BIOMÉRIEUX EPISEQ® CS for clinical pathogens outbreak monitoring

NEW: Next Generation Sequencing Software for HAI outbreak management

BIOMÉRIEUX EPISEQ CS is the software application by bioMérieux to help you better manage healthcare-associated infection (HAI) outbreaks using Next Generation Sequencing (NGS)

Built on bioMérieux’s expertise in microbiology and WGS for advanced epidemiological application

  • Access a higher level of strain discrimination and characterization through whole genome MLST typing
  • Track, contain and prevent the spread of pathogens

Not for Diagnostic Use

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01         UPLOAD

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

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

Download the Illumina application note here (PDF)

02         ANALYSIS

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 and virulome 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 and virulome information

  • Identifies and differentiates outbreak strains from endemic strains

Next Generation Sequencing: your new, powerful solution for HAI

Healthcare-associated infections (HAI), particularly when associated with  antimicrobial resistant organisms, are one of today’s most pressing global healthcare burdens, incurring very high costs both in human and financial terms (see sidebar). The more we know about the pathogens involved in infection transmission or an outbreak, the better we can manage them.

Now, bioMérieux launches a new software to analyze Next Generation Sequencing-based genetic strain typing. NGS sequencers enable whole genome sequencing for the highest possible resolution of microbial. The BIOMÉRIEUX EPISEQ CS provides therefore a high-level bacterial strain characterization that gives extremely precise information about the disease agents suspected to be involved in infection transmission or HAI outbreak. This powerful tool enables healthcare institutions and communities to:

  • Make faster, better-targeted decisions;
  • Implement infection control measures;
  • Conduct improved epidemiological investigation;
  • Reduce the incidence of future cases;
  • Reduce HAI-related healthcare management costs.

The HAI burden – management and prevention

Hospital acquired infections cause significant patient morbidity and mortality around the world: approximately 100,000 related deaths yearly in each the USA and Europe, and far more in low-resource countries. They also incur substantial burdens to health care costs, estimated at €7 billion in Europe; $6.5 billion in USA annually1.

In addition to preventative measures, effective infection control is achieved through active surveillance of infection as well as recognition and intervention of burgeoning disease outbreaks. Molecular epidemiological investigations have become increasingly integral to these functions, and rely on rapid and effective assessment of genetic relatedness among strains2.

1) World Health Organization 2011: Report on the Burden of Endemic Health Care-Associated Infection Worldwide

2) Application of whole genome sequencing for bacterial strain typing in molecular epidemiology, Annals of Nigerian Medicine / Jul-Dec 2014 / Vol 8 | Issue 22015


The Value of Whole Genome Sequencing (WGS) in Clinical Microbiology

WGS has proven to be invaluable for outbreak detection and surveillance. It has been used to define transmission pathways of infectious pathogens and to support outbreak investigations.

Sequencing of the entire genome provides the ultimate resolution for epidemiological studies, as one is able to see every region of the genome and identify subtle differences overlooked by earlier genotypic techniques3.

3) Bacterial whole genome sequencing: The future of clinical bacteriology, Annals of Nigerian Medicine / Jul-Dec 2014 / Vol 8 | Issue 2

With results including Quality Control, MLST, Resistance Markers, Virulence markers* and Phylogenetic tree, you gain a whole picture of the causative agent, with advantages like:

  • Superior resolution of strain typing for accurate identification of HAI, less prone to false-positive and false-negative findings.
  • Next-level epidemiological investigation: Enables exploration of isolates’ virulence genes, antibiotic resistance mechanisms, concordantly with molecular epidemiology investigation.
  • Better understanding of transmission events: high-resolution inference of phylogenomic relationships and of the sequence of transmission events.
  • Unprecedented ability to define strain relationships for epidemiological investigation of bacterial outbreaks, significantly impacting infection control for better patient outcomes and cost control

*for Clostridium DifficileStaphylococcus Aureus, and E.Coli

  • Application of whole genome sequencing 1 for bacterial strain typing in molecular epidemiology.

    JCM Accepted Manuscript Posted Online 28 January 2015

    J. Clin. Microbiol. doi:10.1128/JCM.03385-14

  • Bacterial whole genome sequencing and clinical bacteriology - Annals of Nigerian Medicine / Jul-Dec 2014 / Vol 8 | Issue 2

  • Bacterial whole genome sequencing: The future of clinical bacteriology, Annals of Nigerian Medicine / Jul-Dec 2014 / Vol 8 | Issue 2

Please consult your local bioMérieux representative for product availability in your country

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