Lecture notes

role of the clinical microbiology laboratory

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Module
Clinical and food microbiology (BM6CFM)

Institution
Aston University, Birmingham (Aston)

Aims of the clinical microbiology laboratory. • To provide accurate information about the presence or absence of microorganisms from a clinical specimen • To provide antimicrobial susceptibility information on the microorganism(s) recovered • Accurate diagnosis and sensitivity testing: (...

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Uploaded on August 27, 2024
Number of pages 10
Written in 2023/2024
Type Lecture notes
Professor(s) Jonathan cox
Contains All classes

clinical microbiology
nhs
role of clinical laboratory
aston university

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clinical and food microbiology lecture 1-16

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Role of the clinical microbiology laboratory: from patient to result.

Aims of the clinical microbiology laboratory.
• To provide accurate information about the presence or absence of microorganisms
from a clinical specimen
• To provide antimicrobial susceptibility information on the microorganism(s)
recovered
• Accurate diagnosis and sensitivity testing:
(a) Successful treatment of infection
(b) Aids in preventing spread of infection
(c) Prevents emergence of antibiotic resistance
We need to know the absence of microorganisms in a specimen so that we can rule out a
diagnosis. Also, so that we can treat the patient properly.

From patient to result: the diagnostic template.
1. Request from clinician for sample to be taken.
2. Sample collection.
3. Transport of samples to the clinical microbiology laboratory.
4. Reception of samples.
5. Consideration of safety issues with the sample- risk to people that are testing that
sample.
6. non-culture techniques for diagnosis.
7. Culture techniques for diagnosis.
8. Identification and sensitivity test the organisms.
9. This gives us the result.

NHS hospital trust form.
Clinical details included: this shows the symptoms that the patient is manifesting and
therefore why is the test being taken in the first place.
Important that we have the appropriate sample for the appropriate diagnosis.

STERILE SITES NON-STERILE SITES
• Blood / bone marrow • Upper respiratory tract: streptococci, anaerobes, Candida albicans
• CSF (meningitis infection) (commensals)
• Tissue • Skin: coagulase negative staphylococcus eg S. epidermidis)
• Lower respiratory tract • GI tract: ‘coliforms’,anaerobes ‘faecal flora’
(BAL) • Vagina: lactobacilli, anaerobes
• Bladder • Urethra: skin and faecal flora

Clinical sample collection.

, There are sterile and non-sterile sites where we can obtain clinical samples from patients.
In non-sterile sites it is important to know what commensals are normally found there and
what commensals should not be present there.
To avoid getting commensals which are already present at the site in a UTI test you would
need to obtain a mid-stream urine sample.
Because the first bit of urine will not be sterile.

Examples of specimens received in clinical microbiology.
Midstream urine.
Blood culture- we need to see if we can grow bacteria from people's bloodstream and this is
important because it tells us if a person has sepsis.
Urethral swab- this is inserted down through the urethra, and then it is cultured.
It is useful for STI.
Faeces (stool)- to diagnose gastrointestinal infections.
Toenail clippings- this is for fungal infections that we might get in our toe nails that we may
need to diagnose.
Sputum-this comes from the deep lung. It includes lung tissue, mucus and a lot of other
stuff. It comes out as a solid.

Sample collection: aide-memoire.
• Take appropriate specimen eg. sputum
• Collect specimen before antibiotics are given
• Avoid contamination from normal flora if possible and any contaminated
equipment
• Label specimens correctly and identify any known ‘High Risk’ eg HIV
• Complete request form completely; sufficient clinical information
• Transport sample to the lab as quickly as possible.
• You need to collect the specimen before antibiotics are given this is because the
bacteria could be dead before you can assess the sample if you have given antibiotics
before collecting the specimen. Therefore, you will not end up getting a diagnosis.
Therefore, you may be selecting for organisms that are not causing the infection.
• However, if you suspect meningitis or sepsis, you would get that patient on
intravenous antibiotics before you are thinking about sensitivity testing.
• If you take a broad specimen antibiotic it will decolonize, you're gut. So, it will put
you at higher risk for clostridium difficile colonization.
• Avoid contamination from normal flora- midstream urine- and you need to use
sterile equipment.
• If you are taking a sample from a high-risk person, such as someone with HIV, there
is a chance that they also have TB. So, you need to put the relevant information
down so that it protects people in the clinical lab.
• Sample has to be transported as quickly as possible, because the sample is not in its
optimum environment therefore if you leave it for a while autolysis will happen,
where the bacteria will explode and it will not be viable.

Transport of clinical samples to microbiology.

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