R2M tools and meta-tools: rapid risk assessment for mitigation of crop pathogens & pests

The ability of national agricultural research and extension systems (NARES) and national plant protection organizations (NPPOs) to address emerging pathogen and pest risks is key to national food security.  Many countries globally are in the process of improving their systems.

We are advancing R2M: tools for rapid risk assessment and mitigation planning for crop pathogens and pests at the national or regional level.  These tools will help countries develop their strategies for effective management of crop disease, as well as invasive pathogen/pest management, as building blocks in the development of a global surveillance and mitigation system for crop disease.  We are developing ‘meta-tools’ in the sense that national programs can use these meta-tools to create their own tools for evaluating risk and mitigation strategies.  Tools include the following:

An expert knowledge elicitation (EKE) meta-tool for designing, implementing and analyzing EKE related to diseases and pests

Tools for habitat connectivity analysis to map locations that are candidate priorities for surveillance and management of host-specific pathogens and pests

A framework for trade network analysis, to identify considerations for biosecurity

GeoPathome, a rapid assessment of pathogen and pest risk through trade and geographic proximity

Impact network analysis (INA) for implementing scenario analysis to evaluate regional management options

Our team includes (in alphabetical order) Ashish Adhikari, Katie Alcock, Anudeep Reddy Banda, Sydney Barker, Manoj Choudhary, Berea Etherton, Robert Fontan, Taylor Johnson, Neha Kallamvalli, Krishna Keshav, Nattapol Kraisitudomsook, Ekaterina Krysova, David McDermott, Laurent Lagos Mendoza, Jessica Malosh, Richard Will McCoy, Romaric Mouafo Tchinda, Christopher Perez, Aaron Plex Sulá, Silas Rickards, Jacob Robledo Buritica, Eleni Stilian, Ted Stronkowsky IV, Yvette Zerry

R2M builds on projects including the following:

Andersen, K. F.C. E. Buddenhagen, P. Rachkara, R. Gibson, S. Kalule, D. Phillips, and K. A. Garrett. 2019. Modeling epidemics in seed systems and landscapes to guide management strategies: The case of sweetpotato in Northern Uganda. Phytopathology 109:1519-1532.  [open access link]

Andersen Onofre, K. F., G. A. Forbes, J. Andrade-Piedra, C. E. Buddenhagen, J. C. Fulton, M. Gatto, Z. Khidesheli, R. Mdivani, Y. XingK. A. Garrett. 2021. An integrated seed health strategy and phytosanitary risk assessment: potato in the Republic of Georgia. Agricultural Systems 191:103144. [open access link]

Buddenhagen*C. E.,  J. F. Hernandez Nopsa*K. F. Andersen, J. Andrade-Piedra, G. A. Forbes, P. Kromann, S. Thomas-Sharma, P. Useche, and K. A. Garrett. 2017. Epidemic network analysis for mitigation of invasive pathogens in seed systems: Potato in Ecuador.  Phytopathology 107:1209-1218. [open access link]

Buddenhagen*, C. E.Y. Xing*, J. Andrade Piedra, G. A. Forbes, P. Kromann, I. Navarrete, S. Thomas-Sharma, R. A. ChoudhuryK. F. Andersen, E. Schulte-Geldermann, B. A. EthertonA. I. Plex Sulá, and K. A. Garrett. 2022. Where to invest project efforts for greater benefit: A framework for management performance mapping with examples for potato seed health. Phytopathology 112:1431-1443. [open access link]

Carvajal-Yepes, M., K. Cardwell, A. Nelson, K. A. Garrett, B. Giovani, D. G. O. Saunders, S. Kamoun, J. P. Legg, V. Verdier, J. Lessel, R. A. Neher, R. Day, P. Pardey, M. L. Gullino, A. R. Records, B. Bextine, J. E. Leach, S. Staiger, and J. Tohme. 2019. A global surveillance system for crop diseases. Science 364:1237-1239. [link]

Etherton, B. A., R. A. Choudhury, R. I. Alcalá-Briseño, Y. Xing, A. I. Plex Sulá, D. Carrillo, J. Wasielewski, L. Stelinski, K. A. Grogan, F. Ballen, T. Blare, J. Crane, and K. A. Garrett. 2023. Are avocados toast? A framework to analyze decision-making for emerging epidemics, applied to laurel wilt. Agricultural Systems 206:103615. [open access link]

Etherton, B. A., R. A. Choudhury, R. I. Alcalá Briseño, R. A. Mouafo-Tchinda, A. I. Plex Sulá, M. Choudhury, A. Adhikari, S. L. Lei, N. Kraisitudomsook, J. Robledo Buritica, V. A. Cerbaro, K. Ogero, C. M. Cox, S. P. Walsh, J. Andrade-Piedra, B. A. Omondi, I. Navarrete, M. A. McEwan, and K. A. Garrett. 2024. Disaster plant pathology: Smart solutions for threats to global plant health from natural and human-driven disasters. Phytopathology 114:855-868. [open access link].

Garrett, K. A. 2021. Impact network analysis and the INA R package: Decision support for regional management interventions. Methods in Ecology and Evolution 12:1634-1647. [open access link]

Garrett, K. A., D. P. Bebber, B. A. Etherton, K. M. Gold, A. I. Plex Sulá, and M. G. Selvaraj. 2022. Climate change effects on pathogen emergence: artificial intelligence to translate big data for mitigation.  Annual Review of Phytopathology 60:357-378. [open access link]

Hernandez Nopsa, J. F., G. J. Daglish, D. W. Hagstrum, J. F. Leslie, T. W. Phillips, C. Scoglio, S. Thomas-Sharma, G. H. Walter, and K. A. Garrett. 2015. Ecological networks in stored grain: identifying key nodes for emerging pests and mycotoxins in postharvest networks.  BioScience 65:985-1002. [open access link]

Keshav, K., A. I. Plex Sulá, K. A. Garrett. 2024. geohabnet: Analysis of habitat connectivity. R package version 2.0.1, https://CRAN.R-project.org/package=geohabnet.

Margosian, M. L., K. A. Garrett, J. M. S. Hutchinson, and K. A. With. 2009. Connectivity of the American agricultural landscape: Assessing the national risk of crop pest and disease spread. BioScience 59:141-151. [open access link]

Nduwimana, I., S. Sylla, Y. Xing, A. Simbare, C. Niyongere , K. A. Garrett, B. A. Omondi. 2022. Banana seed exchange systems in Burundi – linking formal and informal systems. Outlook on Agriculture 51:334-348. [open access link]

Sanatkar, M. R., C. Scoglio, B. Natarajan, S. Isard, and K. A. Garrett. 2015. History, epidemic evolution, and model burn-in for a network of annual invasion: Soybean rust. Phytopathology 105:947-955. [open access link]

Sutrave, S., C. Scoglio, S. A. Isard, J. M. S. Hutchinson, and K. A. Garrett. 2012. Identifying highly connected counties compensates for resource limitations when evaluating national spread of an invasive pathogen. PLOS ONE 7:e37793. [open access link]

Thomas-Sharma, S., J. Andrade-Piedra, M. Carvajal Yepes, J. Hernandez Nopsa, M. Jeger, R. Jones, P. Kromann, J. Legg, J. Yuen, G. A. Forbes, and K. A. Garrett. 2017. A risk assessment framework for seed degeneration: Informing an integrated seed health strategy for vegetatively-propagated crops. Phytopathology 107:1123-1135. [open access link]  [Interactive interface for exploring model behavior]

Xing*, Y.J. Hernandez Nopsa*, K. F. Andersen, J. Andrade-Piedra, F. Beed, G. Blomme, M. Carvajal Yepes, D. Coyne, W. Cuellar, G. Forbes, J. Kreuze, J. Kroschel, L. Kumar, J. Legg, M. Parker, E. Schulte-Geldermann, K. Sharma, and K. A. Garrett. 2020. Global cropland connectivity: A risk factor for invasion and saturation by emerging pathogens and pests. BioScience 70:744-758. [open access link]

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