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ONT Genomic Epidemiology (Prokaryotic)

 
 
Characterize AMR, virulence, and plasmids in a single run.
Microsynth's ONT Genomic Epidemiology service deciphers prokaryotic genomes using long-read sequencing and a targeted analysis pipeline for resistance, virulence, and strain typing.

What You Can Achieve

  • Identify species with high-resolution taxonomic profiling
  • Detect antimicrobial resistance (AMR) and virulence genes
  • Reconstruct and analyze plasmids
  • Detect SNPs and structural variants (if reference available)
  • Perform MLST and ANI analyses for epidemiological comparison

Before You Start

To tailor the analysis, please let us know:

  • Which organism(s) or strains are you investigating?
  • Is a reference genome (e.g., NCBI Accession) available?
  • Are you primarily interested in AMR genes, virulence genes, plasmids—or all three?
  • Are there specific genes or features you want to screen?

Modular Workflow

A structured process designed to identify and contextualize genomic traits:

ONT Genomic Epidemiology

Bioinformatics Analysis

Our specialized Genomic Epidemiology pipeline includes:

  • Taxonomic classification via ANI and MLST (if schema exists in PubMLST)
  • AMR gene detection using curated resistance gene databases
  • Virulence factor identification based on public and proprietary annotations
  • Plasmid recovery and reconstruction
  • Variant calling if a reference genome is available
  • Summary visualizations for resistance profiles, plasmid maps, and gene clusters

You receive:

  • Annotated genome and plasmid sequences
  • Gene presence/absence tables (AMR/virulence)
  • MLST and ANI reports
  • Variant tables and visualizations
  • All raw and processed sequencing data

Turnaround Time

  • Results delivered in 3 to 7 days after sample receipt

Dependent on genome complexity and whether a reference is provided.

Sample Requirements

Option 1: Pre-extracted HMW DNA

  • Minimum 1 μg of high-quality gDNA
  • ≥50% of fragments >10–20 kb
  • 260/280 >1.8 and 260/230 between 2.0–2.2
  • ≥30 μl at ≥30 ng/μl

Option 2: Cultures or Colonies (with Extraction)

  • Bacterial cell pellet, isolated colony, or liquid culture
  • Clearly labeled, fresh or properly preserved
  • Include medium type and any special handling notes