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Clinical Laboratories and Pathology Groups

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This collaborative effort with microbiology labs will keep microbiologists at the forefront of infectious disease diagnostics

A partnership of San Diego-based genome sequencing company Illumina, and the French multinational, in vitro diagnostics company bioMérieux, plans to launch a next-generation sequencing (NGS) epidemiology service that will allow microbiologists to rapidly identify strains that threaten hospital inpatients and public health, according to a press release distributed by the Illumina-bioMérieux team.

Illumina-bioMérieux Service to Aid Hospital and Public Health Labs 

Illumina designated sequencing laboratories with Illumina MiSeq® systems will collaborate with microbiologists working in hospital and public health laboratories to prevent, rapidly track, and contain infectious disease agents in hospitals and communities.

The Illumina-bioMérieux partnership will develop applications for microbiology sequencing technologies, beginning with an NGS epidemiological solution for genotyping disease agents. This solution will combine the power of the Illumina MiSeq® system with a proprietary genomic database to provide pathogen analysis. The largest library of bacterial strains in the world, bioMérieux’s culture collection contains over 80,000 references that will be tapped to co-develop a database of unprecedented scope that includes information about virulence and microbial resistance characteristics.

Pathogen Analysis to be Provided by Illumina-Designated Sequencing Labs

These epidemiology services will be provided by designated sequencing laboratories, supported by the secure, cloud-based pathogen database to deliver a standardized report of infectious agents’ genomic profiles, with sequence-level accuracy and depth of information, stated the Illumina-bioMérieux press release.

In announcing the new service, Illumina Chief Executive Jay Flatley said, “We are excited by the opportunity to expand the number of NGS-based applications in the infectious disease market with a solution designed for epidemiology and hospital infection control.”

Jean-Luc Bélingard, Chairman of bioMérieux, said his company’s epidemiology collaboration with Illumina offers an opportunity to provide an innovative solution within hospital settings for sequencing bacteria. “It is particularly suited to the growing need to combat infectious diseases, one of the major global public health challenges today,” he said. “Moreover, this collaboration is a first step that will enable bioMérieux to identify opportunities and fields of application that sequencing can bring to infectious disease diagnostics.”

Service to Accelerate Use of Pathogen Genomics in Public Health Labs

Dr. Leila Luheshi, the Programme Lead for Science at the PHG Foundation, said in a news blog that pathogen genomic data, such as what will be offered by the Illumina-bioMérieux epidemiology service, would have a huge role in improving infectious disease surveillance, and it was great to see this fact underlined by a large-scale commercial collaboration.

Dr. Leila Luheshi

Dr. Leila Luheshi (pictured above), the Programme Lead for Science at the PHG Foundation in Cambridge, England, believes commercially developed “out-of-the-box” genomic solutions, like what is proposed by the Illumina-bioMérieux service, could accelerate use of pathogen genomics by infectious disease scientists.  (Photo copyright PGH Foundations.)


Based in Cambridge, England, the PGH Foundation is a nonprofit organization that provides expert assessment of new technologies, including their scientific basis and clinical relevance to economic and social impact, with independent insights into the potential benefits and consequences for health systems and services.

Luheshi is currently leading a major PGH Foundation project to assess the potential clinical impact of microbial genomics on public health and health services, and to develop policy to support implementation, working in consultation with leading stakeholders.

She said that availability of commercially developed “out of the box solutions” for pathogen genomics may help to accelerate the uptake of genomics, particularly if they provide user-friendly analytical software accessible to non-bioinformatics trained laboratory staff. But Luheshi warned of potential downsides to the use of proprietary systems, “particularly if they do not enable the genomic data generated to be made widely and freely available to other parts of the health system and to legitimate researchers.”

Genetic sequencing would provide scientists precise information about disease agents involved in infection transmission, or as the cause of outbreaks and epidemics. Genetic sequencing of bacteria can help microbiologists identify antibiotic-resistant mechanisms. It also would make it possible to establish a correlation between the different characteristics of an infectious agent to determine the chronology of transmission, and monitor its spread. This information could facilitate and speed decisions by public health clinicians to implement effective measures to contain and stop the spread of the disease agents.

The ultimate goal of this epidemiology service is to contain epidemic, avoid transmission of infectious agents, and improve hospital practices where needed, noted the Illumina-bioMérieux press release. When faced with a suspected epidemic or health crisis, public health and hospital microbiology laboratories will be able to send the relevant isolates to a designated laboratory for sequencing and analysis, using the pathogen database and software developed by the Illumina-bioMérieux partnership. A customized report of the results would be generated and presented in an easily understandable graphical format that identifies the infectious agent, as well as sequence-based genetic variations that could assist in understanding how it is transmitted.

Service to Collaborate with Microbiologists, Not Molecular Diagnostic Labs

While this is the first commercial epidemiology effort to address infectious disease on a genomics level, pathologists can expect to see other biomedical competitors enter this market. What is noteworthy about this proposed service is it represents a significant effort by the Illumina-bioMérieux partnership to collaborate with microbiology laboratories, incorporating these new diagnostic tools into a comprehensive system that would keep microbiologists at the forefront of infectious disease diagnostics.

—Patricia Kirk

Related Information:

Illumina and bioMérieux Enter Agreement to Co-Develop a Next-Generation Sequencing Solution for Epidemiological Monitoring of Bacterial Infections

Illumina Plans Bacterial Genomics Clinical Microbiology Service

Illumina and bioMérieux to Pinpoint Pathogens with Next Gen Sequencing

bioMérieux, Illumina to Launch NGS Epidemiology Solution