Clinical Microbiology Lab

What are the six main functions of a clinical microbiology lab?

1. Diagnosis

2. Guidance for treatment

3. Outbreak detection

4. Support for infection control

5. Collect and collate information

6. Epidemiological studies

What tools are used in diagnosis?

1. Culture

2. Serology

3. Molecular

4. Proteomics

What falls under collect and collate information?

1. Follow trends in resistant pathogens

2. Antimicrobial susceptibility summaries

What do clinical microbiologists provide information on?

1. Appropriate specimen collection/transport

2. Interpretation of laboratory results

3. Managing patients via antimicrobial therapy

4. Infection control issues

What are the four reasons that make it important for how the clinical lab functions?

1. Decreased frustration for both patients and healthcare workers

2. Cost effective use of lab resources

3. Ensure results correspond to the initial clinical question

4. Provide relevant clinical information

What is the laboratory work flow?

1. Collection

2. Transport/storage

3. Accessioning

4. Processing

5. Interpretation/identification

6. Susceptibility testing/molecular testing

7. Reporting/documentation

What is empiric treatment? What do you have to ensure to do when following this path?

It is when you treat a patient before the results come back from the lab. You must confirm your treatment plan with the results once they are received back from the lab.

What are possible issues to consider during specimens collection?

1. Will the specimens provide useful information

2. Choice of the type of specimen

3. Instructions for collection by the patient

4. Transport time to the lab

5. Need for transport media

6. Quality of specimen

7. Risk of false positive or negative result

Are specimens for culture ever placed in formalin/ formaldehyde? Why or why not?

No because formalin kills all bacteria

How do we accession a specimen?

1. First have to identify the specimen

2. Decide if you are going to accept or reject it

3. Is it a life threatening specimen

4. Decide if you want to process in house or refer out to a specialized lab

5. Has to be coded and entered into LIS system

How do we identify the specimen?

1. Is the specimen properly labelled?

2. Has it been properly collected?

3. Time of collection and transport

What are some possible reasons that a specimen may be rejected?

1. Missing information

2. Duplicate

3. Its leaking

4. Poor quality

5. Specimen information does not match the requisition form

6. Too old or improper transport

7. Swab/transport media expired

8. Inappropriate specimen

What are the possible types of specimens?

1. Blood

2. Urine

3. Scrapings

4. Stool

5. Fluids

6. Swabs

What is the role of transport media? What is it?

To maintain viability but inhibit growth. It is a jelly like substance.

What is a common type of transport media? What is a type of transport media used for parasites?

Cary Blair Transport media. SAF for parasites.

What does SAF contain? Why?

Formalin because we are not looking to grow anything as we are looking for eggs

What are the considerations when processing a specimen?

1. Type of specimen we have

2. Which tests are required

3. Does the specimen require additional processing

4. What media is required

5. Incubation conditions

What are possible tests that can be done with a specimen?

1. Culture

2. Serology

3. Molecular

4. Microscopy (gram stain, AFB stain)

What are two types of additional processing?

decontamination and centrifugation

What is an advance in bacterial identification?

Molecular diagnostics

What was molecular diagnostics a huge benefit for? What did it do very little for?

Viral diagnostics but it did not do much for bacterial diagnostics

Why did molecular diagnostics not do much for bacterial diagnostics?

This is because of the cost (it is often cheaper to do a urine culture), sensitivity and molecular diagnostics does not provide susceptibility data.

When looking for a good quality specimen, what should you look for?

Other indicators

When looking at a sputum gram stain, do you want epithelial cells to be present? Why or why not?

No because the presence of epithelial cells indicates contamination from the upper respiratory tract, which can compromise the diagnostic accuracy.

What do neutrophils represent?

Pus

How are sputum/specimens graded?

It is based on the ratio of neutrophils to squamous epithelial cells (cells/LPF).

What is Q0?

Very poor quality specimen as microscopic examination shows oropharyngeal contamination and the specimen will not be processed

What is Q1?

Poor quality specimen and microscopic examination shows oropharyngeal contamination. This specimen has been processed but results should be interpreted with caution and repeat if possible

What is Q2? Q3?

Q2 is good quality specimen and Q3 is very good quality specimen

How long for interpretation/identification for microscopy?

0.5 hour -same day

How long for interpretation/identification for POC?

Rapid streptococcal Ag test/hour

How long for interpretation/identification for culture?

24 hour-3 weeks

How long for interpretation/identification for direct MALDI-TOF?

Same day

How long for interpretation/identification for serological?

Same day/week

How long for interpretation/identification for molecular?

same/ next day for diagnostics and epidemiological studies

How long for interpretation/identification for susceptibility testing?

additional 24-72 hours (longer for mycobacteria)