BioMérieux and Illumina Use Whole Genome Sequencing to Monitor Hospital Infections

By Bio-IT World Staff

January 8, 2016 | Multinational diagnostics company bioMérieux has launched the first commercial system for using whole genome sequencing to monitor outbreaks in hospitals. The solution, called bioMérieux EpiSeq, has been developed in partnership with genomics giant Illumina, and uses Illumina’s MiSeq next-generation sequencers to derive complete bacterial genomes from samples.

“Hospital acquired infections are a problem throughout the whole world,” says Christiane Honisch, Illumina’s Director of Microbiology Market Development. “As with the human genome, we are clearly entering a new era of genomic information. Now that we have the opportunity to use Illumina technology to look at whole genomes, we can get the most accurate fingerprint of the microbe.”

EpiSeq is strictly for the surveillance of ongoing infections, and is not meant to diagnose patients. It will, however, report the presence of any genetic variants conferring virulence traits or antibiotic resistance, to help hospitals plan their responses to outbreaks. These variants will be identified by referencing a bioMérieux-curated database of known pathogen genomes.

Meanwhile, genome-wide information on bacteria sampled from different areas of a hospital can be compared to determine the likely path of an outbreak’s transmission. This information will let customers know where and how an infectious strain entered a hospital, and where there are vulnerabilities in their measures to prevent the spread of hospital acquired infections. Using whole genome sequencing, as opposed to targeting a few known genetic markers, gives EpiSeq greater power to track the relatedness of different bacterial samples.

The tools used in this phylogenetic analysis are proprietary to bioMérieux, says Alain Pluquet, the company’s Chief Technology Officer. “It is based on deep bioMérieux understanding of microbiology,” he says, adding that the analysis is fully automated and will not require any interpretation by lab technicians.

EpiSeq is currently available for surveillance of Staphylococcus aureus, one of the most common causes of healthcare associated infections. The service will expand to cover more species in the near future. “We have a shortlist of probably ten pathogens coming quite soon,” says Pluquet, chosen to address the most pressing needs of hospitals.

Neither Illumina nor bioMérieux is announcing which additional bacteria are being considered for EpiSeq, but among the obvious candidates are Pseudomonas aeruginosa, Escherichia coli, and Clostridium difficile.

BioMérieux is rolling out the service through its network of partner labs, beginning in France, Germany, and the Netherlands. Samples will be sequenced on MiSeqs in these labs, and data will be transferred and stored through the Illumina-developed BaseSpace analysis environment. BioMérieux will report results to customers within seven days of a partner lab receiving samples.

EpiSeq will also be launched in the U.S. and Asia at an unannounced future date.

The EpiSeq analysis workflow could also eventually be made available to hospital labs with their own sequencers, for in-house surveillance of infections. Illumina makes an FDA-cleared version of the MiSeq for clinical use, and some hospital labs have already independently designed next-generation sequencing programs for outbreak monitoring.

“There are plenty of labs that do not have sequencers yet,” says Pluquet. “That said, we will evolve according to our customers’ needs, and if in the future we have customers asking for the bioinformatics part only, we will probably do that.”

“This is the future of managing healthcare associated and hospital acquired infections,” says Honisch. “With the throughput and the price point our technology offers, this is clearly the right approach.”