http://www.fao.org/about/meetings/wgs-on-food-safety-management/en/ Developing a national strategy to bring pathogen genomics into practice. Presentation from the Technical Meeting on the impact of Whole Genome Sequencing (WGS) on food safety management and GMI-9, 23-25 May 2016, Rome, Italy.

1. Developing a national strategy to bring
pathogen genomics into practice
Sobia Raza
GMI 2016, Rome
25th May 2016

2. About us
The PHG Foundation is a pioneering independent
think-tank with a special focus on genomics and other
emerging health technologies that can provide more
accurate and effective personalised medicine.
• Active since 1997
• Member of Cambridge University Health Partners
and Cambridge Institute of Public Health
• Funded by philanthropy, grants, and fees for
commissioned work

3. Our mission
Making science work for health
Harnessing genomic and bioscience research to
deliver improved and affordable healthcare
We provide knowledge, evidence, tools and
opportunities for policymakers to deliver
rational and responsible changes in health
policy and practice.

4. Pathogen Genomics into Practice
Roadmap of policies
and practices
35 supporting
Recommendations
Organisation
specific messages
www.phgfoundation.org/reports/16857
To support the
development and
delivery of
genomics informed
infectious disease
services that are
evidence based,
high quality, and
available
population-wide
on an equitable
basis

5. Bite size briefings
www.phgfoundation.org/id

6. Project Steering Group
• Dr Tom Barlow - Department of Health (from Mar 2014 – Jul 2014)
• Dr Paul Cosford - Public Health England
• Professor Saheer Gharbia - Public Health England London
• Dr Dorian Kennedy - Department of Health (to Mar 2014)
• Professor David Lomas - University College London
• Dr Christine McCartney - Public Health England
• Professor Julian Parkhill - Wellcome Trust Sanger Institute
• Mr Colin Pavelin - Department of Health (from Jul 2014)
• Professor Sharon Peacock - University of Cambridge (to Sep 2014)
• Professor Tim Peto - John Radcliffe Hospital, Oxford
• Dr Estee Torok - University of Cambridge (from Sep 2014)

7. Our team
Dr Hilary Burton
Director
(Consultant in Public Health
Medicine)
Dr Mark Kroese
Deputy Director
(Consultant in Public Health
Medicine)
Dr Philippa Brice
Director External Affairs
Alison Hall
Head of Humanities
Dr Leila Luheshi
Head of Science
Dr Sobia Raza
Data Science – Policy Analyst
Dr Gurdeep Sagoo
Health Economist /
Epidemiologist
Dr Sowmiya Moorthie
Epidemiologist / Scientist

8. Expertise - Stakeholder consultation
PHE microbiology services (Colindale and
regional labs)
NHS microbiology labs (inc. private
providers)
WT Sanger Institute
University research departments
HICF collaborations
Dept. of Health
Food standards agency
EMBL-European Bioinformatics Institute
Global Microbial Identifier
Costello medical consultants
THIS/NPEx
Professional groups Organisations / departments
Epidemiologists
CCDCs
Medical microbiologists
Infectious disease clinicians
Clinical virologists
Infection control nurses
Public health microbiologists
Clinical scientists (microbiology)
Clinical scientists (molecular genetics)
Bioinformaticians
Govt. health policy advisers
Govt. genomics policy advisers
ELSI advisers
Health economists
Research scientists
Clinical informatics experts

9. Workshops
• WS1–
Scoping and horizon scanning to determine current
and future range of applications of pathogen
genomics and identify barriers to implementation
• WS2 –
Work with translational researchers and frontline
service users and deliverers to generate
recommendations to address barriers to
implementation across:
– Service delivery
– Strategic issues
– Data management

10. Engagement
• Engagement event
Discuss report and recommendations with stakeholders:
– Public Health England (PHE)
– Department of Health
– National Health Service (NHS)
– Department for Environment, Food and Rural Affairs (DEFRA)
– Animal and Plant Health Authority (APHA)
– Food Standards Agency (FSA)

11. Assess needs
Configure
Quality assure
Accredit
Evaluate
Establish validly & utility
Standardise data
formats
Wider applications of genomics in infectious disease
Building an evidence base II: cost effectiveness
of PG services
Delivering safe & effective services in a dynamic
technology & knowledge environment
Building an evidence base I: developing, demonstrating &
evaluating clinical utility
ELSI of implementing pathogen genomics
Strategic coordination
& investment
Ensure collation &
curation of samples
& data
Enable & regulate
data access
www.phgfoundation.org/roadmap

12. The catalyst:
A set of real or virtual
structures that amplifies
and integrates the current
activities in pathogen
genomics to accelerate
and increase the
effectiveness of their
impact on patient and
population health.

13. Infectious disease genomics in England-
who’s involved?
• The management of infectious disease is spread across a wide
range of organisations and professional groups
• Each has a different baseline level of awareness and engagement
with genomics and different / multiple roles
Public Health England Wider health system Frontline services
e.g. infection control nurses,
field epidemiologists,
microbiology scientists,
service commissioners
e.g. Department of Health,
NHSE,
Food Standards Agency,
DEFRA,
APHA,
Industry
Remit spans:
Surveillance,
National infection control,
National emergency response,
Specialist microbiology services,
R&D

14. Strategic coordination- what’s required?
One health approach
Forum for frontline
services workforce
Interoperation of services
across organisations
International
collaboration
Cross organisational
leadership
Synergy in the development of
genomics programmes
Interaction with other governments
and representation within
international initiatives
Leadership group to ensure
strategies are aligned and service
delivery is coordinated
National collaborative network to
share knowledge, best practice,
and agree standards

15. Data integration– what’s required?
Incentives Mechanism
How?
An effective data management strategy to realise the benefits for
population health and drive innovation and expansion of genomics
informed services
…and /or a mandate to
share data with public
health authorities.
Adequate infrastructure and
support to facilitate data
deposition at a practical level

16. Data integration– what’s required?
Agreement on:
Timing
Data qualityTransparency
Database
To ensure data is available within
actionable timeframes for public
health and future developments
To ensure proportionate and
responsible release of data
through ELSI evaluation
To aid interoperability and
allow aggregation and analysis
To ensure processes for
sharing are sustainable and
supported

17. How could genomic & clinical data be managed?
A vision of a data management strategy

18. • An effective data management strategy to improve current delivery of
pathogen genomic services and to drive research, innovation and expansion of
future genomics informed services is essential.
• Without strategic coordination of policy and practice across all the relevant
organisations involved in the delivery of pathogen genomics, the effectiveness of
the technology to inform infectious disease management will be undermined
• Clear national strategy is key to supporting local adoption and diffusion of
pathogen genomics and facilitating international infectious disease
management
Conclusions
Local National International

19. How can we work together to support
pathogen genomics implementation?
• Strategic intelligence covering regulatory and public affairs,
health economics and reimbursement issues
• Technology and health service appraisal
• Policy evaluation and development
• Health needs assessment and service review
• Evaluation and implementation planning
Our services:
www.phgfoundation.org/consultancy
Contact:
leila.luheshi@phgfoundation.org
sobia.raza@phgfoundation.org

20. sobia.raza@phgfoundation.org