Table 2.

Teaching Approaches

Strategy	Description	Implementation Examples
Challenge and problem-based tasks	Problem-solving and decision-making exercises	• Use card-based blueprint to order processes and procedures in a typical WGS for AMR surveillance pipeline • Use of fictive case scenarios involving training others in genomics aspects
Case studies	Use of real cases, as published in the literature	• Identify MDR Salmonella enterica subsp. enterica serotype Kentucky lineage expansion [13] • Investigation of a Brazilian epidemic of Mycobacterium abscessus species complex [14] • Klebsiella pneumoniae outbreak investigation [15]
Historical and chronological presentation of processes	Demonstration of lab procedures, visual tours, lab visits, exhibition tour	• Visit to the sequencing facilities at the Sanger Institute • Visit to the exhibition marking the start of the Human Genome Project • Demonstration of library preparation for WGS • Demonstration of best practices for antimicrobial susceptibility testing
Comparative analysis of tools and platforms	Presenting alternative ways of achieving the same/similar result	• Comparison of data merging and consolidation techniques—interactively with spreadsheets versus programmatically with R and Python • Comparison of different databases and software tools used to determine AMR phenotype based on genomic data • Comparison of different ways of interpreting bacterial population structures—MLST trees versus phylogenetic trees obtained from WGS data
Project planning and management techniques	Considering standards and quality control, constraints and limitations, time management; project planning, and constraints (financial, scaling and other)	• Exercise on how to build a computer server that needs to accomplish certain tasks, given a list of hardware components and a fixed budget • Exercise on how to set up a WGS laboratory • QC assessment of libraries and sequencing
Provision of resources	Provision of links to resources and portals, quality control standards, virtual and cloud tools, toolkits	• Software tools: • AMR prediction tools: ARIBA [16], Pathogenwatch [17], AMRFinder [18] • AMR databases: CARD [19], ResFinder [20] • Nucleotide archives: Genbank [21], European Nucleotide Archive [22] • Data integration tools: dataflo (https://dataflo.io/) • Data visualization: Microreact [11] • Pipelines: Nextflow [23] • Phylogeny: RAxML [24] • Genome Assembly: SPAdes [25] • QC tools: FastQC [26], Quast [27], Bactinspector [28], Qualifyr [29] • Typing tools: PubMed MLST (www.pubmlst.org) • The Training and Learning Toolkit
Analysis and evaluation	Consideration and evaluation of participants’ specific contexts	• Big-picture exercise where participants evaluate their own circumstances

Abbreviations: AMR, antimicrobial resistance; MDR, multidrug resistance; MLST, multilocus sequence typing; QC, quality control; WGS, whole genome sequencing.