Application of bacteriophages as a biocontrol strategy for Rhodococcus equi in the soil of horse breeding farms

Abstract

R. equi is a soil saprophyte responsible for bronchopneumonia in young foals. The absence of a vaccine and the rise of multidrug-resistant strains necessitate alternative strategies for managing R. equi and mitigating disease risk. Bacteriophages are now being revisited to combat bacterial pathogens. This thesis aimed to contribute to the understanding of R. equi ecology and demonstrate the efficacy of phages in reducing virulent R. equi in the environment, consequently lowering infection risks to foals.

Initial experiments analysed R. equi isolates for growth patterns and soil factor tolerances, revealing distinct growth behaviours and genomic variations that may be linked to strain virulence. Optimal growth occurred in sterile soil at 30–37℃ and pH 6–9, with minimal variation across soil types.

Soil microbiome analysis revealed increases in Rhodococcus during the foaling season, with observed increases in the proportion of Corynebacteriales in sand soil. Major compositional shifts across soil types may facilitate R. equi persistence.

Five lytic phages were selected for soil decontamination; when used in cocktails, these phages enhanced the host range and killing of R. equi by up to 5 log CFU/g, remaining viable in the soil environment.

Virulent R. equi isolates from soil and infected foals were screened against the phages to determine their lytic potential against circulating isolates. Phages lysed 77% of environmental isolates and 88% of clinical isolates. In natural soil inoculated with mixed historical R. equi, phage cocktails reduced DNA concentrations by 1.1 log CFU/g and the proportion of virulent R. equi by 81.5%. In soil with mixed modern R. equi, reductions were 0.8 log CFU/g and 60%, respectively. Microbiome analysis showed that phage treatments reduced bacterial diversity, affecting Rhodococcus and related genera.

This thesis presents novel applications of phage cocktails as a critical step toward therapeutic use against virulent R. equi populations.