BIOMÉRIEUX EPISEQ^® CS for clinical pathogens outbreak monitoring

FAST AND INTUITIVE WORKFLOW

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.

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 Difficile, Staphylococcus 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