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Mapping pathogen genomics training provision: a structured analysis within a global consortium network.

Alice Matimba1, Kirsty Lee Garson2, Nídia S Trovão3

  • 1Wellcome Sanger Institute, Hinxton, United Kingdom.

Frontiers in Public Health
|May 15, 2026
PubMed
Summary
This summary is machine-generated.

This study surveyed pathogen genomics training, finding most courses are introductory, focus on bioinformatics, and lack formal assessments. This highlights needs for advanced training and standardized evaluation in infectious disease surveillance.

Keywords:
bioinformatics traininggenomic surveillancepathogen genomicspublic health workforce developmenttraining programs

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Area of Science:

  • Public Health
  • Genomics
  • Infectious Disease Surveillance

Background:

  • Pathogen genomics is crucial for infectious disease surveillance and outbreak response.
  • Current pathogen genomics training initiatives are fragmented, hindering visibility into program structure, delivery, and assessment.

Purpose of the Study:

  • To characterize pathogen genomics training initiatives.
  • To identify structural patterns and inform workforce development strategies.

Main Methods:

  • A structured survey was conducted to identify and analyze pathogen genomics training initiatives.
  • Eighty-one courses from 17 countries were analyzed.

Main Results:

  • Most courses (58%) were introductory, focusing on bioinformatics (72%), with limited advanced topics or structured assessments (38% lacked assessments).
  • Training predominantly used local computing resources (93%), with limited use of high-performance computing (HPC) or cloud platforms during sessions.
  • Viral pathogen themes were common, and nearly half (48%) covered broadly applicable genomic methods.

Conclusions:

  • Pathogen genomics training exhibits geographic concentration, a predominance of introductory formats, and variability in assessment and advanced computing infrastructure use.
  • Findings offer insights for strengthening coordinated and sustainable workforce development in pathogen genomics.