From patients to results

Question 1

Aims of the clinical Microbiology Lab:

To provide what?

Providing this leads to what?

Answer 1

• To provide accurate information about the presence or absence of the microorganisms from a clinical specimen.
• To provide antimicrobial susceptibility information

Accurate diagnosis and sensitivity testing leads to:

• Successful treatment of infection
• Aids in preventing the spread of infection
• Prevents emergence of antibiotic resistance

Question 2

What are the 9 steps of the diagnostic template:

Answer 2

1. Request
2. Sample collection
3. Transport of sample
4. Reception
5. Safety issues
6. Non-culture techniques
7. Culture of clinical samples
8. Identification and sensitivity
9. Results

Question 3

Sample Collection:

• Sterile sites
• Non Sterile sites

Answer 3

Sterile sites:

• blood/bone marrow
• CSF
• Tissue
• Lower respiratory tract
• Bladder

Non-sterile sites:

• Upper respiratory tract
• Skin
• GI tract
• Vagina
• Urethra

Question 4

Examples of Clinical specimens:

Answer 4

MSU: mid stream urine
Blood Culture
Urethral swab
Faeces (Stool)
Toe nail clippings
Sputum

Question 5

Transport media for:

Bacteria

Viruses

Answer 5

Bacteria: Stuarts transport media - STM contains charcoal to inactive any toxic bacterial bi-products. used for swabs.

Viruses: Viral transport media (VTM). buffered salt solution containing serum. Contains antimicrobials to control overgrowth of contaminating bacteria and fungi

Refrigeration @ 4 C

Question 6

Advisory committee of dangerous pathogens categorization:

Cat 1
Cat 2
Cat 3
Cat 4

Answer 6

Cat 1 - a biological agent unlikely to cause human disease, (Saprophytic/soil organisms)

Cat 2 - A biological agent that can cause human disease; hazardous to employees; unlikely to spread in the community; effective treatment/prophylaxis. eg. S.aureus, C. difficle, S.pneumoniae, S.pyrogenes, N.gonorrhoeae

Cat 3 - A biological agent that can cause severe human disease; serious hazard to employees, risk of spread in community; effective treatment/prophylaxis eg. mycobacterium tuberculosis

Cat 4 - a biological agent that causes severe human disease; serious hazard to employees; likely to spread in community; no effective treatment/prophylaxis eg. Ebola virus

Question 7

Diagnostic procedures:

Name the non culture techniques:

Answer 7

• Direct microscopy: Light microscopy, stains.
• Antigen detection: use of specific monoclonal antibodies
• Molecular microbiology (NAAT - (PCR))
• Serological responses

Question 8

Culture techniques: Solid Agar

Name the different agars available.

Answer 8

Basic Agar (Nutrient, general purpose).

Enriched Agar (enriched general purpose)
- Horse blood, Chocolate agar.

Selective Agar (selects specific organisms from a sample) 
- Cycloserine cefoxitin fructose agar = CCFA (C.diff)  

Differential agar (differentiates organism within a sample)

• Cystine lactose electrolyte deficient agar (CLED)
• usually chromogenic (changes color)

Question 9

4 Stages of identification

Answer 9

1. Basic ID = Microscopic eg gram stain
2. Generic: basic tests eg macroscopic and microscopic.
3. (most clinical specimens) Full: basic ID plus additional tests eg. Biochemistry eg API (analytical profile index)/MALDI-TOF
4. (outbreaks) Full plus typing eg. genetic fingerprinting and serotyping.

Question 10

Sensitivity Testing: 
What is EUCAST?
Purpose of sensitivity testing? 
European standardized method?
Disc Susceptibility method?

Answer 10

EUCAST: European committee on antimicrobial susceptibility testing

Purpose: Determine sensitivity/resistance of pathogens

European standardized method: For determining sensitivity to antibiotics; provides national standardized sensitivity/resistance data; epidemiologically useful

Disc susceptibility: Determines the sensitivity/resistance of the pathogen.