Introduction to Whole Genome Sequencing in AMR surveillance

The course originally ran over 6 days in February 2021, starting Monday 15 February, and ending Friday 26 February 2021

Recordings and Course material

This course is now freely available for self-learning. Presentations, Zoom recordings from the original course and course material to conduct the exercises have been combined and are available below. Please note that since this course is self-learning, we are not able to provide feedback on work submitted for the exercises beyond the automated response to certain questions.

Course information
Title:

Introduction to Whole Genome Sequencing (WGS) in Antimicrobial Resistance (AMR).

Language of instruction:

English.

Offered as:

Webinar with lectures, exercises and panel discussion.

Duration of course:

6 x ½ days.

Responsible:

Rene S. Hendriksen (DTU), rshe@food.dtu.dk

Course co-responsible:

Pernille Nilsson (DTU), Anthony Smith (NICD, South Africa), Jinal Bhiman (NICD, South Africa), Marco van Zwetselaar (KCRI, Tanzania), Beverly Eygir (NMIMR, Ghana), Iruka N. Okeke (UI, Nigeria).

General course objectives:

The course provides an introduction to Whole Genome Sequencing (WGS) and its use in Antimicrobial resistance (AMR) surveillance.

The participant will upon completion of the course i) know what WGS is and how it can be used and ii) be able to use freely available online tools to perform simple bioinformatics analysis and interpret results.

Learning objectives:

A participant who has met the objectives of the course will be able to:

Describe the potential uses of WGS in public health microbiology
Describe the different sequencing platforms and the technology behind using the correct terminology
Plan sampling/surveillance appropriate for with WGS studies with epidemiology in mind
Perform drag-and-drop bioinformatics using online analysis tools and interpret the results

Content:

The course covers sampling strategies for doing WGS in AMR, sequencing terminology, detailing state-of-the art technology including technical specifics of whole genome sequencing to give the participants a thorough understanding. Furthermore the course covers what the output data looks like, the importance of quality control and the use of online tools to analyse the data for species identification and AMR detection.

The course will comprise of lectures and hands-on exercises that the participants will have to complete and submit answers to in between course days.

Course literature:

No literature required.

Audience:

None and novel users.

Day 1: Why and how to bring WGS into AMR

Speaker/ Presenter	Content/Activity	Slides/Video/ Exercise sub
	Entire day 1 training: incl. Welcome, Introduction, Q&A and wrap-up.	Slides/Video
Rene S. Hendriksen (DTU, Denmark)	[1] The present and future in AMR surveillance. The potential of using WGS in AMR surveillance	Slides/Video
Rene S. Hendriksen (DTU, Denmark)	[2] Application of WGS in public health microbiology: Cholera and Haiti. Genomic epidemiology of the Haitian Cholera outbreak.	Slides/Video
Alessandro Foddai (DTU, Denmark)	[3] Taking epidemiology into account –what to sequence and how much? Note: Attendants are encouraged to review the treatment guidelines for syndromes/ pathogens or organisms in their country (to know what data will help clinicians and public health people in their country or region)	Slides/Video
Jette Sejer Kjeldgaard (DTU, Denmark)	[4] Overview of terminology and different sequencing platforms: Illumina, Ion Torrent, Pacific Biosciences (PacBio), Oxford Nanopore Technologies	Slides/Video

Day 2: Quality control and identification/characterization

	Entire day 2 training: incl. Welcome, Introduction, Q&A and wrap-up	Slides/Video
Mushal Allam (NICD, South Africa)	[5] Basic quality control of raw reads	Slides/Video
Mushal Allam (NICD, South Africa)	[5E] Exercise: Basic quality control of raw reads using FastQC. A tutorial where you learn how to import, view, and check the quality of sequenced data using FastQC. Note: You will perform the exercise on your own computer and can test your knowledge by taking the quiz to to self-evaluate.	Slides/Files/Quiz
Marco van Zwetselaar (KCRI, Tanzania)	[6] Bioinformatics Basics: General introduction to bioinformatics and introducing genome assembly. (60 min)	Slides/Video

Day 3: Bioinformatics with online tools

	Day 3 training: incl. Welcome, Introduction and QA	Slides/Video*
Stanford Kwenda (NICD, South Africa)	[7] Online tools 1: Introduction to online tools. Kmers, MLST and serotyping of Salmonella and E.coli.	Slides/Video
Tolbert Sonda (KCRI, Tanzania)	[8] Online tools 2: CGE Online Bioinformatics Tools. SpeciesFinder, KmerFinder, ResFinder.	Slides/Video
Anthony Smith (NICD, South Africa)	[9] Online tools 3: Presentation of online tools available for microbial identification using sequence analysis: Pathogenwatch, autoMLST, pubMLST-ribosomal MLST.	Video
Anthony Smith (NICD, South Africa)	[9E] Exercise using online tools: Participants will download sequence data and tasked to perform analysis using the presented online tools. (15 min introduction). Note: You will perform the exercise on your own computer and can test your knowledge by taking the quiz to to self-evaluate.	Slides/Files/ Quiz

*Majority of recording missing due to technical issues during zoom recording

Day 4: Phylogeny and Genotype to phenotype

	Entire day 4 training: incl. Welcome, Introduction, Q&A and wrap-up	Slides/Video
Erkison Odih (UI, Nigeria)	[10] Phylogeny: construction, visualization, and interpretation. Tools: Microreact	Slides/Video
Erkison Odih (UI), Sonda Tolbert (KCRI) Ayorinde Afolayan (UI)	[10E] Exercise on phylogeny: Participants will be given an exercise on phylogeny. Note: You will perform the exercise on your own computer and test your knowledge by taking the quiz to to self-evaluate.	Slides/Files/ Quiz
Jette Sejer Kjeldgaard (DTU, Denmark)	[11] Genotype to Phenotype: Prediction of AMR by WGS	Video
Jette Sejer Kjeldgaard (DTU, Denmark)	[11E] Exercise Phenotype based on genotype: Determining phenotype based on genotype. Note: The sequence analysis output files mentioned in the exercise description are no longer available. You need to run the six sequence files through ResFinder before you can evaluate the presence of AMR genes and the predicted phenotypes. You will perform the exercise on your own computer and can test your knowledge by taking the quiz to to self-evaluate.	Slides Excel/Files/ Quiz

Day 5: Results and Nagoya protocol

	Entire day 5 training: incl. Welcome, Introduction, Q&A and wrap-up	Slides/Video
	Going through results from all exercises.
Carolina Dos Santos Ribeiro (RIVM)	[12] The Nagoya protocol: An introduction.	Slides/Video

Day 6: Genomic surveillance

	Entire day 6 training: incl. Welcome, Introduction, Q&A and wrap-up	Slides/Video
Anthony Smith (NICD, South Africa)	[13] Practical examples of genomic surveillance 1. NICD, South Africa: Genomic surveillance of enteric pathogens.	Video
Errol Strain (FDA, USA)	[13] Practical examples of genomic surveillance 2. FDA, USA: Genomic and metagenomics-based surveillance of AMR in the United States under the National Antimicrobial Resistance Monitoring System (NARMS).	Video
Rene S. Hendriksen (DTU, Denmark)	[13] Practical examples of genomic surveillance 3. DTU, Denmark: WGS surveillance in Europe.	Video
Jorge Raul Matheu Alvarez (WHO)	[13] Practical examples of genomic surveillance 4. WHO: Integrated surveillance of AMR and the ESBL Ec tricycle project.	Video
Sofonias K. Tessema (Africa Union, ACDC)	[13] Practical examples of genomic surveillance 5. Africa Union/Africa CDC: Pathogen Genomics for Infectious Disease Control and Elimination in Africa.	Video
	[14] Panel Discussion: Genomic Surveillance (Live) Moderator: Iruka N. Okeke Panel: • Anthony Smith (NICD, South Africa) • Errol Strain (FDA, USA) • Sofonias K. Tessema (Africa Union/ACDC) • Jorge Raul Matheu Alvarez (WHO)
Pernille Nilsson (DTU)	Concluding remarks and close

Introduction to Whole Genome Sequencing in AMR surveillance​