A Loop-Mediated Isothermal Amplification Assay and Sample Preparation Procedure for Sensitive Detection of Xanthomonas fragariae in Strawberry

Survival of Xanthomonas fragariae on Common Materials

Xanthomonas fragariae causes strawberry angular leaf spot (ALS), an important disease for the strawberry nursery industry in North America. To identify potential inoculum sources, the survival of X. fragariae was examined on the surfaces of 11 common materials found in nurseries: corrugated cardboard, cotton balls, cotton cloth (t-shirt), strawberry leaf, sheet metal, plastic, rubber, Tyvek, wood (balsa), glass (microscope slide), and latex (latex glove). Prefabricated rectangular samples (7.62 by 2.54 cm) of each material were immersed in a bacterial suspension for 15 min, after which the samples were stored at approximately 20°C (room temperature) or -4°C (the cold storage temperature for dormant plants in strawberry nurseries) for 1, 3, 7, 14, 30, 60, 90, 180, 270, and 365 days after inoculation (DAI). After the storage period elapsed, bacteria were recovered from the surfaces of each of the samples with phosphate-buffered saline (PBS)-soaked cotton balls. Survival rate was determined with a viability real-time quantitative PCR procedure and in a plant bioassay that involved rub inoculation of strawberry leaflets with the PBS-soaked cotton balls used to recover bacteria from the samples. Results showed that X. fragariae could survive on all surfaces but that survival rate differed among materials and storage temperature. All materials were capable of harboring viable bacteria up to 7 DAI when stored at -4°C based on the formation of lesions on inoculated leaves in the plant bioassay. The longest survival observed was 270 DAI on cardboard stored at -4°C. At room temperature, cardboard, cotton balls, cotton t-shirt, and strawberry leaf tissue supported small bacterial populations up to 14 DAI. The information from this study can be used to improve sanitation practices for ALS management in strawberry nurseries.

Development of a Highly Sensitive Loop-Mediated Isothermal Amplification Incorporated with Flocculation of Carbon Particles for Rapid On-Site Diagnosis of Blood Disease Bacterium Banana

Bananas are one of the most crucial fruit crops worldwide and significantly contribute to food security in developing countries. However, blood disease of bananas caused by Ralstonia syzygii subspecies celebensensis has become a threat to banana production. Rapid and accurate diagnosis of BDB for on-site detection is pivotal at an early stage for an effective disease control strategy. This study developed LAMP with specific primers targeting BDB, followed by a flocculation assay for visualising positive amplification in the LAMP assay. The assay was sensitive to picogram amounts of gDNA (0.5 pg). LAMP assay on BDB gDNA showed flocculation, but negative results on Fusarium oxysporus cubense and Ralstonia solanacaerum confirming the specificity of the assays. Field testing conducted at MARDI headquarters and Taman Pertanian Universiti discovered that the LAMP-flocculation assays were successful in detecting BDB on symptomatic samples as well as on samples from a healthy plot with no symptom observed at the sampling stage, revealing that this assay can detect BDB at an early infection stage. The validation results showed that the LAMP-flocculation assay was comparable with the PCR technique. This newly developed technique is highly specific and sensitive for the early detection of BDB for the adoption of precautionary control measures.

A Long-Amplicon Viability-qPCR Test for Quantifying Living Pathogens that Cause Bacterial Spot in Tomato Seed

Bacterial spot is one of the most serious diseases of tomato. It is caused by four species of Xanthomonas: X. euvesicatoria, X. gardneri, X. perforans, and X. vesicatoria. Contaminated or infected seed can be a major source of inoculum for this disease. The use of certified pathogen-free seed is one of the primary management practices to reduce the inoculum load in commercial production. Current seed testing protocols rely mainly on plating the seed extract and conventional PCR; however, the plating method cannot detect viable but nonculturable cells, and the conventional PCR assay has limited capability to differentiate DNA extracted from viable or dead bacterial cells. To improve the sensitivity and specificity of the tomato seed testing method for bacterial spot pathogens, a long-amplicon quantitative PCR (qPCR) assay coupled with propidium monoazide (PMA-qPCR) was developed to quantify selectively the four pathogenic Xanthomonas species in tomato seed. The optimized PMA-qPCR procedure was evaluated on pure bacterial suspensions, bacteria-spiked seed extracts, and seed extracts of inoculated and naturally infected seed. A crude DNA extraction protocol also was developed, and PMA-qPCR with crude bacterial DNA extracts resulted in accurate quantification of 10⁴ to 10⁸ CFU/ml of viable bacteria when mixed with dead cells at concentrations as high as 10⁷ CFU/ml in the seed extracts. With DNA purified from concentrated seed extracts, the PMA-qPCR assay was able to detect DNA of the target pathogens in seed samples spiked with ≥75 CFU/ml (about 0.5 CFU/seed) of the viable pathogens. Latent class analysis of the inoculated and naturally infected seed samples showed that the PMA-qPCR assay had greater sensitivity than plating the seed extracts on the semiselective modified Tween Medium B and CKTM media for all four target species. Being much faster and more sensitive than dilution plating, the PMA-qPCR assay has potential to be used as a standalone tool or in combination with the plating method to improve tomato seed testing and advance the production of clean seed.

Loop-Mediated Isothermal Amplification assays for on-site detection of the main sweetpotato infecting viruses

Globally, Sweet potato feathery mottle virus (SPFMV) and Sweet potato chlorotic stunt virus (SPCSV) occur frequently and in combination cause sweetpotato virus disease (SPVD). Many viral diseases are economically important and negatively impact the production and movement of germplasm across regions. Rapid detection of viruses is critical for effective control. Detection and quantification of viruses directly from sweetpotato remains a challenge. Current diagnostic tests are not sensitive enough to reliably detect viruses directly from the plant or require expensive laboratory equipment and expertise to perform. We developed a simple and rapid loop-mediated isothermal amplification (LAMP) assay for the detection of SPFMV, SPCSV and begomoviruses related to sweet potato leaf curl virus (SPLCV). Laboratory validation recorded 100 % diagnostic sensitivity for all the three viruses. The LAMP assays were customized for field testing using a lyophilized thermostable isothermal master mix in a ready-to-use form that required no cold chain. The average time to positivity (TTP) was: SPFMV 5-30 min, SPCSV 15-43 min s and begomoviruses 28-45 mins. LAMP on-site testing results were comparable to PCR and RT-PCR confirmatory laboratory tests. The LAMP assay is a powerful tool for rapid sweetpotato virus detection at a reasonable cost and thus could serve as quality control systems for planting materials.

"Shining a LAMP" (Loop-Mediated Isothermal Amplification) on the Molecular Detection of Phytopathogens Phytophthora spp. and Phytophthora cactorum in Strawberry Fields

Phytopathogenic microorganisms belonging to the genus Phytophthora have been recognized many times as causal agents of diseases that lower the yield of many plants important for agriculture. Meanwhile, Phytophthora cactorum causes crown rot and leather rot of berry fruits, mainly strawberries. However, widely-applied culture-based methods used for the detection of pathogens are time-consuming and often inaccurate. What is more, molecular techniques require costly equipment. Here we show a rapid and effective detection method for the aforementioned targets, deploying a simple molecular biology technique, Loop-Mediated Isothermal Amplification (LAMP). We optimized assays to amplify the translation elongation factor 1-α (EF1a) gene for two targets: Phytophthora spp. And Phytophthora cactorum. We optimized the LAMP on pure strains of the pathogens, isolated from organic plantations of strawberry, and successfully validated the assay on biological material from the environment including soil samples, rhizosphere, shoots and roots of strawberry, and with SYBR Green. Our results demonstrate that a simple and reliable molecular detection method, that requires only a thermoblock and simple DNA isolation kit, can be successfully applied to detect pathogens that are difficult to separate from the field. We anticipate our findings to be a starting point for developing easier and faster modifications of the isothermal detection methods and which can be applied directly in the plantation, in particular with the use of freeze-dried reagents and chemistry, allowing observation of the results with the naked eye.

Trends in Molecular Diagnosis and Diversity Studies for Phytosanitary Regulated Xanthomonas

Bacteria in the genus Xanthomonas infect a wide range of crops and wild plants, with most species responsible for plant diseases that have a global economic and environmental impact on the seed, plant, and food trade. Infections by Xanthomonas spp. cause a wide variety of non-specific symptoms, making their identification difficult. The coexistence of phylogenetically close strains, but drastically different in their phenotype, poses an added challenge to diagnosis. Data on future climate change scenarios predict an increase in the severity of epidemics and a geographical expansion of pathogens, increasing pressure on plant health services. In this context, the effectiveness of integrated disease management strategies strongly depends on the availability of rapid, sensitive, and specific diagnostic methods. The accumulation of genomic information in recent years has facilitated the identification of new DNA markers, a cornerstone for the development of more sensitive and specific methods. Nevertheless, the challenges that the taxonomic complexity of this genus represents in terms of diagnosis together with the fact that within the same bacterial species, groups of strains may interact with distinct host species demonstrate that there is still a long way to go. In this review, we describe and discuss the current molecular-based methods for the diagnosis and detection of regulated Xanthomonas, taxonomic and diversity studies in Xanthomonas and genomic approaches for molecular diagnosis.

Development of Real-Time and Colorimetric Loop Mediated Isothermal Amplification Assay for Detection of Xanthomonas gardneri

Xanthomonas gardneri is one of the causal agents of bacterial spot (BS), an economically important bacterial disease of tomato and pepper. Field-deployable and portable loop-mediated isothermal amplification (LAMP)-based instruments provide rapid and sensitive detection of plant pathogens. In order to rapidly and accurately identify and differentiate X. gardneri from other BS-causing Xanthomonas spp., we optimized a new real-time monitoring LAMP-based method targeting the X. gardneri-specific hrpB gene. Specificity and sensitivity of real-time and colorimetric LAMP assays were tested on the complex of bacterial strains pathogenic to tomato and pepper and on plants infected by the pathogen. The assay detection limit was 1 pg/μL of genomic DNA with an assay duration of only 30 min. The use of portable and handheld instruments allows for fast analysis, reducing the diagnosis time, and can contribute to proper disease management and control of X. gardneri. Due to the high efficiency of this method, we suggest its use as a standard diagnostic tool during phytosanitary controls.

Detection of Viable Xanthomonas fragariae Cells in Strawberry Using Propidium Monoazide and Long-Amplicon Quantitative PCR

Xanthomonas fragariae causes angular leaf spot in strawberry. The pathogen's association with its host tissue is thought to be a condition for its survival. Consequently, transmission of the pathogen to field production sites occurs almost exclusively through the movement of contaminated planting stock. The aim of this study was to develop a propidium monoazide (PMA)-quantitative PCR (qPCR) protocol for specific detection of viable X. fragariae cells. The qPCR procedure was developed for two different primer pairs: one producing a long amplicon (863 bp) and the other a short amplicon (61 bp). Both pairs were tested on mixtures of viable and heat-killed bacteria cells, bacteria-spiked strawberry petiole samples, and petioles collected from symptomatic, inoculated plants. The results showed that long-amplicon PMA-qPCR enabled specific and sensitive detection of X. fragariae with a detection limit of 10³ CFU/ml, and it significantly improved PMA efficiency in differentiating viable from dead bacterial cells relative to short-amplicon PMA-qPCR. Based on the delta threshold cycle (C_t) values (i.e., the difference in C_t values between PMA-treated and nontreated samples), the long-amplicon PMA-qPCR was able to suppress the detection of dead X. fragariae cells 1.9- to 3.1-fold across all petiole samples tested. The quantification results from PMA-qPCR for mixtures of viable and dead cells were highly correlated with the predicted bacterial concentrations in a linear relationship (R² = 0.981). This assay can be useful for identifying inoculum sources in the strawberry production cycle, which may lead to improved disease management strategies.

Rapid Detection of Xanthomonas citri pv. fuscans and Xanthomonas phaseoli pv. phaseoli in Common Bean by Loop-Mediated Isothermal Amplification

A single loop-mediated isothermal amplification (LAMP) assay was developed for specific detection of both pathogens that cause bacterial blight in common bean, Xanthomonas phaseoli pv. phaseoli (Xpp) and Xanthomonas citri pv. fuscans (Xcf). The objective was to provide a simple, easy-to-use, specific, and sensitive method to investigate the presence of one or both pathogens in plant material and seeds for routine diagnosis. The detection limits for both pathogens were 10 CFU/ml for cell suspensions and 1 fg of DNA, whereas in conventional PCR, the primers detected up to 10⁵ CFU/ml and 1 ng of DNA. Specificity was confirmed by testing DNA from bean leaves, other Xanthomonas species, common fungal and bacterial bean pathogens, and bacteria from the leaf microbiota. The method was tested with bean leaves inoculated with Xpp, and the pathogen could be detected from 4 h up to 15 days postinoculation, even before disease symptoms were visible. When the method was applied to bacterium detection (Xpp or Xcf) in seed lots from infected plants, the bacterium detection rate was 100% (24 of 24). The pathogens were detected in seeds incubated for just 1 h in saline solution (0.85%), reducing the time needed for bacterium detection. The LAMP assay could be useful as a tool in bean bacterial blight management. Rapid and sensitive detection of bacteria in bean seed lots would reduce the risks of planting highly contaminated seeds in environments favorable to blight multiplication.

Genome-based population structure analysis of the strawberry plant pathogen Xanthomonas fragariae reveals two distinct groups that evolved independently before its species description

Xanthomonas fragariae is a quarantine organism in Europe, causing angular leaf spots on strawberry plants. It is spreading worldwide in strawberry-producing regions due to import of plant material through trade and human activities. In order to resolve the population structure at the strain level, we have employed high-resolution molecular typing tools on a comprehensive strain collection representing global and temporal distribution of the pathogen. Clustered regularly interspaced short palindromic repeat regions (CRISPRs) and variable number of tandem repeats (VNTRs) were identified within the reference genome of X. fragariae LMG 25863 as a potential source of variation. Strains from our collection were whole-genome sequenced and used in order to identify variable spacers and repeats for discriminative purpose. CRISPR spacer analysis and multiple-locus VNTR analysis (MLVA) displayed a congruent population structure, in which two major groups and a total of four subgroups were revealed. The two main groups were genetically separated before the first X. fragariae isolate was described and are potentially responsible for the worldwide expansion of the bacterial disease. Three primer sets were designed for discriminating CRISPR-associated markers in order to streamline group determination of novel isolates. Overall, this study describes typing methods to discriminate strains and monitor the pathogen population structure, more especially in the view of a new outbreak of the pathogen.

Colonization and Movement of Xanthomonas fragariae in Strawberry Tissues

Xanthomonas fragariae causes angular leaf spot of strawberry, an important disease in strawberry growing regions worldwide. To better understand how X. fragariae multiplies and moves in strawberry plants, a green fluorescent protein (GFP)-labeled strain was constructed and used to monitor the pathogen's presence in leaf, petiole, and crown tissue with fluorescence microscopy following natural and wound inoculation in three strawberry cultivars. Taqman PCR was used to quantify bacterial densities in these same tissues regardless of the presence of GFP signal. Results showed X. fragariae colonized leaf mesophyll, the top 1 cm portion of the petiole adjacent to the leaf blade, and was occasionally found colonizing xylem vessels down to the middle of the petioles. The colonization of vascular bundles and the limited systemic movement that was observed appeared to be a passive process, of which the frequency increased with wounding and direct infiltration of bacteria into leaf veins. X. fragariae was able to directly enter petioles and colonize the space under the epidermis. Systemic movement of the bacteria into crown and other uninoculated tissues was not detected visually by GFP. However, X. fragariae was occasionally detected in these tissues by qPCR, but at quantities very near the qPCR detection limit. Petiole tissue harboring bacteria introduced either by direct entry through natural openings or wounds, or by systemic movement from infected foliar tissue, likely serves as a main source of initial inoculum in field plantings.

Development of a recombinase polymerase amplification assay for Vibrio parahaemolyticus detection with an internal amplification control

A novel RPA-IAC assay using recombinase polymerase and an internal amplification control (IAC) for Vibrio parahaemolyticus detection was developed. Specific primers were designed based on the coding sequence for the toxR gene in V. parahaemolyticus. The recombinase polymerase amplification (RPA) reaction was conducted at a constant low temperature of 37 °C for 20 min. Assay specificity was validated by using 63 Vibrio strains and 10 non-Vibrio bacterial species. In addition, a competitive IAC was employed to avoid false-negative results, which co-amplified simultaneously with the target sequence. The sensitivity of the assay was determined as 3 × 10³ CFU/mL, which is decidedly more sensitive than the established PCR method. This method was then used to test seafood samples that were collected from local markets. Seven out of 53 different raw seafoods were detected as V. parahaemolyticus-positive, which were consistent with those obtained using traditional culturing method and biochemical assay. This novel RPA-IAC assay provides a rapid, specific, sensitive, and more convenient detection method for V. parahaemolyticus.

Analysis of the Spatial Pattern of Strawberry Angular Leaf Spot in California Nursery Production

In California, angular leaf spot (ALS) is a common disease in strawberry nursery production, and a major concern for nurseries wishing to export plants. As the spatial pattern of a disease can offer insight into pathogen source, mode of dissemination, and how current crop management practices affect epidemic development, an understanding of the spatial pattern of ALS would allow nursery growers to make informed decisions regarding disease management. Ninety-seven field assessments of disease incidence were performed at different nursery locations in 2014 and 2015 to quantify ALS spatial pattern under commercial conditions. Both point-pattern and geostatistical statistical procedures were used to analyze the data. The spatial pattern of ALS was characterized by a high degree of heterogeneity, as indicated by high median values of the beta-binomial distribution's theta parameter (0.643), and the index of dispersion, D (4.218). The binary power law provided a robust description of the data with estimated slope and intercept parameters significantly greater than 1 and 0, respectively (P < 0.001). Spatial analysis by distance indices (SADIE) detected significant nonrandom spatial arrangements for 64% of the data sets. Analysis of directional disease spread showed a strong spatial association between sampling units along the same planting row. This suggests that recurrent crop operations during the growing season play a significant role in ALS spread and should be taken into account to improve disease control.

Development and Evaluation of ELISA and qRT-PCR for Identification of Squash vein yellowing virus in Cucurbits

Squash vein yellowing virus (SqVYV) causes viral watermelon vine decline. To facilitate detection of SqVYV, enzyme linked-immunosorbent assay (ELISA) and quantitative reverse-transcription polymerase chain reaction (qRT-PCR) diagnostic methods were developed. Both methods were capable of detecting SqVYV in a wide range of cucurbit hosts. ELISA was able to detect virus in infected host tissue diluted to at least 1:2,560, which was sufficient for detection in symptomatic squash and watermelon plants. The qRT-PCR method was capable of reliably detecting as few as 3.4 copies of a cloned fragment of SqVYV genomic RNA with an average cycle threshold (C_t) value of 36.4. The sensitivities and specificities for each detection method were estimated by latent class analysis for a set of inoculated squash and watermelon plants at two sampling scales. The scales were hierarchical, with individual plants representing the upper scale and samples from the plant representing the lower scale. The number of samples per plant varied from 1 to 8, and a plant was diagnosed positive if any of its samples tested positive. For all analyses, a cutoff C_t of 35 was chosen for qRT-PCR, which is approximately 2.5 cycles lower than the lowest C_t value achieved for mock-inoculated plants (presumed to be a false positive). qRT-PCR showed high sensitivities (≥0.99) at both sampling scales for squash and watermelon, whereas the sensitivities for ELISA ranged from 0.58 to 0.76. The specificities for both tests were very similar (≥0.94), with ELISA sometimes outperforming qRT-PCR. These diagnostic methods provide additional tools for the identification of SqVYV and management of SqVYV-induced watermelon vine decline.

An immunoassay-based reverse-transcription loop-mediated isothermal amplification assay for the rapid detection of avian influenza H5N1 virus viremia

Avian influenza virus (AIV) subtype H5N1 attracts particular consideration because it is a continuous threat to animals and public health systems. The viremia caused by AIV H5N1 infection may increase the risk of blood-borne transmission between humans. Therefore, there is a need to rapidly evaluate and implement screening measures for AIV H5N1 viremia that allows for rapid response to this potentially pandemic threat. The present report describes an immunoassay-based reverse-transcription loop-mediated isothermal amplification (immuno-RT-LAMP) assay for the rapid detection of AIV H5N1 in whole blood samples. Using PCR tubes coated with an H5 subtype monoclonal antibody, AIV H5N1 virions were specifically captured from blood samples. After a thermal lysis step, the released viral N1 gene was exponentially amplified using RT-LAMP on either a real-time PCR instrument for quantitative analysis, or in a water bath system for endpoint analysis. The detection limit of the newly developed immuno-RT-LAMP assay was as low as 1.62×10(1) 50% embryo infectious dose/mL of virus in both regular samples and simulated viremia samples. There were no cross-reactions with non-H5N1 influenza viruses or other avian viruses. The reproducibility of the assay was confirmed using intra- and inter-assay tests with variability ranging from 1.05% to 3.37%. Our results indicate that immuno-RT-LAMP is a novel, effective point-of-care virus identification solution for the rapid diagnosis and monitoring of AIV H5N1 in blood samples.