diagnostics Flashcards
why do we want/need to identify the species of a pathogen causing disease? (3 things)
1- use appropriate antibiotics (if needed)
2- anticipate possible sequelae
3- epidemiological surveillance
what are specimens?
clinical patient samples that contain tissue or fluid for microbe testing
which specimens come from sterile sites?
Blood, CSF, Urine, pleural fluid, peritoneal fluid, internal organ tissues
which specimens come from non-sterile sites?
skin, wound abscesses, nose, lung contents
why does the specimen need to preserve the state of the sample?
if the microbe growing within a certain characteristic (aerobic/anaerobic) you would want to preserve that to have accurate results
consider why we collect blood via venipuncture
venipuncture collects blood directly from the vein into an aerobic or anaerobic culture tube (to preserve the state) it also keeps blood sterile.
why is a pH-sensitive sensor used to check for growth?
it glows if bacterial growth has occurred (which should not happen since blood is mostly sterile)
what is the procedure that collects CSF?
Lumbar puncture
what is needle aspiration used for? sterile or non-sterile?
pueral, synovial, or peritoneal fluid (sterile)
wound abscesses (non-sterile)
what are biopsies used for? sterile or non-sterile?
skin when viral or fungal infection is suspected (non sterile)
nasopharyngeal swabs
used to collect non-sterile secretions that may contain viruses or bacteria
what is sputum and in what cases it is collected? what if a patient cannot produce sputum?
a deep lung secretion that results from inflammation and it can be collected by coughing. if a patient cannot produce a bronchoalveolar lavage (BAL) is used
bladder microbiota is ________ so why is a traditional urine sample insufficient?
anaerobic; it is not easily collectible or culturable because it can be contaminated by the skin and urethral microbiota
what is used to collect urine from the bladder instead?
suprapubic puncture or catheterization
what does culture-based biochemical testing involve?
selective and differential media
what are dichotomous keys and what types of tests are they used for?
used to identify different organisms based on observable traits, used for biochemical tests
what is another way of Identification via proteins?
Mass spectrometry generates protein signature/fingerprint but a pure culture is needed for reliable result
what is the most commonly used molecular method?
DNA
PCR
can detect a unique region of a microbial genome
multiplex PCR
can detect multiple genes of the same bacteria to identify strains
what needs to happen first for RNA genomes to be used for PCR applications?
reverse transcriptase to transform RNA into cDNA (complement DNA) then the reporter probes can measure the amount of amplified DNA in the PCR reaction
next generation sequencing
can determine whole-genome sequence of a pure culture, or multiple genomes within a sample/specimen
what is the key method in all immunological methods of pathogen identification?
antibodies
how does ELISA work, difference between antibody capture and antigen capture
detects serum antibodies against a paticular pathogen (antibody capture) or the presence of pathogen antigens in a sample (antigen capture)
antigen
foreign matter that invades the body
antibody
circulate the blood to attack the same antigens that enter the body again (defense)
pros and cons of conventional diagnosis
requires sending a clinical specimen to a specialized lab which makes it slower but more accurate (requires multi-day delay and follow up)
pros and cons of point-of-care testing
rapid diagnostic tests run at the site of patient care meaning they are quick but not as accurate
point of care sensitivity
how small of a concentration can the test detect in the sample
if the sample has less than the threshold = false negative
needs more sensitive confirmatory testing
point of care specificity
how well it can distinguish between closely related targets
if the sample has a similarly related target = false positive
needs to be confirmed with a more specific test
what do we appreciate about immunochromatic assays
immunochromatic assays are modified ELISAs that use antibodies AND antigens. they can test if someone is actively infected (testing for antigen) or has an immune memory against a pathogen (testing for antibody)
