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BioMérieux, Illumina Launch Whole-Genome Sequencing Service to Investigate Staph Outbreaks


NEW YORK (GenomeWeb) – In vitro diagnostics firm BioMérieux and Illumina have partnered to launch a service for sequencing the genomes of Staphyloccus aureus samples.

The service, dubbed EpiSeq, will initially be available in Germany, France, and the Netherlands, but BioMérieux will begin expanding the service to the US, other European countries, and Asia beginning next year, BioMérieux Chief Technology Officer Alain Pluquet told GenomeWeb this week.

The EpiSeq service is the first product to be launched under an agreement that BioMérieux and Illumina made last year to develop NGS-based technologies for microbiology applications. The firms will work together over a four-year renewable period to combine Illumina's MiSeq system with a jointly developed pathogen genome database based on BioMérieux's culture collection containing more than 80,000 references.

Illumina and BioMérieux declined to disclose any financial terms of the agreement or the recently launched EpiSeq service.

Pluquet said that the service will be mainly geared toward hospitals. S. aureus is responsible for around 70 percent of infections in hospitals, so starting with that pathogen was a "no brainer." The "medical value of S. aureus is very high," he said.

The sequencing itself will be performed at one of a network of reference laboratories established by BioMérieux that have the technical capabilities. Illumina will provide the staff training on the MiSeq system, and BioMérieux will generate the report.

Currently, two laboratories will perform the testing — one in Germany and one in France, Pluquet said. As the company broadens access to EpiSeq, it will identify additional laboratories in those respective countries, he added.

The firms settled on a whole-genome sequencing workflow because it "gives us a holisitic picture of the microbe on the genomic level," Christiane Honisch, director of microbiology market development at Illumina, told GenomeWeb.

For instance, she said, if a hospital has an outbreak, it will collect samples that have been swabbed from different locations throughout the hospital — including infected patients, equipment, and sinks — and send all those samples for analysis. The microbes will first be cultured and then the lab will sequence the whole genomes of all the samples. "This is the most accurate fingerprint," she said, and will allow scientists to identify any antimicrobial resistance genes as well as piece together the transmission chain or in some cases figure out whether an outbreak is truly occurring or whether the infections represent isolated incidents.

"We started with S. aureus because it's the organisim with the largest impact on hospital-acquired infections," Honisch said.

Pluquet added that the companies plan to develop similar services for a total of 10 different microbes over the next two years.

Turnaround time from a BioMérieux in-network lab receiving a sample to report generation will be seven days or less, Pluquet said. He declined to disclose the price of the service.

Pluquet added that the service will only be for samples that are in fact S. aureus. It is not a metagenomic sequencing approach to try and identify what pathogen or pathogens are present in a mixed sample. Instead, it is geared to help hospitals track hospital-acquired infections and manage outbreaks.

"The first quality check we do is to make sure it's a Staphyloccus sample," he said. The sequencing then provides more analysis of the pathogen. Pluquet said that there will be two levels of reporting — a more basic level that provides strain typing needed for epidemiological research and a "deeper dive" into the genome.

Currently, hospitals use traditional typing methods such as pulsed field gel electrophoresis, which has a lower resolution than NGS. For instance, five people in the same hospital could all have infections of S. aureus that belong to the same strain, but pulsed-field gel electrophoresis will not be able to distinguish whether those patients' infections are related and occurred along the same transmission chain, or whether the patients became infected from separate transmission events.

Pluquet added that NGS will also have an advantage over PCR-based techniques because it is more comprehensive. "PCR is focused on known mutations," he said. "It is a yes/no approach." On the other hand, NGS is "completely exhaustive." In addition, he said, NGS allows researchers to "analyze and understand the infection and the flow of the infection."

He thinks that NGS-based approaches for studying hospital-borne infections will eventually replace more traditional methods like pulsed-field gel electrophoresis. "We see that sequencing is the technology of the future," he said.

Pluquet added that the EpiSeq service is not designed for diagnosis, but rather for bacterial epidemiology to help hospitals understand and deal with infections and outbreaks. The firm will not pursue regulatory clearances, since the EpiSeq service will not be for in vitro diagnostic purposes.

Dawn Barry, the vice president of applied markets and life sciences at Illumina added that the EpiSeq service was just the first step of the partnership with BioMérieux. Part of the companies' agreement, however, is to "define the regulatory strategy and the next steps," she said.

Some institutions are also starting to implement their own NGS-based protocols for tracking infectious disease.

For instance, Mt. Sinai Hospital has started a study to sequence clinical cases of Clostridium difficile infection in order to monitor potential outbreaks. And the Modernising Medical Microbiology group at the University of Oxford in the UK has developed an NGS-based test for Mycobacterium tuberculosis and has been building up genomic databases of other pathogens in order to monitor them within UK National Health System hospitals.