Genome guided LAMP assay for rapid and reliable detection of Xanthomonas axonopodis pv. vasculorum
Abstract Xanthomonas axonopodis pv. vasculorum (Xav), the causative agent of sugarcane gumming disease, represents a significant threat to global sugarcane production due to its systemic and destructive nature. A field-deployable tool specific to Xav is required for rapid infection detection and tim...
Saved in:
| Main Authors: | , , , , , , , , , , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Nature Portfolio
2025-07-01
|
| Series: | Scientific Reports |
| Subjects: | |
| Online Access: | https://doi.org/10.1038/s41598-025-08291-w |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| _version_ | 1849334964294778880 |
|---|---|
| author | Mitchell Marabella Julia Howard Santosh Bhandari Sally Do Maya Montoya-Pimolwatana Yichen Dou Shefali Dobhal Dario Arizala Stefania Montesinos Sharon A. Andreason Francisco Ochoa-Corona Jon-Paul Bingham Jenee Odani Daniel Jenkins Li Maria Ma Jacqueline Fletcher James P. Stack Mohammad Arif |
| author_facet | Mitchell Marabella Julia Howard Santosh Bhandari Sally Do Maya Montoya-Pimolwatana Yichen Dou Shefali Dobhal Dario Arizala Stefania Montesinos Sharon A. Andreason Francisco Ochoa-Corona Jon-Paul Bingham Jenee Odani Daniel Jenkins Li Maria Ma Jacqueline Fletcher James P. Stack Mohammad Arif |
| author_sort | Mitchell Marabella |
| collection | DOAJ |
| description | Abstract Xanthomonas axonopodis pv. vasculorum (Xav), the causative agent of sugarcane gumming disease, represents a significant threat to global sugarcane production due to its systemic and destructive nature. A field-deployable tool specific to Xav is required for rapid infection detection and timely disease management. This resulted in a loop-mediated isothermal amplification (LAMP) assay targeting the gene region, unique to Xav strains, as a rapid and precise diagnostic assay. The selection of a target gene region was informed by comprehensive in silico genomes analyses of Xav and other closely related Xanthomonas species. The target gene region’s specificity was validation against the NCBI GenBank database and internally sequenced genomes. Primers for both endpoint PCR and LAMP assays were designed using this unique gene. The LAMP assay underwent extensive testing against inclusivity and exclusivity panels. Use of exclusivity panel, comprising 81 strains from related species, other bacterial genera, and host genomes, demonstrated the assay’s specificity with no false positives. The assay exhibited a detection limit of 1 pg, and its effectiveness was unimpeded by crude host lysate (sugarcane). Further validation through multi-device and multi-operator testing underscored the assay’s 100% reproducibility and robustness. Application to infected plant samples resulted in the detection of all infected specimens without any false positives or negatives. This novel LAMP assay is accurate and reliable tool for Xav detection, with promising applications in routine diagnostics, biosecurity measures, microbial forensics, and epidemiological research. |
| format | Article |
| id | doaj-art-a87b0901f71941ad98d3fa4087d1d943 |
| institution | Kabale University |
| issn | 2045-2322 |
| language | English |
| publishDate | 2025-07-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Scientific Reports |
| spelling | doaj-art-a87b0901f71941ad98d3fa4087d1d9432025-08-20T03:45:26ZengNature PortfolioScientific Reports2045-23222025-07-0115111310.1038/s41598-025-08291-wGenome guided LAMP assay for rapid and reliable detection of Xanthomonas axonopodis pv. vasculorumMitchell Marabella0Julia Howard1Santosh Bhandari2Sally Do3Maya Montoya-Pimolwatana4Yichen Dou5Shefali Dobhal6Dario Arizala7Stefania Montesinos8Sharon A. Andreason9Francisco Ochoa-Corona10Jon-Paul Bingham11Jenee Odani12Daniel Jenkins13Li Maria Ma14Jacqueline Fletcher15James P. Stack16Mohammad Arif17Department of Molecular Biosciences and Bioengineering, University of Hawaii at ManoaDepartment of Molecular Biosciences and Bioengineering, University of Hawaii at ManoaDepartment of Plant and Environmental Protection Sciences, University of Hawaii at ManoaDepartment of Molecular Biosciences and Bioengineering, University of Hawaii at ManoaDepartment of Plant and Environmental Protection Sciences, University of Hawaii at ManoaDepartment of Molecular Biosciences and Bioengineering, University of Hawaii at ManoaDepartment of Plant and Environmental Protection Sciences, University of Hawaii at ManoaDepartment of Plant and Environmental Protection Sciences, University of Hawaii at ManoaDepartment of Plant and Environmental Protection Sciences, University of Hawaii at ManoaUSDA Agricultural Research Service, U.S. Vegetable LaboratoryInstitute for Biosecurity and Microbial Forensics, Oklahoma State UniversityDepartment of Molecular Biosciences and Bioengineering, University of Hawaii at ManoaDepartment of Human Nutrition, Food and Animal Sciences, University of Hawaii at ManoaDepartment of Plant and Environmental Protection Sciences, University of Hawaii at ManoaInstitute for Biosecurity and Microbial Forensics, Oklahoma State UniversityInstitute for Biosecurity and Microbial Forensics, Oklahoma State UniversityDepartment of Plant Pathology, Kansas State UniversityDepartment of Plant and Environmental Protection Sciences, University of Hawaii at ManoaAbstract Xanthomonas axonopodis pv. vasculorum (Xav), the causative agent of sugarcane gumming disease, represents a significant threat to global sugarcane production due to its systemic and destructive nature. A field-deployable tool specific to Xav is required for rapid infection detection and timely disease management. This resulted in a loop-mediated isothermal amplification (LAMP) assay targeting the gene region, unique to Xav strains, as a rapid and precise diagnostic assay. The selection of a target gene region was informed by comprehensive in silico genomes analyses of Xav and other closely related Xanthomonas species. The target gene region’s specificity was validation against the NCBI GenBank database and internally sequenced genomes. Primers for both endpoint PCR and LAMP assays were designed using this unique gene. The LAMP assay underwent extensive testing against inclusivity and exclusivity panels. Use of exclusivity panel, comprising 81 strains from related species, other bacterial genera, and host genomes, demonstrated the assay’s specificity with no false positives. The assay exhibited a detection limit of 1 pg, and its effectiveness was unimpeded by crude host lysate (sugarcane). Further validation through multi-device and multi-operator testing underscored the assay’s 100% reproducibility and robustness. Application to infected plant samples resulted in the detection of all infected specimens without any false positives or negatives. This novel LAMP assay is accurate and reliable tool for Xav detection, with promising applications in routine diagnostics, biosecurity measures, microbial forensics, and epidemiological research.https://doi.org/10.1038/s41598-025-08291-wPlant pathogenic bacteriaSugarcaneField-deployablePhytopathogenic |
| spellingShingle | Mitchell Marabella Julia Howard Santosh Bhandari Sally Do Maya Montoya-Pimolwatana Yichen Dou Shefali Dobhal Dario Arizala Stefania Montesinos Sharon A. Andreason Francisco Ochoa-Corona Jon-Paul Bingham Jenee Odani Daniel Jenkins Li Maria Ma Jacqueline Fletcher James P. Stack Mohammad Arif Genome guided LAMP assay for rapid and reliable detection of Xanthomonas axonopodis pv. vasculorum Scientific Reports Plant pathogenic bacteria Sugarcane Field-deployable Phytopathogenic |
| title | Genome guided LAMP assay for rapid and reliable detection of Xanthomonas axonopodis pv. vasculorum |
| title_full | Genome guided LAMP assay for rapid and reliable detection of Xanthomonas axonopodis pv. vasculorum |
| title_fullStr | Genome guided LAMP assay for rapid and reliable detection of Xanthomonas axonopodis pv. vasculorum |
| title_full_unstemmed | Genome guided LAMP assay for rapid and reliable detection of Xanthomonas axonopodis pv. vasculorum |
| title_short | Genome guided LAMP assay for rapid and reliable detection of Xanthomonas axonopodis pv. vasculorum |
| title_sort | genome guided lamp assay for rapid and reliable detection of xanthomonas axonopodis pv vasculorum |
| topic | Plant pathogenic bacteria Sugarcane Field-deployable Phytopathogenic |
| url | https://doi.org/10.1038/s41598-025-08291-w |
| work_keys_str_mv | AT mitchellmarabella genomeguidedlampassayforrapidandreliabledetectionofxanthomonasaxonopodispvvasculorum AT juliahoward genomeguidedlampassayforrapidandreliabledetectionofxanthomonasaxonopodispvvasculorum AT santoshbhandari genomeguidedlampassayforrapidandreliabledetectionofxanthomonasaxonopodispvvasculorum AT sallydo genomeguidedlampassayforrapidandreliabledetectionofxanthomonasaxonopodispvvasculorum AT mayamontoyapimolwatana genomeguidedlampassayforrapidandreliabledetectionofxanthomonasaxonopodispvvasculorum AT yichendou genomeguidedlampassayforrapidandreliabledetectionofxanthomonasaxonopodispvvasculorum AT shefalidobhal genomeguidedlampassayforrapidandreliabledetectionofxanthomonasaxonopodispvvasculorum AT darioarizala genomeguidedlampassayforrapidandreliabledetectionofxanthomonasaxonopodispvvasculorum AT stefaniamontesinos genomeguidedlampassayforrapidandreliabledetectionofxanthomonasaxonopodispvvasculorum AT sharonaandreason genomeguidedlampassayforrapidandreliabledetectionofxanthomonasaxonopodispvvasculorum AT franciscoochoacorona genomeguidedlampassayforrapidandreliabledetectionofxanthomonasaxonopodispvvasculorum AT jonpaulbingham genomeguidedlampassayforrapidandreliabledetectionofxanthomonasaxonopodispvvasculorum AT jeneeodani genomeguidedlampassayforrapidandreliabledetectionofxanthomonasaxonopodispvvasculorum AT danieljenkins genomeguidedlampassayforrapidandreliabledetectionofxanthomonasaxonopodispvvasculorum AT limariama genomeguidedlampassayforrapidandreliabledetectionofxanthomonasaxonopodispvvasculorum AT jacquelinefletcher genomeguidedlampassayforrapidandreliabledetectionofxanthomonasaxonopodispvvasculorum AT jamespstack genomeguidedlampassayforrapidandreliabledetectionofxanthomonasaxonopodispvvasculorum AT mohammadarif genomeguidedlampassayforrapidandreliabledetectionofxanthomonasaxonopodispvvasculorum |