Laboratory Diagnosis Of Infections Flashcards
Role of lab in detection of infections diseases
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
Expectations from the lab in lab diagnosis
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
Expectations of clinician in lab diagnosis
- give as much detail as possible on request form
- order and collect appropriate requests
- understand lab procedures ( working hours , limitations , abilities and rejection policies )
Describe the lab workflow cycle And list briefly what occurs at each cycle
- 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 )
Pearls of wisdom in test selection
- garbage in = garage out ( poor specimen gives poor quality tests )
- literature ( knowledge of disease processes and characteristics )
- available tests
- course of disease
Anatomical sites to collect samples
Which Samples are superior
- skin ( scalpel ) , sputum , saliva , skin swab , spinal tab , nasopharyngeal region , urine , feaces
- fluid and tissue samples are superior to swabs
Basic principles in sample collection
- 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
Collecting blood sample procedure and rules
- 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
How to collect urine , procedure and rules
- 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
How to collect stool , procedures and rules
- use pan bed or collection bin
- only an inch collected using sterile tongue blade
- place specimen in sterile container and keep free from urine
How to collect sputum , procedures and rules
- collect 1st thing in the morning for TB tests
- try not to contaminate with saliva and sinuses fluids
4 important data needed on request forms
- 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 )
List 6 rejection criteria
- leaking container
- mismatch information
- unlabelled container
- improper specimen collection technique
- improper test requested for specimen collected
- delayed transport time
2 categories of detecting infectious disease
1 culture methods
2 non culture methods
List culture methods and give examples
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
List non culture methods and give examples
1 serology - co agglutination reactions , precipitation reactions
2 molecular - PCR , DNA sequencing
2 methods of microbe identification and when is it done
Describe what is AST ( briefly and give examples)
- Manual , automatic
- antimicrobial susceptibility testing ( testing response and effectiveness of therapies of a anti microbial )
- agar dilution , microbroth dilution , gradient dilution , disk diffusion
What is the light source of dark field and fluorescent microscope
When is dark field used
- radiation of the electromagnetic spectrum of diff wavelength compared to light
- when microbe isn’t easily cultured
Reasons for doing microscopy
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
3 ways to identify microbes
1 biochemical reactions
2 molecules assays
3 antisera agglutinations
Describe API index , how it works and Advantages
- 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
Describe the VITEK machine how it works and advantages
- 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
Describe MALDI TOF MS machine , function , how it works
- 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
Function of serology test , when used and examples
And what is detected in the test
-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 )
What does a molecular test amplify , 3 things that are looked for , what is it performed on and function
- 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
What are the components of PCR and how does it occur and when it stop
- 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
Advantages and Disadvantages of PCR
- 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
What is AST used for and the 3 interpretation standards and what to do at each
- 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
Describe the 4 steps in selecting antibiotics for routine testing
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
Give 3 AST methods and examples
1 dilution - broth and gradient dilution And disk diffusion
2 automated AST - MALDI TOF MS , VITEK
3 PCR methods , GeneXpert
Describe disk diffusion how it works , advantages and major use
- 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
What is the review stage of post analytical phase
- 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
What should the report be like and what should it have and do
What can it also be used for
/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
