Multihospital expansion of vancomycin-resistant Enterococcus faecium ST117-CT7799 and transmission of linear plasmids co-carrying vanA and linezolid resistance genes, Comunitat Valenciana, Spain (2022-2024)

Valiente-Mullor, C.; Ruiz-Roldan, L.; Almeida-Santos, A. C.; Antoni, R.; Sanz-Carbonell, A.; Arnal, S.; Sabater, S.; Torres, I.; Gonzalez-Barbera, E.; Vidal-Catala, I.; Tormo, N.; Medina-Gonzalez, R.; Novais, C.; Peixe, L.; Freitas, A. R.; Gonzalez-Candelas, F.

doi:10.64898/2026.06.01.729239

bioRxiv · 10.64898/2026.06.01.729239

Multihospital expansion of vancomycin-resistant Enterococcus faecium ST117-CT7799 and transmission of linear plasmids co-carrying vanA and linezolid resistance genes, Comunitat Valenciana, Spain (2022-2024)

Valiente-Mullor, C.·Ruiz-Roldan, L.·Almeida-Santos, A. C.·Antoni, R.·Sanz-Carbonell, A.·Arnal, S.·Sabater, S.·Torres, I.·Gonzalez-Barbera, E.·Vidal-Catala, I.·Tormo, N.·Medina-Gonzalez, R.·Novais, C.·Peixe, L.·Freitas, A. R.·Gonzalez-Candelas, F.

View original source ↗Export metadata ↓

Abstract

BackgroundVancomycin-resistant Enterococcus faecium (VREfm) is a WHO priority pathogen. In the Comunitat Valenciana (CV), Spain, VREfm prevalence has increased since 2022. We characterized the population structure, transmission patterns and resistance determinants of VREfm across eight hospitals (2021-2024). MethodsEight hospitals reported 870 VREfm cases during 2021-2024. We sequenced 254 VREfm isolates using WGS (Illumina) and inferred relatedness by MLST, cgMLST, and core-genome SNP analyses. Acquired antimicrobial resistance (AMR) genes, bacteriocins, plasmid replicases and putative virulence markers (PVMs) were identified in silico. Thirty-eight representatives underwent Nanopore long-read sequencing and hybrid assembly to resolve plasmids. ResultsThe predominant vancomycin-resistance genotype was vanB (62%; six hospitals), followed by vanA (19%; five hospitals) and vanA+vanB (17%; five hospitals). Eight sequence types (ST) and 15 clonal complexes (CT) were identified, grouped into seven main phylogenetic clades with close relatedness to publicly available genomes from other regions of Spain and Europe. A single lineage, ST117-CT7799, accounted for 198/254 (78%) isolates, persisted during 2022-2024 across seven hospitals and was enriched in the bacteriocin gene bac43 (or T8) (84%). Linezolid-resistance genes optrA and cfr(D) were present in 34% of isolates, most of which also carried vanA (32%). Hybrid assemblies revealed a diverse plasmidome including RepA_N megaplasmids with PVMs and AMR genes, and small Rep3-like plasmids harbouring bacteriocins (bac43, bac51, bacAS9); a 6 kb repA_pB82 plasmid was bac43-positive in 37/38 (97%) fully resolved carriers. Eight strains across four hospitals carried identical linear plasmids co-harbouring vanA, optrA, cfrD genes within a widespread repUS78_pZY2 background, consistent with inter-lineage plasmid transmission. ConclusionsThis first comprehensive genomic analysis of VREfm in CV indicates extensive inter-hospital spread dominated by expansion of ST117-CT7799 and highlights plasmid-mediated convergence of vancomycin and linezolid resistance via linear plasmids. Strengthened infection prevention and genomic surveillance, including long-read sequencing to track linear plasmids, are warranted.

Explore related subjects

microbiology Preprint

Keep this discovery

Explore connections, maps & timelines

BibTeX RIS

Valiente-Mullor, C., Ruiz-Roldan, L., Almeida-Santos, A. C., Antoni, R., Sanz-Carbonell, A., Arnal, S., Sabater, S., Torres, I., Gonzalez-Barbera, E., Vidal-Catala, I., Tormo, N., Medina-Gonzalez, R., Novais, C., Peixe, L., Freitas, A. R., Gonzalez-Candelas, F.. 2026-06-02. Multihospital expansion of vancomycin-resistant Enterococcus faecium ST117-CT7799 and transmission of linear plasmids co-carrying vanA and linezolid resistance genes, Comunitat Valenciana, Spain (2022-2024). https://doi.org/10.64898/2026.06.01.729239

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related preprints

bioRxiv2026

Reverse Transcription Loop-Mediated Isothermal Amplification Combined with Lateral Flow Assay (RT-LAMP-LFA) for Rapid Detection of the 2026 Bundibugyo Virus (BDBV) Outbreak Strain

Making accurate diagnosis is a critical first step in patient management and control for emerging and re-emerging disease outbreaks. Bundibugyo virus (BDBV) is a filovirus that causes Ebola disease, and the 2026 outbreak highlights the need for rapid diagnostic approaches that can be deployed in settings with limited laboratory infrastructure. Here, we developed a reverse transcription loop-mediated isothermal amplification-lateral flow assay (RT-LAMP-LFA) for rapid detection of the 2026 BDBV outbreak strain. LAMP primers were designed based on the genome sequence of the 2026 outbreak strain, and the conservation of the primer binding sites among all available 2026 outbreak genomes was confirmed in silico. LAMP primers were evaluated for analytical specificity and sensitivity using in vitro-transcribed RNA (ivtRNA) from BDBV and other filoviruses, as well as RNA derived from arboviruses and mammalian cells. Amplification products were detected using a Chromatography-Printed Array Strip (C-PAS) lateral flow platform. The newly designed primers specifically detected the presence of BDBV RNA without nonspecific amplification of the other viral or cellular RNA samples tested. Consistent amplification was observed down to 103 copies per reaction. In addition, BDBV viral RNA was successfully amplified, and the amplification products were detected using C-PAS, with the total workflow being completed within 25 min. These findings demonstrate the analytical specificity and sensitivity of the developed RT-LAMP-LFA assay and its compatibility with rapid visual lateral flow detection, supporting its potential application as a point-of-care approach for BDBV detection.

microbiology↗

bioRxiv2026

Divergent methane production and microbial community responses to carbon enrichment in freshwater wetland sediments

Methane (CH4) accumulation in wetland sediments reflects interactions among organic matter, sediment chemistry, and microbial communities. We combined depth-resolved field characterization across four wetland habitats in northern Israel with complementary incubations to examine methane accumulation and responses to labile-carbon enrichment. Sediment cores were characterized using Rock-Eval analysis, porewater chemistry, oxygen profiling at three sites, and mcrA amplicon sequencing. High CH4 concentrations occurred under contrasting conditions: Ein Nimfit (EN) contained approximately 12% total organic carbon and reached 2.1 mM CH4, whereas Ein Afek site EA2 contained approximately 5% carbon and accumulated 0.7-1.7 mM CH4. Both showed sulfate depletion, but EN exhibited pronounced sulfide accumulation, whereas EA2 showed greater dissolved iron and nutrient enrichment. Their classified methanogenic assemblages also differed. EA1 remained methane poor despite increasing carbon content with depth, while EA3 combined low carbon content and CH4 accumulation with detectable methanogens and lower methanogenic diversity. In a 36-day bottle experiments using sediments from two of the four wetland habitats, sucrose-amended EA3 exhibited a transient maximum of 18.8 mmol collected CH4 kg-1 wet sediment during Days 22-29, whereas EN reached its highest collected amount during Days 29-36. Methane proportions increased before the large output increase in EA3 but remained comparatively stable and high in EN. Soluble chemical oxygen demand trajectories and microbial community changes also differed. These findings identify distinct biogeochemical settings supporting methane accumulation and demonstrate methanogenic potential in low-CH4 sediment, emphasizing the complementary information provided by field profiles, microbial characterization, and exploratory enrichment experiments.

microbiology↗

bioRxiv2026

The absence of microbiome in germ-free mice exacerbates the pathogenicity of mouse-adapted SARS-CoV-2 MA10

Germ-free mice, which are devoid of microbiota, provide a powerful system to define the contribution of the microbiome to host responses during infection. Severe COVID-19 outcomes are associated with multiple comorbidities that are themselves characterized by microbiome dysbiosis; however, the causal role of the microbiota in SARS-CoV-2 pathogenesis remains poorly understood. Here, we use germ-free mouse models to evaluate the impact of the microbiome on disease severity following infection with mouse-adapted SARS-CoV-2 MA10. Comparison with conventionally housed mice revealed that the absence of the microbiome markedly exacerbates SARS-CoV-2-induced disease in both C57BL/6 and Swiss Webster backgrounds. Germ-free mice exhibited greater weight loss, impaired lung function, worsened pulmonary pathology, and pronounced alterations in circulating cytokine and chemokine profiles compared with conventional controls. These findings show that resident microbiota limit SARS-CoV-2 pathogenicity and establish germ-free COVID-19 models as a powerful platform to identify protective microbial taxa and microbiota-based interventions to reduce severe disease.

microbiology↗