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Application of Genomics in Infectious Disease

Module description

During this course, you will explore the genomic structure of infectious agents, the implication of acquisition or loss of nucleotides, genes and plasmids on pathogenicity, and the sensitivity of a pathogen to drug treatment.

You will also explore some of the huge resources of freely available sequence data and computational tools on which modern genomics research relies. In addition, you will investigate your own case study and present it to the class in a poster presentation. This module provides an exciting learning opportunity at the forefront of modern biology.

This module is primarily aimed at clinical practitioners, diagnostic service providers, scientists and researchers and those aspiring to specialise within an academic career pathway. You will learn from, with and about your peers, developing a mutual understanding and respect for the positive contributions that each will bring to Genomic Medicine.

This module is delivered in a blended learning structure, combining online resources with three contact days over a one-month period and, for Distance Learners, as an entirely online asynchronous structure.

Module aims - intentions of the module

This module will show how genomics can be used to improve diagnostic accuracy, predict which drugs are likely to be more effective in individual patients and contribute to the monitoring, treatment and control of infectious disease in individuals and populations.

Computer-based practical activities will consolidate use of bioinformatics tools and databases through hands-on analysis of genomics data (e.g. comparative genomics of pathogen genome sequences), and preparation and presentation of a research poster will provide a platform to critically discuss case studies.

Key employability skills include extracting and analysing complex information from web-based resources, and awareness of data driven decision-making. You will be provided with skills relevant to careers in medicine, medical research, and biosciences more broadly.

The content of the module is inspired by, and will inspire, cutting edge research in genomics. The bioinformatics tools and methods that you use will be the same as those used in the convenor’s microbial genomics research, identifying genetic variation from high-throughput DNA sequencing data. You will share learning, and will generate ideas for new research, alongside a leading genomicist and bioinformatician.

Intended Learning Outcomes (ILOs)

ILO: Module-specific skills

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

• 1. Evaluate how sequencing of the genome of infective organisms can be used in infectious disease for diagnosis, sub-classification and strain identity
• 2. Critically evaluate the emerging action of drugs in controlling infection e.g. HIV, TB
• 3. Critically evaluate the molecular basis of organism drug resistance in some infections and how this directs drug research
• 4. Critically evaluate how the genome sequence of pathogens can be used to investigate and manage suspected outbreaks of infection in hospital and community settings
• 5. Evaluate how sequencing of the genome of infective organisms can be used for assessing pathogenicity, antimicrobial resistance, drug selection and epidemic control

ILO: Discipline-specific skills

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

• 6. Explain the principles of epidemiology of infectious diseases
• 7. Explain the underlying principles of laboratory diagnosis, antimicrobial susceptibility testing, and epidemiological typing of pathogens

ILO: Personal and key skills

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

• 8. Critically reflect on personal practice and makes connections between known and unknown areas, to allow for personal development, adaptation and change
• 9. Innovate and respond to new technologies and evaluate these in the context of best practice and the need for improved service delivery
• 10. Communicate accurately and effectively with peers, tutors and the public

Syllabus plan

• 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
• Laboratory diagnosis, including genomic techniques and technologies, and appropriate sample type, analysis and interpretation of genomic data, and the role of bioinformatics
• Role of genomics in: infectious disease diagnosis, prognosis, drug selection, resistance, monitoring, epidemic control and drug research.

Accessibility note: As part of this course you will undertake sessions in the computing laboratory (of up to 80 students) that are typically 2 hrs in duration. Breaks are possible and students are welcome to leave the laboratory for short periods. In the event of unavoidable absence, it is possible to complete the computer practical tasks remotely. The course is available as a blended-learning option, where online asynchronous resources are complemented by in-person attendance at three contact days, which may fall outside of the University’s academic term dates; alternatively, the course can be taken entirely asynchronously online, making it suitable for Distance Learners.

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

Details of learning activities and teaching methods

Formative assessment

Summative assessment (% of credit)

Details of summative 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. The ‘Participation in online discussions’ component is not deferrable due to its practical nature. 

Referral – if you have failed the module overall (i.e. a final overall module mark of less than 50%) you will be referred in assessments as described in the table above. The mark given for a re-assessment taken as a result of referral will be capped at 50%.

Indicative learning resources - Basic reading

• Gardy JL, Loman NJ. Towards a genomics-informed, real-time, global pathogen surveillance system. Nat Rev Genet. 2018;19:9-20. doi: 10.1038/nrg.2017.88.
• Deurenberg RH, Bathoorn E, Chlebowicz MA, Couto N, Ferdous M, García-Cobos S, Kooistra-Smid AM, Raangs EC, Rosema S, Veloo AC, Zhou K, Friedrich AW, Rossen JW. Application of next generation sequencing in clinical microbiology and infection prevention. J Biotechnol. 2017;243:16-24. doi: 10.1016/j.jbiotec.2016.12.022.
• Lakin SM, Dean C, Noyes NR, Dettenwanger A, Ross AS, Doster E, Rovira P, Abdo Z, Jones KL, Ruiz J, Belk KE, Morley PS, Boucher C. MEGARes: an antimicrobial resistance database for high throughput sequencing. Nucleic Acids Res. 2017;45:D574-D580. doi: 10.1093/nar/gkw1009.
• Deng X, den Bakker HC, Hendriksen RS. Genomic Epidemiology: Whole-Genome-Sequencing-Powered Surveillance and Outbreak Investigation of Foodborne Bacterial Pathogens. Annu Rev Food Sci Technol. 2016;7:353-74. doi: 10.1146/annurev-food-041715-033259.

Indicative learning resources - Web based and electronic resources

• ELE page: https://vle.exeter.ac.uk/course/view.php?id=10248
• The role of next generation whole genome sequencing in TB diagnostics– Philip Butcher
• Nature Reviews Microbiology – Dangerous Pathogens

Key words search

Viruses, prokaryotes, infection, drug resistance, outbreaks