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Microbial Genomics

Next-Generation Sequencing Provides Insight into Microbiome

Recent advances include powerful applications for public health

Next-Generation Sequencing Provides Insight into Microbiome
December 22, 2014

Bacteria, viruses, and parasites. Until fairly recently, scientists had only scratched the surface of understanding these microbes and how they interact with all living matter, from plants to animals to humans. Our gut, for example, is home to billions of bacteria, and researchers are now beginning to understand how they influence our immune systems. Food-borne illnesses can be tracked to their source, and infectious disease outbreaks can be identified and managed with greater accuracy. Recent developments in microbial genomics, due in part to next generation sequencing (NGS), are enabling such insights and advancements.

According to Illumina’s Susan Knowles, senior market development manager, “Through the power and high resolution of NGS, researchers are better equipped to discover novel microbes, compare genomes, and study rearrangements that translate to microbial evolution.  This research is enabling advances in several areas of microbial genomics including public health, clinical microbiology and the human microbiome. Those areas in turn have direct impact on human health.”

She notes that in addition to providing higher resolution, NGS allows researchers to characterize “un-culturable” organisms. With traditional methods, scientists estimate that only ~1 percent of bacteria can be grown in a laboratory, which in turn limited organisms to be studied.

Public health advances

One of the more progressive areas of microbial genomics, according to Knowles, is public health infectious disease surveillance, where scientists are constantly searching for new clues about how diseases spread from animal-to-person and person-to-person. Driven by the goal to prevent and control outbreaks in the community, researchers seek to better understand transmission dynamics and track the origins of diseases such as tuberculosis and influenza.

“While epidemiologists know a lot of basic information about disease transmission, we don’t know much about how those diseases behave and evolve during an outbreak,” Knowles explains. “That’s where next-generation sequencing is a powerful factor.” It can help determine if one specific person is infecting several people and where an outbreak began, for example. It can also tell more about the course of outbreaks and how they evolve.

Microbiology collaborations accelerating the field

Recently, Illumina announced a collaboration with bioMerieux, a world leader in the field of in vitro diagnostics, to develop an NGS epidemiological solution offered by service labs for genotyping disease agents. The solution will combine Illumina’s MiSeq® sequencing system with a jointly developed pathogen genome database based on bioMérieux’s culture collection. This collection, which contains over 80,000 references, constitutes one of the largest libraries of bacterial strains in the world, and will contribute to creating a database of unprecedented scope with information about virulence and microbial resistance characteristics.

The ultimate goal of the Illumina and bioMérieux epidemiology solution will be to enable public health and hospital microbiology laboratories to investigate suspected outbreaks and better characterize outbreak strains so hospital infection control and public health officials can take action to minimize transmission and contain an epidemic.

Another high-profile development is the recent partnership between U.S. Agency for International Development (USAID), the Broad Institute of MIT and Harvard and Illumina to aid those in West Africa who are fighting the spread of the Ebola virus. Through the partnership, local and outbreak-deployed personnel will be trained to sequence viral genomes from the outbreak and to extend surveillance operations. Genome sequencing of the virus is critical for genomic surveillance—tracking how the virus is moving and changing in real-time. This information may influence the development of diagnostics, vaccines, and therapies.

“This is an exciting time for those of us in the microbial genomics field,” says Knowles. “Being able to examine bacteria, viruses and parasites may not sound as glamorous as sequencing the human genome, but in terms of progressing public and human health, it’s equally as powerful.”

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