Genomic diversity of multidrug-resistant <i>Rhodococcus equi</i> : novel sequence types, pangenome architecture, and phylogenomic evolution

ABSTRACT Rhodococcus equi is a major cause of life-threatening pneumonia in foals under 6 months of age and an opportunistic pathogen in immunocompromised humans. Although common in soil and equine farm environments, its evolutionary dynamics, virulence architecture, and pathways of antimicrobial resistance (AMR) emergence remain poorly understood. This study integrated phenotypic characterization and whole-genome sequencing of 46 R. equi isolates from horses submitted for necropsy ( n = 45) and equine fecal samples ( n = 1) in Kentucky between January 2022 and December 2023 to define their resistance landscape, virulence potential, and population structure. A high burden of multidrug-resistant (MDR) strains was identified (32.6%), including resistance to rifamycin, macrolides, tetracyclines, sulfonamides, and cephalosporins. Nearly all isolates (97.8%) formed robust biofilms, survived intracellularly in macrophages, and carried key virulence determinants ( vapA , vapH , iupT ). Genomic analysis identified 22 multilocus sequence types (MLSTs), including 20 previously unreported novel sequence types (STs), indicating substantial lineage expansion. Pangenome analysis revealed a large accessory genome and limited core gene conservation; phylogenomic analysis revealed clustering with isolates from humans and other animal hosts, suggesting shared evolutionary ancestry and potential cross-species transmission. These findings highlight R. equi as a One Health concern at the animal-environment-human interface. The discovery of numerous novel STs, together with widespread MDR phenotypes and conserved virulence determinants, underscores the need for strengthened antimicrobial stewardship, enhanced genomic surveillance, and development of alternative therapeutic strategies. This study provides critical insights into the epidemiology, AMR emergence, and evolutionary dynamics of R. equi circulating within equine farm systems and its implications for both equine and human health. IMPORTANCE Rhodococcus equi is a bacterium commonly found in soil and around horse farms. While it is part of the natural environment, it can cause serious diseases, including life-threatening pneumonia in young foals and severe infections in people with weakened immune systems. Despite its importance, much remains unknown about how this pathogen spreads, evolves, and develops resistance to antibiotics. In this study, we combined laboratory testing with genome sequencing of R. equi obtained from necropsied horses to better understand how these bacteria resist antibiotics and form protective biofilms that make infections difficult to treat. Our genomic analyses revealed many previously unrecognized genetic lineages and showed that horse-associated strains share close evolutionary links with isolates from humans and other animals. Together, these findings highlight R. equi as an emerging concern and a potential public health risk, underscoring the importance of responsible antimicrobial use and expanded genomic surveillance to safeguard equine and human health.