Macrolide- and rifampin-resistant Rhodococcus equi on a horse breeding farm, Kentucky, USA

Update on emerging multidrug-resistant Rhodococcus equi

Jose Vázquez-Boland, Jorge Val-Calvo and Mariela Scortti present a brief summary of the main aspects surrounding the recently identified multidrug-resistant Rhodococcus equi that emerged in the USA and the actions being taken to tackle the problem with support from the UK's Horserace Betting Levy Board.

Rhodococcus infection: a 10-year retrospective analysis of clinical experience and antimicrobial susceptibility profile

Rhodococcus equi is an opportunistic pathogen known to cause pulmonary and extrapulmonary disease among immunocompromised patients. Treatment is frequently challenging due to intrinsic resistance to multiple antibiotic classes. While non-equi Rhodococcus spp. are prevalent, their clinical significance is poorly defined. There is also limited data on antibiotic susceptibility testing (AST) of Rhodococcus infection in humans. We conducted a single-center, retrospective cohort study evaluating clinical characteristics, microbiologic profile, and AST of Rhodococcus infections between June 2012 and 2022 at our tertiary academic medical center. Identification of Rhodococcus spp. was performed by Sanger 16S rRNA gene sequencing and/or matrix-assisted laser desorption ionization-time of flight mass spectrometry, and AST was performed by agar dilution. Three hundred twenty-two isolates of Rhodococcus spp. were identified from blood (50%), pulmonary (26%), and bone/joint (12%) sources. R. equi/hoagii, R. corynebacterioides, and R. erythropolis were the most frequently isolated species, with 19% of isolates identified only to genus level. One hundred ninety-nine isolates evaluated for AST demonstrated high-level resistance to amoxicillin/clavulanate, cephalosporins, and aminoglycosides. More than 95% susceptibility to imipenem, vancomycin, linezolid, rifampin, and clarithromycin was observed. Non-equi species showed a significantly more favorable AST profile relative to R. equi. Clinically significant Rhodococcus infection was rare with 10 cases diagnosed (majority due to R. equi) and managed. The majority of patients received 2- or 3-drug combination therapy for 2-6 months, with favorable clinical response. Significant differences in AST were observed between R. equi and non-equi species. Despite high antimicrobial resistance to several antibiotic classes, imipenem and vancomycin remain appropriate empiric treatment options for R. equi. Future research evaluating mechanisms underlying antimicrobial resistance is warranted.

Antimicrobial Residue Accumulation Contributes to Higher Levels of Rhodococcus equi Carrying Resistance Genes in the Environment of Horse-Breeding Farms

Antimicrobial residues excreted in the environment following antimicrobial treatment enhance resistant microbial communities in the environment and have long-term effects on the selection and maintenance of antimicrobial resistance genes (AMRGs). In this study, we focused on understanding the impact of antimicrobial use on antimicrobial residue pollution and antimicrobial resistance (AMR) in the environment of horse-breeding farms. Rhodococcus equi is an ideal microbe to study these associations because it lives naturally in the soil, exchanges AMRGs with other bacteria in the environment, and can cause disease in animals and humans. The environment is the main source of R. equi infections in foals; therefore, higher levels of multidrug-resistant (MDR) R. equi in the environment contribute to clinical infections with MDR R. equi. We found that macrolide residues in the environment of horse-breeding farms and the use of thoracic ultrasonographic screening (TUS) for early detection of subclinically affected foals with R. equi infections were strongly associated with the presence of R. equi carrying AMRGs in the soil. Our findings indicate that the use of TUS contributed to historically higher antimicrobial use in foals, leading to the accumulation of antimicrobial residues in the environment and enhancing MDR R. equi.

The Effects of Antimicrobial Protocols and Other Perioperative Factors on Postoperative Complications in Horses Undergoing Celiotomy: A Retrospective Analysis, 2008-2021

Recognition of antimicrobial resistance in equine practice has increased over the past decade. The objective of this study was to provide an updated retrospective review of antimicrobial regimens in one tertiary referral hospital and to evaluate the association with postoperative complications. A secondary objective was to evaluate other perioperative factors including surgical procedure, anesthetic and recovery parameters, and the effect of perioperative medications on complications and outcomes. A computerized search of medical records was performed to identify horses undergoing exploratory celiotomy from 1 January 2008 to 31 December 2021. A total of 742 celiotomies were performed (608 completed, 134 terminated intraoperatively). Factors recorded were evaluated using logistic regression for the presence of either incisional infection, postoperative ileus, or other complications postoperatively. Antimicrobial type or timing (pre-, intra-, or postoperative) were not associated with decreased risk of incisional infection or postoperative ileus; however, the duration of NSAID use was positively associated with incisional infection (OR 1.14 per day). Lidocaine and alpha-2-agonist administration postoperatively were also associated with increased incidence of postoperative ileus (OR 21.5 and 1.56, respectively). Poor recovery quality (OR 4.69), the addition of other antimicrobials besides penicillin/gentamicin postoperatively (OR 3.63), and an increased number of different NSAID classes used (OR 1.46 per additional) were associated with other complications. Implementation of enterotomy was associated with decreased risk of other complications (OR 0.64). These findings provide an updated summary of factors associated with postoperative complications in horses undergoing celiotomy.

Antimicrobial susceptibility of Rhodococcus equi strains isolated from foals in Chile

Rhodococcus equi is responsible for foal pneumonia worldwide, with a significant economic impact on the production and breeding of horses. In Chile, the first case was reported in 2000, and since then, its incidence has been increasing. Distinctive characteristics of R. equi as an intracellular pathogen in macrophages, emergence of virulence plasmids encoding surface lipoprotein antigens, and appearance of antibiotic resistance against macrolides and rifampicin have significantly complicated the treatment of R. equi pneumonia in foals. Therefore, in vitro susceptibility studies of first-line and newer antibiotics against R. equi are the first step to establishing effective treatments and optimizing new therapeutic options. The aim of the present study is to determine the susceptibility profile of fourteen strains of R. equi isolated from foals in Chile to several antibiotics of the macrolide group including azithromycin, amikacin, tildipirosin and gamithromycin as well as others such as rifampicin, doxycycline and ceftiofur. Identification of R. equi in collected isolates from foals in Chile has been performed by CAMP test and PCR based on detecting of the gene encoding the 16 S rRNA. The presence of genes encoding virulence plasmids was also determined using PCR. Results obtained have demonstrated presence of virulent R. equi strains in Chile. In vitro susceptibility pattern to different antibiotics has shown better results for doxycycline and rifampicin similar to previous studies performed. Current macrolides have been evaluated in order to consider alternative treatment options in a context of emerging resistance to classic macrolides and rifampicin, obtaining better results with gamithromycin (MIC range of 0.125 to 128 mg/ml) than with tildipirosin (MIC range of 16 to 128 mg/ml). An adequate diagnosis of bacterial susceptibility based on antibiograms is necessary to treat the Rhodococcus equi infection in foals.

Rhodococcus equi: challenges to treat infections and to mitigate antimicrobial resistance

Rhodococcus equi, a gram-positive facultative intracellular pathogen and a soil saprophyte, is one of the most common causes of pneumonia in young foals. It poses a threat to the economy in endemic horse-breeding farms and to animal welfare annually. Many farms use thoracic ultrasonographic screening and antimicrobial treatment of subclinically affected foals as a preventive measure against severe R. equi infections. The wide use antimicrobials to treat subclinically affected foals has contributed to the emergence of multidrug resistant (MDR)-R. equi in both clinical isolates from sick foals and in the environment of horse-breeding farms. Alternatives to treat foals infected with MDR-R. equi are scarce and the impact of the emergence of MDR-R. equi in the environment of farms is still unknown. The aim of this review is to discuss the emergence of MDR-R. equi in the United States and the challenges faced to guide antimicrobial use practices. Reduction of antimicrobial use at horse-breeding farms is essential for the preservation of antimicrobial efficacy and, ultimately, human, animal, and environmental health.

Rhodococcus equi-What is New This Decade?

Foals become infected shortly after birth; most develop subclinical pneumonia and 20% to 30% develop clinical pneumonia that requires treatment. It is now well established that the combination of screening programs based on thoracic ultrasonography and treatment of subclinical foals with antimicrobials has led to the development of resistant Rhodococcus equi strains. Thus, targeted treatment programs are needed. Administration of R equi-specific hyperimmune plasma shortly after birth is beneficial as foals develop less severe pneumonia but does not seem to prevent infection. This article provides a summary of clinically relevant research published during this past decade.

Less Typical Courses of Rhodococcus equi Infections in Foals

This article aims to present several interesting and less typical courses of Rhodococcus equi infections in foals, collected during the 2019-2021 foaling seasons in some Polish studs. The study was conducted by the Division of Veterinary Epidemiology and Economics, Warsaw University of Life Sciences-SGGW, and concentrated on ultrasonographic contribution to diagnostics and treatment of the disease. Among many standard cases of rhodococcal pneumonia, some rare ones occurred. The aforementioned issues include the potential contribution of rhodococcal infection to a grave outcome in a prematurely born filly, lost as a yearling, so-called "extrapulmonary disorders" (EPD), a hypothesis of inherited immunodeficiency with grave outcome in a breeding dam line from one stud, and macrolide-induced anhidrosis. The main benefit of this report would be to supplement the general picture of clinical rhodococcosis.

Antimicrobial resistance among Streptococcus equi subspecies zooepidemicus and Rhodococcus equi isolated from equine specimens submitted to a diagnostic laboratory in Kentucky, USA

Background

Surveillance of antimicrobial resistance (AMR) among veterinary pathogens is necessary to identify clinically relevant patterns of AMR and to inform antimicrobial use practices. Streptococcus equi subsp. zooepidemicus and Rhodococcus equi are bacterial pathogens of major clinical importance in horses and are frequently implicated in respiratory tract infections. The objectives of this study were to describe antimicrobial resistance patterns and identify predictors of AMR and multidrug resistance (MDR) (resistance to three or more antimicrobial classes) among equine S. zooepidemicus and R. equi isolates.

Methods

Antimicrobial susceptibility data from equine specimens submitted to the University of Kentucky Veterinary Diagnostic Laboratory between 2012 and 2017 were used in the study. Temporal trends in AMR and MDR were assessed using the Cochran-Armitage test. Logistic regression was used to identify associations between patient characteristics and the following outcomes: (a) MDR among S. zooepidemicus isolates, and (b) resistance to macrolides and ansamycins (rifampin) among R. equi isolates. Logistic regression was also used to investigate whether resistance of S. zooepidemicus and R. equi isolates to an antimicrobial class could be predicted by resistance to other drug classes.

Results

The vast majority of S. zooepidemicus (99.6%) and R. equi isolates (83%) were resistant to at least one antimicrobial agent, but no significant temporal trends in AMR were observed. Approximately half (53.3%) of the S. zooepidemicus isolates were multidrug-resistant, and there was a significant (p < 0.001) increasing temporal trend of MDR among S. zooepidemicus isolates. Resistance to penicillin, which is typically recommended for treatment of suspected S. zooepidemicus infections, also increased during the study period, from 3.3% to 9.5%. Among R. equi isolates, 19.2% were resistant to one or more macrolide antibiotics, 24% were resistant to rifampin, and 15.6% were resistant to both macrolide(s) and rifampin. For both organisms, resistance to an antimicrobial class could be predicted based on resistance profiles to other drug classes. For instance, significant (p < 0.01) predictors of β-lactam resistance among S. zooepidemicus isolates included resistance to macrolides (Odds Ratio (OR) = 14.7) and ansamycins (OR = 9.3). Resistance to phenicols (OR = 3.7) and ansamycins (OR = 19.9) were associated with higher odds of macrolide resistance among R. equi isolates.

Conclusions

The increase in MDR among S. zooepidemicus isolates is concerning. The observed levels of resistance to macrolides and rifampin among R. equi are also worrisome given the limited number of antimicrobials available for treatment of this organism. The findings of this study highlight the importance of ongoing surveillance of AMR to guide treatment decisions and directions for future research.

International Spread of Multidrug-Resistant Rhodococcus equi

A multidrug-resistant clone of the animal and human pathogen Rhodococcus equi, MDR-RE 2287, has been circulating among equine farms in the United States since the 2000s. We report the detection of MDR-RE 2287 outside the United States. Our finding highlights the risk for MDR-RE spreading internationally with horse movements.

Fitness cost conferred by the novel erm(51) and rpoB mutation on environmental multidrug resistant-Rhodococcus equi

Rhodococcus equi is a common cause of severe pneumonia in foals. Emergence of macrolide-resistant R. equi isolated from foals and their environment has been reported in the United States. A novel erm(51) gene was recently identified in R. equi in soil from horse farms in Kentucky. Our objective was to determine the effect of the erm(51) gene and associated rpoB mutation on the fitness of multidrug resistant-R. equi (MDR-R. equi^{erm(51)+, rpoB+}) under different nutrient conditions. Bacterial growth curves were generated for 3 MDR-R. equi^{erm(51)+, rpoB+} isolates and 3 wild-type (WTN) R. equi isolates recovered from environmental samples of farms in central Kentucky. Growth was measured over 30.5 h in brain-heart infusion broth (BHI), minimal medium (MM), and minimal medium without iron (MM-I). All isolates had significantly (P < 0.05) higher growth in BHI compared to either MM or MM-I. MDR-R. equi^{erm(51)+, rpoB+} exhibited significantly lower growth compared to WTN isolates in BHI (nutrient-rich condition), but not in either MM or MM-I (nutrient-restricted conditions). This study indicates that under nutrient-rich conditions fitness of MDR-R. equi^{erm(51)+, rpoB+} is reduced relative to susceptible isolates; however, under nutrient-restricted conditions MDR-R. equi^{erm(51)+, rpoB+} isolates grow similarly to susceptible isolates. These findings indicate that MDR-R. equi^{erm(51)+, rpoB+} might be outcompeted by susceptible isolates in nature when practices to reduce antimicrobial pressure, such as reducing antimicrobial use in foals, are implemented. But it also raises the concern that these resistant genotypes might persist in the environment of horse-breeding farms in the face of selective pressures such as antimicrobials or nutrient restriction.

Transfusion of hyperimmune plasma for protecting foals against Rhodococcus equi pneumonia

The bacterium Rhodococcus equi causes pneumonia in foals that is prevalent at breeding farms worldwide. In the absence of an effective vaccine, transfusion of commercial plasma from donor horses hyperimmunised against R. equi is used by many farms to reduce the incidence of pneumonia among foals at farms where the disease is endemic. The effectiveness of hyperimmune plasma for controlling R. equi pneumonia in foals has varied considerably among reports. The purposes of this narrative review are: 1) to review early studies that provided a foundational basis for the practice of transfusion of hyperimmune plasma that is widespread in the US and in many other countries; 2) to summarise current knowledge of hyperimmune plasma for preventing R. equi pneumonia; 3) to provide an interpretive summary of probable explanations for the variable results among studies evaluating the effectiveness of transfusion of hyperimmune plasma for reducing the incidence of R. equi pneumonia; 4) to review mechanisms by which hyperimmune plasma might mediate protection; and 5) to consider risks of transfusing foals with hyperimmune plasma. Although the weight of evidence supports the practice of transfusing foals with hyperimmune plasma to prevent R. equi pneumonia, many important gaps in our knowledge of this topic remain including the volume/dose of hyperimmune plasma to be transfused, the timing(s) of transfusion, and the mechanism(s) by which hyperimmune plasma mediates protection. Transfusing foals with hyperimmune plasma is expensive, labour-intensive, and carries risks for foals; therefore, alternative approaches for passive and active immunisation to prevent R. equi pneumonia are greatly needed. This article is protected by copyright. All rights reserved.

Novel Quantitative PCR for Rhodococcus equi and Macrolide Resistance Detection in Equine Respiratory Samples

R. equi is an important veterinary pathogen that takes the lives of many foals every year. With the emergence and spread of MDR R. equi to current antimicrobial treatment, new tools that can provide a fast and accurate diagnosis of the disease and antimicrobial resistance profile are needed. Here, we have developed and analytically validated a multiplex qPCR for the simultaneous detection of R. equi and related macrolide resistance genes in equine respiratory samples. The three sets of oligos designed in this study to identify R. equi housekeeping gene choE and macrolide resistance genes erm(46) and erm(51) showed high analytic sensitivity with a limit of detection (LOD) individually and in combination below 12 complete genome copies per PCR reaction, and an amplification efficiency between 90% and 147%. Additionally, our multiplex qPCR shows high specificity in in-silico analysis. Furthermore, it did not present any cross-reaction with normal flora from the equine respiratory tract, nor commonly encountered respiratory pathogens in horses or other genetically close organisms. Our new quantitative PCR is a trustable tool that will improve the speed of R. equi infection diagnosis, as well as helping in treatment selection.

Fecal concentration of Rhodococcus equi determined by quantitative polymerase chain reaction of rectal swab samples to differentiate foals with pneumonia from healthy foals

BACKGROUND

Diagnostic accuracy of real-time, quantitative PCR (qPCR) assays to quantify virulent Rhodococcus equi using rectal swab samples has not been systematically evaluated.

OBJECTIVE

To evaluate the accuracy of qPCR of rectal swab samples to differentiate foals with pneumonia from healthy foals of similar age from the same environment.

ANIMALS

One hundred privately owned foals born in 2021 from 2 farms in New York.

METHODS

An incident case-control study design was used. Rectal swabs were collected from all foals diagnosed with R. equi pneumonia at 2 horse-breeding farms (n = 47). Eligible pneumonia cases (n = 39) were matched by age to up to 2 healthy (n = 53) control foals; rectal swabs were collected from control foals on the day of diagnosis of the index case. DNA was extracted from fecal swabs and the concentration of virulent R. equi (ie, copy numbers of the virulence-associated protein A gene [vapA] per 100 ng fecal DNA) was estimated by qPCR.

RESULTS

The area under the ROC curve for qPCR of fecal swabs was 83.7% (95% CI, 74.9-92.6). At a threshold of 14 883 copies of vapA per 100 ng fecal DNA, specificity of the assay was 83.0% (95% CI, 71.7-92.4) and sensitivity was 79.5% (95% CI, 66.7-92.3).

CONCLUSIONS AND CLINICAL IMPORTANCE

Although fecal concentrations of virulent R. equi are significantly higher in pneumonic foals than healthy foals of similar age in the same environment, qPCR of rectal swabs as reported here lacks adequate diagnostic accuracy for clinical use.

Rhodococcus equi Foal Pneumonia: Update on Epidemiology, Immunity, Treatment, and Prevention

Pneumonia in foals caused by the bacterium Rhodococcus equi has a worldwide distribution and is a common cause of disease and death for foals. The purpose of this narrative review is to summarise recent developments pertaining to the epidemiology, immune responses, treatment, and prevention of rhodococcal pneumonia of foals. Screening tests have been used to implement earlier detection and treatment of foals with presumed subclinical R. equi pneumonia to reduce mortality and severity of disease. Unfortunately, this practice has been linked to the emergence of antimicrobial resistant R. equi in North America. Correlates of protective immunity for R. equi infections of foals remain elusive, but recent evidence indicates that innate immune responses are important both for mediating killing and orchestrating adaptive immune responses. A macrolide antimicrobial in combination with rifampin remains the recommended treatment for foals with R. equi pneumonia. Great need exists to identify which antimicrobial combination is most effective for treating foals with R. equi pneumonia and to limit emergence of antimicrobial-resistant strains. In the absence of an effective vaccine against R. equi, passive immunisation remains the only commercially-available method for effectively reducing the incidence of R. equi pneumonia. Because passive immunisation is expensive, labour-intensive, and carries risks for foals, great need exists to develop alternative approaches for passive and active immunisation.

Synergistic combinations of clarithromycin with doxycycline or minocycline reduce the emergence of antimicrobial resistance in Rhodococcus equi

BACKGROUND

The alarming increase in rifampin and macrolide resistance among Rhodococcus equi isolates highlights the need to identify alternative therapeutic options that can effectively control rhodococcosis in foals while limiting the further development of drug resistance.

OBJECTIVES

To evaluate bacterial killing, antibiotic synergism and mutant prevention concentrations (MPCs) of clarithromycin alone and in combination with doxycycline, minocycline or rifampin against clinical isolates of R equi.

STUDY DESIGN

In vitro experiments.

METHODS

Bacterial time-kill, fractional inhibitory concentration (checkerboard) and mutant prevention concentration assays were evaluated in four clarithromycin- and rifampin-susceptible (ClaS /RifS ) and two clarithromycin- and rifampin-resistant (ClaR /RifR ) R equi clinical strains.

RESULTS

In this study evaluating a limited number of isolates, combinations of clarithromycin with doxycycline or minocycline, but not with rifampin, were generally synergistic in both ClaS /RifS and ClaR /RifR strains as determined by checkerboard testing. In time-kill assays, all antibiotics, both alone and in combination, reduced viable ClaS /RifS R equi by more than 3 log10 at 24 hours compared with control cultures without antibiotics. Combinations of clarithromycin with doxycycline, minocycline or rifampin induced significantly lower MPC values compared with the individual antimicrobials alone for all ClaS /RifS R equi strains, resulting in a narrower mutant selection window (MSW). However, clarithromycin/rifampin combination did not markedly decrease MPCs of the individual antimicrobials in ClaR /RifR R equi isolates, and the observed decrease in MPCs for doxycycline or minocycline did not generally differ when combined with clarithromycin.

MAIN LIMITATIONS

The number of analysed R equi isolates was limited. In vitro outcomes require clinical confirmation.

CONCLUSIONS

Dual therapy combinations consisting of clarithromycin with doxycycline or minocycline merit consideration as a treatment protocol against R equi in foals due to in vitro synergy. These combination therapies may also minimise the emergence of antimicrobial resistance in cases of rhodococcosis.

Antimicrobial resistance spectrum conferred by pRErm46 of emerging macrolide (multidrug)-resistant Rhodococcus equi

Clonal multidrug resistance recently emerged in Rhodococcus equi, complicating the therapeutic management of this difficult-to-treat animal and human pathogenic actinomycete. The currently spreading multidrug-resistant (MDR) "2287" clone arose in equine farms upon acquisition, and co-selection by mass macrolide-rifampin therapy, of the pRErm46 plasmid carrying the erm(46) macrolides-lincosamides-streptogramins resistance determinant, and an rpoB^S531F mutation. Here, we screened a collection of susceptible and macrolide-rifampin-resistant R. equi from equine clinical cases using a panel of 15 antimicrobials against rapidly growing mycobacteria (RGM), nocardiae and other aerobic actinomycetes (NAA). R. equi -including MDR isolates- was generally susceptible to linezolid, minocycline, tigecycline, amikacin and tobramycin according to Staphylococcus aureus interpretive criteria, plus imipenem, cefoxitin and ceftriaxone based on Clinical & Laboratory Standards Institute (CLSI) guidelines for RGM/NAA. Ciprofloxacin and moxifloxacin were in the borderline category according to European Committee on Antimicrobial Susceptibility Testing (EUCAST) criteria. Molecular analyses linked pRErm46 to significantly increased MICs for trimethoprim-sulfamethoxazole and doxycycline in addition to clarithromycin within the RGM/NAA panel, and to streptomycin, spectinomycin and tetracycline resistance. pRErm46 variants with spontaneous deletions in the class 1 integron (C1I) region, observed in ≈30% of erm(46)-positive isolates, indicated that the newly identified resistances were attributable to C1I's sulfonamide (sul1) and aminoglycoside (aaA9) resistance cassettes and adjacent tetRA(33) determinant. Most MDR isolates carried the rpoB^S531F mutation of the 2287 clone, while different rpoB mutations (S531L, S531Y) detected in two cases suggest the emergence of novel MDR R. equi strains.

Antimicrobial Selection for the Equine Practitioner

Antimicrobial drugs play an important, often central, role in the therapeutic management of mature horses and foals with a variety of illnesses, including those requiring critical care. Antimicrobial use must be based on rational principles involving thorough patient evaluation and sound clinical judgment that indicate a high likelihood that the patient has a bacterial infection and that antimicrobials are indicated to promote recovery. The aim of antimicrobial treatment is to inflict an insult on infecting bacteria sufficient to kill the organism or render it susceptible to inactivation by natural host defenses or the local microenvironment without adversely affecting the patient.

Spread of Multidrug-Resistant Rhodococcus equi, United States

Multidrug resistance has been detected in the animal and zoonotic human pathogen Rhodococcus equi after mass macrolide/rifampin antibioprophylaxis in endemically affected equine farms in the United States. Multidrug-resistant (MDR) R. equi emerged upon acquisition of pRERm46, a conjugative plasmid conferring resistance to macrolides, lincosamides, streptogramins, and, as we describe, tetracycline. Phylogenomic analyses indicate that the increasing prevalence of MDR R. equi since it was first documented in 2002 is caused by a clone, R. equi 2287, attributable to coselection of pRErm46 with a chromosomal rpoB^S531F mutation driven by macrolide/rifampin therapy. pRErm46 spillover to other R. equi genotypes has given rise to a novel MDR clone, G2016, associated with a distinct rpoB^S531Y mutation. Our findings illustrate that overuse of antimicrobial prophylaxis in animals can generate MDR pathogens with zoonotic potential. MDR R. equi and pRErm46-mediated resistance are currently disseminating in the United States and are likely to spread internationally through horse movements.

Association between antimicrobial treatment of subclinical pneumonia in foals and selection of macrolide- and rifampicin-resistant Rhodococcus equi strains at horse-breeding farms in central Kentucky

OBJECTIVE

To compare soil concentrations of macrolide- and rifampicin-resistant Rhodococcus equi strains (MRRE) on horse-breeding farms that used thoracic ultrasonographic screening (TUS) to identify foals with subclinical pneumonia combined with subsequent administration of macrolides and rifampin to affected foals (TUS farms) versus soil concentrations on farms that did not (non-TUS farms), determine whether the combined use of TUS and antimicrobial treatment of subclinically affected foals was associated with soil concentration of MRRE, and assess whether there were temporal effects on soil concentrations of MRRE during the foaling season.

SAMPLES

720 soil samples and 20 completed questionnaires from 20 horse-breeding farms (10 TUS farms and 10 non-TUS farms) in central Kentucky.

PROCEDURES

A questionnaire was used to gather information from participating farms about their 2019 foaling season. Soil samples were collected during January, March, May, and July 2019 for bacterial culture and antimicrobial susceptibility testing to identify any isolates of MRRE. Results were compared for TUS farms versus non-TUS farms. Linear mixed-effects modeling was used to evaluate for potential associations between the soil concentration of MRRE and the use of TUS.

RESULTS

Overall, the sum of the mean soil concentrations of MRRE was significantly higher for TUS farms (8.85 log₁₀-transformed CFUs/g) versus non-TUS farms (7.37 log₁₀-transformed CFUs/g).

CONCLUSIONS AND CLINICAL RELEVANCE

Our findings indicated that farms that use TUS to identify foals with subclinical pneumonia for antimicrobial treatment select for antimicrobial-resistant R equi strains. Because prognosis is worse for foals infected with resistant versus nonresistant strains of R equi, prudent use of antimicrobials to treat foals with subclinical pulmonary lesions attributed to R equi is recommended.

Epidemiology and Molecular Basis of Multidrug Resistance in Rhodococcus equi

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.

Host-directed therapy in foals can enhance functional innate immunity and reduce severity of Rhodococcus equi pneumonia

Pneumonia caused by the intracellular bacterium Rhodococcus equi is an important cause of disease and death in immunocompromised hosts, especially foals. Antibiotics are the standard of care for treating R. equi pneumonia in foals, and adjunctive therapies are needed. We tested whether nebulization with TLR agonists (PUL-042) in foals would improve innate immunity and reduce the severity and duration of pneumonia following R. equi infection. Neonatal foals (n = 48) were nebulized with either PUL-042 or vehicle, and their lung cells infected ex vivo. PUL-042 increased inflammatory cytokines in BAL fluid and alveolar macrophages after ex vivo infection with R. equi. Then, the in vivo effects of PUL-042 on clinical signs of pneumonia were examined in 22 additional foals after intrabronchial challenge with R. equi. Foals infected and nebulized with PUL-042 or vehicle alone had a shorter duration of clinical signs of pneumonia and smaller pulmonary lesions when compared to non-nebulized foals. Our results demonstrate that host-directed therapy can enhance neonatal immune responses against respiratory pathogens and reduce the duration and severity of R. equi pneumonia.

Current Trends in Understanding and Managing Equine Rhodococcosis

The aim of this review was to summarize studies on equine rhodococcosis over the last decade. For many years Rhodococcus equi has remained one of the major health challenges in the equine breeding industry worldwide. Recently, many novel approaches and ideas have been described and some of them were initially implemented into the clinical practice. This study reviews a variety of new information about neonatal susceptibility, clinical appearance, considered and applied diagnostic procedures and treatment alternatives, factors limiting accurate prognosis, ideas regarding environmental management and prophylaxis considerations. Although multiple research were conducted, the main problems such as high morbidity and mortality, a lack of reliable prevention strategies and treatment limitations are still unresolved and require further scientific effort.

Relationship between rifampicin resistance and RpoB substitutions of Rhodococcus equi strains isolated in France

OBJECTIVES

Study of the rifampicin resistance of Rhodococcus equi strains isolated from French horses over a 20-year period.

METHODS

Rifampicin susceptibility was tested by disk diffusion (DD) and broth macrodilution methods, and rpoB gene sequencing and MLST were performed on 40 R. equi strains, 50.0% of which were non-susceptible to rifampicin.

RESULTS

Consistency of results was observed between rifampicin susceptibility testing and rpoB sequencing. Strains non-susceptible to rifampicin by DD had a substitution at one of the sites (Asp516, His526 and Ser531) frequently encountered and conferring rifampicin resistance. High-level resistance was correlated with His526Asp or Ser531Leu substitutions; low-level resistance was correlated with Asp516Tyr substitution, a novel substitution for R. equi. Strains susceptible to rifampicin by DD showed no substitution in the three sites, except for two strains carrying, respectively, the His526Asn and Asp516Val substitutions (previously correlated with low-level rifampicin resistance). Both strains were isolated from an animal from which ten other strains were also isolated and found to be rifampicin-non-susceptible by DD. MLST showed the presence of 10 STs (including the novel ST43), but no association was observed with rifampicin resistance.

CONCLUSIONS

This study confirms that certain substitutions in RpoB are more likely to confer high- or low-level rifampicin resistance, describes a new substitution conferring rifampicin resistance in R. equi and suggests non-clonal dissemination of rifampicin-resistant strains in France. Standard DD may miss strains with a low-level rifampicin-resistant substitution; further studies are needed to remedy the absence of R. equi-specific clinical breakpoints.

The novel and transferable erm(51) gene confers macrolides, lincosamides and streptogramins B (MLSB ) resistance to clonal Rhodococcus equi in the environment

The use of mass antimicrobial treatment has been linked to the emergence of antimicrobial resistance in human and animal pathogens. Using whole-genome single-molecule real-time (SMRT) sequencing, we characterized genomic variability of multidrug-resistant Rhodococcus equi isolated from soil samples from 100 farms endemic for R. equi infections in Kentucky. We discovered the novel erm(51)-encoding resistance to MLS_B in R. equi isolates from soil of horse-breeding farms. Erm(51) is inserted in a transposon (TnErm51) that is associated with a putative conjugative plasmid (pRErm51), a mobilizable plasmid (pMobErm51), or both enabling horizontal gene transfer to susceptible organisms and conferring high levels of resistance against MLS_B in vitro. This new resistant genotype also carries a previously unidentified rpoB mutation conferring resistance to rifampicin. Isolates carrying both vapA and erm(51) were rarely found, indicating either a recent acquisition of erm(51) and/or impaired survival when isolates carry both genes. Isolates carrying erm(51) are closely related genetically and were likely selected by antimicrobial exposure in the environment.

Horizontal Spread of Rhodococcus equi Macrolide Resistance Plasmid pRErm46 across Environmental Actinobacteria

Conjugation is one of the main mechanisms involved in the spread and maintenance of antibiotic resistance in bacterial populations. We recently showed that the emerging macrolide resistance in the soilborne equine and zoonotic pathogen Rhodococcus equi is conferred by the erm(46) gene carried on the 87-kb conjugative plasmid pRErm46. Here, we investigated the conjugal transferability of pRErm46 to 14 representative bacteria likely encountered by R. equi in the environmental habitat. In vitro mating experiments demonstrated conjugation to different members of the genus Rhodococcus as well as to Nocardia and Arthrobacter spp. at frequencies ranging from ∼10^-2 to 10^-6 pRErm46 transfer was also observed in mating experiments in soil and horse manure, albeit at a low frequency and after prolonged incubation at 22 to 30°C (environmental temperatures), not 37°C. All transconjugants were able to transfer pRErm46 back to R. equi Conjugation could not be detected with Mycobacterium or Corynebacterium spp. or several members of the more distant phylum Firmicutes such as Enterococcus, Streptococcus, or Staphylococcus Thus, the pRErm46 host range appears to span several actinobacterial orders with certain host restriction within the Corynebacteriales All bacterial species that acquired pRErm46 expressed increased macrolide resistance with no significant deleterious impact on fitness, except in the case of Rhodococcus rhodnii Our results indicate that actinobacterial members of the environmental microbiota can both acquire and transmit the R. equi pRErm46 plasmid and thus potentially contribute to the maintenance and spread of erm(46)-mediated macrolide resistance in equine farms.IMPORTANCE This study demonstrates the efficient horizontal transfer of the Rhodococcus equi conjugative plasmid pRErm46, recently identified as the cause of the emerging macrolide resistance among equine isolates of this pathogen, to and from different environmental Actinobacteria, including a variety of rhodococci as well as Nocardia and Arthrobacter spp. The reported data support the notion that environmental microbiotas may act as reservoirs for the endemic maintenance of antimicrobial resistance in an antibiotic pressurized farm habitat.

Efficacy of the combination of doxycycline and azithromycin for the treatment of foals with mild to moderate bronchopneumonia

BACKGROUND

Given the importance of rifampin in treatment protocols for tuberculosis in people, its use in veterinary medicine is under increasing scrutiny in some countries and alternatives might be needed in the near future.

OBJECTIVES

This study was set up to evaluate whether azithromycin combined with doxycycline is effective for the treatment of bronchopneumonia in foals and noninferior to the combination of azithromycin and rifampin.

STUDY DESIGN

This is a controlled, randomised and double-blinded clinical trial. Two hundred and forty foals on a farm endemic for infections caused by Rhodococcus equi were involved.

METHODS

Foals with ultrasonographic pulmonary lesions (lesion score 10-15 cm) were allocated to 3 groups: azithromycin-doxycycline orally (n = 81); azithromycin-rifampin orally (n = 81); or untreated controls (n = 78). Physical examination and thoracic ultrasonography were performed by individuals unaware of treatment group assignment. Foals that worsened were considered treatment failures and removed from the study.

RESULTS

The proportion of foals that recovered was significantly higher for foals treated with azithromycin-doxycycline (80 of 81) or azithromycin-rifampin (81 of 81) compared with that of control foals (57 of 78). The difference in the percentage of efficacy of azithromycin-rifampin vs azithromycin-doxycycline was 1.2% (90% CI = -0.78% to 3.5%) which did not cross the predetermined noninferiority limit of 10%. Therefore, azithromycin-doxycycline was noninferior to azithromycin-rifampin within the predetermined noninferiority limit.

MAIN LIMITATIONS

The study was performed on a single farm, and recovery rates may differ in other locations.

CONCLUSION

Azithromycin-doxycycline was noninferior to azithromycin-rifampin for the treatment of bronchopneumonia in this farm.

A Common Practice of Widespread Antimicrobial Use in Horse Production Promotes Multi-Drug Resistance

The practice of prophylactic administration of a macrolide antimicrobial with rifampin (MaR) to apparently healthy foals with pulmonary lesions identified by thoracic ultrasonography (i.e., subclinically pneumonic foals) is common in the United States. The practice has been associated epidemiologically with emergence of R. equi resistant to MaR. Here, we report direct evidence of multi-drug resistance among foals treated with MaR. In silico and in vitro analysis of the fecal microbiome and resistome of 38 subclinically pneumonic foals treated with either MaR (n = 19) or gallium maltolate (GaM; n = 19) and 19 untreated controls was performed. Treatment with MaR, but not GaM, significantly decreased fecal microbiota abundance and diversity, and expanded the abundance and diversity of antimicrobial resistance genes in feces. Soil plots experimentally infected with Rhodococcus equi (R. equi) and treated with MaR selected for MaR-resistant R. equi, whereas MaR-susceptible R. equi out-competed resistant isolates in GaM-treated or untreated plots. Our results indicate that MaR use promotes multi-drug resistance in R. equi and commensals that are shed into their environment where they can persist and potentially infect or colonize horses and other animals.

Rhodococcus equi Joint Sepsis and Osteomyelitis Is Associated With a Grave Prognosis in Foals

The most common pathologic manifestation of Rhodococcus equi, a gram-positive, facultative intracellular bacterium, is pyogranulomatous pneumonia in foals and weanlings. Hematogenous spread of bacteria may subsequently occur, resulting in joint sepsis, osteomyelitis, or subcutaneous abscessation. Medical records from horses presenting to the Cornell University Equine Hospital from 1998 to 2018 were reviewed for cases diagnosed with R. equi joint and/or bone infection, and information about case progression and outcome were analyzed. We hypothesized that, despite advances in diagnostic imaging, antimicrobials and antimicrobial delivery methods, the prognosis for R. equi joint sepsis and osteomyelitis remains grave for athletic activity and poor for survival. The 12 cases that met the review criteria had a mortality rate of 84% (10/12), with one case lost to follow up after discharge and one case discharged with a grave prognosis for athleticism.

Clonal Confinement of a Highly Mobile Resistance Element Driven by Combination Therapy in Rhodococcus equi

MDR clades arise upon acquisition of resistance traits, but the determinants of their clonal expansion remain largely undefined. Taking advantage of the unique features of Rhodococcus equi infection control in equine farms, involving the same dual antibiotic treatment since the 1980s (a macrolide and rifampin), this study sheds light into the determinants of multiresistance clonality and the importance of combination therapy in limiting the dissemination of mobile resistance elements. Clinically effective therapeutic alternatives against R. equi foal pneumonia are currently lacking, and the identified macrolide-rifampin MDR clone 2287 has serious implications. Still at early stages of evolution and local spread, R. equi 2287 may disseminate globally, posing a significant threat to the equine industry and, also, public health due to the risk of zoonotic transmission. The characterization of the 2287 clone and its resistance determinants will enable targeted surveillance and control interventions to tackle the emergence of MDR R. equi.

Antibiotic use has been linked to changes in the population structure of human pathogens and the clonal expansion of multidrug-resistant (MDR) strains among healthcare- and community-acquired infections. Here we present a compelling example in a veterinary pathogen, Rhodococcus equi, the causative agent of a severe pulmonary infection affecting foals worldwide. We show that the erm(46) gene responsible for emerging macrolide resistance among equine R. equi isolates in the United States is part of a 6.9-kb transposable element, TnRErm46, actively mobilized by an IS481 family transposase. TnRErm46 is carried on an 87-kb conjugative plasmid, pRErm46, transferable between R. equi strains at frequencies up to 10⁻³. The erm(46) gene becomes stabilized in R. equi by pRErm46’s apparent fitness neutrality and wholesale TnRErm46 transposition onto the host genome. This includes the conjugally exchangeable pVAPA virulence plasmid, enabling the possibility of cotransfer of two essential traits for survival in macrolide-treated foals in a single mating event. Despite its high horizontal transfer potential, phylogenomic analyses show that erm(46) is paradoxically confined to a specific R. equi clone, 2287. R. equi 2287 also carries a unique rpoB^S531F mutation conferring high-level resistance to rifampin, systematically administered together with macrolides against rhodococcal pneumonia on equine farms. Our data illustrate that under sustained combination therapy, several independent “founder” genetic events are concurrently required for resistance, limiting not only its emergence but also, crucially, horizontal spread, ultimately determining multiresistance clonality.

Effect of Macrolide and Rifampin Resistance on Fitness of Rhodococcus equi during Intramacrophage Replication and In Vivo

The soil-dwelling, saprophytic actinomycete Rhodococcus equi is a facultative intracellular pathogen of macrophages and causes severe bronchopneumonia when inhaled by susceptible foals. Standard treatment for R. equi disease is dual-antimicrobial therapy with a macrolide and rifampin. Thoracic ultrasonography and early treatment with antimicrobials prior to the development of clinical signs are used as means of controlling endemic R. equi infection on many farms. Concurrently with the increased use of macrolides and rifampin for chemoprophylaxis and the treatment of subclinically affected foals, a significant increase in the incidence of macrolide- and rifampin-resistant R. equi isolates has been documented. Previously, our laboratory demonstrated decreased fitness of R. equi strains that were resistant to macrolides, rifampin, or both, resulting in impaired in vitro growth in iron-restricted media and in soil. The objective of this study was to examine the effect of macrolide and/or rifampin resistance on intracellular replication of R. equi in equine pulmonary macrophages and in an in vivo mouse infection model in the presence and absence of antibiotics. In equine macrophages, the macrolide-resistant strain did not increase in bacterial numbers over time and the dual macrolide- and rifampin-resistant strain exhibited decreased proliferation compared to the susceptible isolate. In the mouse model, in the absence of antibiotics, the susceptible R. equi isolate outcompeted the macrolide- or rifampin-resistant strains.

Transfusion With 2 L of Hyperimmune Plasma is Superior to Transfusion of 1 L or Less for Protecting Foals Against Subclinical Pneumonia Attributed to Rhodococcus equi

Transfusing foals with Rhodococcus equi hyperimmune plasma (REHIP) is a standard practice at many horse-breeding farms to help prevent R. equi pneumonia. At many large breeding farms, pneumonia is most commonly recognized as subclinical based on thoracic ultrasonography findings. The efficacy of REHIP transfusion and the impact of the volume of plasma transfused for reducing the cumulative incidence of subclinical R. equi pneumonia are unknown. A retrospective cohort study was conducted among foals born and residing through weaning at a large breeding farm. Foals were transfused with either 0 L (n = 2 foals), 1 L (n = 85 foals), or 2 L (n = 62 foals) of REHIP within 36 hours of birth. Volume transfused was principally based on intended use of the foals. All foals at the ranch were routinely screened using thoracic ultrasonography at 5, 7, and 9 weeks of age to detect subclinical pneumonia attributed to R. equi based on farm history. The proportion of the foals receiving < 1 L REHIP that developed subclinical pneumonia (32%; 26/82) was significantly (P = .0068; chi-squared test) greater than that among foals transfused with 2 L of REHIP (12%; 8/68). Despite the important limitations of this observational study, it provides evidence supporting the need for well-designed clinical trials to evaluate the impact of the use and dose of REHIP for preventing subclinical pneumonia. Reducing the incidence of subclinical pneumonia is important because reducing antibiotic treatment of subclinical cases will decrease selection pressure for antimicrobial resistance in R. equi.

In vitro evaluation of complement deposition and opsonophagocytic killing of Rhodococcus equi mediated by poly-N-acetyl glucosamine hyperimmune plasma compared to commercial plasma products

Background

The bacterium Rhodococcus equi can cause severe pneumonia in foals. The absence of a licensed vaccine and limited effectiveness of commercial R. equi hyperimmune plasma (RE‐HIP) create a great need for improved prevention of this disease.

Hypothesis

Plasma hyperimmune to the capsular polysaccharide poly‐N‐acetyl glucosamine (PNAG) would be significantly more effective than RE‐HIP at mediating complement deposition and opsonophagocytic killing (OPK) of R. equi.

Animals

Venipuncture was performed on 9 Quarter Horses.

Methods

The ability of the following plasma sources to mediate complement component 1 (C1) deposition onto either PNAG or R. equi was determined by ELISA: (1) PNAG hyperimmune plasma (PNAG‐HIP), (2) RE‐HIP, and (3) standard non‐hyperimmune commercial plasma (SP). For OPK, each plasma type was combined with R. equi, equine complement, and neutrophils isolated from horses (n = 9); after 4 hours, the number of R. equi in each well was determined by quantitative culture. Data were analyzed using linear mixed‐effects regression with significance set at P < .05.

Results

The PNAG‐HIP and RE‐HIP were able to deposit significantly (P < .05) more complement onto their respective targets than the other plasmas. The mean proportional survival of R. equi opsonized with PNAG‐HIP was significantly (P < .05) less (14.7%) than that for SP (51.1%) or RE‐HIP (42.2%).

Conclusions and Clinical Importance

Plasma hyperimmune to PNAG is superior to RE‐HIP for opsonizing and killing R. equi in vitro. Comparison of these 2 plasmas in field trials is warranted because of the reported incomplete effectiveness of RE‐HIP.

Identification of macrolide- and rifampicin-resistant Rhodococcus equi in environmental samples from equine breeding farms in central Kentucky during 2018

Rhodococcus equi causes severe pneumonia in foals and is most often recognized in people as an opportunistic pathogen. Longitudinal studies examining antimicrobial-resistant R. equi from environmental samples are lacking. We hypothesized that antimicrobial-resistant R. equi would be detectable in the ground (pasture soil or stall bedding) and air at breeding farms with previous documentation of foals infected with resistant isolates, and that concentrations of resistant isolates would increase over time during the foaling season. In this prospective cohort study, ground and air samples were collected from stalls and paddocks in January, March, May and July of 2018 at 10 horse-breeding farms with history of foal pneumonia attributed to macrolide- or Rifampicin-resistant R. equi. Environmental samples were cultured in the presence and absence of macrolides and Rifampicin to select for resistant organisms. Data were analyzed with linear mixed-effects and Hurdle models. Concentrations of total R. equi in bedding or air of stalls were significantly (P < 0.05) higher in January than other months. The proportion of resistant R. equi in soil samples from paddocks was significantly (P < 0.05) higher than stall bedding during all months. For each month, air samples from paddocks had a significantly (P < 0.05) higher proportion of resistant isolates than those from stalls. Fifty-five percent of resistant soil isolates and 34% of resistant air isolates were considered virulent by identification of the vapA gene. Concentrations of resistant R. equi isolates did not increase over time during the foaling season. Antimicrobial-resistant R. equi can persist in the environment at farms with a history of pneumonia caused by resistant R. equi infections, and exposure to resistant isolates in paddocks and stalls appears stable during the foaling season. Resistant isolates in the environment not only pose a risk for disease but also can serve as a repository for dissemination of resistance genes.

Effect of Macrolide and Rifampin Resistance on the Fitness of Rhodococcus equi

Rhodococcus equi is a leading cause of severe pneumonia in foals. Standard treatment is dual antimicrobial therapy with a macrolide and rifampin, but the emergence of macrolide- and rifampin-resistant R. equi isolates is an increasing problem. The objective of this study was to determine the effect of macrolide and/or rifampin resistance on fitness of R. equi Three unique isogenic sets were created, each consisting of four R. equi strains, as follows: a susceptible parent isolate, strains resistant to macrolides or rifampin, and a dual macrolide- and rifampin-resistant strain. Each isogenic set's bacterial growth curve was generated in enriched medium, minimal medium (MM), and minimal medium without iron (MM-I). Bacterial survival in soil was analyzed over 12 months at -20°C, 4°C, 25°C, and 37°C, and the ability of these strains to retain antimicrobial resistance during sequential subculturing was determined. Insertion of the mobile element conferring macrolide resistance had minimal effect on in vitro growth. However, two of three rpoB mutations conferring rifampin resistance resulted in a decreased growth rate in MM. In soil, macrolide- or rifampin-resistant R. equi strains exhibited limited growth compared to that of the susceptible R. equi isolate at all temperatures except -20°C. During subculturing, macrolide resistance was lost over time, and two of three rpoB mutations reverted to the wild-type form. The growth of rifampin-resistant R. equi colonies is delayed under nutrient restriction. In soil, possession of rifampin or macrolide resistance results in decreased fitness. Both macrolide and rifampin resistance can be lost after repeated subculturing.IMPORTANCE This work advances our understanding of the opportunistic environmental pathogen Rhodococcus equi, a disease agent affecting horses and immunocompromised people. R. equi is one of the most common causes of severe pneumonia in young horses. For decades, the standard treatment for R. equi pneumonia in horses has been dual antimicrobial therapy with a macrolide and rifampin; effective alternatives to this combination are lacking. The World Health Organization classifies these antimicrobial agents as critically important for human medicine. Widespread macrolide and rifampin resistance in R. equi isolates is a major emerging problem for the horse-breeding industry and might also adversely impact human health if resistant strains infect people or transfer resistance mechanisms to other pathogens. This study details the impact of antimicrobial resistance on R. equi fitness, a vital step for understanding the ecology and epidemiology of resistant R. equi isolates, and will support development of novel strategies to combat antimicrobial resistance.

Emergence of Resistance to Macrolides and Rifampin in Clinical Isolates of Rhodococcus equi from Foals in Central Kentucky, 1995 to 2017

The objective of this study was to determine the prevalence of Rhodococcus equi strains resistant to macrolides and rifampin over time in clinical samples from foals submitted to diagnostic laboratories in central Kentucky. We performed a retrospective observational study of all clinical samples from foals that were submitted to veterinary diagnostic laboratories in Kentucky between January 1995 and December 2017. Samples were included if the R. equi bacterium was cultured and tested for in vitro susceptibility to erythromycin or rifampin. In vitro susceptibility testing to erythromycin was available for 2,169 isolates of R. equi, while susceptibility testing to both erythromycin and rifampin was available for 1,681 isolates. Rifampin resistance was first detected in 2000, and erythromycin resistance was first detected in 2004. Between 1995 and 2006, the proportion of resistant isolates of R. equi was 0.7% for erythromycin and 2.3% for rifampin. There was a significant (P < 0.001) increase in the proportion of resistant R. equi between 2007 and 2017, with 13.6% of isolates being resistant to erythromycin and 16.1% being resistant to rifampin. Between 2007 and 2017, isolates of R. equi resistant to erythromycin or rifampin were significantly less likely to be isolated from feces than from the respiratory tract, other soft tissues, or musculoskeletal infections. The considerable increase in the prevalence of isolates of R. equi resistant to macrolides and rifampin since 2007 is of concern for both human and animal health.

Current taxonomy of Rhodococcus species and their role in infections

Rhodococcus is a genus of obligate aerobic, Gram-positive, partially acid-fast, catalase-positive, non-motile, and none-endospore bacteria. The genus Rhodococcus was first introduced by Zopf. This bacterium can be isolated from various sources of the environment and can grow well in non-selective medium. A large number of phenotypic characterizations are used to compare different species of the genus Rhodococcus, and these tests are not suitable for accurate identification at the genus and species level. Among nucleic acid-based methods, the most powerful target gene for revealing reliable phylogenetic relationships is 16S ribosomal RNA gene (16S rRNA gene) sequence analysis, but this gene is unable to differentiation some of Rhodococcus species. To date, whole genome sequencing analysis has solved taxonomic complexities in this genus. Rhodococcus equi is the major cause of foal pneumonia, and its implication in human health is related to cases in immunocompromised patients. Macrolide family together with rifampicin is one of the most effective antibiotic agents for treatment rhodococcal infections.

Antimicrobial Resistance in Rhodococcus equi

Pneumonia caused by Rhodococcus equi remains an important cause of disease and death in foals. The combination of a macrolide (erythromycin, azithromycin, or clarithromycin) with rifampin has been the recommended treatment for foals with clinical signs of infection caused by R. equi since the early 1980s with, until recently, only rare reports of resistance. Resistance to macrolides and rifampin in isolates of R. equi cultured from horses is increasing, with isolates resistant to all macrolides and rifampin now being cultured from up to 40% of infected foals at some farms. This text reviews the available data regarding antimicrobial resistance in R. equi , with emphasis on the molecular mechanisms of the recent emergence of resistance to macrolides and rifampin in equine isolates of R. equi .

The Rhodococcus equi virulence protein VapA disrupts endolysosome function and stimulates lysosome biogenesis

Rhodococcus equi (R. equi) is an important pulmonary pathogen in foals that often leads to the death of the horse. The bacterium harbors a virulence plasmid that encodes numerous virulence‐associated proteins (Vaps) including VapA that is essential for intracellular survival inside macrophages. However, little is known about the precise function of VapA. Here, we demonstrate that VapA causes perturbation to late endocytic organelles with swollen endolysosome organelles having reduced Cathepsin B activity and an accumulation of LBPA, LC3 and Rab7. The data are indicative of a loss of endolysosomal function, which leads cells to upregulate lysosome biogenesis to compensate for the loss of functional endolysosomes. Although there is a high degree of homology of the core region of VapA to other Vap proteins, only the highly conserved core region of VapA, and not VapD of VapG, gives the observed effects on endolysosomes. This is the first demonstration of how VapA works and implies that VapA aids R. equi survival by reducing the impact of lysosomes on phagocytosed bacteria.