5. Clinical Microbiology Flashcards
What are the 4 basic steps of Clinical Microbiology testing procedure?
- Sample Collection
- Sample reception area: cross checking of details, specimen and ID
- Data entry: patient details, sample type and request
- Sample testing
What does microscopy/electron microscopy generally involve?
- Direct examination of unstained mounts:
e. g. wet mount
e. g. Indian ink (darkens background not cell)
e. g. dark field microscopy - Examination of stained preps:
e. g. Gram stain (bacteria)
e. g. acid-fast stain
e. g. fluorescence (direct or indirect- immuno-fluorescence)
What are some advantages of general microscopy?
- Rapid (can give a presumptive diagnosis)
- Gives pre-culture information
- Provides diagnosis for many fungi/parasites
- Can identify bacteria with distinctive morphology (vibrio spp) or staining characteristics (Mycobacterium spp)
- Specific fluorescent dyes can be used to indirectly detect organisms via antibodies e.g. Chlamydia trachomatis and T. pallidum
- Easy to use for some sample types e.g. urine of faeces
Advantages of electron microscopy:
- Virus morphology can be distinctive
- Leads to rapid diagnosis
- Once an agent is recognised: PCR, serology can be done
Disadvantages of Microscopy:
- Many pathogens are indistinguishable from normal flora
- Technical difficulties with smears
- To visualise you may make agent inviable (not able to then be cultured)
- Electron microscopy needed for viruses- instrument is expensive and uncommon
What are some common:
- In microbiology lab techniques:
- Out of microbiology lab techniques:
In microbiology lab techniques:
- Microscopy/electron microscopy
- Culture
- Serology
- Molecular testing
Out of microbiology techniques:
- Haematology (WBC count)
- Biochemistry e.g. AST and ALT
- Anatomical physiology
What organisms can culturing be an effective technique for?
- Bacteria
- Fungi
- Viruses
How are bacteria cultured?
- Bacteria are cultured on solid media (agar plates, slope plates) or liquid media (for enrichment or sensitivity
- There are many different media types e.g. enriched, selective, media
- Bacteria are then identified by:
- Morphology
- Growth requirements
- Biochemistry
- Enzymes
- Antigens
- Antibiotic susceptibility testing can also be carried out
How are fungal infections diagnosed?
- A very limited number of fungi actually cause infections
- Superficial infections: microscopic examination- if unclear: culture
- Systemic infections: culture, antigen testing, molecular testing
What media are used when fungi are cultured?
General purpose media: brain heart infusion (BHI) or sabouraud dextrose agar (SDA)
Specialised media:
- SDA with chloraphenicol and cyclohexamide (growth of non-pathogenic normal flora fungi is inhibited so only pathogenic fungi grow)
How are viruses cultured?
- Viruses are cultured using cell cultures
- Before this they were grown in suitable host animals or embryonated eggs
What are the main features of continuous cell lines that are used for culturing viruses?
- Derived from tumour tissue or primary cells treated with chemicals/tumour virus
- Single cell type (uniform population of cells
- Immortal: can propagate indefinitely
- Often different from cell of origin (abnormal)
- Retain viability after freezing at low temps
What is a cytocidal infection?
- An infection that result in cell death
e. g. picornaviruses, herpesviruses and adenoviruses
What is cytopathic effect?
- Microscopic or macroscopic degenerative changes or abnormalities in host cells/tissues caused by the infecting virus
What are the advantages of culturing as a diagnostic technique?
- Results in live organisms
- There can be isolation from normal flora
- Microbe can be fully identified
- Antibiotic sensitivities/resistance can be tested
- Microorganisms can be cultured from almost any site
- Many types of microorganisms can be cultured (bacteria, fungi and viruses)
