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Publications

Browse peer-reviewed publications, book chapters and other scholarly works produced by the Biosecurity research team.

  • 2026
    1. Arizala D, Dobhal S, Alvarez AM, & Arif M (2026). Description of two novel non-pathogenic tomato-associated Clavibacter species: Clavibacter seminis sp. nov. and Clavibacter quasicaliforniensis sp. nov. International Journal of Systematic and Evolutionary Microbiology. https://doi.org/10.1099/ijsem.0.007184
    1. Brandt, P. J., Noden, B. H., Soares, R., & Hoback, W. W. (2026). Influence of fire frequency and vegetation encroachment on the abundance of ticks1 in eastern Oklahoma glades. Southwestern Entomologist, 51(1), 217-230. https://doi.org/10.3958/059.051.0117
    1. Ribeiro-Junior, M.R., Cardwell, K.F., Nascimento, D., Espindola, A.S., Ramachandran, A., Gupta, S.K. and Tyungu, D. (2026). Rapid detection of human and animal respiratory viruses using Microbe Finder (MiFi®). Frontiers in Microbiology, 17, p.1743643. https://doi.org/10.3389/fmicb.2026.1743643
    1. Zhang, J., Olson, J., Wallace, S., & Espindola, A. S. (2026). First Report of Capsicum Chlorosis Virus Infecting Zinnia in the Continental United States. Plant Disease.
  • 2025
    1. Arif, M., Zeng, Q., & Dobhal, S. (2025). Editorial: Research in the identification and control methods of rot diseases in plants. Frontiers in Microbiology. https://doi.org/10.3389/fmicb.2025.1601422
    1. Charkowski, A., & Arif, M. (2025). Pectobacterium. In B. J. Jones, G. W. Sundin, S. A. Miller, E. A. Newberry, & A. Sharma (Eds.), Laboratory guide for identification of plant pathogenic bacteria (4th ed., pp. 233–261). American Phytopathological Society Press.
    1. Chuang, S. C., Dobhal, S., Keith, L. M., Alvarez, A. M., & Arif, M. (2025). Xanthomonas spp. infecting Araceae and Araliaceae: Taxonomy, phylogeny, and potential virulence mechanisms. Biology, 14(7), 766. https://doi.org/10.3390/biology14070766
    1. Chuang, S. C., Dobhal, S., Amore, T. D., Alvarez, A. M., & Arif, M. (2025). Optimal Reference Gene Selection and Potential Target Gene Identification During Xanthomonas phaseoli pv. dieffenbachiae–Anthurium andreanum Infection. Methods and Protocols, 8(4), 72. https://doi.org/10.3390/mps8040072 
    1. Dobhal, S., Hugouvieux-Cotte-Pattat, N., Arizala, D., Sari, G. B., Chaung, S. C., Alvarez, A. M., & Arif, M. (2025). Dickeya ananatis sp. nov., pectinolytic bacterium isolated from pineapple (Ananas comosus). International Journal of Systematic and Evolutionary Microbiology, 75, 006822. https://doi.org/10.1099/ijsem.0.006822
    1. Dobhal, S., Santillana, G., Stulberg, M. J., Arizala, D., Alvarez, A. M., & Arif, M. (2025). Development and validation of genome-informed and multigene-based qPCR and LAMP assays for accurate detection of Dickeya solani: a critical quarantine pathogen threatening the potato industry. Microbiology Spectrum, 13(1), e00784-24. https://doi.org/10.1128/spectrum.00784-24 
    1. Duffeck, M. R., Faris, A. M., Wayadande, A., Olson, J., Wallace, S., Espindola, A. S., ... & Sikora, E. J. (2025). Association of the pathogen Spiroplasma kunkelii with corn stunt symptoms in Oklahoma, Kansas, Missouri, Arkansas, Nebraska, South Dakota, New York, Wisconsin, Minnesota, Indiana, and Alabama during the 2024 growing season. Plant Health Progress, 26(4), 469-476. https://doi.org/10.1094/PHP-03-25-0082-SC 
    1. Harmon, C., Luster, D., Sharma, P., & Cardwell, K. (2025). Focus issue articles on diagnostic assay development and validation: The science of getting it right II. PhytoFrontiers, 5(2), 124–126. https://doi.org/10.1094/PHYTOFR-06-25-0055-FI
    1. Komal, Dobhal, S., Arizala, D., Boluk, G., Alvarez, A. M., & Arif, M. (2025). Complete genome sequence of Dickeya oryzae strain A5272 isolated during pineapple heart rot outbreak in Hawaii. PhytoFrontiers. https://doi.org/10.1094/PHYTOFR-01-25-0001-A
    1. Krause-Sakate, R., Gomes Ruschel, R., Ochoa-Corona, F. M., Andreason, S. A., de Marchi, B. R., Ribeiro-Junior, M. R., Nascimento, D. M., Trujillo, R., Smith, H. A., Hutton, S. F., & Wallace, S. (2025). First detection of Bemisia tabaci MED in Oklahoma and development of a high-resolution melting assay for MEAM1 and MED discrimination. Journal of Economic Entomology, 118(1), 45–56. https://doi.org/10.1093/jee/toae228
    1. Kuhn, J. H., et al. (2025). Annual (2024) taxonomic update of RNA-directed RNA polymerase-encoding negative-sense RNA viruses (realm Riboviria: kingdom Orthornavirae: phylum Negarnaviricota). Journal of General Virology, 106, 002077. https://doi.org/10.1099/jgv.0.002077
    1. 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., Bingham, J. P., Odani, J., Jenkins, D., Ma, L. M., Fletcher, J., Stack, J. P., & Arif, M. (2025). Genome guided LAMP assay for rapid and reliable detection of Xanthomonas axonopodis pv. vasculorum. Scientific Reports, 15, 23093. https://doi.org/10.1038/s41598-025-08291-w 
    1. Martin, F. N., Batuman, O., Luster, D. G., Miles, T. D., Rivera, Y., Sharma, P., Geiser, D., & Cardwell, K. (2025). How controls improve diagnostic assay performance: Hitchhiker’s guide to diagnostic assay controls. PhytoFrontiers, 5(2), 127–137. https://doi.org/10.1094/PHYTOFR-10-24-0118-FI
    2. Mosquera-Yuqui, F., Ramos-Lopez, D., Hu, X., Yang, Y., Mendoza, J. L., Asare, E., Habiger, J., Hurtado-Gonzales, O. P., & Espindola, A. S. (2025). A comparative template-switching cDNA approach for HTS-based multiplex detection of three viruses and one viroid commonly found in apple trees. Scientific Reports, 15(1), 1657. https://doi.org/10.1038/s41598-025-86065-0 
    1. Nascimento, D. M., Sharma, P., & Luster, D. G. (2025). A 2023–2024 literature review of validation standards and diagnostic accuracy. PhytoFrontiers, 5(2), 144–147. https://doi.org/10.1094/PHYTOFR-12-24-0132-FI
    1. Nascimento, D. M., Bodaghi, S., Wang, H., Ribeiro-Junior, M. R., Campos, R., Dang, T., ... & Cardwell, K. F. (2025). Development and Validation of a Suite of E-Probes for Electronic Diagnostic Nucleic Acid Analysis (EDNA) for 20 Graft-Transmissible Pathogens of Citrus Using MiFi and Blind Ring Testing Among Novice Users. PhytoFrontiers, 5(2), 243-253. https://doi.org/10.1094/PHYTOFR-12-24-0140-FI 
    1. Pasha, A., Espindola, A. S., Ziebell, H., & Ochoa-Corona, F. M. (2025). Highly curated and reliable e-probes for detection of viral pathogens in unassembled HTS datasets from hops. PhytoFrontiers, 5(2), 165–173. https://doi.org/10.1094/PHYTOFR-09-24-0106-FI
    1. Paul, S., Paswan, R., Zhang, G., & Ma, L. M. (2025). Dynamic changes in antibiotic resistomes of pecan orchard soils under adaptive multi-paddock (AMP) management. Journal of Applied Microbiology (submitted).
    1. Paul, S., Paswan, R., Zhang, G., & Ma, L. M. (2025). Insights on soil microbial communities in pecan orchards under adaptive multi-paddock grazing using amplicon and shotgun metagenomics. Journal of Applied Microbiology (submitted).
    1. Peña-Zúñiga, L., Espindola, A. S., & Ochoa-Corona, F. M. (2025). Assessment of viral limit of detection in spiked, unassembled high-throughput sequence datasets. PhytoFrontiers, 5(2), 264–271. https://doi.org/10.1094/PHYTOFR-11-24-0121-FI
    1. Proaño-Cuenca, F., Carrera-López, D., Zeller, K., Espindola, A. S., & Cardwell, K. (2025). Integrating in silico and in vitro approaches for detecting Coniothyrium glycines in high-throughput sequencing (HTS) datasets using EDNA-MiFi. PhytoFrontiers, 5(2), 254-263. https://doi.org/10.1094/PHYTOFR-11-24-0128-FI 
    1. Ramos Lopez, D., Flores, F. J., & Espindola, A. S. (2025). MeStanG-resource for high-throughput sequencing standard data sets generation for bioinformatic methods evaluation and validation. Biology, 14(1), 69. https://doi.org/10.3390/biology14010069 
    1. Ribeiro, P. H., Ribeiro-Junior, M. R., Silveira, B. R. R., Ochoa-Corona, F. M., & Krause-Sakate, R. (2025). A rapid, cost-effective RNA recovery of cowpea mild mottle virus (CPMMV) directly from PCR tube adsorption for routine-scale detection in soybean. Viruses, 18(1), 41. https://doi.org/10.3390/v18010041 
    1. Ribeiro-Junior, M. R., Espindola, A., Nascimento, D. M., Barreto da Silva, F. F., Krause-Sakate, R., & Ochoa-Corona, F. M. (2025). An attempt toward the global screening of soybean viruses using EDNA-MiFi-based electronic probes. PhytoFrontiers, 5(2), 236–242. https://doi.org/10.1094/PHYTOFR-12-24-0141-FI
    1. Roy, A., Shao, J., Espindola, A. S., Ramos Lopez, D., Otero-Colina, G., Rivera, Y., Mavrodieva, V. A., Nakhla, M. K., Schneider, W. L., & Cardwell, K. (2025). Detection and in vivo validation of Dichorhavirus e-probes in meta-transcriptomic data via Microbe Finder (MiFi®) discovers a novel host and a possible new strain of orchid fleck virus. Viruses, 17(3), 441. https://doi.org/10.3390/v17030441 
    1. Rubino, L., Abrahamian, P., An, W., Aranda, M. A., Ascencio-Ibañez, J. T., Bejerman, N., ... & Van Doorslaer, K. (2025). Summary of taxonomy changes ratified by the International Committee on Taxonomy of Viruses from the Plant Viruses Subcommittee, 2025. Journal of General Virology, 106(7), 002114. https://doi.org/10.1099/jgv.0.002114 
    1. Sharma, P., Harmon, C., & Cardwell, K. (2025). Diagnostic assay validation network (DAVN) progress and evolution. PhytoFrontiers, 5(2), 148–153. https://doi.org/10.1094/PHYTOFR-11-24-0123-FI
    1. Song, Q., Gao, H., Cheng, L., Ma, L. M., & Mao, Y. (2025). Polyelectrolyte nanocoatings synthesized by initiated chemical vapor deposition for antifouling surfaces against Listeria innocua. LWT – Food Science and Technology. https://doi.org/10.1016/j.lwt.2025.118834
  • 2024
    1. Arizala, D., & Arif, M. (2024). Impact of homologous recombination on core genome evolution and host adaptation of Pectobacterium parmentieri. Genome Biology and Evolution, 16, 1–23. https://doi.org/10.1093/gbe/evae032
    1. Chaung, S. C., Dobhal, S., Pal, K., Amore, T. D., Alvarez, A. M., & Arif, M. (2024). Xanthomonas strains isolated from hosts in the Araceae reveal diverse phylogenetic relationships and origins. Phytopathology. https://doi.org/10.1094/PHYTO-08-23-0265-R
    1. Chuang, S., Dobhal, S., Alvarez, A. M., & Arif, M. (2024). Three new species, Xanthomonas hawaiiensis sp. nov., Stenotrophomonas aracearum sp. nov., and Stenotrophomonas oahuensis sp. nov., isolated from Araceae family. Frontiers in Microbiology. https://doi.org/10.3389/fmicb.2024.1356025
    1. Dewberry, R. J., Sharma, P., Prom, J. L., Kinscherf, N. A., Lowe-Power, T., Mazloom, R., Zang, X., Arif, M., Stulberg, M., Heath, L. S., Eversole, K., Beattie, G. A., Vinatzer, B., & Allen, C. (2024). Genotypic and phenotypic analyses show Ralstonia solanacearum cool virulence is a quantitative trait not restricted to “Race 3 biovar 2.” Phytopathology, 114, 2468–2480. https://doi.org/10.1094/PHYTO-06-24-0187-R
    2. Digiaro, M., Elbeaino, T., Kubota, K., Ochoa-Corona, F. M., & von Bargen, S. (2024). ICTV virus taxonomy profile: Fimoviridae 2024. Journal of General Virology, 105(5), 001943. https://doi.org/10.1099/jgv.0.001943 
    1. Dobhal, S., Chaung, S. C., Arizala, D., Keith, L. M., Alvarez, A. M., & Arif, M. (2024). High-quality complete genome sequence of Xanthomonas phaseoli pv. dieffenbachiae outbreak strain D182: The causative agent of anthurium bacterial blight in Hawai‘i. PhytoFrontiers. https://doi.org/10.1094/PHYTOFR-02-24-0006-A
    1. Dobhal, S., Santillana, G., Stulberg, M. J., Arizala, D., Alvarez, A. M., & Arif, M. (2024). Development and validation of genome-informed and multigene-based qPCR and LAMP assays for accurate detection of Dickeya solani: A critical quarantine pathogen threatening the potato industry. Microbiology Spectrum, 13, e00784-24. https://doi.org/10.1128/spectrum.00784-24
    1. Espindola, A. S. (2024). Simulated high-throughput sequencing datasets are a crucial tool for validating bioinformatic pathogen detection pipelines. Biology, 13(9), 700. https://doi.org/10.3390/biology13090700 
    1. Faris, A. M., Rodrigues Duffeck, M., Olson, J. D., Espindola, A. S., Muller, L., Velasco, S. E., & Zambiasi, J. M. (2024). First report of Dalbulus maidis (DeLong and Wolcott)(Hemiptera: Cicadellidae) in Oklahoma. Insects, 15(10), 778. https://doi.org/10.3390/insects15100778 
    1. Ferrucho, R. L., Marín-Ramírez, G. A., Ochoa-Corona, F., & Ángel-Calle, C. A. (2024). PCR-based detection for the quarantine fungus Colletotrichum kahawae, a biosecurity threat to the coffee (Coffea arabica) industry worldwide. Plant Disease, 108, 2615–2624. https://doi.org/10.1094/PDIS-09-23-1788-SR
    1. Kagambèga, A., Ramadan, H., Dione, M., Bouda, S. C., Hiott, L. M., McMillan, E. A., Sharma, P., Gupta, S. K., Barro, N., Jackson, C. R., & Frye, J. G. (2024). Genome analysis of Salmonella enterica serovar Enteritidis strains isolated from poultry and humans in Burkina Faso. Microbiology Resource Announcements, 13(6), e01024-23. https://doi.org/10.1128/mra.01024-23
    1. Marabella, M., Howard, J., Bhandari, S., Do, S., Montoya-Pimolwatana, M., Dou, Y., ... & Arif, M. (2024). Loop-mediated Isothermal Amplification (LAMP) assay for reliable detection of Xanthomonas axonopodis pv. vasculorum. BioRxiv. https://www.biorxiv.org/content/10.1101/2024.02.07.579270v1 
    1. Michele Digiaro, M., Elbeaino, T., Kubota, K., Ochoa-Corona, F. M., & von Bargen, S. (2024). ICTV virus taxonomy profile: Fimoviridae 2024. Journal of General Virology, 105, 001943. https://doi.org/10.1099/jgv.0.001943 
    1. Montesinos, S., Tyagi, G., Feng, Z., Hampson, E., Adhikari, A., Minaai, M., ... & Arif, M. (2024). Genome-guided, field-deployable loop-mediated isothermal amplification (LAMP) assay for specific detection of Dickeya dadantii. bioRxiv. https://doi.org/10.1101/2024.05.04.592507 
    1. Ribeiro-Junior, M. R., Barreto da Silva, F., Marubayashi, J. M., et al. (2024). Molecular identification of thrips species in Brazilian agroecosystems. Phytoparasitica, 52, 79. https://doi.org/10.1007/s12600-024-01198-8
  • 2023
    1. Bocsanczy, A. M., Espindola, A. S., Cardwell, K., & Norman, D. J. (2023). Development and validation of e-probes with the MiFi system for detection of Ralstonia solanacearum species complex in blueberries. PhytoFrontiers, 3(1), 137-147. https://doi.org/10.1094/PHYTOFR-04-22-0043-FI 
    1. Cardwell, K. F., Harmon, C. L., Luster, D. G., Stack, J. P., Hyten, A. M., Sharma, P., & Nakhla, M. K. (2023). The need and a vision for a diagnostic assay validation network. PhytoFrontiers, 3(1), 9–17. https://doi.org/10.1094/PHYTOFR-05-22-0056-F
    1. Cardwell, K. F., Harmon, C. L., Stack, J. P., & Sharma, P. (2023). Focus issue articles on diagnostic assay development and validation: The science of getting it right. PhytoFrontiers, 3(1), 5–8. https://doi.org/10.1094/PHYTOFR-02-23-0014-FI
    1. Czajkowski, R., Arif, M., & Chapman, T. (2023). Editorial: Genome-wide analyses of Pectobacterium and Dickeya species, volume II. Frontiers in Plant Science. https://doi.org/10.3389/fpls.2023.1224293
    1. Dang, T., Wang, H., Espindola, A. S., Habiger, J., Vidalakis, G., & Cardwell, K. (2023). Development and statistical validation of e-probe diagnostic nucleic acid analysis (EDNA) assays for the detection of citrus pathogens from raw high-throughput sequencing data. PhytoFrontiers, 3(1), 113-123. https://doi.org/10.1094/PHYTOFR-05-22-0047-FI 
    1. Groth-Helms, D., Rivera, Y., Martin, F. N., Arif, M., Sharma, P., & Castlebury, L. A. (2023). Terminology and guidelines for diagnostic assay development and validation: A proposal for best practices. PhytoFrontiers, 3(1), 23–35. https://doi.org/10.1094/PHYTOFR-05-22-0059-FI
    1. Geiser, D. M., Martin, F. N., Espindola, A. S., Brown, J. K., Bell, T. H., Yang, Y., & Kang, S. (2023). Knowledge gaps, research needs, and opportunities in plant disease diagnostic assay development and validation. PhytoFrontiers, 3(1), 51-63. https://doi.org/10.1094/PHYTOFR-05-22-0057-FI 
    1. Harmon, C. L., Castlebury, L. A., Boundy-Mills, K., Broders, K. D., Hyten, A. M., Jacobs, J. L., ... & Sharma, P. (2023). Standards of diagnostic validation: Recommendations for reference collections. PhytoFrontiers, 3(1), 43-50. https://doi.org/10.1094/PHYTOFR-05-22-0050-FI 
    2. Klair, D., Dobhal, S., Ahmad, A., Hassan, Z. U., Uyeda, J., Silva, J., Wang, K. H., Kim, S., Alvarez, A. M., & Arif, M. (2023). Exploring taxonomic and functional microbiome of Hawaiian stream and spring irrigation water systems using Illumina and Oxford Nanopore sequencing platforms. Frontiers in Microbiology. https://doi.org/10.3389/fmicb.2023.1039292
    1. Kuhn, J. H., Abe, J., Adkins, S., Alkhovsky, S. V., Avšič-Županc, T., Ayllón, M. A., ... & Stenglein, M. D. (2023). Annual (2023) taxonomic update of RNA-directed RNA polymerase-encoding negative-sense RNA viruses (realm Riboviria: kingdom Orthornavirae: phylum Negarnaviricota). Journal of General Virology, 104(8), 001864. https://doi.org/10.1099/jgv.0.001864 
    1. Lowe-Power, T., Sharma, P., Alfenas-Zerbini, P., Alvarez, B., Arif, M., et al. (2023). Letter to the editor: The Ralstonia research community rejects the proposal to classify phylotype I Ralstonia into the new species Ralstonia nicotianae. PhytoFrontiers. https://doi.org/10.1094/PHYTOFR-06-23-0071-LE
    1. Ma, L., Lopez, N., & Zhang, G. (2023). Draft whole-genome sequences of competitive exclusion Ligilactobacillus salivarius strains for poultry. Microbiology Resource Announcements, 12(10), e00316-23. https://doi.org/10.1128/MRA.00316-23
    1. Ma, L., Lopez, N., & Zhang, G. (2023). Draft whole-genome sequences of Bacillus strains of potential probiotics for poultry. Microbiology Resource Announcements, 12(10), e00315-23. https://doi.org/10.1128/MRA.00315-23
    1. Narayanan, S., Espindola, A. S., Malayer, J., Cardwell, K., & Ramachandran, A. (2023). Development and evaluation of Microbe Finder (MiFi)®: A novel in silico diagnostic platform for pathogen detection from metagenomic data. Journal of Medical Microbiology, 72(6), 001720. https://doi.org/10.1099/jmm.0.001720 
    1. Olmedo-Velarde, A., Ochoa-Corona, F. M., Larrea-Sarmiento, A. E., Elbeaino, T., & Flores, F. (2023). In-silico prediction of RT-qPCR-high resolution melting for broad detection of emaraviruses. PLOS ONE, 18(5), e0272980. https://doi.org/10.1371/journal.pone.0272980
    1. Paudel, S., Dobhal, S., Lowe-Power, T., Schlub, R. L., Hu, J., Caitilyn, A., Alvarez, A. M., & Arif, M. (2023). “RSSC-Lineage Multiplex PCR” assay detects and differentiates Ralstonia solanacearum, R. pseudosolanacearum, R. syzygii, and the R3bv2 subgroup. PhytoFrontiers. https://doi.org/10.1094/PHYTOFR-07-23-0087-R
    1. Ruschel, R. G., Taylor, M., Ochoa-Corona, F. M., Amirudeen, A. K. J., Druciarek, T., & Paret, M. (2023). An artificial positive control for routine detection of rose rosette virus and Phyllocoptes fructiphilus that fit most primers for PCR, LAMP and RPA-based assays. Annals of Applied Biology, 183(1), 67–79. https://doi.org/10.1111/aab.12834
    1. Sharma, P., & Luster, D. G. (2023). Perspective: State of the field of plant pathogen diagnostic assay development and validation. PhytoFrontiers, 3(1), 18–22. https://doi.org/10.1094/PHYTOFR-05-22-0054-FI
  • 2022
    1. Arif, M., Czajkowski, R., & Chapman, T. (2022). Editorial: Genome-wide analyses of Pectobacterium and Dickeya species. Frontiers in Plant Science. https://doi.org/10.3389/fpls.2022.822829
    1. Arizala, D., Dobhal, S., Alvarez, A. M., & Arif, M. (2022). Elevation of Clavibacter michiganensis subsp. californiensis to species level as Clavibacter californiensis sp. nov., merging and re-classification of Clavibacter michiganensis subsp. chilensis and Clavibacter michiganensis subsp. phaseoli as Clavibacter phaseoli sp. nov. based on complete genome in silico analyses. International Journal of Systematic and Evolutionary Microbiology, 72(9). https://doi.org/10.1099/ijsem.0.005427
    1. Arizala, D., Dobhal, S., Babler, B., Crockford, A., Rioux, R. A., Alvarez, A. M., & Arif, M. (2022). Development of a multiplex TaqMan qPCR targeting unique genomic regions for the specific and sensitive detection of Pectobacterium species and P. parmentieri. Journal of Applied Microbiology, 132(4), 3089–3110. https://doi.org/10.1111/jam.15447
    1. Boluk, G., Dobhal, S., Arizala, D., Alvarez, A. M., & Arif, M. (2022). Dickeya colocasiae sp. nov. isolated from wetland taro, Colocasia esculenta. bioRxiv. https://doi.org/10.1101/2022.01.14.476417
    1. Cevallos, F., PeÑa-ZuÑiga, L., Ochoa-Corona, F., & Damicone, J. (2022). Frequency and genetic variability of the avirulence gene AvrLm4-7 among Leptosphaeria maculans isolates collected in Oklahoma, USA. Canadian Journal of Plant Pathology, 44(6), 892-906. https://doi.org/10.1080/07060661.2022.2077449 
    1. Cho, S., Hiott, L. M., House, S. L., Woodley, T. A., McMillan, E. A., Sharma, P., ... & Frye, J. G. (2022). Analysis of Salmonella enterica isolated from a mixed-use watershed in Georgia, USA: antimicrobial resistance, serotype diversity, and genetic relatedness to human isolates. Applied and Environmental Microbiology, 88(10), e00393-22. https://doi.org/10.1128/aem.00393-22 
    1. Claros, N. A., Shires, M., Mollov, D., Hammond, J., Jordan, R., Ochoa-Corona, F., ... & Salamanca, L. R. (2022). Rose rosette disease: A diagnostic guide. Plant Health Progress, 23(4), 482-491. https://doi.org/10.1094/PHP-05-22-0047-DG 
    1. DeLude, A., Wells, R., Boomla, S., Chuang, S., Urena, F., Shipman, A., Rubas, N., Kuehu, D. L., Bickerton, B., Peterson, T., Dobhal, S., Arizala, D., Klair, D., Ochoa-Corona, F. M., Ali, M. E., Odani, J., Bingham, J. P., Jenkins, D., Fletcher, J., Stack, J. P., Alvarez, A. M., & Arif, M. (2022). Loop-mediated isothermal amplification (LAMP) assay for specific and rapid detection of Dickeya fangzhongdai targeting a unique genomic region. Scientific Reports, 12, 19193. https://doi.org/10.1038/s41598-022-22023-4
    1. Espindola, A. S., Cardwell, K., Martin, F. N., Hoyt, P. R., Marek, S. M., Schneider, W., & Garzon, C. D. (2022). A step towards validation of high-throughput sequencing for the identification of plant pathogenic oomycetes. Phytopathology, 112(9), 1859–1866. https://doi.org/10.1094/PHYTO-11-21-0454-R 
    2. Harmon, C. L., Akey, B. L., Ochoa-Corona, F. M., Ramachandran, A., & Sharma, P. (2022). Training, tests, and tech: Deployment of diagnostic tools for biosecurity. In K. Cardwell & K. Bailey (Eds.), Tactical sciences for biosecurity in animal and plant systems (pp. 222–261). IGI Global. https://doi.org/10.4018/978-1-7998-7935-0.ch007
    1. Kagambèga, A., McMillan, E. A., Bouda, S. C., Hiott, L. M., Ramadan, H., Soro, D. K., Sharma, P., Gupta, S. K., Barro, N., Jackson, C. R., & Frye, J. G. (2022). Resistance genes, plasmids, multilocus sequence typing (MLST), and phenotypic resistance of non-typhoidal Salmonella isolated from slaughtered chickens in Burkina Faso. Antibiotics, 11(6), 782. https://doi.org/10.3390/antibiotics11060782
    1. Klair, D., Arizala, D., Dobhal, S., Boluk, G., Alvarez, A. M., & Arif, M. (2022). Pectobacterium colocasium sp. nov. isolated from taro (Colocasia esculenta). bioRxiv. https://doi.org/10.1101/2022.02.08.479620
    1. Kuhn, J. H., Adkins, S., Alkhovsky, S. V., et al. (2022). 2022 taxonomic update of phylum Negarnaviricota (Riboviria: Orthornavirae), including the large orders Bunyavirales and Mononegavirales. Archives of Virology, 167, 2857–2906. https://doi.org/10.1007/s00705-022-05546-z
    1. Ribeiro Junior, M. R., Barreto da Silva, F., Marubayashi, J. M., Uzan, J., Nogueira, A. M., Muller, C., Nascimento, D. M., Yuki, V. A., Narita, N., Pavan, M. A., Ochoa-Corona, F. M., & Krause Sakate, R. (2022). Molecular and biological characterization of an isolate of the potyvirus passiflora virus Y naturally infecting soybean (Glycine max) in Brazil. Archives of Virology. https://doi.org/10.1007/s00705-022-05605-5
    1. Salazar, A., Ochoa-Corona, F. M., Talley, J. L., & Noden, B. H. (2022). An elution independent collection device (EICD) for rapid collection of Anaplasma marginale DNA from blood samples. Acta Tropica, 225, 106201. https://doi.org/10.1016/j.actatropica.2021.106201 
    1. Zhang, J., Arif, M., Shen, H., Sun, D., Pu, X., Hu, J., Lin, B., & Yang, Q. (2022). Genomic comparisons and phenotypic diversity of Dickeya zeae strains causing bacterial soft rot of banana in China. Frontiers in Plant Science, 13. https://doi.org/10.3389/fpls.2022.822829
  • 2021
    1. Arif, M., Busot, G. Y., Mann, R., Rodoni, B., & Stack, J. P. (2021). Field-deployable recombinase polymerase amplification assay for specific, sensitive and rapid detection of the U.S. select agent and toxigenic bacterium, Rathayibacter toxicus. Biology, 10, 620. https://doi.org/10.3390/biology10070620
    1. Arif, M., Busot, G. Y., Mann, R., Rodoni, B., & Stack, J. P. (2021). Multiple internal controls enhance reliability for PCR and real time PCR detection of Rathayibacter toxicus. Scientific Reports, 11, 8365. https://doi.org/10.1038/s41598-021-87815-6
    1. Boluk, G., Arizala, D., Dobhal, S., Zhang, J., Hu, J., Alvarez, A. M., & Arif, M. (2021). Genomic and phenotypic biology of novel strains of Dickeya zeae isolated from pineapple and taro in Hawaii: Insights into genome plasticity, pathogenicity, and virulence determinants. Frontiers in Plant Science. https://doi.org/10.3389/fpls.2021.663851
    1. Dang, T., Espindola, A., Vidalakis, G., & Cardwell, K. (2021). An in silico detection of a citrus viroid from raw high-throughput sequencing data. In Viroids: Methods and Protocols (pp. 275-283). New York, NY: Springer US. https://doi.org/10.1007/978-1-0716-1464-8_23 
    1. Diaz, C., Smith, M., Rohla, C., Zhang, G., Molina, S., & Ma, L. (2021). Prevalence of Shiga toxin-producing Escherichia coli and Salmonella in native pecan orchards as influenced by waiting periods between grazing and harvest. Journal of Food Protection, 85(1), 36–43. https://doi.org/10.4315/JFP-21-163
    1. Domingo, R., Perez, C., Klair, D., Vu, H., Candelaria-Tochiki, A., Wang, X., Camson, A., Uy, J. N., Salameh, M., Arizala, D., Dobhal, S., Boluk, G., Bingham, J. P., Ochoa-Corona, F., Ali, M. E., Stack, J. P., Fletcher, J., Odani, J., Jenkins, D., Alvarez, A. M., & Arif, M. (2021). Genome-informed loop-mediated isothermal amplification assay for specific detection of Pectobacterium parmentieri in infected potato tissues and soil. Scientific Reports, 11, 21948. https://doi.org/10.1038/s41598-021-01196-4
    1. Espindola, A. S., & Cardwell, K. F. (2021). Microbe Finder (MiFi®): Implementation of an interactive pathogen detection tool in metagenomic sequence data. Plants, 10(2), 250. https://doi.org/10.3390/plants10020250 
    1. Espindola, A. S., Sempertegui-Bayas, D., Bravo-Padilla, D. F., Freire-Zapata, V., Ochoa-Corona, F., & Cardwell, K. F. (2021). TASPERT: Target-specific reverse transcript pools to improve HTS plant virus diagnostics. Viruses, 13(7), 1223. https://doi.org/10.3390/v13071223 
    1. Kagambèga, A., Belem, S., McMillan, E. A., Hiott, L. M., Ramadan, H., Soro, D. K., ... & Frye, J. G. (2021). Genome analysis of Salmonella strains isolated from imported frozen fish in Burkina Faso. Annals of Microbiology, 71(1), 32. https://doi.org/10.1186/s13213-021-01642-8 
    1. Kagambèga, A., Hiott, L. M., Boyle, D. S., McMillan, E. A., Sharma, P., Gupta, S. K., ... & Frye, J. G. (2021). Serotyping of sub-Saharan Africa Salmonella strains isolated from poultry feces using multiplex PCR and whole genome sequencing. BMC Microbiology, 21(1), 29. https://doi.org/10.1186/s12866-021-02085-6 
    1. Klair, D., Silva, J., Arizala, D., Boluk, G., Dobhal, S., Ahmad, A. A., ... & Arif, M. (2021). First Report of Pectobacterium brasiliense causing soft rot on mizuna (Brassica rapa var. japonica) in the United States. Plant Disease, 105(12), 4149. https://doi.org/10.1094/PDIS-03-21-0644-PDN 
    1. Klair, D., Boluk, G., Silva, J., Arizala, D., Dobhal, S., & Arif, M. (2021). First report of bacterial soft rot disease on pak choi (Brassica rapa subsp. chinensis) caused by Pectobacterium brasiliense in the United States. Plant Disease, 105(7), 2011. https://doi.org/10.1094/PDIS-08-20-1854-PDN 
    2. Larrea-Sarmiento, A., Stack, J. P., Alvarez, A. M., & Arif, M. (2021). Multiplex recombinase polymerase amplification assay developed using unique genomic regions for rapid on-site detection of genus Clavibacter and C. nebraskensis. Scientific Reports, 11, 12017. https://doi.org/10.1038/s41598-021-91336-7
    1. McMillan, E. A., Nguyen, L. H. T., Hiott, L. M., Sharma, P., Jackson, C. R., Frye, J. G., & Chen, C. Y. (2021). Genomic comparison of conjugative plasmids from Salmonella enterica and Escherichia coli encoding beta-lactamases and capable of mobilizing kanamycin resistance Col-like plasmids. Microorganisms, 9(11), 2205. https://doi.org/10.3390/microorganisms9112205 
    1. Ramachandran, S., Dobhal, S., Alvarez, A. M., & Arif, M. (2021). Improved multiplex TaqMan qPCR assay with universal internal control offers reliable and accurate detection of Clavibacter michiganensis. Journal of Applied Microbiology. https://doi.org/10.1111/jam.15017
    1. Rattner, R., Thapa, S. P., Dang, T., Osman, F., Selvaraj, V., Maheshwari, Y., ... & Yokomi, R. (2021). Genome analysis of Spiroplasma citri strains from different host plants and its leafhopper vectors. BMC Genomics, 22(1), 373. https://doi.org/10.1186/s12864-021-07637-8 
    1. Salazar, A., Ochoa-Corona, F. M., Talley, J. L., & Noden, B. H. (2021). Recombinase polymerase amplification (RPA) with lateral flow detection for three Anaplasma species of importance to livestock health. Scientific Reports, 11, 15962. https://doi.org/10.1038/s41598-021-95402-y
    1. Salazar, A., Ochoa-Corona, F. M., Olson, J. D., Babu, B., & Paret, M. (2021). Probing loop-mediated isothermal amplification (LAMP) targeting two gene-fragments of rose rosette virus. PLoS One, 16(11), e0256510. https://doi.org/10.1371/journal.pone.0256510
  • 2020
    1. Andreason, S. A., Arif, M., Brown, J. K., Ochoa-Corona, F., & Wayadande, A. (2020). Exploring the use of high-resolution melting analysis and helicase-dependent amplification for discrimination of Bemisia tabaci cryptic species and Trialeurodes vaporariorum. Journal of Economic Entomology, 113(5), 2511–2520. https://doi.org/10.1093/jee/toaa180
    1. Arizala, D., Dobhal, S., Paudel, S., Boluk, G., Silva, J., Ahmad, A. A., ... & Arif, M. (2020). First report of Pectobacterium brasiliense causing bacterial soft rot and blackleg diseases of potato in Hawaii. Plant Disease, 104(2515), 10-1094. https://doi.org/10.1094/PDIS-02-20-0395-PDN 
    1. Arizala, D., Dobhal, S., Paudel, S., Gunarathne, S., Boluk, G., & Arif, M. (2020). First report of bacterial soft rot and blackleg on potato caused by Pectobacterium parmentieri in Hawaii. Plant Disease, 104(3), 970. https://doi.org/10.1094/PDIS-09-19-1894-PDN 
    1. Boluk, G., Arizala, D., Ocenar, J., Mokwele, J., Silva, J., Dobhal, S., ... & Arif, M. (2020). First report of Pectobacterium brasiliense causing soft rot on Brassica oleracea var. sabellica in Hawaii, United States. Plant Disease, 104(2721), 10-1094. https://doi.org/10.1094/PDIS-04-20-0701-PDN 
    1. Boundy‐Mills, K., McCluskey, K., Elia, P., Glaeser, J. A., Lindner, D. L., Nobles Jr, D. R., ... & Wertz, J. E. (2020). Preserving US microbe collections sparks future discoveries. Journal of applied microbiology, 129(2), 162-174. https://doi.org/10.1111/jam.14525 
    1. Cho, S., Gupta, S. K., McMillan, E., Sharma, P., Ramadan, H., Jove, T., Jackson, C. R., & Frye, J. G. (2020). Genomic analysis of multidrug resistant Escherichia coli from surface water in Northeast Georgia, USA: Presence of a ST131 epidemic strain containing blaCTX-M-15 on a phage. Microbial Drug Resistance, 26(5), 447–455. https://doi.org/10.1089/mdr.2019.03
    1. Dobhal, S., Boluk, G., Babler, B., Stulberg, M. J., Rascoe, J., Nakhla, M. K., ... & Arif, M. (2020). Comparative genomics reveals signature regions used to develop a robust and sensitive multiplex TaqMan real‐time qPCR assay to detect the genus Dickeya and Dickeya dianthicola. Journal of applied microbiology, 128(6), 1703-1719. https://doi.org/10.1111/jam.14579 
    1. Fletcher, J., Barnaby, N. G., Burans, J., Melcher, U., Luster, D. G., Nutter Jr, F. W., ... & Corona, F. M. O. (2020). Forensic plant pathology. In Microbial Forensics (pp. 49-70). Academic Press. https://doi.org/10.1016/B978-0-12-382006-8.00007-4 
    1. Kuhn, J. H., Adkins, S., Alioto, D., Alkhovsky, S. V., Amarasinghe, G. K., Anthony, S. J., ... & Oliveira, R. C. (2020). 2020 taxonomic update for phylum Negarnaviricota (Riboviria: Orthornavirae), including the large orders Bunyavirales and Mononegavirales. Archives of virology, 165(12), 3023-3072. https://doi.org/10.1007/s00705-020-04731-2 
    1. Paudel, S., Dobhal, S., Alvarez, A. M., & Arif, M. (2020). Taxonomy and phylogenetic research on Ralstonia solanacearum species complex: a complex pathogen with extraordinary economic consequences. Pathogens, 9(11), 886. https://doi.org/10.3390/pathogens9110886 
    1. Ramadan, H., Gupta, S. K., Sharma, P., Ahmed, M., Hiott, L. M., Barrett, J. B., Woodley, T. A., Frye, J. G., & Jackson, C. R. (2020). Circulation of emerging NDM-5 producing Escherichia coli among humans and dogs in Egypt. Zoonoses and Public Health, 67(3), 324–329. https://doi.org/10.1111/zph.12676
    1. Ramos, K., Sivaprasad, Y., Guevara, F., Ochoa-Corona, F., Viera, W., & Flores, F. (2020). Occurrence of potato yellowing virus in naranjilla (Solanum quitoense) in Ecuador. Journal of Plant Pathology, 102, 597. https://doi.org/10.1007/s42161-019-00479-0
    1. Rydzak, P., Ochoa-Corona, F. M., Whitfield, A. E., & Wayadande, A. C. (2020). Combining multiplex PCR and high-resolution melting for the detection and discrimination of arthropod transmitted viruses of cereals. Journal of Virological Methods, 278, 113823. https://doi.org/10.1016/j.jviromet.2020.113823
    2. Sharma, P., Gupta, S. K., Adenipekun, E. O., Barrett, J. B., Hiott, L. M., Woodley, T. A., Iwalokun, B. A., Oluwadun, A., Ramadan, H., Frye, J. G., & Jackson, C. R. (2020). Genome analysis of multidrug resistant Escherichia coli isolated from poultry in Nigeria. Foodborne Pathogens and Disease, 17(1), 1–7. https://doi.org/10.1089/fpd.2019.2659
    1. Sharma, P., Gupta, S. K., Barrett, J. B., Hiott, L. M., Woodley, T. A., Kariyawasam, S., Frye, J. G., & Jackson, C. R. (2020). Comparison of antimicrobial resistance and pan-genome of clinical and non-clinical Enterococcus cecorum from poultry using whole-genome sequencing. Foods, 9(6), 686. https://doi.org/10.3390/foods9060686
    1. Vazquez-Iglesias, I., Ochoa-Corona, F. M., Tang, J., Robinson, R., Clover, G. R. G., Fox, A., & Boonham, N. (2020). Facing rose rosette virus: A risk to European rose cultivation. Plant Pathology, 69(9), 1603–1617. https://doi.org/10.1111/ppa.13255
    1. Yasuhara-Bell, J., Arif, M., Busot, G. Y., Mann, R., Rodoni, B., & Stack, J. P. (2020). Comparative genomic analysis confirms five genetic populations of the select agent, Rathayibacter toxicus. Microorganisms, 8(3), 366. https://doi.org/10.3390/microorganisms8030366 
    1. Zhang, J., Arif, M., Shen, H., Hu, J., Sun, D., Pu, X., ... & Lin, B. (2020). Genomic divergence between Dickeya zeae strain EC2 isolated from rice and previously identified strains, suggests a different rice foot rot strain. PLoS One, 15(10), e0240908. https://doi.org/10.1371/journal.pone.0240908