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, Rhodococcus parequi, found during phylogenomic investigations of a global collection of strains identified as Rhodococcus (Prescottella) equi. Strain PAM 2766^T 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 2766^T in the same Rhodococcus sublineage as R. equi, together with Rhodococcus agglutinans, Rhodococcus defluvii, Rhodococcus soli, Rhodococcus subtropicus, Rhodococcus spongiicola and Rhodococcus xishaensis. PAM 2766^T is most closely related to, but sufficiently distinct from, R. equi DSM 20307 ^T 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^T draft genome is ~5.3 Mb in size with 68.98% G+C mol content. PAM 2766^T is strictly aerobic and 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 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^T 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 2766^T (=CETC 30995^T=NCTC 14987^T).