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inf & imm > Week 1 Sample Collection > Flashcards

Week 1 Sample Collection Flashcards

1
Q

What are the 4 main ways of diagnosing an infection and what do they test for?

A

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

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2
Q

What is in the diagnostic testing pathway (when sending samples to diagnose an infx)?

A

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

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3
Q

What are the body sites that contain large numbers of commensal bacterial flora?

A

SMUGGD (GodDamn SMU Good)
- GIT
- Distal urethra and perineum
- Skin
- Mouth and upper throat
- Upper RT and some parts of lower RT
- Genital tract

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4
Q

What are sterile body sites?

A

Sites in the body that should not have any detectable organisms

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5
Q

Where are the normally sterile body sites? (IMPT)

A
  • Blood
  • CSF
  • Vitreous fluid in the eye
  • Joint fluid and tissue
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6
Q

What levels of bacteria are there in the parts of the urinary system?

A

Sterile
- Urine from upper urinary tract (kidney, ureter, bladder)

Some bacteria
- Urine after passing through the distal urethra

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7
Q

What levels of bacteria are there in the parts of the respiratory system?

A

Little to no:
- Lower respiratory tract (near alveoli)

Large amounts:
- Upper respiratory tract

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8
Q

What are the benefits of using a swab to collect specimens?

A
  • Easy to use
  • Low cost
  • Readily available
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9
Q

What is a limitation of using a swab for specimen collection?

A

If there is pus or infected fluid, it would be better to just send a sample of that to improve diagnostic yield

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10
Q

When should a swab be collected?

A
  • 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
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11
Q

How to take a swab sample from an exposed wound with signs of infection?

A

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

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12
Q

What are fastidious bacteria and what are some examples?

A

Fastidious
- Needs special media to allow them to survive outside the human body

Examples
- Neisseria gonorrhea, Chlamydia trachomatis, viruses and anaerobic bacteria

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13
Q

Describe the various transport media available for swabs and what they are used for.
- Virus
- Anaerobes
- Aerobes
- N. gonorrheae

A

IMAGE

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14
Q

Describe the common swab type for bacterial culture. (IMPT)

A
  • Rayon bud tip
  • gel-like Amies transport media
  • Suitable for aerobic/anaerobic cultures and screening
  • Not suitable for bacterial/viral PCR and viral culture
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15
Q

Descibe the most common swab type for viral culture and viral PCR. (IMPT)

A
  • 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
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16
Q

Describe the most common swab type for bacterial culture and PCR. (IMPT)

A
  • Flocked swab
  • Liquid Amies media / e-Swab
  • Suitable for aerobic/anaerobic culture, bacterial PCR and screening
  • Not suitable for viral culture and PCR
17
Q

What is formalin used for?

A

Used in histopathology as a tissue preservative but cannot be used in microbiology tests as it kills all microbes to preserve the tissue.

18
Q

What are the types of urine samples and how sterile are they? (IMPT)

A

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

19
Q

What are the principles of non-invasive urine collection?

A
  • Obtain as clean as a specimen as possible (MSU and CCU)
  • Reduce contamination from urethra and perineal region
20
Q

What are the principles of urine collection for catheter specimen urine (CSU)?

A
  • 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
21
Q

How do you collect catheter specimen urine?

A
  • 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.
22
Q

What are the types of respiratory samples and how clean are they?

A
  • 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
23
Q

Describe whether throat and mouth samples can be used as a respiratory specimen.

A
  • 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
24
Q

What are the principles of sputum collection?

A
  • 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
25
Q

What are the sterile fluids in the body?

A
  • Joint aspirate
  • CSF
  • Blood
  • Aspirates from internal body organs
26
Q

What are the principles of invasive collection of sterile site samples?

A
  • Clean and disinfect hands then clean puncture site thoroughly
  • Disinfect puncture site but allow it to airdry
  • Sterile no-touch techniques
27
Q

What is the turn-around-time for non-culture results?

A

Blood tests: 1-3 days

Microscopy: 1-2 days

PCR: 1-3 days

28
Q

What is the turn-around-time for culture results?

A

Aerobic culture: 2-5 days

Viral culture: 7-21 days

TB culture: 10-42 days

29
Q

What does presence of bacteria in sterile body sites show?

A
  • Infection
  • Contamination (by organisms that are not from the intended site culture, and are often from sampling technique or superficial site)
30
Q

What does presence of bacteria in non-sterile sites mean?

A
  • Infection
  • Contamination
  • Colonisation
31
Q

What is a viable count and what is it for UTI?

A

Viable count:
- How much bacteria was present in the urine
- 100,000 cfu/ml is likely a UTI

32
Q

What is the common dipstix interpretation for UTI? (IMPT)

A

WBC ++
- May have hematuria
- Protein ++ or pyuria possible

33
Q

What are some signs that the urine sample is contaminated?

A
  • Results show mixed bacterial growth (MBG)
  • Epithelial cells (could also show that urine is not MSU)

inf & imm (19 decks)

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