Implementation of Whole Genome Sequencing (WGS) in ... Implementation of Whole Genome Sequencing (WGS)

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  • Implementation of Whole Genome Sequencing (WGS) in

    Microbiology Reference Services

    Prof Matt Holden, University of St Andrew and Health Protection Scotland on

    behalf of the Dr Camilla Wiuff, Strategic Lead Microbiology, Health Protection

    Scotland and the WGS Service Transformation Group

    Healthcare Science Annual Event, 70th Anniversary of the NHS Celebrating Achievement Building Influence

    28th June 2018

    https://www.google.co.uk/url?sa=i&rct=j&q=&esrc=s&source=images&cd=&cad=rja&uact=8&ved=0ahUKEwiU1Y-exbLZAhXC7BQKHZeZAqQQjRwIBw&url=https://www.aspenpeople.co.uk/NSSstrategy/about.htm&psig=AOvVaw0d3yd7Gbm2D7CgcnZaGWsu&ust=1519148995012446

  • Whole Genome Sequencing and Genomics

    https://www.google.co.uk/url?sa=i&rct=j&q=&esrc=s&source=images&cd=&cad=rja&uact=8&ved=0ahUKEwiU1Y-exbLZAhXC7BQKHZeZAqQQjRwIBw&url=https://www.aspenpeople.co.uk/NSSstrategy/about.htm&psig=AOvVaw0d3yd7Gbm2D7CgcnZaGWsu&ust=1519148995012446

  • • WGS is a new technique that allows us to read the genetic code of bacteria to

    guide optimal treatment, track their spread and break the chain of disease

    transmission.

    • WGS generates more accurate and comprehensive intelligence

    about pathogens than any other technique.

    • WGS will transform how we investigate and

    control outbreaks and how we manage

    infected patients.

    WGS is a game changer in the global fight against infection

    https://www.google.co.uk/url?sa=i&rct=j&q=&esrc=s&source=images&cd=&cad=rja&uact=8&ved=0ahUKEwiU1Y-exbLZAhXC7BQKHZeZAqQQjRwIBw&url=https://www.aspenpeople.co.uk/NSSstrategy/about.htm&psig=AOvVaw0d3yd7Gbm2D7CgcnZaGWsu&ust=1519148995012446

  • • Prior to 2013, individual Scottish reference laboratories had established

    collaborative WGS research projects with academic partners

    • However, there was no coordinated approach to implementing WGS in

    public health microbiology (PHM) services

    • A national workshop on future WGS based PHM services initiated a

    coordinated approach to introduction of WGS technology in two

    reference centres in Glasgow and Edinburgh (2015)

    The journey to WGS in public health microbiology in Scotland

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  • Our strategic objective

    ....is to implement and provide a sustainable,

    resilient, responsive, high quality and cost

    effective microbial WGS capability for NHS

    Scotland.

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  • Clinical governance

    Since 2015 the national steering group, WGS Implementation Group,

    has driven and overseen structured implementation of WGS

    Since 2017, the WGS IG was included in the Scottish Health

    Protection Network’s (SHPN) coordination of national public health

    developments

    Operational developments

    The WGS Service Transformation Group has contributed to

    development of all parts of the service, including laboratory

    methodology and setup, bio-informatics analysis and IT built

    The WGS Implementation Group

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  • WGS Service Transformation Group (WGS STG)

    Camilla Wiuff

    Matt Holden

    John MacDonald

    Derek Brown

    Sharif Shaaban

    Roisin Ure

    Henry Mather

    John Coia

    Lesley Alison

    Anne Holmes

    Louise Seagar

    Ian Laurenson

    Kate Templeton

    https://www.google.co.uk/url?sa=i&rct=j&q=&esrc=s&source=images&cd=&cad=rja&uact=8&ved=0ahUKEwiU1Y-exbLZAhXC7BQKHZeZAqQQjRwIBw&url=https://www.aspenpeople.co.uk/NSSstrategy/about.htm&psig=AOvVaw0d3yd7Gbm2D7CgcnZaGWsu&ust=1519148995012446

  • Collaborative working Service transformation within budgetary constraints

    Coordination of WGS service transformation

    Strategic direction

    Options appraisal

    Funding

    Clinical/

    Scientific developm

    ents

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  • • Options appraisal of WGS providers resulted in ‘2-site

    reference laboratory model’ with organism/clinical area

    specialised services

    Service design and planning

    • The model provides service flexibility,

    responsiveness, resilience, scalability and

    strategic oversight that will allow optimal

    response to public health threats and

    emergencies

    • Utilising the expertise and clinical

    leadership of existing reference

    laboratory and HPS teams

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  • Designing the architecture of the service

    Microbial WGS Service Model 11 of 16

    Sample Originator

    Reference Laboratory

    HPS International

    Repositories

    High Performance

    Computing

    EMBL-

    EBI

    DNA Extraction

    DNA Library

    Preparation

    Sample

    Reception

    Genome

    Assembly/

    Mapping

    and Annotation

    Identify and

    interpret variation

    Report Results

    Epidemiological

    Analysis

    Buffer

    Buffer

    Sequencing QC

    HPS Staff

    ECOSS

    GenBank

    Run QC

    Sample Collection

    and Dispatch

    Wider Clinical and

    Public Health

    Advice

    DDBJ