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Vázquez-Boland J, Val-Calvo J, Scortti M. Update on emerging multidrug-resistant Rhodococcus equi. Vet Rec 2024; 194:e4071. [PMID: 38488609 DOI: 10.1002/vetr.4071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
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.
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Affiliation(s)
- Jose Vázquez-Boland
- Microbial Pathogenesis Laboratory, Biomedical Sciences-Infection Medicine, College of Medicine and Veterinary Medicine, IRR Building South, University of Edinburgh, Edinburgh, EH16 4UU
| | - Jorge Val-Calvo
- Microbial Pathogenesis Laboratory, Biomedical Sciences-Infection Medicine, College of Medicine and Veterinary Medicine, IRR Building South, University of Edinburgh, Edinburgh, EH16 4UU
| | - Mariela Scortti
- Microbial Pathogenesis Laboratory, Biomedical Sciences-Infection Medicine, College of Medicine and Veterinary Medicine, IRR Building South, University of Edinburgh, Edinburgh, EH16 4UU
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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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Mitchell SW, Moran RA, Elbourne LDH, Chapman B, Bull M, Muscatello G, Coleman NV. Impacts of Domestication and Veterinary Treatment on Mobile Genetic Elements and Resistance Genes in Equine Fecal Bacteria. Appl Environ Microbiol 2023; 89:e0159022. [PMID: 36988354 PMCID: PMC10057962 DOI: 10.1128/aem.01590-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 02/05/2023] [Indexed: 03/09/2023] Open
Abstract
Antimicrobial resistance in bacteria is a threat to both human and animal health. We aimed to understand the impact of domestication and antimicrobial treatment on the types and numbers of resistant bacteria, antibiotic resistance genes (ARGs), and class 1 integrons (C1I) in the equine gut microbiome. Antibiotic-resistant fecal bacteria were isolated from wild horses, healthy farm horses, and horses undergoing veterinary treatment, and isolates (9,083 colonies) were screened by PCR for C1I; these were found at frequencies of 9.8% (vet horses), 0.31% (farm horses), and 0.05% (wild horses). A collection of 71 unique C1I+ isolates (17 Actinobacteria and 54 Proteobacteria) was subjected to resistance profiling and genome sequencing. Farm horses yielded mostly C1I+ Actinobacteria (Rhodococcus, Micrococcus, Microbacterium, Arthrobacter, Glutamicibacter, Kocuria), while vet horses primarily yielded C1I+ Proteobacteria (Escherichia, Klebsiella, Enterobacter, Pantoea, Acinetobacter, Leclercia, Ochrobactrum); the vet isolates had more extensive resistance and stronger PC promoters in the C1Is. All integrons in Actinobacteria were flanked by copies of IS6100, except in Micrococcus, where a novel IS5 family element (ISMcte1) was implicated in mobilization. In the Proteobacteria, C1Is were predominantly associated with IS26 and also IS1, Tn21, Tn1721, Tn512, and a putative formaldehyde-resistance transposon (Tn7489). Several large C1I-containing plasmid contigs were retrieved; two of these (plasmid types Y and F) also had extensive sets of metal resistance genes, including a novel copper-resistance transposon (Tn7519). Both veterinary treatment and domestication increase the frequency of C1Is in equine gut microflora, and each of these anthropogenic factors selects for a distinct group of integron-containing bacteria. IMPORTANCE There is increasing acknowledgment that a "one health" approach is required to tackle the growing problem of antimicrobial resistance. This requires that the issue is examined from not only the perspective of human medicine but also includes consideration of the roles of antimicrobials in veterinary medicine and agriculture and recognizes the importance of other ecological compartments in the dissemination of ARGs and mobile genetic elements such as C1I. We have shown that domestication and veterinary treatment increase the frequency of occurrence of C1Is in the equine gut microflora and that, in healthy farm horses, the C1I are unexpectedly found in Actinobacteria, while in horses receiving antimicrobial veterinary treatments, a taxonomic shift occurs, and the more typical integron-containing Proteobacteria are found. We identified several new mobile genetic elements (plasmids, insertion sequences [IS], and transposons) on genomic contigs from the integron-containing equine bacteria.
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Affiliation(s)
- Scott W. Mitchell
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia
| | - Robert A. Moran
- Institute of Microbiology and Infection, School of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Liam D. H. Elbourne
- School of Natural Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Belinda Chapman
- Quantal Bioscience Pty Ltd, Carlingford, New South Wales, Australia
| | - Michelle Bull
- Quantal Bioscience Pty Ltd, Carlingford, New South Wales, Australia
| | - Gary Muscatello
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia
| | - Nicholas V. Coleman
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia
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Analysis of Gut Microbial Communities and Resistance Genes in Pigs and Chickens in Central China. Animals (Basel) 2022; 12:ani12233404. [PMID: 36496925 PMCID: PMC9736826 DOI: 10.3390/ani12233404] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 11/24/2022] [Accepted: 12/01/2022] [Indexed: 12/07/2022] Open
Abstract
BACKGROUND Basic data concerning the gut microbiota of the main animal husbandry breeds (pigs and chickens) are scarce in China. The dynamics of gut microbiota (pigs and chickens) in China and antibiotic resistance genes carried by microorganisms in the natural environment are unknown. METHODS Free range and factory-farmed Gushi chickens and Huainan pigs were divided into eight groups. Faecal samples were collected from each group, and the metagenomic sequencing method was used to detect each group of samples. RESULTS The resistance genes showed the following trend, from high to low relative abundance: tetW was the highest, followed by tetW/N/W, then lnuA; and others from high to low were mdtB, lnuC, ANT6-la, ErmB, mdtC, ErmQ, tetBP, vatE, evgS, acrB, cpxA, mefA, Escherichia coli-ampC, tetL, yojl, AcrF and mdtA. All groups administered enrofloxacin and oregano oil did not develop a drug-resistant phenotype during the 5-day treatment period, as grouped in this trial. In 2022, after Announcement No. 194 of the Ministry of Agriculture and Rural Affairs in China, the antimicrobial resistance (AMR) trend declined, but it did not fundamentally change, presumably due to the impact of environmental pollution caused by the long-term use of antimicrobials.
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Natarajan H, Xu S, Crowley AR, Butler SE, Weiner JA, Bloch EM, Littlefield K, Benner SE, Shrestha R, Ajayi O, Wieland-Alter W, Sullivan D, Shoham S, Quinn TC, Casadevall A, Pekosz A, Redd AD, Tobian AAR, Connor RI, Wright PF, Ackerman ME. Antibody attributes that predict the neutralization and effector function of polyclonal responses to SARS-CoV-2. BMC Immunol 2022; 23:7. [PMID: 35172720 PMCID: PMC8851712 DOI: 10.1186/s12865-022-00480-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 02/07/2022] [Indexed: 01/19/2023] Open
Abstract
BACKGROUND While antibodies can provide significant protection from SARS-CoV-2 infection and disease sequelae, the specific attributes of the humoral response that contribute to immunity are incompletely defined. METHODS We employ machine learning to relate characteristics of the polyclonal antibody response raised by natural infection to diverse antibody effector functions and neutralization potency with the goal of generating both accurate predictions of each activity based on antibody response profiles as well as insights into antibody mechanisms of action. RESULTS To this end, antibody-mediated phagocytosis, cytotoxicity, complement deposition, and neutralization were accurately predicted from biophysical antibody profiles in both discovery and validation cohorts. These models identified SARS-CoV-2-specific IgM as a key predictor of neutralization activity whose mechanistic relevance was supported experimentally by depletion. CONCLUSIONS Validated models of how different aspects of the humoral response relate to antiviral antibody activities suggest desirable attributes to recapitulate by vaccination or other antibody-based interventions.
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Affiliation(s)
- Harini Natarajan
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Dartmouth College, Hanover, NH, USA
| | - Shiwei Xu
- Program in Quantitative Biological Sciences, Dartmouth College, Hanover, NH, USA
| | - Andrew R Crowley
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Dartmouth College, Hanover, NH, USA
| | - Savannah E Butler
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Dartmouth College, Hanover, NH, USA
| | - Joshua A Weiner
- Thayer School of Engineering, Dartmouth College, 14 Engineering Drive, Hanover, NH, 03755, USA
| | - Evan M Bloch
- Department of Pathology, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Kirsten Littlefield
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Sarah E Benner
- Department of Pathology, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Ruchee Shrestha
- Department of Pathology, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Olivia Ajayi
- Department of Pathology, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Wendy Wieland-Alter
- Department of Pediatrics, Geisel School of Medicine at Dartmouth, Dartmouth-Hitchcock Medical Center, Lebanon, NH, USA
| | - David Sullivan
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
- Department of Medicine, Division of Infectious Diseases, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Shmuel Shoham
- Department of Medicine, Division of Infectious Diseases, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Thomas C Quinn
- Department of Medicine, Division of Infectious Diseases, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Arturo Casadevall
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
- Department of Medicine, Division of Infectious Diseases, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Andrew Pekosz
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Andrew D Redd
- Department of Medicine, Division of Infectious Diseases, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Aaron A R Tobian
- Department of Pathology, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Ruth I Connor
- Department of Pediatrics, Geisel School of Medicine at Dartmouth, Dartmouth-Hitchcock Medical Center, Lebanon, NH, USA
| | - Peter F Wright
- Department of Pediatrics, Geisel School of Medicine at Dartmouth, Dartmouth-Hitchcock Medical Center, Lebanon, NH, USA
| | - Margaret E Ackerman
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Dartmouth College, Hanover, NH, USA.
- Program in Quantitative Biological Sciences, Dartmouth College, Hanover, NH, USA.
- Thayer School of Engineering, Dartmouth College, 14 Engineering Drive, Hanover, NH, 03755, USA.
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