Knowledge guides

LG15: Microbiology

Epidemiology, pathophysiology, and clinical sciences

Advanced Trainees will have in-depth knowledge of the topics listed under each clinical sciences heading.

For the statistical and epidemiological concepts listed, trainees should be able to describe the underlying rationale, the indications for using one test or method over another, and the calculations required to generate descriptive statistics.

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Investigations, procedures, and clinical assessment tools

Advanced Trainees will know the scientific foundation of each investigation and procedure, including relevant anatomy and physiology. They will be able to interpret the reported results of each investigation or procedure.

Advanced Trainees will know how to explain the investigation or procedure to patients, families, and carers, and be able to explain procedural risk and obtain informed consent where applicable.

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Important specific issues

Advanced Trainees will identify important specialty-specific issues and the impact of these on diagnosis, management and outcomes.

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  • Consideration of samples and volume, including yield versus risk of collection
  • Diagnostic stewardship, and:
    • considerations of cost-effectiveness
    • its role in optimal diagnostic testing
    • the prevention of harm from inappropriate use of diagnostic testing
  • Human microbiome, colonising organisms that constitute normal flora at different body sites, and the features of pathological infection
  • Microbiologic results for a particular infectious disease or syndrome, considering:
    • accuracy, such as standard error and coefficient of variation
    • disease prevalence
    • pre-test probability
    • risk of false positives and negatives
    • sensitivity and specificity
  • Specimen selection, collection, and transportation for a particular infectious disease or syndrome
  • Spread and transmission of infectious disease

PCH

  • Common organisms for those age groups
  • Spectrum of pathogenic organisms by age, particularly in the first few months to years of life, such as cause of sepsis
Methods of microbiological investigations
  • Antigen detection methods
  • Antimicrobial susceptibility testing
  • Disc diffusion
  • Genotypic methods and further susceptibility tests
  • Metagenomic analysis
  • Methods, such as:
    • automated methods
    • minimum inhibitory concentration
  • Microscopy and culture:
    • identification of commonly encountered groups of pathogens based on features, such as:
      • biochemical tests
      • colony characteristics
      • gram stain
      • growth requirements
      • mass spectrometry
      • molecular techniques
      • motility
    • microscopy for parasites
  • Molecular methods:
    • common methods used in laboratory identification of bacteria, fungi, parasites, and viruses, such as:
      • nucleic acid amplification commercial kits versus in-house
      • polymerase chain reaction (PCR) tests
      • role of the reference laboratory
  • Serology:
    • antibody detection
    • role in interpretation of common serological tests, with consideration to:
      • patient factors such as immunosuppression and administration of blood products
      • the role of convalescent serology
      • timing of illness
  • Specimen types:
    • blood:
      • blood culture systems
      • limitations of blood culture media
      • volume of blood required
    • cerebrospinal fluid (CSF):
      • triage of testing on small, volume-critical specimens
      • use and limitations of CSF diagnostics methods for important central nervous system infections, such as:
        • brain lesions
        • encephalitis
        • meningitis
    • faecal pathogens detected by:
      • antigen
      • culture
      • PCR
    • mycobacteria:
      • culture
      • drug susceptibility testing and limitations
      • PCR
      • specific stains, such as:
        • fluorescent
        • Ziehl-Neelsen
    • sputum:
      • contaminated specimen
      • limitations of sputum microscopy
    • sterile tissues and fluids
    • swabs
    • tissue
    • urine:
      • cell counts
      • culture
      • red cell morphology
  • Whole genome sequencing
Microbiology laboratory service in the investigation, diagnosis, and management of infection
  • Pre-analytic considerations, such as selecting correct:
    • patient identification
    • sample type and volume
    • timing of collection
    • transport requirements and timing
Aboriginal and Torres Strait Islander peoples and Māori
  • Advice to clinicians regarding critical / urgent microbiology results, or for commonly misunderstood diagnostic test results
  • Appropriate microbiological tests for clinical investigation, and facilitation of specimens with complex or critical testing requirements
  • Biosafety and biosecurity in the lab with regards to Australian / New Zealand standards and Security Sensitive Biological Agents (SSBA) Regulatory Scheme
  • Common sources of error in each stage of the testing cycle, and how to mitigate them
  • Considerations and requirements when introducing new laboratory tests, including concepts of verification and validation
  • Laboratory information systems, including:
    • interactions with the electronic health record
    • limitations
    • utilisation for audit purposes
  • National and international antimicrobial guidelines
  • Notifiable disease recognition and notification
  • Quality assurance and control in the laboratory
  • Risks and management of laboratory exposures
  • Testing for antimicrobial resistant organisms, such as:
    • carbapenem-resistant organisms