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

We present the description of the new species, Rhodococcus parequi, found during phylogenomic investigations of a global collection of strains identified as Rhodococcus
(Prescottella) equi. Strain PAM 2766T was isolated from horse-breeding farm soil in Normandy, France, and was indistinguishable from R. equi based on the usual identification tests. Whole genome phylogenetic analyses located PAM 2766T in the same Rhodococcus sublineage as R. equi, together with Rhodococcus agglutinans, Rhodococcus defluvii, Rhodococcus soli, Rhodococcus subtropicus, Rhodococcus spongiicola and Rhodococcus xishaensis. PAM 2766T is most closely related to, but sufficiently distinct from R. equi DSM 20307 T to be considered as a separate species. Average Nucleotide Identity (ANI) and Average Amino Acid Identity (AAI) values are 88.60% and 92.35, respectively, well below the species cutoff. The PAM 2766T draft genome is ~5.3 Mb in size with 68.98% G+C mol content. PAM 2766T is aerobic, non-motile, and produces smooth, creamy to buff-coloured colonies very similar to those of R. equi. It phenotypically differs from the latter by the ability to grow at 5ºC, 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 2766T belongs to a novel species, for which the name Rhodococcus parequi sp. nov. is proposed. R. parequi was avirulent in macrophage infection assays and is assumed to be non-pathogenic. The type strain is PAM 2766T (= CETC 30995T = NCTC 14987T).