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Brochu AS, Dumonceaux TJ, Valenzuela M, Bélanger R, Pérez-López E. A New Multiplex TaqMan qPCR for Precise Detection and Quantification of Clavibacter michiganensis in Seeds and Plant Tissue. PLANT DISEASE 2024; 108:2272-2282. [PMID: 38381965 DOI: 10.1094/pdis-06-23-1194-sr] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/23/2024]
Abstract
Bacterial canker of tomato caused by Clavibacter michiganensis (Cm) is one of the most devastating bacterial diseases affecting the tomato industry worldwide. As the result of Cm colonization of the xylem, the susceptible host shows typical symptoms of wilt, marginal leaf necrosis, stem cankers, and ultimately plant death. However, what makes Cm an even more dangerous pathogen is its ability to infect seeds and plants without causing symptoms. Unfortunately, there are no resistant cultivars or effective chemical or biological control methods available to growers against Cm. Its control relies heavily on prevention. The implementation of a rapid and accurate detection tool is imperative to monitor the presence of Cm and prevent its spread. In this study, we developed a specific and sensitive multiplex TaqMan qPCR assay to detect Cm and distinguish it from related bacterial species that affect tomato plants. Two Cm chromosomal virulence-related genes, rhuM and tomA, were used as specific targets. The plant internal control tubulin alpha-3 was included in each of the multiplexes to improve the reliability of the assay. Specificity was evaluated with 37 bacterial strains including other Clavibacter spp. and related and unrelated bacterial pathogens from different geographic locations affecting a wide variety of hosts. Results showed that the assay is able to discriminate Cm strains from other related bacteria. The assay was validated on tissue and seed samples following artificial infection, and all tested samples accurately detected the presence of Cm. The tool described here is highly specific, sensitive, and reliable for the detection of Cm and allows the quantification of Cm in seeds, roots, stems, and leaves. The diagnostic assay can also be adapted for multiple purposes such as seed certification programs, surveillance, biosafety, the effectiveness of control methods, border protection, and epidemiological studies.[Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Anne-Sophie Brochu
- Département de Phytologie, Faculté des Sciences de l'Agriculture et de l'Alimentation, Université Laval, Québec City, Canada
- Centre de Recherche et d'Innovation sur les Végétaux (CRIV), Université Laval, Québec City, Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec City, Canada
- L'Institute EDS, Université Laval, Québec City, Canada
| | - Tim J Dumonceaux
- Agriculture and Agri-Food Canada Saskatoon Research and Development Centre, Saskatoon, SK, Canada
| | - Miryam Valenzuela
- Molecular Microbiology and Environmental Biotechnology Laboratory, Department of Chemistry & Center of Biotechnology Dr. Daniel Alkalay Lowitt, Universidad Tecnica Federico Santa Maria, Valparaiso 2390123, Chile
| | - Richard Bélanger
- Département de Phytologie, Faculté des Sciences de l'Agriculture et de l'Alimentation, Université Laval, Québec City, Canada
- Centre de Recherche et d'Innovation sur les Végétaux (CRIV), Université Laval, Québec City, Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec City, Canada
| | - Edel Pérez-López
- Département de Phytologie, Faculté des Sciences de l'Agriculture et de l'Alimentation, Université Laval, Québec City, Canada
- Centre de Recherche et d'Innovation sur les Végétaux (CRIV), Université Laval, Québec City, Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec City, Canada
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Sen Y, van der Wolf J, Visser RGF, van Heusden S. Bacterial Canker of Tomato: Current Knowledge of Detection, Management, Resistance, and Interactions. PLANT DISEASE 2015; 99:4-13. [PMID: 30699746 DOI: 10.1094/pdis-05-14-0499-fe] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Clavibacter michiganensis subsp. michiganensis is the causal agent of bacterial canker of tomato. The disease was first described in 1910 in Michigan, USA. C. michiganensis subsp. michiganensis (from now on called clavibacter) was initially thought to be a phloem parasite, but was later found to be a xylem-invading bacterium. The host range comprises mainly solanaceous crops such as tomato, pepper, and eggplant. Strains show great variability in virulence and are usually described as being hypervirulent, hypovirulent, or nonvirulent. Clavibacter lacks a type III secretion system, and only a few virulence factors have been experimentally determined from the many putative virulence factors. As the molecular mode of infection by clavibacter is unknown, researchers have avoided intensive work on this organism. Genetic plant mechanisms conferring resistance to clavibacter are apparently complex, and breeders have yet to develop disease-resistant cultivars.
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Affiliation(s)
- Yusuf Sen
- Wageningen UR Plant Breeding, Wageningen University and Research Centre, Wageningen, The Netherlands, and Graduate School Experimental Plant Sciences, Wageningen, The Netherlands
| | - Jan van der Wolf
- Plant Research International Biointeractions and Plant Health, Wageningen, The Netherlands
| | - Richard G F Visser
- Wageningen UR Plant Breeding, Wageningen University and Research Centre, Wageningen, The Netherlands
| | - Sjaak van Heusden
- Wageningen UR Plant Breeding, Wageningen University and Research Centre, Wageningen, The Netherlands
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Phylogenetic analysis and polyphasic characterization of Clavibacter michiganensis strains isolated from tomato seeds reveal that nonpathogenic strains are distinct from C. michiganensis subsp. michiganensis. Appl Environ Microbiol 2012; 78:8388-402. [PMID: 23001675 DOI: 10.1128/aem.02158-12] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The genus Clavibacter comprises one species and five subspecies of plant-pathogenic bacteria, four of which are classified as quarantine organisms due to the high economic threat they pose. Clavibacter michiganensis subsp. michiganensis is one of the most important pathogens of tomato, but the recommended diagnostic tools are not satisfactory due to false-negative and/or -positive results. To provide a robust analysis of the genetic relatedness among a worldwide collection of C. michiganensis subsp. michiganensis strains, relatives (strains from the four other C. michiganensis subspecies), and nonpathogenic Clavibacter-like strains isolated from tomato, we performed multilocus sequence-based analysis and typing (MLSA and MLST) based on six housekeeping genes (atpD, dnaK, gyrB, ppK, recA, and rpoB). We compared this "framework" with phenotypic and genotypic characteristics such as pathogenicity on tomato, reaction to two antisera by immunofluorescence and to five PCR identification tests, and the presence of four genes encoding the main C. michiganensis subsp. michiganensis pathogenicity determinants. We showed that C. michiganensis subsp. michiganensis is monophyletic and is distinct from its closest taxonomic neighbors. The nonpathogenic Clavibacter-like strains were identified as C. michiganensis using 16S rRNA gene sequencing. These strains, while cross-reacting with C. michiganensis subsp. michiganensis identification tools, are phylogenetically distinct from the pathogenic strains but belong to the C. michiganensis clade. C. michiganensis subsp. michiganensis clonal complexes linked strains from highly diverse geographical origins and also strains isolated over long periods of time in the same location. This illustrates the importance of seed transmission in the worldwide dispersion of this pathogen and its survival and adaptation abilities in a new environment once introduced.
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Cho MS, Lee JH, Her NH, Kim C, Seol YJ, Hahn JH, Baeg JH, Kim HG, Park DS. A quantitative and direct PCR assay for the subspecies-specific detection of Clavibacter michiganensis subsp. michiganensis based on a ferredoxin reductase gene. J Microbiol 2012; 50:496-501. [PMID: 22752914 DOI: 10.1007/s12275-012-1611-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2011] [Accepted: 03/09/2012] [Indexed: 10/28/2022]
Abstract
The Gram-positive bacterium Clavibacter michiganensis subsp. michiganensis is the causal agent of canker disease in tomato. Because it is very important to control newly introduced inoculum sources from commercial materials, the specific detection of this pathogen in seeds and seedlings is essential for effective disease control. In this study, a novel and efficient assay for the detection and quantitation of C. michiganensis subsp. michiganensis in symptomless tomato and red pepper seeds was developed. A pair of polymerase chain reaction (PCR) primers (Cmm141F/R) was designed to amplify a specific 141 bp fragment on the basis of a ferredoxin reductase gene of C. michiganensis subsp. michiganensis NCPPB 382. The specificity of the primer set was evaluated using purified DNA from 16 isolates of five C. michiganensis subspecies, one other Clavibacter species, and 17 other reference bacteria. The primer set amplified a single band of expected size from the genomic DNA obtained from the C. michiganensis subsp. michiganensis strains but not from the other C. michiganensis subspecies or from other Clavibacter species. The detection limit was a single cloned copy of the ferredoxin reductase gene of C. michiganensis subsp. michiganensis. In conclusion, this quantitative direct PCR assay can be applied as a practical diagnostic method for epidemiological research and the sanitary management of seeds and seedlings with a low level or latent infection of C. michiganensis subsp. michiganensis.
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Affiliation(s)
- Min Seok Cho
- National Academy of Agricultural Science, Rural Development Administration, Suwon, 441-707, Republic of Korea
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de León L, Siverio F, López MM, Rodríguez A. Clavibacter michiganesis subsp. michiganensis, a Seedborne Tomato Pathogen: Healthy Seeds Are Still the Goal. PLANT DISEASE 2011; 95:1328-1338. [PMID: 30731794 DOI: 10.1094/pdis-02-11-0091] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Affiliation(s)
- Leandro de León
- Instituto Canario de Investigaciones Agrarias (ICIA). Tenerife, Canary Islands, Spain
| | - Felipe Siverio
- Laboratorio de Sanidad Vegetal de la Consejería de Agricultura, Ganadería, Pesca y Alimentación del Gobierno de Canarias. Tenerife, Canary Islands, Spain
| | - María M López
- Instituto Valenciano de Investigaciones Agrarias (IVIA). Moncada, Valencia, Spain
| | - Ana Rodríguez
- Instituto Canario de Investigaciones Agrarias (ICIA). Tenerife, Canary Islands, Spain, and Universidad de La Laguna, Tenerife, Canary Islands, Spain
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Olivier V, Baloche A, Drouin A, Audusseau C, Paillard S, Soubelet H. Internal methods comparison study and inter-laboratory study on Clavibacter michiganensis subsp. michiganensis in tomato seeds1. ACTA ACUST UNITED AC 2010. [DOI: 10.1111/j.1365-2338.2010.02380.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Kim HY, Park HJ, Ko G. Hollow-fiber ultrafiltration for the concentration and simultaneous recovery of multiple pathogens in contaminated foods. J Food Prot 2009; 72:2547-52. [PMID: 20003737 DOI: 10.4315/0362-028x-72.12.2547] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
We investigated the possibility of using hollow-fiber ultrafiltration (HUF) for the simultaneous recovery of multiple microorganisms in food samples. MS2 bacteriophage, E. coli, Bacillus subtilis spores, and murine norovirus (MNV) were each inoculated into 5 liters of either distilled water (DW) or glycine elution buffer and then concentrated using hollow-fiber polysulfone ultrafilters. The resulting concentrates were further analyzed by either cultivation or TaqMan real-time reverse transcription PCR assay. The overall average recovery rates were 7.1% in DW and 17.1% in glycine elution buffer. When the virus, vegetative bacteria, and bacterial spores were simultaneously inoculated into DW, glycine, or Tris-HCl elution buffers, on average 16.8% of inoculated microorganisms were recovered by HUF. The addition of 3% beef extract blocking buffer to HUF increased the total recovery rate to 46.1%, with incremental recovery rates increasing sharply for B. subtilis spores and MNV. Use of HUF resulted in E. coli recovery rates of 68.0% on lettuce and 66.2% on ham and MNV recovery rates of 1.5% on lettuce and 5.8% on ham. Our study demonstrates that HUF can be effective at simultaneously recovering and concentrating diverse bacterial and viral pathogens from foods.
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Affiliation(s)
- Hee-Yeon Kim
- Department of Environmental Health and Institute of Health and Environment, School of Public Health, Seoul National University, Seoul, Korea
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Horká M, Horký J, Matoušková H, Šlais K. Free flow and capillary isoelectric focusing of bacteria from the tomatoes plant tissues. J Chromatogr A 2009; 1216:1019-24. [DOI: 10.1016/j.chroma.2008.12.024] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2008] [Revised: 12/08/2008] [Accepted: 12/10/2008] [Indexed: 11/16/2022]
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Cholera toxin subunit B detection in microfluidic devices. Anal Bioanal Chem 2008; 393:177-86. [DOI: 10.1007/s00216-008-2364-6] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2008] [Revised: 08/18/2008] [Accepted: 08/20/2008] [Indexed: 11/26/2022]
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Solid-phase capture of pathogenic bacteria by using gangliosides and detection with real-time PCR. Appl Environ Microbiol 2008; 74:2254-8. [PMID: 18263751 DOI: 10.1128/aem.02601-07] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We developed a method for concentrating pathogens from samples without enrichment. Immobilized gangliosides concentrated bacteria for detection with real-time PCR. A sensitivity of approximately 4 CFU/ml (3 h) in samples without competing microflora was achieved. Samples with competing microflora had a sensitivity of 40,000 CFU/ml. The variance was less than one cycle.
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de León L, Rodríguez A, López MM, Siverio F. Evaluation of the efficacy of immunomagnetic separation for the detection of Clavibacter michiganensis subsp. michiganensis in tomato seeds. J Appl Microbiol 2007; 104:776-86. [PMID: 17927739 DOI: 10.1111/j.1365-2672.2007.03595.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
AIMS To evaluate the effectiveness of the optimized immunomagnetic separation (IMS)-plating protocol in relation to other culture, serological and molecular techniques currently used for Clavibacter michiganensis subsp. michiganensis in seed-testing laboratories. METHODS AND RESULTS Bacterial suspensions, tomato seed extracts spiked with the pathogen and naturally infected seeds were IMS-plated for the detection of C. m. subsp. michiganensis. These results were compared with plating on general (YPGA) and semiselective (mSCM) media, double-antibody sandwich enzyme-linked immunosorbent assay (DAS-ELISA), immunofluorescent assay (IF) or polymerase chain reaction (PCR). Different seed lots and pathogen strains were also tested. IMS-plating allowed the detection of less than 10 CFU ml(-1) of pathogen in all assayed samples. The mSCM medium provided positive results for 10 CFU ml(-1) in naturally infected seeds, but up to 14 days was necessary for the typical colonies of the target to be come visible. By serological techniques, 10(3) and up to 10(4) CFU ml(-1) were detected by IF and ELISA, respectively. DNA extraction was required to obtain positive results by PCR in seed extracts containing 10(3) CFU ml(-1) or more. CONCLUSIONS Among the evaluated methods, IMS-plating provided the best results regarding sensitivity and specificity for C. m. subsp. michiganensis detection, allowing the recovery of viable bacteria from seed extracts. SIGNIFICANCE AND IMPACT OF THE STUDY IMS-plating increases isolation rates of C. m. subsp. michiganensis and could improve standard protocols currently used for routine analysis.
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Affiliation(s)
- L de León
- Departamento de Protección Vegetal, Instituto Canario de Investigaciones Agrarias (ICIA), La Laguna, Tenerife, Canary Islands, Spain
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