Module information

Module details

Molecular Pathology in Infection Sciences
Module code

Aim of this module

This module will provide the trainee with the knowledge and understanding of the molecular pathology of infection. In the work-based module they will be expected to apply this knowledge as they learn to perform molecular methods used in microbiology and gain experience of the interpretation of patient results in a variety of clinical settings.

Work-based content


# Learning outcome Competency Action
# 1 Learning outcome 1,2 Competency

Interpret request forms and recommend the most appropriate investigation strategy to investigate molecular pathology samples.

Action View
# 2 Learning outcome 1,4 Competency

Receive, process and store common molecular pathology specimens.

Action View
# 3 Learning outcome 2,3 Competency

Perform and critically evaluate the results from a range of molecular assays used to detect and genotype micro-organisms, including:

  • nucleic acid extraction
  • polymerase chain reaction (PCR) and RT-PCR
  • the range of quantitative assays used in your laboratory.
Action View
# 4 Learning outcome 2,3 Competency

Use manual, semi-automated and automated equipment deployed in the molecular pathology laboratory.

Action View
# 5 Learning outcome 3,4 Competency

Conform to requirements for internal quality control (IQC) and external quality assessment (EQA) for molecular diagnostic testing.

Action View
# 6 Learning outcome 4 Competency

Use laboratory and hospital information systems to identify and record patient demographics, clinical details and relevant laboratory results.

Action View
# 7 Learning outcome 4,5 Competency

Produce basic interpretative reports on common molecular pathology investigations.

Action View
# 8 Learning outcome 1,2 Competency

Control infection risks in accordance with departmental protocols.

Action View
# 9 Learning outcome 1,2 Competency

Minimise risks and hazards in compliance with health and safety policies.

Action View


You must complete:

  • 1 case-based discussion(s)
  • 1 of the following DOPS/ OCEs:
Receive a range of clinical samples, book them in to the appropriate IT system and select the appropriate investigations that are required DOPS
Perform a nucleic acid extraction on a range of specimen types DOPS
Perform and interpret a nucleic acid amplification test DOPS
Perform and interpret nucleic acid sequencing DOPS
Use laboratory IT systems for handling, processing and storage of patient data DOPS
Perform and critically evaluate the results from a range of molecular assays used to detect, and genotype microoranisms. Evaluate the sensitivity and specificity of the assay DOPS
An appropriate activity agreed with your Training Officer OCE

Learning outcomes

  1. Interpret routine requests for molecular pathology investigations in microbiology in the correct clinical context and process the specimens that accompany those requests.
  2. Perform the range of basic laboratory techniques used in the workplace to investigate the molecular pathology of microbial infection.
  3. Apply the principles of internal quality control and external quality assessment and draw conclusions about assay performance.
  4. Use laboratory IT systems for handling, processing and storage of patient data and laboratory results. To include an introduction to bioinformatics.
  5. Produce a basic interpretive report on molecular laboratory results in the context of infection.

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. Explain the molecular pathology of important microbial infections.
  2. Describe the design, operation and performance of a range of molecular investigations used in the detection and management of microbial infections.
  3. Discuss and evaluate the role of molecular technology in the provision of information for management and treatment of microbial infections.
  4. Describe and apply relevant health and safety issues associated with the molecular investigation of microbial infections.
  5. Discuss and evaluate the appropriate quality management systems.
  6. Discuss the partnership between the clinical microbiology laboratory and other clinical specialisms in the investigation of the molecular pathology of infection and patient care.

Indicative content

  • Cell biology, meiosis and mitosis, chromosome segregation
  • Chromosome structure and function
  • Mechanisms of origin of numerical and structural abnormalities, and behaviour of structural chromosome anomalies at meiosis
  • Nucleic acid structure and function, chemical structure of DNA, and replication, transcription and translation
  • Genome structure in microorganisms
  • Interaction between cells and molecular components of microorganisms
  • Scientific basis of molecular testing in infectious disease
  • Molecular science methodology in the investigation of infectious disease, with examples:
    • DNA extraction, PCR, DNA sequencing, blotting
    • RNA extraction, reverse transcription polymerase chain reaction (RT-PCR)
    • Application of DNA-based testing for gene mapping, linkage and mutation detection
    • Sensitivity and specificity of molecular scientific tests
    • Proteomics
    • Next generation sequencing/whole genome sequencing
    • Potential application of new molecular tests and molecular epidemiology
  • Management of molecular science data, including basic bioinformatics

Clinical experiences

Important information

Clinical experiential learning is the range of activities trainees may undertake in order to gain the experience and evidence to demonstrate their achievement of module competencies and assessments. The list is not definitive or mandatory, but training officers should ensure, as best training practice, that trainees gain as many of these clinical experiences as possible. They should be included in training plans, and once undertaken they should support the completion of module assessments and competencies within the e-portfolio.


  • Investigate and report on of the clinical situations in which molecular investigations are performed.
  • Investigate, discuss and report on recent developments in molecular testing and how these may improve the scope and/or quality of investigation of micro-organisms in your laboratory, including the impact on these potential improvements on the care of the public and patients.
  • Prepare a portfolio of significant clinical cases reported in your presence and be able to list clinical outcomes and the main learning points that impact on service delivery, patient/public care and your own practice.
  • Critically appraise the internal quality control and external quality assessment of two molecular diagnostic methods and draw conclusions about method performance and quality.
  • Observe, discuss and report on the clinical and laboratory investigation of the molecular pathology of important microbial infections.
  • Review and report on the partnership between the clinical microbiology laboratory and other clinical specialisms in the investigation of the molecular pathology of infection and the importance of this partnership for service delivery and for patient/public experience and care.