Validation of four real‐time TaqMan PCRs for the detection of Ralstonia solanacearum and/or Ralstonia pseudosolanacearum and/or Clavibacter michiganensis subsp. sepedonicus in potato tubers using a statistical regression approach

A new DNA extraction method and a new multiplex real‐time TaqMan PCR test for detection of Ralstonia solanacearum, Ralstonia pseudosolanacearum and Clavibacter michiganensis subsp. sepedonicus in asymptomatic potato tubers are presented. This new multiplex PCR and three published TaqMan PCRs for detection of R. solanacearum and/or R. pseudosolanacearum and/or R. syzygii spp. and/or C. michiganensis subsp. sepedonicus were validated using linear regression analysis for estimating the Ct values and its variation at 5 × 10³ bacteria mL^?1. The three published PCRs that have been validated are Massart et al. (2014, detecting R. solanacearum and C. michiganensis subsp. sepedonicus), Weller et al. (1999, detecting R. solanacearum, R. pseudosolanacearum and R. syzygii spp.) and Gudmestad et al. (2009, detecting C. michiganensis subsp. sepedonicus). All tested PCRs were fit for purpose for their target organisms. The PCR tests have different target genes, allowing one of the sets to be used as first screening test and another as second screening test for the detection of R. solanacearum and/or R. pseudosolanacearum and/or C. michiganensis subsp. sepedonicus in asymptomatic potato tubers.     

Performance of real‐time PCR and immunofluorescence for the detection of Clavibacter michiganensis subsp. sepedonicus and Ralstonia solanacearum in potato tubers in routine testing

This paper describes a comparison study of test methods and supports the use of real‐time polymerase chain reaction (PCR) for the detection of Clavibacter michiganensis subsp. sepedonicus and Ralstonia solanacearum in potato tubers in routine testing. These 2 bacteria are quarantine organisms under European Union (EU) regulatory control and testing for (latent) infections of these bacteria in seed potatoes is mandatory. Real‐time PCR tests were performed on 276 routine potato tuber samples, including samples infected with either C. michiganensis subsp. sepedonicus or R. solanacearum, and the performance of these real‐time PCR tests was compared with that of immunofluorescence (IF). Real‐time PCR tests, using different primer sets and extraction and PCR protocols, proved to be sensitive and specific for the detection of C. michiganensis subsp. sepedonicus and R. solanacearum in potato tubers in routine testing, and performed at least as well as IF. Real‐time PCR is a good addition to the detection protocols as laid down in EU regulations (EU Council Directives 2006/56/EC and 2006/63/EC).     

Repetitive Sequence-derived PCR Profiling Using the BOX-A1R Primer for Rapid Identification of the Plant Pathogen Clavibacter Michiganensis Subspecies Sepedonicus

Repetitive sequence-derived PCR using the BOX-A1R primer was used to generate genomic fingerprints of Clavibacter michiganensis subspecies sepedonicus, the causal agent of bacterial ring rot disease of potato. A total of 35 C. michiganensis subsp. sepedonicus strains were selected for study in order to represent the widest possible historical, morphological and geographical diversity of the organism. Comparison was made with genomic fingerprints of C. michiganensis subsp. michiganensis, C. michiganensis subsp. insidiosus, C. michiganensis subsp. tessellarius, C. michiganensis subsp. nebraskensis as well as other related Gram positive plant pathogens. The resultant genomic fingerprints and subsequent cluster analysis show C. michiganensis subsp. sepedonicus to form a remarkably homogeneous group with approximately 84% similarity between all of the strains tested. There was no evidence to suggest that fingerprints varied with historic, morphological or geographic diversity. In addition, C. michiganensis subsp. sepedonicus isolated from asymptomatic sugar beet had the same fingerprint as those which were isolated as potato pathogens. This group was easily distinguished from the clusters formed by the other subspecies of C. michiganensis and Gram positive plant pathogens. The potential for this technique to be used as a relatively rapid method to replace the time consuming and sometimes inconclusive eggplant bioassay test is discussed.     

Rapid Identification of Clavibacter michiganensis Subspecies Sepedonicus based on the Stable Low Molecular Weight RNA (LMW RNA) Profiles

Clavibacter michiganensis subsp. sepedonicus causes potato ring rot disease. The identification process for this bacterium is complex and long. This work demonstrates that the stable low-molecular-weight (LMW) RNA profiles allow their rapid identification. Staircase electrophoresis in polyacrylamide gels was used to analyze the LMW RNA profiles of 54 strains of C. michiganensis subsp. sepedonicus from different geographic origins. The profiles of several strains of other subspecies of C. michiganensis and other pathogens of potatoes were also analyzed. All the strains of C. michiganensis subsp. sepedonicus had the same LMW RNA profile. They had a band in class 2 of tRNA that was absent in the other subspecies of the species C. michiganensis. Also, the LMW RNA of C. michiganensis subsp. sepedonicus was different with respect to the LMW RNA profiles of other pathogens of potato. The results indicate the possible utilization of LMW RNA profiles in identification of the bacteria causing potato ring rot disease.     

Rapid Identification of Clavibacter michiganensis Subspecies sepedonicus Using Two Primers Random Amplified Polymorphic DNA (TP-RAPD) Fingerprints

Twenty strains of Clavibacter michiganensis subsp. sepedonicus from different geographic origins and other reference strains of the same and different species, including other potato pathogens, were analysed with a new procedure named TP-RAPD that originates fingerprints of bacterial species. This procedure uses two primers to amplify the 16S rDNA gene. At 45 °C of annealing, the PCR product electrophoresed in agarose gels produced a band pattern that was different in all bacterial species studied as well as in the subspecies of C. michiganensis. All strains of C. michiganensis subsp. sepedonicus displayed the same TP-RAPD number of pattern. Unlike Gram negative bacteria, Gram positives of high G + C content, such as Clavibacter, produced low bands in TP-RAPD. By using a different set of two primers also based in the 16S rDNA sequence from Escherichia coli a more adequate amplification of Gram positives of high G + C including a greater number of bands was obtained. TP-RAPD patterns using the new set of primers described in this work is a reliable and fast method to identify C. michiganensis subsp. sepedonicus.     

Development of the simultaneous detection of Ralstonia solanacearum race 3 and Clavibacter michiganensis subsp. sepedonicus in potato tubers by a multiplex real-time PCR assay

Clavibacter michiganensis subsp. sepedonicus and Ralstonia solanacearum (Smith) Yabuuchi et al. race 3 are the causal agents of ring-rot and brown-rot of potato respectively. These diseases represent a serious threat to potato production in temperate climates. Both bacteria are listed as A2 pests in the EPPO region and as zero-tolerance quarantine organisms in the European Union. All the detection tests developed so far were only focused on the detection of a single pathogen while the absence of both bacteria has to be certified in the seed tubers. We have therefore developed a new multiplex real-time PCR assay to simultaneously detect both bacteria in a single assay. Additionally, the reliability of this molecular diagnostic test has been improved by the simultaneous amplification of an internal control, corresponding to a potato gene co-extracted from the sample. The polyvalence and the specificity of each set of bacterial primers and probes were evaluated on more than 90 bacterial strains. The limit of detection of this triplex real-time protocol was similar to those observed with other molecular protocols previously developed for the individual detection of one of these bacteria. A concordance of 100 % was obtained in a blind test mimicking the routine application of the technology. In conclusion, this new protocol represents a straightforward and convenient method potentially adapted to primary screening of potato tubers.     

Evaluation of the API 50CH and API ZYM systems for rapid characterization of Clavibacter michiganensis subsp. sepedonicus, causal agent of potato ring rot

API 50CH and API ZYM systems were used to characterize fifty-three strains of Clavibacter michiganensis subsp. sepedonicus from different geographic locations and several reference strains of the same and different species, including other potato pathogens. Clavibacter michiganensis subsp. sepedonicus strains displayed a high level of homogeneity, both in carbohydrate utilization and in enzymatic activity. Using API 50CH and API ZYM it was possible to differentiate C. michiganensis subsp. sepedonicus strains from the remaining taxa analysed in this study, which included representative strains of the other subspecies of C. michiganensis as well as other bacterial pathogens affecting potatoes. Therefore, these systems could be used as an effective method to characterize C. michiganensis subsp. sepedonicus. Such a procedure would constitute an alternative system to the conventional nutritional and physiological identification tests currently included in the official methods employed in the European Union to detect and identify this bacterium. The results obtained with the API systems agreed with the current taxonomic classification of C. michiganensis, clearly separating sepedonicus from the other subspecies belonging to this species.     

Euphresco inter‐laboratory comparison (2009–2012) on detection of Clavibacter michiganensis subsp. sepedonicus and Ralstonia solanacearum in potato tubers: proposal to include TaqMan® real‐time PCR as a primary (core) screening test in EU/EPPO standard methods

In the European Union (EU) potato production is surveyed for Clavibacter michiganensis subsp. sepedonicus (potato ring rot) and Ralstonia solanacearum (potato brown rot) under Commission Directives 93/85/EEC with its amendment 2006/56/EC and 98/57/EEC with its amendment 2006/63/EC. A regular update of the Directives is required in view of developments in understanding of the biology of these organisms and the diagnostics recommended for their detection and identification. Three inter‐laboratory tests (ILT1, ILT2 and ILT3) were performed from 2009 to 2012 as part of a Euphresco Phytosanitary ERA‐NET project to assess performance of current official methods for C. michiganensis subsp. sepedonicus and R. solanacearum. A major aim of the ILTs was to generate data on the performance of real‐time PCR protocols to support their introduction as primary (core) screening tests for both pathogens. In ILT1, 29 laboratories from 23 countries participated, in ILT2, 23 laboratories from 18 countries and in ILT3 42 laboratories from 24 countries. Relative accuracies for real‐time PCR tests averaged 92% for R. solanacearum and 96% for C. michiganensis subsp. sepedonicus) and compared with existing primary (core) screening tests (immunofluorescence, conventional PCR, semi‐selective plating and bioassay) in terms of analytical sensitivity, analytical specificity and robustness. It was concluded that all methods tested, including real‐time PCR, can be considered as equivalent. Therefore TaqMan ^® real‐time PCR is recommended for inclusion in EU Directives and EPPO Standards as a reliable primary (core) screening method.     

Evaluation of antagonistic bacteria for suppression of bacterial ring rot of potato

Bacterial strains with potential for biological control of bacterial ring rot of potato caused byClavibacter michiganensis subsp.sepedonicus were isolated from the surface of potato tubers. Eighty-eight potential biocontrol candidates, selected on the basis ofin vitro antibiosis toC. m. sepedonicus, produced inhibition zones with radii ranging from 0.5 to 16 mm on test plates. All antagonistic isolates were screened in the greenhouse for biocontrol activity on micropropagated potato plantlets root-inoculated withC. m. sepedonicus. Eight strains consistently prevented infection of plantlets but there was no significant correlation between the width of the inhibition zone in thein vitro assay and ring rot suppression in the plant bioassay. Three strains that showed a high level of biological control potential were identified as a saprophytic enteric bacterium (strain 7G), anArthrobacter sp. (strain 16C), and a soil coryneform bacterium (strain 18A). These were tested in a field plot by co-inoculating cut seed potato tubers withC. m. sepedonicus and antagonists. Strains 7G and 18A significantly increased plant stand whereas 16C decreased disease incidence. The relative number of ostensibly ring rot-free progeny tubers was generally greater when antagonists were present.     

Polymorphism analysis of housekeeping genes for identification and differentiation of <Emphasis Type="Italic">Clavibacter michiganensis</Emphasis> subspecies

The utility of polymorphism analysis was determined for differentiation of the following subspecies of the Gram-positive plant pathogenic bacterium, Clavibacter michiganensis: C. m. subsp. michiganensis, C. m. subsp. sepedonicus, C. m. subsp. insidiosus C. m. subsp. nebraskensis, and C. m. subsp. tessellarius. Specific primers designed for amplification of the housekeeping genes recA, rpoB, and rpoD generated 827-, 1037-, and 862-bp DNA fragments, respectively. PCR products obtained from 40 C. michiganensis strains were analysed using RFLP with four restriction endonucleases, and those PCR products with specific RFLP patterns were sequenced. The genotypes discriminated after PCR–RFLP were specific for each subspecies and also allowed for differentiation of C. m. subsp. michiganensis strains. Sequence analysis of the recA, rpoB, and rpoD gene fragments also distinguished C. michiganensis subspecies and was useful for phylogenetic analysis of all subspecies. For rapid, inexpensive, and effective differentiation of the five subspecies in this research, we recommend the amplification of recA and/or rpoD gene fragments and digestion of the PCR products with the restriction endonuclease FnuDII.     

In Planta - Complementation of Clavibacter Michiganensis Subsp. sepedonicus Strains Deficient in Cellulase Production or HR Induction Restores Virulence

Clavibacter michiganensis subsp. sepedonicus, a Gram positive bacterium that causes bacterial ring rot of potato, was studied in eggplant, an alternate host, using strains that differed in phenotype. Two factors affecting virulence, the ability to induce a hypersensitive response (HR) and cellulase production, were studied. A plasmid-free isolate of C. michiganensis subsp. sepedonicus that causes HR on tobacco but is unable to produce cellulase multiplied efficiently in planta, but caused only weak symptoms. In contrast, a strain that is unable to induce HR on tobacco but produces cellulase was impaired in the ability to multiply in the host and caused no symptoms. When the two non-virulent strains were coinoculated into eggplants, typical disease symptoms developed. This enhancement was not due to formation of a new phenotype or significant increases in population density of either of the strains. Our results suggest that both cellulase production and the ability to induce HR are required for a successful infection process and disease induction by C. michiganensis subsp. sepedonicus. Our results additionally suggest that the ability to induce HR on non-host plants is required for multiplication in the host plant, whereas cellulase expression is necessary for induction of disease symptoms.     

Bacterial diseases of potatoes in the major potato-growing areas in Turkey1

In 1988 and 1989 bacterial diseases of potatoes in Central Anatolia were investigated by utilizing the EC method for the detection of ring-rot bacterium (Clavibacter michiganensis ssp. sepedonicus) and using selective medium. 91 samples containing 200 tubers from commercial and farmers’ stores in Central Anatolia were tested for the presence of C.m.sepedonicus and about 50 tubers of each sample were also tested for the presence of soft-rot erwinias. Five different bacteria that cross-reacted with C.m.spedonicus antisera were isolated from heel-end extracts. All cross-reacted bacteria differed from C.m.sepedonicus morphologically and none of them was pathogenic on eggplant. C.m. sepedonicus was not detected, but Erwinia carotouora ssp. carotouora and Erwinia carotovora ssp. atroseptica were present in 7 and 17% of the samples respectively.     

植物病原棒形杆菌属分类最新进展

植物病原棒形杆菌属Clavibacter的分类随着研究的深入和鉴定技术水平的不断进步一直在发生着变化,之前普遍认可的观点为该属仅含有1个种,即密执安棒形杆菌C. michiganensis,种下又分为5个亚种,分别为密执安亚种C. michiganensis subsp. michiganensis、诡橘亚种C. michiganensis subsp. insidiosus、尼布拉斯加亚种C. michiganensis subsp. nebraskensis、环腐亚种C. michiganensis subsp. sepedonicus和花叶亚种C. michiganensis subsp. tessellarius。最近几年又有4个新亚种陆续被报道,分别为菜豆亚种C. michiganensis subsp. phaseoli、辣椒亚种C. michiganensis subsp. capsici、加利福尼亚亚种C. michiganensis subsp. californiensis和智利亚种C. michiganensis subsp. chilensis。随着全基因组分析和多基因分析技术在细菌分类上的应用,之前被广泛认可的4个亚种(诡橘亚种、尼布拉斯加亚种、环腐亚种和花叶亚种)及新亚种辣椒亚种也曾被建议定义为种,即C. insidiosus、C. nebraskensis、C. sepedonicus、C. tessellarius和C. capsici。为便于研究人员了解该属最新的分类研究现状,本文对植物病原棒形杆菌属的分类历史及最新分类现状进行了系统梳理,期望为该属病原菌的风险评估、检测鉴定等研究提供分类学参考。     

Evaluation of a diagnostic microarray for the detection of major bacterial pathogens of potato from tuber samples

Potato can be infected with many bacterial pathogens, the detection of which is necessary in seed certification. In this study, a diagnostic microarray previously tested for specificity of probes for detecting the potato bacteria causing blackleg and soft rot (Pectobacterium atrosepticum, Pectobacterium carotovorum, and Dickeya spp.), ring rot (Clavibacter. michiganensis subsp. sepedonicus), scab (Streptomyces scabies and Streptomyces turgidiscabies) and brown rot (Ralstonia solanacearum) from pure culture was evaluated for analytical sensitivity when testing directly from tuber samples. The microarray readily detected all the bacterial species when 100 ng of the target bacterial DNA from pure culture was mixed with DNA from soil microbes and potato. However, detection was inconsistent when total DNA isolated directly from infected tubers or enriched bacterial culture was used. While the high specificity of the probes could be confirmed from the results of the DNA cocktail experiment used as a control, the study demonstrated that the level of analytical sensitivity of the microarray under the tested condition was not sufficient to detect bacteria directly from tubers. Therefore, in addition to the cost and organizational complexities, the low analytical sensitivity and limited reproducibility of the microarray are constraints for establishing the platform for routine detection of potato bacterial pathogens from tuber samples.     

Analysis of the toxicity of purothionins and hordothionins for plant pathogenic bacteria

Purothionins (PTHs) and hordothionins (HTHs) were purified by cation-exchange chromatography from petroleum-ether extracts of wheat and barley flour respectively. The HTHs could be separated into two fractions, HTH-1 and HTH-2. Radial diffusion assays and micro-plate broth dilution assays with a number of plant pathogenic bacteria showed that these proteins were toxic forClavibacter michiganensis subsp.michiganensis, the causal agent of bacterial canker on tomato,C. m. subsp.sepedonicus, the causal agent of ring rot on potato, andXanthomonas campestris pv.vesicatoria, the causal agent of a spot disease on tomato and pepper. Only minor differences in toxicity between PTHs and HTHs, and between HTH-1 and HTH-2, were detected. Minor differences in toxicity of these thionins were also detected for different strains of these bacteria. The use of these plant proteins for engineering bacterial disease resistance into solanaceous crops will be discussed.     

Test performance study for detection of Ralstonia solanacearum and Clavibacter sepedonicus in potato tubers with TaqMan PCR

A test performance study (TPS) was organized in 2018 with ten official testing laboratories to evaluate the performance of different real-time PCR tests for the detection of Clavibacter sepedonicus and/or Ralstonia solanacearum in potato tubers. Participants were sent spiked potato extracts with low (0.8–1.2 × 10⁴ cfu mL^-1), medium (1.6–2.4 × 10⁵ cfu mL^-1) and high (1.6–2.4 × 10⁷ cfu mL^-1) bacterial loads, DNA extracts thereof and heel-end cores from symptomatic potato tubers. The four real-time PCR tests in this TPS for detection of C. sepedonicus were considered fit for purpose as principal screening methods. Two real-time PCRs in this TPS were considered fit for purpose as principal screening methods for detection of R. solanacearum. A third real-time PCR missed 23% of the DNA samples from low-level R. solanacearum spikes and is considered not fit for purpose as a principal screening method. Correct identification of spiked samples was lower when DNA extraction from the spiked samples was performed by the participating laboratories, highlighting the importance of appropriate DNA extraction protocols.     

A more sensitive and rapid multiplex RT-PCR assay combining with magnetic nanobeads for simultaneous detection of viruses in sweet potato

An improved multiplex RT-PCR assay combined with magnetic nanobeads (MNB-RT-PCR) was developed for simultaneous detection of four sweet potato viruses, Sweet potato virus G (SPVG), Sweet potato feathery mottle virus (SPFMV), Sweet potato virus C (SPVC) and Sweet potato chlorotic fleck virus (SPCFV). Four primer pairs specific for each virus were designed and the corresponding PCR products were 169, 357, 516 and 900 bp in length for SPVG, SPFMV, SPVC and SPCFV, respectively. The specificity of the method was tested using different combinations of virus templates, and the identities of the amplification products were confirmed by sequencing. The limits of detection for all four viruses by single and multiplex MNB-RT-PCR assays were comparable. The assay was further evaluated using laboratory and field samples compared with a conventional CTAB-RT-PCR assay, and the comparative results showed that the MNB-RT-PCR assay was more rapid and sensitive. These results suggest that the multiplex MNB-RT-PCR assay is an effective and preferable method for virus detection in sweet potato.     

Verbreitung der Bakteriellen Ringfäule der Kartoffel (Clavibacter michiganensis ssp. sepedonicus) durch kontaminierte Lagerkisten

In field trials performed by the Institute for Plant Protection of the Bavarian State Research Center for Agriculture (LfL) in Freising in 2001 and 2002, it was studied, whether Clavibacter michiganensis ssp. sepedonicus (Cms), the bacterial ring rot pathogen of potato, could be transmitted to seed potatoes by the use of contaminated crates. Healthy seed tubers were brought into contact with Cms before planting by (i) storage in freshly contaminated crates at 8°C for 4 weeks, (ii) storage at unregulated cellar temperature (between 1 and 15°C) for 8 months in crates, which were already contaminated and empty at filling time for 5 months and (iii) storage in freshly contaminated crates at 4°C for 5 months. Infections of stems and tubers of the plants were determined by polymerase chain reaction (PCR) and indirect immunofluorescence antibody staining (IFAS). Storage of healthy tubers in contaminated crates produced infected plants in all three treatments: PCR results of the tubers were positive in 2 (ii) to 9% (i) of the plants.     

Simultaneous and selective detection of two major soft rot pathogens of potato: Pectobacterium atrosepticum (Erwinia carotovora subsp. atrosepticum) and Dickeya spp. (Erwinia chrysanthemi)

Dickeya spp. and Pectobacterium atrosepticum are major pathogens of potato. Current methods to detect these soft-rotting bacteria require separate identification steps. Here we describe a simple method allowing simultaneous detection of both pathogens based on multiplex PCR. The sensitivity of the primer sets was first examined on purified genomic DNA of the type strains Dickeya chrysanthemi 2048^T and P. atrosepticum 1526^T. The specificity and detection limits of the primer sets were successfully tested on 61 strains belonging to various Dickeya and Pectobacterium species, on artificially inoculated and on naturally contaminated potato plants. This new method provides a gain in time and materials, the main advantages for large-scale processes such as pathogen-free seed certification.     

Accreditation process in the National Phytosanitary laboratory in Latvia1

The National Phytosanitary laboratory is the only laboratory in Latvia that provides testing of samples for regulated pests in the phytosanitary field. In 2001 a decision was made to implement Quality Assurance systems in the laboratory and obtain accreditation. From 2001 to 2003 preparation for accreditation took place in the laboratory. During this time a client of the laboratory, Sanitary Border Inspection of Latvia (SBI), arranged three audits to assess the activities of the laboratory in accordance with the requirements of ISO 17025. After a time and labour‐consuming preparation process on 2003‐12‐29 all the necessary documents including a Quality manual, two methods and procedures were submitted to the Latvian National Accreditation Bureau (LATAK). The first audit by LATAK was carried out in March 2005. After elimination of all non‐conformities, accreditation for two methods was received in 2005 (Method for detection and identification of Clavibacter michiganensis subsp. sepedonicus in potato tubers and Method for detection and identification of Ralstonia solanacearum in potato tubers). The Quality Assurance System was implemented and applies to the whole laboratory. Every year LATAK experts carry out monitoring visits and each time imperfections are found they must be eliminated or improved.