PHPS41100 Precision Medicine in Infectio

Academic Year 2021/2022

Advances in precision medicine as applied to the study of infectious disease, have been enabled by developments in next generation sequencing (NGS) technologies. These have benefited from developments in high throughput data analysis techniques, and the ability to leverage information that provides a sound basis for decision making. Increasingly, genome-based approaches to diagnose infection and to inform individual patient treatment regimens are a reality in modern medicine. In addition, the speed with which genome data can now be generated and interpreted allows for the introduction of real-time, targeted outbreak control measures at a population level.

The focus of this module is to introduce the student to the concept of precision medicine through the use of relevant applications from the individual patient and societal perspective. At the patient level, there are many potential approaches including the use of companion diagnostics and antimicrobial susceptibility testing (AST) for optimising patient specific treatment regimens. Further depth can be obtained using approaches such as metagenomic analysis that provides a powerful tool for the detection of potential pathogens where traditional diagnostic techniques struggle. At the population level, real-life experiences with precision molecular-based epidemiology techniques illustrate the power of such tools and the targeted population-level public health and control interventions that are possible. A case in point is the application of these strategies applied to the control of the 2014 Ebola outbreak in West Africa. Further, as genomic data from food and environmental samples is increasingly used to guide the development of targeted food safety policies and procedures, the module will also address the application of genomics to food safety and the impact of host and environmental factors on the host gut microbiome and human health.

The module will be divided into four learning segments; i) precision medicine in the clinic, ii) precision molecular epidemiology, iii) introduction to precision food safety and iv) introduction to phylogenetic analysis of viral genomes.

Factors governing the design of the experimental and analytical approach to precision medicine in infectious disease will be explored in detail.

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Curricular information is subject to change

Learning Outcomes:

This module is designed to enable students to comprehend and appreciate the technologies underpinning precision medicine. They will also gain an appreciation of the challenges and opportunities that the genomics era can offer to the study of infectious disease. Through guided examples, students will gain an early understanding of how these new tools can be applied to the management and applied control of local and global infections/outbreaks.
Students will learn:
1. The technical concepts underpinning genome based approaches to diagnosis of infectious disease;
2. To interpret genome based diagnostic data for viral infectious pathogens (such as HIV-1; influenza virus and SARS-CoV-2, among others);
3. How metagenomics can be applied to syndromic investigation in patients;
4. The genomic tools required to investigate and describe the epidemiology of an outbreak of infectious disease
5. The power of precision epidemiology in understanding outbreak dynamics
6. An understanding of precision food safety;
7. To recognise and understand the application of phylogenetic analysis to bacterial and viral genomic sequences;
8. To critique of relevant scientific literature

Indicative Module Content:

1. Introduction to precision medicine and infectious disease
2. Interpretation of genome-based molecular diagnostics
3. Metagenomics and its application to pathogen detection
4. Metagenomics and pathogen detection –experimental design
5. Impact of WGS on global Influenza Vaccination Programme
6. Ebola and other emerging infectious diseases – application of genomics in preparedness
7. Application of genomics to control of SARS-CoV-2 epidemic
8. Application of genomics to precision food safety
9. Microbiome and human health
10. Introduction to the phylogenetic analysis of infectious pathogens
11. Critical evaluation of relevant scientific literature

Student Effort Hours: 
Student Effort Type Hours


Seminar (or Webinar)


Specified Learning Activities


Autonomous Student Learning




Approaches to Teaching and Learning:
Face to Face lectures; Specified Learning Activities; Autonomous Student Learning 
Requirements, Exclusions and Recommendations

Not applicable to this module.

Module Requisites and Incompatibles
Not applicable to this module.
Assessment Strategy  
Description Timing Open Book Exam Component Scale Must Pass Component % of Final Grade
Assignment: Identify the presence of potentially harmful bacteria in datasets from environmental samples by using available bioinformatics tools and propose next steps to confirm the risk and ameliorate it Coursework (End of Trimester) n/a Graded No


Carry forward of passed components
Resit In Terminal Exam
Summer No
Please see Student Jargon Buster for more information about remediation types and timing. 
Feedback Strategy/Strategies

• Feedback individually to students, post-assessment

How will my Feedback be Delivered?

There will be an opportunity for students to get individual feedback on their graded assignment post assessment either by email or face to face.

Name Role
Dr Michael Carr Lecturer / Co-Lecturer
Dr Cillian F De Gascun Lecturer / Co-Lecturer
Professor Séamus Fanning Lecturer / Co-Lecturer
Dr Gabo Gonzalez Lecturer / Co-Lecturer
Dr Guerrino Macori Tutor
Dr Joanne O'Gorman Tutor