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Gao Y, Song B, Wang M, Yang F, Yu C, Chen H. Complete genome sequence of Erwinia amylovora PBI209 isolated from a necrotic flower of Pyrus sinkiangensis in China. Microbiol Resour Announc 2024; 13:e0029124. [PMID: 38967467 PMCID: PMC11320953 DOI: 10.1128/mra.00291-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Accepted: 06/20/2024] [Indexed: 07/06/2024] Open
Abstract
Here, we report the complete genome sequence of Erwinia amylovora PBI209 that causes fire blight isolated from a necrotic flower of Pyrus sinkiangensis in Xinjiang, China. The genome consists of 3,800,955 bp, with 3,403 protein-coding genes and a guanine-cytosine content of 53.61%.
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Affiliation(s)
- Ya Gao
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Bo Song
- Institute of Plant Protection, Xinjiang Academy of Agricultural Sciences, Urumqi, China
- Key Laboratory of Integrated Pest Management on Crops in Northwestern Oasis, Ministry of Agriculture and Rural Affairs, Urumqi, China
- Xinjiang Key Laboratory of Agricultural Biosafety Urumqi, Urumqi, China
| | - Meihong Wang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Fenghuan Yang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Chao Yu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Huamin Chen
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
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de Pedro Jové R, Sebastià P, Valls M. Identification of Type III Secretion Inhibitors for Plant Disease Management. Methods Mol Biol 2021; 2213:39-48. [PMID: 33270191 DOI: 10.1007/978-1-0716-0954-5_4] [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] [Indexed: 12/17/2023]
Abstract
Bacterial plant pathogens are among the most devastating threats to agriculture. To date, there are no effective means to control bacterial plant diseases due to the restrictions in the use of antibiotics in agriculture. A novel strategy under study is the use of chemical compounds that inhibit the expression of key bacterial virulence determinants. The type III secretion system is essential for virulence of many Gram-negative bacteria because it injects into the plant host cells bacterial proteins that interfere with their immune system. Here, we describe the methodology to identify bacterial type III secretion inhibitors, including a series of protocols that combine in planta and in vitro experiments. We use Ralstonia solanacearum as a model because of the number of genetic tools available in this organism and because it causes bacterial wilt, one of the most threatening plant diseases worldwide. The procedures presented can be used to evaluate the effect of different chemical compounds on bacterial growth and virulence.
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Affiliation(s)
- Roger de Pedro Jové
- Department of Genetics, University of Barcelona, Barcelona, Catalonia, Spain
- Centre for Research in Agricultural Genomics (CSIC-IRTA-UAB-UB), Bellaterra, Catalonia, Spain
| | - Pau Sebastià
- Centre for Research in Agricultural Genomics (CSIC-IRTA-UAB-UB), Bellaterra, Catalonia, Spain
| | - Marc Valls
- Department of Genetics, University of Barcelona, Barcelona, Catalonia, Spain.
- Centre for Research in Agricultural Genomics (CSIC-IRTA-UAB-UB), Bellaterra, Catalonia, Spain.
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Jones HJ, Shield CG, Swift BM. The Application of Bacteriophage Diagnostics for Bacterial Pathogens in the Agricultural Supply Chain: From Farm-to-Fork. PHAGE (NEW ROCHELLE, N.Y.) 2020; 1:176-188. [PMID: 36147287 PMCID: PMC9041468 DOI: 10.1089/phage.2020.0042] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Bacteriophages (phages) have great potential not only as therapeutics but as diagnostics. Indeed, they have been developed and used to diagnose and detect bacterial infections, primarily in human clinical settings. The ability to rapidly detect and control bacterial pathogens in agriculture is of primary importance to maintain food security, improve animal health, and prevent the passage of zoonotic pathogens into the human population. Culture-based detection methods are often labor-intensive, and require further confirmatory tests, increasing costs and processing times needed for diagnostics. Molecular detection methods such as polymerase chain reaction are commonly used to determine the safety of food, however, a major drawback is their inability to differentiate between viable and nonviable bacterial pathogens in food. Phage diagnostics have been proven to be rapid, capable of identifying viable pathogens and do not require cultivation to detect bacteria. Phage detection takes advantage of the specificity of interaction between phage and their hosts. Furthermore, phage detection is cost effective, which is vitally important in agricultural supply chains where there is a drive to keep costs down to ensure that the cost of food does not increase. The full potential of phage detection/diagnostics is not wholly realized or commercialized. This review explores the current use and potential future scope of phage diagnostics and their application to various bacterial pathogens across agriculture and food supply chains.
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Affiliation(s)
- Helen J. Jones
- Pathobiology and Population Sciences, Royal Veterinary College, Hatfield, United Kingdom
| | - Christopher G. Shield
- Pathobiology and Population Sciences, Royal Veterinary College, Hatfield, United Kingdom
| | - Benjamin M.C. Swift
- Pathobiology and Population Sciences, Royal Veterinary College, Hatfield, United Kingdom
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Zurn JD, Norelli JL, Montanari S, Bell R, Bassil NV. Dissecting Genetic Resistance to Fire Blight in Three Pear Populations. PHYTOPATHOLOGY 2020; 110:1305-1311. [PMID: 32175827 DOI: 10.1094/phyto-02-20-0051-r] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Fire blight, caused by the bacterial pathogen Erwinia amylovora, is a persistent problem for pear (Pyrus spp.) growers in the United States. Growing resistant cultivars is one of the best options for managing fire blight. The cultivars Potomac and Old Home and the selection NJA2R59T69 display resistance to fire blight. As such, three mapping populations (El Dorado × Potomac, Old Home × Bartlett, and NJA2R59T69 × Bartlett) were developed to identify genomic regions associated with resistance to fire blight. Progeny were phenotyped during 2017 and 2018 by inoculating multiple actively growing shoots of field-grown seedling trees with E. amylovora isolate E153n via the cut-leaf method. Genotyping was conducted using the recently developed Axiom Pear 70 K Genotyping Array and chromosomal linkage groups were created for each population. An integrated two-way pseudo-testcross approach was used to map quantitative trait loci (QTLs). Resistance QTLs were identified on chromosome 2 for each population. The QTLs identified in the El Dorado × Potomac and Old Home × Bartlett populations are in the same region as QTLs that were previously identified in Harrow Sweet and Moonglow. The QTL in NJA2R59T69 mapped proximally to the previously identified QTLs and originated from an unknown Asian or occidental source. Future research will focus on further characterizing the resistance regions and developing tools for DNA-informed breeding.
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Affiliation(s)
- Jason D Zurn
- United States Department of Agriculture-Agricultural Research Service (USDA-ARS) National Clonal Germplasm Repository, Corvallis, OR, U.S.A
| | - John L Norelli
- USDA-ARS Appalachian Fruit Research Laboratory, Kearneysville, WV, U.S.A
| | - Sara Montanari
- Department of Plant Sciences, University of California Davis, Davis, CA, U.S.A
| | - Richard Bell
- USDA-ARS Appalachian Fruit Research Laboratory, Kearneysville, WV, U.S.A
| | - Nahla V Bassil
- United States Department of Agriculture-Agricultural Research Service (USDA-ARS) National Clonal Germplasm Repository, Corvallis, OR, U.S.A
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Puigvert M, Solé M, López‐Garcia B, Coll NS, Beattie KD, Davis RA, Elofsson M, Valls M. Type III secretion inhibitors for the management of bacterial plant diseases. MOLECULAR PLANT PATHOLOGY 2019; 20:20-32. [PMID: 30062690 PMCID: PMC6430469 DOI: 10.1111/mpp.12736] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
The identification of chemical compounds that prevent and combat bacterial diseases is fundamental for crop production. Bacterial virulence inhibitors are a promising alternative to classical control treatments, because they have a low environmental impact and are less likely to generate bacterial resistance. The major virulence determinant of most animal and plant bacterial pathogens is the type III secretion system (T3SS). In this work, we screened nine plant extracts and 12 isolated compounds-including molecules effective against human pathogens-for their capacity to inhibit the T3SS of plant pathogens and for their applicability as virulence inhibitors for crop protection. The screen was performed using a luminescent reporter system developed in the model pathogenic bacterium Ralstonia solanacearum. Five synthetic molecules, one natural product and two plant extracts were found to down-regulate T3SS transcription, most through the inhibition of the regulator hrpB. In addition, for three of the molecules, corresponding to salicylidene acylhydrazide derivatives, the inhibitory effect caused a dramatic decrease in the secretion capacity, which was translated into impaired plant responses. These candidate virulence inhibitors were then tested for their ability to protect plants. We demonstrated that salicylidene acylhydrazides can limit R. solanacearum multiplication in planta and protect tomato plants from bacterial speck caused by Pseudomonas syringae pv. tomato. Our work validates the efficiency of transcription reporters to discover compounds or natural product extracts that can be potentially applied to prevent bacterial plant diseases.
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Affiliation(s)
- Marina Puigvert
- Department of GeneticsUniversity of BarcelonaBarcelona08028CataloniaSpain
- Centre for Research in Agricultural Genomics (CSIC‐IRTA‐UAB‐UB)Bellaterra08193CataloniaSpain
| | - Montserrat Solé
- Centre for Research in Agricultural Genomics (CSIC‐IRTA‐UAB‐UB)Bellaterra08193CataloniaSpain
| | - Belén López‐Garcia
- Centre for Research in Agricultural Genomics (CSIC‐IRTA‐UAB‐UB)Bellaterra08193CataloniaSpain
| | - Núria S. Coll
- Centre for Research in Agricultural Genomics (CSIC‐IRTA‐UAB‐UB)Bellaterra08193CataloniaSpain
| | - Karren D. Beattie
- Griffith Institute for Drug DiscoveryGriffith UniversityQld4111Australia
| | - Rohan A. Davis
- Griffith Institute for Drug DiscoveryGriffith UniversityQld4111Australia
| | | | - Marc Valls
- Department of GeneticsUniversity of BarcelonaBarcelona08028CataloniaSpain
- Centre for Research in Agricultural Genomics (CSIC‐IRTA‐UAB‐UB)Bellaterra08193CataloniaSpain
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Born Y, Fieseler L, Thöny V, Leimer N, Duffy B, Loessner MJ. Engineering of Bacteriophages Y2:: dpoL1-C and Y2:: luxAB for Efficient Control and Rapid Detection of the Fire Blight Pathogen, Erwinia amylovora. Appl Environ Microbiol 2017; 83:e00341-17. [PMID: 28389547 PMCID: PMC5452800 DOI: 10.1128/aem.00341-17] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Accepted: 04/03/2017] [Indexed: 01/08/2023] Open
Abstract
Erwinia amylovora is the causative agent of fire blight, a devastating plant disease affecting members of the Rosaceae Alternatives to antibiotics for control of fire blight symptoms and outbreaks are highly desirable, due to increasing drug resistance and tight regulatory restrictions. Moreover, the available diagnostic methods either lack sensitivity, lack speed, or are unable to discriminate between live and dead bacteria. Owing to their extreme biological specificity, bacteriophages are promising alternatives for both aims. In this study, the virulent broad-host-range E. amylovora virus Y2 was engineered to enhance its killing activity and for use as a luciferase reporter phage, respectively. Toward these aims, a depolymerase gene of E. amylovora virus L1 (dpoL1-C) or a bacterial luxAB fusion was introduced into the genome of Y2 by homologous recombination. The genes were placed downstream of the major capsid protein orf68, under the control of the native promoter. The modifications did not affect viability of infectivity of the recombinant viruses. Phage Y2::dpoL1-C demonstrated synergistic activity between the depolymerase degrading the exopolysaccharide capsule and phage infection, which greatly enhanced bacterial killing. It also significantly reduced the ability of E. amylovora to colonize the surface of detached flowers. The reporter phage Y2::luxAB transduced bacterial luciferase into host cells and induced synthesis of large amounts of a LuxAB luciferase fusion. After the addition of aldehyde substrate, bioluminescence could be readily monitored, and this enabled rapid and specific detection of low numbers of viable bacteria, without enrichment, both in vitro and in plant material.IMPORTANCE Fire blight, caused by Erwinia amylovora, is the major threat to global pome fruit production, with high economic losses every year. Bacteriophages represent promising alternatives to not only control the disease, but also for rapid diagnostics. To enhance biocontrol efficacy, we combined the desired properties of two phages, Y2 (broad host range) and L1 (depolymerase for capsule degradation) in a single recombinant phage. This phage showed enhanced biocontrol and could reduce E. amylovora on flowers. Phage Y2 was also genetically engineered into a luciferase reporter phage, which transduces bacterial bioluminescence into infected cells and allows detection of low numbers of viable target bacteria. The combination of speed, sensitivity, and specificity is superior to previously used diagnostic methods. In conclusion, genetic engineering could improve the properties of phage Y2 toward better killing efficacy and sensitive detection of E. amylovora cells.
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Affiliation(s)
- Yannick Born
- Institute of Food, Nutrition, and Health, ETH Zurich, Zürich, Switzerland
- Agroscope, Research Division Plant Protection, Wädenswil, Switzerland
| | - Lars Fieseler
- Institute of Food, Nutrition, and Health, ETH Zurich, Zürich, Switzerland
| | - Valentin Thöny
- Institute of Food, Nutrition, and Health, ETH Zurich, Zürich, Switzerland
| | - Nadja Leimer
- Institute of Food, Nutrition, and Health, ETH Zurich, Zürich, Switzerland
| | - Brion Duffy
- Agroscope, Research Division Plant Protection, Wädenswil, Switzerland
| | - Martin J Loessner
- Institute of Food, Nutrition, and Health, ETH Zurich, Zürich, Switzerland
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Gusberti M, Klemm U, Meier MS, Maurhofer M, Hunger-Glaser I. Fire Blight Control: The Struggle Goes On. A Comparison of Different Fire Blight Control Methods in Switzerland with Respect to Biosafety, Efficacy and Durability. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2015; 12:11422-47. [PMID: 26378562 PMCID: PMC4586684 DOI: 10.3390/ijerph120911422] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Revised: 08/27/2015] [Accepted: 09/01/2015] [Indexed: 12/03/2022]
Abstract
Fire blight (FB), caused by Erwinia amylovora, is one of the most important pome fruit pathogens worldwide. To control this devastating disease, various chemical and biological treatments are commonly applied in Switzerland, but they fail to keep the infection at an acceptable level in years of heavy disease pressure. The Swiss authorities therefore currently allow the controlled use of the antibiotic streptomycin against FB in years that are predicted to have heavy infection periods, but only one treatment per season is permitted. Another strategy for controlling Erwinia is to breed resistant/tolerant apple cultivars. One way of accelerating the breeding process is to obtain resistant cultivars by inserting one or several major resistance genes, using genetic engineering. To date, no study summarizing the impact of different FB control measures on the environment and on human health has been performed. This study consequently aims to compare different disease-control measures (biological control, chemical control, control by antibiotics and by resistant/tolerant apple cultivars obtained through conventional or molecular breeding) applied against E. amylovora, considering different protection goals (protection of human health, environment, agricultural diversity and economic interest), with special emphasis on biosafety aspects. Information on each FB control measure in relation to the specified protection goal was assessed by literature searches and by interviews with experts. Based on our results it can be concluded that the FB control measures currently applied in Switzerland are safe for consumers, workers and the environment. However, there are several gaps in our knowledge of the human health and environmental impacts analyzed: data are missing (1) on long term studies on the efficacy of most of the analyzed FB control measures; (2) on the safety of operators handling streptomycin; (3) on residue analyses of Equisetum plant extract, the copper and aluminum compounds used in apple production; and (4) on the effect of biological and chemical control measures on non-target fauna and flora. These gaps urgently need to be addressed in the near future.
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Affiliation(s)
- Michele Gusberti
- Institute of Integrative Biology Zurich, Plant Pathology Group, Swiss Federal Institute of Technology, Zurich CH-8092, Switzerland.
| | - Urs Klemm
- Swiss Expert Committee for Biosafety, Bern CH-3003, Switzerland.
| | - Matthias S Meier
- Swiss Expert Committee for Biosafety, Bern CH-3003, Switzerland.
- Research Institute of Organic Agriculture (FiBL), Frick CH-5070, Switzerland.
| | - Monika Maurhofer
- Institute of Integrative Biology Zurich, Plant Pathology Group, Swiss Federal Institute of Technology, Zurich CH-8092, Switzerland.
- Swiss Expert Committee for Biosafety, Bern CH-3003, Switzerland.
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Piqué N, Miñana-Galbis D, Merino S, Tomás JM. Virulence Factors of Erwinia amylovora: A Review. Int J Mol Sci 2015; 16:12836-54. [PMID: 26057748 PMCID: PMC4490474 DOI: 10.3390/ijms160612836] [Citation(s) in RCA: 77] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2015] [Revised: 05/22/2015] [Accepted: 05/26/2015] [Indexed: 01/31/2023] Open
Abstract
Erwinia amylovora, a Gram negative bacteria of the Enterobacteriaceae family, is the causal agent of fire blight, a devastating plant disease affecting a wide range of host species within Rosaceae and a major global threat to commercial apple and pear production. Among the limited number of control options currently available, prophylactic application of antibiotics during the bloom period appears the most effective. Pathogen cells enter plants through the nectarthodes of flowers and other natural openings, such as wounds, and are capable of rapid movement within plants and the establishment of systemic infections. Many virulence determinants of E. amylovora have been characterized, including the Type III secretion system (T3SS), the exopolysaccharide (EPS) amylovoran, biofilm formation, and motility. To successfully establish an infection, E. amylovora uses a complex regulatory network to sense the relevant environmental signals and coordinate the expression of early and late stage virulence factors involving two component signal transduction systems, bis-(3'-5')-cyclic di-GMP (c-di-GMP) and quorum sensing. The LPS biosynthetic gene cluster is one of the relatively few genetic differences observed between Rubus- and Spiraeoideae-infecting genotypes of E. amylovora. Other differential factors, such as the presence and composition of an integrative conjugative element associated with the Hrp T3SS (hrp genes encoding the T3SS apparatus), have been recently described. In the present review, we present the recent findings on virulence factors research, focusing on their role in bacterial pathogenesis and indicating other virulence factors that deserve future research to characterize them.
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Affiliation(s)
- Núria Piqué
- Departament de Microbiologia i Parasiologia Sanitàries, Facultat de Farmàcia, Universitat de Barcelona, Av. Joan XXIII s/n, 08028 Barcelona, Spain.
| | - David Miñana-Galbis
- Departament de Microbiologia i Parasiologia Sanitàries, Facultat de Farmàcia, Universitat de Barcelona, Av. Joan XXIII s/n, 08028 Barcelona, Spain.
| | - Susana Merino
- Departament de Microbiologia, Facultat de Biologia, Universitat de Barcelona, Av. Diagonal 643, 08071 Barcelona, Spain.
| | - Juan M Tomás
- Departament de Microbiologia, Facultat de Biologia, Universitat de Barcelona, Av. Diagonal 643, 08071 Barcelona, Spain.
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Duffy B, Holliger E, Walsh F. Streptomycin use in apple orchards did not increase abundance of mobile resistance genes. FEMS Microbiol Lett 2013; 350:180-9. [PMID: 24164283 DOI: 10.1111/1574-6968.12313] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2013] [Revised: 09/26/2013] [Accepted: 10/22/2013] [Indexed: 11/26/2022] Open
Abstract
Streptomycin is used as a first-line defense and tetracycline as a second-line defense, in the fight against fire blight disease in apple and pear orchards. We have performed the first study to quantitatively analyze the influence of streptomycin use in agriculture on the abundance of streptomycin and tetracycline resistance genes in apple orchards. Flowers, leaves, and soil were collected from three orchard sites in 2010, 2011, and 2012. Gene abundance distribution was analyzed using two-way anova and principal component analysis to investigate relationships between gene abundance data over time and treatment. The mobile antibiotic resistance genes, strA, strB, tetB, tetM, tetW, and the insertion sequence IS1133, were detected prior to streptomycin treatment in almost all samples, indicating the natural presence of these resistance genes in nature. Statistically significant increases in the resistance gene abundances were occasional, inconsistent, and not reproducible from one year to the next. We conclude that the application of streptomycin in these orchards was not associated with sustained increases in streptomycin or tetracycline resistance gene abundances.
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Affiliation(s)
- Brion Duffy
- Federal Department of Economic Affairs, Education and Research EAER, Research Station Agroscope Changins-Wädenswil ACW, Wädenswil, Switzerland
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Smits TH, Rezzonico F, López MM, Blom J, Goesmann A, Frey JE, Duffy B. Phylogenetic position and virulence apparatus of the pear flower necrosis pathogen Erwinia piriflorinigrans CFBP 5888T as assessed by comparative genomics. Syst Appl Microbiol 2013; 36:449-56. [DOI: 10.1016/j.syapm.2013.04.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2013] [Revised: 04/18/2013] [Accepted: 04/18/2013] [Indexed: 10/26/2022]
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Born Y, Fieseler L, Klumpp J, Eugster MR, Zurfluh K, Duffy B, Loessner MJ. The tail-associated depolymerase ofErwinia amylovoraphage L1 mediates host cell adsorption and enzymatic capsule removal, which can enhance infection by other phage. Environ Microbiol 2013; 16:2168-80. [DOI: 10.1111/1462-2920.12212] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2013] [Revised: 07/05/2013] [Accepted: 07/10/2013] [Indexed: 01/21/2023]
Affiliation(s)
- Yannick Born
- Institute of Food, Nutrition and Health; ETH Zurich; Zürich CH-8092 Switzerland
- Phytopathology; Research Station Agroscope Changins-Wädenswil ACW; Wädenswil CH-8820 Switzerland
| | - Lars Fieseler
- Institute of Food, Nutrition and Health; ETH Zurich; Zürich CH-8092 Switzerland
| | - Jochen Klumpp
- Institute of Food, Nutrition and Health; ETH Zurich; Zürich CH-8092 Switzerland
| | - Marcel R. Eugster
- Institute of Food, Nutrition and Health; ETH Zurich; Zürich CH-8092 Switzerland
| | - Katrin Zurfluh
- Institute of Food, Nutrition and Health; ETH Zurich; Zürich CH-8092 Switzerland
| | - Brion Duffy
- Phytopathology; Research Station Agroscope Changins-Wädenswil ACW; Wädenswil CH-8820 Switzerland
| | - Martin J. Loessner
- Institute of Food, Nutrition and Health; ETH Zurich; Zürich CH-8092 Switzerland
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Malnoy M, Martens S, Norelli JL, Barny MA, Sundin GW, Smits THM, Duffy B. Fire blight: applied genomic insights of the pathogen and host. ANNUAL REVIEW OF PHYTOPATHOLOGY 2012; 50:475-94. [PMID: 22702352 DOI: 10.1146/annurev-phyto-081211-172931] [Citation(s) in RCA: 92] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
The enterobacterial phytopathogen Erwinia amylovora causes fire blight, an invasive disease that threatens a wide range of commercial and ornamental Rosaceae host plants. The response elicited by E. amylovora in its host during disease development is similar to the hypersensitive reaction that typically leads to resistance in an incompatible host-pathogen interaction, yet no gene-for-gene resistance has been described for this host-pathogen system. Comparative genomic analysis has found an unprecedented degree of genetic uniformity among strains of E. amylovora, suggesting that the pathogen has undergone a recent genetic bottleneck. The genome of apple, an important host of E. amylovora, has been sequenced, creating new opportunities for the study of interactions between host and pathogen during fire blight development and for the identification of resistance genes. This review includes recent advances in the genomics of both host and pathogen.
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Affiliation(s)
- Mickael Malnoy
- Department of Biology and Genomics of Fruit Plants, FEM IASMA Research and Innovation Center, Foundation Edmund Mach di San Michele all'Adige, Trento, Italy.
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13
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Braun-Kiewnick A, Altenbach D, Oberhänsli T, Bitterlin W, Duffy B. A rapid lateral-flow immunoassay for phytosanitary detection of Erwinia amylovora and on-site fire blight diagnosis. J Microbiol Methods 2011; 87:1-9. [DOI: 10.1016/j.mimet.2011.06.015] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2011] [Revised: 06/13/2011] [Accepted: 06/18/2011] [Indexed: 10/18/2022]
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14
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Born Y, Fieseler L, Marazzi J, Lurz R, Duffy B, Loessner MJ. Novel virulent and broad-host-range Erwinia amylovora bacteriophages reveal a high degree of mosaicism and a relationship to Enterobacteriaceae phages. Appl Environ Microbiol 2011; 77:5945-54. [PMID: 21764969 PMCID: PMC3165370 DOI: 10.1128/aem.03022-10] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2010] [Accepted: 07/05/2011] [Indexed: 12/16/2022] Open
Abstract
A diverse set of 24 novel phages infecting the fire blight pathogen Erwinia amylovora was isolated from fruit production environments in Switzerland. Based on initial screening, four phages (L1, M7, S6, and Y2) with broad host ranges were selected for detailed characterization and genome sequencing. Phage L1 is a member of the Podoviridae, with a 39.3-kbp genome featuring invariable genome ends with direct terminal repeats. Phage S6, another podovirus, was also found to possess direct terminal repeats but has a larger genome (74.7 kbp), and the virus particle exhibits a complex tail fiber structure. Phages M7 and Y2 both belong to the Myoviridae family and feature long, contractile tails and genomes of 84.7 kbp (M7) and 56.6 kbp (Y2), respectively, with direct terminal repeats. The architecture of all four phage genomes is typical for tailed phages, i.e., organized into function-specific gene clusters. All four phages completely lack genes or functions associated with lysogeny control, which correlates well with their broad host ranges and indicates strictly lytic (virulent) lifestyles without the possibility for host lysogenization. Comparative genomics revealed that M7 is similar to E. amylovora virus ΦEa21-4, whereas L1, S6, and Y2 are unrelated to any other E. amylovora phage. Instead, they feature similarities to enterobacterial viruses T7, N4, and ΦEcoM-GJ1. In a series of laboratory experiments, we provide proof of concept that specific two-phage cocktails offer the potential for biocontrol of the pathogen.
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Affiliation(s)
- Yannick Born
- Agroscope Changins-Wädenswil ACW, Swiss National Competence Center for Fire Blight, 8820 Wädenswil, Switzerland
- Institute of Food, Nutrition, and Health, ETH Zürich, 8092 Zürich, Switzerland
| | - Lars Fieseler
- Institute of Food, Nutrition, and Health, ETH Zürich, 8092 Zürich, Switzerland
| | - Janine Marazzi
- Institute of Food, Nutrition, and Health, ETH Zürich, 8092 Zürich, Switzerland
| | - Rudi Lurz
- Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Brion Duffy
- Agroscope Changins-Wädenswil ACW, Swiss National Competence Center for Fire Blight, 8820 Wädenswil, Switzerland
| | - Martin J. Loessner
- Institute of Food, Nutrition, and Health, ETH Zürich, 8092 Zürich, Switzerland
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Smits THM, Duffy B. Genomics of iron acquisition in the plant pathogen Erwinia amylovora: insights in the biosynthetic pathway of the siderophore desferrioxamine E. Arch Microbiol 2011; 193:693-9. [DOI: 10.1007/s00203-011-0739-0] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2011] [Revised: 06/27/2011] [Accepted: 07/21/2011] [Indexed: 10/17/2022]
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Smits THM, Rezzonico F, Kamber T, Blom J, Goesmann A, Ishimaru CA, Frey JE, Stockwell VO, Duffy B. Metabolic versatility and antibacterial metabolite biosynthesis are distinguishing genomic features of the fire blight antagonist Pantoea vagans C9-1. PLoS One 2011; 6:e22247. [PMID: 21789243 PMCID: PMC3137637 DOI: 10.1371/journal.pone.0022247] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2011] [Accepted: 06/17/2011] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Pantoea vagans is a commercialized biological control agent used against the pome fruit bacterial disease fire blight, caused by Erwinia amylovora. Compared to other biocontrol agents, relatively little is currently known regarding Pantoea genetics. Better understanding of antagonist mechanisms of action and ecological fitness is critical to improving efficacy. PRINCIPAL FINDINGS Genome analysis indicated two major factors Contribute to biocontrol activity: competition for limiting substrates and antibacterial metabolite production. Pathways for utilization of a broad diversity of sugars and acquisition of iron were identified. Metabolism of sorbitol by P. vagans C9-1 may be a major metabolic feature in biocontrol of fire blight. Biosynthetic genes for the antibacterial peptide pantocin A were found on a chromosomal 28-kb genomic island, and for dapdiamide E on the plasmid pPag2. There was no evidence of potential virulence factors that could enable an animal or phytopathogenic lifestyle and no indication of any genetic-based biosafety risk in the antagonist. CONCLUSIONS Identifying key determinants contributing to disease suppression allows the development of procedures to follow their expression in planta and the genome sequence contributes to rationale risk assessment regarding the use of the biocontrol strain in agricultural systems.
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Affiliation(s)
- Theo H. M. Smits
- Swiss National Competence Center for Fire Blight, Division of Plant Protection, Agroscope Changins-Wädenswil ACW, Wädenswil, Switzerland
| | - Fabio Rezzonico
- Swiss National Competence Center for Fire Blight, Division of Plant Protection, Agroscope Changins-Wädenswil ACW, Wädenswil, Switzerland
| | - Tim Kamber
- Swiss National Competence Center for Fire Blight, Division of Plant Protection, Agroscope Changins-Wädenswil ACW, Wädenswil, Switzerland
| | - Jochen Blom
- CeBiTec, Bielefeld University, Bielefeld, Germany
| | | | - Carol A. Ishimaru
- Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota, United States of America
| | - Jürg E. Frey
- Swiss National Competence Center for Fire Blight, Division of Plant Protection, Agroscope Changins-Wädenswil ACW, Wädenswil, Switzerland
| | - Virginia O. Stockwell
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America
| | - Brion Duffy
- Swiss National Competence Center for Fire Blight, Division of Plant Protection, Agroscope Changins-Wädenswil ACW, Wädenswil, Switzerland
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Smits THM, Rezzonico F, Duffy B. Evolutionary insights from Erwinia amylovora genomics. J Biotechnol 2010; 155:34-9. [PMID: 21040749 DOI: 10.1016/j.jbiotec.2010.10.075] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2010] [Revised: 10/14/2010] [Accepted: 10/22/2010] [Indexed: 11/30/2022]
Abstract
Evolutionary genomics is coming into focus with the recent availability of complete sequences for many bacterial species. A hypothesis on the evolution of virulence factors in the plant pathogen Erwinia amylovora, the causative agent of fire blight, was generated using comparative genomics with the genomes E. amylovora, Erwinia pyrifoliae and Erwinia tasmaniensis. Putative virulence factors were mapped to the proposed genealogy of the genus Erwinia that is based on phylogenetic and genomic data. Ancestral origin of several virulence factors was identified, including levan biosynthesis, sorbitol metabolism, three T3SS and two T6SS. Other factors appeared to have been acquired after divergence of pathogenic species, including a second flagellar gene and two glycosyltransferases involved in amylovoran biosynthesis. E. amylovora singletons include 3 unique T3SS effectors that may explain differential virulence/host ranges. E. amylovora also has a unique T1SS export system, and a unique third T6SS gene cluster. Genetic analysis revealed signatures of foreign DNA suggesting that horizontal gene transfer is responsible for some of these differential features between the three species.
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Affiliation(s)
- Theo H M Smits
- Agroscope Changins-Wädenswil ACW, Division of Plant Protection, Swiss National Competence Center for Fire Blight, CH-8820 Wädenswil, Switzerland.
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Smits THM, Rezzonico F, Kamber T, Blom J, Goesmann A, Frey JE, Duffy B. Complete genome sequence of the fire blight pathogen Erwinia amylovora CFBP 1430 and comparison to other Erwinia spp. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2010; 23:384-393. [PMID: 20192826 DOI: 10.1094/mpmi-23-4-0384] [Citation(s) in RCA: 115] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Fire blight, caused by the enterobacterium Erwinia amylovora, is a devastating disease of rosaceous plants that has global economic importance for apple and pear production and trade. The complete genome of E. amylovora CFBP 1430 was sequenced, annotated, and compared with the genomes of other Erwinia spp. Several singleton and shared features of the E. amylovora CFBP 1430 genome were identified that offer a first view into evolutionary aspects within the genus Erwinia. Comparative genomics identified or clarified virulence and fitness determinants and secretion systems. Novel insights revealed in the genome of E. amylovora CFBP 1430 hold potential for exploitation to improve the design of more effective fire blight control strategies.
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Affiliation(s)
- Theo H M Smits
- Agroscope Changins-Wädenswil ACW, Division of Plant Protection, Swiss National Competence Center for Fire Blight, Wädenswil, Switzerland
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Smits THM, Jaenicke S, Rezzonico F, Kamber T, Goesmann A, Frey JE, Duffy B. Complete genome sequence of the fire blight pathogen Erwinia pyrifoliae DSM 12163T and comparative genomic insights into plant pathogenicity. BMC Genomics 2010; 11:2. [PMID: 20047678 PMCID: PMC2827408 DOI: 10.1186/1471-2164-11-2] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2009] [Accepted: 01/04/2010] [Indexed: 11/10/2022] Open
Abstract
Background Erwinia pyrifoliae is a newly described necrotrophic pathogen, which causes fire blight on Asian (Nashi) pear and is geographically restricted to Eastern Asia. Relatively little is known about its genetics compared to the closely related main fire blight pathogen E. amylovora. Results The genome of the type strain of E. pyrifoliae strain DSM 12163T, was sequenced using both 454 and Solexa pyrosequencing and annotated. The genome contains a circular chromosome of 4.026 Mb and four small plasmids. Based on their respective role in virulence in E. amylovora or related organisms, we identified several putative virulence factors, including type III and type VI secretion systems and their effectors, flagellar genes, sorbitol metabolism, iron uptake determinants, and quorum-sensing components. A deletion in the rpoS gene covering the most conserved region of the protein was identified which may contribute to the difference in virulence/host-range compared to E. amylovora. Comparative genomics with the pome fruit epiphyte Erwinia tasmaniensis Et1/99 showed that both species are overall highly similar, although specific differences were identified, for example the presence of some phage gene-containing regions and a high number of putative genomic islands containing transposases in the E. pyrifoliae DSM 12163T genome. Conclusions The E. pyrifoliae genome is an important addition to the published genome of E. tasmaniensis and the unfinished genome of E. amylovora providing a foundation for re-sequencing additional strains that may shed light on the evolution of the host-range and virulence/pathogenicity of this important group of plant-associated bacteria.
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Affiliation(s)
- Theo H M Smits
- Swiss National Competence Center for Fire Blight, Division of Plant Protection, Agroscope Changins-Wädenswil ACW, Wädenswil, Switzerland
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Rezzonico F, Stockwell VO, Duffy B. Plant agricultural streptomycin formulations do not carry antibiotic resistance genes. Antimicrob Agents Chemother 2009; 53:3173-7. [PMID: 19414583 PMCID: PMC2704632 DOI: 10.1128/aac.00036-09] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2009] [Revised: 03/10/2009] [Accepted: 04/23/2009] [Indexed: 11/20/2022] Open
Abstract
Streptomycin is used in plant agriculture for bacterial disease control, particularly against fire blight in pome fruit orchards. Concerns that this may increase environmental antibiotic resistance have led to bans or restrictions on use. Experience with antibiotic use in animal feeds raises the possible influence of formulation-delivered resistance genes. We demonstrate that agricultural streptomycin formulations do not carry producer organism resistance genes. By using an optimized extraction procedure, Streptomyces 16S rRNA genes and the streptomycin resistance gene strA were not detected in agricultural streptomycin formulations. This diminishes the likelihood for one potential factor in resistance development due to streptomycin use.
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Affiliation(s)
- Fabio Rezzonico
- Agroscope Changins-Wädenswil, ACW, Swiss National Competence Center for Fire Blight, Wädenswil, Switzerland
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