Module overview
You 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
Learning Outcomes
Learning Outcomes
Having successfully completed this module you will be able to:
- Critically evaluate the molecular basis of organism drug resistance in some infections and how this directs drug research
- Critically evaluate the emerging action of drugs in controlling infection e.g. HIV, TB
- Discuss and appraise how the genome sequence of pathogens can be used to track cross infection and outbreaks of infections among the population
- 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.
- Evaluate how sequencing of the genome of infective organisms can be used in infectious disease for assessing diagnosis, sub-classification and strain identity.
- Explain the differences between prokaryote and eukaryote genomes
Syllabus
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.
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.
| Type | Hours |
|---|---|
| Independent Study | 122 |
| Teaching | 28 |
| Total study time | 150 |
Resources & Reading list
Internet Resources
Online Tutorials: Nature Reviews Microbiology – Dangerous Pathogens.
Clinical and biological insights from viral genome sequencing.
100,000 Genomes Project Protocol (Section 3.3.3).
Viruses Special Issue "Next Generation Sequencing: New Developments and Discoveries in Virology".
Centers for Disease Control and Prevention (CDC), Public Health Genomics Epidemiology.
PHE Public Health Genomics ePathGen module (tutorials & case studies).
Genomic insights into tuberculosis.
Online Tutorials: NYU Genomics Lectures – Lectures 7,8,9,10.
A to Z guide to Infectious diseases.
PHG Foundation Report "Pathogen Genomes into Practice (parts I & II, pp17-88)".
From Theory to Practice: Translating Whole-Genome Sequencing (WGS) into the Clinic.
Clinical use of whole genome sequencing for Mycobacterium tuberculosis.
DNA Sequencing Predicts 1st-Line Tuberculosis Drug Susceptibility Profiles.
Centers for Disease Control and Prevention (CDC), Public Health Genomics Pathogen Genomics.
Assessment
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%.
Summative
This is how we’ll formally assess what you have learned in this module.
| Method | Percentage contribution |
|---|---|
| Written assignment | 50% |
| Written assignment | 50% |
Referral
This is how we’ll assess you if you don’t meet the criteria to pass this module.
| Method | Percentage contribution |
|---|---|
| Written assignment | 100% |
Repeat Information
Repeat type: Internal & External