Resistome & Virulome Analysis (AMR Surveillance) — Hands-on

Build end-to-end workflows to profile antimicrobial resistance (AMR) genes and virulence factors from shotgun metagenomes for clinical, environmental, wastewater and food safety use-cases. You'll map reads/contigs to curated databases, quantify ARGs/VFs with proper normalization, track mobile genetic elements and context, and generate decision-ready surveillance reports aligned with One Health frameworks.

Resistome & Virulome Analysis (AMR Surveillance)

Help Desk · WhatsApp

Session Index

Session 1 — Databases, Concepts & Intake Session 2 — Read/Contig-Level ARG & VF Calling Session 3 — Mobile Elements, Context & Risk Session 4 — Dashboards, Reporting & GLASS

Session 1

Fee: Rs 8800

Databases, Concepts & Intake

ARG & VF ontology and curation

CARD / ResFinder / MEGARes / ARG-ANNOT VFDB / Victors / PATRIC updates & versioning

Study design & intake

matrix (clinical, wastewater, soil, food) mock communities & controls metadata (MIxS-AMR)

Normalization concepts

CPM/RPKM/TPM vs. per 16S/rrn internal standards & spike-ins compositional awareness

Session 2

Fee: Rs 11800

Read/Contig-Level ARG & VF Calling

Short-read pipelines

RGI (CARD) / AMRFinderPlus DeepARG / ShortBRED SRST2 / KMA

Assembly-based screening

ABRicate (CARD/ResFinder/VFDB) Prokka + HMM searches sensitivity/specificity trade-offs

Quantification & thresholds

%identity/coverage rules resistance classes/mechanisms FDR & confidence flags

Session 3

Fee: Rs 14800

Mobile Elements, Context & Risk

Mobilome & context detection

PlasmidFinder / MOB-suite IntegronFinder / ISfinder linking ARGs→contigs→MAGs

Co-occurrence & transmission

network & synteny views source attribution (host taxa) time-series drift

Risk & priority scoring

clinically relevant ARGs/VFs critical AB classes (WHO) wastewater sentinel metrics

Session 4

Fee: Rs 18800

Dashboards, Reporting & GLASS Alignment

Visualization & reporting

heatmaps / sankey / chord ARG class stacks & VF panels Quarto dashboards

Surveillance frameworks

WHO GLASS mapping (overview) One Health indicators reporting templates & SOPs

Compositional DA & QA checks

ANCOM-BC / ALDEx2 batch/confounders mock replays & limits of detection

PDF

Resistome & Virulome Analysis (AMR Surveillance) Training | CARD/ResFinder, RGI/AMRFinderPlus, Mobilome & Dashboards

Resistome & Virulome Analysis (AMR Surveillance) — Hands-on