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Godoi APDS, Sobral GG, da Silva Vieira JC, Carneiro GF, Conceição FR, da Silva ER, Mendonça M. Phenotypical and molecular characterization of Rhodococcus equi isolated from foals in the Agreste region of Pernambuco - Brazil. Braz J Microbiol 2025; 56:1321-1331. [PMID: 40048142 PMCID: PMC12095708 DOI: 10.1007/s42770-025-01640-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2024] [Accepted: 02/13/2025] [Indexed: 05/22/2025] Open
Abstract
Equine rhodococcosis is caused by Rhodococcus equi, an intracellular coccobacillus whose main virulence factor is a plasmid that harbors genes encoding proteins from the Vap family, with the vapA gene being the most important in equine isolates. Furthermore, other factors observed in R. equi strains, such as antimicrobial resistance and biofilm production, may represent significant challenges in the treatment of affected animals. The objective of this study was to characterize four isolates of R. equi from foals in the state of Pernambuco, Brazil. All isolates were identified as R. equi through biochemical tests, amplification of the choE gene, and sequencing of 16 S rRNA. PCR analysis revealed that three isolates were positive for the plasmid virulence genes (vapA, -C, -D, -E, -F, -H and traA), although vapD was absent in one of the three isolates. One isolate did not present any virulence genes, possibly due to the loss of the plasmid after repeated passages at 37ºC. In the antimicrobial susceptibility test, all isolates were susceptible to erythromycin, clarithromycin, azithromycin, rifampicin, gentamicin, and doxycycline. However, all isolates were capable of forming biofilms, with moderate biofilm formation in isolates Rhodo1 and Rhodo2, and weak biofilm formation in isolates Rhodo3 and Rhodo4, which may be associated with increased antimicrobial tolerance. This molecular characterization demonstrated, for the first time, the presence of the virulence plasmid in R. equi isolates from foals in Northeast Brazil, as well as their capacity for biofilm formation.
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Affiliation(s)
- Alysson Paulo Dos Santos Godoi
- Departamento de Medicina Veterinária, Universidade Federal Rural de Pernambuco, Rua Dom Manuel de Medeiros, Recife, Pernambuco, 52171-900, Brazil
- Programa de Pós-Graduação em Sanidade e Reprodução de Animais de Produção, Universidade Federal do Agreste de Pernambuco, Avenida Bom Pastor, Boa Vista, Garanhuns, 55292-270, Pernambuco, Brazil
| | - Gilvannya Gonçalves Sobral
- Departamento de Medicina Veterinária, Universidade Federal Rural de Pernambuco, Rua Dom Manuel de Medeiros, Recife, Pernambuco, 52171-900, Brazil
| | - Júlio César da Silva Vieira
- Programa de Pós-Graduação em Sanidade e Reprodução de Animais de Produção, Universidade Federal do Agreste de Pernambuco, Avenida Bom Pastor, Boa Vista, Garanhuns, 55292-270, Pernambuco, Brazil
| | - Gustavo Ferrer Carneiro
- Departamento de Medicina Veterinária, Universidade Federal Rural de Pernambuco, Rua Dom Manuel de Medeiros, Recife, Pernambuco, 52171-900, Brazil
| | - Fabricio Rochedo Conceição
- Centro de Desenvolvimento Tecnológico, Núcleo de Biotecnologia, Universidade Federal de Pelotas, Campus Capão do Leão, Pelotas, 96010-610, Rio Grande do Sul, Brazil
| | - Elizabete Rodrigues da Silva
- Programa de Pós-Graduação em Sanidade e Reprodução de Animais de Produção, Universidade Federal do Agreste de Pernambuco, Avenida Bom Pastor, Boa Vista, Garanhuns, 55292-270, Pernambuco, Brazil
| | - Marcelo Mendonça
- Programa de Pós-Graduação em Sanidade e Reprodução de Animais de Produção, Universidade Federal do Agreste de Pernambuco, Avenida Bom Pastor, Boa Vista, Garanhuns, 55292-270, Pernambuco, Brazil.
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Gallegos AL, Nashmias ME, Zubimendi JP, Hernández MA, Acosta V, Tejerizo GAT, Quelas JI, Silva RA, Alvarez HM. Adaptive responses of Rhodococcus aetherivorans L13 to oligotrophy: genome and transcriptomic analysis. Curr Genet 2025; 71:10. [PMID: 40220062 DOI: 10.1007/s00294-025-01314-z] [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: 01/02/2025] [Revised: 03/22/2025] [Accepted: 03/27/2025] [Indexed: 04/14/2025]
Abstract
The wide ecological distribution of actinobacteria suggests that they have developed efficient mechanisms to adapt to extremely nutritionally deficient (oligotrophic) conditions. The impact of nutrient limitation typically observed in oligotrophic areas on bacteria remains to be assessed for many species. The non-model Rhodococcus aetherivorans L13can grow under oligotrophic conditions, even without an added carbon source. Oligotrophic cells of L13 undergo physiological and morphological changes compared to glucose-grown cells, including forming short-fragmenting cells, producing an extracellular polymeric substance, and a 26-fold decrease in respiratory activity. We conducted genome sequencing of L13 and assembled the entire genome, subsequently comparing the abundance of gene transcripts in oligotrophic cells to those of glucose-grown cells, to explore the oligotrophy-responsive mechanisms at the genetic level. The genome comprises 6,543,485 base pairs, distributed across a single chromosome and six extrachromosomal plasmids (one linear and five circular). RNA-Seq analysis revealed the significant dysregulation of 2,665 genes (44% of the total genes detected). Results suggested a profound reorganization of its carbon and energy metabolism, including the activation of (i) mechanisms for utilizing air components; (ii) various dehydrogenases involved in aldehyde and alcohol metabolism, (iii) several enzymes involved in C2 metabolism, glyoxylate shunt, and TCA bypass routes, and downregulation of several genes that encode CO2 releasing-decarboxylase enzymes. Our results suggested that the adaptation strategy of L13 to oligotrophic conditions is supported by a combination of metabolic events, including low metabolic activity, the activation of C2 and ketoacids metabolism, and the display of a carbon conservative metabolic program.
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Affiliation(s)
- Andrea L Gallegos
- INBIOP (Instituto de Biociencias de la Patagonia), Facultad de Ciencias Naturales y Ciencias de la Salud, Consejo Nacional de Investigaciones Científicas y Técnicas, Universidad Nacional de la Patagonia San Juan Bosco, Ruta Provincial N° 1, Km 4-Ciudad Universitaria 9000, Comodoro Rivadavia, Chubut, Argentina
| | - María E Nashmias
- YPF Tecnología SA (Y-TEC), Av. del Petróleo Argentino s/n (1923), Berisso, Buenos Aires, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), CABA, Godoy Cruz 2290 (C1425FQB), Argentina
| | - Juan Pablo Zubimendi
- YPF Tecnología SA (Y-TEC), Av. del Petróleo Argentino s/n (1923), Berisso, Buenos Aires, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), CABA, Godoy Cruz 2290 (C1425FQB), Argentina
| | - Martín A Hernández
- INBIOP (Instituto de Biociencias de la Patagonia), Facultad de Ciencias Naturales y Ciencias de la Salud, Consejo Nacional de Investigaciones Científicas y Técnicas, Universidad Nacional de la Patagonia San Juan Bosco, Ruta Provincial N° 1, Km 4-Ciudad Universitaria 9000, Comodoro Rivadavia, Chubut, Argentina
| | - Verónica Acosta
- Facultad de Ingeniería, Consejo Nacional de Investigaciones Científicas y Técnicas, CIT Golfo San Jorge. (CONICET), Universidad Nacional de la Patagonia San Juan Bosco, Ruta Provincial N° 1, Km 4-Ciudad Universitaria 9000, Comodoro Rivadavia, Chubut, Argentina
| | - Gonzalo A Torres Tejerizo
- Instituto de Biotecnología y Biología Molecular, Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, CCT-La Plata-CONICET, Universidad Nacional de La Plata, La Plata, Argentina
| | - Juan I Quelas
- YPF Tecnología SA (Y-TEC), Av. del Petróleo Argentino s/n (1923), Berisso, Buenos Aires, Buenos Aires, Argentina.
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), CABA, Godoy Cruz 2290 (C1425FQB), Argentina.
| | - Roxana A Silva
- INBIOP (Instituto de Biociencias de la Patagonia), Facultad de Ciencias Naturales y Ciencias de la Salud, Consejo Nacional de Investigaciones Científicas y Técnicas, Universidad Nacional de la Patagonia San Juan Bosco, Ruta Provincial N° 1, Km 4-Ciudad Universitaria 9000, Comodoro Rivadavia, Chubut, Argentina.
| | - Héctor M Alvarez
- INBIOP (Instituto de Biociencias de la Patagonia), Facultad de Ciencias Naturales y Ciencias de la Salud, Consejo Nacional de Investigaciones Científicas y Técnicas, Universidad Nacional de la Patagonia San Juan Bosco, Ruta Provincial N° 1, Km 4-Ciudad Universitaria 9000, Comodoro Rivadavia, Chubut, Argentina.
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Vazquez-Boland JA, Val-Calvo J, Duquesne F, Decorosi F, Viti C, Petry S, Scortti M. Rhodococcus parequi sp. nov., a new species isolated from equine farm soil closely related to the pathogen Rhodococcus equi. Int J Syst Evol Microbiol 2025; 75:006679. [PMID: 40063668 PMCID: PMC11893733 DOI: 10.1099/ijsem.0.006679] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2024] [Accepted: 02/02/2025] [Indexed: 03/14/2025] Open
Abstract
We present the description of the new species, Rhodococcus parequi, found during phylogenomic investigations of a global collection of strains identified as Rhodococcus (Prescottella) equi. Strain PAM 2766T was isolated from horse-breeding farm soil in Normandy, France, and was indistinguishable from R. equi based on the usual identification tests. Whole-genome phylogenetic analyses located PAM 2766T in the same Rhodococcus sublineage as R. equi, together with Rhodococcus agglutinans, Rhodococcus defluvii, Rhodococcus soli, Rhodococcus subtropicus, Rhodococcus spongiicola and Rhodococcus xishaensis. PAM 2766T is most closely related to, but sufficiently distinct from, R. equi DSM 20307 T to be considered a separate species. The average nt identity (ANI) and average aa identity (AAI) values are 88.60% and 92.35, respectively, well below the species cutoff. The PAM 2766T draft genome is ~5.3 Mb in size with 68.98% G+C mol content. PAM 2766T is strictly aerobic and non-motile and produces smooth, creamy to buff-coloured colonies very similar to those of R. equi. It phenotypically differs from the latter by the ability to grow at 5 °C, a strongly positive urease test at 24 h and specificities in the carbon and nitrogen source utilization profile as determined by phenotype microarray screens. Our data indicate that PAM 2766T belongs to a novel species, for which the name Rhodococcus parequi sp. nov. is proposed. R. parequi was avirulent in macrophage infection assays and is assumed to be non-pathogenic. The type strain is PAM 2766T (=CETC 30995T=NCTC 14987T).
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Affiliation(s)
- José A. Vazquez-Boland
- Microbial Pathogenomics Laboratory, Edinburgh Medical School (Biomedical Sciences), University of Edinburgh, Edinburgh, UK
| | - Jorge Val-Calvo
- Microbial Pathogenomics Laboratory, Edinburgh Medical School (Biomedical Sciences), University of Edinburgh, Edinburgh, UK
| | - Fabien Duquesne
- ANSES, Laboratory for Animal Health, Physiopathology and Epidemiology of Equine Diseases Unit, Goustranville, France
| | - Francesca Decorosi
- Department of Agriculture, Food, Environment and Forestry, University of Florence, Florence, Italy
| | - Carlo Viti
- Department of Agriculture, Food, Environment and Forestry, University of Florence, Florence, Italy
| | - Sandrine Petry
- ANSES, Laboratory for Animal Health, Physiopathology and Epidemiology of Equine Diseases Unit, Goustranville, France
| | - Mariela Scortti
- Microbial Pathogenomics Laboratory, Edinburgh Medical School (Biomedical Sciences), University of Edinburgh, Edinburgh, UK
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de Oliveira ACFM, Vieira BD, de Felício R, Silva LDSE, Veras AADO, Graças DAD, Silva A, Azevedo Baraúna R, Barretto Barbosa Trivella D, Schneider MPC. A metabologenomics approach reveals the unexplored biosynthetic potential of bacteria isolated from an Amazon Conservation Unit. Microbiol Spectr 2025; 13:e0099624. [PMID: 39656018 PMCID: PMC11705897 DOI: 10.1128/spectrum.00996-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Accepted: 11/05/2024] [Indexed: 01/11/2025] Open
Abstract
The Amazon, an important biodiversity hotspot, remains poorly explored in terms of its microbial diversity and biotechnological potential. The present study characterized the metabolic potential of Gram-positive strains of the Actinomycetes and Bacilli classes isolated from soil samples of an Amazon Conservation Unit. The sequencing of the 16S rRNA gene classified the strains ACT015, ACT016, and FIR094 within the genera Streptomyces, Rhodococcus, and Brevibacillus, respectively. Genome mining identified 33, 17, and 14 biosynthetic gene clusters (BGCs) in these strains, including pathways for the biosynthesis of antibiotic and antitumor agents. Additionally, 40 BGCs (62,5% of the total BGCs) were related to unknown metabolites. The OSMAC approach and untargeted metabolomics analysis revealed a plethora of metabolites under laboratory conditions, underscoring the untapped chemical diversity and biotechnological potential of these isolates. Our findings illustrated the efficacy of the metabologenomics approach in elucidating secondary metabolism and selecting BGCs with chemical novelty.IMPORTANCEThe largest rainforest in the world is globally recognized for its biodiversity. However, until now, few studies have been conducted to prospect natural products from the Amazon microbiome. In this work, we isolated three free-living bacterial species from the microbiome of pristine soils and used two high-throughput technologies to reveal the vast unexplored repertoire of secondary metabolites produced by these microorganisms.
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Affiliation(s)
- Ana Carolina Favacho Miranda de Oliveira
- Biological Engineering Laboratory, Innovation Space, Guamá Science and Technology Park, Belém, Pará, Brazil
- Center of Genomics and Systems Biology, Institute of Biological Sciences, Federal University of Pará, Belém, Pará, Brazil
| | - Bruna Domingues Vieira
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, São Paulo, Brazil
| | - Rafael de Felício
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, São Paulo, Brazil
| | - Lucas da Silva e Silva
- Center of Genomics and Systems Biology, Institute of Biological Sciences, Federal University of Pará, Belém, Pará, Brazil
| | | | - Diego Assis das Graças
- Biological Engineering Laboratory, Innovation Space, Guamá Science and Technology Park, Belém, Pará, Brazil
| | - Artur Silva
- Biological Engineering Laboratory, Innovation Space, Guamá Science and Technology Park, Belém, Pará, Brazil
| | - Rafael Azevedo Baraúna
- Biological Engineering Laboratory, Innovation Space, Guamá Science and Technology Park, Belém, Pará, Brazil
| | - Daniela Barretto Barbosa Trivella
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, São Paulo, Brazil
| | - Maria Paula Cruz Schneider
- Biological Engineering Laboratory, Innovation Space, Guamá Science and Technology Park, Belém, Pará, Brazil
- Center of Genomics and Systems Biology, Institute of Biological Sciences, Federal University of Pará, Belém, Pará, Brazil
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Kakuda T, Sato T, Takuhara M, Hagiuda H, Suzuki Y. LysR-Type Transcriptional Regulator VirR Responds to Temperature and pH and Directly Activates the Transcription of virS-Containing Operon in Rhodococcus equi. Int J Microbiol 2025; 2025:6618952. [PMID: 39802684 PMCID: PMC11724031 DOI: 10.1155/ijm/6618952] [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: 07/15/2024] [Accepted: 12/06/2024] [Indexed: 01/16/2025] Open
Abstract
Rhodococcus equi-a facultative intracellular pathogen of macrophages-causes bronchopneumonia in foals and patients who are immunocompromised. Virulent strains of R. equi possess a virulence-associated plasmid, which encodes a 15- to 17-kDa surface protein called virulence-associated protein A (VapA). VapA expression is regulated by temperature and pH. Two transcriptional regulators, VirR and VirS, are involved in the transcriptional regulation of vapA. VirR regulates VapA expression through VirS. However, whether VirR directly regulates virS transcription is unclear. In this study, we examined VirR binding to the promoter region of the icgA operon, which contains virS, using the electrophoretic mobility shift assay and DNase I footprinting. VirR bound DNA fragments containing the virR-icgA intergenic region. Transcription from the promoter in this region was VirR-dependent and regulated by temperature and pH. The VirR-binding site contained the LysR-type transcriptional regulator-binding consensus motif, T-N11-A. A point mutation (L98E) in the putative ligand-binding pocket of VirR constitutively activated the icgA promoter. However, no apparent difference was observed in the electrophoretic mobility shift assay and DNase I footprinting using the icgA promoter when L98E VirR was compared with wild-type VirR. A bacterial two-hybrid system identified an interaction between VirR and RpoA. Our data reveal that VirR binds the promoter of the icgA operon and directly activates its transcription. Furthermore, the regulation of VapA expression in response to temperature and pH is mediated by VirR.
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Affiliation(s)
- Tsutomu Kakuda
- Laboratory of Animal Hygiene, School of Veterinary Medicine, Kitasato University, Higashi 23-35-1, Towada Aomori 034-8628, Japan
| | - Takashi Sato
- Laboratory of Animal Hygiene, School of Veterinary Medicine, Kitasato University, Higashi 23-35-1, Towada Aomori 034-8628, Japan
| | - Mari Takuhara
- Laboratory of Animal Hygiene, School of Veterinary Medicine, Kitasato University, Higashi 23-35-1, Towada Aomori 034-8628, Japan
| | - Hirofumi Hagiuda
- Laboratory of Animal Hygiene, School of Veterinary Medicine, Kitasato University, Higashi 23-35-1, Towada Aomori 034-8628, Japan
| | - Yasunori Suzuki
- Laboratory of Animal Hygiene, School of Veterinary Medicine, Kitasato University, Higashi 23-35-1, Towada Aomori 034-8628, Japan
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Miranda-CasoLuengo R, Yerlikaya Z, Luo H, Cheng C, Blanco A, Haas A, Meijer WG. The N-terminal domain is required for cell surface localisation of VapA, a member of the Vap family of Rhodococcus equi virulence proteins. PLoS One 2024; 19:e0298900. [PMID: 38421980 PMCID: PMC10903876 DOI: 10.1371/journal.pone.0298900] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Accepted: 01/31/2024] [Indexed: 03/02/2024] Open
Abstract
Rhodococcus equi pneumonia is an important cause of mortality in foals worldwide. Virulent equine isolates harbour an 80-85kb virulence plasmid encoding six virulence-associated proteins (Vaps). VapA, the main virulence factor of this intracellular pathogen, is known to be a cell surface protein that creates an intracellular niche for R. equi growth. In contrast, VapC, VapD and VapE are secreted into the intracellular milieu. Although these Vaps share very high degree of sequence identity in the C-terminal domain, the N-terminal domain (N-domain) of VapA is distinct. It has been proposed that this domain plays a role in VapA surface localization but no direct experimental data provides support to such hypothesis. In this work, we employed R. equi 103S harbouring an unmarked deletion of vapA (R. equi ΔvapA) as the genetic background to express C-terminal Strep-tagged Vap-derivatives integrated in the chromosome. The surface localization of these proteins was assessed by flow cytometry using the THE2122;-NWSHPQFEK Tag FITC-antibody. We show that VapA is the only cell surface Vap encoded in the virulence plasmid. We present compelling evidence for the role of the N-terminal domain of VapA on cell surface localization using fusion proteins in which the N-domain of VapD was exchanged with the N-terminus of VapA. Lastly, using an N-terminally Strep-tagged VapA, we found that the N-terminus of VapA is exposed to the extracellular environment. Given the lack of a lipobox in VapA and the exposure of the N-terminal Strep-tag, it is possible that VapA localization on the cell surface is mediated by interactions between the N-domain and components of the cell surface. We discuss the implications of this work on the light of the recent discovery that soluble recombinant VapA added to the extracellular medium functionally complement the loss of VapA.
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Affiliation(s)
- Raúl Miranda-CasoLuengo
- UCD School of Biomolecular and Biomedical Science and UCD Conway Institute of Biomolecular & Biomedical Research, University College Dublin, Dublin, Ireland
| | - Zeynep Yerlikaya
- UCD School of Biomolecular and Biomedical Science and UCD Conway Institute of Biomolecular & Biomedical Research, University College Dublin, Dublin, Ireland
- Department of Microbiology, School of Veterinary Medicine, Firat University, Elazığ, Türkiye
| | - Haixia Luo
- UCD School of Biomolecular and Biomedical Science and UCD Conway Institute of Biomolecular & Biomedical Research, University College Dublin, Dublin, Ireland
| | - Cheng Cheng
- UCD School of Biomolecular and Biomedical Science and UCD Conway Institute of Biomolecular & Biomedical Research, University College Dublin, Dublin, Ireland
| | - Alfonso Blanco
- Flow Cytometry Core Technology, UCD Conway Institute of Biomolecular & Biomedical Research, University College Dublin, Dublin, Ireland
| | - Albert Haas
- Institute for Cell Biology, University of Bonn, Bonn, Germany
| | - Wim G. Meijer
- UCD School of Biomolecular and Biomedical Science and UCD Conway Institute of Biomolecular & Biomedical Research, University College Dublin, Dublin, Ireland
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Li T, Xu B, Chen H, Shi Y, Li J, Yu M, Xia S, Wu S. Gut toxicity of polystyrene microplastics and polychlorinated biphenyls to Eisenia fetida: Single and co-exposure effects with a focus on links between gut bacteria and bacterial translocation stemming from gut barrier damage. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 908:168254. [PMID: 37923278 DOI: 10.1016/j.scitotenv.2023.168254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 10/25/2023] [Accepted: 10/29/2023] [Indexed: 11/07/2023]
Abstract
Microplastics' (MPs) ability to sorb and transport polychlorinated biphenyls (PCBs) in soil ecosystems warrants significant attention. Although organisms mainly encounter pollutants through the gut, the combined pollution impact of MPs and PCBs on soil fauna gut toxicity remains incompletely understood. Consequently, this study examined the gut toxicity of polystyrene MPs (PS-MPs) and PCB126 on Eisenia fetida, emphasizing the links between gut bacteria and bacterial translocation instigated by gut barrier impairment. Our findings underscored that E. fetida could ingest PS-MPs, which mitigated the PCB126 accumulation in E. fetida by 9.43 %. Exposure to PCB126 inhibited the expression of gut tight junction (TJ) protein genes. Although the presence of PS-MPs attenuated this suppression, it didn't alleviate gut barrier damage and bacterial translocation in the co-exposure group. This group demonstrated a significantly increased level of gut bacterial load (BLT, ANOVA, p = 0.005 vs control group) and lipopolysaccharide-binding protein (LBP, ANOVA, all p < 0.001 vs control, PCB, and PS groups), both of which displayed significant positive correlations with antibacterial defense. Furthermore, exposure to PS-MPs and PCB126, particularly within the co-exposure group, results in a marked decline in the dispersal ability of gut bacteria. This leads to dysbiosis (Adonis, R2 = 0.294, p = 0.001), with remarkable signature taxa such as Janthinobacterium, Microbacterium and Pseudomonas, being implicated in gut barrier dysfunction. This research illuminates the mechanism of gut toxicity induced by PS-MPs and PCB126 combined pollution in earthworms, providing novel insights for the ecological risk assessment of soil.
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Affiliation(s)
- Tongtong Li
- Department of Applied Biology, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, China
| | - Baohua Xu
- Department of Applied Biology, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, China
| | - Hao Chen
- Department of Applied Biology, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, China
| | - Ying Shi
- Department of Applied Biology, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, China
| | - Jun Li
- Jiangxi Key Laboratory of Natural Product and Functional Food, College of Food Science and Engineering, Jiangxi Agricultural University, Nanchang 330045, China
| | - Mengwei Yu
- Department of Applied Biology, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, China
| | - Shaohui Xia
- Department of Applied Biology, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, China
| | - Shijin Wu
- Department of Applied Biology, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, China.
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8
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Herrero OM, Alvarez HM. Fruit residues as substrates for single-cell oil production by Rhodococcus species: physiology and genomics of carbohydrate catabolism. World J Microbiol Biotechnol 2024; 40:61. [PMID: 38177966 DOI: 10.1007/s11274-023-03866-z] [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: 08/09/2023] [Accepted: 12/03/2023] [Indexed: 01/06/2024]
Abstract
Strains belonging to R. opacus, R. jostii, R. fascians, R. erythropolis and R. equi exhibited differential ability to grow and produce lipids from fruit residues (grape marc and apple pomace), as well as single carbohydrates, such as glucose, gluconate, fructose and sucrose. The oleaginous species, R. opacus (strains PD630 and MR22) and R. jostii RHA1, produced higher yields of biomass (5.1-5.6 g L-1) and lipids (38-44% of CDW) from apple juice wastes, in comparison to R. erythropolis DSM43060, R. fascians F7 and R. equi ATCC6939 (4.1-4.3 g L-1 and less than 10% CDW of lipids). The production of cellular biomass and lipids were also higher in R. opacus and R. jostii (6.8-7.2 g L-1 and 33.9-36.5% of CDW of lipids) compared to R. erythropolis, R. fascians, and R. equi (3.0-3.6 g L-1 and less than 10% CDW of lipids), during cultivation of cells on wine grape waste. A genome-wide bioinformatic analysis of rhodococci indicated that oleaginous species possess a complete set of genes/proteins necessary for the efficient utilization of carbohydrates, whereas genomes from non-oleaginous rhodococcal strains lack relevant genes coding for transporters and/or enzymes for the uptake, catabolism and assimilation of carbohydrates, such as gntP, glcP, edd, eda, among others. Results of this study highlight the potential use of the oleaginous rhodococcal species to convert sugar-rich agro-industrial wastes, such as apple pomace and grape marc, into single-cell oils.
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Affiliation(s)
- O Marisa Herrero
- Instituto de Biociencias de la Patagonia (INBIOP), Universidad Nacional de la Patagonia San Juan Bosco y CONICET, Km 4-Ciudad Universitaria, 9000, Comodoro Rivadavia, Chubut, Argentina
| | - Héctor M Alvarez
- Instituto de Biociencias de la Patagonia (INBIOP), Universidad Nacional de la Patagonia San Juan Bosco y CONICET, Km 4-Ciudad Universitaria, 9000, Comodoro Rivadavia, Chubut, Argentina.
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9
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Liu L, Yu W, Cai K, Ma S, Wang Y, Ma Y, Zhao H. Identification of vaccine candidates against rhodococcus equi by combining pangenome analysis with a reverse vaccinology approach. Heliyon 2023; 9:e18623. [PMID: 37576287 PMCID: PMC10413060 DOI: 10.1016/j.heliyon.2023.e18623] [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: 04/27/2023] [Revised: 07/12/2023] [Accepted: 07/24/2023] [Indexed: 08/15/2023] Open
Abstract
Rhodococcus equi (R. equi) is a zoonotic opportunistic pathogen that can cause life-threatening infections. The rapid evolution of multidrug-resistant R. equi and the fact that there is no currently licensed effective vaccine against R. equi warrant the need for vaccine development. Reverse vaccinology (RV), which involves screening a pathogen's entire genome and proteome using various web-based prediction tools, is considered one of the most effective approaches for identifying vaccine candidates. Here, we performed a pangenome analysis to determine the core proteins of R. equi. We then used the RV approach to examine the subcellular localization, host and gut flora homology, antigenicity, transmembrane helices, physicochemical properties, and immunogenicity of the core proteins to select potential vaccine candidates. The vaccine candidates were then subjected to epitope mapping to predict the exposed antigenic epitopes that possess the ability to bind with major histocompatibility complex I/II (MHC I/II) molecules. These vaccine candidates and epitopes will form a library of elements for the development of a polyvalent or universal vaccine against R. equi. Sixteen R. equi complete proteomes were found to contain 6,238 protein families, and the core proteins consisted of 3,969 protein families (∼63.63% of the pangenome), reflecting a low degree of intraspecies genomic variability. From the pool of core proteins, 483 nonhost homologous membrane and extracellular proteins were screened, and 12 vaccine candidates were finally identified according to their antigenicity, physicochemical properties and other factors. These included four cell wall/membrane/envelope biogenesis proteins; four amino acid transport and metabolism proteins; one cell cycle control, cell division and chromosome partitioning protein; one carbohydrate transport and metabolism protein; one secondary metabolite biosynthesis, transport and catabolism protein; and one defense mechanism protein. All 12 vaccine candidates have an experimentally validated 3D structure available in the protein data bank (PDB). Epitope mapping of the candidates showed that 16 MHC I epitopes and 13 MHC II epitopes with the strongest immunogenicity were exposed on the protein surface, indicating that they could be used to develop a polypeptide vaccine. Thus, we utilized an analytical strategy that combines pangenome analysis and RV to generate a peptide antigen library that simplifies the development of multivalent or universal vaccines against R. equi and can be applied to the development of other vaccines.
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Affiliation(s)
- Lu Liu
- College of Veterinary Medicine, Xinjiang Agricultural University, Urumqi 830052, Xinjiang, China
| | - Wanli Yu
- College of Veterinary Medicine, Xinjiang Agricultural University, Urumqi 830052, Xinjiang, China
| | - Kuojun Cai
- College of Veterinary Medicine, Xinjiang Agricultural University, Urumqi 830052, Xinjiang, China
| | - Siyuan Ma
- College of Veterinary Medicine, Xinjiang Agricultural University, Urumqi 830052, Xinjiang, China
| | - Yanfeng Wang
- College of Veterinary Medicine, Xinjiang Agricultural University, Urumqi 830052, Xinjiang, China
| | - Yuhui Ma
- Zhaosu Xiyu Horse Industry Co., Ltd. Zhaosu County 835699, Yili Prefecture, Xinjiang, China
| | - Hongqiong Zhao
- College of Veterinary Medicine, Xinjiang Agricultural University, Urumqi 830052, Xinjiang, China
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10
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Lara-Moreno A, Merchán F, Morillo E, Zampolli J, Di Gennaro P, Villaverde J. Genome analysis for the identification of genes involved in phenanthrene biodegradation pathway in Stenotrophomonas indicatrix CPHE1. Phenanthrene mineralization in soils assisted by integrated approaches. Front Bioeng Biotechnol 2023; 11:1158177. [PMID: 37214282 PMCID: PMC10192627 DOI: 10.3389/fbioe.2023.1158177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 04/14/2023] [Indexed: 05/24/2023] Open
Abstract
Phenanthrene (PHE) is a highly toxic compound, widely present in soils. For this reason, it is essential to remove PHE from the environment. Stenotrophomonas indicatrix CPHE1 was isolated from an industrial soil contaminated by polycyclic aromatic hydrocarbons (PAHs) and was sequenced to identify the PHE degrading genes. Dioxygenase, monooxygenase, and dehydrogenase gene products annotated in S. indicatrix CPHE1 genome were clustered into different trees with reference proteins. Moreover, S. indicatrix CPHE1 whole-genome sequences were compared to genes of PAHs-degrading bacteria retrieved from databases and literature. On these basis, reverse transcriptase-polymerase chain reaction (RT-PCR) analysis pointed out that cysteine dioxygenase (cysDO), biphenyl-2,3-diol 1,2-dioxygenase (bphC), and aldolase hydratase (phdG) were expressed only in the presence of PHE. Therefore, different techniques have been designed to improve the PHE mineralization process in five PHE artificially contaminated soils (50 mg kg-1), including biostimulation, adding a nutrient solution (NS), bioaugmentation, inoculating S. indicatrix CPHE1 which was selected for its PHE-degrading genes, and the use of 2-hydroxypropyl-β-cyclodextrin (HPBCD) as a bioavailability enhancer. High percentages of PHE mineralization were achieved for the studied soils. Depending on the soil, different treatments resulted to be successful; in the case of a clay loam soil, the best strategy was the inoculation of S. indicatrix CPHE1 and NS (59.9% mineralized after 120 days). In sandy soils (CR and R soils) the highest percentage of mineralization was achieved in presence of HPBCD and NS (87.3% and 61.3%, respectively). However, the combination of CPHE1 strain, HPBCD, and NS showed to be the most efficient strategy for sandy and sandy loam soils (LL and ALC soils showed 35% and 74.6%, respectively). The results indicated a high degree of correlation between gene expression and the rates of mineralization.
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Affiliation(s)
- Alba Lara-Moreno
- Department of Agrochemistry, Environmental Microbiology and Soil Conservation, Institute of Natural Resources and Agrobiology of Seville, Spanish National Research Council (IRNAS-CSIC), Seville, Spain
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Seville, Seville, Spain
| | - Francisco Merchán
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Seville, Seville, Spain
| | - Esmeralda Morillo
- Department of Agrochemistry, Environmental Microbiology and Soil Conservation, Institute of Natural Resources and Agrobiology of Seville, Spanish National Research Council (IRNAS-CSIC), Seville, Spain
| | - Jessica Zampolli
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milano, Italy
| | - Patrizia Di Gennaro
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milano, Italy
| | - Jaime Villaverde
- Department of Agrochemistry, Environmental Microbiology and Soil Conservation, Institute of Natural Resources and Agrobiology of Seville, Spanish National Research Council (IRNAS-CSIC), Seville, Spain
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11
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Haubenthal T, Hansen P, Krämer I, Gindt M, Jünger-Leif A, Utermöhlen O, Haas A. Specific preadaptations of Rhodococcus equi cooperate with its Virulence-associated protein A during macrophage infection. Mol Microbiol 2023; 119:285-301. [PMID: 36627747 DOI: 10.1111/mmi.15026] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 01/03/2023] [Accepted: 01/04/2023] [Indexed: 01/12/2023]
Abstract
Gram-positive Rhodococcus equi (Prescotella equi) is a lung pathogen of foals and immunocompromised humans. Intra-macrophage multiplication requires production of the bacterial Virulence-associated protein A (VapA) which is released into the phagosome lumen. VapA pH-neutralizes intracellular compartments allowing R. equi to multiply in an atypical macrophage phagolysosome. Here, we show that VapA does not support intra-macrophage growth of several other bacterial species demonstrating that only few bacteria have the specific preadaptations needed to profit from VapA. We show that the closest relative of R. equi, environmental Rhodococcus defluvii (Prescotella defluvii), does not multiply in macrophages at 37°C even when VapA is present because of its thermosensitivity but it does so once the infection temperature is lowered providing rare experimental evidence for 'thermal restriction'. Using growth experiments with isolated macrophage lysosomes and modified infection schemes we provide evidence that R. equi resists the attack by phagolysosome contents at low pH for several hours. During this time, R. equi produces and secretes VapA which enables it to grow at the expense of lysosome constituents. We present arguments that, under natural infection conditions, R. equi is VapA-less during the initial encounter with the host. This has important implications for vaccine development.
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Affiliation(s)
| | - Philipp Hansen
- Institute for Cell Biology, University of Bonn, Bonn, Germany
| | - Ina Krämer
- Institute for Cell Biology, University of Bonn, Bonn, Germany
| | - Mélanie Gindt
- Institute for Cell Biology, University of Bonn, Bonn, Germany
| | | | - Olaf Utermöhlen
- Institute for Medical Microbiology, Immunology and Hygiene, University of Cologne, Germany
| | - Albert Haas
- Institute for Cell Biology, University of Bonn, Bonn, Germany
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12
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Adhesion of Rhodococcus bacteria to solid hydrocarbons and enhanced biodegradation of these compounds. Sci Rep 2022; 12:21559. [PMID: 36513758 PMCID: PMC9748138 DOI: 10.1038/s41598-022-26173-3] [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: 06/25/2022] [Accepted: 12/12/2022] [Indexed: 12/15/2022] Open
Abstract
Adhesive activities of hydrocarbon-oxidizing Rhodococcus bacteria towards solid hydrocarbons, effects of adhesion on biodegradation of these compounds by rhodococcal cells and adhesion mechanisms of Rhodococcus spp. were studied in this work. It was shown that efficiency of Rhodococcus cells' adhesion to solid n-alkanes and polycyclic aromatic hydrocarbons (PAHs) varied from 0.0 to 10.6·106 CFU/cm2. R. erythropolis IEGM 212 and R. opacus IEGM 262 demonstrated the highest (≥ 4.3·106 CFU/cm2) adhesion. The percentage biodegradation of solid hydrocarbons (n-hexacosane and anthracene as model substrates) by Rhodococcus cells was 5 to 60% at a hydrocarbon concentration of 0.2% (w/w) after 9 days and strongly depended on cell adhesive activities towards these compounds (r ≥ 0.71, p < 0.05). No strict correlation between the adhesive activities of rhodococcal cells and physicochemical properties of bacteria and hydrocarbons was detected. Roughness of the cell surface was a definitive factor of Rhodococcus cell adhesion to solid hydrocarbons. Specific appendages with high adhesion force (≥ 0.6 nN) and elastic modulus (≥ 6 MPa) were found on the surface of Rhodococcus cells with high surface roughness. We hypothesized that these appendages participated in the adhesion process.
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13
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Weisberg AJ, Miller M, Ream W, Grünwald NJ, Chang JH. Diversification of plasmids in a genus of pathogenic and nitrogen-fixing bacteria. Philos Trans R Soc Lond B Biol Sci 2022; 377:20200466. [PMID: 34839700 PMCID: PMC8628075 DOI: 10.1098/rstb.2020.0466] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Members of the agrobacteria-rhizobia complex (ARC) have multiple and diverse plasmids. The extent to which these plasmids are shared and the consequences of their interactions are not well understood. We extracted over 4000 plasmid sequences from 1251 genome sequences and constructed a network to reveal interactions that have shaped the evolutionary histories of oncogenic virulence plasmids. One newly discovered type of oncogenic plasmid is a mosaic with three incomplete, but complementary and partially redundant virulence loci. Some types of oncogenic plasmids recombined with accessory plasmids or acquired large regions not known to be associated with pathogenicity. We also identified two classes of partial virulence plasmids. One class is potentially capable of transforming plants, but not inciting disease symptoms. Another class is inferred to be incomplete and non-functional but can be found as coresidents of the same strain and together are predicted to confer pathogenicity. The modularity and capacity for some plasmids to be transmitted broadly allow them to diversify, convergently evolve adaptive plasmids and shape the evolution of genomes across much of the ARC. This article is part of the theme issue 'The secret lives of microbial mobile genetic elements'.
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Affiliation(s)
- Alexandra J. Weisberg
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
| | - Marilyn Miller
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
| | - Walt Ream
- Department of Microbiology, Oregon State University, Corvallis, OR 97331, USA
| | - Niklaus J. Grünwald
- Horticultural Crops Research Laboratory, United States Department of Agriculture and Agricultural Research Service, Corvallis, OR 97330, USA
| | - Jeff H. Chang
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
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Vail KJ, da Silveira BP, Bell SL, Cohen ND, Bordin AI, Patrick KL, Watson RO. The opportunistic intracellular bacterial pathogen Rhodococcus equi elicits type I interferon by engaging cytosolic DNA sensing in macrophages. PLoS Pathog 2021; 17:e1009888. [PMID: 34473814 PMCID: PMC8443056 DOI: 10.1371/journal.ppat.1009888] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 09/15/2021] [Accepted: 08/12/2021] [Indexed: 11/18/2022] Open
Abstract
Rhodococcus equi is a major cause of foal pneumonia and an opportunistic pathogen in immunocompromised humans. While alveolar macrophages constitute the primary replicative niche for R. equi, little is known about how intracellular R. equi is sensed by macrophages. Here, we discovered that in addition to previously characterized pro-inflammatory cytokines (e.g., Tnfa, Il6, Il1b), macrophages infected with R. equi induce a robust type I IFN response, including Ifnb and interferon-stimulated genes (ISGs), similar to the evolutionarily related pathogen, Mycobacterium tuberculosis. Follow up studies using a combination of mammalian and bacterial genetics demonstrated that induction of this type I IFN expression program is largely dependent on the cGAS/STING/TBK1 axis of the cytosolic DNA sensing pathway, suggesting that R. equi perturbs the phagosomal membrane and causes DNA release into the cytosol following phagocytosis. Consistent with this, we found that a population of ~12% of R. equi phagosomes recruits the galectin-3,-8 and -9 danger receptors. Interestingly, neither phagosomal damage nor induction of type I IFN require the R. equi’s virulence-associated plasmid. Importantly, R. equi infection of both mice and foals stimulates ISG expression, in organs (mice) and circulating monocytes (foals). By demonstrating that R. equi activates cytosolic DNA sensing in macrophages and elicits type I IFN responses in animal models, our work provides novel insights into how R. equi engages the innate immune system and furthers our understanding how this zoonotic pathogen causes inflammation and disease. Rhodococcus equi is a facultative intracellular bacterial pathogen of horses and other domestic animals, as well as an opportunistic pathogen of humans. In human patients, Rhodococcus pneumonia bears some pathological similarities to pulmonary tuberculosis, and poses a risk for misdiagnosis. In horses, R. equi infection has a major detrimental impact on the equine breeding industry due to a lack of an efficacious vaccine and its ubiquitous distribution in soil. Given the prevalence of subclinical infection and high false positive rate in current screening methods, there exists a critical need to identify factors contributing to host susceptibility. Here, we use a combination of bacterial genetics and animal models to investigate innate immune responses during R. equi infection. We found that R. equi modulates host immune sensing to elicit a type I interferon response in a manner resembling that of M. tuberculosis. We also found that the danger sensors galectin-3, -8, and -9 are recruited to a population of R. equi-containing vacuoles, independent of expression of VapA. Our research identifies innate immune sensing events and immune transcriptional signatures that may lead to biomarkers for clinical disease, more accurate screening methods, and insight into susceptibility to infection.
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Affiliation(s)
- Krystal J. Vail
- Department of Microbial Pathogenesis and Immunology, Texas A&M Health Science Center, Bryan, Texas, United States of America
- Department of Veterinary Pathology, Texas A&M University, College Station, Texas, United States of America
| | - Bibiana Petri da Silveira
- Department of Large Animal Clinical Sciences, Texas A&M University, College Station, Texas, United States of America
| | - Samantha L. Bell
- Department of Microbial Pathogenesis and Immunology, Texas A&M Health Science Center, Bryan, Texas, United States of America
| | - Noah D. Cohen
- Department of Large Animal Clinical Sciences, Texas A&M University, College Station, Texas, United States of America
| | - Angela I. Bordin
- Department of Large Animal Clinical Sciences, Texas A&M University, College Station, Texas, United States of America
| | - Kristin L. Patrick
- Department of Microbial Pathogenesis and Immunology, Texas A&M Health Science Center, Bryan, Texas, United States of America
| | - Robert O. Watson
- Department of Microbial Pathogenesis and Immunology, Texas A&M Health Science Center, Bryan, Texas, United States of America
- * E-mail:
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15
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Rampacci E, Marenzoni ML, Cannalire R, Pietrella D, Sabatini S, Giovagnoli S, Felicetti T, Pepe M, Passamonti F. Ethidium bromide exposure unmasks an antibiotic efflux system in Rhodococcus equi. J Antimicrob Chemother 2021; 76:2040-2048. [PMID: 33855442 DOI: 10.1093/jac/dkab121] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Accepted: 03/16/2021] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND This study introduces a newly created strain (Rhodococcus equiEtBr25) by exposing R. equi ATCC 33701 to ethidium bromide (EtBr), a substrate for MDR transporters. Such an approach allowed us to investigate the resulting phenotype and genetic mechanisms underlying the efflux-mediated resistance in R. equi. METHODS R. equi ATCC 33701 was stimulated with increasing concentrations of EtBr. The antimicrobial susceptibility of the parental strain and R. equiEtBr25 was investigated in the presence/absence of efflux pump inhibitors (EPIs). EtBr efflux was evaluated by EtBr-agar method and flow cytometry. The presence of efflux pump genes was determined by conventional PCR before to quantify the expression of 30 genes coding for membrane transporters by qPCR. The presence of erm(46) and mutations in 23S rRNA, and gyrA/gyrB was assessed by PCR and DNA sequencing to exclude the occurrence of resistance mechanisms other than efflux. RESULTS R. equi EtBr25 showed an increased EtBr efflux. Against this strain, the activity of EtBr, azithromycin and ciprofloxacin was more affected than that of rifampicin and azithromycin/rifampicin combinations. Resistances were reversed by combining the antimicrobials with EPIs. Gene expression analysis detected a marked up-regulation of REQ_RS13460 encoding for a Major Facilitator Superfamily (MFS) transporter. G→A transition occurred in the transcriptional repressor tetR/acrR adjacent to REQ_RS13460. CONCLUSIONS Exposure of R. equi to EtBr unmasked an efflux-mediated defence against azithromycin and ciprofloxacin, which seemingly correlates with the overexpression of a specific MFS transporter. This genotype may mirror an insidious low-level resistance of clinically important isolates that could be countered by EPI-based therapies.
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Affiliation(s)
- Elisa Rampacci
- Department of Veterinary Medicine, University of Perugia, via San Costanzo 4, 06126 Perugia, Italy
| | - Maria Luisa Marenzoni
- Department of Veterinary Medicine, University of Perugia, via San Costanzo 4, 06126 Perugia, Italy
| | - Rolando Cannalire
- Department of Pharmacy, University of Naples "Federico II", via D. Montesano 49, 80131 Napoli, Italy
| | - Donatella Pietrella
- Department of Medicine and Surgery, University of Perugia, via Gambuli 1, 06156 Perugia, Italy
| | - Stefano Sabatini
- Department of Pharmaceutical Sciences, University of Perugia, via del Liceo 1, 06123 Perugia, Italy
| | - Stefano Giovagnoli
- Department of Pharmaceutical Sciences, University of Perugia, via del Liceo 1, 06123 Perugia, Italy
| | - Tommaso Felicetti
- Department of Pharmaceutical Sciences, University of Perugia, via del Liceo 1, 06123 Perugia, Italy
| | - Marco Pepe
- Department of Veterinary Medicine, University of Perugia, via San Costanzo 4, 06126 Perugia, Italy
| | - Fabrizio Passamonti
- Department of Veterinary Medicine, University of Perugia, via San Costanzo 4, 06126 Perugia, Italy
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16
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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: 2.5] [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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17
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Antimicrobial resistance spectrum conferred by pRErm46 of emerging macrolide (multidrug)-resistant Rhodococcus equi. J Clin Microbiol 2021; 59:e0114921. [PMID: 34319806 DOI: 10.1128/jcm.01149-21] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
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 rpoBS531F 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 rpoBS531F mutation of the 2287 clone, while different rpoB mutations (S531L, S531Y) detected in two cases suggest the emergence of novel MDR R. equi strains.
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18
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Suzuki Y, Kubota H, Madarame H, Takase F, Takahashi K, Sasaki Y, Kakuda T, Takai S. Pathogenicity and genomic features of vapN-harboring Rhodococcus equi isolated from human patients. Int J Med Microbiol 2021; 311:151519. [PMID: 34280738 DOI: 10.1016/j.ijmm.2021.151519] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2021] [Revised: 05/20/2021] [Accepted: 07/01/2021] [Indexed: 11/16/2022] Open
Abstract
Rhodococcus equi is a saprophytic soil bacterium and intracellular pathogen that causes refractory suppurative pneumonia in foals and has emerged as a pathogenic cause of zoonotic disease. Several studies have reported human infections caused by R. equi harboring a recently described third type of virulence plasmid, the ruminant-associated pVAPN, which carries the vapN virulence determinant. Herein, we analyzed pathogenicity and genomic features of nine vapN-harboring R. equi isolated from human patients with and without HIV/AIDS. Four of these strains showed significant VapN production and proliferation in cultured macrophages. These strains were lethally pathogenic after inoculation with 1.0 × 108 CFU in mice and reproduced a necrotizing granulomatous inflammation in the liver and spleen similar to that observed in humans. Additionally, we determined entire genome sequences of all nine strains. Lengths of sequences were 5.0-5.3 Mbp, and GC contents were 68.7 %-68.8 %. All strains harbored a 120- or 125-kbp linear plasmid carrying vapN (Type I or Type II pVAPN) classified on the basis of differences in the distal sequences on the 3' side. Interestingly, VapN production differed significantly among strains harboring nearly identical types of pVAPN with variation limited to several SNPs and short base pair indels. The pVAPN sequences possessed by the VapN-producing strains did not retain any common genetic characteristics, and more detailed analyses, including chromosomal genes, are needed to further elucidate the VapN expression mechanism.
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Affiliation(s)
- Yasunori Suzuki
- Laboratory of Animal Hygiene, Kitasato University School of Veterinary Medicine, Aomori, Japan.
| | - Hiroaki Kubota
- Department of Microbiology, Tokyo Metropolitan Institute of Public Health, Tokyo, Japan
| | - Hiroo Madarame
- Laboratory of Small Animal Clinics, Veterinary Teaching Hospital, Azabu University, Kanagawa, Japan
| | - Fumiaki Takase
- Laboratory of Animal Hygiene, Kitasato University School of Veterinary Medicine, Aomori, Japan
| | - Kei Takahashi
- Laboratory of Animal Hygiene, Kitasato University School of Veterinary Medicine, Aomori, Japan
| | - Yukako Sasaki
- Laboratory of Animal Hygiene, Kitasato University School of Veterinary Medicine, Aomori, Japan
| | - Tsutomu Kakuda
- Laboratory of Animal Hygiene, Kitasato University School of Veterinary Medicine, Aomori, Japan
| | - Shinji Takai
- Laboratory of Animal Hygiene, Kitasato University School of Veterinary Medicine, Aomori, Japan
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Álvarez-Narváez S, Giguère S, Cohen N, Slovis N, Vázquez-Boland JA. Spread of Multidrug-Resistant Rhodococcus equi, United States. Emerg Infect Dis 2021; 27:529-537. [PMID: 33496218 PMCID: PMC7853588 DOI: 10.3201/eid2702.203030] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
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 rpoBS531F 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 rpoBS531Y 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.
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20
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Sangkanjanavanich N, Kakuda T, Suzuki Y, Sasaki Y, Takai S. Identification of genes required for the fitness of Rhodococcus equi during the infection of mice via signature-tagged transposon mutagenesis. J Vet Med Sci 2021; 83:1182-1190. [PMID: 34108307 PMCID: PMC8437726 DOI: 10.1292/jvms.21-0256] [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: 11/22/2022] Open
Abstract
Rhodococcus equi is a Gram-positive facultative intracellular bacterium that causes pyogranulomatous pneumonia in foals and immunocompromised people. In the present study, signature-tagged transposon mutagenesis was applied for the negative selection of R. equi mutants that cannot survive in vivo. Twenty-five distinguishable plasmid-transposon (plasposon) vectors by polymerase chain reaction (PCR), each containing a unique oligonucleotide tag, were constructed and used to select the transposon mutants that have in vivo fitness defects using a mouse systemic infection model. Of the 4,560 transposon mutants, 102 mutants were isolated via a real-time PCR-based screening as the mutants were unable to survive in the mouse model. Finally, 50 single transposon insertion sites were determined via the self-cloning strategy. The insertion of the transposon was seen on the virulence plasmid in 15 of the 50 mutants, whereas the remaining 35 mutants had the insertion of transposon on the chromosome. The chromosomal mutants contained transposon insertions in genes involved in cellular metabolism, DNA repair and recombination, gene regulation, non-ribosomal peptide synthesis, and unknown functions. Additionally, seven of the chromosomal mutants showed a reduced ability to multiply in the macrophages in vitro. In this study, we have identified several biosynthetic pathways as fitness factors associated with the growth within macrophages and survival in mice.
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Affiliation(s)
- Nuttapone Sangkanjanavanich
- Laboratory of Animal Hygiene, School of Veterinary Medicine, Kitasato University, Higashi 23-35-1, Towada, Aomori 034-8628, Japan
| | - Tsutomu Kakuda
- Laboratory of Animal Hygiene, School of Veterinary Medicine, Kitasato University, Higashi 23-35-1, Towada, Aomori 034-8628, Japan
| | - Yasunori Suzuki
- Laboratory of Animal Hygiene, School of Veterinary Medicine, Kitasato University, Higashi 23-35-1, Towada, Aomori 034-8628, Japan
| | - Yukako Sasaki
- Laboratory of Animal Hygiene, School of Veterinary Medicine, Kitasato University, Higashi 23-35-1, Towada, Aomori 034-8628, Japan
| | - Shinji Takai
- Laboratory of Animal Hygiene, School of Veterinary Medicine, Kitasato University, Higashi 23-35-1, Towada, Aomori 034-8628, Japan
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21
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Allegro AR, Barhoumi R, Bordin AI, Bray JM, Cohen ND. Uptake and replication in Acanthamoeba castellanii of a virulent (pVAPA-positive) strain of Rhodococcus equi and its isogenic, plasmid-cured strain. Vet Microbiol 2021; 257:109069. [PMID: 33862330 DOI: 10.1016/j.vetmic.2021.109069] [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: 10/14/2020] [Accepted: 04/07/2021] [Indexed: 11/16/2022]
Abstract
Rhodococcus equi is a soil saprophytic bacterium and intracellular pathogen that causes pneumonia in foals. Strains of R. equi that are virulent in foals contain a plasmid that encodes a virulence-associated protein A (VapA) necessary for replication in macrophages. Because other intracellular pathogens survive and replicate inside amoebae, we postulated that the VapA-bearing plasmid (pVAPA) confers a survival advantage for R. equi against environmental predators like amoebae. To test this hypothesis, we compared phagocytosis by and survival in Acanthamoeba castellanii of isogenic strains of pVAPA-positive and pVAPA-negative R. equi. Phagocytosis of the pVAPA-negative strain by A. castellanii was significantly (P < 0.0001) greater than the pVAPA-positive strain. Intracellular replication of the pVAPA-positive strain in A. castellanii was significantly (P < 0.0001) greater than the pVAPA-negative strain during both 48 h and 9 days. These results indicate that the presence of the VapA plasmid reduces uptake and aids replication of R. equi in A. castellanii.
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Affiliation(s)
- Angelica R Allegro
- Equine Infectious Disease Laboratory, Department of Large Animal Clinical Sciences, College of Veterinary Medicine & Biomedical Sciences, Texas A&M University, College Station, TX, 77843-4475, United States
| | - Rola Barhoumi
- Image Analysis Laboratory, Department of Veterinary Integrative Biosciences, College of Veterinary Medicine & Biomedical Sciences, Texas A&M University, College Station, TX, 77843-4458, United States
| | - 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, 77843-4475, United States
| | - 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, TX, 77843-4475, United States
| | - 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, 77843-4475, United States.
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22
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Detection of Rhodococcus fascians, the Causative Agent of Lily Fasciation in South Korea. Pathogens 2021; 10:pathogens10020241. [PMID: 33672562 PMCID: PMC7924060 DOI: 10.3390/pathogens10020241] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 02/10/2021] [Accepted: 02/18/2021] [Indexed: 12/03/2022] Open
Abstract
Rhodococcus fascians is an important pathogen that infects various herbaceous perennials and reduces their economic value. In this study, we examined R. fascians isolates carrying a virulence gene from symptomatic lily plants grown in South Korea. Phylogenetic analysis using the nucleotide sequences of 16S rRNA, vicA, and fasD led to the classification of the isolates into four different strains of R. fascians. Inoculation of Nicotiana benthamiana with these isolates slowed root growth and resulted in symptoms of leafy gall. These findings elucidate the diversification of domestic pathogenic R. fascians and may lead to an accurate causal diagnosis to help reduce economic losses in the bulb market.
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23
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Pátek M, Grulich M, Nešvera J. Stress response in Rhodococcus strains. Biotechnol Adv 2021; 53:107698. [PMID: 33515672 DOI: 10.1016/j.biotechadv.2021.107698] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 01/13/2021] [Accepted: 01/15/2021] [Indexed: 12/13/2022]
Abstract
Rhodococci are bacteria which can survive under various extreme conditions, in the presence of toxic compounds, and in other hostile habitats. Their tolerance of unfavorable conditions is associated with the structure of their cell wall and their large array of enzymes, which degrade or detoxify harmful compounds. Their physiological and biotechnological properties, together with tools for their genetic manipulation, enable us to apply them in biotransformations, biodegradation and bioremediation. Many such biotechnological applications cause stresses that positively or negatively affect their efficiency. Whereas numerous reviews on rhodococci described their enzyme activities, the optimization of degradation or production processes, and corresponding technological solutions, only a few reviews discussed some specific effects of stresses on the physiology of rhodococci and biotechnological processes. This review aims to comprehensively describe individual stress responses in Rhodococcus strains, the interconnection of different types of stresses and their consequences for cell physiology. We examine here the responses to (1) environmental stresses (desiccation, heat, cold, osmotic and pH stress), (2) the presence of stress-inducing compounds (metals, organic compounds and antibiotics) in the environment (3) starvation and (4) stresses encountered during biotechnological applications. Adaptations of the cell envelope, the formation of multicellular structures and stresses induced by the interactions of hosts with pathogenic rhodococci are also included. The roles of sigma factors of RNA polymerase in the global regulation of stress responses in rhodococci are described as well. Although the review covers a large number of stressful conditions, our intention was to provide an overview of the selected stress responses and their possible connection to biotechnological processes, not an exhaustive survey of the scientific literature. The findings on stress responses summarized in this review and the demonstration of gaps in current knowledge may motivate researchers working to fill these gaps.
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Affiliation(s)
- Miroslav Pátek
- Institute of Microbiology of the CAS, v. v. i., Prague, Czech Republic.
| | - Michal Grulich
- Institute of Microbiology of the CAS, v. v. i., Prague, Czech Republic.
| | - Jan Nešvera
- Institute of Microbiology of the CAS, v. v. i., Prague, Czech Republic.
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24
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Petry S, Sévin C, Kozak S, Foucher N, Laugier C, Linster M, Breuil MF, Dupuis MC, Hans A, Duquesne F, Tapprest J. Relationship between rifampicin resistance and RpoB substitutions of Rhodococcus equi strains isolated in France. J Glob Antimicrob Resist 2020; 23:137-144. [PMID: 32992034 DOI: 10.1016/j.jgar.2020.08.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 08/05/2020] [Accepted: 08/14/2020] [Indexed: 01/09/2023] Open
Abstract
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.
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Affiliation(s)
- Sandrine Petry
- ANSES, Laboratory for Animal Health in Normandy, Physiopathology and Epidemiology of Equine Diseases Unit, Goustranville, France.
| | - Corinne Sévin
- ANSES, Laboratory for Animal Health in Normandy, Physiopathology and Epidemiology of Equine Diseases Unit, Goustranville, France
| | - Sofia Kozak
- ANSES, Laboratory for Animal Health in Normandy, Physiopathology and Epidemiology of Equine Diseases Unit, Goustranville, France
| | - Nathalie Foucher
- ANSES, Laboratory for Animal Health in Normandy, Physiopathology and Epidemiology of Equine Diseases Unit, Goustranville, France
| | - Claire Laugier
- ANSES, Laboratory for Animal Health in Normandy, Physiopathology and Epidemiology of Equine Diseases Unit, Goustranville, France
| | - Maud Linster
- ANSES, Laboratory for Animal Health in Normandy, Physiopathology and Epidemiology of Equine Diseases Unit, Goustranville, France
| | - Marie-France Breuil
- ANSES, Laboratory for Animal Health in Normandy, Physiopathology and Epidemiology of Equine Diseases Unit, Goustranville, France
| | | | - Aymeric Hans
- ANSES, Laboratory for Animal Health in Normandy, Physiopathology and Epidemiology of Equine Diseases Unit, Goustranville, France
| | - Fabien Duquesne
- ANSES, Laboratory for Animal Health in Normandy, Physiopathology and Epidemiology of Equine Diseases Unit, Goustranville, France
| | - Jackie Tapprest
- ANSES, Laboratory for Animal Health in Normandy, Physiopathology and Epidemiology of Equine Diseases Unit, Goustranville, France
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25
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Khan N, Martínez-Hidalgo P, Humm EA, Maymon M, Kaplan D, Hirsch AM. Inoculation With a Microbe Isolated From the Negev Desert Enhances Corn Growth. Front Microbiol 2020; 11:1149. [PMID: 32636811 PMCID: PMC7316896 DOI: 10.3389/fmicb.2020.01149] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Accepted: 05/06/2020] [Indexed: 11/13/2022] Open
Abstract
Corn (Zea mays L.) is not only an important food source, but also has numerous uses, including for biofuels, fillers for cosmetics, glues, and so on. The amount of corn grown in the U.S. has significantly increased since the 1960's and with it, the demand for synthetic fertilizers and pesticides/fungicides to enhance its production. However, the downside of the continuous use of these products, especially N and P fertilizers, has been an increase in N2O emissions and other greenhouse gases into the atmosphere as well as run-off into waterways that fuel pollution and algal blooms. These approaches to agriculture, especially if exacerbated by climate change, will result in decreased soil health as well as human health. We searched for microbes from arid, native environments that are not being used for agriculture because we reasoned that indigenous microbes from such soils could promote plant growth and help restore degraded soils. Employing cultivation-dependent methods to isolate bacteria from the Negev Desert in Israel, we tested the effects of several microbial isolates on corn in both greenhouse and small field studies. One strain, Dietzia cinnamea 55, originally identified as Planomicrobium chinense, significantly enhanced corn growth over the uninoculated control in both greenhouse and outside garden experiments. We sequenced and analyzed the genome of this bacterial species to elucidate some of the mechanisms whereby D. cinnamea 55 promoted plant growth. In addition, to ensure the biosafety of this previously unknown plant growth promoting bacterial (PGPB) strain as a potential bioinoculant, we tested the survival and growth of Caenorhabditis elegans and Galleria mellonella (two animal virulence tests) as well as plants in response to D. cinnamea 55 inoculation. We also looked for genes for potential virulence determinants as well as for growth promotion.
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Affiliation(s)
- Noor Khan
- Department of Molecular, Cell & Developmental Biology, University of California, Los Angeles, Los Angeles, CA, United States
| | - Pilar Martínez-Hidalgo
- Department of Molecular, Cell & Developmental Biology, University of California, Los Angeles, Los Angeles, CA, United States.,Department of Biology, Geology, Physics and Inorganic Chemistry, Universidad Rey Juan Carlos, Madrid, Spain
| | - Ethan A Humm
- Department of Molecular, Cell & Developmental Biology, University of California, Los Angeles, Los Angeles, CA, United States
| | - Maskit Maymon
- Department of Molecular, Cell & Developmental Biology, University of California, Los Angeles, Los Angeles, CA, United States
| | - Drora Kaplan
- Department of Environmental Hydrology and Microbiology, Zuckerberg Institute for Water Research, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Beersheba, Israel
| | - Ann M Hirsch
- Department of Molecular, Cell & Developmental Biology, University of California, Los Angeles, Los Angeles, CA, United States.,Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, United States
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26
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Savory EA, Weisberg AJ, Stevens DM, Creason AL, Fuller SL, Pearce EM, Chang JH. Phytopathogenic Rhodococcus Have Diverse Plasmids With Few Conserved Virulence Functions. Front Microbiol 2020; 11:1022. [PMID: 32523572 PMCID: PMC7261884 DOI: 10.3389/fmicb.2020.01022] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Accepted: 04/27/2020] [Indexed: 11/13/2022] Open
Abstract
Rhodococcus is a genus of Gram-positive bacteria with species that can cause growth deformations to a large number of plant species. This ability to cause disease is hypothesized to be dependent on a cluster of three gene loci on an almost 200 kb-sized linear plasmid. To reevaluate the roles of some of the genes in pathogenicity, we constructed and characterized deletion mutants of fasR and four fas genes. Findings confirmed that fasR, which encodes a putative transcriptional regulator, is necessary for pathogenesis. However, three of the fas genes, implicated in the metabolism of plant growth promoting cytokinins, are dispensable for the ability of the pathogen to cause disease. We also used long-read sequencing technology to generate high quality genome sequences for two phytopathogenic strains in which virulence genes are diverged in sequence and/or hypothesized to have recombined into the chromosome. Surprisingly, findings showed that the two strains carry extremely diverse virulence plasmids. Ortholog clustering identified only 12 genes present on all three virulence plasmids. Rhodococcus requires a small number of horizontally acquired traits to be pathogenic and the transmission of the corresponding genes, via recombination and conjugation, has the potential to rapidly diversify plasmids and bacterial populations.
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Affiliation(s)
- Elizabeth A Savory
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States
| | - Alexandra J Weisberg
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States
| | - Danielle M Stevens
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States
| | - Allison L Creason
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States
| | - Skylar L Fuller
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States
| | - Emma M Pearce
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States
| | - Jeff H Chang
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States.,Center for Genome Research and Biocomputing, Oregon State University, Corvallis, OR, United States
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27
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Assessment of Antimicrobial Susceptibility of Virulent Strains of Rhodococcus equi Isolated From Foals and Soil of Horse Breeding Farms With and Without Endemic Infections. J Equine Vet Sci 2020; 91:103114. [PMID: 32684259 DOI: 10.1016/j.jevs.2020.103114] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Revised: 03/27/2020] [Accepted: 04/27/2020] [Indexed: 12/21/2022]
Abstract
Rhodococcus equi is an opportunistic, intracellular saprophyte that causes severe pyogranulomatous pneumonia in foals. The bacterium displays in vitro susceptibility to many antibiotics. The highest efficacy against R. equi in vitro and in vivo is achieved by using a combination of rifampicin and macrolide antibiotics. Recent years have seen an upward trend in the minimum inhibitory concentration (MIC) of rifampicin and erythromycin, suggesting increasing resistance of R. equi to these antibiotics. The aim of the study was to determine the antimicrobial activity of 24 selected antibiotics against R. equi strains isolated from dead foals and from the environment of horse breeding farms with and without endemic R. equi infections. Minimum inhibitory concentration gradient strips were used to determine the lowest concentration of the antibiotic that inhibited the growth of R. equi. Based on normal MIC distribution, an epidemiologic cutoff values (ECOFF) were assessed for particular antibiotics and R. equi strains. The results were compared with ECOFFs for S. aureus, according to the European Committee on Antimicrobial Susceptibility Testing data. The data indicate that the lowest MIC values were obtained for clarithromycin, rifampicin, imipenem, and vancomycin. The majority of R. equi strains can be classified as wild type in relation to the majority of antibiotics. A small percentage of strains presented non-WT (NWT) with the exception of SXT, for which 35% of strains were classified as NWT. The lack of interpretative criteria for R. equi creates a real problem in the assessment of antibiotic sensitivity both for clinical and scientific purposes.
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28
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Vázquez-Boland JA, Scortti M, Meijer WG. Conservation of Rhodococcus equi (Magnusson 1923) Goodfellow and Alderson 1977 and rejection of Rhodococcus hoagii (Morse 1912) Kämpfer et al. 2014. Int J Syst Evol Microbiol 2020; 70:3572-3576. [PMID: 32375930 PMCID: PMC7395624 DOI: 10.1099/ijsem.0.004090] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Revised: 01/07/2020] [Accepted: 02/18/2020] [Indexed: 01/07/2023] Open
Abstract
A recent taxonomic study confirmed the synonymy of Rhodococcus equi (Magnusson 1923) Goodfellow and Alderson 1977 and Corynebacterium hoagii (Morse 1912) Eberson 1918. As a result, both R. equi and C. hoagii were reclassified as Rhodococcus hoagii comb. nov. in application of the principle of priority of the Prokaryotic Code. Because R. equi is a well-known animal and zoonotic human pathogen, and a bacterial name solidly established in the veterinary and medical literature, we and others argued that the nomenclatural change may cause error and confusion and be potentially perilous. We have now additionally found that the nomenclatural type of the basonym C. hoagii, ATCC 7005T, does not correspond with the original description of the species C. hoagii in the early literature. Its inclusion as the C. hoagii type on the Approved Lists 1980 results in a change in the characters of the taxon and in C. hoagii designating two different bacteria. Moreover, ATCC 7005, the only strain in circulation under the name C. hoagii, does not have a well documented history; it is unclear why it was deposited as C. hoagii and a possible mix-up with a Corynebacterium (Rhodococcus) equi isolate is a reasonable assumption. We therefore request the rejection of Rhodococcus hoagii as a nomen ambiguum, nomen dubium and nomen perplexum in addition to nomen periculosum, and conservation of the name Rhodococcus equi, according to Rules 56ab of the Code.
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Affiliation(s)
- José A. Vázquez-Boland
- Microbial Pathogenesis Group, Edinburgh Medical School (Biomedical Sciences - Infection Medicine), University of Edinburgh, Chancellor’s Building, Little France campus, Edinburgh EH16 4SB, UK
| | - Mariela Scortti
- Microbial Pathogenesis Group, Edinburgh Medical School (Biomedical Sciences - Infection Medicine), University of Edinburgh, Chancellor’s Building, Little France campus, Edinburgh EH16 4SB, UK
| | - Wim G. Meijer
- UCD School of Biomolecular and Biomedical Science, University College Dublin, Dublin 4, Ireland
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29
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Mourenza Á, Collado C, Bravo-Santano N, Gil JA, Mateos LM, Letek M. The extracellular thioredoxin Etrx3 is required for macrophage infection in Rhodococcus equi. Vet Res 2020; 51:38. [PMID: 32156317 PMCID: PMC7063783 DOI: 10.1186/s13567-020-00763-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Accepted: 02/18/2020] [Indexed: 01/19/2023] Open
Abstract
Rhodococcus equi is an intracellular veterinary pathogen that is becoming resistant to current antibiotherapy. Genes involved in preserving redox homeostasis could be promising targets for the development of novel anti-infectives. Here, we studied the role of an extracellular thioredoxin (Etrx3/REQ_13520) in the resistance to phagocytosis. An etrx3-null mutant strain was unable to survive within macrophages, whereas the complementation with the etrx3 gene restored its intracellular survival rate. In addition, the deletion of etrx3 conferred to R. equi a high susceptibility to sodium hypochlorite. Our results suggest that Etrx3 is essential for the resistance of R. equi to specific oxidative agents.
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Affiliation(s)
- Álvaro Mourenza
- Department of Molecular Biology, Area of Microbiology, University of León, León, Spain
| | - Cristina Collado
- Department of Molecular Biology, Area of Microbiology, University of León, León, Spain
| | | | - José A Gil
- Department of Molecular Biology, Area of Microbiology, University of León, León, Spain
| | - Luís M Mateos
- Department of Molecular Biology, Area of Microbiology, University of León, León, Spain.
| | - Michal Letek
- Department of Molecular Biology, Area of Microbiology, University of León, León, Spain.
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30
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A Novel Screening Strategy Reveals ROS-Generating Antimicrobials That Act Synergistically against the Intracellular Veterinary Pathogen Rhodococcus equi. Antioxidants (Basel) 2020; 9:antiox9020114. [PMID: 32012850 PMCID: PMC7070597 DOI: 10.3390/antiox9020114] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Revised: 01/20/2020] [Accepted: 01/26/2020] [Indexed: 12/13/2022] Open
Abstract
Rhodococcus equi is a facultative intracellular pathogen that causes infections in foals and many other animals such as pigs, cattle, sheep, and goats. Antibiotic resistance is rapidly rising in horse farms, which makes ineffective current antibiotic treatments based on a combination of macrolides and rifampicin. Therefore, new therapeutic strategies are urgently needed to treat R. equi infections caused by antimicrobial resistant strains. Here, we employed a R. equi mycoredoxin-null mutant strain highly susceptible to oxidative stress to screen for novel ROS-generating antibiotics. Then, we used the well-characterized Mrx1-roGFP2 biosensor to confirm the redox stress generated by the most promising antimicrobial agents identified in our screening. Our results suggest that different combinations of antibacterial compounds that elicit oxidative stress are promising anti-infective strategies against R. equi. In particular, the combination of macrolides with ROS-generating antimicrobial compounds such as norfloxacin act synergistically to produce a potent antibacterial effect against R. equi. Therefore, our screening approach could be applied to identify novel ROS-inspired therapeutic strategies against intracellular pathogens.
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31
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Frederick J, Hennessy F, Horn U, de la Torre Cortés P, van den Broek M, Strych U, Willson R, Hefer CA, Daran JMG, Sewell T, Otten LG, Brady D. The complete genome sequence of the nitrile biocatalyst Rhodocccus rhodochrous ATCC BAA-870. BMC Genomics 2020; 21:3. [PMID: 31898479 PMCID: PMC6941271 DOI: 10.1186/s12864-019-6405-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Accepted: 12/16/2019] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Rhodococci are industrially important soil-dwelling Gram-positive bacteria that are well known for both nitrile hydrolysis and oxidative metabolism of aromatics. Rhodococcus rhodochrous ATCC BAA-870 is capable of metabolising a wide range of aliphatic and aromatic nitriles and amides. The genome of the organism was sequenced and analysed in order to better understand this whole cell biocatalyst. RESULTS The genome of R. rhodochrous ATCC BAA-870 is the first Rhodococcus genome fully sequenced using Nanopore sequencing. The circular genome contains 5.9 megabase pairs (Mbp) and includes a 0.53 Mbp linear plasmid, that together encode 7548 predicted protein sequences according to BASys annotation, and 5535 predicted protein sequences according to RAST annotation. The genome contains numerous oxidoreductases, 15 identified antibiotic and secondary metabolite gene clusters, several terpene and nonribosomal peptide synthetase clusters, as well as 6 putative clusters of unknown type. The 0.53 Mbp plasmid encodes 677 predicted genes and contains the nitrile converting gene cluster, including a nitrilase, a low molecular weight nitrile hydratase, and an enantioselective amidase. Although there are fewer biotechnologically relevant enzymes compared to those found in rhodococci with larger genomes, such as the well-known Rhodococcus jostii RHA1, the abundance of transporters in combination with the myriad of enzymes found in strain BAA-870 might make it more suitable for use in industrially relevant processes than other rhodococci. CONCLUSIONS The sequence and comprehensive description of the R. rhodochrous ATCC BAA-870 genome will facilitate the additional exploitation of rhodococci for biotechnological applications, as well as enable further characterisation of this model organism. The genome encodes a wide range of enzymes, many with unknown substrate specificities supporting potential applications in biotechnology, including nitrilases, nitrile hydratase, monooxygenases, cytochrome P450s, reductases, proteases, lipases, and transaminases.
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Affiliation(s)
- Joni Frederick
- Protein Technologies, CSIR Biosciences, Meiring Naude Road, Brummeria, Pretoria, South Africa
- Electron Microscope Unit, University of Cape Town, Rondebosch, 7701 South Africa
- Present Address: LadHyx, UMR CNRS 7646, École Polytechnique, 91128 Palaiseau, France
| | - Fritha Hennessy
- Protein Technologies, CSIR Biosciences, Meiring Naude Road, Brummeria, Pretoria, South Africa
| | - Uli Horn
- Meraka, CSIR, Meiring Naude Road, Brummeria, 0091 South Africa
| | - Pilar de la Torre Cortés
- Industrial Microbiology, Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Marcel van den Broek
- Industrial Microbiology, Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Ulrich Strych
- Biology and Biochemistry, University of Houston, 4800 Calhoun Road, Houston, TX 77204 USA
- Present Address: Department of Pediatrics, Section of Tropical Medicine, Baylor College of Medicine, 1102 Bates Avenue, Houston, TX 77030 USA
| | - Richard Willson
- Biology and Biochemistry, University of Houston, 4800 Calhoun Road, Houston, TX 77204 USA
- Chemical and Biomolecular Engineering, University of Houston, 4800 Calhoun Road, Houston, TX 77204 USA
| | - Charles A. Hefer
- Bioinformatics and Computational Biology Unit, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, 0002 South Africa
- Present Address: AgResearch Limited, Lincoln Research Centre, Private Bag 4749, Christchurch, 8140 New Zealand
| | - Jean-Marc G. Daran
- Industrial Microbiology, Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Trevor Sewell
- Electron Microscope Unit, University of Cape Town, Rondebosch, 7701 South Africa
| | - Linda G. Otten
- Biocatalysis, Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Dean Brady
- Protein Technologies, CSIR Biosciences, Meiring Naude Road, Brummeria, Pretoria, South Africa
- Molecular Sciences Institute, School of Chemistry, University of the Witwatersrand, PO, Wits, 2050 South Africa
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Comparative Genomic Analysis of Rhodococcus equi: An Insight into Genomic Diversity and Genome Evolution. Int J Genomics 2019; 2019:8987436. [PMID: 31950028 PMCID: PMC6948317 DOI: 10.1155/2019/8987436] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Revised: 07/24/2019] [Accepted: 08/11/2019] [Indexed: 12/03/2022] Open
Abstract
Rhodococcus equi, a member of the Rhodococcus genus, is a gram-positive pathogenic bacterium. Rhodococcus possesses an open pan-genome that constitutes the basis of its high genomic diversity and allows for adaptation to specific niche conditions and the changing host environments. Our analysis further showed that the core genome of R. equi contributes to the pathogenicity and niche adaptation of R. equi. Comparative genomic analysis revealed that the genomes of R. equi shared identical collinearity relationship, and heterogeneity was mainly acquired by means of genomic islands and prophages. Moreover, genomic islands in R. equi were always involved in virulence, resistance, or niche adaptation and possibly working with prophages to cause the majority of genome expansion. These findings provide an insight into the genomic diversity, evolution, and structural variation of R. equi and a valuable resource for functional genomic studies.
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Kumpf A, Partzsch A, Pollender A, Bento I, Tischler D. Two Homologous Enzymes of the GalU Family in Rhodococcus opacus 1CP- RoGalU1 and RoGalU2. Int J Mol Sci 2019; 20:ijms20225809. [PMID: 31752319 PMCID: PMC6888414 DOI: 10.3390/ijms20225809] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Revised: 11/15/2019] [Accepted: 11/16/2019] [Indexed: 01/15/2023] Open
Abstract
Uridine-5’-diphosphate (UDP)-glucose is reported as one of the most versatile building blocks within the metabolism of pro- and eukaryotes. The activated sugar moiety is formed by the enzyme UDP-glucose pyrophosphorylase (GalU). Two homologous enzymes (designated as RoGalU1 and RoGalU2) are encoded by most Rhodococcus strains, known for their capability to degrade numerous compounds, but also to synthesize natural products such as trehalose comprising biosurfactants. To evaluate their functionality respective genes of a trehalose biosurfactant producing model organism—Rhodococcus opacus 1CP—were cloned and expressed, proteins produced (yield up to 47 mg per L broth) and initially biochemically characterized. In the case of RoGalU2, the Vmax was determined to be 177 U mg−1 (uridine-5’-triphosphate (UTP)) and Km to be 0.51 mM (UTP), respectively. Like other GalUs this enzyme seems to be rather specific for the substrates UTP and glucose 1-phosphate, as it accepts only dTTP and galactose 1-phoshate in addition, but both with solely 2% residual activity. In comparison to other bacterial GalU enzymes the RoGalU2 was found to be somewhat higher in activity (factor 1.8) even at elevated temperatures. However, RoGalU1 was not obtained in an active form thus it remains enigmatic if this enzyme participates in metabolism.
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Affiliation(s)
- Antje Kumpf
- Environmental Microbiology, Institute of Biosciences, TU Bergakademie Freiberg, Leipziger Str. 29, 09599 Freiberg, Germany; (A.P.); (A.P.)
- EMBL Hamburg, Notkestr. 85, 22607 Hamburg, Germany;
- Microbial Biotechnology, Faculty of Biology & Biotechnology, Ruhr University Bochum, Universitätsstr. 150, 44780 Bochum, Germany
- Correspondence: (A.K.); (D.T.); Tel.: +49-234-32-22082 (A.K.); +49-234-32-22656 (D.T.)
| | - Anett Partzsch
- Environmental Microbiology, Institute of Biosciences, TU Bergakademie Freiberg, Leipziger Str. 29, 09599 Freiberg, Germany; (A.P.); (A.P.)
| | - André Pollender
- Environmental Microbiology, Institute of Biosciences, TU Bergakademie Freiberg, Leipziger Str. 29, 09599 Freiberg, Germany; (A.P.); (A.P.)
| | - Isabel Bento
- EMBL Hamburg, Notkestr. 85, 22607 Hamburg, Germany;
| | - Dirk Tischler
- Microbial Biotechnology, Faculty of Biology & Biotechnology, Ruhr University Bochum, Universitätsstr. 150, 44780 Bochum, Germany
- Correspondence: (A.K.); (D.T.); Tel.: +49-234-32-22082 (A.K.); +49-234-32-22656 (D.T.)
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Mourenza Á, Bravo-Santano N, Pradal I, Gil JA, Mateos LM, Letek M. Mycoredoxins Are Required for Redox Homeostasis and Intracellular Survival in the Actinobacterial Pathogen Rhodococcus equi. Antioxidants (Basel) 2019; 8:antiox8110558. [PMID: 31731720 PMCID: PMC6912445 DOI: 10.3390/antiox8110558] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 11/11/2019] [Accepted: 11/13/2019] [Indexed: 12/11/2022] Open
Abstract
Rhodococcus equi is a facultative intracellular pathogen that can survive within macrophages of a wide variety of hosts, including immunosuppressed humans. Current antibiotherapy is often ineffective, and novel therapeutic strategies are urgently needed to tackle infections caused by this pathogen. In this study, we identified three mycoredoxin-encoding genes (mrx) in the genome of R. equi, and we investigated their role in virulence. Importantly, the intracellular survival of a triple mrx-null mutant (Δmrx1Δmrx2Δmrx3) in murine macrophages was fully impaired. However, each mycoredoxin alone could restore the intracellular proliferation rate of R. equi Δmrx1Δmrx2Δmrx3 to wild type levels, suggesting that these proteins could have overlapping functions during host cell infection. Experiments with the reduction-oxidation sensitive green fluorescent protein 2 (roGFP2) biosensor confirmed that R. equi was exposed to redox stress during phagocytosis, and mycoredoxins were involved in preserving the redox homeostasis of the pathogen. Thus, we studied the importance of each mycoredoxin for the resistance of R. equi to different oxidative stressors. Interestingly, all mrx genes did have overlapping roles in the resistance to sodium hypochlorite. In contrast, only mrx1 was essential for the survival against high concentrations of nitric oxide, while mrx3 was not required for the resistance to hydrogen peroxide. Our results suggest that all mycoredoxins have important roles in redox homeostasis, contributing to the pathogenesis of R. equi and, therefore, these proteins may be considered interesting targets for the development of new anti-infectives.
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Affiliation(s)
- Álvaro Mourenza
- Department of Molecular Biology, Area of Microbiology, University of León, 24071 León, Spain; (Á.M.); (I.P.); (J.A.G.)
| | | | - Inés Pradal
- Department of Molecular Biology, Area of Microbiology, University of León, 24071 León, Spain; (Á.M.); (I.P.); (J.A.G.)
| | - Jose A. Gil
- Department of Molecular Biology, Area of Microbiology, University of León, 24071 León, Spain; (Á.M.); (I.P.); (J.A.G.)
| | - Luis M. Mateos
- Department of Molecular Biology, Area of Microbiology, University of León, 24071 León, Spain; (Á.M.); (I.P.); (J.A.G.)
- Correspondence: (L.M.M.); (M.L.)
| | - Michal Letek
- Health Sciences Research Centre, University of Roehampton, London SW15 4JD, UK;
- Correspondence: (L.M.M.); (M.L.)
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Clonal Confinement of a Highly Mobile Resistance Element Driven by Combination Therapy in Rhodococcus equi. mBio 2019; 10:mBio.02260-19. [PMID: 31615959 PMCID: PMC6794481 DOI: 10.1128/mbio.02260-19] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
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 rpoBS531F 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.
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36
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Thapa SP, Davis EW, Lyu Q, Weisberg AJ, Stevens DM, Clarke CR, Coaker G, Chang JH. The Evolution, Ecology, and Mechanisms of Infection by Gram-Positive, Plant-Associated Bacteria. ANNUAL REVIEW OF PHYTOPATHOLOGY 2019; 57:341-365. [PMID: 31283433 DOI: 10.1146/annurev-phyto-082718-100124] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Gram-positive bacteria are prominent members of plant-associated microbial communities. Although many are hypothesized to be beneficial, some are causative agents of economically important diseases of crop plants. Because the features of Gram-positive bacteria are fundamentally different relative to those of Gram-negative bacteria, the evolution and ecology as well as the mechanisms used to colonize and infect plants also differ. Here, we discuss recent advances in our understanding of Gram-positive, plant-associated bacteria and provide a framework for future research directions on these important plant symbionts.
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Affiliation(s)
- Shree P Thapa
- Department of Plant Pathology, University of California, Davis, California 95616, USA
| | - Edward W Davis
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon 97331, USA;
- Molecular and Cellular Biology Program, Oregon State University, Corvallis, Oregon 97331, USA
- Center for Genome Research and Biocomputing, Oregon State University, Corvallis, Oregon 97331, USA
| | - Qingyang Lyu
- Department of Plant Pathology, University of California, Davis, California 95616, USA
| | - Alexandra J Weisberg
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon 97331, USA;
| | - Danielle M Stevens
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon 97331, USA;
- Integrative Genetics and Genomics, University of California, Davis, California 95616, USA
| | - Christopher R Clarke
- Genetic Improvement for Fruits and Vegetables Laboratory, Agricultural Research Service, US Department of Agriculture, Beltsville, Maryland 20705, USA
| | - Gitta Coaker
- Department of Plant Pathology, University of California, Davis, California 95616, USA
| | - Jeff H Chang
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon 97331, USA;
- Molecular and Cellular Biology Program, Oregon State University, Corvallis, Oregon 97331, USA
- Center for Genome Research and Biocomputing, Oregon State University, Corvallis, Oregon 97331, USA
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37
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Bujold AR, Lani NR, Sanz MG. Strain-to-strain variation of Rhodococcus equi growth and biofilm formation in vitro. BMC Res Notes 2019; 12:519. [PMID: 31426832 PMCID: PMC6701102 DOI: 10.1186/s13104-019-4560-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Accepted: 08/10/2019] [Indexed: 01/01/2023] Open
Abstract
OBJECTIVE Rhodococcus equi is an opportunistic pathogen that causes disease worldwide in young foals and immunocompromised humans. The interactions of R. equi with the host immune system have been described; however, most studies have been conducted using a few well-characterized strains. Because biological differences between R. equi strains are not well characterized, it is unknown if experimental results will replicate when different strains are used. Therefore, our objective was to compare the growth and biofilm formation of low-passage-rate clinical isolates of R. equi to higher-passage-rate, commonly studied isolates to determine whether strain-to-strain variation exists. RESULTS Twelve strains were used: 103+, ATCC 33701, UKVDL206 103S harboring a GFP-expressing plasmid, a plasmid-cured 33701 (higher-passage-rate) and seven low-passage clinical isolates. Generation time in liquid revealed fast, moderate-fast, moderate-slow, and slow-growing isolates. The higher-passage-rate isolates were among the moderate-slow growing strains. A strain's rate of growth did not correspond to its ability to form biofilm nor to its colony size on solid media. Based on our results, care should be taken not to extrapolate in vitro work that may be conducted using different R. equi strains. Further work is needed to evaluate the effect that the observed differences may have on experimental results.
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Affiliation(s)
- Adina R Bujold
- Department of Veterinary Clinical Sciences, Washington State University, Pullman, WA, USA
| | - Nicholas R Lani
- Department of Veterinary Clinical Sciences, Washington State University, Pullman, WA, USA
| | - Macarena G Sanz
- Department of Veterinary Clinical Sciences, Washington State University, Pullman, WA, USA.
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Paterson ML, Ranasinghe D, Blom J, Dover LG, Sutcliffe IC, Lopes B, Sangal V. Genomic analysis of a novel Rhodococcus (Prescottella) equi isolate from a bovine host. Arch Microbiol 2019; 201:1317-1321. [PMID: 31302711 PMCID: PMC6790187 DOI: 10.1007/s00203-019-01695-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Revised: 06/06/2019] [Accepted: 06/20/2019] [Indexed: 01/02/2023]
Abstract
Rhodococcus (Prescottella) equi causes pneumonia-like infections in foals with high mortality rates and can also infect a number of other animals. R. equi is also emerging as an opportunistic human pathogen. In this study, we have sequenced the genome of a novel R. equi isolate, B0269, isolated from the faeces of a bovine host. Comparative genomic analyses with seven other published R. equi genomes, including those from equine or human sources, revealed a pangenome comprising of 6876 genes with 4141 genes in the core genome. Two hundred and 75 genes were specific to the bovine isolate, mostly encoding hypothetical proteins of unknown function. However, these genes include four copies of terA and five copies of terD genes that may be involved in responding to chemical stress. Virulence characteristics in R. equi are associated with the presence of large plasmids carrying a pathogenicity island, including genes from the vap multigene family. A BLAST search of the protein sequences from known virulence-associated plasmids (pVAPA, pVAPB and pVAPN) revealed a similar plasmid backbone on two contigs in bovine isolate B0269; however, no homologues of the main virulence-associated genes, vapA, vapB or vapN, were identified. In summary, this study confirms that R. equi genomes are highly conserved and reports the presence of an apparently novel plasmid in the bovine isolate B0269 that needs further characterisation to understand its potential involvement in virulence properties.
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Affiliation(s)
- Megan L Paterson
- Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, NE1 8ST, UK
| | - Diyanath Ranasinghe
- Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, NE1 8ST, UK
| | - Jochen Blom
- Bioinformatics and Systems Biology, Justus-Liebig-Universität, Giessen, Germany
| | - Lynn G Dover
- Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, NE1 8ST, UK
| | - Iain C Sutcliffe
- Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, NE1 8ST, UK
| | - Bruno Lopes
- School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Foresterhill, Aberdeen, AB25 2ZD, UK
| | - Vartul Sangal
- Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, NE1 8ST, UK.
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Vázquez‐Boland JA, Meijer WG. The pathogenic actinobacterium Rhodococcus equi: what's in a name? Mol Microbiol 2019; 112:1-15. [PMID: 31099908 PMCID: PMC6852188 DOI: 10.1111/mmi.14267] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/25/2019] [Indexed: 12/17/2022]
Abstract
Rhodococcus equi is the only recognized animal pathogenic species within an extended genus of metabolically versatile Actinobacteria of considerable biotechnological interest. Best known as a horse pathogen, R. equi is commonly isolated from other animal species, particularly pigs and ruminants, and causes severe opportunistic infections in people. As typical in the rhodococci, R. equi niche specialization is extrachromosomally determined, via a conjugative virulence plasmid that promotes intramacrophage survival. Progress in the molecular understanding of R. equi and its recent rise as a novel paradigm of multihost adaptation has been accompanied by an unusual nomenclatural instability, with a confusing succession of names: "Prescottia equi", "Prescotella equi", Corynebacterium hoagii and Rhodococcus hoagii. This article reviews current advances in the genomics, biology and virulence of this pathogenic actinobacterium with a unique mechanism of plasmid-transferable animal host tropism. It also discusses the taxonomic and nomenclatural issues around R. equi in the light of recent phylogenomic evidence that confirms its membership as a bona fide Rhodococcus.
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Affiliation(s)
- José A. Vázquez‐Boland
- Microbial Pathogenesis Group, Edinburgh Medical School (Biomedical Sciences – Infection Medicine)University of EdinburghChancellor's Building, Little France campusEdinburghEH16 4SBUK
| | - Wim G. Meijer
- UCD School of Biomolecular and Biomedical ScienceUniversity College DublinDublin 4Ireland
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40
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Gregson BH, Metodieva G, Metodiev MV, Golyshin PN, McKew BA. Differential Protein Expression During Growth on Medium Versus Long-Chain Alkanes in the Obligate Marine Hydrocarbon-Degrading Bacterium Thalassolituus oleivorans MIL-1. Front Microbiol 2018; 9:3130. [PMID: 30619200 PMCID: PMC6304351 DOI: 10.3389/fmicb.2018.03130] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Accepted: 12/04/2018] [Indexed: 02/02/2023] Open
Abstract
The marine obligate hydrocarbonoclastic bacterium Thalassolituus oleivorans MIL-1 metabolizes a broad range of aliphatic hydrocarbons almost exclusively as carbon and energy sources. We used LC-MS/MS shotgun proteomics to identify proteins involved in aerobic alkane degradation during growth on medium- (n-C14) or long-chain (n-C28) alkanes. During growth on n-C14, T. oleivorans expresses an alkane monooxygenase system involved in terminal oxidation including two alkane 1-monooxygenases, a ferredoxin, a ferredoxin reductase and an aldehyde dehydrogenase. In contrast, during growth on long-chain alkanes (n-C28), T. oleivorans may switch to a subterminal alkane oxidation pathway evidenced by significant upregulation of Baeyer-Villiger monooxygenase and an esterase, proteins catalyzing ketone and ester metabolism, respectively. The metabolite (primary alcohol) generated from terminal oxidation of an alkane was detected during growth on n-C14 but not on n-C28 also suggesting alternative metabolic pathways. Expression of both active and passive transport systems involved in uptake of long-chain alkanes was higher when compared to the non-hydrocarbon control, including a TonB-dependent receptor, a FadL homolog and a specialized porin. Also, an inner membrane transport protein involved in the export of an outer membrane protein was expressed. This study has demonstrated the substrate range of T. oleivorans is larger than previously reported with growth from n-C10 up to n-C32. It has also greatly enhanced our understanding of the fundamental physiology of T. oleivorans, a key bacterium that plays a significant role in natural attenuation of marine oil pollution, by identifying key enzymes expressed during the catabolism of n-alkanes.
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Affiliation(s)
- Benjamin H Gregson
- School of Biological Sciences, University of Essex, Colchester, United Kingdom
| | - Gergana Metodieva
- School of Biological Sciences, University of Essex, Colchester, United Kingdom
| | - Metodi V Metodiev
- School of Biological Sciences, University of Essex, Colchester, United Kingdom
| | - Peter N Golyshin
- School of Biological Sciences, Bangor University, Bangor, United Kingdom.,School of Natural Sciences, College of Environmental Sciences and Engineering, Bangor University, Bangor, United Kingdom
| | - Boyd A McKew
- School of Biological Sciences, University of Essex, Colchester, United Kingdom
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Ito K, Harada M, Nakajima N, Yamamura S, Tomita M, Suzuki H, Amachi S. Genomic Analysis of Rhodococcus sp. Br-6, a Bromate Reducing Bacterium Isolated From Soil in Chiba, Japan. J Genomics 2018; 6:122-126. [PMID: 30510597 PMCID: PMC6275400 DOI: 10.7150/jgen.27741] [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: 06/08/2018] [Accepted: 07/26/2018] [Indexed: 11/06/2022] Open
Abstract
Bromate is a byproduct of the ozone disinfection of drinking water. It is a genotoxic carcinogen and causes renal cell tumors in rats. Physicochemical removal of bromate is very difficult, making microbial reduction of bromate to bromide a promising approach to eliminate bromate from water. Rhodococcus sp. Br-6, isolated from soil, can efficiently reduce bromate by using acetate as an electron donor. We determined the draft genome sequence of Rhodococcus sp. Br-6 for the potential practical application of the bromate-reducing bacterium. Core genome phylogeny suggests that the Br-6 strain is most closely related to R. equi. The Br-6 genome contains genes encoding multiple isoforms of diaphorase, previously found to be involved in Br-6-mediated bromate reduction. The genes identified in the present study could be effective targets for experimental studies of microbial bromate reduction in the future.
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Affiliation(s)
- Kohei Ito
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, Japan.,Faculty of Environment and Information Studies, Keio University, Fujisawa, Kanagawa, Japan
| | - Masafumi Harada
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, Japan.,Faculty of Environment and Information Studies, Keio University, Fujisawa, Kanagawa, Japan
| | - Nobuyoshi Nakajima
- Center for Environmental Biology and Ecosystem Studies, National Institute for Environmental Studies, Tsukuba, Ibaraki, Japan
| | - Shigeki Yamamura
- Center for Environmental Biology and Ecosystem Studies, National Institute for Environmental Studies, Tsukuba, Ibaraki, Japan.,Center for Regional Environmental Research, National Institute for Environmental Studies, Tsukuba, Ibaraki, Japan
| | - Masaru Tomita
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, Japan.,Faculty of Environment and Information Studies, Keio University, Fujisawa, Kanagawa, Japan
| | - Haruo Suzuki
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, Japan.,Faculty of Environment and Information Studies, Keio University, Fujisawa, Kanagawa, Japan
| | - Seigo Amachi
- Graduate School of Horticulture, Chiba University, Matsudo City, Chiba, Japan
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42
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Bargen K, Scraba M, Krämer I, Ketterer M, Nehls C, Krokowski S, Repnik U, Wittlich M, Maaser A, Zapka P, Bunge M, Schlesinger M, Huth G, Klees A, Hansen P, Jeschke A, Bendas G, Utermöhlen O, Griffiths G, Gutsmann T, Wohlmann J, Haas A. Virulence‐associated protein A fromRhodococcus equiis an intercompartmental pH‐neutralising virulence factor. Cell Microbiol 2018; 21:e12958. [DOI: 10.1111/cmi.12958] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Revised: 08/17/2018] [Accepted: 09/04/2018] [Indexed: 12/26/2022]
Affiliation(s)
- Kristine Bargen
- Division of Biophysics, Cell Biology InstituteUniversity of Bonn Bonn Germany
| | - Mirella Scraba
- Division of Biophysics, Cell Biology InstituteUniversity of Bonn Bonn Germany
| | - Ina Krämer
- Division of Biophysics, Cell Biology InstituteUniversity of Bonn Bonn Germany
| | - Maren Ketterer
- Division of Biophysics, Cell Biology InstituteUniversity of Bonn Bonn Germany
| | | | - Sina Krokowski
- Division of Biophysics, Cell Biology InstituteUniversity of Bonn Bonn Germany
| | - Urska Repnik
- Department of BiosciencesUniversity of Oslo Oslo Norway
| | - Michaela Wittlich
- Division of Biophysics, Cell Biology InstituteUniversity of Bonn Bonn Germany
| | - Anna Maaser
- Division of Biophysics, Cell Biology InstituteUniversity of Bonn Bonn Germany
| | - Pia Zapka
- Division of Biophysics, Cell Biology InstituteUniversity of Bonn Bonn Germany
| | - Madeleine Bunge
- Division of Biophysics, Cell Biology InstituteUniversity of Bonn Bonn Germany
| | | | - Gitta Huth
- Division of Biophysics, Cell Biology InstituteUniversity of Bonn Bonn Germany
| | - Annette Klees
- Division of Biophysics, Cell Biology InstituteUniversity of Bonn Bonn Germany
| | - Philipp Hansen
- Division of Biophysics, Cell Biology InstituteUniversity of Bonn Bonn Germany
| | - Andreas Jeschke
- Division of Biophysics, Cell Biology InstituteUniversity of Bonn Bonn Germany
| | - Gerd Bendas
- Pharmaceutical InstituteUniversity of Bonn Bonn Germany
| | - Olaf Utermöhlen
- Institute for Medical Microbiology, Immunology and Hygiene, University Medical Center, and Center for Molecular Medicine Köln, and German Center for Infection Research (DCIF) Cologne Germany
| | | | | | - Jens Wohlmann
- Division of Biophysics, Cell Biology InstituteUniversity of Bonn Bonn Germany
- Department of BiosciencesUniversity of Oslo Oslo Norway
| | - Albert Haas
- Division of Biophysics, Cell Biology InstituteUniversity of Bonn Bonn Germany
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43
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Lasek R, Szuplewska M, Mitura M, Decewicz P, Chmielowska C, Pawłot A, Sentkowska D, Czarnecki J, Bartosik D. Genome Structure of the Opportunistic Pathogen Paracoccus yeei ( Alphaproteobacteria) and Identification of Putative Virulence Factors. Front Microbiol 2018; 9:2553. [PMID: 30410477 PMCID: PMC6209633 DOI: 10.3389/fmicb.2018.02553] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Accepted: 10/05/2018] [Indexed: 12/17/2022] Open
Abstract
Bacteria of the genus Paracoccus are common components of the microbiomes of many naturally- and anthropogenically shaped environments. One species, Paracoccus yeei, is unique within the genus because it is associated with opportunistic human infections. Therefore, strains of P. yeei may serve as an interesting model to study the transition from a saprophytic to a pathogenic lifestyle in environmental bacteria. Unfortunately, knowledge concerning the biology, genetics and genomic content of P. yeei is fragmentary; also the mechanisms of pathogenicity of this bacterium remain unclear. In this study we provide the first insight into the genome composition and metabolic potential of a clinical isolate, P. yeei CCUG 32053. This strain has a multipartite genome (4,632,079 bp) composed of a circular chromosome plus eight extrachromosomal replicons pYEE1–8: 3 chromids and 5 plasmids, with a total size of 1,247,173 bp. The genome has been significantly shaped by the acquisition of genomic islands, prophages (Myoviridae and Siphoviridae phage families) and numerous insertion sequences (ISs) representing seven IS families. Detailed comparative analysis with other complete genomic sequences of Paracoccus spp. (including P. yeei FDAARGOS_252 and TT13, as well as non-pathogenic strains of other species in this genus) enabled us to identify P. yeei species-specific genes and to predict putative determinants of virulence. This is the first attempt to identify pathoadaptive genetic information of P. yeei and to estimate the role of the mobilome in the evolution of pathogenicity in this species.
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Affiliation(s)
- Robert Lasek
- Department of Bacterial Genetics, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Magdalena Szuplewska
- Department of Bacterial Genetics, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Monika Mitura
- Department of Bacterial Genetics, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Przemysław Decewicz
- Department of Bacterial Genetics, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Cora Chmielowska
- Department of Bacterial Genetics, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Aleksandra Pawłot
- Department of Bacterial Genetics, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Dorota Sentkowska
- Department of Bacterial Genetics, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Jakub Czarnecki
- Department of Bacterial Genetics, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Dariusz Bartosik
- Department of Bacterial Genetics, Faculty of Biology, University of Warsaw, Warsaw, Poland
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44
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Kalinowski M, Grądzki Z, Jarosz Ł, Adaszek Ł. Molecular analysis of the chromosomal 16S rRNA gene and vapA plasmid gene of Polish field strains of R. equi. PLoS One 2018; 13:e0204024. [PMID: 30252885 PMCID: PMC6155501 DOI: 10.1371/journal.pone.0204024] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Accepted: 08/31/2018] [Indexed: 12/29/2022] Open
Abstract
Rhodococcus equi (R. hoagii) is an opportunistic pathogen commonly found in foals up to 6 months old and animal environment. The R. equi genome contains genetically stable chromosomal DNA and an 80–90 kb plasmid containing vapA gene, responsible for virulence. Most reports from around the world focus on the determination of R. equi plasmid profiles. Few studies have attempted to determine differences in nucleotide sequences between virulent strains of R. equi isolated from foals and breeding environment. The aim of the study was to perform a molecular analysis of a fragment of the chromosomal gene encoding the 16S rRNA subunit and the vapA plasmid gene of virulent R. equi strains isolated on Polish studs from foals and from the breeding environment of horses. The sequencing method was used to compare the primary structure of fragments of the chromosomal and plasmid DNA of the virulent R. equi strains. The sequences of 22 clinical and 18 environmental R. equi isolates were compared with the sequences of the gene fragments of reference strains available in the NCBI GenBank database. All sequenced 16S rRNA amplicons of Polish field strains were identical and showed 99.5% similarity to the four randomly selected sequences of this gene fragment in the GenBank database. The results confirm that fragments of the 16S rRNA gene of R. equi strains are highly conserved and do not undergo variation in field conditions. Analysis of the sequencing results for the vapA gene fragment of the strains used in our study revealed two polymorphic variants and clear differences between the sequences of strains isolated from foals and from soil samples. Presumably, R. equi strains present in the breeding environment are more exposed than clinical strains to adverse external factors. This may result in changes in the DNA sequence due to natural selection.
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Affiliation(s)
- Marcin Kalinowski
- Department of Epizootiology and Clinic of Infectious Diseases, Faculty of Veterinary Medicine, University of Life Sciences in Lublin, Lublin, Poland
- * E-mail:
| | - Zbigniew Grądzki
- Department of Epizootiology and Clinic of Infectious Diseases, Faculty of Veterinary Medicine, University of Life Sciences in Lublin, Lublin, Poland
| | - Łukasz Jarosz
- Department of Epizootiology and Clinic of Infectious Diseases, Faculty of Veterinary Medicine, University of Life Sciences in Lublin, Lublin, Poland
| | - Łukasz Adaszek
- Department of Epizootiology and Clinic of Infectious Diseases, Faculty of Veterinary Medicine, University of Life Sciences in Lublin, Lublin, Poland
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45
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Bordin AI, Gressler LT, Alexander ERC, Sule P, Cirillo JD, Edwards JF, Cohen ND. Guinea pig infection with the intracellular pathogen Rhodococcus equi. Vet Microbiol 2018; 215:18-22. [PMID: 29426401 DOI: 10.1016/j.vetmic.2017.11.019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Revised: 10/04/2017] [Accepted: 11/17/2017] [Indexed: 11/29/2022]
Abstract
Rhodococcus equi is an opportunistic, intracellular pathogen that causes pyogranulomatous pneumonia in foals and immunocompromised people. Currently, there is no experimental model of R. equi pneumonia other than intra-bronchial experimental infection of foals with R. equi, which is labor-intensive and costly. This study's objective was to develop a guinea pig (GP) model of R. equi pneumonia that would facilitate development of novel approaches for controlling and preventing this disease. Guinea pigs were infected with either 101, 102, 103, or 104 colony forming units (CFUs) of a virulent strain of R. equi using a Madison aerosol chamber, or 106 or 107 CFUs of this strain intratracheally. Animals were monitored daily for clinical signs of pneumonia, and were euthanized and necropsied on days 1, 3, 7, or 35 post-infection (PI). Lung homogenates were plated onto selective agar to determine bacterial load. No clinical signs of disease were observed regardless of the inoculum dose or infection method. No bacteria were recovered from GPs euthanized at 35 days PI. Histology and immunostaining of T-cells, B-cells, and macrophages in lungs showed that inflammatory responses in infected GPs were similarly unremarkable irrespective of dose or route of infection. Guinea pigs appear to be resistant to pulmonary infection with virulent R. equi even at doses that reliably produce clinical pneumonia in foals.
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Affiliation(s)
- Angela I Bordin
- Equine Infectious Disease Laboratory, Department of Large Animal Clinical Sciences, Texas A&M University, College Station, TX, USA.
| | - Leticia T Gressler
- Equine Infectious Disease Laboratory, Department of Large Animal Clinical Sciences, Texas A&M University, College Station, TX, USA
| | - Ellen Ruth C Alexander
- Equine Infectious Disease Laboratory, Department of Large Animal Clinical Sciences, Texas A&M University, College Station, TX, USA
| | - Preeti Sule
- Department of Microbial Pathogenesis and Immunology, Texas A&M Health Science Center, College Station, TX, USA
| | - Jeffrey D Cirillo
- Department of Microbial Pathogenesis and Immunology, Texas A&M Health Science Center, College Station, TX, USA
| | - John F Edwards
- Department of Veterinary Pathobiology, Texas A&M University, College Station, TX, USA
| | - Noah D Cohen
- Equine Infectious Disease Laboratory, Department of Large Animal Clinical Sciences, Texas A&M University, College Station, TX, USA.
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46
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Wright LM, Carpinone EM, Bennett TL, Hondalus MK, Starai VJ. VapA of Rhodococcus equi binds phosphatidic acid. Mol Microbiol 2017; 107:428-444. [PMID: 29205554 DOI: 10.1111/mmi.13892] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Revised: 11/28/2017] [Accepted: 12/03/2017] [Indexed: 12/30/2022]
Abstract
Rhodococcus equi is a multihost, facultative intracellular bacterial pathogen that primarily causes pneumonia in foals less than six months in age and immunocompromised people. Previous studies determined that the major virulence determinant of R. equi is the surface bound virulence associated protein A (VapA). The presence of VapA inhibits the maturation of R. equi-containing phagosomes and promotes intracellular bacterial survival, as determined by the inability of vapA deletion mutants to replicate in host macrophages. While the mechanism of action of VapA remains elusive, we show that soluble recombinant VapA32-189 both rescues the intramacrophage replication defect of a wild type R. equi strain lacking the vapA gene and enhances the persistence of nonpathogenic Escherichia coli in macrophages. During macrophage infection, VapA was observed at both the bacterial surface and at the membrane of the host-derived R. equi containing vacuole, thus providing an opportunity for VapA to interact with host constituents and promote alterations in phagolysosomal function. In support of the observed host membrane binding activity of VapA, we also found that rVapA32-189 interacted specifically with liposomes containing phosphatidic acid in vitro. Collectively, these data demonstrate a lipid binding property of VapA, which may be required for its function during intracellular infection.
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Affiliation(s)
- Lindsay M Wright
- Department of Infectious Diseases, University of Georgia, Athens, GA 30602, USA
| | - Emily M Carpinone
- Department of Microbiology, University of Georgia, Athens, GA 30602, USA
| | - Terry L Bennett
- Department of Microbiology, University of Georgia, Athens, GA 30602, USA
| | - Mary K Hondalus
- Department of Infectious Diseases, University of Georgia, Athens, GA 30602, USA
| | - Vincent J Starai
- Department of Infectious Diseases, University of Georgia, Athens, GA 30602, USA.,Department of Microbiology, University of Georgia, Athens, GA 30602, USA
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47
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Ceniceros A, Dijkhuizen L, Petrusma M. Molecular characterization of a Rhodococcus jostii RHA1 γ-butyrolactone(-like) signalling molecule and its main biosynthesis gene gblA. Sci Rep 2017; 7:17743. [PMID: 29255143 PMCID: PMC5735094 DOI: 10.1038/s41598-017-17853-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Accepted: 12/01/2017] [Indexed: 01/25/2023] Open
Abstract
Rhodococcus genome sequence analysis has revealed a surprisingly large (and unexplored) potential for the production of secondary metabolites. Also, putative γ-butyrolactone gene clusters have been identified in some Rhodococci. These signalling molecules are known to regulate secondary metabolism in Streptomyces. This work provides evidence for synthesis of a γ-butyrolactone(-like) molecule by Rhodococci (RJB), the first report in the Rhodococcus genus. The Rhodococcus jostii RHA1 RJB molecule was detected by a reporter system based on the γ-butyrolactone receptor protein (ScbR) of Streptomyces coelicolor. This RJB is structurally identical to 6-dehydro SCB2, the predicted precursor of the S. coelicolor γ-butyrolactone SCB2. The R. jostii RHA1 key RJB biosynthesis gene was identified (gblA): Deletion of gblA resulted in complete loss of RJB synthesis whereas higher RJB levels were detected when gblA was overexpressed. Interaction of the RJB molecule with ScbR indicates that communication may occur between these two Actinomycete genera in their natural habitat. Furthermore, RJB may provide a highly relevant tool for awakening cryptic secondary metabolic gene clusters in Rhodococci. This study provides preliminary evidence that R. jostii RHA1 indeed synthesizes diffusible molecules with antimicrobial activity, but a possible role for RJB in this remains to be established.
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Affiliation(s)
- Ana Ceniceros
- Microbial Physiology, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Nijenborgh 7, 9747AG, Groningen, The Netherlands
| | - Lubbert Dijkhuizen
- Microbial Physiology, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Nijenborgh 7, 9747AG, Groningen, The Netherlands.
| | - Mirjan Petrusma
- Microbial Physiology, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Nijenborgh 7, 9747AG, Groningen, The Netherlands
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48
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Savory EA, Fuller SL, Weisberg AJ, Thomas WJ, Gordon MI, Stevens DM, Creason AL, Belcher MS, Serdani M, Wiseman MS, Grünwald NJ, Putnam ML, Chang JH. Evolutionary transitions between beneficial and phytopathogenic Rhodococcus challenge disease management. eLife 2017; 6:30925. [PMID: 29231813 PMCID: PMC5726852 DOI: 10.7554/elife.30925] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Accepted: 11/03/2017] [Indexed: 02/02/2023] Open
Abstract
Understanding how bacteria affect plant health is crucial for developing sustainable crop production systems. We coupled ecological sampling and genome sequencing to characterize the population genetic history of Rhodococcus and the distribution patterns of virulence plasmids in isolates from nurseries. Analysis of chromosome sequences shows that plants host multiple lineages of Rhodococcus, and suggested that these bacteria are transmitted due to independent introductions, reservoir populations, and point source outbreaks. We demonstrate that isolates lacking virulence genes promote beneficial plant growth, and that the acquisition of a virulence plasmid is sufficient to transition beneficial symbionts to phytopathogens. This evolutionary transition, along with the distribution patterns of plasmids, reveals the impact of horizontal gene transfer in rapidly generating new pathogenic lineages and provides an alternative explanation for pathogen transmission patterns. Results also uncovered a misdiagnosed epidemic that implicated beneficial Rhodococcus bacteria as pathogens of pistachio. The misdiagnosis perpetuated the unnecessary removal of trees and exacerbated economic losses. All organisms live in a world teeming with bacteria. Some bacteria are beneficial and, for example, provide their hosts with nutrients. Others cause harm, for example, by stealing nutrients and causing disease. Many bacteria can also gain DNA from other bacteria, and the genes encoded within the new DNA can help them to live with other organisms. This can start the bacteria on an evolutionary path to becoming beneficial or harmful. Rhodococcus are bacteria that live in association with many species of plants, including trees. Most are harmless but some cause disease. Plants infected with harmful Rhodococcus can show deformed growth, which causes major losses to the nursery industry. Savory, Fuller, Weisberg et al. set out to understand how disease-causing Rhodococcus are introduced into nurseries, if they are transferred between nurseries, whether they persist in nurseries, and how to limit their spread. It turns out that harmless Rhodococcus are beneficial to plants. However, if these harmless bacteria gain a certain DNA molecule – called a virulence plasmid – they can convert into harmful bacteria. Further analysis showed that some nurseries repeatedly acquired the harmful bacteria. The pattern of affected nurseries suggested that some might have purchased diseased plants from a common provider. In other cases, the sources remained a mystery. Savory et al. also report that, contrary to previous findings, there is no evidence to support the diagnosis that Rhodococcus without a virulence plasmid are responsible for an unusual growth problem that has plagued the pistachio industry. In recent years, this incorrect diagnosis led to trees being unnecessarily destroyed, worsening the economic losses. These findings suggest that genes moving between bacteria can dramatically change how those bacteria interact with the organisms in which they live. It needs to be shown whether this is an exceptional process, unique to only certain groups of bacteria, or if it is more widespread in nature. These findings could inform future disease management strategies to better protect agricultural systems.
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Affiliation(s)
- Elizabeth A Savory
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, United States
| | - Skylar L Fuller
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, United States.,Molecular and Cellular Biology Program, Oregon State University, Corvallis, United States
| | - Alexandra J Weisberg
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, United States
| | - William J Thomas
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, United States
| | - Michael I Gordon
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, United States
| | - Danielle M Stevens
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, United States
| | - Allison L Creason
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, United States.,Molecular and Cellular Biology Program, Oregon State University, Corvallis, United States
| | - Michael S Belcher
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, United States
| | - Maryna Serdani
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, United States
| | - Michele S Wiseman
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, United States
| | - Niklaus J Grünwald
- Horticultural Crops Research Laboratory, United States Department of Agriculture and Agricultural Research Service, Corvallis, United States
| | - Melodie L Putnam
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, United States
| | - Jeff H Chang
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, United States.,Molecular and Cellular Biology Program, Oregon State University, Corvallis, United States.,Center for Genome Research, Oregon State University, Corvallis, United States
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49
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Chandramani-Shivalingappa P, Bhandari M, Wiechert SA, Gilbertie J, Jones DE, Sponseller BA. Induction of Reactive Intermediates and Autophagy-Related Proteins upon Infection of Macrophages with Rhodococcus equi. SCIENTIFICA 2017; 2017:8135737. [PMID: 29230347 PMCID: PMC5688232 DOI: 10.1155/2017/8135737] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Accepted: 10/01/2017] [Indexed: 06/07/2023]
Abstract
Rhodococcus equi (R. equi) is an intracellular macrophage-tropic pathogen with potential for causing fatal pyogranulomatous pneumonia in foals between 1 and 6 months of age. In this study, we sought to determine whether infection of macrophages with R. equi could lead to the induction of autophagy. Murine bone marrow derived macrophages (BMDM) were infected with R. equi for various time intervals and analyzed for upregulation of autophagy proteins and accumulation of autophagosomes relative to uninfected controls. Western blot analysis showed a progressive increase in LC3-II and Beclin1 levels in a time-dependent manner. The functional accumulation of autophagosomes detected with monodansylcadaverine further supported the enhanced induction of autophagy in BMDM infected with R. equi. In addition, infection of BMDM with R. equi induced generation of reactive oxygen species (ROS) in a time-dependent manner. These data are consistent with reports documenting the role of ROS in induction of autophagy and indicate that the infection of macrophages by R. equi elicits innate host defense mechanisms.
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Affiliation(s)
- Prashanth Chandramani-Shivalingappa
- Department of Veterinary Microbiology and Preventive Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA 50011, USA
- Division of Pulmonary, Critical Care, and Sleep Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Mahesh Bhandari
- Department of Veterinary Microbiology and Preventive Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA 50011, USA
| | - Sarah A. Wiechert
- Department of Veterinary Microbiology and Preventive Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA 50011, USA
| | - Jessica Gilbertie
- Department of Veterinary Microbiology and Preventive Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA 50011, USA
| | - Douglas E. Jones
- Department of Veterinary Pathology, College of Veterinary Medicine, Iowa State University, Ames, IA 50011, USA
| | - Brett A. Sponseller
- Department of Veterinary Microbiology and Preventive Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA 50011, USA
- Department of Veterinary Clinical Sciences, College of Veterinary Medicine, Iowa State University, Ames, IA 50011, USA
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50
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MacArthur I, Anastasi E, Alvarez S, Scortti M, Vázquez-Boland JA. Comparative Genomics of Rhodococcus equi Virulence Plasmids Indicates Host-Driven Evolution of the vap Pathogenicity Island. Genome Biol Evol 2017; 9:1241-1247. [PMID: 28369330 PMCID: PMC5434932 DOI: 10.1093/gbe/evx057] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/20/2017] [Indexed: 01/16/2023] Open
Abstract
The conjugative virulence plasmid is a key component of the Rhodococcus equi accessory genome essential for pathogenesis. Three host-associated virulence plasmid types have been identified: the equine pVAPA and porcine pVAPB circular variants, and the linear pVAPN found in bovine (ruminant) isolates. We recently characterized the R. equi pangenome (Anastasi E, et al. 2016. Pangenome and phylogenomic analysis of the pathogenic actinobacterium Rhodococcus equi. Genome Biol Evol. 8:3140–3148.) and we report here the comparative analysis of the virulence plasmid genomes. Plasmids within each host-associated type were highly similar despite their diverse origins. Variation was accounted for by scattered single nucleotide polymorphisms and short nucleotide indels, while larger indels—mostly in the plasticity region near the vap pathogencity island (PAI)—defined plasmid genomic subtypes. Only one of the plasmids analyzed, of pVAPN type, was exceptionally divergent due to accumulation of indels in the housekeeping backbone. Each host-associated plasmid type carried a unique PAI differing in vap gene complement, suggesting animal host-specific evolution of the vap multigene family. Complete conservation of the vap PAI was observed within each host-associated plasmid type. Both diversity of host-associated plasmid types and clonality of specific chromosomal-plasmid genomic type combinations were observed within the same R. equi phylogenomic subclade. Our data indicate that the overall strong conservation of the R. equi host-associated virulence plasmids is the combined result of host-driven selection, lateral transfer between strains, and geographical spread due to international livestock exchanges.
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Affiliation(s)
- Iain MacArthur
- Division of Infection and Immunity, The Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Elisa Anastasi
- Division of Infection and Immunity, The Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Sonsiray Alvarez
- Division of Infection and Immunity, The Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Mariela Scortti
- Division of Infection and Immunity, The Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom.,Edinburgh Medical School (Biomedical Sciences), University of Edinburgh, Edinburgh, United Kingdom
| | - José A Vázquez-Boland
- Division of Infection and Immunity, The Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom.,Edinburgh Medical School (Biomedical Sciences), University of Edinburgh, Edinburgh, United Kingdom.,Centre for Immunity, Infection and Evolution, University of Edinburgh, Edinburgh, United Kingdom
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