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Microbiology > Clinical Specimen Basics > Flashcards

Clinical Specimen Basics Flashcards

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Biology 101 flashcards
1
Q

Multiple diagnostic methods can be used depending on the organism. Describe the methods of direct observation and culture?

A

Direct observation: stain is quick but lower in sensitivity

Culture is common for bacteria, fungi, and occasional viruses

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2
Q

Parasites are best detected using what diagnostic method?

A

Detected best by direct observation but immunoassay and molecular assays useful for some
Larger tissue parasites may require biopsy or body imaging

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3
Q

Immunoassays can detect organisms directly or can be designed to do what?

A

detect antibody response of host to infection

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4
Q

How many negative tests are needed to exclude some organisms?

A

3 negative test

dont take all 3 specimens in one day

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5
Q

What is precision?

A

How consistent the test values are

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6
Q

What is accuracy?

A

How close are the test values to the true value

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7
Q

In terms of negative and positive results what is the best test ?

A

fewest number of false positives and negatives

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8
Q

What are the formulas for sensitivity, specificity, PPV and NPV

A 
Sensitivity= a/(a+c)
Specificity = d/(b+d) 
PPV= a/(a+b) (percent of all positive test that are true positives is the PPV) 
NPV = d/(c+d)
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9
Q

What is a predicted value of a test?

A

is a measure (%) of the times that the value (positive or negative) is the true value

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10
Q

If the population has a disease prevalence of 1% in the general population, there will be how many true positive and how many false positives per 100 random tests that are 98% sensitive ?

A

1 true positive
2 false positives
this means that 67% of the positives will be false positives
predictive value of a positive is only 33%

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11
Q

What tests are the key method of detection?

A

cultures

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12
Q

What are traditional methods?

A

blood agar, extracts from plants and animals and live animal cells of various species

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13
Q

What are alternatives to cultures?

A

Immunoassays

  • detection of specific microbes using antigen capture immunoassay
  • detect of antibodies to microbes using specific antibody capture
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14
Q

IgM is a marker of what? IgG is a marker for what?

A

IgM: acute infection
IgG: can be a marker of recent or old infection

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15
Q

What is the immunodiagnosis steps of an acute infection?

A
  1. Draw an acute serum: within the first week or as soon as possible before 14 days
  2. Draw a convalescent serum 3-6 weeks after the first serum : look for a 4 fold or greater titer increase due to IgG (usually titers go up 1:64 or more after an acute infection)
  3. Most tests today use ELISA, so the serum titer is given as an optical density.
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16
Q

What are antibody titer tests?

A

Results are highest dilution of serum still giving a positive Rx

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17
Q

Larger centralized automated labs will provide what in terms of accuracy and cost of tests

A

Higher accuracy

lower cost tests

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18
Q

In an emergency setting you need STAT tests, what is a trade off for speed in terms of accuracy and costs?

A

slight decrease in test accuracy and higher costs per tests

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19
Q

What do you do if you miss the acute titer?

A

Draw a convalescent titer when titer is high. 3-6 weeks after the start of the infection
a very high convalescent titer, and if the clinical symptoms agree, the infection can be presumptively confirmed

20
Q

Does a single positive antibody allow for a definitive confirmation of acute infections?

A 
nope 
exceptions are the chronic infections: 
Lyme Disease 
HIV infection 
Hepatitis infection
21
Q

In diagnosis of chronic infections the acute phase is usually missed. For HIV and Lyme, you do assays to check for presence of a variety of antibody types to increase test specificity. Why do you test for a panel of antibodies to surface and internal proteins?

A

helps eliminate false positive reactions due to just one or two cross reacting common antigens between closely related microbes

22
Q

A western blot procedure for HIV and lyme is one way to produce what?

A

produce a variety of separate antigens from the virus or bacterium of interest so that these antigens can be used to test for distant antibodies from the patient

23
Q

For diagnosis of hep B you check for what?

A

check for several antibody markers for viral antigens and human antibodies against the virus
PCR for hep B virus titer

24
Q

For HIV and Hep C, you can also check for virus antigen or virus DNA or RNA, how do you check this?

A

Antigen Immunoassay

PCR for nucleic acid

25
Q

Ab titer in a baby drops or increases each month after birth?

A

drops

26
Q

Check antibody titer for agents suspected (CMV, Toxo). What is the timeline for checking babies?

A

Test at birth (Cord blood serum)
Test baby again after 3 or 4 months
if baby is negative for infection: IgM should not be present and IgG titer from mother will drop at rate of 50% loss every month and will never go back up

27
Q

If a baby is positive for infection what will be the IgM and IgG?

A

IgM will be positive

IgG titers eventually go up

28
Q

Rising and continous IgM is a marker of what?

A

Acute Infection

29
Q

IgG is usually what kind of marker?

A

lifelong

30
Q

What are some characteristics of third generation immunoassays?

A

Very convenient to perform
Sensitivity and specificity still just okay typical of enzyme immunoassays
Single Analyze test

31
Q

What is the test used for influenza?

A

Binax NOW influenza

one of the easiest to use, read the result after 15 minutes

32
Q

Fourth generation assays, what are some features?

A

Simultaneous detection (antigen and antibody)
Kits made with superior reagents (monoclonal antibodies or recombinant antigens)
New improved detection technology

33
Q

Name the tests in the order of increasing sensitivity

A

EIA then RIA/FIA then DELFIA then Nucleic acid amplification

34
Q

what is an example of nucleic acid amplification test

A

PCR

35
Q

What is real time PCR?

A

Simple to perform due to complex chemistry
A colored light producing reaction occurs in a tube
reaction tubes do not have to be handled or opened after putting in the specimen

36
Q

Explain tests and timelines for chikungunya and dengue diagnosis

A

Sometimes you need two types of test for dx:
days 2-6 of illness (PCR is best because it detects circulating virus in blood)
days 7-14, ELISA test for IgM in blood
days 6-8, both tests are Ok

37
Q

What are some new technologies that bypass culture? (high cost)

A

Mass sequencing replaces cultures (detect multiple pathogens)
Molecular array chips (multiple microbes)

38
Q

What is a low cost new technology to supplement culture?

A

MALDI-TOF
For about the effort and time that it takes to do a gram stain of a bacterial colony, it is now possible to identify the colony
Accuracy higher than traditional culture

39
Q

In regards to technology, it is important to make sure you patients understand what?

A

tests are FDA approved with a certain % of false positive and negative reactions as a given

40
Q

In regards to technology, it is important that tests can be set up to be better screening tests or better _________ tests.

A

confirmatory

it is unusual to have a single test that does it all

41
Q

What are the guidelines for specimen handling?

A 
Disinfection 
Quantity and timing 
Device for collection and transport 
Transport time 
Storage time
42
Q

If a specimen is rejected by the lab it should be saved by the lab at what temp?

A

4C

43
Q

What are situations for rejection of specimens that are beyond salvage?

A

Misidentification of specimen
Culture specimens received in fixative
Dried out specimen on swab
Quantity insufficient for tests ordered

44
Q

A sample can be rejected due to serious compromise. what are situations in which the specimen has been compromised?

A

Improper storage temp
Improper transport medium
Improper transport time
Leaky specimen

45
Q

What organisms require prompt culture if specified by doctor?

A

Haemophilus ducreyi
Anaerobes in regular transport tubes
Neisseria gonorrhoeae in joint fluid

Microbiology (39 decks)

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