Application of Genomics in Infectious Diseases

BIOL67971 Application of Genomics in Infectious Diseases 15 Semester 1 Postgraduate Taught Level 7 Sara Gago Unit coordinator 1 FHEQ level (Framework for Higher Education Qualifications) ' Masters/Integrated Masters P4 ' European Credit Transfer & Accumulation System Rating : 7.5 Genomic approaches are changing the way we investigate incidents of infectious disease at levels from the single case of infection through to outbreaks and global surveillance. While some technical approaches used in the study of infectious disease may overlap with those used in human genomics, there are many differences in the genetics of microorganisms and the methodology used which needs to be illustrated within this unit. The unit is intended to give the student an in-depth knowledge of the relevance of genomics to infectious disease, to provide hands on experience in carrying out and interpreting appropriate analyses and to develop specialist knowledge in infectious disease genomics. <div>Genomic approaches are changing the way we investigate incidents of infectious disease at levels from the single case of infection through to outbreaks and global surveillance. While some of the philosophies and technical approaches used in the study of infectious disease may overlap with those used in human genomics, there are many differences in the genetics of microorganisms and the methodology used which will be covered in this unit. The unit is intended to give the student an in-depth knowledge of the relevance of genomics to infectious disease, to provide hands on experience in carrying out and interpreting appropriate analyses and to develop specialist knowledge in infectious disease genomics.</div> <div> The aim of this module is that the student will have a greater understanding of 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 and control of infectious disease in individuals and populations.</div>  <ul> <li> Explain the principles of epidemiology of infectious diseases.</li> <li> Critically evaluate how the genome sequence of pathogens can be used to investigate and manage suspected outbreaks of infection in hospital and community settings.</li> <li> Explain the underlying principles of laboratory diagnosis, antimicrobial susceptibility testing, and epidemiological typing of pathogens.</li> <li> Critically evaluate the emerging action of drugs in controlling infection eg virus, bacteria and fungi</li> <li> Evaluate how sequencing of the genome of infective organisms can be used in infectious disease for diagnosis, sub-classification and strain identity.</li> <li> Evaluate how sequencing of the genome of infective organisms can be used in infectious disease for assessing pathogenicity, antimicrobial resistance, drug selection and epidemic control.</li> <li> Critically evaluate the molecular basis of organism drug resistance and how this directs to drug search.</li></ul> <ul> <li> To assess the most appropriate genomic approaches to address an infection-related question</li> <li> Critical evaluation of genomic analysis of pathogens as a means to inform antimicrobial treatments</li> <li> Critical evaluation of utility of purely genomic approaches to investigate incidents of infectious disease</li></ul>  <ul> <li> Choose and apply bioinformatics methodology commonly used for compiling microbial genomes or compare strains.</li> <li> Choose and apply bioinformatics methodology commonly used for identify microbial communities in clinical samples.</li></ul> <ul> <li> Bioinformatics methodology</li> <li> Confidence to interpret infectious disease bioinformatics analysis</li> <li> Report writing</li> <li> Scientific discussion</li></ul>   <div> Learning will focus on a case-based approach to ensure relevance to clinical practice. A range of formats will be used in both face-to-face and e-learning.Lectures, problem-based learning, case studies, group work and interactive seminars.</div>  2 Written assignment (inc essay) 80% 7 Oral assessment/presentation 20% Formative feedback will be provided in a draft of the written assignment before submission. Feedback on presentations will be provided in a dedicate course work session. MSc Genomic Medicine FT MSc Genomic Medicine FT PGDT Taught Component Optional MSc Genomic Medicine FT MSc Genomic Medicine FT (HEE) PGDT Taught Component Optional MSc Genomic Medicine PT MSc Genomic Medicine PT PGDT Taught Component Optional MSc Genomic Medicine PT MSc Genomic Medicine PT (HEE) PGDT Taught Component Optional PG Diploma Genomic Medicine FT PG Diploma Genomic Medicine FT PGDT Taught Component Optional PG Diploma Genomic Medicine FT PGDip Genomic Medicine FT(HEE) PGDT Taught Component Optional PG Diploma Genomic Medicine PT PG Diploma Genomic Medicine PT PGDT Taught Component Optional PG Diploma Genomic Medicine PT PGDip Genomic Medicine PT(HEE) PGDT Taught Component Optional PG Cert Genomic Medicine FT PG Cert Genomic Medicine FT PGDT Taught Component Optional PG Cert Genomic Medicine FT PGCert GenomicMedicine FT(HEE) PGDT Taught Component Optional PG Cert Genomic Medicine PT PG Cert Genomic Medicine PT PGDT Taught Component Optional PG Cert Genomic Medicine PT PG Cert Genomic Med PT (HEE) PGDT Taught Component Optional Genomic Medicine - CPD Genomic Medicine - CPD PGDT Taught Component Optional Genomic Medicine - CPD Genomic Medicine - CPD (HEE) PGDT Taught Component Optional MRes Genomic Medicine MRes Genomic Medicine PGDT Taught Component Optional N Includes but is not limited to:Books:The genetics of bacteria and their viruses. Studies in basic genetics and molecular biology. HAYES, W. 1964 pp. xii +740 pp.Reviews and Original Articles:<ul> <li> 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 Feb 10;243:16-24. doi: 10.1016/j.jbiotec.2016.12.022.</li> <li> Edwards DJ, Holt KE(2015). "Beginner’s guide to comparative bacterial genome analysis using next generation sequence data. Microbial Informatics and Experimentation, a 3:2.</li> <li> Golubchik T, Batty EM, Miller RR, Farr H, Young BC et al (2013). Within-host evolution of Staphylococcus aureus during asymptomatic carriage. PLoS ONE 8(5) e61319.</li> <li> Gomez CA, Budvytiene I, Zemek AJ, Banaei N. Performance of Targeted Fungal Sequencing for Culture-Independent Diagnosis of Invasive Fungal Disease. Clin Infect Dis. 2017 Nov 29;65(12):2035-2041. doi: 10.1093/cid/cix728.</li> <li> Harris SR, Cartwright EJ, Török ME, Holden MT, Brown NM, Ogilvy-Stuart AL, Ellington MJ, Quail MA, Bentley SD, Parkhill J, Peacock SJ (2013). Whole-genome sequencing for analysis of an outbreak of meticillin-resistant Staphylococcus aureus: a descriptive study. Lancet Infect Dis. 13(2): 130-6.</li> <li> Roetzer A, Diel R, Kohl TA, Ruckert C, Nubel U et al (2013) Whole Genome Sequencing Versus Traditional Genotyping for Investigation of a Mycobacterium tuberculosis Outbreak: A Longtitudinal Molecular Epidemiological Study. PLoS Med(2); e1001387.</li> <li> Rossen JWA, Friedrich AW, Moran-Gilad J; ESCMID Study Group for Genomic and Molecular Diagnostics (ESGMD). Practical issues in implementing whole-genome-sequencing in routine diagnostic microbiology. Clin Microbiol Infect. 2018 Apr;24(4):355-360. doi: 10.1016/j.cmi.2017.11.001.</li></ul> Websites:<a href="https://www.ecdc.europa.eu/">https://www.ecdc.europa.eu</a>https://www.gov.uk/government/organisations/public-health-england  0 0 150