Dr Marie Anne Chattaway Pathogen Lead for Salmonella Services Gastrointestinal Bacteria Reference Unit National Infection Service PHE, Colindale

Managing the Transition of Implementing WGS Training PHE staff with the change

EURL-AR Training Course September 2017, Copenhagen

GBRU provide a range of specialised services

•National reference service for identification and typing of gastrointestinal (GI) bacterial pathogens

•National surveillance, outbreak detection and investigation.

•Research and development, training and education.

•Response to emerging GI bacterial infections (e.g non-O157 VTEC, enteroinvasive E. coli), Identification and strain characterisation for major global enteric pathogens (Salmonella, E. coli, VTEC, Listeria monocytogenes , Campylobacter, Shigella, Yersinia, Vibrio, Clostridia, Bacillus, Helicobacter).

2 Training PHE staff with the WGS change

Challenge: PHE was the first organisation in the world to routinely use WGS as a replacement for traditional microbiological typing techniques to provide identification, typing and surveillance services. How did we manage the transition for staff to this radical change?

3 Training PHE staff with the WGS change

Validation of WGS Assay

Is new method as sensitive as

previous method?

Have customers been informed of

the change?

Are the results fit for purpose?

Will turnaround times be affected?

What will the cost be?

Does the output of results affect stakeholders

analysis?

What MOLIS development is

required?

Are Bioinformatics pipelines in place?

What training is required?

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People

Process Tools

Change

Change Management Model

Assess

Design

Implement

Manage Change

Evaluate

Safety and Quality Validation of change

Merge processes Systems of work

Phased based change Change RA

Staff engagement Culture

Competency Delegation IPR targets

Surge Capacity Expertise

Capital Bids Surge Capacity

Contingency Planning

Calibration

All Challenges are interlinked

Quality, Safety & Governance

Updating systems and following current standards

Staff Expertise

Staff retention, contingency planning, development, surge

capacity

Technology & Culture

Changing culture in NIS with technological advances

Organisational Change

Ensuring NIS adapt and meet PHEs mission

Service Provision

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A polyphasic and multidisciplinary training approach is needed

What will the use of WGS as a replacement for traditional techniques look like?

Pathogen Expertise

Laboratory Results

Surveillance Data

Clinical Picture

Bioinformatics Analysis

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Safety Quality

Governance Research Funding

Budgeting Informatics Modelling Business Training

Management Stakeholders Global Health

Multidisciplinary Approach

KEY: ENGAGE WITH STAFF! Continually engage with staff at all levels throughout the change process

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Assess the training needs for the new

processes: Do we have the right skill mix?

Microbiologists Bioinformatics

Informatics (LIMS)

Anonymous feedback

Monthly Updates

Workshops

Weekly Seminars

Action: Get staff to understand that they

have transferable skills and still needed for the

future.

Microbiologists

Bioinformatics

LIMS

Give feedback

Review

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Validation

SOPs

Worksheets

Risk Assessments

Competency assessments

Audit process for GAPS

Documentation

ISO 15189

Need to ensure correct documentation is in place

Training of staff to meet requirements to move into genomics

Didn’t have extra funds for new staff so we had to use the staff resource we had available

Continually engage with staff at all levels

Training plans for staff – applicable to current and new staff

Involving staff in the Development process – next few slides

Training aids: SOPs worksheets and competency documents

Different grades requires different levels of training, lower grades tend to be section specific and higher grades need to understand the full end to end process.

Weekly gastro seminar series to gain understanding of application and not just the technique for all staff

Validation training on interpretation of results – There is a two stage validation process (technical and medical) and follow up work maybe needed

Validation projects involves senior staff, microbiologists and bioinformatics – an integrated approach.

Rotation of staff across the unit for resilience.

IPR targets set for staff across the department

Co-publication of manuscripts will involve all relevant grades of staff

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10

Lysis & enzymatic

steps Run the

QiaSymphony DNA extraction

Quantify DNA

extracts

Transfer DNA to Sequencing

Service

Samples arrive

Glomax - Promega

LabChip – Perkin Elmer

Laboratory side: Need to ensure the system is defined and protocol and staff are trained

Slide by Satheesh Nair

Training PHE staff with the WGS change

Example: Daily High-Throughput DNA extraction

Laboratory Training

Methods

Organisms processed: Salmonella, E.coli, Shigella, Listeria and Campylobacter

Plating out and inoculating broths/plates

Recognising contamination and purifying.

Inactivation of cultures

Qiasymphony extraction on HG2/HG3 inactivated broths

Submission to sequencing service on genesifter platform

Ideal Skill mix

Senior HealthCare Scientist/BMS to supervise and troubleshoot and offer support

Experienced/medium grade scientist

X 2 low grade support staff

Approach:

Was able to use GBRU microbiologists and retrain staff.

Rotation was implemented across GBRU for improved resilience, enhancement of skills and staff interest

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Need to ensure Laboratory Information Management Systems (LIMS) are updated

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Previous – Biochemistry, serology, PCR

Now – NGS quality metrics, ID, genes,

serogroup

Informatics Training

Methods

LIMS workflows that need updating: Salmonella, E.coli, Shigella, Listeria and Campylobacter

Designing new LIMS workflows that are pathogen specific and fit for purpose for WGS outputs.

Developing and changing steps in MOLIS as appropriate.

Developing queries of outputs

Ideal Skill mix

Experienced Informatics Data manager

X 3 LIMS super-users for the different pathogen areas

Approach:

Only have one data manager staff member

Trained X 3 microbiologists in LIMS skills to help support workflow changes.

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Need to ensure Bioinformatics pipeline is in place

Export Text (from bioinformatics)

GDW

Monophasic Typhimurium PCR

Preliminary sequence types

Upload to Short Read Archive

SnapperDB GeneFinder AMR

MOLIS Slide from: Phil Ashton/Satheesh Nair

NCBI BioProject accession: PRJNA248064

Bioinformatics Training

Methods

Development of script for high through-put data processing

Monitoring and troubleshooting with each batch of data release

Development of cluster tools for outbreak detection

Data analysis for validation of new processes

Phylogenetic tree generation and outbreak support in OCTs

Ideal Skill mix

Centralised PHE Bioinformaticians

Senior GBRU Bioinformatics Lead

X 3 GBRU supporting Bioinformaticians

Pathogen specific bioinformaticians within the unit are essential

Approach:

Only had 2 Bioinformatician. Converted X 1 microbiologist post when a BMS had left the department. Currently have an additional microbiologist on a project secondment.

We are training microbiologists and bioinformaticians in genomic analysis

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Need to ensure microbiologists can interpret, analyse and report results in a fit for purpose manner to our service users

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Final Validation

ID and typing

information on report

Report atypical

outbreaks

Biological Assessment

Fits in with clinical picture

Is further work

needed

Initial Assessment Quality Metrics Contamination,

pipeline issues

Microbiological Validation Training

Methods

Assessment of WGS data quality metrics

Recognising contamination of results, bioinformatic pipeline and importing issues

Assessment of results with senders findings and clinical picture

Organising further microbiological work where appropriate.

Assessment of multiple tests undertaken for atypical/rare strains for reporting.

Recognising potential outbreaks that may not be part of the clustering pipeline.

Ensuring all samples are reported – samples will be in different stages of testing

Need two staff for each pathogen – one for technical validation and one for medical validation

Ideal Skill mix for resilience

X 4 Specific Senior Pathogen Leads /Experts

X 4 Supporting high grade BMS/Healthcare Scientists

X 8 supporting medium grade Scientists

Approach:

We do not have the resource to have staff dedicated to validation only. Validation is integrated as part of the staffs workload with other tasks.

All pathogen leads involved in the development projects and designed the validation process.

With the replacement of traditional techniques with WGS, there was a pool of microbiologists that could be retrained.

Appropriately graded and experienced microbiologists were trained in the technical validation process.

High grade and experience microbiologists were trained in the technical and medical validation process.

Atypical and Complex pathogens/situations are handled by the pathogen Lead.

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Validation

Reporting to customer (communication)

Sequencing Bioinformatics

DNA extraction Day 1

Library Prep Day 2-3

Sequencing Day 4-5

Bioinformatics Validation Reporting

Day 6-7

Overview of Process implemented and training undertaken

Competency Training

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Practical supervisory sign off in 3 stages

Step by Step Training Plan sign off

Knowledge assessment sign off

Conclusions Training staff with the WGS change has been an integrated, polyphasic and engaged approach.

The staff have come along with the journey rather then trained in a new technique after implementation.

May not always have the ideal grade of staff available for the different sections and need to be adaptable during the transition phase.

WGS is always evolving with addition of new pathogens and new trouble shooting issues so monitoring/reviewing is continual.

The feedback from staff is essential for understanding the troubled areas and what action needs to be taken where staff are unhappy.

Feedback needs to be given back to staff as part of the engagement process

Planned training and competency sign off ensures staff are fully competent.

This approach has enabled retention of skilled microbiologists, improved resilience and rotation of staff into different areas enabling a high retention of staff.

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BIG THANK YOU TO ALL OF Bacterial Reference Department, Genomic Sequencing Unit, BIOINFORMATICS, GBRU, PHE AND EVERYONE INVOLVED IN THIS GROUNDBREAKING CHANGE!!

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