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Hu B, Gao S, Zhang H, Li Q, Li G, Zhang S, Xing Y, Huang Y, Han S, Tian Y, Zhang W, He H. Whole-genome sequencing and pathogenicity analysis of Rhodococcus equi isolated in horses. BMC Vet Res 2024; 20:362. [PMID: 39129003 PMCID: PMC11318318 DOI: 10.1186/s12917-024-04167-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2024] [Accepted: 07/01/2024] [Indexed: 08/13/2024] Open
Abstract
BACKGROUND Rhodococcus equi (R. equi) is a Gram-positive zoonotic pathogen that frequently leads to illness and death in young horses (foals). This study presents the complete genome sequence of R. equi strain BJ13, which was isolated from a thoroughbred racehorse breeding farm in Beijing, China. RESULTS The BJ13 genome has a length of 5.30 Mb and consists of a complete chromosome and a plasmid measuring 5.22 Mb and 0.08 Mb, respectively. We predicted 4,929 coding gene open reading frames, along with 52 tRNAs and 12 rRNAs. Through analysis of mobile genetic elements, we identified 6 gene islands and 1 prophage gene. Pathogenic system analysis predicted the presence of 418 virulence factors and 225 drug resistance genes. Secretion system analysis revealed the prediction of 297 secreted proteins and 1,106 transmembrane proteins. BJ13 exhibits genomic features, virulence-associated genes, potential drug resistance, and a virulence plasmid structure that may contribute to the evolution of its pathogenicity. Lastly, the pathogenicity of the isolated strain was assessed through animal experiments, which resulted in inflammatory reactions or damage in the lungs, liver, and spleen of mice. Moreover, by the 7th day post-infection, the mortality rate of the mice reached 50.0%, indicating complex immune regulatory mechanisms, including overexpression of IL-10 and increased production of pro-inflammatory cytokines like TNF-α. These findings validate the strong pathogenicity of the isolated strain and provide insights for studying the pathogenic mechanisms of Rhodococcus equi infection. CONCLUSIONS The complete genome sequence of R. equi strain BJ13 provides valuable insights into its genomic characteristics, virulence potential, drug resistance, and secretion systems. The strong pathogenicity observed in animal experiments underscores the need for further investigation into the pathogenic mechanisms of R. equi infection.
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Affiliation(s)
- Bin Hu
- College of Animal Science and Veterinary Medicine, Henan Institute of Science and Technology, Xinxiang, China
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Sichao Gao
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Anhui University of Science and Technology, Huainan, China
| | - Hao Zhang
- University of Chinese Academy of Sciences, Beijing, China
| | - Qiaoqiao Li
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Anhui University of Science and Technology, Huainan, China
| | - Gaojian Li
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Shuairan Zhang
- College of Shenyang Institute of Technology, Shenyang, Liaoning, China
| | - Yanan Xing
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yanyi Huang
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Shuyi Han
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Ying Tian
- Beijing Wildlife Rescue and Rehabilitation Center, Beijing, China
| | - Wei Zhang
- Beijing Wildlife Rescue and Rehabilitation Center, Beijing, China
| | - Hongxuan He
- College of Animal Science and Veterinary Medicine, Henan Institute of Science and Technology, Xinxiang, China.
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Alvarez Narvaez S, Sanchez S. Exploring the Accessory Genome of Multidrug-Resistant Rhodococcus equi Clone 2287. Antibiotics (Basel) 2023; 12:1631. [PMID: 37998833 PMCID: PMC10669575 DOI: 10.3390/antibiotics12111631] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 11/15/2023] [Accepted: 11/16/2023] [Indexed: 11/25/2023] Open
Abstract
Decades of antimicrobial overuse to treat respiratory disease in foals have promoted the emergence and spread of zoonotic multidrug-resistant (MDR) Rhodococcus equi worldwide. Three main R. equi MDR clonal populations-2287, G2106, and G2017-have been identified so far. However, only clones 2287 and G2016 have been isolated from sick animals, with clone 2287 being the main MDR R. equi recovered. The genetic mechanisms that make this MDR clone superior to the others at infecting foals are still unknown. Here, we performed a deep genetic characterization of the accessory genomes of 207 R. equi isolates, and we describe IME2287, a novel genetic element in the accessory genome of clone 2287, potentially involved in the maintenance and spread of this MDR population over time. IME2287 is a putative self-replicative integrative mobilizable element (IME) carrying a DNA replication and partitioning operon and genes encoding its excision and integration from the R. equi genome via a serine recombinase. Additionally, IME2287 encodes a protein containing a Toll/interleukin-1 receptor (TIR) domain that may inhibit TLR-mediated NF-kB signaling in the host and a toxin-antitoxin (TA) system, whose orthologs have been associated with antibiotic resistance/tolerance, virulence, pathogenicity islands, bacterial persistence, and pathogen trafficking. This new set of genes may explain the success of clone 2287 over the other MDR R. equi clones.
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Affiliation(s)
- Sonsiray Alvarez Narvaez
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA 30602, USA
| | - Susan Sanchez
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA 30602, USA
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Higgins C, Huber L. Rhodococcus equi: challenges to treat infections and to mitigate antimicrobial resistance. J Equine Vet Sci 2023:104845. [PMID: 37295760 DOI: 10.1016/j.jevs.2023.104845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 06/01/2023] [Accepted: 06/03/2023] [Indexed: 06/12/2023]
Abstract
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.
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Affiliation(s)
- Courtney Higgins
- Department of Pathobiology, College of Veterinary Medicine, Auburn University, 1130 Wire Road, Auburn, Alabama, USA 36832.
| | - Laura Huber
- Department of Pathobiology, College of Veterinary Medicine, Auburn University, 1130 Wire Road, Auburn, Alabama, USA 36832.
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4
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Swanner KKD, Patel R, Nguyen TT, Patel FN, Magadia R, Rifai AO, Davenport M. A Rare Presentation of Rhodococcus Equi Bacteremia as a Result of Right Upper Arm Cellulitis: A Case Report and Literature Review. Cureus 2023; 15:e38295. [PMID: 37255906 PMCID: PMC10226525 DOI: 10.7759/cureus.38295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2023] [Accepted: 04/29/2023] [Indexed: 06/01/2023] Open
Abstract
Rhodococcus equi is an emerging opportunistic pathogen in immunocompromised patients. Owing to its resemblance to Mycobacterium, Nocardia, and Corynebacterium, R. equi is frequently misdiagnosed as a contaminant, which can result in treatment delays. A 65-year-old man with a history of end-stage renal disease (ESRD) presented to the emergency room with pain and increased swelling in his right upper extremity. Shortly after he arrived in the emergency room, his condition deteriorated. Intravenous vancomycin was administered after collecting blood cultures. The blood cultures grew Rhodococcus equi, and oral azithromycin and oral rifampin were added for a 14-day course of treatment. The patient recovered without any further complications and was subsequently discharged home. R. equi is a partially acid-fast actinomycete that spreads through contact with grazing animals and contaminated soil. R. equi invades macrophages to survive and causes infection within a host. In this particular case, the patient worked on a farm taking care of goats. He was exposed to the bacteria after falling and sustaining multiple lacerations to the right arm. This case is unique due to the development of bacteremia with R. equi, an uncommon cause of bacteremia that led to cardiopulmonary arrest. The treatment with oral azithromycin combined with oral rifampin and intravenous vancomycin was effective for the complete resolution of the infection.
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Affiliation(s)
| | - Riya Patel
- College of Medicine, Alabama College of Osteopathic Medicine, Dothan, USA
| | - Thuy T Nguyen
- Internal Medicine, Alabama College of Osteopathic Medicine, Dothan, USA
| | - Felicia N Patel
- Internal Medicine, Alabama College of Osteopathic Medicine, Dothan, USA
| | - Raul Magadia
- Department of Infectious Diseases, Regional Medical Center, Anniston, USA
| | - Ahmad O Rifai
- Nephrology, The Virtual Nephrologist, Panama City Beach, USA
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5
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Xu X, Liang H, Song Y, Wang D, Wei Q, Wang Y. HIV complicated with Rhodococcus equi infection: A case report. INFECTIOUS MEDICINE 2022; 1:281-284. [DOI: 10.1016/j.imj.2022.10.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/24/2023]
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Rivera-Velez A, Huber L, Sinha S, Cohen ND. Fitness cost conferred by the novel erm(51) and rpoB mutation on environmental multidrug resistant-Rhodococcus equi. Vet Microbiol 2022; 273:109531. [PMID: 35944389 DOI: 10.1016/j.vetmic.2022.109531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 08/02/2022] [Accepted: 08/03/2022] [Indexed: 11/25/2022]
Abstract
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. equierm(51)+, rpoB+) under different nutrient conditions. Bacterial growth curves were generated for 3 MDR-R. equierm(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. equierm(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. equierm(51)+, rpoB+ is reduced relative to susceptible isolates; however, under nutrient-restricted conditions MDR-R. equierm(51)+, rpoB+ isolates grow similarly to susceptible isolates. These findings indicate that MDR-R. equierm(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.
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Affiliation(s)
- Andres Rivera-Velez
- Department of Large Animal Clinical Sciences, College of Veterinary Medicine & Biomedical Sciences, Texas A&M University, College Station, TX 77843, USA.
| | - Laura Huber
- Pathobiology Department, College of Veterinary Medicine, Auburn University, 1130 wire Rd, Auburn, AL 36832, USA.
| | - Samiran Sinha
- Department of Statistics, Texas A&M University, College Station, TX 77843, USA.
| | - Noah D Cohen
- Department of Large Animal Clinical Sciences, College of Veterinary Medicine & Biomedical Sciences, Texas A&M University, College Station, TX 77843, USA.
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7
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Kahn SK, Cohen ND, Bordin AI, Coleman MC, Heird JC, Welsh TH. Transfusion of hyperimmune plasma for protecting foals against Rhodococcus equi pneumonia. Equine Vet J 2022; 55:376-388. [PMID: 35834170 DOI: 10.1111/evj.13858] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 07/08/2022] [Indexed: 11/03/2022]
Abstract
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.
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Affiliation(s)
- Susanne K Kahn
- Equine Infectious Disease Laboratory, Department of Large Animal Clinical Sciences, College of Veterinary Medicine & Biomedical Sciences, Texas A&M University, College Station, TX, USA
| | - Noah D Cohen
- Equine Infectious Disease Laboratory, Department of Large Animal Clinical Sciences, College of Veterinary Medicine & Biomedical Sciences, Texas A&M University, College Station, TX, USA
| | - Angela I Bordin
- Equine Infectious Disease Laboratory, Department of Large Animal Clinical Sciences, College of Veterinary Medicine & Biomedical Sciences, Texas A&M University, College Station, TX, USA
| | - Michelle C Coleman
- Department of Large Animal Clinical Sciences, College of Veterinary Medicine & Biomedical Sciences, Texas A&M University, College Station, TX, USA
| | - James C Heird
- Department of Animal Science, College of Agriculture & Life Sciences, Texas A&M University, College Station, TX, USA
| | - Thomas H Welsh
- Department of Animal Science, College of Agriculture & Life Sciences, Texas A&M University, College Station, TX, USA
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8
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Narváez SÁ, Fernández I, Patel NV, Sánchez S. Novel Quantitative PCR for Rhodococcus equi and Macrolide Resistance Detection in Equine Respiratory Samples. Animals (Basel) 2022; 12:1172. [PMID: 35565598 PMCID: PMC9099730 DOI: 10.3390/ani12091172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 04/22/2022] [Accepted: 04/28/2022] [Indexed: 11/16/2022] Open
Abstract
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.
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Affiliation(s)
- Sonsiray Álvarez Narváez
- Poultry Diagnostic and Research Center, Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, GA 30602, USA
| | - Ingrid Fernández
- Athens Veterinary Diagnostic Laboratory, Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA 30602, USA; (I.F.); (N.V.P.); (S.S.)
| | - Nikita V. Patel
- Athens Veterinary Diagnostic Laboratory, Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA 30602, USA; (I.F.); (N.V.P.); (S.S.)
| | - Susan Sánchez
- Athens Veterinary Diagnostic Laboratory, Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA 30602, USA; (I.F.); (N.V.P.); (S.S.)
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9
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Cohen ND, Flores-Ahlschewde P, Gonzales GM, Kahn SK, da Silveira BP, Bray JM, King EE, Blair CC, Bordin AI. Fecal concentration of Rhodococcus equi determined by quantitative polymerase chain reaction of rectal swab samples to differentiate foals with pneumonia from healthy foals. J Vet Intern Med 2022; 36:1146-1151. [PMID: 35475581 PMCID: PMC9151472 DOI: 10.1111/jvim.16438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 04/04/2022] [Accepted: 04/12/2022] [Indexed: 11/29/2022] Open
Abstract
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.
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Affiliation(s)
- Noah D Cohen
- Equine Infectious Disease Laboratory, Department of Large Animal Clinical Sciences, College of Veterinary Medicine & Biomedical Sciences, Texas A&M University, College Station, Texas, USA
| | | | - Giana M Gonzales
- Equine Infectious Disease Laboratory, Department of Large Animal Clinical Sciences, College of Veterinary Medicine & Biomedical Sciences, Texas A&M University, College Station, Texas, USA
| | - Susanne K Kahn
- Equine Infectious Disease Laboratory, Department of Large Animal Clinical Sciences, College of Veterinary Medicine & Biomedical Sciences, Texas A&M University, College Station, Texas, USA
| | - Bibiana Petri da Silveira
- Equine Infectious Disease Laboratory, Department of Large Animal Clinical Sciences, College of Veterinary Medicine & Biomedical Sciences, Texas A&M University, College Station, Texas, USA
| | - Jocelyne M Bray
- Equine Infectious Disease Laboratory, Department of Large Animal Clinical Sciences, College of Veterinary Medicine & Biomedical Sciences, Texas A&M University, College Station, Texas, USA
| | - Emily E King
- Rood & Riddle Equine Hospital in Saratoga, Saratoga Springs, New York, USA
| | - Caroline C Blair
- Equine Infectious Disease Laboratory, Department of Large Animal Clinical Sciences, College of Veterinary Medicine & Biomedical Sciences, Texas A&M University, College Station, Texas, USA
| | - Angela I Bordin
- Equine Infectious Disease Laboratory, Department of Large Animal Clinical Sciences, College of Veterinary Medicine & Biomedical Sciences, Texas A&M University, College Station, Texas, USA
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10
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Bordin AI, Huber L, Sanz M, Cohen N. Rhodococcus equi Foal Pneumonia: Update on Epidemiology, Immunity, Treatment, and Prevention. Equine Vet J 2022; 54:481-494. [PMID: 35188690 DOI: 10.1111/evj.13567] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 02/03/2022] [Accepted: 02/17/2022] [Indexed: 11/25/2022]
Abstract
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.
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Affiliation(s)
- Angela I Bordin
- Equine Infectious Disease Laboratory, Department of Large Animal Clinical Sciences, College of Veterinary Medicine & Biomedical Sciences, Texas A&M University, College Station, Texas, 77843-4475, USA
| | - Laura Huber
- Department of Pathobiology, College of Veterinary Medicine, Auburn University, Auburn, Alabama, 36849, USA
| | - Macarena Sanz
- Department of Veterinary Clinical Sciences, College of Veterinary Medicine, Washington State University, Pullman, Washington, 99164-6610, USA
| | - Noah Cohen
- Equine Infectious Disease Laboratory, Department of Large Animal Clinical Sciences, College of Veterinary Medicine & Biomedical Sciences, Texas A&M University, College Station, Texas, 77843-4475, USA
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11
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Song Y, Xu X, Huang Z, Xiao Y, Yu K, Jiang M, Yin S, Zheng M, Meng H, Han Y, Wang Y, Wang D, Wei Q. Genomic Characteristics Revealed Plasmid-Mediated Pathogenicity and Ubiquitous Rifamycin Resistance of Rhodococcus equi. Front Cell Infect Microbiol 2022; 12:807610. [PMID: 35252029 PMCID: PMC8891757 DOI: 10.3389/fcimb.2022.807610] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 01/27/2022] [Indexed: 11/22/2022] Open
Abstract
Rhodococcus equi is a zoonotic pathogen that can cause fatal disease in patients who are immunocompromised. At present, the epidemiology and pathogenic mechanisms of R. equi infection are not clear. This study characterized the genomes of 53 R. equi strains from different sources. Pan-genome analysis showed that all R. equi strains contained 11481 pan genes, including 3690 core genes and 602 ~ 1079 accessory genes. Functional annotation of pan genome focused on the genes related to basic lifestyle, such as the storage and expression of metabolic and genetic information. Phylogenetic analysis based on pan-genome showed that the R. equi strains were clustered into six clades, which was not directly related to the isolation location and host source. Also, a total of 84 virulence genes were predicted in 53 R. equi strains. These virulence factors can be divided into 20 categories related to substance metabolism, secreted protein and immune escape. Meanwhile, six antibiotic resistance genes (RbpA, tetA (33), erm (46), sul1, qacEdelta 1 and aadA9) were detected, and all strains carried RbpA related to rifamycin resistance. In addition, 28 plasmids were found in the 53 R. equi strains, belonging to Type-A (n = 14), Type-B (n = 8) and Type-N (n = 6), respectively. The genetic structures of the same type of plasmid were highly similar. In conclusion, R. equi strains show different genomic characteristics, virulence-related genes, potential drug resistance and virulence plasmid structures, which may be conducive to the evolution of its pathogenesis.
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Affiliation(s)
- Yang Song
- National Pathogen Resource Center, Chinese Center for Disease Control and Prevention (China CDC), Beijing, China
| | - Xinmin Xu
- Department of Clinical Laboratory, Beijing Ditan Hospital, Capital Medical University, Beijing, China
| | - Zhenzhou Huang
- Center for human Pathogenic Culture Collection, National Institute for Communicable Disease Control and Prevention, China CDC, Beijing, China
| | - Yue Xiao
- Center for human Pathogenic Culture Collection, National Institute for Communicable Disease Control and Prevention, China CDC, Beijing, China
| | - Keyi Yu
- Center for human Pathogenic Culture Collection, National Institute for Communicable Disease Control and Prevention, China CDC, Beijing, China
| | - Mengnan Jiang
- National Pathogen Resource Center, Chinese Center for Disease Control and Prevention (China CDC), Beijing, China
| | - Shangqi Yin
- Department of Clinical Laboratory, Beijing Ditan Hospital, Capital Medical University, Beijing, China
| | - Mei Zheng
- Department of Clinical Laboratory, Beijing Ditan Hospital, Capital Medical University, Beijing, China
| | - Huan Meng
- Department of Clinical Laboratory, Beijing Ditan Hospital, Capital Medical University, Beijing, China
| | - Ying Han
- Department of Clinical Laboratory, Beijing Ditan Hospital, Capital Medical University, Beijing, China
| | - Yajie Wang
- Department of Clinical Laboratory, Beijing Ditan Hospital, Capital Medical University, Beijing, China
- *Correspondence: Qiang Wei, ; Duochun Wang, ; Yajie Wang,
| | - Duochun Wang
- Center for human Pathogenic Culture Collection, National Institute for Communicable Disease Control and Prevention, China CDC, Beijing, China
- *Correspondence: Qiang Wei, ; Duochun Wang, ; Yajie Wang,
| | - Qiang Wei
- National Pathogen Resource Center, Chinese Center for Disease Control and Prevention (China CDC), Beijing, China
- *Correspondence: Qiang Wei, ; Duochun Wang, ; Yajie Wang,
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Nielsen SS, Bicout DJ, Calistri P, Canali E, Drewe JA, Garin‐Bastuji B, Gonzales Rojas JL, Gortázar C, Herskin M, Michel V, Miranda Chueca MÁ, Padalino B, Pasquali P, Roberts HC, Spoolder H, Ståhl K, Velarde A, Viltrop A, Winckler C, Baldinelli F, Broglia A, Kohnle L, Alvarez J. Assessment of listing and categorisation of animal diseases within the framework of the Animal Health Law (Regulation (EU) No 2016/429): antimicrobial-resistant Rhodococcus equi in horses. EFSA J 2022; 20:e07081. [PMID: 35136423 PMCID: PMC8808660 DOI: 10.2903/j.efsa.2022.7081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Rhodococcus equi (R. equi) was identified among the most relevant antimicrobial-resistant (AMR) bacteria in the EU for horses in a previous scientific opinion. Thus, it has been assessed according to the criteria of the Animal Health Law (AHL), in particular criteria of Article 7 on disease profile and impacts, Article 5 on its eligibility to be listed, Annex IV for its categorisation according to disease prevention and control rules as in Article 9 and Article 8 for listing animal species related to the bacterium. The assessment has been performed following a methodology previously published. The outcome is the median of the probability ranges provided by the experts, which indicates whether each criterion is fulfilled (lower bound ≥ 66%) or not (upper bound ≤ 33%), or whether there is uncertainty about fulfilment. Reasoning points are reported for criteria with uncertain outcome. According to the assessment here performed, it is uncertain whether AMR R. equi can be considered eligible to be listed for Union intervention according to Article 5 of the AHL (10-66% probability). According to the criteria in Annex IV, for the purpose of categorisation related to the level of prevention and control as in Article 9 of the AHL, the AHAW Panel concluded that the bacterium does not meet the criteria in Sections 1 and 2 (Categories A and B; 5-10% and 10-33% probability of meeting the criteria, respectively), and the AHAW Panel is uncertain whether it meets the criteria in Sections 3, 4 and 5 (Categories C, D and E; 10-66% probability of meeting the criteria in all three categories). The animal species to be listed for AMR R. equi according to Article 8 criteria are mainly horses and other species belonging to the Perissodactyla and Artiodactyla orders.
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Reuss SM. Rhodococcus equi
, extrapulmonary disorders and lack of response to therapy. EQUINE VET EDUC 2021. [DOI: 10.1111/eve.13583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- S. M. Reuss
- Boehringer Ingelheim Animal Health USA, Inc. Duluth Georgia USA
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Żychska M, Witkowski L, Klementowska A, Rzewuska M, Kwiecień E, Stefańska I, Czopowicz M, Szaluś-Jordanow O, Mickiewicz M, Moroz A, Bonecka J, Kaba J. Rhodococcus equi-Occurrence in Goats and Clinical Case Report. Pathogens 2021; 10:pathogens10091141. [PMID: 34578172 PMCID: PMC8472617 DOI: 10.3390/pathogens10091141] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 08/31/2021] [Accepted: 09/01/2021] [Indexed: 01/11/2023] Open
Abstract
Background: Rhodococcus equi infection is commonly known in equine medicine to cause frequently fatal rhodococcosis. Infections in other species and people are also reported. Clinical manifestation in goats is relatively similar to horses and humans, but data regarding bacterium prevalence are scarce. Thus, the study aimed to estimate the occurrence of R. equi in goats. Methods: During post mortem examination, submandibular, mediastinal, and mesenteric lymph nodes were collected. Standard methods were used for bacteria isolation and identification. Results: A total of 134 goats were examined, and 272 lymph node samples were collected. R. equi was isolated from four animals. All four isolates carried the choE gene, and one also had traA and pVAPN plasmid genes. Conclusions: To the authors’ best knowledge, this is the first report of R. equi occurrence and genetic diversity in goats. The results may help create a model for treating rhodococcosis in other animal species and assessing the role of meat contamination as a potential source of human infection. This research should be considered a pilot study for further application of the goat as a model of R. equi infection in horses and humans.
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Affiliation(s)
- Monika Żychska
- Division of Veterinary Epidemiology and Economics, Institute of Veterinary Medicine, Warsaw University of Life Sciences-SGGW, 02-776 Warsaw, Poland; (M.Ż.); (A.K.); (M.C.); (M.M.); (A.M.); (J.K.)
| | - Lucjan Witkowski
- Division of Veterinary Epidemiology and Economics, Institute of Veterinary Medicine, Warsaw University of Life Sciences-SGGW, 02-776 Warsaw, Poland; (M.Ż.); (A.K.); (M.C.); (M.M.); (A.M.); (J.K.)
- Correspondence: ; Tel.: +48-22-593-6111
| | - Agnieszka Klementowska
- Division of Veterinary Epidemiology and Economics, Institute of Veterinary Medicine, Warsaw University of Life Sciences-SGGW, 02-776 Warsaw, Poland; (M.Ż.); (A.K.); (M.C.); (M.M.); (A.M.); (J.K.)
| | - Magdalena Rzewuska
- Department of Preclinical Sciences, Institute of Veterinary Medicine, Warsaw University of Life Sciences-SGGW, 02-786 Warsaw, Poland; (M.R.); (E.K.); (I.S.)
| | - Ewelina Kwiecień
- Department of Preclinical Sciences, Institute of Veterinary Medicine, Warsaw University of Life Sciences-SGGW, 02-786 Warsaw, Poland; (M.R.); (E.K.); (I.S.)
| | - Ilona Stefańska
- Department of Preclinical Sciences, Institute of Veterinary Medicine, Warsaw University of Life Sciences-SGGW, 02-786 Warsaw, Poland; (M.R.); (E.K.); (I.S.)
| | - Michał Czopowicz
- Division of Veterinary Epidemiology and Economics, Institute of Veterinary Medicine, Warsaw University of Life Sciences-SGGW, 02-776 Warsaw, Poland; (M.Ż.); (A.K.); (M.C.); (M.M.); (A.M.); (J.K.)
| | - Olga Szaluś-Jordanow
- Department of Small Animal Diseases with Clinic, Institute of Veterinary Medicine, Warsaw University of Life Sciences-SGGW, 02-776 Warsaw, Poland; (O.S.-J.); (J.B.)
| | - Marcin Mickiewicz
- Division of Veterinary Epidemiology and Economics, Institute of Veterinary Medicine, Warsaw University of Life Sciences-SGGW, 02-776 Warsaw, Poland; (M.Ż.); (A.K.); (M.C.); (M.M.); (A.M.); (J.K.)
| | - Agata Moroz
- Division of Veterinary Epidemiology and Economics, Institute of Veterinary Medicine, Warsaw University of Life Sciences-SGGW, 02-776 Warsaw, Poland; (M.Ż.); (A.K.); (M.C.); (M.M.); (A.M.); (J.K.)
| | - Joanna Bonecka
- Department of Small Animal Diseases with Clinic, Institute of Veterinary Medicine, Warsaw University of Life Sciences-SGGW, 02-776 Warsaw, Poland; (O.S.-J.); (J.B.)
| | - Jarosław Kaba
- Division of Veterinary Epidemiology and Economics, Institute of Veterinary Medicine, Warsaw University of Life Sciences-SGGW, 02-776 Warsaw, Poland; (M.Ż.); (A.K.); (M.C.); (M.M.); (A.M.); (J.K.)
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15
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Ivshina IB, Kuyukina MS, Krivoruchko AV, Tyumina EA. Responses to Ecopollutants and Pathogenization Risks of Saprotrophic Rhodococcus Species. Pathogens 2021; 10:974. [PMID: 34451438 PMCID: PMC8398200 DOI: 10.3390/pathogens10080974] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 07/29/2021] [Accepted: 07/30/2021] [Indexed: 11/17/2022] Open
Abstract
Under conditions of increasing environmental pollution, true saprophytes are capable of changing their survival strategies and demonstrating certain pathogenicity factors. Actinobacteria of the genus Rhodococcus, typical soil and aquatic biotope inhabitants, are characterized by high ecological plasticity and a wide range of oxidized organic substrates, including hydrocarbons and their derivatives. Their cell adaptations, such as the ability of adhering and colonizing surfaces, a complex life cycle, formation of resting cells and capsule-like structures, diauxotrophy, and a rigid cell wall, developed against the negative effects of anthropogenic pollutants are discussed and the risks of possible pathogenization of free-living saprotrophic Rhodococcus species are proposed. Due to universal adaptation features, Rhodococcus species are among the candidates, if further anthropogenic pressure increases, to move into the group of potentially pathogenic organisms with "unprofessional" parasitism, and to join an expanding list of infectious agents as facultative or occasional parasites.
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Affiliation(s)
- Irina B. Ivshina
- Perm Federal Research Center UB RAS, Institute of Ecology and Genetics of Microorganisms UB RAS, 13 Golev Str., 614081 Perm, Russia; (M.S.K.); (A.V.K.); (E.A.T.)
- Department of Microbiology and Immunology, Perm State University, 15 Bukirev Str., 614990 Perm, Russia
| | - Maria S. Kuyukina
- Perm Federal Research Center UB RAS, Institute of Ecology and Genetics of Microorganisms UB RAS, 13 Golev Str., 614081 Perm, Russia; (M.S.K.); (A.V.K.); (E.A.T.)
- Department of Microbiology and Immunology, Perm State University, 15 Bukirev Str., 614990 Perm, Russia
| | - Anastasiia V. Krivoruchko
- Perm Federal Research Center UB RAS, Institute of Ecology and Genetics of Microorganisms UB RAS, 13 Golev Str., 614081 Perm, Russia; (M.S.K.); (A.V.K.); (E.A.T.)
- Department of Microbiology and Immunology, Perm State University, 15 Bukirev Str., 614990 Perm, Russia
| | - Elena A. Tyumina
- Perm Federal Research Center UB RAS, Institute of Ecology and Genetics of Microorganisms UB RAS, 13 Golev Str., 614081 Perm, Russia; (M.S.K.); (A.V.K.); (E.A.T.)
- Department of Microbiology and Immunology, Perm State University, 15 Bukirev Str., 614990 Perm, Russia
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