Rapid, specific, simple, in-field detection of Xanthomonas campestris pathovar musacearum by loop-mediated isothermal amplification

A retrospective analysis comparing metagenomic next-generation sequencing with conventional microbiology testing for the identification of pathogens in patients with severe infections

Introduction

The application value of metagenomic next-generation sequencing (mNGS) in detecting pathogenic bacteria was evaluated to promote the rational and accurate use of antibiotics. A total of 180 patients with severe infections were included in this study.

Methods

Based on their different symptoms, bronchoalveolar lavage fluid (BALF) or blood samples were collected for conventional microbiological testing (CMT) and mNGS.

Results

The results indicated that the etiological diagnosis rate of mNGS (78.89%) was significantly higher than that of CMT (20%) (p<0.001). Notably, mNGS exhibited greater sensitivity towards rare pathogens such as Chlamydia pneumoniae, Mycobacterium tuberculosis complex, and Legionella pneumophila, which were undetectable by CMT. Additionally, 64 cases underwent blood culture, BALF culture, and mNGS testing. Analysis revealed that the positive rate of blood culture (3.1%) was lower than that of BALF (25%), and the positive rate of CMT from both types was significantly lower than that of mNGS (89.1%) (p<0.001). In this study, 168 mNGS results were accepted, and 116 patients had their antibiotic therapy adjustment based on mNGS. Paired analysis indicated that white blood cell count (WBC), procalcitonin (PCT), C-reactive protein (CRP), and neutrophil (NEU) percentage provided valuable therapeutic guidance. The survival rate of patients was 55.36%, influenced by patient physical condition and age.

Discussion

Our data indicated that mNGS had significant auxiliary value in the clinical diagnosis and treatment for critically ill patients, especially for those with negative CMT results and clinically undefined infections. mNGS could broaden the detection scope, especially for special pathogens, and improve the detection rate, providing powerful assistance for early clinical diagnosis and treatment.

Colorimetric LAMP Assay for Detection of Xanthomonas phaseoli pv. manihotis in Cassava Through Genomics: A New Approach to an Old Problem

Bacterial blight caused by Xanthomonas phaseoli pv. manihotis (Xpm) is considered the main bacterial disease that affects cassava, causing significant losses when not properly managed. In the present study, a fast, sensitive, and easy-to-apply method to detect Xpm via colorimetric loop-mediated isothermal amplification (LAMP) was developed. To ensure the use of a unique-to-the-target pathovar core region for primer design, 74 complete genomic sequences of Xpm together with different bacterial species and pathovars were used for comparative genomics. A total of 42 unique genes were used to design 27 LAMP primer sets, from which nine primers were synthesized, and only one (Xpm_Lp1 primer set) showed sufficient efficiency in preliminary tests. The sensitivity, assessed by a serial dilution of the type strain (IBSBF 278) DNA, yielded high sensitivity, detecting up to 100 fg. The LAMP primers showed high specificity, did not cross-react with other bacterial species or other pathovars tested, and amplified only the Xpm isolates. Tests confirmed the high efficiency of the protocol using infected or inoculated macerated cassava leaves without the need for additional sample treatment. The LAMP test developed in this study was able to detect Xpm in a fast, simple, and sensitive way, and it can be used to monitor the disease under laboratory and field conditions.

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.

Rapid identification of the invasive Small hive beetle (Aethina tumida) using LAMP

BACKGROUND

Small hive beetle (SHB), Aethina tumida is an invasive pest of managed honey bees and has invaded Europe from Africa. The main risk point identified for incursions of this pest into the UK is imports of package bees and queens. Surveillance of this pest, carried out by the National Bee Unit, involves monitoring imports of live bees and routine screening of sentinel apiaries around the UK through collection of hive debris for visual inspection of pests. Currently, no molecular methods are used for screening hive debris for this pest in the UK. A new invasion of this pest would likely occur at low levels and might present with partial specimens broken up in the hive or eggs from the beetle, difficult to identify by visual inspection. Therefore, we sought to develop a fast and sensitive method for detecting SHB in hive debris by developing a loop-mediated isothermal amplification (LAMP) assay.

RESULT

The LAMP assay was able to detect the SHB in 19 to 25.37 min and did not cross-react with any non-target species tested. The assay was sensitive and could detect 12pg of DNA and it was able to detect less than 1 mg of tissue in a 30 g complex matrix of honey bee hive debris. The assay could successfully amplify from crude extracts of partial tissue specimens.

CONCLUSION

This tool will allow rapid field screening of suspect beetle specimens and laboratory screening of hive debris for a notifiable exotic pest of honey bees. © 2020 Crown copyright. Pest Management Science © 2020 Society of Chemical Industry.

Development of PCR, LAMP and qPCR Assays for the Detection of Aflatoxigenic Strains of Aspergillus flavus and A. parasiticus in Hazelnut

Aspergillus flavus and A. parasiticus are two species able to produce aflatoxins in foodstuffs, and in particular in hazelnuts, at harvest and during postharvest phase. As not all the strains of these species are aflatoxin producers, it is necessary to develop techniques that can detect aflatoxigenic from not aflatoxigenic strains. Two assays, a LAMP (loop-mediated isothermal amplification) and a real time PCR with TaqMan^® probe were designed and validated in terms of specificity, sensitivity, reproducibility, and repeatability. The capability of the strains to produce aflatoxins was measured in vitro and both assays showed to be specific for the aflatoxigenic strains of A. flavus and A. parasiticus. The limit of detection of the LAMP assay was 100–999 picograms of DNA, while the qPCR detected 160 femtograms of DNA in hazelnuts. Both techniques were validated using artificially inoculated hazelnuts and naturally infected hazelnuts. The qPCR was able to detect as few as eight cells of aflatoxigenic Aspergillus in naturally infected hazelnut. The combination of the LAMP assay, which can be performed in less than an hour, as screening method, with the high sensitivity of the qPCR, as confirmation assay, is able to detect aflatoxigenic strains already in field, helping to preserve the food safety of hazelnuts.

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.

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.

LAMP Detection of Four Plant-Pathogenic Oomycetes and Its Application in Lettuce Fields

In Kagawa Prefecture, Japan, the pathogens Phytophthora pseudolactucae, Pythium irregulare, Pythium uncinulatum, and Pythium spinosum have caused huge losses in lettuce production. We used loop-mediated isothermal amplification (LAMP) to analyze soil and plants in lettuce fields for the presence of these four pathogens. To develop an effective on-site detection method, we contrasted the Plant-LAMP and Plant Culture-LAMP procedures for plant samples, and five soil DNA extraction methods for soil samples. Plant-LAMP and a Soil DNA Isolation kit were selected to analyze three fields for the pathogen species present, infected sites, and level of soil contamination. We found that the same wilting symptoms could be caused by Phytophthora or Pythium, or a mixture of species from both genera. Ph. pseudolactucae infects the pith of the lettuce in aboveground parts, whereas Pythium spp. mainly infect roots. Ph. pseudolactucae and Py. uncinulatum caused disease more frequently than the other two pathogens. Furthermore, not all of the pathogens existed in the soil near infected lettuce plants. Therefore, the LAMP method can be used to diagnose pathogenic oomycetes in the field, and will be useful in the development of control strategies in lettuce production.

Rapid Sample Preparation and LAMP for Phytoplasma Detection

Loop-mediated isothermal AMPlification (LAMP) allows the rapid detection of pathogens by polymerase-mediated amplification of target nucleic acid sequences at a single incubation temperature. LAMP can be combined with very simple sample preparation/crude DNA extraction protocols, allowing the method to be used away from the laboratory for in-field detection. Equally, these benefits can also be leveraged to provide a rapid method suited to high-throughput diagnostic laboratories. In this chapter we described a crude DNA extraction protocol suitable for use in the field and provide a protocol for real-time detection using LAMP.

A highly specific tool for identification of Xanthomonas vasicola pv. musacearum based on five Xvm-specific coding sequences

Xanthomonas vasicola pv. musacearum (Xvm) is a bacterial pathogen responsible for the economically important Xanthomonas wilt disease on banana and enset crops in Sub-Saharan Africa. Given that the symptoms are similar to those of other diseases, molecular diagnosis is essential to unambiguously identify this pathogen and distinguish it from closely related strains not pathogenic on these hosts. Currently, Xvm identification is based on polymerase chain reaction (PCR) with GspDm primers, targeting the gene encoding general secretory protein D. Experimental results and examination of genomic sequences revealed poor specificity of the GspDm PCR. Here, we present and validate five new Xvm-specific primers amplifying only Xvm strains.

Comparative Evaluation of the LAMP Assay and PCR-Based Assays for the Rapid Detection of Alternaria solani

Early blight (EB), caused by the pathogen Alternaria solani, is a major threat to global potato and tomato production. Early and accurate diagnosis of this disease is therefore important. In this study, we conducted a loop-mediated isothermal amplification (LAMP) assay, as well as conventional polymerase chain reaction (PCR), nested PCR, and quantitative real-time PCR (RT-qPCR) assays to determine which of these techniques was less time consuming, more sensitive, and more accurate. We based our assays on sequence-characterized amplified regions of the histidine kinase gene with an accession number (FJ424058). The LAMP assay provided more rapid and accurate results, amplifying the target pathogen in less than 60 min at 63°C, with 10-fold greater sensitivity than conventional PCR. Nested PCR was 100-fold more sensitive than the LAMP assay and 1000-fold more sensitive than conventional PCR. qPCR was the most sensitive among the assays evaluated, being 10-fold more sensitive than nested PCR for the least detectable genomic DNA concentration (100 fg). The LAMP assay was more sensitive than conventional PCR, but less sensitive than nested PCR and qPCR; however, it was simpler and faster than the other assays evaluated. Despite of the sensitivity, LAMP assay provided higher specificity than qPCR. The LAMP assay amplified A. solani artificially, allowing us to detect naturally infect young potato leaves, which produced early symptoms of EB. The LAMP assay also achieved positive amplification using diluted pure A. solani culture instead of genomic DNA. Hence, this technique has greater potential for developing quick and sensitive visual detection methods than do other conventional PCR strategies for detecting A. solani in infected plants and culture, permitting early prediction of disease and reducing the risk of epidemics.

Xanthomonas campestris pv. musacearum: a major constraint to banana, plantain and enset production in central and east Africa over the past decade

TAXONOMY

Bacteria; Phylum Proteobacteria; Class Gammaproteobacteria; Order Xanthomonadales; Family Xanthomonadaceae; Genus Xanthomonas; currently classified as X. campestris pv. musacearum (Xcm). However, fatty acid methyl ester analysis and genetic and genomic evidence suggest that this pathogen is X. vasicola and resides in a separate pathovar.

ISOLATION AND DETECTION

Xcm can be isolated on yeast extract peptone glucose agar (YPGA), cellobiose cephalexin agar and yeast extract tryptone sucrose agar (YTSA) complemented with 5-fluorouracil, cephalexin and cycloheximide to confer semi-selectivity. Xcm can also be identified using direct antigen coating enzyme-linked immunosorbent assay (DAC-ELISA), species-specific polymerase chain reaction (PCR) using GspDm primers and lateral flow devices that detect latent infections.

HOST RANGE

Causes Xanthomonas wilt on plants belonging to the Musaceae, primarily banana (Musa acuminata), plantain (M. acuminata × balbisiana) and enset (Ensete ventricosum).

DIVERSITY

There is a high level of genetic homogeneity within Xcm, although genome sequencing has revealed two major sublineages.

SYMPTOMS

Yellowing and wilting of leaves, premature fruit ripening and dry rot, bacterial exudate from cut stems.

DISTRIBUTION

Xcm has only been found in African countries, namely Burundi, Ethiopia, Democratic Republic of the Congo, Kenya, Rwanda, Tanzania and Uganda.

ECOLOGY AND EPIDEMIOLOGY

Xcm is transmitted by insects, bats, birds and farming implements. Long-distance dispersal of the pathogen is by the transportation of latently infected plants into new areas.

MANAGEMENT

The management of Xcm has relied on cultural practices that keep the pathogen population at tolerable levels. Biotechnology programmes have been successful in producing resistant banana plants. However, the deployment of such genetic material has not as yet been achieved in farmers' fields, and the sustainability of transgenic resistance remains to be addressed.

Evaluation of a loop-mediated isothermal amplification assay based on hrpZ gene for rapid detection and identification of Pseudomonas syringae pv. lachrymans in cucumber leaves

AIMS

Cucumber angular leaf spot caused by Pseudomonas syringae pv. lachrymans (Psl) is an important and destructive disease worldwide, and no effective technique has been developed for the control of the pathogen. Detection of infection or latent in cucumber plants is critical to evaluate disease progress and strengthening management to avoid a serious epidemic in the fields. In this paper, we developed a rapid and sensitive method for detection of Psl using an isothermal method known as loop-mediated amplification (LAMP).

METHODS AND RESULTS

A set of six primers was designed to amplify the gene coding for the hrpZ, and conditions for detection were optimized to complete in 60 min at 67°C, and the amplification were confirmed through gel electrophoresis or visually inspected using calcein stain. The specificity of LAMP primers set was widely validated on Psl and nontarget strains. In sensitivity testing, LAMP allowed detection as low as 10⁴  CFU per ml bacterial cells without DNA extraction. The novel method was also applied for detecting Psl in infected cucumber leaves, and even the early onset of disease can be detected by the assay.

CONCLUSIONS

This study confirmed that the novel developed LAMP assay is an easy, rapid and sensitive method for the detection of Psl in infected leaves.

SIGNIFICANCE AND IMPACT OF THE STUDY

The method is suitable for direct detection of Psl without strain enrichment and complex DNA extraction from samples in the field, and hence it has the capability to be used for on-site disease diagnosis and field surveys.

Rapid and Sensitive Detection of Didymella bryoniae by Visual Loop-Mediated Isothermal Amplification Assay

Didymella bryoniae is a pathogenic fungus that causes gummy stem blight (GSB) in Cucurbitaceae crops (e.g., cantaloupe, muskmelon, cucumber, and watermelon). GSB produces lesions on the stems and leaves, and can also be spread by seeds. Here, we developed a rapid, visual, and sensitive loop-mediated amplification (LAMP) assay for D. bryoniae detection based on sequence-characterized amplified regions (GenBank accession nos GQ872461 and GQ872462) common to the two random amplification of polymorphic DNA group genotypes (RGI and RGII) of D. bryoniae; ideal conditions for detection were optimized for completion in 45 min at 63°C. The sensitivity and specificity of the LAMP assay were further analyzed in comparison with those of a conventional polymerase chain reaction (PCR). The sensitivity of the LAMP assay was 1000-fold higher than that of conventional PCR with a detection limit of 0.1 fg μL(-1) of targeted DNA. The LAMP assay could be accomplished in about 45 min, with the results visible to the naked eye. The assay showed high specificity in discriminating all D. bryoniae isolates from seven other fungal pathogens that occur in Cucurbitaceae crops. The LAMP assay also detected D. bryoniae infection in young muskmelon leaves with suspected early symptoms of GSB disease. Hence, the technique has great potential for developing rapid and sensitive visual detection methods for the D. bryoniae pathogen in crops and seeds. This method has potential application in early prediction of disease and reducing the risk of epidemics.

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

Xanthomonas fragariae is a bacterium that causes angular leaf spot of strawberry. Asymptomatic infection is common and contributes to the difficulties in disease management. The aim of this study was to develop a loop-mediated isothermal amplification (LAMP) assay as an efficient method for detection of asymptomatic infections of X. fragariae. In addition, a new method of sample preparation was developed that allows sampling of a larger amount of plant tissue, hence increasing the detection rate in real-life samples. The sample preparation procedure includes an overnight incubation of strawberry tissues in phosphate-buffered saline (PBS), followed by a quick sample concentration and a boiling step to extract DNA for amplification. The detection limit of the LAMP assay was approximately 2×10(3) CFU/mL for pure bacteria culture and 300 CFU/mL for bacteria spiked strawberry leaf and petiole samples. LAMP provided a 2-3 fold lower detection limit than the standard qPCR assay but was faster, and more user-friendly. The LAMP assay should serve as a rapid, sensitive and cost-effective tool for detecting asymptomatic infections of X. fragariae in strawberry nursery stock and contribute to improved disease management.