Pathogen fingerprinting for precise outbreak analysis

The 1928 platform uses core genome multilocus sequence typing (cgMLST) for transmission analysis. This method is robust and enables reliable comparisons across large sample sets. We generate our own cgMLST schemes which consists of conserved genes that can be used to generate a “pathogen fingerprint”. By visualising the number of identical genes found in phylogenetic trees, large sample sets can be compared and groups of closely related samples can be identified as possible outbreaks. The method also allows for new samples to be compared to historical data previously uploaded. An alternative to use cgMLST for clustering is to use Single Nucleotide Polymorphism (SNP) analysis. This will generate a phylogenetic tree based alterations of single nucleotides in the whole genome.

Analysis includes:

  • Quality control including sample quality

  • Automatic species identification

  • cgMLST for more than 25 species and SNP analysis for all species

  • Antimicrobial resistance and virulence markers

  • Epidemiological metadata

Epidemiologic typing

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