📚 Syllabus & Course Curriculum
Antimicrobial Resistance (AMR)
Module-by-module breakdown of Metagenomic Analysis of AMR and HGT, from foundations to a certified capstone project.
Foundations
• Resistance mechanisms: efflux, target modification and enzymatic inactivation
• Conjugation, transformation and transduction as routes of gene movement
• Resistome and mobilome as distinct objects requiring distinct analysis
Sequencing
• Shotgun metagenomics against amplicon approaches for resistance gene detection
• Read QC, host read removal and adapter handling with fastp and Bowtie2
• Depth requirements — low-abundance resistance genes are missed at shallow depth
Detection
• CARD, ResFinder and AMRFinderPlus, and their differing curation philosophies
• Read-based against assembly-based detection and the sensitivity trade-off
• Identity and coverage thresholds and the false positives loose settings produce
Context
• Assembly with metaSPAdes and binning with MetaBAT for genomic context
• Plasmid, integron and transposon identification with mobileOG and PlasmidFinder
• Host attribution and why short reads frequently cannot support the claim
Inference
• Gene presence is not resistance phenotype — the limits of genotypic prediction
• Evidence needed to argue a horizontal transfer event actually occurred
• Comparative and longitudinal designs for tracking resistome change
Earn government-registered certification in Metagenomic Analysis of AMR and HGT
e-Certificate and e-Marksheet issued on successful completion.
