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Microbiology > Laboratory Diagnosis Of Infections > Flashcards

Laboratory Diagnosis Of Infections Flashcards

1
Q

Role of lab in detection of infections diseases

A

1 detection of infectious microbes
2 anti microbes testing
3 provide timely and good quality results
4 provide advice on appropriate specimen collection
5 detection of outbreaks
6 detect possible bioterrorism events
7 infection prevention and control

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2
Q

Expectations from the lab in lab diagnosis

A 
1 timely and good quality results 
2 ongoing validation of tests 
3 quality control of all tests 
4 information dissemination 
5 initial verification of all tests
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3
Q

Expectations of clinician in lab diagnosis

A
  • give as much detail as possible on request form
  • order and collect appropriate requests
  • understand lab procedures ( working hours , limitations , abilities and rejection policies )
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4
Q

Describe the lab workflow cycle And list briefly what occurs at each cycle

A
  • pre analytical phase : what are the signs and symptoms present which may be an infection aids in test selection (test selection , specimen collection and transport )
  • analytical phase - numerous tests done to determine infectious disease present ( microscopy , culture methods , non culture methods , susceptibility testing )
  • post analytical phase ( test review , report and dissemination )
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5
Q

Pearls of wisdom in test selection

A
  • garbage in = garage out ( poor specimen gives poor quality tests )
  • literature ( knowledge of disease processes and characteristics )
  • available tests
  • course of disease
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6
Q

Anatomical sites to collect samples

Which Samples are superior

A
  • skin ( scalpel ) , sputum , saliva , skin swab , spinal tab , nasopharyngeal region , urine , feaces
  • fluid and tissue samples are superior to swabs
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7
Q

Basic principles in sample collection

A
  • wear ppe
  • deliver sample within reasonable time range ( avoids overgrowths which contaminate )
  • use leak proof containers
  • submit adequate volumes where possible
  • label containers accurately
  • ideally collects samples before giving antibiotics as this skews results
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8
Q

Collecting blood sample procedure and rules

A
  • draw blood when temp rising
  • septic techniques ( ensure skin is sterile before and after )
  • 2 cultures 40-60 Mins apart and diff locations and about 10-15 ml blood
  • don’t draw form IV catheters
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9
Q

How to collect urine , procedure and rules

A
  • clean area around urethra
  • start midstream and fill 5-10 ml of leak proof container
  • label accurately
  • clearly explain procedure to patient
  • take specimen to lab quickly
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10
Q

How to collect stool , procedures and rules

A
  • use pan bed or collection bin
  • only an inch collected using sterile tongue blade
  • place specimen in sterile container and keep free from urine
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11
Q

How to collect sputum , procedures and rules

A
  • collect 1st thing in the morning for TB tests

- try not to contaminate with saliva and sinuses fluids

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12
Q

4 important data needed on request forms

A
  • type of specimen submitted ( helps know what test to undergo )
  • anatomical site of specimen collection ( gives insight on microbes found there )
  • method of specimen collection
  • specific pathogens being sought ( aids to optimize culture conditions )
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13
Q

List 6 rejection criteria

A
  • leaking container
  • mismatch information
  • unlabelled container
  • improper specimen collection technique
  • improper test requested for specimen collected
  • delayed transport time
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14
Q

2 categories of detecting infectious disease

A

1 culture methods

2 non culture methods

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15
Q

List culture methods and give examples

A

1 microscopy( to seek out defining features of microbes ) - fluorescent , dark field microscopy , light , stains

2 culture ( replicates microbes natural environment to amplify it and isolate ) - selective , differential , chromogenic

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16
Q

List non culture methods and give examples

A

1 serology - co agglutination reactions , precipitation reactions

2 molecular - PCR , DNA sequencing

17
Q

2 methods of microbe identification and when is it done

Describe what is AST ( briefly and give examples)

A
  • Manual , automatic
  • antimicrobial susceptibility testing ( testing response and effectiveness of therapies of a anti microbial )
  • agar dilution , microbroth dilution , gradient dilution , disk diffusion
18
Q

What is the light source of dark field and fluorescent microscope

When is dark field used

A
  • radiation of the electromagnetic spectrum of diff wavelength compared to light
  • when microbe isn’t easily cultured
19
Q

Reasons for doing microscopy

A

1 to validate quality of microbe which aids in culture technique selection
2 determine if cultured organism is contaminate or pathogenic
3 guide treatment decisions by aiding in identification of microbe

20
Q

3 ways to identify microbes

A

1 biochemical reactions
2 molecules assays
3 antisera agglutinations

21
Q

Describe API index , how it works and Advantages

A
  • analytical profile index ( for identification)
  • rapid identification of bacteria
  • has panels with microtubule with dehydrated substrates that are metabolized by bacterial suspension
  • biochemical profile determined by color change and colors converted into numerical code wc is read from index and microbe identified
22
Q

Describe the VITEK machine how it works and advantages

A
  • miniature microbroth
  • used to identify and AST automatically
  • has advanced calorimetric tech to determine individual biochemical reactions of a microbes in cards
  • rapid testing
  • real time
  • cost effective
23
Q

Describe MALDI TOF MS machine , function , how it works

A
  • automated identification machine , AST and sub-typing
  • protein based
  • place sample on sample plate and matrix over it
  • ion of organism are excited by electrons from machine and these ions are accelerated to a spectrophotometry and read by a computer to identify a microbe
24
Q

Function of serology test , when used and examples

And what is detected in the test

A

-to monitor infections and effectiveness of therapies

  • when Pathogens are difficult to grow
  • to assess immune status
  • diagnose active infections ( see a specific IG or antigen and confirm )
  • precipitation reactions
  • co agglutination reactions
  • antigens , small particles presented by APC to induce immune response
  • antigens ( bodies response to pathogens )
25
Q

What does a molecular test amplify , 3 things that are looked for , what is it performed on and function

A
  • nucleic acids
  • genes or part of a gene of ( virulence , specific species or resistance genes to a certain therapy )
  • performed direct on specimen or cultured specimen
  • to identify , surveillance and AST
26
Q

What are the components of PCR and how does it occur and when it stop

A
  • tag polymerase , nucleotides , primers , mix buffer , DNA Sequence , PCR tube

-undergoes a cycle of
1 denature DNA sequence
2 annealing ( forming leading and lagging ends )
3 extension ( joining of lagging ends )

-when components are depleted

27
Q

Advantages and Disadvantages of PCR

A
  • can detect fastidious
  • can detect even dead microbes
  • can amplify minute quantities
  • can detect diff species of microbes at the same time
  • false positives due to contamination
  • can’t diff between dead and viable cells
  • expensive and technical expertise
  • will only look for a specific organism
28
Q

What is AST used for and the 3 interpretation standards and what to do at each

A
  • antimicrobial susceptibility testing
    /used to
  • detect resistance mechanisms, predict patient outcome and control infections
1 susceptible- recommended doses will treat 
2 resistant - antimicrobial won’t work 
3 intermediate ( buffer zone ) - higher doses for ideal clinical outcome
29
Q

Describe the 4 steps in selecting antibiotics for routine testing

A

1 customer service ( consult with pharmacy and infection control orgs on what antibiotics are present and what organisms are seen )
2 antibiotic to be included in institution formulary ( inform phamarcies on selected antibiotic )
3 test the antimicrobial against species according to EUCAST guidelines )
4 availability of drug for testing

30
Q

Give 3 AST methods and examples

A

1 dilution - broth and gradient dilution And disk diffusion
2 automated AST - MALDI TOF MS , VITEK
3 PCR methods , GeneXpert

31
Q

Describe disk diffusion how it works , advantages and major use

A
  • place antimicrobial on agar plate with microbes present
  • look at zone of inhibition around disk at the drugs
  • flexible drug selection , low cost , minimum expertise needed and instrument readers to prevent errors
  • gives quantitative numbers which can be translated to dosage
32
Q

What is the review stage of post analytical phase

A
  • ensuring that’s the test was done according to guidelines

- have we identified what we needed to identify and is it in accordance with information given on request form

33
Q

What should the report be like and what should it have and do

What can it also be used for

A

/interpretable
/selection of antimicrobial
/ alternative antimicrobial if organisms resistant to narrow spectrum
/ clinical guidelines to aid clinician to influence clinical decisions

  • fed into public health stats
  • implement infection control measures
  • improve antibiotic prescription polices

Microbiology (5 decks)

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