Week 1 Sample Collection Flashcards
What are the 4 main ways of diagnosing an infection and what do they test for?
1) Culture (bacterial and viral)
- To grow any possible organisms in the sample
2) Molecular testing (PCR)
- To detect nucleic acid/RNA/DNA
3) Serology (blood test)
- To detect Ab formed following exposure to the organism
4) Microscopy (Gram stain, AFB, fungal mic.)
- To see the organisms under a microscope
- Quick results but hard to do well
What is in the diagnostic testing pathway (when sending samples to diagnose an infx)?
1) Determine priority of the test
- Which is the most important sample
- When to collect it
2) Determine specimen type
3) Determine collection and transport
- Swab
- Containers
- Labels
- How to transport
4) Interpret results
What are the body sites that contain large numbers of commensal bacterial flora?
SMUGGD (GodDamn SMU Good)
- GIT
- Distal urethra and perineum
- Skin
- Mouth and upper throat
- Upper RT and some parts of lower RT
- Genital tract
What are sterile body sites?
Sites in the body that should not have any detectable organisms
Where are the normally sterile body sites? (IMPT)
- Blood
- CSF
- Vitreous fluid in the eye
- Joint fluid and tissue
What levels of bacteria are there in the parts of the urinary system?
Sterile
- Urine from upper urinary tract (kidney, ureter, bladder)
Some bacteria
- Urine after passing through the distal urethra
What levels of bacteria are there in the parts of the respiratory system?
Little to no:
- Lower respiratory tract (near alveoli)
Large amounts:
- Upper respiratory tract
What are the benefits of using a swab to collect specimens?
- Easy to use
- Low cost
- Readily available
What is a limitation of using a swab for specimen collection?
If there is pus or infected fluid, it would be better to just send a sample of that to improve diagnostic yield
When should a swab be collected?
- When there are signs of local infection (pain, swelling, redness, pus, abscess)
- When there are signs of systemic infection (fever, cough) and a nasopharyngeal swab is needed to diagnose a viral respiratory infection
- When screening for MDO/multi-drug resistant organisms (MRSA, VRE, CPO) even if no local signs of infection are present
How to take a swab sample from an exposed wound with signs of infection?
1) Remove superficial debris (as true pathogens are usually only present in the deeper tissues)
2) Take a deep sample from a representative part
3) Swab with firm pressure and rotate the swab
4) Press into wound to collect fluid if any
What are fastidious bacteria and what are some examples?
Fastidious
- Needs special media to allow them to survive outside the human body
Examples
- Neisseria gonorrhea, Chlamydia trachomatis, viruses and anaerobic bacteria
Describe the various transport media available for swabs and what they are used for.
- Virus
- Anaerobes
- Aerobes
- N. gonorrheae
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Describe the common swab type for bacterial culture. (IMPT)
- Rayon bud tip
- gel-like Amies transport media
- Suitable for aerobic/anaerobic cultures and screening
- Not suitable for bacterial/viral PCR and viral culture
Descibe the most common swab type for viral culture and viral PCR. (IMPT)
- Flocked swab
- Universal transport media (UTM)
- UTM provides a supportive environment for viruses, chlamydia and mycoplasma
- Contains antibiotics to prevent bacterial overgrowth in the sample
- Suitable for viral culture, antigen and PCR, and chlamydia PCR
- Not suitable for bacterial PCR, aerobic and anaerobic cultures
Describe the most common swab type for bacterial culture and PCR. (IMPT)
- Flocked swab
- Liquid Amies media / e-Swab
- Suitable for aerobic/anaerobic culture, bacterial PCR and screening
- Not suitable for viral culture and PCR
What is formalin used for?
Used in histopathology as a tissue preservative but cannot be used in microbiology tests as it kills all microbes to preserve the tissue.
What are the types of urine samples and how sterile are they? (IMPT)
1) Renal aspirate (from kidneys)
- Sterile specimen
- Invasive procedure
2) Supra-pubic aspirate (from bladder)
- Sterile
- Invasive
3) Midstream and clean catch urine
- “Clean” but non-sterile
- Non-invasive
4) In-out catheter urine
- “Clean” but non-sterile
5) Catheter urine
- Often colonised
- Non-invasive
What are the principles of non-invasive urine collection?
- Obtain as clean as a specimen as possible (MSU and CCU)
- Reduce contamination from urethra and perineal region
What are the principles of urine collection for catheter specimen urine (CSU)?
- Obtain a fresh sample
- Reduce contamination from urine in the urine drainage collection bag
~ Catheters are usual sterile on the first insertion but quickly become
colonized with bacteria
~ Long-term catheters will always grow bacteria
How do you collect catheter specimen urine?
- If required, clamp tubing a few cm from the sampling port, which should be cleaned first
- Attach syringe to the sample port and aspirate the required amount each.
What are the types of respiratory samples and how clean are they?
- Throat/Mouth samples
~ Heavily colonised with bacteria
~ Non-invasive - Endotracheal aspirate
- Sputum
~ Clean to clean-contaminated
~ Non-invasive - Bronchial lavage
~ Clean but not sterile
~ Invasive
Describe whether throat and mouth samples can be used as a respiratory specimen.
- Will often be rejected as unusable
- May often show epithelial cells on microscopy
- Not representative of the bacteria in the air sacs as sample is only saliva/mucus from the back of the throat, instead of being from the base of the lungs
What are the principles of sputum collection?
- Collect in the morning
- Before breakfast to avoid contamination
- Rinse mouth with water only, no toothpaste or mouthwash
- Patient sits up to cough hard in order to bring up a sample as close to the alveoli/base of lung as possible
- Patient to take several deep breaths, in through nose and out of mouth, to loosen sputum secretions
