module

Advanced Topics in Pathogen Evolution

Description - summary of the module content

Module description

Pathogens, or disease causing microorganisms, are ubiquitous and affect almost all parts of our everyday life. Their interactions with their hosts are dynamic, complex, and in many cases still not fully understood. As any other organism, pathogens aim to survive and reproduce, but in doing so, they can incur significant fitness costs on their hosts. Hosts, in response, have evolved various mechanisms to defend against pathogens, exerting selection pressure on the pathogens and leading to further evolutionary change. The main aim of this module is to provide you with an in-depth overview of the causes and consequences of pathogen evolution, how we study them and how we can ultimately use this information to develop new tools in our fight against infectious diseases. Through a series of research-led lectures, discussions, and hands-on practicals you will be exposed to a wide range of current topics related to pathogen evolution, including host-pathogen coevolution, evolution of virulence, antibiotic resistance, genetic diversity, genomic parasites, and emerging infectious diseases. Emphasis will further be put upon modern approaches and methodologies employed to investigate these evolutionary dynamics, from genome sequencing and bioinformatic analyses, to laboratory model system, to computer simulations. The module will be delivered by a team of researchers working at the cutting edge of their respective disciplines at our Penryn Campus and will provide you with a broad ranging understanding of key principles, modern methodologies, and open questions in the field of pathogen evolution.

Module aims - intentions of the module

This module deals with the frontiers of Pathogen Evolution. The module aims to provide a synthetic understanding of the scientific processes in general, but in particular to provide an in-depth understanding of the wide range of aspects underpinning pathogen evolution, spanning host-pathogen coevolution, evolution of virulence, antibiotic resistance, genetic diversity, genomic parasites, and emerging infectious diseases. Our attention to cutting edge approaches and methodologies used to investigate pathogen evolution spans genetic sequences and sequence analysis, phylogenetic comparative analysis, evolutionary model system, and mathematical modelling. You will first be introduced to these topics and methods and then skilled in how they relate to research at the frontiers of our current understanding in pathogen evolution.

This module will ensure that you will have the appropriate understanding of the theoretical and practical principles underlying pathogen evolution, in particular those that are relevant to your research project. The main aim of this module is to provide you with the ability to critically assess current scientific literature and methodologies across the field, which will greatly facilitate the planning and execution of your independent research project. The module will also equip you very well for a future research-oriented career.

Intended Learning Outcomes (ILOs)

ILO: Module-specific skills

On successfully completing the module you will be able to...

• 1. Describe, fully and systematically, key concepts and approaches in pathogen evolution
• 2. Critically and independently assess the research area
• 3. Conduct a literature review of a current research topic in the research areas covered

ILO: Discipline-specific skills

On successfully completing the module you will be able to...

• 4. Discuss ideas and construct coherent arguments (both in writing and orally) based on their independent and critical assessment of the discipline
• 5. Solve practical and theoretical problems in evolutionary biology
• 6. Critically assess scientific literature

ILO: Personal and key skills

On successfully completing the module you will be able to...

• 7. Professionally present new ideas and results (both in writing and orally)
• 8. Prioritise, generate, and summarise data relevant to the testing of rational hypotheses
• 9. Present written reports in a clear, concise, and logical manner
• 10. Think critically, and critically appraise and logically solve problems

Syllabus plan

Syllabus plan

Taught content

The module will include lectures and group discussions on the frontiers of our knowledge in key fields in Pathogen Evolution. Topics may change, but will typically include the following:

• Host-parasite Interactions and Co-evolution
• Evolution of Virulence
• Mechanisms and Effect of Pathogen Genetic / Antigenic Diversity
• Pathogen Population Structure
• Evolution of Antibiotic Resistance
• Genomic Parasites (Transposable Elements, Retroviruses)
• Role of Host Microbiota in Disease Ecology and Evolution
• Infectious Disease Emergence and Surveillance
• Pathogen Evolution in Natural Populations

Practical activities

The module will also include a strong practical component, focussed on key approaches in Pathogen Evolution. Topics may change, but will typically include the following:

• Genetic Sequencing
• Utilising Sequence Data
• Experimental Evolution
• Evolutionary Quantitative Genetic Analysis
• Mathematical Modelling

Learning and teaching

Learning activities and teaching methods (given in hours of study time)

Details of learning activities and teaching methods

Assessment

Formative assessment

Summative assessment (% of credit)

Details of summative assessment

Re-assessment

Details of re-assessment (where required by referral or deferral)

Re-assessment notes

Deferral – if you miss an assessment for certificated reasons judged acceptable by the Mitigation Committee, you will normally be either deferred in the assessment or an extension may be granted. The mark given for a re-assessment taken as a result of deferral will not be capped and will be treated as it would be if it were your first attempt at the assessment.

Referral – if you have failed the module overall (i.e. a final overall module mark of less than 50%) you will be required to redo the relevant assessment. If you are successful on referral, your overall module mark will be capped at 50%.

Resources

Indicative learning resources - Basic reading

The module will draw extensively on primary published research papers in peer-reviewed journals.

The following would serve as excellent background reading to support the learning in key areas

• Prescott’s Microbiology (McGraw Hill, 11^th edition)
• Brock Biology of Microorganisms (Pearson, 15^th edition)

Module has an active ELE page

Key words search

Pathogens, evolution, antibiotic resistance, virulence, coevolution