Pathogen Surveillance Training Curricula

Click here for the training survey

The Pathogen Surveillance Training Curriculum aims to provide a recommended set of courses with topic areas and indicative content for implementing pathogen surveillance and applied genomic epidemiology training within public health. The curriculum includes foundational and pathogen-specific courses, targeted to specific job descriptions (i.e., persona) in public health facilities.

Basic Foundational Courses

The Foundational Courses are aimed at building generic, wet-laboratory, and bioinformatics knowledge and skills to adequately equip public health personas.

Generic Foundational Course
Bioinformatics Foundational Course
Wet-lab Foundational Course

Module Code	Pathogen	Persona	Module Title
G01	All pathogens	Wet laboratory personnel	An Introduction to Basic Molecular and Microbial Biology
G01	All pathogens	Dry laboratory personnel	An Introduction to Basic Molecular and Microbial Biology
G01	All pathogens	Managerial personnel	An Introduction to Basic Molecular and Microbial Biology
G02	All pathogens	Wet laboratory personnel	Introduction to Traditional, Field, and Genomic Epidemiology
G02	All pathogens	Dry laboratory personnel	Introduction to Traditional, Field, and Genomic Epidemiology
G02	All pathogens	Managerial personnel	Introduction to Traditional, Field, and Genomic Epidemiology
G03	All pathogens	Wet laboratory personnel	An Overview of the Role of Genomic Epidemiology in Pathogen Genomic Surveillance
G03	All pathogens	Dry laboratory personnel	An Overview of the Role of Genomic Epidemiology in Pathogen Genomic Surveillance
G03	All pathogens	Managerial personnel	An Overview of the Role of Genomic Epidemiology in Pathogen Genomic Surveillance
G04	All pathogens	Wet laboratory personnel	Fundamentals of Biostatistics
G04	All pathogens	Dry laboratory personnel	Fundamentals of Biostatistics
G04	All pathogens	Managerial personnel	Fundamentals of Biostatistics
G05	All pathogens	Wet laboratory personnel	Fundamentals of Pathogen Genomic Surveillance Study Design
G05	All pathogens	Dry laboratory personnel	Fundamentals of Pathogen Genomic Surveillance Study Design
G05	All pathogens	Managerial personnel	Fundamentals of Pathogen Genomic Surveillance Study Design
G06	All pathogens	Wet laboratory personnel	Introduction to Genomic Sequencing and NGS
G06	All pathogens	Dry laboratory personnel	Introduction to Genomic Sequencing and NGS
G06	All pathogens	Managerial personnel	Introduction to Genomic Sequencing and NGS
G07	All pathogens	Wet laboratory personnel	Introduction to Public Health Research and Pathogen Surveillance Ethics and Policies
G07	All pathogens	Dry laboratory personnel	Introduction to Public Health Research and Pathogen Surveillance Ethics and Policies
G07	All pathogens	Managerial personnel	Introduction to Public Health Research and Pathogen Surveillance Ethics and Policies
G08	All pathogens	Wet laboratory personnel	Introduction to Data Sharing and Dissemination
G08	All pathogens	Dry laboratory personnel	Introduction to Data Sharing and Dissemination
G08	All pathogens	Managerial personnel	Introduction to Data Sharing and Dissemination
G09	All pathogens	Wet laboratory personnel	Introduction to Antimicrobial Resistance (AMR).
G09	All pathogens	Dry laboratory personnel	Introduction to Antimicrobial Resistance (AMR).
G09	All pathogens	Managerial personnel	Introduction to Antimicrobial Resistance (AMR).

Module Code	Pathogen	Persona	Module Title
B01	All pathogens	Dry laboratory personnel	Introduction to Unix/Linux, Command Line, and Shell Scripting.
B02	All pathogens	Dry laboratory personnel	Introduction to Version Control.
B03	All pathogens	Dry laboratory personnel	Informatics skills
B04	All pathogens	Dry laboratory personnel	Introduction to Programming
B05	All pathogens	Dry laboratory personnel	Introduction to R Programming for Data Analysis
B06	All pathogens	Dry laboratory personnel	Data Management and Basic Analytics
B07	All pathogens	Dry laboratory personnel	Phylogenetics
B08	All pathogens	Dry laboratory personnel	Virtual Environments and Containerization
B09	All pathogens	Dry laboratory personnel	Workflow management systems
B10	All pathogens	Dry laboratory personnel	Ontologies, standards, data curation and submission
B11	All pathogens	Dry laboratory personnel	Data Visualisation and Report Generation

Module Code	Pathogen	Persona	Module Title
W01	All pathogens	Wet laboratory personnel	Introduction to Biosafety and Biosecurity
W02	All pathogens	Wet laboratory personnel	Basic Laboratory Requirements Set-Up
W03	All pathogens	Wet laboratory personnel	Introduction to Fundamental Laboratory Skills and Calculations
W04	All pathogens	Wet laboratory personnel	Basic Molecular Techniques for NGS Implementation

Pathogen-Specific Courses

The Pathogen-Specific Courses build on the Foundational Courses and focus on building pathogen-specific knowledge and skills to effectively prepare public health personas for pathogen genomic surveillance.

Module Code	Pathogen	Persona	Module Title
BA01	Bacterial	Wet laboratory personnel	Study Design for Bacterial Pathogen Surveillance
BA01	Bacterial	Dry laboratory personnel	Study Design for Bacterial Pathogen Surveillance
BA01	Bacterial	Managerial personnel	Study Design for Bacterial Pathogen Surveillance
BA02	Bacterial	Wet laboratory personnel	Bacterial Sample Preparation, Library Preparation and DNA Sequencing
BA03	Bacterial	Dry laboratory personnel	Bacterial NGS Data Processing
BA04a	Bacterial	Dry laboratory personnel	Bacterial Pathogen Data Analysis
BA04a	Bacterial	Dry laboratory personnel	Bacterial Pathogen Data Analysis
BA4b	Bacterial	Dry laboratory personnel	Bacterial Bioinformatics Analytical workflows
BA05	Bacterial	Dry laboratory personnel	Bacterial Phylogenetics
BA06	Bacterial	Dry laboratory personnel	Antibacterial Resistance Identification and Tracking
BA07	Bacterial	Dry laboratory personnel	BA07. Metagenomics/16S rRNA Amplicon for Bacterial Surveillance

Module Code	Pathogen	Persona	Module Title
V01	Viral	Wet laboratory personnel	Study Design and Sequencing Strategies for Viral Pathogen Surveillance
V01	Viral	Dry laboratory personnel	Study Design and Sequencing Strategies for Viral Pathogen Surveillance
V01	Viral	Managerial personnel	Study Design and Sequencing Strategies for Viral Pathogen Surveillance
V02	Viral	Wet laboratory personnel	Sample Processing and Library Preparation for Viral Pathogens (Theory and Wet-lab Practical)
V03	Viral	Wet laboratory personnel	ARTIC Viral Amplicon Sequencing
V03a	Viral	Wet laboratory personnel	Illumina Workflow for Viral Genome Sequencing
V03b	Viral	Wet laboratory personnel	ONT Workflow for Viral Genome Sequencing
V04	Viral	Dry laboratory personnel	Introduction to Viral NGS Data Processing
V04a		Dry laboratory personnel	Nextclade and Pangolin
V04b	Viral	Dry laboratory personnel	Galaxy Workflow (or other selected workflow(s))
V05	Viral	Dry laboratory personnel	Advanced Bioinformatics Analysis for Viruses

Module Code	Pathogen	Persona	Module Title
M01	Malaria	Wet laboratory personnel	Introduction to Malaria Biology and Genomic Epidemiology
M01	Malaria	Dry laboratory personnel	Introduction to Malaria Biology and Genomic Epidemiology
M01	Malaria	Managerial personnel	Introduction to Malaria Biology and Genomic Epidemiology
M02p	Malaria	Wet laboratory personnel	Malaria Pathogen Surveillance Design
M02p	Malaria	Dry laboratory personnel	Malaria Pathogen Surveillance Design
M02p	Malaria	Managerial personnel	Malaria Pathogen Surveillance Design
M02v	Malaria	Wet laboratory personnel	Malaria Vector Surveillance Design
M02v	Malaria	Dry laboratory personnel	Malaria Vector Surveillance Design
M02v	Malaria	Managerial personnel	Malaria Vector Surveillance Design
M03	Malaria	Wet laboratory personnel	Sample processing and library preparation for malaria (Theory and wet lab practical)
M03a	Malaria	Wet laboratory personnel	Population Genomics and Adaptive Evolution in P.falciparum
M04	Malaria	Dry laboratory personnel	Introduction to Malaria Bioinformatics
M04a	Malaria	Dry laboratory personnel	Intermediate Malaria Bioinformatics: SNP Calling Tools
M04b	Malaria	Dry laboratory personnel	Intermediate Malaria Bioinformatics: Microhaplotype Calling Tools
M05p	Malaria	Dry laboratory personnel	Malaria Pathogen Analytics
M05v	Malaria	Dry laboratory personnel	Introduction to Malaria Vector Biology (Theory)
M06v	Malaria	Dry laboratory personnel	Whole Genome Analysis for Malaria Vector (Theory and Wet-lab Practical)
M07v	Malaria	Dry laboratory personnel	Malaria Vector Transcriptomics Data Analysis
M08	Malaria	Wet laboratory personnel	M08. Using Malaria Genomic Data for Decision-Making
M08	Malaria	Dry laboratory personnel	M08. Using Malaria Genomic Data for Decision-Making
M08	Malaria	Managerial personnel	M08. Using Malaria Genomic Data for Decision-Making

Module Code	Pathogen	Persona	Module Title
P01	Parasitic	Wet laboratory personnel	Study Design for Parasitic Pathogen Surveillance
P01	Parasitic	Dry laboratory personnel	Study Design for Parasitic Pathogen Surveillance
P01	Parasitic	Managerial personnel	Study Design for Parasitic Pathogen Surveillance
P02	Parasitic	Wet laboratory personnel	Sample Processing and Library Preparation for Parasitic Pathogens (Theory and Wet-lab Practical)
P03	Parasitic	Dry laboratory personnel	Introduction to Parasitic NGS Data Processing
P04	Parasitic	Dry laboratory personnel	NGS Data Analysis Using the Artemis Genome Browser and Annotation Tool
P05	Parasitic	Dry laboratory personnel	Using Parasitic Databases and Resources

Module Code	Pathogen	Persona	Module Title
F01	Fungi	Wet laboratory personnel	Study Design and Sequencing Strategies for Fungal Pathogen Surveillance
F01	Fungi	Dry laboratory personnel	Study Design and Sequencing Strategies for Fungal Pathogen Surveillance
F01	Fungi	Managerial personnel	Study Design and Sequencing Strategies for Fungal Pathogen Surveillance
F02	Fungi	Wet laboratory personnel	Overview of Fungal Pathogen Surveillance Using NGS
F03	Fungi	Dry laboratory personnel	Introduction to Fungal Databases
F04	Fungi	Wet laboratory personnel	Fungal Sample Processing and Library Preparation (Theory and Wet-lab Practical)
F05	Fungi	Dry laboratory personnel	Phylogenetics and Visualization for Fungal Genomes
F06	Fungi	Dry laboratory personnel	Antifungal Resistance (AMR)

Module Code	Pathogen	Persona	Module Title
MG01	Metagenomics	Wet laboratory personnel	Introduction to Metagenomics and Use Cases
MG01	Metagenomics	Dry laboratory personnel	Introduction to Metagenomics and Use Cases
MG01	Metagenomics	Managerial personnel	Introduction to Metagenomics and Use Cases
MG02	Metagenomics	Dry laboratory personnel	Study Design and Lab Setup for Metagenomics
MG02	Metagenomics	Wet laboratory personnel	Study Design and Lab Setup for Metagenomics
MG02	Metagenomics	Managerial personnel	Study Design and Lab Setup for Metagenomics
MG03	Metagenomics	Wet laboratory personnel	Sample Processing and Library Preparation for Metagenomics (Theory and Wet-lab Practical)
MG04	Metagenomics	Dry laboratory personnel	Introduction to Metagenomics Data Analysis
MG05	Metagenomics	Wet laboratory personnel	Metagenomics Data Analysis. iSeq 100 Loading
MG06	Metagenomics	Wet laboratory personnel	Quality Control, Sample QC, Sequencing Run QC
MG07	Metagenomics	Dry laboratory personnel	Metagenomics Analysis. Cloud-based Metagenomics Platform for Researchers

We are inviting individuals with expertise in genomic epidemiology, bioinformatics, and applied pathogen surveillance to register their interest in participating in the ongoing development of our curriculum. This is an exciting opportunity to contribute to the development and implementation of a standardised, scalable, adaptable, and dynamic curriculum that can be applied globally. Click here to participate.