Train the Trainer in Data Science for Pathogen Genomics and Surveillance

There is a growing need for specialised expertise in data science to support the work of researchers and healthcare professionals including clinical scientists, specialist registrars or consultants in medical microbiology in the UK, as the nature of their work changes and needs to incorporate big data, sequencing and genomics.
While curricula in the UK teach some genomics and data analysis and interpretation to these audiences, most training is left to advanced professional courses through postgraduate programmes and other independent training providers.

This proposal is motivated by the great demand in training for data science skills for genomics related to infectious pathogens, and a growing need for skilled trainers. Our goal is to enhance training capacity across the UK, able to provide education in Data Science for Pathogen Genomics and Surveillance for healthcare professionals working in the field of clinical microbiology.

We plan to achieve this by 1) implementing a series of Train-the-trainer (Tt) courses 2) offering mentorship and encouraging networking and 3) building and publishing freely available training resources. While regular training courses provide individual participants with skills on how to analyse and interpret their own data, TtT approaches apply the concept of forward teaching and equip professionals who are already knowledgeable in pathogen genomics data science with the skills needed to train others.

A key focus will be training participants in teaching and facilitation skills. We will also develop a project-based learning approach, where participants will be mentored to build their own training materials. This will be followed by in-person sessions, where they will demonstrate how they will deliver training to others and will receive feedback on their teaching methods. Participants will be supported to deliver training in their research or work environments, through mentorship and networking.
By the end of the project, we will publish freely available, ready-to-use training resources for use by trainers in data science for pathogen genomics in the UK.
This proposal brings together the expertise of the Centre for Genomic Pathogen Surveillance (CGPS) and the Wellcome Genome Campus Advanced Courses and Scientific Conferences (ACSC), who have previously collaborated in running several courses, including "Train-the-trainer Capacity Building for Genomic Surveillance of AMR in LMICs" (2019, Wellcome Genome Campus).

CGPS works to translate the analysis of pathogen spread and AMR research into public health benefit, by the generation of open-access tools for the interpretation of local sequence data in a global context. CGPS has experience in all aspects required to build capacity in genomic AMR surveillance, drawn from running an NIHR Global Health Research Unit, in collaboration with laboratories from Colombia, India, Nigeria and The Philippines.


ACSC have over 30 years experience in delivery of training courses for researchers and healthcare professionals. Key courses include Genomics of Clinical Microbiology and Genomics for Clinical Virology, which are primarily targeted at genomics researchers and healthcare professionals including clinical scientists, specialist registrars or consultants in medical microbiology in the UK. Online Future Learn MOOC courses developed by ACSC (https://www.futurelearn.com/search?q=bacterial+genomes) attract tens of thousands of participants every year. To date, ~13% of the online participants are from the UK (10,7k from the UK out of 79k total).

In summary, this project will develop a framework for new training resources tailored to professionals in clinical microbiology fields, enabling use of data science tools to enhance healthcare in the UK. Emphasising on mentorship and network building, the programme will provide a sustainable, standardised and scalable training model both for TtT and for direct training.

There is a growing need for strengthening training capacity in data science, tailored specifically for pathogen genomics and surveillance, for professionals who incorporate genomics and sequencing in microbiology and clinical diagnostics, perform bioinformatics analyses and interpret data from genomic analysis, routinely conduct pathogen surveillance and work on large-scale national projects the to track samples, link metadata, analyse and interpret sequencing data during disease outbreaks and pandemics. The increased demand for these skills requires building capacity by training educators and professionals with relevant skills to provide specific training in Data Science for Pathogen Genomics and Surveillance. We plan to achieve this in three steps. First, we will assess the current training needs for data science and pathogen genomics among healthcare professionals working in the field of clinical microbiology. With guidance from our scientific and clinical advisory boards, we will design and deliver 3 Train-the-trainer courses that integrate pedagogical and scientific concepts, which will enable participants to transfer to others knowledge and skills in data collection, linkage, analysis and interpretation for pathogen genomics and surveillance. The first modules of the course will run virtually and will expand participants' pedagogy and scientific knowledge. Then, a project-based learning approach, where participants will be mentored to build their own training materials will be applied. This will be followed by in-person modules, where they will demonstrate delivering training to others and will receive feedback on their methods. Furthermore, participants will be supported to deliver training in their work environments, through mentorship and networking. An evaluation framework will be designed to follow-up trainees and determine impact on professional development, careers and genomic data science skills among professionals in clinical microbiology.