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for clinical pathogens outbreak monitoring

01       |       02       |       03






01         UPLOAD

Min. coverage recommended: 45x   -      Min. sequencing length: 150 PE

From your personal account you can directly upload your Illumina® FASTQ or assembled FASTA files. 

           Download the Illumina application note here (PDF). 

02         ANALYZE

Using a straightforward credit system you will get access to the cloud service that performs the genomic characterization and a phylogenetic analysis of the strains based on whole genome MLST of the strains.

03         REPORT

An easy to interpret report is available once the analysis is complete.

You now have decisive data to further investigate a potential outbreak or cluster, including resistome, virulome and plasmid information.

The report provides the most precise information on both sample and group level to address your needs during an outbreak situation:


  • Confirms the strain identification

  • Determines genetic relatedness among your own strains and
    the strains in the knowledge base

  • Provides resistome, virulome and plasmid information

  • Identifies and differentiates outbreak strains from endemic strains

WHOLE GENOME SEQUENCING is at the core of the analysis


Using whole-genome sequencing (WGS), EPISEQ® CS analyzes every single region across the genome to identify subtle differences often overlooked by other genotypic techniques. It offers the highest possible resolution of microbial genomes, providing extremely precise information about genes involved in infection and transmission of HAIs. This cutting-edge level of bacterial strain characterization allows you to quickly identify the source and define the transmission pathways of infectious pathogens. WGS plays a critical role in the support of outbreak investigations as well as epidemiological studies, ultimately improving overall infection control programs.

wgMLST - the technique of choice 

For each of the samples you analyze using EPISEQ® CS, the de novo assembled genome is screened for the presence of loci using BLAST.


Every locus that is found in the genome is matched against the allele database of the corresponding organism. 


A called allele has a valid start and stop codon, has no internal stop codons, has a length dividable by 3, and no non-ACGT bases. Only called alleles are included in the wgMLST allelic profile (i.e., a list of all the called loci) of the sample which are used to calculate similarities between the samples.


The categorical distance coefficient is used (match or no match between the allele numbers) to calculate the similarities and UPGMA is used as clustering algorithm. 


The allele numbers of the conventional MLST loci are screened against the corresponding MLST database and if a match is found the MLST sequence type is recorded.

wgMLST results are finally used to:

  • Check the user-defined species identity.

  • Allow robust genome-based phylogenies.

  • Provide core genome-based quality statistics indicating completeness, and as such quality of the wgMLST analysis.

  • Provide conventional genomic typing information, i.e. MLST.



Peacock S. Bring microbial sequencing to hospitals. Nature 509: 557-559 (2014)

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