Journal Article

Multi-host distribution of Rhodococcus equi (Prescottella equi) strains and their phylogenomic clustering

Stevens, Marc J. A., Kittl, Sonja, Schulthess, Bettina, Schmitt, Sarah, Keller, Peter M., Schrenzel, Jacques, Cernela, Nicole, Ghielmetti, Giovanni, Biggel, Michael, Stephan, Roger

2025

Overview

Background Rhodococcus equi is an intracellular bacterial pathogen that can cause infections in various hosts, including humans and animals. Host-associated virulence plasmids have been identified as key contributors to the pathogenicity of R. equi and potentially play a role in determining the host tropism of the bacteria. The investigation of additional clinical and environmental isolates is likely to provide novel insights into the population structure, infection pathways, and drug resistance of this important pathogen. We combined whole-genome sequencing and antimicrobial-susceptibility testing of 37 selected R. equi isolates from animal, human, and environmental sources, collected in Switzerland over a 21 year period. In addition, we gathered a total of 251 whole-genome sequences and 141 multi-locus sequence (MLST) typing records from public sources. Although large geographical areas are not represented due to missing genomes we used a phylogenetic approach to define diversity patterns, distribution, and host tropism of R. equi . Results Horse isolates, irrespective of the country of isolation, exhibited distinct sequence types (ST), notably ST-1 and ST-24 among others, and carried the VAPA plasmid, implying a strain-specific affinity for particular plasmid types. Several STs including ST-62 and ST-76 associated with the VAPN plasmid included both human and ruminant isolates from Switzerland, hinting at a potential common infection source. Similarly, isolates from porcine and human sources, documented in various European countries and China, exhibited common ST, including ST-18 and ST-36, and were found to harbour VAPB plasmids upon testing, suggesting potential zoonotic implications. Conclusions Using a genomic approach we report host-specific strains that serve as carriers of virulence-associated plasmids, indicating an adaptation strategy within distinct R. equi lineages. The existence of shared plasmid profiles between farm animals and humans suggests a common infection source. Our results contribute to an improved understanding of the global genetic diversity of virulent and environmental R. equi strains, which will benefit from additional molecular epidemiological studies including strains from unrepresented geographical areas.

• Publisher: BioMed Central,BioMed Central Ltd,Springer Nature B.V,BMC
• Subject: Abscesses / Acquired immune deficiency syndrome / Actinomycetales Infections - microbiology / Actinomycetales Infections - veterinary / AIDS / Animal human relations / Animals / Anopheles / Anti-Bacterial Agents - pharmacology / Antibiotics / Antimicrobial agents / Antiretroviral drugs / Bacteria / Bacteria, Pathogenic / Bacterial infections / Biological Microscopy / Biomedical and Life Sciences / Clustering / Comparative genomics / Distribution / DNA sequencing / Drug resistance / Drug resistance in microorganisms / Drug therapy / Epidemiology / Gene sequencing / Genes / Genetic aspects / Genetic diversity / Genome, Bacterial / Genomes / Genomics / Gram-positive bacteria / Health aspects / HIV / Hogs / Horse Diseases - microbiology / Horses - microbiology / Host specificity / Host tropism / Host-associated virulence plasmids / Host-bacteria relationships / Human immunodeficiency virus / Humans / Identification and classification / Imipenem / Immune system / Infection / Infections / Life Sciences / Microbial Sensitivity Tests / Microbiology / Multilocus Sequence Typing / Mycology / Nucleotide sequence / Nucleotide sequencing / Parasitology / Pathogenicity / Pathogens / Phylogenomics / Phylogeny / Plasmids / Plasmids - genetics / Pneumonia / Population structure / Rhodococcus equi / Rhodococcus equi - classification / Rhodococcus equi - drug effects / Rhodococcus equi - genetics / Rhodococcus equi - isolation & purification / Rhodococcus equi - pathogenicity / Strains (organisms) / Susceptibility testing / Switzerland / Taxonomy / Tetracycline / Tetracyclines / Tropism / Virology / Virulence / Virulence (Microbiology) / Virulence Factors - genetics / Whole Genome Sequencing