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The University of Southampton

MEDI6127 Applications of Genomics in Infectious Disease

Module Overview

The student will learn about the genomic structure of infectious agents, implication of acquisition or loss of nucleotides, genes and plasmids on pathogenicity, sensitivity of a pathogen to drug treatment and response to the host.

Aims and Objectives

Module Aims

From this module the student will understand how genomics can be used to provide more accurate diagnosis, predict which drugs are likely to be more effective and monitor treatment and control of infectious disease in individuals and populations.

Learning Outcomes

Learning Outcomes

Having successfully completed this module you will be able to:

  • Explain the differences between prokaryote and eukaryote genomes
  • Discuss and appraise how the genome sequence of pathogens can be used to track cross infection and outbreaks of infections among the population
  • Critically evaluate the emerging action of drugs in controlling infection e.g. HIV, TB
  • Critically evaluate the molecular basis of organism drug resistance in some infections and how this directs drug research
  • Evaluate how sequencing of the genome of infective organisms can be used in infectious disease for assessing diagnosis, sub-classification and strain identity.
  • Evaluate how sequencing of the genome of infective organisms can be used in infectious disease for assessing pathogenicity, drug resistance and drug selection; and for epidemic control.


• Infection as a cause of national and global morbidity and mortality • Transmission of human infections: person to person, food and waterborne, sexually transmitted, vector-borne • Prokaryotes, their genome, replication and population genetics • Genomic characterisation of viruses: DNA and RNA genomes, single-stranded, double stranded, segmented • Genomic comparisons of microbial strains in the context of outbreaks and transmissions in hospitals and the community • Anti-infective drug action • Mutation rate and drug resistance • Genomic evidence of individual susceptibility to specific infection • Role of genomics in: infectious disease diagnosis, prognosis, drug selection, resistance, monitoring, epidemic control, drug research.

Special Features

The module will be taught by an international faculty, at the forefront of their respective academic disciplines and professions. Adult learning methods will be used throughout and an emphasis placed upon interactive learning, practical demonstration and the interpretation of clinical scenarios to reinforce learning. Extensive e-learning facilities will be available to foster independent study

Learning and Teaching

Teaching and learning methods

The module will comprise two blocks of two days' intensive on-site teaching, each followed by a period of independent study. A variety of learning and teaching methods will be adopted to promote a wide range of skills and meet the differing learning styles of the group. The on-site teaching will include seminars, practical demonstrations, discussions and exercises surrounding interpretation of data and clinical scenarios, and specialist lectures given by a range of academic and health care professionals. This will ensure a breadth and depth of perspective, giving a good balance between background theories and principles and practical experience. Off-site independent learning will take place on the virtual learning environment hosted by the UoS.

Independent Study122
Total study time150

Resources & Reading list

Broad Institute for Infectious Diseases.

BioMed Central Genomics of infectious diseases special issue – articles from Genome Biology & Genome Medicine.

Evaluation of Whole-Genome Sequencing for Mycobacterial Species Identification and Drug Susceptibility Testing in a Clinical Setting: a Large-Scale Prospective Assessment of Performance against Line Probe Assays and Phenotyping.

Genomic insights into tuberculosis.

Beginner’s guide to comparative bacterial genome analysis using next-generation sequence data. Microbial Informatics and Experimentation. 2013;3:2.

A to Z guide to Infectious diseases.

PHE Public Health Genomics ePathGen module (tutorials & case studies).

Clinical use of whole genome sequencing for Mycobacterium tuberculosis.

DNA Sequencing Predicts 1st-Line Tuberculosis Drug Susceptibility Profiles.

PHG Foundation Report "Pathogen Genomes into Practice (parts I & II, pp17-88)".

Viruses Special Issue "Next Generation Sequencing: New Developments and Discoveries in Virology".

Online Resource: The role of next generation whole genome sequencing in TB diagnostics - Philip Butcher.

Centers for Disease Control and Prevention (CDC), Public Health Genomics Epidemiology.

Interpreting whole genome sequencing for investigating tuberculosis transmission: a systematic review.

Genomics and infectious disease: a call to identify the ethical, legal and social implications for public health and clinical practice – Genome Medicine 6:106 2014.

Online Tutorials: NYU Genomics Lectures – Lectures 7,8,9,10.

Rapid antibiotic-resistance predictions from genome sequence data for Staphylococcus aureus and Mycobacterium tuberculosis.

From Theory to Practice: Translating Whole-Genome Sequencing (WGS) into the Clinic.

Centers for Disease Control and Prevention (CDC), Public Health Genomics Pathogen Genomics.

Online Tutorials: Nature Reviews Microbiology – Dangerous Pathogens.

Clinical and biological insights from viral genome sequencing.

100,000 Genomes Project Protocol (Section 3.3.3).


Assessment Strategy

The assessment for the module provides you with the opportunity to demonstrate achievement of the learning outcomes. There will be two components to the assessment i) 1500 word written assignment 1, and ii) 1500 word written assignment 2. The pass mark for the module and all assessed components is 50%. If you do not achieve the pass mark on this module by achieving 50% or more in all components, you may still pass by compensation. To do this, you must achieve a qualifying mark of 40% on each assessed component. Each of the component marks is then combined, using the appropriate weighting, to give an overall mark for the module. If this overall mark is greater than or equal to 50% you will have passed the module. If your overall mark is less than 50% when the weighting has been applied to the components, you will have failed the module. If you have not achieved 40% or more on all components, you cannot use compensation and have failed the module. If you have failed the module, you will have the opportunity to submit work at the next referral (re-sit) opportunity using the method outlined below. You must achieve the pass mark in all referred components. On passing your referrals, your final module mark will be capped at 50%.


MethodPercentage contribution
Written assignment  (1500 words) 50%
Written assignment  (1500 words) 50%


MethodPercentage contribution
Written assignment  (2500 words) 100%

Repeat Information

Repeat type: Internal & External

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