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Precision metagenomics lets you detect all potential pathogens and drug resistance mechanisms in one workflow, providing more comprehensive and definitive information upfront.

Identify All Relevant Pathogens with Just One Workflow and Easy Analysis

Precision metagenomics offers an efficient and comprehensive approach for characterizing the microbial environment

Published:Jun 02, 2023
|3 min read
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Headshot of Robert Schlaberg
Robert Schlaberg, MD, MPH, is a VP and distinguished scientist (Infectious Disease) within the Emerging Applications & Partnerships group at Illumina. Prior to joining Illumina, Robert was a co-founder and chief medical officer of IDbyDNA, an assistant professor of Pathology at the University of Utah School of Medicine, and a medical director at ARUP Laboratories.

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What is precision metagenomics, and what are its advantages for pathogen detection versus other molecular diagnostic assays such as multiplex PCR testing?

The term “metagenomics” does not have a consistent definition, but generally, it is an approach to describe the composition of a microbial community, in this case, with genomic tools. While traditional metagenomics is broad and provides a high-level overview, PCR is on the other end of the spectrum: it is very specific and sensitive, but it can only detect one organism at a time. Precision metagenomics fits somewhere in between those extremes by allowing for reliable and sensitive detection, as well as genomic characterization of organisms, at the species, strain, or genotype level.

How does adopting a precision metagenomics platform improve an infectious disease lab?

Rather than running a battery of culture, antigen-based, microscopy, PCR, or shotgun metagenomics tests, precision metagenomics lets you detect all potential pathogens and drug resistance mechanisms in one workflow, providing more comprehensive and definitive information upfront. When we conducted clinical research studies for urinary tract infections (UTIs), we detected over 30 percent more relevant pathogens with precision metagenomics rather than culture-based tests. With respiratory tract infections, we could use it to detect unexpected pathogens that were otherwise unlikely to be recognized. For example, we detected mumps virus, which most labs would not have specifically looked for since it is uncommon but undetected circulation has important public health implications.

What challenges do labs face when adopting precision metagenomics, and how does Illumina's Explify platform address these challenges?

The greatest barrier has been data analysis. Precision metagenomic analysis produces millions of individual DNA sequences for a single sample that need to be compared to millions of reference sequences in a complex, broad detection catalog of relevant pathogens. In addition, to  ensure the accuracy of their workflow, labs must perform quality control that is as complex as next-generation sequencing.

Illumina's Explify platform addresses these challenges through its point-and-click-based analysis designed to be used by someone without bioinformatics expertise. The platform has tailored sequence data comparison, algorithmics, and interpretation (i.e., providing answers instead of just the raw catalog) and does not require you to purchase additional hardware (thanks to cloud-based access) nor develop analytics expertise to make sense of your data.

How do you think precision metagenomics will impact the future of molecular diagnostics?

Despite the known shortcomings of existing methods, the previous complexity of NGS workflows and high costs of sequencing-based approaches prevented their wide use. As those barriers are increasingly removed, and with more automation, there will be wider and scalable adoption of precision metagenomics for comprehensive testing beyond only the most complicated cases. Through a platform like Explify, labs can perform consistent precision metagenomics workflows and detailed analysis to comprehensively characterize the microbial environment. The approach allows for efficiency and accuracy, while leaving room for discovery and serendipity, which are vital to the scientific process.

Illumina approval code M-GL-01772.