Enterococci are gram-positive bacteria that normally colonize the intestinal tracts of humans and animals, where they usually live as harmless commensals. Yet two species in particular, Enterococcus faecalis and Enterococcus faecium, are among the most important causes of opportunistic and healthcare-associated infections. Enterococcus faecium is notorious for its capacity to acquire resistance to penicillins and, increasingly, to glycopeptides such as vancomycin, an antibiotic class introduced in 1955 that kills bacteria by binding to peptidoglycan precursors and blocking cell wall synthesis. Vancomycin-resistant enterococci were first described more than two decades after the drug’s introduction, and among resistant E. faecium isolates the vanB genotype has become the most prevalent in several European countries. VanB-type resistance is known for phenotypic variability, meaning that laboratory phenotype does not always reliably reflect the underlying resistance genes, a property that has now proven consequential in a dramatic way.

The public health stakes are considerable. The World Health Organization’s 2024 Bacterial Priority Pathogens List classifies vancomycin-resistant E. faecium as a high-priority pathogen, and according to the European Centre for Disease Prevention and Control the mean vancomycin resistance rate among European E. faecium isolates stands at roughly 20 percent. Austria had long reported comparatively low figures, with the national action program on antibiotic resistance documenting a resistance rate of just 3 percent among invasive isolates in 2023. That picture changed abruptly. After years without any invasive vancomycin-resistant E. faecium infections, the diagnostic laboratory serving Graz and the wider region observed the resistance rate among E. faecium-positive blood cultures climb to 6 percent in 2024 and then to 20 percent in the first half of 2025. By June 2025, thirty-one resistant isolates had been collected, and virtually all could be attributed to a single previously unreported lineage, ST117/CT7799.

The outbreak’s first signal appeared in February 2024, when automated VITEK2 susceptibility testing flagged vancomycin resistance in a clinical E. faecium isolate even though disk diffusion, gradient testing, and broth microdilution all failed to confirm it under routine conditions. When the laboratory reorganized its workflow to route all enterococcal isolates through automated testing and systematically re-examined results, five further isolates with the same distinctive phenotype emerged within months. All came from specimens obtained for genuine infection diagnostics rather than screening, and every case was confirmed as vanB-type resistance by molecular PCR. Retrospective review of raw instrument data found no evidence of this phenotype in the laboratory’s records before 2024, strongly suggesting a genuinely new arrival. Early cases clustered around invasive procedures performed at a single hospital, and a second transmission chain later surfaced among urology patients who had undergone double-J catheterization in an operating room shared with surgeons. Notably, environmental surface sampling by the hospital infection control team failed to locate the organism, and nearly all affected patients had either been hospitalized for at least four days or had recent inpatient care history with the same provider.

To characterize the outbreak, the team subjected twenty non-duplicate isolates to whole genome sequencing using both Illumina short-read and Oxford Nanopore long-read platforms, achieving highly concordant results between technologies. Core genome multilocus sequence typing based on 1,423 loci revealed a strikingly homogeneous cluster: even isolates sampled sixteen months apart differed by no more than six alleles, far below the cluster threshold of three alleles used for assignment once the clonal relationship was established. The nearest local control strain, isolated at the same site during the same period, differed by 159 alleles, and the closest reference strain from the Robert Koch Institute collection differed by 142 alleles. Searches of the cross-national surveillance platform MiGenomeSurv showed the next closest relative still 76 alleles away, confirming that CT7799 represents an entirely novel lineage. The clone was provisionally named VREfmstyr, after Styria, the Austrian federal state where it was first isolated.

Genomic analysis also illuminated the genetic architecture of resistance. All outbreak isolates carried a complete copy of the transposon Tn1549, the mobile element responsible for vanB-mediated vancomycin resistance, inserted into the chromosome. Long-read assemblies proved essential: short-read assemblies fragmented the transposon across three contigs, obscuring its structure, whereas long reads revealed three matching blocks separated by two intervening regions of 1,494 and 1,417 base pairs containing insertion sequence elements, including an ISL3-like transposase of the ISEfa11 family and an IS3-like ISEnfa3-family transposase alongside a helix-turn-helix domain protein. An additional IS91 transposase was found inserted in a YodL domain protein upstream of the vanB gene cluster. All seven vancomycin resistance genes, vanB, vanY-B, vanW-B, vanH-B, vanX-B, vanR-B, and vanS-B, were identical across every outbreak isolate, underscoring the clone’s remarkable genetic stability despite months of circulation. Based on the classification scheme of the Norwegian VRE study group, the vanB cassette appears to be a hybrid between variants typically associated with different sequence types, hinting at a recombination event in the strain’s recent history.

The true significance of the study, however, lies in its systematic evaluation of diagnostic methods, and the results are sobering. Broth microdilution, the reference standard for antimicrobial susceptibility testing, correctly identified only 16 of 31 isolates, or 52 percent, as vancomycin resistant when read after the standard 24 hours of incubation, even though all control strains behaved as expected. Extending incubation to 48 hours eventually pushed minimum inhibitory concentrations above the susceptibility breakpoint for all isolates, but the growth around concentrations of 2 milligrams per liter and above was so sparse that even trained personnel could easily overlook it. Gradient testing from two different manufacturers failed to detect resistance in every single case at 24 hours, and disk diffusion was equally deceptive: all isolates produced inhibition zone diameters clearly wider than the 12-millimeter resistance threshold, and the zone edges lacked the fuzzy appearance that typically signals vancomycin resistance. Only VITEK2 automated testing, which correctly flagged all 31 isolates under routine settings, proved reliable, a finding that diverges from earlier studies reporting only 81 percent sensitivity for low-MIC resistant strains and possibly reflecting improvements in newer test cards and software.

Screening carried a similar message of failure. When seven representative isolates were plated on kanamycin-vancomycin agar and four commercially available chromogenic VRE screening media, three of the four commercial agars yielded no growth at all after 24 hours, and the sole medium showing some activity was only weakly positive for four isolates and negative for the remaining three. Prolonging incubation to 48 and even 72 hours improved results only marginally and inconsistently across manufacturers, while the outbreak strain failed entirely to grow on kanamycin-vancomycin agar. These findings matter because VRE often constitutes only a small fraction of the intestinal enterococcal population, making selective screening media indispensable for controlling transmission, and because prior research has already shown that sensitivity drops sharply for strains with vancomycin minimum inhibitory concentrations below 16 milligrams per liter. Only CHROMagar VRE proved dependable after standard incubation, and even that required confirming results under the study’s specific conditions.

Intriguingly, when a representative isolate was exposed to vancomycin on a gradient strip for more than 100 hours, single colonies eventually grew within the inhibition zone, and after two passages the derivative consistently displayed a minimum inhibitory concentration of at least 32 milligrams per liter. Sequencing revealed that this resistant derivative carried a single nucleotide substitution in the vanS-B gene, the sensor kinase that regulates the vancomycin resistance operon, causing an amino acid change from serine to arginine at position 243. This observation suggests that the outbreak clone’s occult phenotype stems from a regulatory mutation or arrangement that dampens resistance expression, and that vancomycin pressure can select for compensatory variants restoring full resistance. The authors caution, however, that whether the insertion elements or the specific allele differences in vanR-B, vanY-B, and vanW-B are causally responsible for the difficult-to-detect phenotype remains an open question demanding further investigation.

The implications reach well beyond Styria. Because many diagnostic laboratories worldwide rely on 24-hour disk diffusion zone readings to determine vancomycin susceptibility, a strain with this phenotype could spread through hospitals without triggering any alarm, quietly colonizing patients and contaminating environments while appearing fully susceptible on paper. The research team recommends that laboratories verify the adequacy of their screening media and incubation times, and adapt their susceptibility testing protocols by prolonging incubation, adding molecular vanB PCR testing, or employing automated VITEK2 analysis. Given the clone’s demonstrated epidemic potential, its absence from all prior surveillance databases, and the growing proportion of invasive infections it now accounts for in the region, surveillance studies will be essential to determine whether ST117/CT7799 remains a local phenomenon or whether laboratories across Europe and beyond must urgently reassess whether their diagnostic procedures can catch a superbug designed, by evolutionary accident, to stay invisible.

Subject of Research: Emergence and diagnostic challenges of a novel vancomycin-resistant Enterococcus faecium clone (ST117/CT7799) in Austria

Article Title: Emergence of a Novel, Phenotypically Difficult‐to‐Detect Vancomycin‐Resistant Enterococcus faecium Clone (ST117/CT7799)

Article References: Forstner, P., Uitz, C., Dabernig‐Heinz, J., Wagner, G. E., Bender, J., Fischer, M., Siebenhofer, D., Werner, G., Busche, T., Klages, L. J., Rückert‐Reed, C., Steinmetz, I., & Dichtl, K. (2026). Emergence of a Novel, Phenotypically Difficult‐to‐Detect Vancomycin‐Resistant Enterococcus faecium Clone (ST117/CT7799). MicrobiologyOpen, 15(5), Article e70393. https://doi.org/10.1002/mbo3.70393

Image Credits: AI Generated

DOI: 10.1002/mbo3.70393

Keywords: vancomycin-resistant Enterococcus faecium, VRE, ST117/CT7799, hospital outbreak, antimicrobial resistance, vanB operon, Tn1549 transposon, whole genome sequencing, diagnostics, Austria, infection control, cgMLST

Enterococcus faecium is not an exotic microbe. It lives quietly in the human gut, but in hospitals it has become a leading cause of bloodstream infections, wound infections and endocarditis, particularly in patients weakened by surgery, broad-spectrum antibiotics or invasive devices. What makes E. faecium a global public health threat is its extraordinary capacity to acquire resistance. The emergence of vancomycin-resistant E. faecium, known as VREfm, has drastically narrowed treatment options, because vancomycin has long been one of the few reliable drugs against enterococcal infections. The World Health Organization has flagged vancomycin-resistant enterococci as high-priority targets for new antibiotic development, and genomic surveillance has become the sharpest available tool for tracking how these bacteria spread and evolve inside hospitals.

In the new study, the two clinical isolates, designated EF_35 and EF_38, were recovered from surgical site infections in two different hospitalised patients treated in obstetrics and gynaecology departments. Both patients had developed post-operative wound infections, a well-known complication of caesarean sections and other surgical procedures. The research team performed antibiotic susceptibility testing, whole-genome sequencing and a battery of bioinformatic analyses designed to answer three key questions: what resistance genes did the bacteria carry, on what mobile elements were those genes located, and how closely related were the two isolates to each other and to E. faecium genomes reported elsewhere in the world.

The answer to the relatedness question was striking. Multilocus sequence typing placed both isolates in sequence type 80, or ST80, a lineage belonging to clonal complex CC17, the group of hospital-adapted E. faecium strains that has spread through healthcare systems worldwide since it first emerged as a nosocomial clone. Even more telling, whole-genome single nucleotide polymorphism analysis revealed that the two isolates differed by only eight genomic SNPs. In practical terms, bacteria from different patients that differ by only a handful of SNPs are considered closely related, strongly suggesting a common source or direct transmission within the hospital environment. An interval of twenty days between the two isolations fits the classic pattern of a nascent hospital outbreak, in which a single strain moves between patients, surfaces or healthcare workers before being detected.

Genetically, the isolates were textbook multidrug-resistant VREfm. Phenotypic testing confirmed resistance to vancomycin, and the genomes harboured genes conferring resistance to aminoglycosides and macrolides as well. This stacking of resistance determinants is what makes CC17 lineages so successful in hospitals: a patient colonised by such a strain who then develops an infection has very few oral or intravenous options, and clinicians are pushed toward last-line agents such as linezolid or daptomycin, drugs that are expensive, toxic and themselves threatened by emerging resistance.

The centrepiece of the genomic analysis was the vanA operon, the genetic machinery that renders enterococci resistant to vancomycin and teicoplanin. Vancomycin normally works by binding the D-Ala-D-Ala termini of peptidoglycan precursors, blocking cell-wall synthesis. The vanA system rewires that target: it enzymatically remodels cell-wall precursors to end in D-Ala-D-Lac instead, an terminus to which vancomycin binds with drastically reduced affinity, while simultaneously degrading the normal precursors. In both Algerian isolates, the researchers found the vanA operon embedded within a Tn1546 transposon-like element, the mobile genetic unit first characterised in the 1990s in the French reference strain E. faecium BM4147 and since then responsible for disseminating glycopeptide resistance around the globe.

Crucially, that Tn1546 element was not sitting on the chromosome. It was located on a rep17-type plasmid, a replicon family related to the well-known pRUM plasmids that circulate among hospital E. faecium strains. Plasmids are circular, self-replicating DNA molecules that can transfer horizontally between bacteria, sometimes across species boundaries, and they are widely regarded as the primary vehicles by which resistance genes move through hospital microbial communities. Recent work has shown that plasmids were central to the recent emergence of E. faecium as a major nosocomial pathogen, so pinpointing which plasmid carries a resistance cassette in a given region provides both an evolutionary and an epidemiological clue.

One detail of the plasmid’s cargo raised the stakes considerably. Alongside the vanA-Tn1546 cassette, the rep17 plasmid also carried a specific resistance locus, designated locus 3, composed of the genes ant(6), sat(4) and aph(3′). This exact gene combination has drawn attention because it has been found in vancomycin-resistant Staphylococcus aureus, the feared VRSA isolates in which the vanA operon has jumped from enterococci into staphylococcal genomes, including cases in which the entire vanA locus integrated into the S. aureus chromosome. The presence of the same Tn1546-associated aminoglycoside locus on an E. faecium plasmid in Algeria raises, as the authors note, the possibility that such a plasmid could transfer the vanA operon into a staphylococcal genome. Although VRSA remains rare worldwide, each documented case has followed precisely this route of plasmid-mediated gene transfer from enterococci to staphylococci, so plasmids of this architecture are watched as potential launching pads for that dangerous jump.

For Algeria specifically, the study fills in an important piece of a growing picture. Earlier reports documented the first vancomycin-resistant enterococcal cases in the country in 2008, the emergence of glycopeptide-resistant E. faecium in subsequent years, molecular characterisation of related vanA E. faecium healthcare-associated infections, and a 2021 survey showing high frequency and diversity of VRE in Algerian healthcare settings, followed by the detection of vanA-positive E. faecium CC17 even in hospital wastewater. The new genomic data demonstrate that the epidemic VREfm ST80 clone is not merely present but actively evolving within Algerian hospitals, carrying the same mobile resistance elements described on other continents. Genomic surveillance of this kind, the authors argue, is essential for detecting clonal transmission early enough to interrupt it with infection-control measures, from hand hygiene and environmental disinfection to active screening and isolation of colonised patients.

The technical approach also illustrates how modern clinical microbiology increasingly relies on whole-genome sequencing as a routine investigative tool. By combining sequencing with tools for plasmid detection and typing, transposon annotation, resistome identification and SNP-based phylogenetic comparison, the team could reconstruct, from two wound isolates, a narrative of clonal spread, plasmid-borne resistance and cross-genus transmission risk that older methods such as pulsed-field gel electrophoresis could only hint at. The genomes of both isolates have been deposited in GenBank under accession numbers JBAIVL000000000 and JBAIVM000000000, making them available for future comparative studies across the Mediterranean region and beyond.

The broader message is sobering but not hopeless. VREfm ST80 is now documented on multiple continents, and the genetic elements that give it its armour are inherently mobile. Yet the same mobility that makes the threat means surveillance works: identifying a rep17 plasmid carrying Tn1546-vanA in a specific hospital department tells infection-control teams exactly what to look for and where to intervene. For obstetric and gynaecology patients, who undergo some of the most common surgeries in medicine, keeping this clone from gaining a foothold is a matter of routine vigilance, genomic alertness and the unglamorous but decisive practice of infection prevention.

As the antibiotic crisis looms larger, the genetic adaptation of VREfm underscores the urgent need for novel therapeutic strategies. The team, under the guidance of senior author Daria Van Tyne, Ph.D., utilized their Enhanced Detection System for Healthcare-Associated Transmission (EDS-HAT) to trace the lineage and prevalence of VREfm strains over six years. Their findings indicate a shift in strain variation; the number of VREfm strains has dramatically decreased from approximately eight distinct strains in 2017 to just two predominant strains by the end of 2022.

The evolution of these strains is marked by their newfound ability to produce bacteriocins—naturally occurring antimicrobial peptides that target and kill closely related bacterial species. This adaptation not only enhances their survival but also facilitates the eradication of competing strains, thus providing them with optimal nutritional resources for reproduction. Researchers are alarmed by this development, as it indicates a potentially dangerous trend where drug-resistant strains could outpace treatment efforts.

The ramifications of these findings extend beyond local hospital settings. By analyzing a vast repository of over 15,000 VREfm genomic sequences collected from various locations worldwide, the research team confirmed that the observed adaptations were not unique to their institution. The convergence of these adaptations globally poses a significant risk to existing healthcare protocols. Emma Mills, the lead author of the study and a dedicated graduate student, expressed her astonishment at the scale of the genomic shift, likening the bacterial survival strategy to a ruthless competition for resources among pathogens.

The resistance and adaptation of VREfm are particularly troublesome for immunocompromised individuals who are often treated with antibiotics that exacerbate their condition by reducing the diversity of their microbiota. The elimination of effective strains of VREfm not only endangers patients already battling infections but also raises alarms for future therapeutic interventions. The traditional global healthcare framework must grapple with the implications of this bacterium’s evolution and its fortified resistance.

This study has profound implications for antibiotic development as well. Daria Van Tyne posits that narrowing diversity among VREfm strains might simplify therapeutic strategies by focusing on fewer, but more potent, targets. Such a paradigm shift in antibiotic development could pave the way for strategically weaponizing bacteriocins against formidable bacterial foes. The potential to harness bacteriocins as targeted therapies presents an inviting avenue for combating drug resistance; this could lead to innovative treatments in the fight against bacterial infections.

Moreover, the findings highlight the importance of real-time data analysis in tracking pathogen evolution and outbreaks. The authors emphasize the critical role of genomic sequencing and computational algorithms in early pathogen detection, which could significantly enhance clinical responses to infection outbreaks. This study exemplifies how merging cutting-edge technology with microbiological research can yield new insights that are paramount for public health.

Despite the grim nature of these revelations, the study does not suggest that the newly adapted strains are more virulent or lethal to patients than previous strains. The researchers acknowledge that understanding the evolutionary pressures within healthcare settings catalyzed these changes is a crucial aspect of future investigations. It is vital for healthcare systems to remain vigilant and adaptive in their approaches to infection control and treatment in light of these developments.

As scholars continue to unravel the complexities of VREfm evolution, the research community is urged to cultivate interdisciplinary collaborations that encompass microbiology, genomics, and clinical medicine. Drawing on diverse expertise will foster innovative solutions that address the persistent challenges posed by antimicrobial resistance. The socio-economic implications of these findings further warrant attention, as they suggest that healthcare costs related to drug-resistant infections may escalate if timely interventions are not implemented.

This groundbreaking research serves as a clarion call for health authorities and medical institutions to reassess their strategies for combating bacterial infections. Incorporating real-time genomic data in clinical decision-making will be essential to curbing the spread of resistant organisms. As the challenge of drug-resistant bacteria intensifies, collective efforts must be mobilized to ensure that advancements in science translate into tangible health benefits for communities worldwide.

In conclusion, the emerging dominance of specific VREfm strains, combined with their remarkable adaptability, necessitates an urgent reconsideration of antimicrobial stewardship, healthcare policies, and treatment methodologies. The scientific community must remain committed to collaborative research, continuous surveillance, and innovative solutions in the face of evolving pathogens. Only through proactive engagement and targeted interventions can the looming threat of antimicrobial resistance be mitigated effectively.

Subject of Research: Evolution of vancomycin-resistant Enterococcus faecium
Article Title: Bacteriocin production facilitates nosocomial emergence of vancomycin-resistant Enterococcus faecium
News Publication Date: March 21, 2025
Web References: Nature Microbiology
References: Available upon request.
Image Credits: Emma Mills
Keywords: vancomycin-resistant Enterococcus faecium, antibiotic resistance, bacteriocins, genomic evolution, antimicrobial therapy, public health, drug development, healthcare-associated infections, microbiology, infectious diseases.