Module 1: Introduction to Whole Genome Sequencing in AMR surveillance

Day 1 WGS in AMR surveillance - presentation - pdf​

Day 2 WGS in AMR surveillance - presentation - pdf

​Day 3 WGS in AMR surveillance - presentation - pdf

​Day 4 WGS in AMR surveillance - presentation - pdf

Day 5 WGS in AMR surveillance - presentation - pdf

​Day 6 WGS in AMR surveillance - presentation - pdf​

Recordings of each day:

Day 1 WGS in AMR surveillance - recording - video

Day 2 WGS in AMR surveillance - recording - video

Day 3 WGS in AMR surveillance - recording - video

Day 4 WGS in AMR surveillance - recording - video

Day 5 WGS in AMR surveillance - recording - video

Day 6 WGS in AMR surveillance - recording - video

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Exercises

5E:

9E:

10E:

11E:

​11E Excel sheet

Individual presentations

The present and future in AMR surveillance

Application of WGS in public health microbiology: Cholera and Haiti.

[3] Taking epidemiology into account –what to sequence and how much?

Overview of terminology and different sequencing platforms

Basic quality control of raw reads

Bioinformatics Basics: General introduction to bioinformatics and introducing genome assembly.

Online tools 1

Online tools 2

Online tools 3

Phylogeny

Genotype to Phenotype

The Nagoya protocol

13-1 NICD, South Africa: Genomic surveillance of enteric pathogens

13-2 FDA, USA: Genomic and metagenomics based surveillance of AMR in the United States under the National Antimicrobial Resistance Monitoring System (NARMS)

13-3 DTU, Denmark: WGS surveillance in Europe

13-4 Africa Union/Africa CDC: Pathogen Genomics for Infectious Disease Control and Elimination in Africa

13-5 WHO: Integrated surveillance of AMR and the ESBL Ec tricycle project.​

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