tools-only Pathogen Typing - Usage Guide
Overview
Identify bacterial strain types using MLST, cgMLST, and SNP-based approaches for outbreak investigation and surveillance.
Prerequisites
conda install -c bioconda mlst
pip install chewbbaca pandas
Quick Start
Tell your AI agent what you want to do:
- "Type my Salmonella isolates with MLST"
- "Run cgMLST on these E. coli genomes"
- "Find which isolates cluster together"
Example Prompts
Basic MLST
"Determine the sequence type of my bacterial genome"
"Run MLST on all FASTAs in this directory"
Core Genome MLST
"Run cgMLST and identify outbreak clusters"
"Calculate allelic distances between my isolates"
Outbreak Investigation
"Which isolates are within 5 allele differences?"
"Identify transmission clusters from my typing results"
What the Agent Will Do
- Identify organism and select appropriate scheme
- Run MLST/cgMLST typing
- Parse results into structured format
- Calculate distances between isolates
- Identify clusters based on thresholds
- Report sequence types and cluster assignments
Tips
- Scheme selection - mlst auto-detects; specify if known
- cgMLST thresholds - Pathogen-specific (E. coli: 10, Salmonella: 7)
- Novel STs - Submit new types to PubMLST for official designation
- Assembly quality - Poor assemblies may give incomplete profiles
- Mixed cultures - MLST assumes clonal isolates