yields 4 molecules etc
How do you test for mycobacterium?
- ZN stain (red) on sputum/pus
- PCR on sputum if smear positive/CSF
- Liquid culture + LJ slopes
- Role of IGRA being assessed - cell mediated
What is meant by category 3 pathogens?
- duty to warn lab staff - “danger of infection”
- eg. TB, typhoid
- if suspected, query/label the sample of risk!
What do we do with E Coli infection?
- culture stool on sorbitol macconkey agar
- bile salts select E coli
- E coli O157 most common strain
- Verotoxin gene probe
What microbiology tests can you do to diagnose/confirm Varicella virus?
- vesicle fluid - PCR
- viral swab - culture
- serum Varicella-Zoster IgM
What microbiology tests can you do to test for Herpes Simplex virus?
- vesicle fluid - PCR
- viral swab - culture
What microbiological tests are appropriate for diagnosis of HIV?
- antibody testing - screening test (EIA), confirmatory test + repeat (EIA)
- viral load (NAAT) - quantification of virus in blood
- resistance testing (sequencing) - look for mutations known to confer resistance
What is the temperature and duration constituating pyrexia of unkown origin?
- T > 38.3
- > 3 weeks
What are the causes of pyrexia of unknown origin?
- Infections (tb, infective endocarditis, abscess)
- Neoplasm (lymphoma)
- Connective tissue disorders (temporal arteritis, sarcoid, SLE)
- Others (factitious)
