Back Module: S-CM-S1

Techniques in Microbiology

Module information

Module details

Title
Techniques in Microbiology
Type
Specialist
Module code
S-CM-S1
Credits
20
Phase
2
Requirement
Compulsory

Aim of this module

This module aims to provide trainees with experience of the range of techniques used in microbiology. Trainees will select, perform and interpret tests for a range of common infections and suggest options for management based on local, national and international guidelines.

Trainees will also appreciate the wider context of these results, including the need to inform public health or infection control, and referral to specialist and reference laboratories. They will also work with the process for validation and verification of a new diagnostic assay, and the requirements for quality assurance and management in microbiology.

Work-based content

Training activities

# Learning outcome Training activity Type Action
# 1 Learning outcome 1, 2, 3, 4 Training activities

Select, perform and interpret tests for STIs using the following techniques and suggest options for management:

  • Microscopy
  • Culture, identification and AST
  • Molecular assays
  • Serology for syphilis
 Type DTA Action View
# 2 Learning outcome 1,2,3 Training activities

Select, perform and interpret tests for genitourinary infections, including UTIs using the following techniques and suggest options for management:

  • Culture, identification and AST
  • Microscopy including automated methods
 Type DTA Action View
# 3 Learning outcome 1,2,3 Training activities

Select, perform and interpret tests for fungal and parasitological causes of genitourinary infections using the following techniques and suggest options for management:

  • Microscopy
  • Culture, identification and AST
 Type DTA Action View
# 4 Learning outcome 1,2,3,5 Training activities

Select, perform and interpret tests for bloodstream infections caused by bacteria and fungi using the following techniques and suggest options for management:

  • Blood cultures
  • Microscopy
  • Culture, identification and antimicrobial susceptibility testing, including detection of resistant organisms
  • Rapid diagnostics
 Type DTA Action View
# 5 Learning outcome 1,2,3,4 Training activities

Select, perform and interpret serology tests for common viral investigations, including the following and suggest options for management:

  • Blood borne viruses
  • Hepatitis screening
  • Antenatal screens
  • Rashes in pregnancy
 Type DTA Action View
# 6 Learning outcome 1,2,3,5 Training activities

Select, perform and interpret tests for parasitological infections using the following techniques and suggest options for management:

  • Microscopy
  • Serology
  • Rapid antigen detection

Applied to the following sample sources:

  • Blood
  • Stool
  • Eyes
  • Genitals
  • Urine
 Type DTA Action View
# 7 Learning outcome 1,2,3,4,5 Training activities

Select, perform and interpret tests for bacterial and viral causes of respiratory infection using the following techniques and suggest options for management:

  • Microscopy
  • Culture, identification and AST
  • Molecular assays
  • Urinary antigen
 Type DTA Action View
# 8 Learning outcome 1,2,3 Training activities

Select, perform and interpret tests for common fungal causes of respiratory infection using the following techniques and suggest options for management:

  • Microscopy
  • Culture, identification and AST
 Type DTA Action View
# 9 Learning outcome 1,2,3 Training activities

Select, perform and interpret tests for bacterial causes of gastrointestinal infection using the following techniques and suggest options for management:

  • Microscopy
  • Culture, identification and AST
  • Serogrouping
 Type DTA Action View
# 10 Learning outcome 1,2,3,4 Training activities

Select, perform, and interpret tests for viral causes of gastrointestinal infection using the following techniques and suggest options for management:

  • Molecular assays

and/or

  • Antigen detection
 Type DTA Action View
# 11 Learning outcome 1,2,3 Training activities

Select, perform and interpret tests for bacterial and fungal causes of central nervous system infection using the following techniques and suggest options for management:

 

  • Microscopy and cell count
  • Culture, identification and antimicrobial susceptibility testing
  • Antigen/antibody detection, eg, pneumococcus, cryptococcus and syphilis
 Type DTA Action View
# 12 Learning outcome 1,2,3,4 Training activities

Select, perform and interpret tests for viral causes of central nervous system infection using the following techniques and suggest options for management:

  • Microscopy and cell count
  • Molecular assays
 Type DTA Action View
# 13 Learning outcome 1,2,3 Training activities

Select, perform, and interpret tests for bacterial and fungal infections associated with the following specimens and suggest options for management:

  • Bone and joint
  • PD
  • Ascitic fluids
  • Sterile and non-sterile tissues
  • Sterile and non-sterile fluids
  • Shunts, lines and other prosthetic material
 Type DTA Action View
# 14 Learning outcome 1,2,3,4,5 Training activities

Select, perform and interpret tests for the detection of Mycobacterium tuberculosis and non-tuberculous Mycobacteria to include:

  • Sample prep
  • Microscopy
  • Molecular
  • Culture

And suggest management of infections caused by Mycobacteria including the interpretation of drug resistance.

 Type DTA Action View
# 15 Learning outcome 1,2,3 Training activities

Select, perform and interpret tests for bacterial and fungal causes of superficial skin, soft tissue and nail infections using the following techniques and suggest options for management:

  • Microscopy
  • Culture, identification and AST
 Type DTA Action View
# 16 Learning outcome 3,5 Training activities

Select, perform and interpret tests for the detection of multidrug resistance, including extended susceptibility testing, using the following techniques and suggest options for management:

  • Disk diffusion
  • Gradient strips
  • Microbroth dilution
  • Molecular assays
  • Automated methods
  • Culture methods
 Type DTA Action View
# 17 Learning outcome 3,5 Training activities

Select and interpret tests for Therapeutic Dose Monitoring of antimicrobials

 Type DTA Action View
# 18 Learning outcome 2,3,4 Training activities

Interpret results from anti-viral resistance assays to include:

  • CMV
  • HIV
  • Hep B
  • Hep C
 Type DTA Action View
# 19 Learning outcome 1,4,6 Training activities

Perform a nucleic acid extraction and manual PCR, including interpretation and reporting from standard curves, troubleshooting common faults and issues

 Type ETA Action View
# 20 Learning outcome 6 Training activities

Perform a validation or verification of a diagnostic assay or method and draft a report for laboratory approval

 Type ETA Action View

Assessments

Complete 4 Case-Based Discussions

Complete 4 DOPS or OCEs

Direct Observation of Practical Skills Titles

  • Perform a manual cell count and Gram stain of a CSF sample.
  • Report a positive blood culture, including organism ID and sensitivities and perform further testing required.
  • Perform a manual serological test for an infectious disease.
  • Process samples from a sterile site.
  • Perform microscopy and culture to identify dermatophytes.

Observed Clinical Event Titles

  • Provide advice on the management of a patient with difficile infection.
  • Communicate a respiratory virus results needing an infection control intervention.
  • Interpret the result of syphilis serology.
  • Interpret the curves from a molecular assay and report.
  • Present validation or verification results to an internal meeting.

Learning outcomes

# Learning outcome
1

Select and perform tests to investigate common infections from a range of sample types following guidance and fulfilling health and safety requirements
2

Interpret the results of tests used to investigate common infections from a range of sample types with consideration of laboratory quality assurance and quality control
3

Identify options for management of common infections based on test results and clinical context, considering infection control, guidelines and public health requirements
4

Perform and interpret molecular techniques for the investigation of common infections following guidance and fulfilling health and safety requirements
5

Select and interpret tests for the investigation and management of drug resistant pathogens
6

Evaluate assay performance according to quality assurance frameworks

Clinical experiences

Clinical experiences help you to develop insight into your practice and a greater understanding of your specialty's impact on patient care. Clinical experiences should be included in your training plan and you may be asked to help organise your experiences. Reflections and observations from your experiences may help you to advance your practice and can be used to develop evidence to demonstrate your awareness and appreciation of your specialty.

Activities

To develop a broader understanding of their specialty practice and support the completion of assessments and competencies, a trainee should;

  • Attend multidisciplinary team meetings where patients with infections are discussed to appreciate the care provided to patients and the roles of the multidisciplinary team involved in the patient pathway.
  • Attend ward rounds involving where patients with infections are being managed to appreciate the care provided to patients and the roles of the multidisciplinary team involved in the patient pathway.
  • Attend a GUM clinic to appreciate the care provided to patients and the roles of the multidisciplinary team involved in the patient pathway.
  • Visit a regional or national reference laboratory to appreciate the role of the reference labs in the provision of microbiological tests and services.

Academic content (MSc in Clinical Science)

Important information

The academic parts of this module will be detailed and communicated to you by your university. Please contact them if you have questions regarding this module and its assessments. The module titles in your MSc may not be exactly identical to the work-based modules shown in the e-portfolio. Your modules will be aligned, however, to ensure that your academic and work-based learning are complimentary.

Learning outcomes

  1. Critically evaluate the range of techniques, including culture, microscopy, serology, automated and molecular techniques used in the diagnosis of common infections.
  2. Discuss the aetiology, pathogenesis, clinical presentation, epidemiology and laboratory diagnosis of common genitourinary, respiratory, gastrointestinal, and neurological infections.
  3. Evaluate the key national guidelines in the management of common genitourinary, respiratory, gastrointestinal, and neurological infections with awareness of case rates within the UK and EU.
  4. Explain the structure and mode of action of a broad range of antimicrobial agents, including antibiotics, antivirals, and antifungals.
  5. Appraise the application and performance of a range of techniques used in the assessment, surveillance, and monitoring of antimicrobial therapy, including identification of antimicrobial resistance.
  6. Evaluate the role of the clinical microbiology laboratory in the provision of information for antimicrobial treatment of infections including multi-drug-resistant infections.
  7. Justify the role of specialist microbiology laboratories in the management of patients.

Indicative content

  • Microbiological Diagnostics of Common Infections:
    • Microbiological culture, including selection of appropriate culture media for a range of common bacteria and fungi.
    • Laboratory dentification of common bacteria and fungi isolates.
    • Microscopy, including appropriate stains for common pathogens.
    • Identification and quantification of white and red blood cells in CSF and sterile fluids or tissues.
    • Understanding of serological assay types and interpretation.
    • Principles of PCR, including nucleic acid extraction, primer and probe design and use, interpretation of amplification curves, and basic troubleshooting.
    • Methods for anti-microbial susceptibility testing, including disk diffusion, gradient strips, microbroth dilution, molecular assays, automated methods, and culture methods.
    • Methods of anti-viral resistance testing, including PCR and whole genome sequencing (WGS).
    • Methods for therapeutic dose monitoring of antimicrobials.
    • Interpretation of anti-microbial susceptibility testing and therapeutic dose monitoring of antimicrobials.
    • The range and use of rapid diagnostics and point of care testing.
    • Other techniques for identification of pathogens and their use such as MALDI-ToF, immunofluorescence, 16S, PFGE, MLST or WGS.
    • The role of the reference laboratories.

 

  • Aetiology, Clinical Presentation, and Management of Common Infections:
    • Understanding of the epidemiology and mechanism of sepsis.
    • Interpretation of blood cultures and other diagnostic tests for the septic patient.
    • Understanding of the epidemiology of bacterial and viral gastrointestinal infection in the UK and the differences observed in other counties in the world.
    • Presentation of common gastrointestinal infections in the UK and in returning travellers and their management.
    • Understanding of the range of bacterial, viral, and fungal pathogens implicated in respiratory infections seen in primary and secondary care.
    • Aetiology of community, hospital and ventilator acquired pneumonia.
    • Understanding of the epidemiology of bacterial and viral pathogens responsible for meningitis; in the UK and in returning travellers and their management.
    • Indications for CSF sampling and interpretation of diagnostic results, including biochemical histological, and microbial for different CNS conditions.
    • Presentation, aetiology, and management of CNS infections, including encephalitis, meningitis, abscess, post-surgical complications of neurosurgery (including device infections) and prion disease.
    • Pathogenesis, transmission, and presentation of infections caused by tuberculous and non-tuberculous mycobacteria in the UK and worldwide.
    • National and global strategies for treatment, monitoring and eradication of tuberculosis.
    • Notifiable diseases and pathogens with particular public health concern.

 

  • Antimicrobials and Resistance:
    • The mechanism of action of each class of antimicrobials.
    • Common mechanisms of resistance in pathogens, and their detection.
    • Infection control and public health implications of multi-drug resistant organisms including, but not limited to, ESBLs, VREs, CPEs, MRSA and MDR/XDR-TB.

Module assigned to

Specialties

Specialty code Specialty title Action
Specialty code SLS2-1-23 Specialty title Clinical Microbiology [2023] Action View
Specialty code SLS2-1-24 Specialty title Clinical Microbiology [2024] Action View
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