Loop-mediated Isothermal Amplification (LAMP) assay for reliable detection of Xanthomonas axonopodis pv. vasculorum

Marabella, M.; Howard, J.; Bhandari, S.; Do, S.; Montoya-Pimolwatana, M.; Dou, Y.; Dobhal, S.; Arizala, D.; Montesinos, S.; Andreason, S. A.; Ochoa-Corona, F. M.; Bingham, J.-P.; Odani, J.; Jenkins, D.; Ma, L. M.; Fletcher, J.; Stack, J. P.; Arif, M.

doi:10.1101/2024.02.07.579270

bioRxiv · 10.1101/2024.02.07.579270

Loop-mediated Isothermal Amplification (LAMP) assay for reliable detection of Xanthomonas axonopodis pv. vasculorum

Marabella, M.·Howard, J.·Bhandari, S.·Do, S.·Montoya-Pimolwatana, M.·Dou, Y.·Dobhal, S.·Arizala, D.·Montesinos, S.·Andreason, S. A.·Ochoa-Corona, F. M.·Bingham, J.-P.·Odani, J.·Jenkins, D.·Ma, L. M.·Fletcher, J.·Stack, J. P.·Arif, M.

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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. Despite the economic implications, a field-deployable, Xav-specific diagnostic tool has not been developed. This resulted in a loop-mediated isothermal amplification (LAMP) assay targeting the pelL gene, unique to Xav strains, as a rapid and precise diagnostic assay. The selection of the pelL gene was informed by comprehensive in silico analyses of Xav genomes and related Xanthomonas species and other close relatives. Validation against the NCBI GenBank database and internally sequenced genomes confirmed the genes exclusivity to Xav. Subsequent primers for both endpoint PCR and LAMP assays were designed using the pelL gene region. 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 assays 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 assays 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.

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Marabella, M., Howard, J., Bhandari, S., Do, S., Montoya-Pimolwatana, M., Dou, Y., Dobhal, S., Arizala, D., Montesinos, S., Andreason, S. A., Ochoa-Corona, F. M., Bingham, J.-P., Odani, J., Jenkins, D., Ma, L. M., Fletcher, J., Stack, J. P., Arif, M.. 2024-02-08. Loop-mediated Isothermal Amplification (LAMP) assay for reliable detection of Xanthomonas axonopodis pv. vasculorum. https://doi.org/10.1101/2024.02.07.579270

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