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Pulmonology (CP) > 24 - Diagnostics for Detection of Infectious Diseases in Respiratory Tract Infections > Flashcards

24 - Diagnostics for Detection of Infectious Diseases in Respiratory Tract Infections Flashcards

1
Q

WHat are teh 2 forms of infection for mycobacterium tuberculosis?

A

latent (90%) and active (10%)

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2
Q

What are the symptoms for latent TB and how do you test for it?

A

Asymptomatic, noncontagisou

Test the patient’s T cells for reactivity against M tuberculosis (TB Quantiferon)

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3
Q

What are the symptoms of active tuberculosis? How do you test for it ?

A

persistent cough, fever/chills, night sweats

upper lobe predominant nodular disease with areas of bronchiectasis

contagious

*test by culturing for mycobacterium in sputum

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4
Q

why would doing PCR for TB of patietns blood not help diagnose TB?

A

TB usually isn’t found in the blood

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5
Q

Who is at risk of progressing from latent Tb to active TB and what is the risk? How do we prevent this progression?

A

immuncompetent: 10% lifetime

immunocomromised (ex AIDs): 10-15%/year

prevent progresion

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6
Q

What is the Mantoux tuberculin skin test?

A
  • TST/PPD
  • Tuberculin purified protein derivative (PPD) subcutaneous
  • read between 48-72 hours looking at area of induration, inexpensive screen
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7
Q

How do we interpret the TST/PPD?

A

Look at area of induration!

  • interpretation stratified by risk/exposure
    • >5mm high risk
      • HIV, recent contact with TB+, suppressed (prednisone, TNFa inhibitors)
    • > 10nm medium risk
      • recent immigration from endemic region, IV drug users, laboratory/healthcare workers
    • >15mm low risk
      • low risk populations, pre-employment screening
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8
Q

What is the sensitivity and specificity of the TST/PPD test?

A
  • Sensitivity: 85-95%
    • false negative in patients with HIV. immunosuppression or overwhelming infection (anergic)
  • Specificity 80-90%
    • false positive if had BCG, cross-reactivity with other Myco spp.
    • somehwat subjective (induration vs erythema)
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9
Q

What is the Quantiferon (IGRA) test for TB?

A
  • uses TB specific peptides (ESAT-6, CFP, TB7.7) and measures T-cell mediated IFN-y response against M. tuberculosis
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10
Q

What are the advantages of the Quantiferon TB test?

A
  • specific for MTB: not cross reactive with BCG, M kansassii, M sulgai, M marinum
  • in-tube, whole blood test, no need for patient follow-up
  • automated, internal standard curve on each plate
    • sensitivity 75-85% (in culture confirmed cases)
    • specificity >99%
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11
Q

What are the disadvantages to the Quantiferon test?

A
  • 50%/test reagent stability
  • pre-analytic steps contribute to variablity
    • collection (0-16 h window for incubation), transport (RT), mixing
    • 5-30% unresolved rate
  • package insert for TNFa inhibitors
  • no equivocal range, no risk based interpretation
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12
Q

Which test TST/PPD or Quantiferon (IGRA) is better for people from TB endemic areas

A

Quantiferon! If they are from an endemic rea they likely received the BCG vaccine which will give them a false positive TST/PPD

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13
Q

What is the advantage os using a flourescent stain versus a non-fluourescent stain?

A

the fluorescent stain allows the lab to identify organisms that are present in lower quantities

the fluorescent stain allows the technologist to “pick out” organisms from a clinical matrix

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14
Q

What are the 2 methods to the direct exam “Smear” test? What are benefits to each? what are the major drawbacks?

A
  1. Acid-Fast
    • cheap, easy
    • Ziehl-Neelson/Kinyoun stain
      • carbol fischin (heat or phenol to increase uptake)
        • decolorize
      • methylene blue or brilliant greeen
  2. Auramine-Rhodamine (fluourescent)
    • binds acid fast cell wall
    • more sensitive, still fairly cheap
      • requires fluourescent microscope

major drawbacks: specificity…species specific morphology. You know it is mycobacterium, but not necessarily mycobacterium tuberculosis

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15
Q

So the Quantiferon will tell us that it is mycobacterium, but not if it is mycobacterium tuberculosis. How can we test for sure that it si mycobacterium tuberculosis?

A

PCR! Very commonly used, even more specific would be to do sequencing (which will also tell you about resitance)

You can also do a culutre, but this takes 8 weeks to get results!

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16
Q

What are some advantages of PCR vs smear or culture when looking for mycobacterium tuberculosis?

A
  • MUCH faster! only 2 hours vs 19-25 days culture
    • important bc potentially can save money, make appropriate treatment decision, and get patients out of isolation faster!
  • specificity: much more specific than smear positive
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17
Q

What are the disadvantages to doing PCR to test for mycobacterium tuberculosis?

A
  • money! especially in resource limited countries where TB is endemic. It is cheap, but not when you have to do a TON of them
  • it requires electricity
  • it requires technical expertise
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18
Q

WHat is the gold standar in TB testing?

A

culture!

  • Medium
    • Lowstein-Jensen
      • egg, potato flour, malachite green, glycerol
      • suitable for most mycobacterium (toxic to RGM, M.bovis)
      • may liquify if bacterial contamination is high
    • Middlebrook
      • defined medium
      • more permissive-bacteria grow faster (not toxic to RGM)
      • it is clear aka easier to spot colonies
      • can be agar or broth
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19
Q

What is a phenotypic antimicrobial suseptibility testing (AST)?

A
  • broth or agar methods
  • drug concentration
    • single concentration “critical concentration”
      • inhibitory 95% of wild type isolates
  • hold time
    • 3 weeks
  • required for all strains
    • test initial isolate, repeat if patient fails to concert to smear negative in 3 months
    • test only first line drugs unless MDR, then test second line

not done as often anymore bc it is slow and molecular AST is fast! (sequencing or PCR)

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20
Q

What is a molecular antimicrobial suseptibility test?

A

sequence the bacteria or PCR for resistance genes

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21
Q

What is DNA sequencing?

A

the process of determining the precise order of nucleotides within DNA molecule

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22
Q

What is Sanger sequencing?

A
  • “PCR on steroids”
  • Sequencing that is done primarily by hand. Is much slower than next gen
  • take a sample, break apart DNA and add small primers, assign each letter A, T, G etc a color and determine the sequence
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23
Q

what is Next generation sequencing? What are some advantages and disadvantages?

A

basically the same thing as Sanger sequencing but more automated! MUCH faster!

  • Advantages
    • much cheaper vs snager sequencing
    • much more data-can sequence a human genome in a week vs 10 years with sanger
    • can identify minor populations
  • Disadvantage
    • expensive
    • time consuming
    • difficult to assemble
24
Q

What are the top 4 drugs to treat TB? How good are we at detecting their molecular resisitance via sequencing?

A
  • Rifampin: mutation in rpoB
    • detects 95-98%
  • Isoniazid
    • detects 95% of mutations
  • Ethambutol: mutations in embB prevent binding of drug
    • detects 80% of mutations
  • Pyrazinamide
    • detects 85% of mutations

so we are pretty good. some drugs have more possible mutations than others so we are better at detecting some drugs than others

25
Q

In a patient with HIV and shortness of breath what 4 things should be considered?

A

pneumocystis jirovecii pneumonia

CMV pneumonitis

bacterial pneumonia

influenza

26
Q

Based on the CT and Chest Xradiograph, what test would tield the etiologic agent of infection?

A

direct fluorescent antigen screen for pneumocystis jirovecii

27
Q

What kind of organism is pneumocystis jirovecii an what does it cause? who does it typically infect?

A
  • A ubiquitous unicellular eukaryote, P. jirovecii
  • causative agent of pneumocystis pneumonia
    • pneumonia symptoms
    • CXR classically with bilateral diffuse interstitial infiltrates
    • elevated LDH (less useful in non-HIV patients)
  • Rare cause of infection in the gerneal population, usually is in immunocompromised population
28
Q

Pneumocystis jirovecii is a frequent cause of morbiditiy and mortality in patients who are immunocompromised. What kind of people fall into this category?

A

Patients who are mmore severely immunocompromised:

  • AIDs
    • patients with CD4 count under 200 are most at risk
    • patients with CD4 count under 300 with a previous infection
  • Indivuals with hematologic malignancies
  • organ transplant recipients
  • those receiveing long-term steroid or cytotoxic therapy
    • >20mg of prednisone/day
    • systemic vasculitis, autoimmune deficiencies
    • thymic dysplasia, sever combined immunodeficiency, hypogammaglobulinemia
29
Q

What kind of specimens are used to diagnose Pneumocystis jirovecii?

A
  • induced sputum
  • bronchoalveolar lavage (BAL) material (sensitivity as high as 90% and specificity is 82%)
  • tissue
    • transbronchial biopsy, open lung biopsy

Cannot be grown in culture!!! diagnosis relies on morphologic identification of organism

30
Q

What are some techniques for identifying Pneumocystis jirovecii?

A
  • Microscopy
    • identify trophozoites and cysts
    • stains:
      • intracystic stages (Giemsa)
      • cyst walls (silver stains)
  • immunoflurouescene microscopy using monoclonal antibodies can identify the orgnaisms with higher sensitivity thn conventional microsopy
31
Q

What can we identify for Pneumocystis jirovecci with a GIemsa stain?

A

trophozoites , only the nuclei stain purple

32
Q

What can we identify with a silver stain for pneumocystis jirovecii?

A

cysts! only the walls of the cysts will stain, the intracystic bodies are not visible

the cysts are saucer shaped

33
Q

What do we see with indirect immunofluroescene to look at pneumocystis jirovecii?

A

green color signals antibody bidining to cyst

has a honey combing look

34
Q

What does poor sensitivity mean?

What does poor specificity mean?

A

seNsitivity=Negative (double check the negatives)

sPecificity=Positive (double check the positives)

35
Q

What is the limitation of the rapid limitation of rapid influenza test that must be considered?

A

the test suffers from poor sensitivity and negatives must be confirmed on PCR

36
Q

What are advantages to the EIA-Antigen (rapid flu test)

A
  • advantages:
    • rapid (15-40min)
    • amenable to point of care testing
    • moderate or waived complexity
    • can do one-zies
  • disadvantages
    • cannot perform more than 5 at a time
    • unable to assess specimen quality
    • subjective read
    • less sensitive than other methods

**inexpensive, highly specific read, but not good at the negative results

37
Q

What is the methodology of the rapid flu test?

A

testing paper has antibody and you add the sample, looking to see if there is antigen that will bind to the anibody in your sample

38
Q

So what does a negative rapid flu test mean?

A

not a lot! Might as well flip a coin! it has low sensitivity and it has a lot of human error (QUIPS) because the test is difficult to read

39
Q

What are advantages of respiratory virus PCR?

A
  • advantages: more rapid than a clture (1 day vs 10days) and more sensitive than other rapid tests
  • disadvantages: expensive, unable to assess specimen quality, need highly trained professional, dedicated facility with specialized equipment
40
Q

What is the gold standard test for respiratory viruses?

A

PCR!

41
Q

Why is it difficult to diagnose a respiratory tract infection?

A
  • respiratory tract most common site of infection
  • symptoms alone are not sufficient for clinicians to determine optimal patient management (true infection, bacterial, viral)
  • wide array of pathogens!
42
Q

What are the most common pathogens ordered/detected? What are some other pathogens that are requested?

A

Flu/RSV remain the most common pathogens ordered/detected

other pathogens: human metapneumovirus, parainfluenza, adenovirus, rhinovirus, B. pertussis

43
Q

What are really good sources to diagnose pneumonia? What are pretty good sources? what are meh sources?

A
  • Really good
    • blood culture
    • pleural fluid or effusion
    • lung biopsy
  • pretty good sources
    • BAL or bronchial brush
    • trach secretions collected at the time of endotracheal tube placement
  • Meh specimens include
    • endotracheal secretions
    • sputum (except for CF patients)
    • NP (except for pertussis)
44
Q

what culture should you always do when looking for pneumonia?

A

sputum culutre! It depends on the circumstances what other cultures you collect. but you shoudl always do this one

45
Q

What symptoms characterize community acquired pneumonia? How is diagnosis best made?

A
  • characterized by lobar or segmental consolidation, fevers, chills, toxic appearance, pleuritic pain with or without effusion
  • diagnosis best made with sputum gram stain and culture and blood cultures (>50% of cases are culture negative)
  • most cases are treated empirically
46
Q

Who are the usual suspects to cause pneumonia? Who are the less common agents? Who are the rare agents?

A

Usual: Streptococcus pneumoniae, Haemophilus influenzae, Moraxella catarrhalis

Less common: S. aureus, Mycoplasma pneumoniae, Chlamydia pneumoniae, Legionella species, endemic fungi

rarely: Francisella, Pasteurella, N meningitidis, mixed aerobic/anaerobic bacteria (aspiration)

47
Q

What are the most common causes of nosocomial pneumonia? WHat makes diagnosis difficult?

A
  • enteric (Klebsiella, Enterobacter, Serratia) or environmental gram-negative rods (pseudomonas, Acinetobacter, Stenotrophomonas) and occasionally S. aureus and environmental fungi (especially in immunocompromised patients)
  • made with quantitative cultures of”
    • BAL > 103 cfu/ml threshold
    • Endotracheal aspirate > 106 cfu/ml threshold
48
Q

What is a gram stain based on? What things do we look at to decide the quality of a specimen?

A

Gram stains are based on bacterial cell wall composition

Quality of specimen:

  • type: sputum vs BAL
  • location of bacteria: intracellular vs extracellular
  • variety of bacteria: abundant single morph vs heterogenous
  • presence of host cells: PMN vs epi vs ciliated epi

2:1 ratio of PMN/Epi OR 25 PMN/field, ciliated epis

49
Q

What is the leading cause of community acquired pneumonia? WHat are the gram stain and culture sensitivities? How does treatment with an antibiotic influence the specificity?

A

Pneumococcal pneumonia (meaning caused by strep pneumo)

gram stain 57%

culture (sputum) 80%

If you are able to get a culutre within 24 hours of starting antibiotic that is still pretty good no antibiotic sensitivity is 93% and 24 hours is 29%

50
Q

What is an example of a selective media? Differential media? Selective and differential media?

A
  • Selective: bactrim blood agar for S. pneumoniae
  • Differential: blood agar plates for streptococcus pyogenes
  • Selective and differential: mannitol salt agar for staphylococcus aureus
51
Q

How do we best obtain a pure culutre?

A

on a solid media, less sure in liquid medias

each bacteria in theory arises from a single bacterium deposited on the surface of the petri dish, and each colony consits of a pure clone fo cells

52
Q

What are the benefits of quantitative culture compared to qualitative? When would qualitative be better?

A
  • Quantitative culture increases the specificity of the culture compared to qualitative culture
    • the respiratory tract is not sterile, quantitative culture may aide in distinguishing between colonization and a pathogen
  • Qualitative culture is more useful for “dirty” specimens like sputum
    • look for predominance of pathogens compared to oral flora
53
Q

How do we diagnose laten tuberculosis? How about active TB?

A
  • PPD or Quantiferon ELISA by looking for acivated macrophaged in patient’s blood
  • Active TB is made through the detection of bacteria in patient specimens by culture, direct stining or molecular techniques
54
Q

How do we typically diagnose PJP?

A

via visualization of cysts in a patient specimen via flurouescene or silver staining

55
Q

the diagnosis of respiratory tests can be ______ or ______. Performance on tests can vary significantly based on ________.

A

The diagnosis of repsiratory viruses can be broad or narrow performance of tests can vary significantly based on the method

56
Q

Ensure that you consider the ________ of viruses and ________ when choosing the best test for an individual patient.

A

Ensure that you consider the seasonality of viruses and patient status when choosing the best test for an individual patient.

Pulmonology (CP) (23 decks)

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