Colorado State University Sequencing Solutions: Revolutionizing Understanding of Antimicrobial Resistance with Genome Analysis

Photo credit: Joe A. Mendoza, Colorado State University

Antimicrobial resistant-microbes (AMRs) pose a serious threat to public health. AMRs are found in people, animals, food, and the environment. They spread from animals to people, and from person to person.

To solve this problem, Dr. Morley and his team are studying the genetic makeup of all of the organisms throughout the environments involved in animal (e.g. beef and dairy cattle) food production, not just one isolated bacteria at a time. Dr. Morley commented that you can’t tell the health of a forest by only looking at a single blade of grass. Rather, the health of a forest is determined by investigating the mixture of plant species. For this reason, they are examining genomic sequences of entire microbial communities (metagenomes) in samples of feed, wastewater, manure, soil, and meat. By analyzing these complex ecosystems, they can better understand how antimicrobial resistance genes develop and evolve.

The team is making progress with this enormous task by using high-throughput sequencing and “big data” computer programs. They are building cloud computing resources called “AMR++” and “AMRStratus”, designed with the intention of making genomic software tools more accessible to non-computer scientists. This will help scientists track how bacteria spread resistance genes, discover where resistance genes originate, and access vital information about AMR genomes. 

This project includes education and training components. The team develops curricula to promote widespread literacy of applied genomics. By increasing the understanding of genetic analysis techniques, the team is training the next generation of agricultural scientists. 

This “next generation sequencing” technology uncovers cutting-edge opportunities to develop innovative tools, advances safe production methods, and creates a paradigm shift for the life sciences.

People in agriculture are committed to promoting public health. I have had outstanding teachers and mentors during my training. I now have the great reward to train promising and dedicated young scientists.

– Dr. Paul Morley

Retaking The Field Volume 3 “Retaking the Field: Empowering Agricultural Sciences for Health” is a collaborative report from eleven universities and the SoAR Foundation. The report — the third in SoAR’s series — explores the success of research projects funded by the Agriculture and Food Research Initiative (AFRI), the flagship competitive grants program of the USDA’s National Institute of Food and Agriculture (NIFA). It is part of SoAR’s broader education and advocacy initiative to encourage additional federal support for food and agricultural research. View The Issue
Retaking the Field Volume 3: The Case for a Surge in Agricultural Research Click to download report

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