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Drug-resistant bacteria are evolving into weapons of an antimicrobial genetic tool
A drug-resistant strain of bacteria that has adapted to health settings in recent years to weaponize an antimicrobial genetic tool, eliminating its cousins and replacing them as the dominant strain. Scientists at the University of Pittsburgh School of Medicine made the discovery while combing local hospital data — and then confirmed it was a global phenomenon. The finding, published today in Nature Microbiology, may be the impetus for new approaches in developing therapeutics against some of the world's deadliest bacteria. It also validates a new use for a developed at Pitt and UPMC...
Drug-resistant bacteria are evolving into weapons of an antimicrobial genetic tool
A drug-resistant strain of bacteria that has adapted to health settings in recent years to weaponize an antimicrobial genetic tool, eliminating its cousins and replacing them as the dominant strain. Scientists at the University of Pittsburgh School of Medicine made the discovery while combing local hospital data — and then confirmed it was a global phenomenon.
The finding, published today inNatural microbiologyMay be the impetus for new approaches to developing therapeutics against some of the world's deadliest bacteria. It also validates a new use for a system developed at Pitt and UPMC that combines genomic sequencing with computer algorithms to quickly detect infectious disease outbreaks.
Our lab has a front row seat to the parade of pathogens moving through the hospital environment. And when we took a step back and zoomed out, it quickly became apparent that big changes were afoot with one of the world's more difficult bacteria. “
Daria van Tyne, Ph.D.,,Senior Author,Associate Professor of Medicine in Pitt's Division of Infectious Diseases
The Advanced Healthcare Detection System (EDS-HAS) analyzes the genetic signatures of infections in hospitalized patients and FLAGS patterns, allowing clinicians to intervene and stop potential outbreaks in real time. But lead author Emma Mills, a microbiology and immunology graduate student in Van Tyne's lab, realized that Eds-Hat was also a treasure trove of detailed historical information that could inform her about the evolution of bacteria over time.
Mills focused on vancomycin-resistantEnterococcus faecium(VREFM), so called because it cannot be eradicated with the popular antibiotic vancomycin. Vrefm kills about 40% of the people it infects and is a particular plague for immunocompromised and hospitalized patients.
After analyzing the genome sequences of 710 VREFM infection samples from hospital patients, Mills found that the diversity of VREFM strains ranged from about eight fairly evenly distributed types to two dominant strains, in 2018, from the end of 2022, in four years, in four years, in four years, in four years.
Upon closer inspection, Mills found that the dominant strains had acquired the ability to produce a bacteriocin, which is an antimicrobial that bacteria use to kill or inhibit each other. They had this new ability to destroy the other VREFM strains with weapons and provided them with unrestricted access to nutrients for easier reproduction.
This further piqued Mills' curiosity: if this was happening at the local hospital, was it happening elsewhere? No previous research publications had examined the possibility that this was a global phenomenon. Therefore, she consulted a publicly available library of more than 15,000 VREFM genomes collected worldwide from 2002 to 2022. Sure enough, what she observed locally was also happening worldwide.
“This was a completely unexpected discovery – I was surprised to see such a dramatic signal,” Mills said. “Once these strains are in an institutional setting like a hospital and matched against other VRE strains in a patient's gut, they take over.
Van Tyne said the finding has no immediate clinical implications - it does not appear that the bacteriocin-wielding VREFMs make patients sicker than their predecessors. However, it could point to possible avenues for developing new therapies.
"The diversity of the VRE population appears to be narrowing from many different types that cause few infections. This means that we may soon have only a single target for which therapeutics such as antibiotics or phage therapy can be designed," said Van Tyne. “It also suggests that bacteriokines are very powerful and we may be able to weaponize them for our own purposes.”
Additional authors of the study include Katharine Hewlett, Alexander B. Smith, Ph.D., and Joseph P. Zackular, Ph.D., of Children's Hospital of Philadelphia; and Marissa P. Griffith, Lora Pless, Ph.D., Alexander J. Sundermann, Dr.Ph, and Lee H. Harrison, MD, of Pitt.
This research was funded by National Institutes of Health Grants R01AI165519, R01AI127472, and R35GM138369.
Sources:
Mills, E.G.,et al. (2025). Bacteriocin production facilitates nosocomial emergence of vancomycin-resistant Enterococcus faecium. Nature Microbiology. doi.org/10.1038/s41564-025-01958-0.