Priority Pathogens List

Published: 2025-05-28

Objectives

The objectives of generating a priority pathogens list are:

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.

All this information can be found in Github

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

Figure 1: Number of pathogens found in the lists of each organization. A total of 198 pathogens from 98 families were included.

Figure 2: Venn diagram of the pathogens shared between NIAID, WHO and ECDC

Figure 3: Number of pathogens per type.

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

Note that pathogens may belong to multiple categories simultaneously.

Figure 4: Number of pathogens in each of the priority types, among the 198 in the list.

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 22 pathogens is selected for PDN priority consideration, based on the inclusion criteria.
Pathogens with a priority score ≥ 12 are marked with highest_priority: true.