The Centers for Disease Control and Prevention (CDC) has reported that at least 2 million illnesses and 23,000 deaths are caused each year in the United States by antibiotic-resistant bacteria, and scientists at the U.S. Food and Drug Administration (FDA) are using cutting-edge technology called whole genome sequencing (WGS) to help identify the presence of antibiotic-resistant bacteria as early as possible, as well as to take steps in controlling their further spread.

“For the first time, we can rapidly determine the entire collection of known antibiotic resistance genes in an individual bacterium. This is allowing new insights into the nature and magnitude of the resistance threat,” says Patrick McDermott, Ph.D., director of FDA’s National Antimicrobial Resistance Monitoring System (NARMS). “And, because the database of resistance genes is growing, due to work by scientists around the globe, we can see what others are nding and quickly ascertain if resistance threats emerging in other countries also are present in the United States.”

WGS has been an important tool in the investigation of MCR-1, a gene that causes resistance to colistin, a drug considered of last resort to treat some serious infections. Since Chinese scientists first discovered MCR-1 in November 2015, NARMS teams have looked at the DNA sequence of genes for more than 100,000 individual bacteria in the national database.

“Within a matter of hours, it was now possible to determine that this new resistance gene was not present in any of these thousands of isolates,” says McDermott. “We didn’t have to go back to the laboratory to perform new experiments. We could just look at the DNA data.”

Later studies conducted by NARMS scientists, this time using selective enrichment of animal samples, found two instances of MCR-1 in swine from the U.S. out of 2,000 samples examined.

The resulting difficulty in finding resistant organisms, along with the fact that the drug is not provided to U.S. food animals, suggests that colistin resistance poses a low risk to public health in this country. NARMS intends to continue monitoring for the MCR-1 gene, watching for any changes in the situation.

“Antibiotic resistance is an international challenge,” said McDermott. “The ultimate goal is to preserve the effectiveness of antibiotics for use in both humans and animals.”