A study led by the Bact_Drugs Lab at UCIBIO-Porto, published in Genome Medicine, reveals how Enterococcus faecium uses "linear plasmids" and antimicrobial peptides to outcompete rivals and evade infection control.
Researchers from the Bact_Drugs Lab at UCIBIO-Porto have published a long-term genomic surveillance study focusing on one of the World Health Organization’s (WHO) high-priority pathogens: vancomycin-resistant Enterococcus faecium (VREfm). The study, recently featured in the journal Genome Medicine, provides a rare, decade-long look at how this bacterium evolves within a major hospital setting.
The research article, titled “Twelve years of genomic surveillance of vancomycin-resistant Enterococcus faecium: emergence of linear vanA and bacteriocin-carrying plasmids challenging infection control,” was developed during the PhD thesis of Ana C. Almeida-Santos, under the supervision of Ana R. Freitas, Carla Novais, and Luísa Peixe. Ana C. Almeida-Santos completed her European Doctorate at the Faculty of Pharmacy of University of Porto in Pharmaceutical Sciences, with a specialty in Microbiology.
A 12-Year Evolutionary Journey
In collaboration with international experts from Denmark and Spain, the UCIBIO team analyzed the trajectory of VREfm in a Porto-based hospital between 2010 and 2021. By combining traditional microbiology with cutting-edge whole-genome sequencing and in-depth plasmid analysis, the researchers identified major clonal shifts. Essentially, older strains being replaced by newer, more competitive versions.
One of the study’s most striking findings is the expanding repertoire of bacteriocins, peptides produced by the bacteria that act as natural antibiotics to kill off rival strains. The authors demonstrate that certain VREfm clones carry specific bacteriocin "toolkits" that may help them dominate the hospital environment, explaining why previously common lineages have started to disappear.
The hidden threat: linear plasmids
The study also highlights a technological breakthrough in hospital surveillance. By using long-read sequencing to create "hybrid assemblies,” the team detected linear vanA plasmids. These mobile DNA elements, which carry the genes for vancomycin resistance, are notoriously difficult to detect using standard short-read sequencing or traditional laboratory methods.
“Bacterial pathogens are continually evolving and adapting,” explains Ana R. Freitas, co-leader of the study. “Hospital antimicrobial resistance surveillance needs to go beyond simple case counts. We must track within-species diversity and mobile genetic elements to truly understand and prevent the spread of multidrug-resistant pathogens.”
Why this matters
E. faecium is a common inhabitant of the human gut that has evolved into a leading cause of healthcare-associated infections globally. When it develops resistance to vancomycin, a "last-resort" antibiotic, treatment becomes significantly more difficult. Because these bacteria can persist in the hospital environment and colonize patients silently, understanding their genetic "cloaking" mechanisms and competitive advantages is vital for modern infection control.
As Luísa Peixe, co-leader of the study and head of the Bact_Drugs Lab, notes, this research underscores the importance of integrating advanced genomic tools into routine hospital surveillance to stay one step ahead of bacterial evolution.
Original article:
Almeida-Santos, A.C., Tedim, A.P., Duarte, B. et al. Twelve years of genomic surveillance of vancomycin-resistant Enterococcus faecium: emergence of linear vanA and bacteriocin-carrying plasmids challenging infection control. Genome Med 18, 56 (2026). https://doi.org/10.1186/s13073-026-01656-4