diagnostics

Question 1

why do we want/need to identify the species of a pathogen causing disease? (3 things)

Answer 1

1- use appropriate antibiotics (if needed)
2- anticipate possible sequelae
3- epidemiological surveillance

Question 2

what are specimens?

Answer 2

clinical patient samples that contain tissue or fluid for microbe testing

Question 3

which specimens come from sterile sites?

Answer 3

Blood, CSF, Urine, pleural fluid, peritoneal fluid, internal organ tissues

Question 4

which specimens come from non-sterile sites?

Answer 4

skin, wound abscesses, nose, lung contents

Question 5

why does the specimen need to preserve the state of the sample?

Answer 5

if the microbe growing within a certain characteristic (aerobic/anaerobic) you would want to preserve that to have accurate results

Question 6

consider why we collect blood via venipuncture

Answer 6

venipuncture collects blood directly from the vein into an aerobic or anaerobic culture tube (to preserve the state) it also keeps blood sterile.

Question 7

why is a pH-sensitive sensor used to check for growth?

Answer 7

it glows if bacterial growth has occurred (which should not happen since blood is mostly sterile)

Question 8

what is the procedure that collects CSF?

Answer 8

Lumbar puncture

Question 9

what is needle aspiration used for? sterile or non-sterile?

Answer 9

pueral, synovial, or peritoneal fluid (sterile)
wound abscesses (non-sterile)

Question 10

what are biopsies used for? sterile or non-sterile?

Answer 10

skin when viral or fungal infection is suspected (non sterile)

Question 11

nasopharyngeal swabs

Answer 11

used to collect non-sterile secretions that may contain viruses or bacteria

Question 12

what is sputum and in what cases it is collected? what if a patient cannot produce sputum?

Answer 12

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

Question 13

bladder microbiota is ________ so why is a traditional urine sample insufficient?

Answer 13

anaerobic; it is not easily collectible or culturable because it can be contaminated by the skin and urethral microbiota

Question 14

what is used to collect urine from the bladder instead?

Answer 14

suprapubic puncture or catheterization

Question 15

what does culture-based biochemical testing involve?

Answer 15

selective and differential media

Question 16

what are dichotomous keys and what types of tests are they used for?

Answer 16

used to identify different organisms based on observable traits, used for biochemical tests

Question 17

what is another way of Identification via proteins?

Answer 17

Mass spectrometry generates protein signature/fingerprint but a pure culture is needed for reliable result

Question 18

what is the most commonly used molecular method?

Answer 18

DNA

Question 19

PCR

Answer 19

can detect a unique region of a microbial genome

Question 20

multiplex PCR

Answer 20

can detect multiple genes of the same bacteria to identify strains

Question 21

what needs to happen first for RNA genomes to be used for PCR applications?

Answer 21

reverse transcriptase to transform RNA into cDNA (complement DNA) then the reporter probes can measure the amount of amplified DNA in the PCR reaction

Question 22

next generation sequencing

Answer 22

can determine whole-genome sequence of a pure culture, or multiple genomes within a sample/specimen

Question 23

what is the key method in all immunological methods of pathogen identification?

Answer 23

antibodies

Question 24

how does ELISA work, difference between antibody capture and antigen capture

Answer 24

detects serum antibodies against a paticular pathogen (antibody capture) or the presence of pathogen antigens in a sample (antigen capture)

Question 25

antigen

Answer 25

foreign matter that invades the body

Question 26

antibody

Answer 26

circulate the blood to attack the same antigens that enter the body again (defense)

Question 27

pros and cons of conventional diagnosis

Answer 27

requires sending a clinical specimen to a specialized lab which makes it slower but more accurate (requires multi-day delay and follow up)

Question 28

pros and cons of point-of-care testing

Answer 28

rapid diagnostic tests run at the site of patient care meaning they are quick but not as accurate

Question 29

point of care sensitivity

Answer 29

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

Question 30

point of care specificity

Answer 30

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

Question 31

what do we appreciate about immunochromatic assays

Answer 31

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)