Objective
Strengthened laboratory preparedness and responsiveness to detect highly pathogenic infectious agents of Risk Group 3 (RG3) bacteria and Risk Group 4 (RG4) viruses. This includes quality assurance of diagnostic methods, the evaluation of new diagnostic approaches and the improvement of biosafety and biosecurity systems in highly specialized SHARP partner laboratories (EMERGE Laboratory Network).
Specific objectives
- Improved laboratory preparedness ensuring the application of best practices and quality assured methods for detection and analyses of highly pathogenic infectious agents in SHARP partner laboratories.
- Improved and consolidated biorisk management in SHARP partner laboratories dedicated to the diagnostics of highly pathogenic infectious agents.
Outputs & activities
The work package is structured in specific tasks and working groups. Special funding is granted to task leaders, co-leaders and designated working group leaders to carry out specific defined activities in cooperation with all WP7 partners, while basic funding is granted to all WP7 partners to cover essential activities, such as participation in External Quality Assurance Exercises (EQAE), meetings and training courses. Special attention is attributed to partners from low GNI Member States to allow their participation in the various tasks of the Work Package.
Deliverables
- Report on quality assurance of diagnostics of highly infectious pathogens (yearly EQAEs) applied in microbiological SHARP partner laboratories.
- Report on assessment and recommendations for modern molecular diagnostic methods and for Antimicrobial Susceptibility Testing (AST) for selected highly pathogenic bacteria.
- Recommendations for biorisk management in high containment facilities.
Milestones
- Implementation of EQAEs
- Specific diagnostic tasks
- Programme for self-evaluation of laboratory biosecurity
People and partners
Partner labs of WP7 / EMERGE Laboratory Network
Work package lead: RKI (contact: EMERGE-Coordination(at)rki.de)
Co-lead: INMI
Updates
External Quality assurance Exercises (EQAEs)
Two rounds of bacterial and viral EQAEs have been conducted (February – March 2020 and June – July 2021)
Training
Most training courses were postponed due to the pandemic. Two courses were carried out as online courses.
Diagnostic approaches
Diagnostic capabilities available in WP7 partner laboratories have been surveyed.
Working Group on Next Generation Sequencing (NGS)
An online survey was circulated among WP7 partners to assess the availability and type of NGS platforms, work processes and bioinformatics support.
A SARS-CoV-2 specific sequencing protocol was set up and used for rapid informed public health decision making in the Netherlands and to investigate several outbreaks. An automated data analysis tool was developed to enable real-time data analysis to generate consensus sequences. See more here.
Working Group on Basic Diagnostic
Various activities had to be postponed due to the pandemic.
Working Group on Antimicrobial Susceptibility Testing (AST)
A study design for the testing of strain collections was developed and introduced in the partner laboratories. Reference strains were used to establish the methods in partner laboratories for inter-laboratory validation.
Collaboration with the European Committee for AST (EUCAST) was continued, and the definition of breakpoints for AST for selected Risk Group 3 bacteria (Bacillus anthracis, Brucella melitensis, Francisella tularensis) was initialized.
Laboratory biorisk management
A “SHARP Tool for Enhancing Laboratory Biorisk Management” has been drafted.
Maintenance of the EMERGE Laboratory Network
To keep the functionality of this grown structure, existing since 2008, a number of options are currently pursued. The partner laboratories have repeatedly underlined the benefits and added value gained by the network activities with regard to diagnostic quality assurance and self-evaluation.
