Cattle as reservoirs of clinically relevant Enterococcus: A One Health genomic perspective

Authors

  • Inês M. Ribeiro UCIBIO - Applied Molecular Biosciences Unit, University Institute of Health Sciences (1H-TOXRUN, IUCS CESPU) - Avenida Central de Gandra 1317, 4585-116 Gandra, Portugal; Associate Laboratory i4HB - Institute for Health and Bioeconomy, University Institute of Health Sciences - CESPU – Gandra, Portugal https://orcid.org/0009-0002-1253-9954
  • Ana C. Almeida-Santos UCIBIO - Applied Molecular Biosciences Unit, Faculdade de Farmácia, Universidade do Porto – Porto, Portugal; Associate Laboratory i4HB, Instituto para a Saúde e a Bioeconomia, Faculdade de Farmácia, Universidade do Porto – Porto, Portugal
  • Maria J. Teixeira UCIBIO - Applied Molecular Biosciences Unit, University Institute of Health Sciences (1H-TOXRUN, IUCS CESPU) - Avenida Central de Gandra 1317, 4585-116 Gandra, Portugal; Associate Laboratory i4HB - Institute for Health and Bioeconomy, University Institute of Health Sciences - CESPU – Gandra, Portugal
  • A. Ribeiro UCIBIO - Applied Molecular Biosciences Unit, University Institute of Health Sciences (1H-TOXRUN, IUCS CESPU) - Avenida Central de Gandra 1317, 4585-116 Gandra, Portugal; Associate Laboratory i4HB - Institute for Health and Bioeconomy, University Institute of Health Sciences - CESPU – Gandra, Portugal
  • Carla Campos Instituto Português de Oncologia do Porto Francisco Gentil, Rua Dr. António Bernardino de Almeida – Porto, Portugal; Escola Superior de Saúde, Instituto Politécnico do Porto, Rua Dr. António Bernardino de Almeida – Porto, Portugal
  • Nuno V. Brito UCIBIO - Applied Molecular Biosciences Unit, University Institute of Health Sciences (1H-TOXRUN, IUCS CESPU) - Avenida Central de Gandra 1317, 4585-116 Gandra, Portugal; Associate Laboratory i4HB - Institute for Health and Bioeconomy, University Institute of Health Sciences - CESPU – Gandra, Portugal; Center for Research and Development in Agrifood Systems and Sustainability, Higher Agricultural School, Polytechnic Institute of Viana do Castelo, Rua Escola Industrial e Comercial de NunʼÁlvares - Viana Do Castelo, Portugal
  • Rui Dantas FERA— Federação Nacional das Associações de Raças Autóctones – Guimarães, Portugal
  • Luís Pinho Department of Veterinary Clinics, Abel Salazar Biomedical Sciences Institute, University of Porto – Porto, Portugal
  • Sandra Quinteira UCIBIO - Applied Molecular Biosciences Unit, University Institute of Health Sciences (1H-TOXRUN, IUCS CESPU) - Avenida Central de Gandra 1317, 4585-116 Gandra, Portugal; Associate Laboratory i4HB - Institute for Health and Bioeconomy, University Institute of Health Sciences - CESPU – Gandra, Portugal; CIBIO - Research Center in Biodiversity and Genetic Resources, InBIO, Research Network in Biodiversity and Evolutionary Biology, Associated Laboratory, University of Porto, Campus de Vairão, Rua Padre Armando Quintas 7,4485-661 Vairão, Portugal; BIOPOLIS Program in Genomics, Biodiversity and Land Planning, Campus de Vairão – Vairão, Portugal
  • Carla Miranda UCIBIO - Applied Molecular Biosciences Unit, University Institute of Health Sciences (1H-TOXRUN, IUCS CESPU) - Avenida Central de Gandra 1317, 4585-116 Gandra, Portugal; Associate Laboratory i4HB - Institute for Health and Bioeconomy, University Institute of Health Sciences - CESPU – Gandra, Portugal; LAQV-REQUIMTE— Associated Laboratory for Green Chemistry of the Network of Chemistry and Technology, University NOVA of Lisbon, Campus da Caparica – Caparica, Portugal
  • Luísa Peixe UCIBIO - Applied Molecular Biosciences Unit, Faculdade de Farmácia, Universidade do Porto – Porto, Portugal; Associate Laboratory i4HB, Instituto para a Saúde e a Bioeconomia, Faculdade de Farmácia, Universidade do Porto – Porto, Portugal
  • Carla Novais UCIBIO - Applied Molecular Biosciences Unit, Faculdade de Farmácia, Universidade do Porto – Porto, Portugal; Associate Laboratory i4HB, Instituto para a Saúde e a Bioeconomia, Faculdade de Farmácia, Universidade do Porto – Porto, Portugal
  • Ana R. Freitas UCIBIO - Applied Molecular Biosciences Unit, University Institute of Health Sciences (1H-TOXRUN, IUCS CESPU) - Avenida Central de Gandra 1317, 4585-116 Gandra, Portugal; Associate Laboratory i4HB - Institute for Health and Bioeconomy, University Institute of Health Sciences - CESPU – Gandra, Portugal; UCIBIO - Applied Molecular Biosciences Unit, Faculdade de Farmácia, Universidade do Porto – Porto, Portugal; Associate Laboratory i4HB, Instituto para a Saúde e a Bioeconomia, Faculdade de Farmácia, Universidade do Porto – Porto, Portugal

DOI:

https://doi.org/10.48797/sl.2026.401

Keywords:

Selected Oral Communication

Abstract

Background: Enterococcus spp. are opportunistic pathogens and One Health indicators of antimicrobial resistance (AMR) [1]. Cattle remain understudied reservoirs of multidrug-resistant (MDR) enterococci [2]. This study assessed the occurrence of clinically relevant antibiotic-resistant Enterococcus in cattle farms in Northern Portugal, comparing intensive dairy systems and native breeds under extensive conditions. Methods: A total of 120 fecal swabs were collected from Holstein-Friesian (n=60) and autochthonous breeds (n=60) across 20 farms (65 calves, 55 adults; 2023). Samples were pre-enriched with or without antibiotics (ampicillin/vancomycin/florfenicol) and plated on Slanetz–Bartley-agar, without/with those antibiotics. Identification (MALDI-TOF MS), susceptibility testing (9 antibiotics; EUCAST/CLSI) and whole-genome sequencing (Illumina) for 13 MDR isolates were performed. Prevalence was calculated per sample [3]. Results: Enterococcus were detected in 62% of samples, with frequent species co-occurrence, mainly E. faecium (Efm-67%), E. hirae (52%), E. faecalis (45%). Resistance to tetracycline (32%), erythromycin (30%), high-level-streptomycin (28%), ampicillin/ciprofloxacin (22% each), chloramphenicol (18%), linezolid (9%), and high-level-gentamicin (6%) was observed. MDR occurred in 26% of samples, mainly in calves and intensive farms. Linezolid resistance (LinR) genes (optrA, poxtA, cfr) were detected across species, mainly in intensive farms, with variable phenotypes (MIC 2-8mg/L). Ampicillin resistance was confined to E. faecium, including ST18 and ST80 lineages associated with hospital settings. One ST80 isolate carried vanHAX despite phenotypic susceptibility, suggesting a vancomycin-variable genotype. AmpR-ST80 CT9962 was restricted to one farm, whereas LinR-ST18-CT9964 spanned farms/cities (Fig.1). Efm showed mixed hospital/community virulence profiles, with clade A1 lineages (ST18/ST80/ST1693) harboring hospital-associated markers (ptsD/orf1481/IS16/full pili-clusters). Bacteriocin genes (0–6) were diverse; ST18 carried bacAS5 linked to hospital strains. Plasmid replicases (mostly Inc18) included hospital-associated plasmids in ST18 (rep_pNB2354p1) and ST80 (rep_pRUM). Conclusions: Cattle may act as reservoirs of enterococci resistant to critically important antibiotics. The detection of hospital-adapted E. faecium clones in intensive farming systems highlight potential transmission, supporting the urgent need for integrated One Health surveillance.

Figure 1. Distribution of E. faecium clones and hospital-associated markers across different farms based on whole-genome sequencing (WGS). Bars represent the number of isolates per sequence type (ST) and core-genome type (CT), colored by production system (intensive vs extensive). Icons indicate the number of farms where each clone was detected. Hospital-associated markers (e.g., ptsD, orf1481, IS16, pili clusters) were identified in specific lineages, particularly within clade A1. LinR= linezolid-resistant; LinS = linezolid-susceptible.

References

1. Torres, C. et al. Antimicrobial Resistance in Enterococcus spp. of animal origin. Microbiol Spectr 2018, 6(4), doi:10.1128/microbiolspec.arba-0032-2018

2. Gião, J. et al. Antimicrobial Susceptibility of Enterococcus Isolates from Cattle and Pigs in Portugal: Linezolid Resistance Genes optrA and poxtA. Antibiotics 2022, 11(5), 615, doi:10.3390/antibiotics11050615

3. Finisterra, L. et al. Industrial dog food is a vehicle of multidrug-resistant enterococci carrying virulence genes often linked to human infections. Int J Food Microbiol 2021, 358, 109284, doi:10.1016/j.ijfoodmicro.2021.109284

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Published

2026-05-05

How to Cite

Ribeiro, I. M., Almeida-Santos, A. C., Teixeira, M. J., Ribeiro, A., Campos, C., Brito, N. V., Dantas, R., Pinho, L., Quinteira, S., Miranda, C., Peixe, L., Novais, C., & Freitas, A. R. (2026). Cattle as reservoirs of clinically relevant Enterococcus: A One Health genomic perspective. Scientific Letters, 1(Sup 1). https://doi.org/10.48797/sl.2026.401

Issue

Vol. 1 No. Sup 1 (2026)

Section

Oral Communications

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Copyright (c) 2026 Inês M. Ribeiro, Ana C. Almeida-Santos, Maria J. Teixeira, A. Ribeiro, Carla Campos, Nuno V. Brito, Rui Dantas, Luís Pinho, Sandra Quinteira, Carla Miranda, Luísa Peixe, Carla Novais, Ana R. Freitas

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