Epidemiology and Molecular Basis of Multidrug Resistance in Rhodococcus equi

Abstract

The development and spread of antimicrobial resistance are major concerns for human and animal health. The effects of the overuse of antimicrobials in domestic animals on the dissemination of resistant microbes to humans and the environment are of concern worldwide. Rhodococcus equi is an ideal model to illustrate the spread of antimicrobial resistance at the animal-human-environment interface because it is a natural soil saprophyte that is an intracellular zoonotic pathogen that produces severe bronchopneumonia in many animal species and humans. Globally, R. equi is most often recognized as causing severe pneumonia in foals that results in animal suffering and increased production costs for the many horse-breeding farms where the disease occurs. Because highly effective preventive measures for R. equi are lacking, thoracic ultrasonographic screening and antimicrobial chemotherapy of subclinically affected foals have been used for controlling this disease during the last 20 years. The resultant increase in antimicrobial use attributable to this "screen-and-treat" approach at farms where the disease is endemic has likely driven the emergence of multidrug-resistant (MDR) R. equi in foals and their environment. This review summarizes the factors that contributed to the development and spread of MDR R. equi, the molecular epidemiology of the emergence of MDR R. equi, the repercussions of MDR R. equi for veterinary and human medicine, and measures that might mitigate antimicrobial resistance at horse-breeding farms, such as alternative treatments to traditional antibiotics. Knowledge of the emergence and spread of MDR R. equi is of broad importance for understanding how antimicrobial use in domestic animals can impact the health of animals, their environment, and human beings.

Keywords: Rhodococcus equi; antibiotic resistance; antimicrobial agents; environmental microbiology; horizontal gene transfer; microbial genetics; zoonotic infections.

FIG 1

Proportions (percentages and 95% exact binomial confidence intervals) of clinical isolates of R. equi resistant to macrolides or rifampin for the time periods from 1995 to 2000 (n = 260 for macrolides and n = 80 for rifampin), 2001 to 2006 (n = 465 and 260, respectively), 2007 to 2012 (n = 614 and 260, respectively), and 2013 to 2017 (n = 839 and 837, respectively). Data were collected from 3 veterinary diagnostic laboratories in the U.S. state of Kentucky. (Reproduced from reference .)

FIG 2

Illustration representing the hypothesized causal effect of the use of thoracic ultrasound screening for early identification of Rhodococcus equi infections followed by prophylactic chemotherapy of subclinically affected foals and the emergence of MDR R. equi in clinical isolates and the environment of horse-breeding farms. The illustration also represents the cycle of shedding and reinfection of foals with MDR R. equi after antimicrobial treatment.

FIG 3

Phylogenetic tree of 93 Rhodococcus equi isolates based on core-genome SNP analysis using ParSNP (85). The genomes analyzed are from 125 environmental and 43 clinical R. equi isolates originating from the United States plus 23 isolates representative of the genomic diversity of the species, including the reference genome strain 103S and the type strain DSM 20307^T. All genomes are available in GenBank. (Accession numbers can be found in references , , , and 63). Numbers at the nodes indicate bootstrap values for 1,000 replicates. Tip labels appear in the following order: (i) strain designation (number), (ii) isolate origin, (iii) geographical origin, and (iv) year of collection and phenotype (M, MLS_B resistant only; MR, macrolide and rifampin resistant [no letters indicate susceptible isolates]). Colors designate different resistance genotypes, with MDR R. equi carrying erm(51) in red, MDR R. equi carrying erm(46) in blue, strains resistant to MLS_B only in purple, and susceptible strains in black. Additionally, MDR R. equi strains carrying erm(46) that are part of clone G2016 appear in green. Clonal clades appear collapsed in the main tree and amplified inside the squares. The tree graph was constructed with FigTree (http://tree.bio.ed.ac.uk/software/figtree/).

FIG 4

Principal-component analysis (PCA) plot based on the SNP variant calls obtained in the phylogenetic analysis of Rhodococcus equi. Shapes represent isolate sample origins (clinical or environmental). Colors represent macrolide- and rifampin-resistant phenotypes and if they are carrying either erm(46) or erm(51). PCA analysis and representation were performed using the ggfortify package in R software (version 3.6.1; https://cran.r-project.org/web/packages/ggfortify/index.html).

FIG 5

Illustration representing hypothesized scenarios of the impact of reducing selective pressure on the prevalence of MDR Rhodococcus equi in the environment. The first panel represents the emergence of MDR R. equi in the environment of horse-breeding farms due to increased antimicrobial use driving selective pressure. Outcome 1 describes a reduction in the prevalence of MDR R. equi in the environment as a consequence of reduced antimicrobial use. In this scenario, resistant bacteria, likely less fit because they are carrying an extra plasmid with resistance genes, would be outcompeted by susceptible ones in the soil. Alternatively, in outcome 2, MDR R. equi adapts genetically to compensate for the loss of fitness conferred by acquiring resistance genes. Moreover, MDR R. equi, in this scenario, can exchange resistance genes with other bacteria in the soil. These 2 factors contribute to allow MDR R. equi to persist in the environment even when selective pressure is reduced.