The study published in bioRxiv highlights a novel method for linking antimicrobial resistance genes and other mobile genetic elements to their hosts directly from microbiome samples without having to culture constituent microbes. The new method is based on Phase Genomics’ ProxiMeta™ Hi-C microbiome discovery platform.
The findings demonstrate a solution to a major bottleneck in the study and tracking of AMR.
Current technology is hampered by its inability to identify hosts responsible for the spread of AMR from complex microbiome communities. According to the World Health Organization if new methods for combatting AMR are not discovered, each year AMR is expected to cause 10 million deaths worldwide by 2050. The new study offers a powerful new way of detecting and understanding the ecology of the spread of AMR across complex microbial communities and can potentially lead to better culture-independent diagnostics and treatments.
“Understanding the host range of AMR genes is especially difficult since these sequences are frequently transferred between bacterial strains and species on plasmids and other mobile elements,” said Ivan Liachko Ph.D., Founder and CEO of Phase Genomics. “Conventional shotgun sequencing approaches can’t connect mobile elements with the organisms they occupy, but our technology not only generates genomes for hundreds of previously undiscovered organisms, but can also assign mobile elements to these new genomes. Future applications of this method could enable real-time tracking of AMR in hospitals or in other contexts where AMR affects public health.”
“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 (AMR) genes,” said Dr. Eva Top, Professor of Biological Sciences at the University of Idaho and lead author on the paper.
In the study, Phase Genomics’ ProxiMeta Hi-C platform examined complex microbiome communities sampled from wastewater. Findings yielded hundreds of new bacterial genomes. Additionally, the data was used to directly assign sequences like plasmids and AMR genes to their hosts, even when these hosts were novel strains and species.
Additional findings, graphics, and video related to the study is available on the Phase Genomics website here. Phase Genomics is currently involved in additional studies tracking AMR 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.
Source: globenewswire.com
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