Programme Parameters
Foundation
3 Days (4.5 Hrs)
Online (e-LMS)
• No prior experience required — basic computer literacy is sufficient.
• A laptop or desktop with a stable internet connection.
• Willingness to complete assignments and the capstone project.
About This Course
Bioinformatics Approach to Antimicrobial Resistance & HGT takes a genomics-and-methods view of one of the great public-health challenges. You learn the bioinformatic workflow for AMR: identifying resistance genes and their genetic context, and — distinctively — reconstructing horizontal gene transfer to understand how resistance moves between organisms via plasmids and mobile elements. The course connects these analyses to surveillance and the wider dynamics of resistance spread. You finish able to reason about a bioinformatics investigation of AMR and its transmission. A verified e-Certificate of competency and e-Marksheet from the Deep Science & Technology Consortium.
🎯 Program Aim
This course covers a bioinformatics approach to antimicrobial resistance (AMR) and horizontal gene transfer (HGT) — analysing genomic data to find resistance genes and trace their spread.
📋 Course Objectives
1. Identify resistance genes and their genetic context.
2. Analyse mobile elements and plasmids.
3. Reconstruct horizontal gene transfer events.
4. Trace how resistance spreads between organisms.
5. Connect analysis to AMR surveillance.
👥 Who Should Enroll?
• Microbiology and genomics researchers
• Bioinformatics and AMR-surveillance staff
• Public-health scientists
• Students of bioinformatics
🚀 Key Learning Outcomes
• A bioinformatics understanding of AMR and HGT.
• A resistance-spread analysis perspective.
• A public-health genomics foundation.
• A verified e-Certificate of competency and e-Marksheet from the Deep Science & Technology Consortium.
💎 What You'll Gain
Live & Recorded Sessions
Lifetime access to class recordingse-Certificate on Completion
Cryptographically verified credentialPost-Programme Support
Direct access to mentors & councilHands-On Experience
Notebooks, real-world code & datasetsCurriculum Outline
Working from Sequenced Genomes
• Illumina and Nanopore data, and why long reads resolve plasmids
• Assembly with SPAdes or Flye and assessing quality with QUAST and BUSCO
• Species confirmation and contamination screening before anything else
Identifying Resistance Determinants
• ResFinder, CARD-RGI and AMRFinderPlus and their different curation choices
• Acquired genes against chromosomal point mutations conferring resistance
• Genotype-to-phenotype concordance and where prediction reliably fails
Locating Genes on Mobile Elements
• Plasmid reconstruction, replicon typing and MOB typing
• Integrons, transposons and insertion sequences flanking resistance genes
• Chromosomal against plasmid location and its epidemiological weight
Tracing Spread Between Isolates
• MLST, cgMLST and core genome SNP analysis for relatedness
• Recombination masking before tree building with Gubbins
• Distinguishing clonal expansion from independent horizontal acquisition
Surveillance and Communication
• Submission to public databases and the metadata standards expected
• Outbreak reporting and the SNP thresholds used, with their limits
• Writing a genomic AMR report that a microbiologist can act on
Technical Specifications
| Parameter | Requirement |
|---|---|
| Covered Tool / Platform | Python |
| Covered Tool / Platform | R/Bioconductor |
| Covered Tool / Platform | BLAST |
| Covered Tool / Platform | Biopython |
| Covered Tool / Platform | Galaxy |
| Covered Tool / Platform | UniProt |
| Covered Tool / Platform | NCBI |
| Covered Tool / Platform | PyMOL |
Programme Faculty & Mentors
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