Antibiotic Resistance Genomics: WGS, Bioinformatics & Resistance Gene Characterization

Aim

Workshop Objectives

Workshop Structure

Day 1: Bacterial Whole-Genome Sequencing, Data Quality Control & Genomic Profiling

Topics Covered:

• Introduction to antimicrobial resistance (AMR) and its global research significance.
• Molecular mechanisms of antibiotic resistance in bacterial pathogens.
• Genetic basis of resistance: Acquired genes, point mutations and horizontal gene transfer.
• Whole-genome sequencing (WGS) technologies: Illumina and Oxford Nanopore.
• Applications of bacterial WGS in resistance genomics and microbial biotechnology.
• Retrieval of bacterial genomic datasets from NCBI SRA and GenBank.
• Understanding FASTQ, FASTA and paired-end sequencing data.
• NGS quality assessment: Phred scores, GC content and sequencing errors.
• Read trimming, adapter removal and quality filtering using fastp.
• Bacterial species identification and sequencing contamination assessment.
• Interpretation of sequencing quality reports using FastQC and MultiQC.

Hands-On 1: Bacterial WGS Data Retrieval & Quality Assessment

Retrieve a curated bacterial WGS dataset, perform read quality assessment and preprocessing using Galaxy, and generate a sequencing quality report.

Tools: NCBI SRA | Galaxy | FastQC | fastp | MultiQC

Day 2: Bacterial Genome Assembly, Antibiotic Resistance Gene Detection & Functional Annotation

Topics Covered:

• Principles of bacterial genome assembly and genomic reconstruction.
• De novo genome assembly using SPAdes.
• Genome assembly evaluation: Contigs, N50, genome size and coverage.
• Assessment of bacterial genome assembly quality using QUAST.
• Introduction to antibiotic resistance genes (ARGs) and major resistance gene families.
• Bioinformatics approaches for identifying acquired ARGs and resistance-associated mutations.
• Antibiotic resistance gene detection using NCBI AMRFinderPlus.
• Introduction to the Comprehensive Antibiotic Resistance Database (CARD).
• Resistance gene identification and annotation using CARD Resistance Gene Identifier (RGI).
• Classification of ARGs by antibiotic class and molecular resistance mechanism.
• Interpretation of sequence identity, alignment coverage and gene detection confidence.

Hands-On 2: Antibiotic Resistance Gene Detection & Characterization

Analyze a curated bacterial genome assembly using NCBI AMRFinderPlus, identify resistance-associated genes, and characterize selected ARGs using CARD annotations.

Tools: Galaxy | SPAdes | QUAST | NCBI AMRFinderPlus | CARD/RGI

Day 3: Molecular Resistance Characterization, Comparative Resistome Analysis & Genomic Epidemiology

Topics Covered:

• Molecular characterization of antibiotic resistance genes and genetic variants.
• Functional annotation of ARGs and associated resistance mechanisms.
• Classification of resistance determinants using the CARD Antibiotic Resistance Ontology.
• Plasmid-associated resistance genes and horizontal gene transfer.
• Introduction to bacterial resistomes and comparative resistome analysis.
• Resistance gene distribution and profiling across bacterial isolates.
• Antibiotic resistance gene presence–absence matrix generation.
• Multilocus sequence typing (MLST) and bacterial strain characterization.
• Introduction to genomic epidemiology and pathogen surveillance using NCBI Pathogen Detection.
• Genotype–phenotype correlation using genomic predictions and antibiotic susceptibility testing (AST) data.
• Python-based visualization of resistance gene distribution and comparative resistome profiles.
• Scientific interpretation of genomic resistance patterns and prediction limitations.

Hands-On 3: Comparative Resistome Profiling & ARG Visualization

Analyze curated antibiotic resistance gene profiles from multiple bacterial isolates, generate an ARG presence–absence matrix, and visualize comparative resistome patterns through heatmaps using Python in Google Colab.

Tools: CARD | NCBI Pathogen Detection | Google Colab | Python (pandas, Matplotlib)

Who Should Enrol?

Important Dates

Workshop Outcomes

Fee Structure