Week 1 Sample Collection

Question 1

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

Answer 1

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

Question 2

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

Answer 2

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

Question 3

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

Answer 3

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

Question 4

What are sterile body sites?

Answer 4

Sites in the body that should not have any detectable organisms

Question 5

Where are the normally sterile body sites? (IMPT)

Answer 5

• Blood
• CSF
• Vitreous fluid in the eye
• Joint fluid and tissue

Question 6

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

Answer 6

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

Some bacteria
- Urine after passing through the distal urethra

Question 7

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

Answer 7

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

Large amounts:
- Upper respiratory tract

Question 8

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

Answer 8

• Easy to use
• Low cost
• Readily available

Question 9

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

Answer 9

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

Question 10

When should a swab be collected?

Answer 10

• 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

Question 11

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

Answer 11

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

Question 12

What are fastidious bacteria and what are some examples?

Answer 12

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

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

Question 13

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

Answer 13

IMAGE

Question 14

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

Answer 14

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

Question 15

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

Answer 15

• 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

Question 16

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

Answer 16

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

Question 17

What is formalin used for?

Answer 17

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

Question 18

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

Answer 18

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

Question 19

What are the principles of non-invasive urine collection?

Answer 19

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

Question 20

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

Answer 20

• 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

Question 21

How do you collect catheter specimen urine?

Answer 21

• 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.

Question 22

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

Answer 22

• 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

Question 23

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

Answer 23

• 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

Question 24

What are the principles of sputum collection?

Answer 24

• 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

Question 25

What are the sterile fluids in the body?

Answer 25

- Joint aspirate - CSF - Blood - Aspirates from internal body organs

Question 26

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

Answer 26

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

Question 27

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

Answer 27

Blood tests: 1-3 days Microscopy: 1-2 days PCR: 1-3 days

Question 28

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

Answer 28

Aerobic culture: 2-5 days Viral culture: 7-21 days TB culture: 10-42 days

Question 29

What does presence of bacteria in sterile body sites show?

Answer 29

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

Question 30

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

Answer 30

- Infection - Contamination - Colonisation

Question 31

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

Answer 31

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

Question 32

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

Answer 32

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

Question 33

What are some signs that the urine sample is contaminated?

Answer 33

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