CDC Sleuthing Helps Decipher Drug-Resistant Infection Rise

CDC Sleuthing Helps Decipher Drug-Resistant Infection Rise

June 7, 2026

Key Points:

• New research from the Centers for Disease Control and Prevention aims to explain the sudden increase in drug-resistant infections caused by NDM-producing carbapenem-resistant Enterobacterales (NDM-CRE) in the U.S. between 2019-2023.
• Most of the NDM-CRE cases were caused by only a handful of strains from a few species, chiefly Klebsiella pneumoniae (~50%) and Escherichia coli (~31%).
• An additional, new high-risk clone began to emerge more recently in 2022, a K. pneumoniae lineage called ST45.
• The researchers are working with state and local public health labs to utilize whole genome sequencing data to help rapidly identify outbreaks of drug-resistant infections.

Washington, D.C.-Previous research from the Centers for Disease Control and Prevention (CDC) found that a dangerous variety of bacteria that cause drug-resistant infections, called NDM-producing carbapenem-resistant Enterobacterales (NDM-CRE), has become much more common in the United States, increasing by 461% from 2019-2023. Now, in a new study presented at ASM Microbe 2026, researchers set out to better understand what was behind this sudden increase, examining if it was driven by closely related strains or, instead, by many different, unrelated bacteria.

To conduct their study, state and local public health labs decoded the full genetic blueprint of more than 8,000 NDM-CRE bacteria that caused human infections through a process called whole genome sequencing. This work was done through the Antimicrobial Resistance Laboratory Network (AR Lab Network), which includes labs from all 50 states. Scientists from CDC's Division of Healthcare Quality Promotion analyzed this data to determine the genetic similarities between the bacteria causing these infections.

The researchers found that most of the NDM-CRE cases were caused by only a handful of strains from a few species, chiefly Klebsiella pneumoniae (~50%) and Escherichia coli (~31%), both of which are known to cause healthcare-associated infections. Most of these strains have previously been designated as "high-risk clones" because they are more likely to cause outbreaks of drug-resistant infections in hospitals. An additional, new high-risk clone that only began to emerge more recently in 2022 was also identified-a K. pneumoniae lineage called ST45. It appears to be carrying a plasmid (a piece of DNA that can be shared among bacteria) causing drug resistance that was also found in other previously recognized strains.

"Since NDM-CRE is largely spread by these high-risk clones, surveillance efforts and research into new treatments and diagnostics should prioritize these strains," said corresponding study author Richard Stanton, Ph.D., a bioinformatician in the Prevention and Response Branch of the Divisions of Healthcare Quality Promotion, which is part of CDC's National Center for Emerging and Zoonotic Infectious Diseases. "Additional, new high-risk clones can also rapidly emerge, making it important to recognize these emerging threats through genomic surveillance, like the whole genome sequencing done by the AR Lab Network."

Stanton said the researchers are working with state and local public health labs to best utilize whole genome sequencing data to rapidly identify outbreaks of infections caused by drug-resistant bacteria like NDM-CRE, which can help stem its overall spread and minimize threats to patients.

"The spread of these nearly untreatable bacteria is being driven by a small number of highly successful bacterial strains that have acquired NDM. New resistant strains can emerge quickly once they acquire these genes, as well," Stanton said. "This underscores the importance of ongoing genomic surveillance to catch these emerging threats early."

The researchers said the work would not be possible without the efforts of state and local public health partners from all 50 states working together through the AR Lab Network.