Application of Genomics in Infectious Disease

Module titleApplication of Genomics in Infectious Disease
Module codeBIOM567
Academic year2018/9
Credits15
Module staff

Dr David Studholme (Convenor)

Duration: Term123
Duration: Weeks

4

Number students taking module (anticipated)

40

Description - summary of the module content

Module description

The analysis of whole genomes has revolutionised biological research in recent years. Determining the complete genome sequence of almost any microbial pathogen is now within the reach of most research bioscientists. Furthermore, recent technological advances have made it possible to study gene expression and epigenetic modifications on a genome-wide scale. Many of these genomics technologies are based on microarrays and massively-parallel sequencing methods (“next-generation sequencing” or NGS). To gain the maximum benefit from these advances now requires new approaches to biological and biomedical research and an increasing role for computational analysis of biological sequence data (bioinformatics). In this module, you will learn about the cutting-edge technologies that are driving advances in our understanding of pathogen genomes and how these methods offer potential for more accurate diagnosis, predict which drugs are likely to be more effective and monitor treatment and control of infectious disease in individuals and populations.

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 as a group task and present it to the class in a group 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.

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 classes will consolidate use of internet-based bioinformatics tools and databases through hands-on analysis of genomics data (e.g. comparative genomics of pathogen genome sequences), and poster sessions 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 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 in infectious disease for assessing: diagnosis, sub-classification and strain identity, pathogenicity, drug resistance and drug selection; and for 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

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
  • Role of genomics in: infectious disease diagnosis, prognosis, drug selection, resistance, monitoring, epidemic control, drug research.

Learning and teaching

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

Scheduled Learning and Teaching ActivitiesGuided independent studyPlacement / study abroad
181320

Details of learning activities and teaching methods

CategoryHours of study timeDescription
Scheduled Learning and Teaching3Lectures
Scheduled Learning and Teaching15Workshops
Guided Independent Study5Preparation for scheduled teaching and learning
Guided Independent Study10Tutor guided online discussion forum
Guided Independent Study10Preparation of poster
Guided Independent Study22Preparation and performing data handling and scientific writing exercise
Guided Independent Study85Online resources and independent guided literature research

Assessment

Formative assessment

Form of assessmentSize of the assessment (eg length / duration)ILOs assessedFeedback method
Online quizzesWeekly1-6Written
Participation in online discussion forumWeekly1-9Oral

Summative assessment (% of credit)

CourseworkWritten examsPractical exams
10000

Details of summative assessment

Form of assessment% of creditSize of the assessment (eg length / duration)ILOs assessedFeedback method
Poster on a relevant published research study50A31-9Oral and written
Data handling and scientific writing exercise501000 words plus tables and diagrams1-6Written

Re-assessment

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

Original form of assessmentForm of re-assessmentILOs re-assessedTimescale for re-assessment
Poster on a relevant published research studyPoster on a relevant published research study1-9August Ref/ Def
Data handling and scientific writing exerciseData handling and scientific writing exercise1-6August Ref/ Def

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 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%.

Resources

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, GarcĂ­a-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

Module has an active ELE page

Key words search

Viruses, prokaryotes, infection, drug resistance, outbreaks

Credit value15
Module ECTS

7.5

Module pre-requisites

None

Module co-requisites

None

NQF level (module)

7

Available as distance learning?

No

Origin date

01/12/2015

Last revision date

01/03/2018