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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?
4 Training PHE staff with the WGS change
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
5 Training PHE staff with the WGS change
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
6 Training PHE staff with the WGS change
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
7 Training PHE staff with the WGS change
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
8 Training PHE staff with the WGS change
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
9 Training PHE staff with the WGS change
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
11 Training PHE staff with the WGS change
Need to ensure Laboratory Information Management Systems (LIMS) are updated
12 Training PHE staff with the WGS change
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.
13 Training PHE staff with the WGS change
14 Training PHE staff with the WGS change
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
15 Training PHE staff with the WGS change
Need to ensure microbiologists can interpret, analyse and report results in a fit for purpose manner to our service users
16 Training PHE staff with the WGS change
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.
17 Training PHE staff with the WGS change
18 Training PHE staff with the WGS change
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
19 Training PHE staff with the WGS change r
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.
20 Training PHE staff with the WGS change
BIG THANK YOU TO ALL OF Bacterial Reference Department, Genomic Sequencing Unit, BIOINFORMATICS, GBRU, PHE AND EVERYONE INVOLVED IN THIS GROUNDBREAKING CHANGE!!
21 Training PHE staff with the WGS change