Introduction to Clinical Microbiology
Overview
Clinical microbiology is the laboratory discipline concerned with microorganisms and their relationship to human infection and disease.
Depending on laboratory scope, clinical microbiology may include bacteriology, mycology, parasitology, virology, antimicrobial susceptibility testing, and related diagnostic services.
Major groups of organisms
Bacteria
Bacteria are prokaryotic microorganisms with diverse structures, metabolic properties, and clinical significance.
Fungi
Fungi include yeasts and moulds. Laboratory investigation may involve direct examination, culture, identification, and susceptibility testing in selected circumstances.
Parasites
Parasites include protozoa and helminths. Detection may involve microscopy, antigen detection, molecular methods, or other approaches depending on the organism and test.
Viruses
Viruses require host cells for replication and are investigated using methods such as antigen detection, molecular amplification, serology, or culture in specialized settings.
The microbiology testing pathway
A broad workflow can include:
- Appropriate test request
- Correct specimen selection
- Collection and labeling
- Appropriate transport
- Direct examination where indicated
- Culture or another detection method
- Identification
- Antimicrobial susceptibility testing where appropriate
- Result review and reporting
The exact workflow depends on the specimen and diagnostic question.
Why specimen quality is critical
Microbiology is particularly dependent on specimen quality because contamination, inappropriate collection, or delay can alter what is recovered or detected.
Important factors include:
- Correct anatomical site
- Appropriate collection method
- Adequate volume
- Suitable container
- Appropriate transport conditions
- Timing relative to antimicrobial therapy when relevant
- Prevention of contamination
Specific requirements should be taken from validated laboratory procedures and current testing guidance.
Culture and identification
Culture uses appropriate media and incubation conditions to support recovery of selected organisms. Identification can then use phenotypic, biochemical, immunological, mass-spectrometric, molecular, or other validated approaches.
Antimicrobial susceptibility testing
Antimicrobial susceptibility testing evaluates an organism's response to selected antimicrobial agents.
Interpretation depends on the:
- Organism
- Antimicrobial agent
- Testing method
- Applicable breakpoint standard
- Current version of the laboratory's adopted guideline
LabGoTo's microbiology knowledge resources should therefore be used alongside the current standard adopted by the laboratory rather than treating a static reference as universally applicable.
Quality considerations
Microbiology quality management includes specimen acceptance, media and reagent quality, equipment monitoring, environmental controls, organism identification controls, susceptibility-testing quality control, staff competency, documentation, and biosafety.
Key points
- Clinical microbiology investigates microorganisms associated with human disease.
- Correct specimen collection and transport are fundamental.
- Culture, identification, and susceptibility testing are method- and organism-dependent.
- Antimicrobial susceptibility interpretation requires the current applicable breakpoint standard.
- Biosafety and quality management are integral to microbiology.
References
- NCBI. MeSH: Microbiology.
- World Health Organization. Laboratory quality management resources.
- Clinical and Laboratory Standards Institute. Current applicable microbiology standards should be used by laboratories adopting CLSI methods.