Antibiotic resistance is difficult enough to control when laboratories can see it. A newly described hospital outbreak in south-eastern Austria shows a more troubling possibility: a resistant bacterial clone can spread while several standard laboratory methods repeatedly make it look susceptible to an important antibiotic.
Researchers investigating a prolonged outbreak of vancomycin-resistant Enterococcus faecium, or VREfm, identified a previously undescribed ST117/CT7799 lineage with an unusually difficult-to-detect resistance phenotype. The study, published in MicrobiologyOpen, found that disk diffusion and gradient testing misclassified every outbreak isolate tested under routine conditions, while standard 24-hour broth microdilution detected resistance in only about half. An automated VITEK 2 system, by contrast, correctly classified all 31 isolates.
The finding matters because E. faecium is an important cause of healthcare-associated infection and vancomycin resistance can sharply narrow treatment options. If resistant strains are classified as susceptible, infection-control teams may underestimate transmission and clinicians may receive misleading susceptibility information.
An outbreak that became difficult to ignore
The investigation began after laboratories serving the University Hospital of Graz and more than 1,600 medical practices in south-eastern Austria observed an unusual increase in vancomycin-resistant E. faecium. The laboratory had seen no invasive VREfm infections for years. By 2024, however, VREfm accounted for 6% of E. faecium-positive blood cultures, rising to 20% in the first half of 2025.
The researchers examined the first 31 non-duplicate isolates with the distinctive phenotype, recovered between February 2024 and June 2025 from routine diagnostic specimens rather than screening samples. Fifteen came from urine, six from wound swabs, five from blood cultures and five from samples obtained during invasive procedures.
The epidemiological pattern strongly suggested healthcare transmission. Thirty of the 31 patients, or 97%, had either been in hospital for at least four days when the specimen was collected or had received inpatient care from the same healthcare provider during the previous six months. Many cases were associated with invasive procedures. Environmental sampling did not identify the strain, so the investigation could not establish a specific environmental reservoir.
Genome sequencing showed a tightly related clone
To determine whether the cases represented a common outbreak rather than unrelated resistant infections, the team used whole-genome sequencing. Twenty outbreak isolates were sequenced using short-read and long-read technologies, allowing the researchers to compare their genomes and investigate the genetic basis of vancomycin resistance.
All sequenced isolates belonged to the same E. faecium ST117/CT7799 lineage. Despite samples being collected as much as 16 months apart, the outbreak genomes differed by no more than six alleles across the core-genome multilocus sequence typing analysis. Contemporary local control strains were far more distant, differing by at least 159 alleles, while the closest reference strain differed by 142. The closest relative found through the cross-national MiGenomeSurv platform was still 76 alleles away.
The genomes contained the complete Tn1549 transposon carrying the vanB resistance system. Molecular testing confirmed vanB-type resistance in the early cases. This created an important mismatch: the bacteria carried a recognised vancomycin-resistance mechanism, yet several conventional phenotype-based tests struggled to reveal it within routine laboratory time frames.
Several routine tests missed the resistance
The researchers directly compared susceptibility-testing approaches. After 24 hours, broth microdilution classified no more than 16 of 31 isolates as vancomycin resistant, a sensitivity of about 52% in this collection. Disk diffusion and gradient tests misclassified all of the outbreak isolates under the tested routine conditions. Longer incubation improved detection, indicating that the resistance phenotype became more apparent with additional growth time.
The contrast with automated testing was striking. VITEK 2 correctly classified all 31 isolates as resistant. The team also assessed four commercial screening agars designed to identify vancomycin-resistant enterococci. Only one of the four reliably detected the new clone after 24 hours.
These results do not mean that disk diffusion, gradient testing or broth microdilution are generally unreliable for VRE. Rather, they show that this particular clone expresses resistance in a way that can fall into a diagnostic blind spot. That distinction is important because laboratory performance observed for one unusual lineage should not be generalised to every vancomycin-resistant enterococcus.
Why a hidden resistance phenotype matters
Diagnostic systems are part of infection control. Hospitals use laboratory results not only to guide individual treatment but also to recognise clusters, trigger isolation precautions and monitor the movement of resistant organisms. A strain that repeatedly tests susceptible could therefore remain epidemiologically quieter than its true transmission pattern warrants.
The Austrian experience illustrates that risk. Early cases were sporadic, but new detections became continuous from November 2024. Once the laboratory reorganised its workflow to use automated susceptibility testing for all enterococci and retested earlier material, additional isolates with the same phenotype emerged. Whole-genome sequencing then demonstrated that the cases formed a highly homogeneous outbreak lineage.
The study therefore supports a broader principle in antimicrobial-resistance surveillance: unusual disagreement between molecular resistance markers and phenotypic tests should be investigated rather than dismissed. Where local epidemiology suggests transmission, laboratories may need complementary methods, extended incubation or molecular confirmation to avoid relying on a single apparently reassuring result.
Important limits to the findings
This was an outbreak investigation centred on a specific regional healthcare network, not a population survey of European hospitals. The 31 isolates were selected because they displayed the phenotype under investigation, so the study cannot estimate how common CT7799 is outside the affected setting. Its geographical distribution remains uncertain.
Not every isolate underwent whole-genome sequencing, although sequencing of 20 isolates demonstrated a highly concordant clonal lineage. The environmental investigation also failed to locate a source, meaning the exact transmission pathway could not be reconstructed. Associations with hospital care and invasive procedures are strong epidemiological clues but do not prove the route for every patient.
Most importantly, the diagnostic results describe the tested platforms, incubation conditions and this particular resistance phenotype. Laboratories use different workflows and local validation procedures. The findings should prompt verification and surveillance rather than an assumption that every laboratory using one of these methods will miss VRE.
A warning for antimicrobial-resistance surveillance
The emergence of ST117/CT7799 adds another layer to the antimicrobial-resistance problem. Resistance can spread biologically, but its apparent prevalence also depends on whether diagnostic systems can recognise it. In this outbreak, a genetically coherent vanB-positive clone exposed a substantial gap between genotype and several routine phenotypic methods.
The immediate priority is to determine whether the lineage has spread beyond the region in which it was identified. More broadly, the work shows why surveillance systems need enough flexibility to investigate unexpected testing patterns. A resistant organism that is hard to detect can undermine both clinical decision-making and the infection-control data used to contain it.
Source Information
Study: 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, e70393.
DOI: 10.1002/mbo3.70393
Study type: Retrospective hospital outbreak investigation with antimicrobial susceptibility testing and whole-genome sequencing.
