🦠 PDN Priority Pathogens List

This repository is part of the PDN (Pathogen Data Network) initiative and contains a curated, updatable list of priority pathogens. The aim is to centralize information from various international organizations and establish a harmonized and structured reference list for research and public health decision-making.

• 🦠 PDN Priority Pathogens List
  • Objectives
  • Methodology
    • Taxonomic standardization
    • Data sources
  • Priority Type Classification
    • Prioritization logic
      • Inclusion criteria
      • Score and ranking
      • Final selection
  • Outputs
  • Updating
    • Example usage

Objectives

• Aggregate pathogen prioritization lists from leading public health and research organizations.
• Provide a unified reference with consistent taxonomy and annotation.
• Support pathogen surveillance, pandemic preparedness, and biosecurity efforts.
• Make prioritization data machine-readable, as many official lists are only available in formats (PDFs or websites) that are not readily accessible for automated analysis.

Methodology

Taxonomic standardization

• Pathogens are named using scientific species names whenever possible.
• When species-level resolution is not feasible, the genus name is used.
• Viral naming follows ICTV (International Committee on Taxonomy of Viruses) recommendations.
• Additional or common names are listed under the Also known as field.

Data sources

The prioritization list integrates information from international and national agencies, using their publicly available priority lists. Each source is referenced below:

Organization	Acronym	Link	List Name	Source URLs
National Institute of Allergy and Infectious Diseases	NIAID	niaid.nih.gov	NIAID Biodefense Pathogens, Research, Wiriya's document	1, 2, 3
European Centre for Disease Prevention and Control	ECDC	ecdc.europa.eu	Disease-based list	Link
World Health Organization	WHO	who.int	WHO priority pathogen lists (scientific framework, bacteria, fungi)	1, 2, 3
Africa Centres for Disease Control and Prevention	AFRICACDC	africacdc.org	Epidemic-prone diseases prioritization	Link
Centers for Disease Control and Prevention (USA)	CDC	cdc.gov	AMR Threats Report 2021-2022	Link

You can consult the live Google Sheet used for this repository.

Priority Type Classification

Each pathogen is categorized into one or more "priority types", based on its inclusion in the above lists. These allow grouping pathogens by relevance across thematic areas.

Unique priority types used:

- Pandemic preparedness
- Biodefense/Bioterrorism
- vaccine-preventable
- STI
- AMR/Nosocomial infection
- Animal disease
- Neglected Tropical Diseases
- Other

Pathogens may belong to multiple categories simultaneously.

Prioritization logic

Inclusion criteria

• Included if the pathogen appears in at least --two of the following global health agency lists--: WHO, NIAID, ECDC.

  • Note: Fungal pathogens are only prioritized by WHO and NIAID and are not present in ECDC or Africa CDC lists.

• Additionally, the pathogen must be listed under at least --two distinct priority categories--, excluding "Animal disease".

Score and ranking

Each pathogen is assigned a composite --priority score--, calculated based on:

• Number of appearances in key organizational lists (WHO, NIAID, ECDC) ×1

• Number of appearances in broader organizational sets (WHO, NIAID, ECDC, AFRICACDC) ×2

• Number of different priority types (excluding "Animal disease") ×1

• Whether the pathogen has been detected in wastewater monitoring ×1

• Additional adjustment for underepresentation:

  • Fungi: +3
  • Protozoan parasites: +4

This score is stored in the field Priority score.

The full ranked list is available in complete_priority_pathogens.json, including the computed priority score and the derived Priority order.

Final selection

• A total of --50 pathogens-- from --33 families-- were retained after filtering.
• From this list, a subset of --26 pathogens-- is selected for PDN priority consideration, based on the inclusion criteria.
• Pathogens with a --priority score ≥ 12-- are marked with Highest priority: true.

Outputs

• complete_priority_pathogens.csv: Raw data table from the Google Sheet.
• complete_priority_pathogens.json: Full list with all processed entries and scores.
• pdn_priority_pathogens.json: Subset of 50 priority pathogens, filtered by inclusion criteria.

Each pathogen entry includes:

• Priority type (as list)
• prioritized_by (list of sources)
• Priority scored
• Priority order
• Highest priority (boolean)

Updating

Run the script generate_pathogens_list.py to pull the latest data and regenerate all outputs.

Example usage

1. Install dependencies:

pip install -r requirements.txt

2. Run the script:

python generate_pathogens_list.py

This will generate the updated .csv and .json files based on the current Google Sheet data.