3. The Knowledge principle: Improving the One Health Surveillance knowledge base

Purpose

The Knowledge principle defines that better surveillance planning, data integration and interpretation needs efficient and continuous knowledge exchange and joined knowledge evolution between all One Health parties.

Therefore, the purpose of this principle is to provide surveillance professionals and stakeholders with guidance on available knowledge resources that may be used to foster an One Health approach within their area of work, or to increase the value of their sector-specific surveillance reports for future One Health analysis.

Scope

The Knowledge principle focus on providing a resource to exchange knowledge on

  • existing surveillance data collections
  • established methods for surveillance data analysis and interpretation
  • current methods for surveillance planning
  • experiences with implementation of new technologies supporting surveillance

Although many surveillance systems and data are already shared with EFSA and ECDC, there are several additional national surveillance systems that are not. The results from these surveillance systems can be difficult to access as reports are often only published in the national language and not listed in scientific databases (e.g. PubMed).

Overall, the solutions & tools provided under the Knowledge principle aim to collate and improve access to surveillance data, improve knowledge of methods to interpret and analyse surveillance data and elucidate new technologies supporting surveillance. Furthermore, each is designed to be maintainable in a collaborative manner. Together, these solutions and tools are expected to support cross-sector, as well as within sector surveillance activities in the future.

Methods

OH Knowledge Base – Surveillance systems

The OH Knowledge Base – Surveillance systems consist of:

(1) an inventory of existing surveillance systems carried out in different countries including links to the literature or websites. The objective was to generate a comprehensive list of surveillance systems in the One Health approach. It was accomplished by collaboration between One Health EJP H2020 ORION project and EFSA/ECDC using similar terminology in describing the surveillance systems. The interface of the inventories provides users with easy and intuitive search functions. The first version is published at https://shiny.fli.de/ife-apps/EJPOrion_WP2Epi/.

2) a database that provides an overview of the common statistical methods used for surveillance data within the EU. Furthermore, it also contains a selection of links to literature, sample calculations in R and software solutions on the internet recommended for surveillance data. This enables a comparison between the existing methods and the methods actually used in surveillance projects and inspires institutes to consider new data analytical methodologies. The first version is published at https://shiny.fli.de/ife-apps/toolsdatabase/.

(3) a literature database gathering reports, scientific literature, and web resources. The collection of the literature is carried out using a literature database (Zotero, https://www.zotero.org/groups/2204615/ejp_orion_wp2epi_data_sources_surveillance_systems/library). As Zotero requires registration, contributors need to be invited. Nevertheless, to be able to access the resources without registration, the database will be accessible via the web applications too.

OH Knowledge Base - The Sequencing for Surveillance Handbook

The Sequencing for Surveillance (SfS) Handbook is a web-based resource containing best practice advice and hands on experience for how to set up and use sequencing for surveillance in a OH-supporting manner . The handbook currently consists of the following sections:

  • public guidance documents from institutions such as EFSA and ECDC
  • descriptions of infrastructural solutions for sequencing and analysis
  • review of bioinformatics tools and pipelines used for analyzing and typing foodborne pathogens
  • databases and other resources needed to perform analyses for species specific analyses
  • guidance on how to use typing data for surveillance and outbreak detection, including clustering guidelines

As part of the infrastructure and pipeline sections, the handbook will include guidelines on how institutions can best process their data and how data can be shared between institutions. In addition, we are creating a prototype analysis system for Listeria, which will serve as a test case for guidelines on how to analyze NGS data in a reproducible and reliable way.

Link: https://oh-sfs-handbook.readthedocs.io/en/latest/

RAKIP Model Repository

The ‘Risk Assessment Modelling and Knowledge Integration Platform’ (RAKIP) partners BfR, ANSES and DTU Food developed the RAKIP Model Repository with the aim of supporting modellers, scientists, risk assessors and risk managers in their efforts to share and re-use mathematical models as well as data analysis procedures across One Health sectors. The RAKIP Model Repository is a curated web-based database currently populated with executable mathematical models relevant for food safety. These models are provided in the Food Safety Knowledge eXchange (FSKX) format, an open exchange format that can include data, model scripts, visualization scripts, simulation settings and harmonized metadata on the model / data. The RAKIP model repository provides a user-friendly interface to access, filter and download the FSKX model file. Registered users can also execute, edit or join models online.

Link to the resource: https://knime.bfr.berlin/landingpage/RAKIP-Model-Repository

Link to the description of the resource: https://foodrisklabs.bfr.bund.de/rakip-web-portal/

Manual for One Health Surveillance Dashboards

This is an online dashboard inventory and practical manual to facilitate the design and implementation of One Health Surveillance dashboards using open source tools. More information is available at the Dashboard Information Centre here. The Dashboard Information Centre is a “living document” that contains an inventory of planned, ongoing and finished dashboard projects, a practical manual and a best practice guide to the development of One Health Surveillance dashboards. It covers the following topics: i) information context and end-user considerations; ii) technical and legal barriers associated with cross sector data sharing; iii) the pitfalls and biases of coanalysing One Health data; iv) the selection of the most suitable technical implementation. It is meant to be used as a “companion” when planning or developing a dashboard.

The Dashboard Information Centre is available here. User manual for construction and implementation of One Health dashboards using open source tools (source codes):, https://zenodo.org/record/7398545#.Y43KOMuZOUk

A practical manual to the use of dashboards in One Health Surveillance practice, including recommendations for sustainability:, https://zenodo.org/record/7398589#.Y49j7HbMJlZ

Webinar: Vaccine and Infection Control days 2021 Norway (Vaksine- og smitteverndager 2021)

The vaccine and infection control days in 2021 shed light on various current topics within vaccination and infection control and are mainly intended for health personnel who work with infection control and / or vaccines in both municipal and specialist health services.

Link: https://www.fhi.no/om/kurs-og-konferanser/webinar-vaksine–og-smitteverndager-2021/

Examples & Lessons learned

Several One Health EJP H2020 ORION project partners carry out national pilot studies to test methods from the Knowledge principle regarding usability within a cross sectional approach. Findings from these pilot studies can be found under the project Deliverable 2.7 ( Zenodo: https://doi.org/10.5281/zenodo.5062653).