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International journal of systematic and evolutionary microbiology2025; 75(3); 006679; doi: 10.1099/ijsem.0.006679

Rhodococcus parequi sp. nov., a new species isolated from equine farm soil closely related to the pathogen Rhodococcus equi.

Abstract: We present the description of the new species, , found during phylogenomic investigations of a global collection of strains identified as () . Strain PAM 2766 was isolated from horse-breeding farm soil in Normandy, France, and was indistinguishable from based on the usual identification tests. Whole-genome phylogenetic analyses located PAM 2766 in the same sublineage as , together with , , , , and . PAM 2766 is most closely related to, but sufficiently distinct from, DSM 20307 to be considered a separate species. The average nt identity (ANI) and average aa identity (AAI) values are 88.60% and 92.35, respectively, well below the species cutoff. The PAM 2766 draft genome is ~5.3 Mb in size with 68.98% G+C mol content. PAM 2766 is strictly aerobic and non-motile and produces smooth, creamy to buff-coloured colonies very similar to those of . It phenotypically differs from the latter by the ability to grow at 5 °C, a strongly positive urease test at 24 h and specificities in the carbon and nitrogen source utilization profile as determined by phenotype microarray screens. Our data indicate that PAM 2766 belongs to a novel species, for which the name sp. nov. is proposed. was avirulent in macrophage infection assays and is assumed to be non-pathogenic. The type strain is PAM 2766 (=CETC 30995=NCTC 14987).
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Publication Date: 2025-03-10 PubMed ID: 40063668PubMed Central: PMC11893733DOI: 10.1099/ijsem.0.006679Google 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.

Rhocococcus parequi sp. nov. is a newly identified bacterial species isolated from soil on an equine farm in France. Although closely related to the pathogenic Rhodococcus equi, this new species can be differentiated based on genomic and phenotypic characteristics.

Overview of the Research

  • The study describes a newly discovered species, Rhodococcus parequi sp. nov., found during genomic studies of bacteria previously thought to be Rhodococcus equi.
  • A key strain, PAM 2766, was isolated from soil on a horse-breeding farm in Normandy, France.
  • This strain was very similar to Rhodococcus equi by common identification methods but differed significantly at the whole-genome level.

Isolation and Identification

  • Strain PAM 2766 was collected from equine farm soil, an environment associated with Rhodococcus equi, a known pathogen of horses.
  • Initial identification tests could not distinguish PAM 2766 from Rhodococcus equi due to similar colonial morphology and phenotypic traits.
  • However, advanced genetic analysis revealed important differences, prompting reclassification.

Genomic Analysis

  • Whole-genome phylogenetic analysis placed PAM 2766 within the Rhodococcus equi sublineage but as a distinct species.
  • PAM 2766’s genome size is around 5.3 megabases with a high G+C content (68.98%), characteristic of the genus Rhodococcus.
  • Key metrics comparing PAM 2766 to Rhodococcus equi DSM 20307 showed:
    • Average nucleotide identity (ANI) of 88.60%
    • Average amino acid identity (AAI) of 92.35%
  • These values fall well below the accepted thresholds for species identity, confirming PAM 2766 represents a new species.

Phenotypic Characteristics

  • PAM 2766 grows as smooth, creamy to buff-coloured colonies similar to Rhodococcus equi, explaining why usual tests failed to distinguish them.
  • Distinct phenotypic traits of PAM 2766 include:
    • Ability to grow at low temperature (5 °C), unlike Rhodococcus equi.
    • Strongly positive urease activity at 24 hours, differing from R. equi.
    • Unique carbon and nitrogen source utilization profiles shown by detailed phenotype microarray analysis.

Pathogenicity and Implications

  • Macrophage infection assays showed PAM 2766 is avirulent, suggesting it is non-pathogenic, unlike Rhodococcus equi which is pathogenic to horses.
  • This is important for understanding risks associated with soil microbes on equine farms.
  • The discovery improves diagnostic accuracy to distinguish pathogenic R. equi from closely related harmless species, which is critical for veterinary health management.

Conclusion and Nomenclature

  • The researchers propose classification of this strain as a novel species Rhodococcus parequi sp. nov.
  • The type strain is designated as PAM 2766 (=CETC 30995=NCTC 14987).
  • This work highlights the power of genomic tools to refine bacterial taxonomy beyond traditional methods.

Cite This Article

APA
Vazquez-Boland JA, Val-Calvo J, Duquesne F, Decorosi F, Viti C, Petry S, Scortti M. (2025). Rhodococcus parequi sp. nov., a new species isolated from equine farm soil closely related to the pathogen Rhodococcus equi. Int J Syst Evol Microbiol, 75(3), 006679. https://doi.org/10.1099/ijsem.0.006679

Publication

International journal of systematic and evolutionary microbiology
ISSN: 1466-5034
NlmUniqueID: 100899600
Country: England
Language: English
Volume: 75
Issue: 3
PII: 006679

Researcher Affiliations

Vazquez-Boland, José A
  • Microbial Pathogenomics Laboratory, Edinburgh Medical School (Biomedical Sciences), University of Edinburgh, Edinburgh, UK.
Val-Calvo, Jorge
  • Microbial Pathogenomics Laboratory, Edinburgh Medical School (Biomedical Sciences), University of Edinburgh, Edinburgh, UK.
Duquesne, Fabien
  • ANSES, Laboratory for Animal Health, Physiopathology and Epidemiology of Equine Diseases Unit, Goustranville, France.
Decorosi, Francesca
  • Department of Agriculture, Food, Environment and Forestry, University of Florence, Florence, Italy.
Viti, Carlo
  • Department of Agriculture, Food, Environment and Forestry, University of Florence, Florence, Italy.
Petry, Sandrine
  • ANSES, Laboratory for Animal Health, Physiopathology and Epidemiology of Equine Diseases Unit, Goustranville, France.
Scortti, Mariela
  • Microbial Pathogenomics Laboratory, Edinburgh Medical School (Biomedical Sciences), University of Edinburgh, Edinburgh, UK.

MeSH Terms

  • Rhodococcus / classification
  • Rhodococcus / genetics
  • Rhodococcus / isolation & purification
  • Animals
  • Phylogeny
  • Soil Microbiology
  • Horses / microbiology
  • DNA, Bacterial / genetics
  • Bacterial Typing Techniques
  • Rhodococcus equi / genetics
  • Rhodococcus equi / classification
  • France
  • Genome, Bacterial
  • RNA, Ribosomal, 16S / genetics
  • Base Composition
  • Farms
  • Sequence Analysis, DNA

Conflict of Interest Statement

The authors declare that there are no conflicts of interest.

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Citations

This article has been cited 3 times.
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  3. Val-Calvo J, Scortti M, Göker M, Vázquez-Boland JA. Leveraging the subgenus category to address monophyletic genus over-splitting: illustration with recently proposed Mycobacteriales genera.. Int J Syst Evol Microbiol 2025 Sep;75(9).
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