README.md

Bioinformatics for AMR Research

A workshop for the One Health Summer Institute's Introduction to Bioinformatics sessions

Goals of the workshop

• Overview of methods for bacterial genomics and molecular epidemiology
• Introduction to databases and tools for the analysis of antimicrobial resistance genes

Workshop program (2021-06-16)

• Introduction and overview of bioinformatics for AMR: methods and databases
• Hands-on activity with the Comprehensive Antimicrobial Resistance Database (CARD): using RGI to analyze genomes and plasmids
• Hands-on work with Galaxy: de novo ssembly of a MRSA genome and analysis of antimicrobial resistance genes

Resources

Workshop slides and hands-on activities

• Introduction and overview PDF slides
• Using CARD and RGI to characterize the resistome of bacterial plasmids and genomes
• Genome Assembly of MRSA using Illumina MiSeq Data (with Galaxy)

Other slides

• Torsten Seemann's presentation slides

Papers

Reviews

• A Primer on Infectious Disease Bacterial Genomics (Lynch et al., 2016)
• A Primer on Microbial Bioinformatics for non-bionformaticians (Carrico et al., 2018)
• Best practices for analysing microbiomes (Knight et al., 2018)

Bacterial genomics (single species)

• Surveillance of Enterococcus spp . reveals distinct species and antimicrobial resistance diversity across a One-Health continuum (Zaheer et al., 2019)
• Characterization of Non-O157 Escherichia coli from Cattle Faecal Samples in the North-West Province of South Africa (Bumunang et al, 2019)

Metagenomics (resistome)

• Comparative diversity of microbiomes and Resistomes in beef feedlots, downstream environments and urban sewage influent

Databases

• CARD: The Comprehensive Antibiotic Resistance Database
• NCBI AMRFinderPlus
• MEGARes database

Videos

• State of the CARD 2021 Presentations and Demonstrations

Virus resources

• ViralZone
• ViPR Virus Pathogen Resource