Title Infectious Disease Pathology and Host Pathogen Interaction
Type Stage Two
Code HBI121
Requirement Compulsory

Module objective

By the end of this module the Clinical Scientist in HSST will be able to analyse, synthesise and apply their knowledge and understanding of the aetiology of infection and be able to apply this knowledge to selection of appropriate clinical diagnostic methodologies. They will be able to appraise and evaluate the current understanding of molecular biology of infection (including a broad range of pathogens) and host–pathogen interactions at a cellular and molecular level. They will also be able to interpret the laboratory procedures and relate to others the considerations when performing metagenomics experiments and a working knowledge of how to perform bioinformatics analyses that assess and help with the interpretation of metagenomics data. The Clinical Scientist in HSST will also be expected to consistently demonstrate the attitudes and behaviours necessary for the role of a CCS.

Knowledge and understanding

By the end of this module the Clinical Scientist in HSST will be able to analyse, synthesise, evaluate and critically apply their expert knowledge of infection to the clinical management of patients, including:

  • Molecular pathology of infectious disease (e.g. toxin production, cell invasion).
  • Protein–protein interactions (in particular host–receptor binding by pathogen surface proteins).
  • Protein modelling, including modelling the interaction of antimicrobials with their targets.
  • Immunological responses to pathogens.
  • Microbiomes.
  • Sequencing of microbiomes (enrichment and subtraction methods in the laboratory).

Technical and clinical skills

By the end of this module the Clinical Scientist in HSST will have a critical understanding of current evidence and its application to the performance and mastery of a range of technical skills and will be apply to apply this to the diagnosis, typing and surveillance of infectious disease, and will:

  • Search pathogen genomes for proteins that are involved in the pathogenesis of disease, including toxins, surface proteins and drug resistance targets.
  • Use software that predicts potentially immunologically -relevant epitopes.
  • Analyse protein–protein networks involving host and pathogen proteins in order to interpret which proteins form important nodes in host-pathogen pathways,
  • Analyse microbiomes using 16S deep sequencing.
  • Analyse microbiomes using amplicon sequencing, metagenomics and other techniques as they move from research into routine use (e.g RNASeq, proteomics and long-read sequencing such as nanopore).

By the end of this module the Clinical Scientist in HSST will be expected to critically reflect and apply in practice a range of clinical and communication skills with respect to bioinformatics analysis of pathogen sequence and host–pathogen interactions. The Clinical Scientist will communicate effectively with the public, patients, carers, clinicians, academics and other healthcare professionals, and will:

  • Apply bioinformatics expertise to the clinical interpretation of infectious disease and its consequences.

Attitudes and behaviours

This module has no attitude and behaviours information.


Code Title Action
HBI1-1-20 Clinical Bioinformatics - Genomics [v1] View