Module - Molecular Pathology in Infection Sciences (SLS202)


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 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.

Work-based Competencies

Learning outcome Title Knowledge
1 1,2

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

  • Principles, scientific basis and clinical application of commonly performed analytical procedures in molecular pathology.
  • The repertoire, specimen requirements, ordering and turnaround times of the molecular pathology investigations performed by the department.
  • Reasons for and sources of referral of molecular pathology samples.
  • The range of appropriate investigations and their selection.
2 1,4

Receive, process and store common molecular pathology specimens.

  • Minimum data set required for identification of samples and the importance of ensuring that this is complete and correct.
  • The repertoire, specimen and storage requirements.
  • Factors affecting sample integrity and appropriate corrective action.
  • Procedures for handling samples which may contain category 2, 3 and 4 pathogens.
  • Types and implications of hazards and risks associated with handling of specimens and relevant control measures.
  • The quality management process that ensures the correct location and storage of documentation and specimens at each stage of the process.
  • Infection risk from blood samples.
  • Health and safety requirements of working with molecular diagnostic systems.
  • Safe laboratory practices, including principles of decontamination of equipment and work areas.
  • Quality assurance procedures and their application.
  • Local and national health and safety policies and procedures and their application.
  • Relevant records, their importance and how to complete these correctly.
  • The procedures for assuring confidentiality of patient information.
3 2,3

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.
  • The principles of PCR.
  • The significance of contamination and sensitivity of PCR. 
  • Hazards and risks associated with PCR.
  • Relevant current quality control procedures.
  • Characteristics of substandard reactions.
  • Factors affecting the integrity of samples and reagents, including lability and contamination.
  • Factors affecting integrity of reagents used in the tests conducted and relevant sensitivities to conditions of cold, heat and light.
  • Principles of electrophoresis of nucleic acids.
  • Principles of radioactive and fluorescent image detection.
4 2,3

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

  • Principles and scientific basis of automated analysers.
  • Principles and methods of laboratory investigations and clinical findings in testing molecular pathology samples.
  • Quality standards in the use of manual, semi-automated and automated equipment deployed in the molecular pathology laboratory.
5 3,4

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

  • The application of IQC and EQA methods used in molecular diagnostic testing.
  • The implications of non-conformance.
6 4

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

  • The procedures for assuring confidentiality of patient information.
  • Laboratory and hospital information systems.
  • Use of microcomputer software for molecular applications, including an introduction to bioinformatics.
7 4,5

Produce basic interpretative reports on common molecular pathology investigations.

  • The information to be included in an interpretative report.
  • How to construct an interpretative report and the format required for presentation.
  • Limits of responsibility in the authorisation and issue of interpretative reports.
  • Clinical conditions that may require urgent action and how to instigate such action.
  • Normal and abnormal results and their significance to the clinical question or condition.
  • The preparation of reports and the reporting process for patients being investigated for infection using molecular diagnostic testing.
8 1,2

Control infection risks in accordance with departmental protocols.

  • Protocols and requirements for hygiene and infection control related to the relevant range of investigations, including preparation, conduct and completion of investigation.
  • Protocol for hand washing and how effective hand washing contributes to control of infection.
  • The importance, range and correct application of aseptic techniques in the investigation of molecular pathology samples.
  • Risks and hazards associated with non-compliance.
9 1,2

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

  • The relevant health and safety regulations for laboratory and clinical investigations.
  • The specific health and safety regulations for the specialism, type of specimen/sample and investigation.
  • The potential hazards and risks and the actions to be taken to minimise these.
  • Responsibilities and scope of practice of laboratory personnel involved in performing investigations and reporting those investigations to users.

Work-based assessment

Complete 1 Case-Based Discussion(s)
Complete 1 of the following DOPS and/or OCEs
Type Title
DOPS 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
OCE An appropriate activity agreed with your Training Officer