Antimicrobial Agents & Resistance

Bioinformatics Program Can Predict Antibiotic Resistance

A new bioinformatics program that uses an algorithm called MetaCherchant can track the spread of antibiotic resistance genes in gut microbiota DNA or in genome samples from soil, water, or sewage.

“We can evaluate the spread of resistance within a single bacterial community, such as the gut [microbiome], as well as between different communities,” said lead author Evgenii Olekhnovich of ITMO University in St. Petersburg, Russia.  “This allows us, for example, to identify global pathways of antibiotic resistance spread through the environment.”

Since gut microbiota can share resistance genes with pathogens, determining how this process occurs is important.  The team thinks their new tool will contribute to the development of more effective antimicrobial therapies and curb the spread of superbugs.

“We created a tool that enables scientists to have a closer look at the difference between gene surroundings in two or more samples of microbiota,” said co-author Vladimir Ulyantsev.  “We can analyze [microbiome] samples collected from different people or from the same person at different times, for example before and after antibiotic treatment, and suggest how a particular resistance gene could spread from one microbial species to another.”

“Using MetaCherchant, we can analyze how [the microbiome] contributes to the spread of resistance to a particular antibiotic class…and find drugs with low resistance risk…[that will] help us adjust and tune specific therapies,” added Olekhnovich.

For more information, go to the October 28 issue of Bioinformatics.