University of Idaho Study Discovers Hosts Responsible for Spread of Antibiotic Resistance in Wastewater Leveraging New Technology Platform

SEATTLE, Wash, May 30, 2019, University of Idaho researchers in collaboration with Phase Genomics published a new study in The ISME Journal, the Multidisciplinary Journal of Microbial Ecology, utilizing ProxiMetaTM to capture the spread of antibiotic resistance on the molecular-level within a complex, environmental microbiome community. 

The study, titled Linking the Resistome and Plasmidome to the Microbiome, employees new technology from Phase Genomics. The Seattle-based biotech is the leader in proximity-ligation genome assembly. The study highlights a novel culture-free method based on Phase Genomics’ ProxiMeta™ microbiome discovery platform.

“Developing improved identification of natural carriers of ARGs provides new strategies to curtail the spread of the global human health crisis of antibiotic resistance.” said Dr. Thibault Stalder, Research support Scientist in Biological Sciences at the University of Idaho and author on the paper. “Without having to culture individual isolates, this method offers a new approach to identify the bacterial reservoirs of mobile genetic elements such as plasmids that carry antimicrobial resistance genes.”

In the study, researchers examined complex microbiome communities sampled from the wastewater treatment plant in Moscow, Idaho. In the findings, researchers discovered dozens of new bacterial genomes. Additionally, the data was used to directly assign sequences from plasmids and ARG genes to their hosts, even when these hosts genomes different from known bacteria. Additional studies previously revealed ARGs in habitats such as soil, rivers, human and animal guts, and wastewater treatment implicating them all as plausible reservoirs for ARGs.

“This study demonstrates how new advancements in genomics can help researchers remove a major roadblock in tracking antibiotic resistance,” said Ivan Liachko Ph.D., Founder and CEO of Phase Genomics. “Conventional shotgun sequencing approaches can’t connect mobile elements carrying ARGs with the organisms they occupy. Our technology generates genomes for hundreds of previously undiscovered organisms and assigns mobile elements to these new genomes. This method could enable real-time tracking of ARGs.”

The World Health Organization predicts that ARG could cause 10 million deaths annually by 2050 if new methods for combatting this global crisis are not developed. The new study offers a powerful and novel way of detecting and understanding the ecology of the spread of ARG across complex microbial communities and can potentially lead to better culture-independent diagnostics and treatments.

Phase Genomics is currently involved in additional studies tracking ARG and enabling microbiome discovery.

ABOUT PHASE GENOMICS – Phase Genomics applies Hi-C and other proximity-ligation methods to enable chromosome-scale genome assembly, metagenomic deconvolution, as well as analysis of structural genomic variation and genome architecture.  They offer a comprehensive portfolio of laboratory and computational services and products, including Hi-C kits for plants, animals, microbes, and human samples as well as industry-leading genome and metagenome assembly and analysis software. 

Based in Seattle, WA, the company was founded in 2015 by a team of genome scientists, software engineers, and entrepreneurs.  The company’s mission is to empower scientists with genomic tools that accelerate breakthrough discoveries.

ABOUT THE UNIVERSITY OF IDAHO – The University of Idaho, home of the Vandals, is Idaho’s land-grant, national research university. From its residential campus in Moscow, U of I serves the state of Idaho through educational centers in Boise, Coeur d’Alene and Idaho Falls, nine research and Extension centers, plus Extension offices in 42 counties. Home to nearly 12,000 students statewide, U of I is a leader in student-centered learning and excels at interdisciplinary research, service to businesses and communities, and in advancing diversity, citizenship and global outreach. U of I competes in the Big Sky Conference. Learn more at

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