School of Bioinformatics · Microbial & evolutionary genomics
Bacterial Genomics & Antimicrobial Resistance
Whole-genome sequencing is now central to antimicrobial-resistance surveillance and outbreak investigation. This course teaches the bacterial genomics workflow used in public-health and clinical microbiology research.
Course overview
Bacterial Genomics & Antimicrobial Resistance follows isolates from reads to public-health questions: assembly and QC, species confirmation, multilocus sequence typing, detection of resistance genes and mutations, plasmids and virulence factors.
You build pangenomes and core-genome SNP phylogenies, estimate transmission relationships in an outbreak dataset, and learn the limits of genotype-to-phenotype prediction for resistance.
Learning outcomes
By the end of the course you will be able to:
- Assemble and quality-check bacterial genomes
- Confirm species and assign MLST types
- Detect AMR genes, point mutations, plasmids and virulence factors
- Build pangenomes and core-genome SNP phylogenies
- Interpret genomic relatedness in an outbreak investigation
Skills you will practise
Eligibility and prerequisites
Who can apply
- Students and graduates of B.Sc., M.Sc., B.Tech., M.Tech., B.Pharm., M.Pharm., MBBS, BDS, B.V.Sc. or a PhD programme in the life sciences, biotechnology, bioinformatics, pharmacy, medicine, agriculture, chemistry, statistics or computer science
- Researchers, faculty and industry professionals moving into data-driven biology
- Final-year students may apply before their results are declared
Prerequisites
- Linux command line
- Undergraduate microbiology
Best suited to
- Microbiologists and public-health researchers
- Clinical microbiology postgraduates
- Students interested in AMR surveillance
Module-wise syllabus
6 modules. Each pairs instructor-led sessions with a hands-on lab on public data.
Topics
- QC and assembly
- Species identification
- Contamination checks
Topics
- MLST and cgMLST
- Serotyping
- Nomenclature databases
Topics
- AMR gene and mutation detection
- Plasmids and mobile elements
- Genotype versus phenotype
Topics
- Core and accessory genomes
- Panaroo
- Gene presence–absence analysis
Topics
- Core-genome SNP alignment
- Recombination
- Transmission inference
Topics
- Analysis
- Interpretation
- Communication
Practical sessions and projects
Capstone project
Investigate an outbreak
Analyse a public set of bacterial genomes to type isolates, predict resistance and infer relatedness, and summarise the findings for a public-health audience.
Assessed on the correctness of the analysis, the quality of the code and the reasoning in the write-up. A pass is required for the certificate.
- From reads to genomes
Assemble ten clinical isolates and confirm their species and assembly quality.
- Typing
Type the isolates and summarise their sequence types.
- Resistance and virulence
Predict resistance profiles and compare them with laboratory susceptibility results.
- Pangenomes
Build a pangenome and find accessory genes associated with resistant isolates.
- Phylogenies and outbreaks
Reconstruct an outbreak phylogeny and identify likely transmission clusters.
- Project: a surveillance report
Produce a genomic surveillance report for a set of isolates with typing, resistance and relatedness.
Software, tools and datasets
Software and tools
All software is free and open source or free for academic use. Recommended computer: 8 GB RAM, 30 GB free disk, Linux, macOS or Windows with WSL2.
Datasets
- Public Klebsiella pneumoniae and E. coli isolates: Typing and AMR detection.NCBI Pathogen Detection (public)
- Published outbreak sequencing datasets: Transmission analysis.ENA / SRA
Core reading
- Feldgarden M et al. (2021). AMRFinderPlus and the Reference Gene Catalog facilitate examination of the genomic links among antimicrobial resistance, stress response, and virulence. Scientific Reports 11:12728.
- Tonkin-Hill G et al. (2020). Producing polished prokaryotic pangenomes with the Panaroo pipeline. Genome Biology 21:180.
Duration, format and fees
- Next cohort
- Dates are sent with your admission offer
- Timetable
- Three evening or weekend sessions a week (IST), plus a lab clinic; intensive and weekend-only schedules on request
- Payment
- Secure online payment link with your admission offer (UPI, cards, net banking). Instalments on request for fees above ₹15,000.
- Refunds
- See the refund and cancellation policy.
Instructor
The instructor for each cohort is named in your admission offer and on this page when the cohort is announced. Vedicgen instructors are selected for hands-on research or industry experience in the subject they teach, and every course is reviewed by a second subject expert.
Questions about who teaches a cohort? [email protected]
Certificate
Learners who complete the course and pass its capstone receive a Vedicgen certificate of completion for Bacterial Genomics & Antimicrobial Resistance, issued by Vivofold, stating the guided hours and skills assessed. Each certificate has a unique ID and QR code that anyone can check.
Apply for Bacterial Genomics & Antimicrobial Resistance
Apply
Send the form below. It takes about five minutes.
Review
An adviser confirms your fit and format within two working days.
Offer
You receive dates, timetable and a secure payment link.
Onboard
Set-up guide, pre-reading and joining links.
Frequently asked questions
In the live cohort, modules are taught in instructor-led sessions with a weekly lab clinic where you work on real public data with help at hand; every session is recorded. The self-paced format uses the same lessons, labs and datasets with mentor review of your capstone. Both formats end with an assessed project reviewed for the code and the science.
A laptop with at least 8 GB of RAM and about 30 GB of free disk space, running Linux, macOS, or Windows with WSL2. Installation instructions are sent before the first session, and lab clinics help with any set-up problems.
Yes. Learners who complete the course and pass its assessment receive a Vedicgen certificate of completion, issued by Vivofold. Every certificate carries a unique ID and a QR code that anyone, including an employer or admissions office, can check on the certificate verification page.
Apply with the form on this page. Live and in-person cohorts run through the year; the dates, timetable and joining details of the next cohort are sent with your admission offer and listed on this page once announced. Self-paced enrolment opens as soon as your application is accepted.
Yes. No course runs longer than four weeks, and the length is customisable: choose the standard schedule, an intensive one- to two-week schedule, weekends only, or a custom timetable. Pick your preference on the application form; colleges and teams can book their own dates.
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