Systems for Pathogens 1 Flashcards
What is in a name
Names provide us with the opportunities to define boundaries
It is up to the test system to define these boundaries and provide a measure that informs us
What is a pathogen
A microbe CAPABLE of causing a specific degree of host damage
How can we define a pathogen
Commensal Non pathogen (in host)
- PRESENT but NOT CAPABLE of causing disease in the host - good bacteria
Zoonotic Non pathogen (in carrier)
- PRESENT but only CAPABLE of causing disease in ANOTHER host
Commensal Opportunist (in host)
- PRESENT and CAPABLE of causing disease in the host but only in certain circumstances
Are all positive samples, diagnostic of disease
No,
We only get the infection once the pathogen is active, not when it is latent
How should you take samples for testing from
Sterile sites must be free from contamination
- eg. Skin flora in blood cultures
Non sterile sites require decontamination of normal flora
- eg Faeces, Mouth, Skin
Samples with high volume or relatively low infected pathogen load require concentration (centrifugation, filtering)
What happens in the sample preparation phase
Culture:
- Enrichment
- Purifacation
- Amplification
Direct:
- Concentration
- Sample treatment
How do we use the samples for analysis
- Molecular DNA/RNA
- Gross morphology (Microscopy)
- Chemical composition (HPLC MassSpec)
Why do we use light microscopy for analysis
Used to visualise bigger samples
- Trichomonas vaginalis
- Schistosoma mansonii
- Entamoeba histolytica
- Strongyloides (thread worm)
Why do we use electron microscopy for analysis
Used to visualise smaller samples such as viruses
Why do we use Direct bacterial staining of Sample
- Used to differentiate what type of bacteria by their cell wall type
- Change the needed antibiotic for that infection
- Visualise other elements such as capsids
Why do we use Immunofluorescent staining for analysis
Able to identify specific antigens present using immunofluorescent tagging
What are the advantages in using microscopy
- Easy to perform
- Rapid screening
- Some parasites have SPECIFIC morphology
- Specific Immunoflourescence staining possible
What are the disadvantages in using microscopy
Not Sensitive, screening sputum smears requires at least 10,000 orgs per ml to be visualised
- General stains are not specific
- Labour intensive (expensive)
- Requires specialist interpretive expertise (more expensive)
What media are used to grow bacteria
- Non Selective Media
eg. Blood Agar - Semi Selective Media
eg. MacConkey Agar, DCA, CLED - Selective growth temperatures eg. Campylobacter species
In what ways can we select for the atmosphere type the culture is grown in
- Aerobic culture
- Microaerophilic Culture
- Anaerobic culture
How can wee use a combination of selection to grow a culture
Selective temperature and Selective atmosphere
- Campylobacter grows at 42°C and at 10% CO₂
How is classical metabolic testing used
Differentiates what metabolic pathways exist in a culture
- Catalase
- Indole test
How can we systematically classify bacteria
Each organism has specific requirements to grow, when we isolate each condition we can identify what it is
How does viral cell cultures work
Grow cells in culture and allow virus to infect it
When virus exerts its cytopathic effect and bursts out of cells we can identify it
How can we identify viruses
Culture & microscopy
- Requires permissive cell lines, eg.Vero cells (Kidney epithelial)
for Measles (M orbillivir
us) - Cytopathic Effect Immunofluorescent staining of culture
Direct Antigen Detection
- ELISA eg. Influenza Virus
What are the advantages of identification with cell culture
- Cheap simple, reliable reagents
- Sensitive
- Validated specificity
- Direct in vivo measurement of effectiveness of therapy
- Easily archived
What are the disadvantages of identification with cell culture
- Some pathogens cannot be grown
- Some pathogens cannot be well differentiated by biochemistry alone
- Slow: culture requires at least overnight incubation
- Some pathogens grow too slowly to aid rapid diagnosis
- Labour intensive (expensive)
- Requires specialist interpretive expertise (more expensive)
