Investigation of Rhodococcus equi bacteriophages from Australian horse breeding farms

Abstract

Rhodococcus equi is the cause of pneumonia in foals and significant economic losses to the equine industry. Alarmingly, R. equi antimicrobial resistance is rising and no vaccine is available. A potential alternative to manage R. equi disease on farms could involve bacteriophages (phages), which are viruses that infect specific bacteria. This thesis aims to progress development of phage‑mediated strategies to combat R. equi pneumonia by expanding the collection and knowledge of R. equi phages, exploring interactions with their hosts, their distribution on Australian horse farms and their impact on R. equi burden and disease.

22 R. equi isolates used for phage isolation and host range testing were screened for virulence factors and distinguished according to MLST, phylogeny, colony morphology and genetic features potentially influencing phage resistance.

Phages were detected in 33 horse farm samples, with 21 phages purified. All 10 phages examined under TEM were siphoviruses. Among 12 sequenced phages, nine did not carry any detectable genes associated with lysogeny, bacterial virulence or antimicrobial resistance, indicative of potential for use in decontamination or therapy. Six phages were novel whilst the others were related to Texas phages, with seven different genetic phage groups overall.

Some features that may have contributed to the variation seen in phage host range and plaquing efficiency and R. equi susceptibility to phage infection were assessed through WGS, including phage tail fibre proteins and enzymes, prophages, plasmids, and mutations affecting R. equi mycolic acid production. R. equi capsule and pilus loci were diverse and were not associated with phage sensitivity.

Phage and R. equi detection (by qPCR) in faeces was more likely in foals less than two months or found in small yards. Such foals were more commonly diagnosed with R. equi pneumonia, and their yards perhaps could be targeted for phage decontamination of R. equi to reduce disease risk.