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BMC microbiology2025; 25(1); 447; doi: 10.1186/s12866-025-04152-8

Multi-host distribution of Rhodococcus equi (Prescottella equi) strains and their phylogenomic clustering.

Abstract: Rhodococcus equi is an intracellular bacterial pathogen that can cause infections in various hosts, including humans and animals. Host-associated virulence plasmids have been identified as key contributors to the pathogenicity of R. equi and potentially play a role in determining the host tropism of the bacteria. The investigation of additional clinical and environmental isolates is likely to provide novel insights into the population structure, infection pathways, and drug resistance of this important pathogen. We combined whole-genome sequencing and antimicrobial-susceptibility testing of 37 selected R. equi isolates from animal, human, and environmental sources, collected in Switzerland over a 21 year period. In addition, we gathered a total of 251 whole-genome sequences and 141 multi-locus sequence (MLST) typing records from public sources. Although large geographical areas are not represented due to missing genomes we used a phylogenetic approach to define diversity patterns, distribution, and host tropism of R. equi. Results: Horse isolates, irrespective of the country of isolation, exhibited distinct sequence types (ST), notably ST-1 and ST-24 among others, and carried the VAPA plasmid, implying a strain-specific affinity for particular plasmid types. Several STs including ST-62 and ST-76 associated with the VAPN plasmid included both human and ruminant isolates from Switzerland, hinting at a potential common infection source. Similarly, isolates from porcine and human sources, documented in various European countries and China, exhibited common ST, including ST-18 and ST-36, and were found to harbour VAPB plasmids upon testing, suggesting potential zoonotic implications. Conclusions: Using a genomic approach we report host-specific strains that serve as carriers of virulence-associated plasmids, indicating an adaptation strategy within distinct R. equi lineages. The existence of shared plasmid profiles between farm animals and humans suggests a common infection source. Our results contribute to an improved understanding of the global genetic diversity of virulent and environmental R. equi strains, which will benefit from additional molecular epidemiological studies including strains from unrepresented geographical areas.
© 2025. The Author(s).
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Publication Date: 2025-07-21 PubMed ID: 40691552PubMed Central: PMC12278488DOI: 10.1186/s12866-025-04152-8Google Scholar: Lookup
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Summary

This research summary has been generated with artificial intelligence and may contain errors and omissions. Refer to the original study to confirm details provided. Submit correction.

The researchers investigated how the bacterial pathogen Rhodococcus equi, responsible for diverse infections in humans and animals, varies across different hosts and geographical locations. Genomic sequencing and antimicrobial tests were conducted on 37 R. equi samples gathered from humans, animals, and the environment over a 21 year period in Switzerland. The genetic diversity and potential factors determining host susceptibility to R. equi were analyzed.

Methodology

  • The team used whole-genome sequencing and antimicrobial susceptibility tests on 37 selected Rhodococcus equi samples. These samples were isolated from various sources, including animals, humans, and the environment, over a span of 21 years in Switzerland.
  • Additional information came from 251 whole-genome sequences and 141 multi-locus sequence (MLST) typing records which were sourced from public databases.
  • Even though the data lacked genomes from large geographical areas, a phylogenetic approach was used to study the bacteria’s diversity patterns, distribution, and host tropism.

Key Findings

  • Horse isolates, regardless of their country of origin, demonstrated distinctive sequence types – notably ST-1 and ST-24 and it was fond that they carried the VAPA plasmid. This indicates a potential affinity for strain-specific plasmid types.
  • Certain sequence types, such as ST-62 and ST-76 which were associated with the VAPN plasmid, included both human and ruminant isolates from Switzerland, implying a possible common source of infection.
  • Isolates from pigs and humans sourced from various European countries and China showed common sequence types (ST-18 and ST-36) and tested positive for carrying VAPB plasmids, implying potential zoonotic connections.

Conclusions

  • The genomic approach used in this research revealed host-specific strains that carry virulence-associated plasmids, demonstrating an adaptation strategy within distinct R. equi lineages.
  • The shared plasmid profiles observed between farm animals and humans point towards a shared infection source.
  • The study contributes to an enhanced understanding of the genetic diversity in virulent and environmental R. equi strains worldwide. However, more research, encompassing strains from underrepresented geographical areas, is necessary for a more comprehensive interpretation.

Cite This Article

APA
Ghielmetti G, Stevens MJA, Schmitt S, Kittl S, Cernela N, Biggel M, Schulthess B, Keller PM, Schrenzel J, Stephan R. (2025). Multi-host distribution of Rhodococcus equi (Prescottella equi) strains and their phylogenomic clustering. BMC Microbiol, 25(1), 447. https://doi.org/10.1186/s12866-025-04152-8

Publication

BMC microbiology
ISSN: 1471-2180
NlmUniqueID: 100966981
Country: England
Language: English
Volume: 25
Issue: 1
Pages: 447
PII: 447

Researcher Affiliations

Ghielmetti, Giovanni
  • Institute for Food Safety and Hygiene, Section of Veterinary Bacteriology, University of Zurich, Winterthurerstrasse 270, Zurich, 8057, Switzerland. giovanni.ghielmetti@uzh.ch.
Stevens, Marc J A
  • Institute for Food Safety and Hygiene, University of Zurich, Winterthurerstrasse 272, Zurich, 8057, Switzerland.
Schmitt, Sarah
  • Institute for Food Safety and Hygiene, Section of Veterinary Bacteriology, University of Zurich, Winterthurerstrasse 270, Zurich, 8057, Switzerland.
Kittl, Sonja
  • Institute of Veterinary Bacteriology, Department of Infectious Diseases and Pathobiology, University of Bern, Laenggassstrasse 122, Bern, 3001, Switzerland.
Cernela, Nicole
  • Institute for Food Safety and Hygiene, University of Zurich, Winterthurerstrasse 272, Zurich, 8057, Switzerland.
Biggel, Michael
  • Institute for Food Safety and Hygiene, University of Zurich, Winterthurerstrasse 272, Zurich, 8057, Switzerland.
Schulthess, Bettina
  • Institute of Medical Microbiology, University of Zurich, Gloriastrasse 28/30, Zurich, 8006, Switzerland.
Keller, Peter M
  • Institute for Infectious Diseases, University of Bern, Friedbühlstrasse 51, Bern, 3010, Switzerland.
  • Present address: Clinical Bacteriology and Mycology, University Hospital Basel, Petersgraben 4, Basel, 4031, Switzerland.
Schrenzel, Jacques
  • Bacteriology Laboratory, Division of Laboratory Medicine, Department of Diagnostics, Geneva University Hospitals, Rue Gabrielle-Perret-Gentil 4, Geneva, 1211, Switzerland.
Stephan, Roger
  • Institute for Food Safety and Hygiene, Section of Veterinary Bacteriology, University of Zurich, Winterthurerstrasse 270, Zurich, 8057, Switzerland.

MeSH Terms

  • Rhodococcus equi / genetics
  • Rhodococcus equi / classification
  • Rhodococcus equi / isolation & purification
  • Rhodococcus equi / drug effects
  • Rhodococcus equi / pathogenicity
  • Animals
  • Phylogeny
  • Humans
  • Horses / microbiology
  • Actinomycetales Infections / microbiology
  • Actinomycetales Infections / veterinary
  • Whole Genome Sequencing
  • Plasmids / genetics
  • Multilocus Sequence Typing
  • Genome, Bacterial
  • Switzerland
  • Microbial Sensitivity Tests
  • Horse Diseases / microbiology
  • Virulence Factors / genetics
  • Virulence
  • Anti-Bacterial Agents / pharmacology

Conflict of Interest Statement

Declarations. Ethics approval and consent to participate: All clinical samples and data were collected during routine patient care. No personal information, photos, or images are contained in the study. The data have been anonymized, enabling analysis in accordance with Swiss law and ethical regulations. Under the Human Research Act and the Swiss Animal Welfare Act, no ethical approval or patient consent is required for quality-focused assessments of clinical samples. Consent for publication: Not applicable. Competing interests: The authors declare no competing interests.

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Citations

This article has been cited 1 times.
  1. Yerlikaya Z, Karagülle B, Otlu B, Muz A. From Paddock to Foal: Prevalence and Genotypic Diversity of Rhodococcus equi on Stud Farms in Türkiye. Vet Sci 2026 Jan 10;13(1).
    doi: 10.3390/vetsci13010072pubmed: 41600728google scholar: lookup
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