Pathogen typing and epidemiology

Infectious diseases impact public health globally. Pathogen outbreaks affect the life of patients and create a high economical burden. Early detection and control of outbreaks is therefore key to protecting public health.

Whole genome analysis offers unique advantages when used for typing and characterizing microbial isolates. Whole genome data reveals the full picture providing taxonomic information and insight into factors like antimicrobial resistance. Once a pathogenic microbe is typed and characterized, comparative whole genome SNP analysis is the most accurate path to tracking a pathogen contamination back to the source.

While crucial for outbreak control, whole genome analysis also enables quality control of starter cultures and biotechnologically valuable strains.







Feature overview

Isolate management

Samples, sample information (metadata) and results can be accessed from a convenient analysis dashboard.


Preconfigured and customizable workflows streamline typing. In one analysis workflow, taking raw whole genome isolate data as input, you confirm the identity and characteristics of microbes, revealing:

  • NGS-MLST (Multi locus sequence typing)
  • Taxonomy
  • Closest known reference genome
  • Antimicrobial resistance genes
  • Likely sample contamination

Phylogenetic analysis

Preconfigured and customizable workflows streamline phylogenetic analysis:

  • K-mer based trees from raw reads, assembled contigs, and closed genomes.
  • Whole-genome SNP trees for accurate outbreak investigation and source tracking of pathogen isolates.

Outbreak trees can help monitor outbreaks and are essential for source tracking of pathogens. Useful features:

  • Trees are interactively linked to Analysis Dashboards.
  • Trees can be explored in the context of typing results, epidemiological metadata, and other custom sample information.

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