Researchers use game theory to successfully identify bacterial antibiotic resistance

October 09, 2019

PULLMAN, Wash. - Washington State University researchers have developed a novel way to identify previously unrecognized antibiotic-resistance genes in bacteria.

By employing machine learning and game theory, the researchers were able to determine with 93 to 99 percent accuracy the presence of antibiotic-resistant genes in three different types of bacteria.

The researchers, including graduate student Abu Sayed Chowdhury and Professor Shira Broschat in the School of Electrical Engineering and Computer Science, and Douglas Call in the Paul Allen School of Global Animal Health, report on their work in the high-profile journal, Scientific Reports.

The increasing prevalence of antibiotic-resistant bacteria is a growing problem around the world. Every year, millions of people in the U.S. are infected with drug-resistant pathogens, and thousands of people die from pneumonia or bloodstream infections that become impossible to treat.

In recent years, researchers have been working to make use of genome sequencing to identify antibiotic-resistant genes, looking for similar sequences of genes in public databases. This works for identifying well-known antibiotic-resistant genes, but doesn't hold up with new or unusual genes.

"There appears to be a vast reservoir of antibiotic resistance genes in the natural world," said Call. "This tool allows us to identify presumed resistance genes that would not be recognizable based on simple sequence comparisons with public databases."

In their work, the WSU team decided to use game theory, a tool that is used in several fields, especially economics, to model strategic interactions between game players, to help identify antibiotic resistant genes.

In game theory, models determine how the behavior of one participant affects and depends on the behavior of other players.

Using their machine learning algorithm and game theory approach, the researchers looked at the interactions of several features of the genetic material, including its structure and the physiochemical, evolutionary, and composition properties of protein sequences rather than simply its sequence similarity.

"This novel game theory approach is especially powerful because features are chosen on the basis of how well they work together as a whole to identify likely antimicrobial-resistance genes -- taking into account both the relevance and interdependency of features," said Broschat.

The researchers were able to use the approach with high accuracy to identify antimicrobial-resistance genes.

"With the growth in both antimicrobial resistance and the number of available sequenced genomes, using machine learning to predict antimicrobial resistance represents a significant development in providing new and more accurate tools in the field," she said.
-end-
The researchers will next be working to improve their model and to develop a user-friendly and publicly available version to predict antimicrobial resistance. The work was funded in part by the Carl M. Hansen Foundation.

Washington State University

Related Antimicrobial Articles from Brightsurf:

Antimicrobial peptides with anticancer properties
Announcing a new article publication for BIO Integration journal. In this article the authors Zhong, Cuiyu; Zhang, Lei; Huang, Jiandong; Huang, Songyin; Yao, Yandan from Sun Yat-sen University, Guangzhou, China; Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, China and Shenzhen Institutes of Advanced Technology, Guangdong, China review antimicrobial peptides with anticancer properties.

Treating COVID-19 could lead to increased antimicrobial resistance
Research led by the University of Plymouth suggests the increased use of antibiotics in the treatment of COVID-19 patients could be placing an additional burden on waste water treatment works, particularly those serving large or emergency hospitals

To prevent antimicrobial resistance, vaccinate the world's kids
Childhood vaccination may be a powerful tool in the fight against antimicrobial resistance in low- and middle-income countries, finds a new analysis led by researchers University of California, Berkeley.

Aquaculture at the crossroads of global warming and antimicrobial resistance
Antimicrobial resistance is responsible for some 700 000 deaths each year worldwide.

Who will lead the global surveillance of antimicrobial resistance via sewage?
In the journal Science, a DTU professor calls for someone to carry on a global surveillance of antimicrobial resistance and infectious diseases via sewage.

Sequencing sewage for antimicrobial resistance surveillance
In this Policy Forum, Frank Aarestrup and Mark Woolhouse advocate for the immediate establishment of a global antimicrobial resistance surveillance system based on the metagenomic sequencing of human sewage.

Novel composite antimicrobial film could take a bite out of foodborne illnesses
A novel composite film -- created by the bonding of an antimicrobial layer to conventional, clear polyethylene plastic typically used to vacuum-package foods such as meat and fish -- could help to decrease foodborne illness outbreaks, according to researchers in Penn State's College of Agricultural Sciences.

Squid pigments have antimicrobial properties
Ommochromes, the pigments that color the skin of squids and other invertebrates, could be used in the food and health sectors for their antioxidant and antimicrobial properties.

Antimicrobial resistance poses significant risk to people, the economy
CCA expert panel study provides new data on potential impact of antimicrobial resistance in Canada.

Antimicrobial resistance is drastically rising
An international team of researchers led by ETH has shown that antimicrobial-resistant infections are rapidly increasing in animals in low and middle income countries.

Read More: Antimicrobial News and Antimicrobial Current Events
Brightsurf.com is a participant in the Amazon Services LLC Associates Program, an affiliate advertising program designed to provide a means for sites to earn advertising fees by advertising and linking to Amazon.com.