Sp. Nov., a New Species Isolated from Equine Farm Soil Closely Related to the Pathogen

Overview

Journal Int J Syst Evol Microbiol

Specialty Microbiology

Date 2025 Mar 10

PMID 40063668

Authors

Jose A Vazquez-Boland

Jorge Val-Calvo

Fabien Duquesne

Francesca Decorosi

Carlo Viti

Sandrine Petry

Mariela Scortti

Affiliations

Soon will be listed here.

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).

References

Hondalus M, Mosser D . Survival and replication of Rhodococcus equi in macrophages. Infect Immun. 1994; 62(10):4167-75. PMC: 303092. DOI: 10.1128/iai.62.10.4167-4175.1994. View

Kim M, Oh H, Park S, Chun J . Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes. Int J Syst Evol Microbiol. 2014; 64(Pt 2):346-351. DOI: 10.1099/ijs.0.059774-0. View

Zhang D, Su Z, Li L, Tang W . sp. nov. and sp. nov., from marine sponges. Int J Syst Evol Microbiol. 2021; 71(7). DOI: 10.1099/ijsem.0.004863. View

Kusuma A, Fenylestari G, Ammar F, Nououi I, Goodfellow M . sp. nov. a new member of the lineage isolated from sediment of a neutral hot spring and reclassification of (Ramaprasad . 2018) as a later heterotypic synonym of (Kruse 1896) Goodfellow and Alderson 1977 (Approved Lists 1980). Int J Syst Evol Microbiol. 2024; 74(1). DOI: 10.1099/ijsem.0.006236. View

Bartos O, Chmel M, Swierczkova I . The overlooked evolutionary dynamics of 16S rRNA revises its role as the "gold standard" for bacterial species identification. Sci Rep. 2024; 14(1):9067. PMC: 11032355. DOI: 10.1038/s41598-024-59667-3. View

Ripio M, Geoffroy C, Dominguez G, ALOUF J, Vazquez-Boland J . The sulphydryl-activated cytolysin and a sphingomyelinase C are the major membrane-damaging factors involved in cooperative (CAMP-like) haemolysis of Listeria spp. Res Microbiol. 1995; 146(4):303-13. DOI: 10.1016/0923-2508(96)81053-9. View

Prescott J . Rhodococcus equi: an animal and human pathogen. Clin Microbiol Rev. 1991; 4(1):20-34. PMC: 358176. DOI: 10.1128/CMR.4.1.20. View

Gonzalez-Iglesias P, Scortti M, MacArthur I, Hapeshi A, Rodriguez H, Prescott J . Mouse lung infection model to assess Rhodococcus equi virulence and vaccine protection. Vet Microbiol. 2014; 172(1-2):256-64. DOI: 10.1016/j.vetmic.2014.03.026. View

Chalita M, Kim Y, Park S, Oh H, Cho J, Moon J . EzBioCloud: a genome-driven database and platform for microbiome identification and discovery. Int J Syst Evol Microbiol. 2024; 74(6). PMC: 11261700. DOI: 10.1099/ijsem.0.006421. View

10.

Goris J, Konstantinidis K, Klappenbach J, Coenye T, Vandamme P, Tiedje J . DNA-DNA hybridization values and their relationship to whole-genome sequence similarities. Int J Syst Evol Microbiol. 2007; 57(Pt 1):81-91. DOI: 10.1099/ijs.0.64483-0. View

11.

Goodfellow M, Beckham A, Barton M . Numerical classification of Rhodococcus equi and related actinomycetes. J Appl Bacteriol. 1982; 53(2):199-207. DOI: 10.1111/j.1365-2672.1982.tb04677.x. View

12.

Yoon S, Ha S, Kwon S, Lim J, Kim Y, Seo H . Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies. Int J Syst Evol Microbiol. 2016; 67(5):1613-1617. PMC: 5563544. DOI: 10.1099/ijsem.0.001755. View

13.

Round J, Roccor R, Li S, Eltis L . A Fatty Acyl Coenzyme A Reductase Promotes Wax Ester Accumulation in Rhodococcus jostii RHA1. Appl Environ Microbiol. 2017; 83(20). PMC: 5626984. DOI: 10.1128/AEM.00902-17. View

14.

Halbert N, Reitzel R, Martens R, Cohen N . Evaluation of a multiplex polymerase chain reaction assay for simultaneous detection of Rhodococcus equi and the vapA gene. Am J Vet Res. 2005; 66(8):1380-5. DOI: 10.2460/ajvr.2005.66.1380. View

15.

Vazquez-Boland J, Meijer W . The pathogenic actinobacterium Rhodococcus equi: what's in a name?. Mol Microbiol. 2019; 112(1):1-15. PMC: 6852188. DOI: 10.1111/mmi.14267. View

16.

Ocampo-Sosa A, Lewis D, Navas J, Quigley F, Callejo R, Scortti M . Molecular epidemiology of Rhodococcus equi based on traA, vapA, and vapB virulence plasmid markers. J Infect Dis. 2007; 196(5):763-9. DOI: 10.1086/519688. View

17.

Jain C, Rodriguez-R L, Phillippy A, Konstantinidis K, Aluru S . High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries. Nat Commun. 2018; 9(1):5114. PMC: 6269478. DOI: 10.1038/s41467-018-07641-9. View

18.

Giguere S, Hondalus M, Yager J, Darrah P, Mosser D, Prescott J . Role of the 85-kilobase plasmid and plasmid-encoded virulence-associated protein A in intracellular survival and virulence of Rhodococcus equi. Infect Immun. 1999; 67(7):3548-57. PMC: 116543. DOI: 10.1128/IAI.67.7.3548-3557.1999. View

19.

Baek J, Baek W, Jeong S, Lee S, Jin H, Jeon C . sp. nov., a benzophenone-3-degrading bacterium, isolated from stream sediment. Int J Syst Evol Microbiol. 2022; 72(6). DOI: 10.1099/ijsem.0.005433. View

20.

Riesco R, Trujillo M . Update on the proposed minimal standards for the use of genome data for the taxonomy of prokaryotes. Int J Syst Evol Microbiol. 2024; 74(3). PMC: 10963913. DOI: 10.1099/ijsem.0.006300. View