bio-epidemiological-genomics-pathogen-typing

Version Compatibility

Reference examples tested with: mlst 2.23+, numpy 1.26+, pandas 2.2+, scanpy 1.10+, scipy 1.12+

Before using code patterns, verify installed versions match. If versions differ:

• Python: pip show <package> then help(module.function) to check signatures
• CLI: <tool> --version then <tool> --help to confirm flags

If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying.

Pathogen Typing

"Type my bacterial isolates by MLST" → Assign multi-locus sequence types to bacterial genomes for isolate characterization, outbreak clone identification, and strain tracking.

• CLI: mlst assembly.fasta for 7-gene MLST typing
• CLI: chewBBACA.py AlleleCall for core genome MLST (cgMLST)

MLST with mlst Tool

# Install mlst
conda install -c bioconda mlst

# Basic MLST typing
mlst genome.fasta
# Output: genome.fasta  ecoli  ST131  adk(53) fumC(40) gyrB(47) ...

# Batch typing
mlst *.fasta > typing_results.tsv

# Specify scheme
mlst --scheme senterica genome.fasta

# List available schemes
mlst --list

# Include allele sequences in output
mlst --csv genome.fasta > results.csv

Parse MLST Results

import pandas as pd
import subprocess

def run_mlst(fasta_files, scheme=None):
    '''Run MLST on multiple genomes

    Returns DataFrame with:
    - Sample name
    - Scheme (auto-detected or specified)
    - Sequence type (ST)
    - Allele profiles

    ST interpretation:
    - Known ST: Matches existing type in database
    - Novel allele: New allele combination, may be unreported ST
    - Failed: Unable to determine (poor assembly or wrong scheme)
    '''
    cmd = ['mlst'] + fasta_files
    if scheme:
        cmd.extend(['--scheme', scheme])

    result = subprocess.run(cmd, capture_output=True, text=True)

    lines = result.stdout.strip().split('\n')
    data = [line.split('\t') for line in lines]

    return pd.DataFrame(data, columns=['file', 'scheme', 'ST'] +
                       [f'locus{i}' for i in range(1, len(data[0])-2)])