AMR Surveillance - Usage Guide

AMR Surveillance - Usage Guide

Overview

Detect and track antimicrobial resistance genes using AMRFinderPlus for surveillance and clinical interpretation.

Prerequisites

conda install -c bioconda ncbi-amrfinderplus
amrfinder -u  # Update database

Quick Start

Tell your AI agent what you want to do:

• "Screen my genomes for AMR genes"
• "Track AMR trends across my surveillance samples"
• "Generate an AMR surveillance report"

Example Prompts

Gene Detection

"Find all resistance genes in these bacterial genomes"

"Check for carbapenemase genes in my Klebsiella isolates"

Surveillance Analysis

"How has ESBL prevalence changed over the past year?"

"Are there any emerging resistance patterns in my data?"

Clinical Interpretation

"What antibiotics should be avoided for this isolate?"

"Generate a resistance report for clinical review"

What the Agent Will Do

1. Run AMRFinderPlus on genome assemblies
2. Parse results and filter high-confidence hits
3. Summarize by drug class
4. Track trends over time if longitudinal data
5. Flag emerging or critical resistance
6. Generate interpretable reports

Tips

• Organism flag - Use --organism for point mutation detection
• Quality - Filter by coverage >90% and identity >90%
• Database - Update regularly with amrfinder -u
• Critical genes - Prioritize carbapenemases and MCR
• Context - Combine with strain typing for outbreak analysis