One Sample. One Test. Comprehensive Result.
Nucleic acid sequence-based infectious disease diagnostics offer incredible advantages over current diagnostic testing technology. Quick metagenome sequences from any sample matrix can be queried to simultaneously identify or rule out multiple pathogen types including close genotypic species and strains in a single sample with a single procedure.
Comprehensive Detection
Identifies disease-causing pathogens in the metagenome in a single diagnostic test.
Multiplex Capability
Screen for multiple pathogen types simultaneously in one test from a single sample.
Strain-Level Sensitivity
Sensitive enough to identify and differentiate closely related strains.
Results in Minutes
Delivers results within minutes on a standard laptop computer, no dedicated hardware required.
LIMS Compatible
Laboratory information management system compatible for seamless integration into existing workflows.
Regulatory Validated
Validated for regulatory ‘Freedom from Disease’ certification.
The Science
The big hurdle for sequence-based infectious disease diagnostics has been the complexity involved in managing and analyzing enormous amounts of data. MiFi’s patented technology uses specially curated target-specific in-silico nucleic acid probes for sensitive and specific detection of unique pathogen signatures in metagenomic data.
MiFi diagnostic probes have proven useful in simultaneously detecting or ruling out presence of multiple causal agents of complex disease etiology such as animal and human respiratory disease, vector-transmitted parasites, nosocomial infectious pathogens, GI-tract pathogens, foreign animal diseases, and more. For crop-based agriculture, MiFi has been proven effective with multiplex screening of cutting materials and seeds to declare ‘Freedom from’ any and all known exotic pathogens.
MiFi® is ready to deploy for reservoir and hospital monitoring, epidemiology and population dynamics research, drug resistance tracking, agriculture certification, veterinary medicine diagnostics, and food safety quality assurance.
MiFi probes detect fungal, bacterial, parasite, viroid and/or virus in any tissue or sample matrix.
Applications
Validated across a broad range of industries and disease contexts.
- Animal & human respiratory disease
- Vector-transmitted parasites
- Nosocomial infectious pathogens
- GI-tract pathogens
- Foreign animal diseases
- Crop pathogen screening & ‘Freedom from’ certification
- Reservoir & hospital monitoring
- Epidemiology & population dynamics
- Drug resistance tracking
- Food safety quality assurance
Publications & Citations
The science is proven effective and extensively peer-reviewed.
- Ribeiro-Junior, M.R., Cardwell, K.F., Nascimento, D., Espindola, A.S., Ramachandran, A., Gupta, S.K., Tyungu, D. 2026. Rapid detection of human and animal respiratory viruses using Microbe Finder (MiFi®). Frontiers in Microbiology, Volume 17. DOI: 10.3389/fmicb.2026.1743643
- Dippenaar, M., Maree, H.J., Bester, R. 2026. From reads to results: comparing Oxford Nanopore to Illumina sequencing for citrus virus surveillance. BMC Genomics. DOI: 10.1186/s12864-026-12637-7
- 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™, Volume 5, Issue 2: 254–263. DOI: 10.1094/PHYTOFR-11-24-0128-FI
- Peña-Zúñiga, L., Espindola, A., Hagen, D., Ali, A., Ochoa-Corona, F. 2025. Assessment of Viral Limit of Detection in Spiked, Unassembled High-Throughput Sequencing Datasets. PhytoFrontiers™, Volume 5, Issue 2: 264–271. DOI: 10.1094/PHYTOFR-11-24-0121-FI
- Nascimento, D.M., Bodaghi, S., Wang, H., Ribeiro-Junior, M.R., Campos, R., Dang, T., Osman, F., et al. 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™, Volume 5, Issue 2: 243–253. DOI: 10.1094/PHYTOFR-12-24-0140-FI
- Ribeiro-Junior, M.R., Espindola, A., Nascimento, D.M., Barreto da Silva, 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™, Volume 5, Issue 2: 236–242. DOI: 10.1094/PHYTOFR-12-24-0141-FI
- 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, Volume 17, Issue 3: 441. DOI: 10.3390/v17030441
- 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 high-throughput sequencing datasets from hops. PhytoFrontiers™, Volume 5, Issue 2: 165–173. DOI: 10.1094/PHYTOFR-09-24-0106-FI
- 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, Volume 15, Article 1657. DOI: 10.1038/s41598-025-86065-0
- 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™, Volume 3, Issue 1: 113–123. DOI: 10.1094/PHYTOFR-05-22-0047-FI
- 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™, Volume 3, Issue 1: 137–147. DOI: 10.1094/PHYTOFR-04-22-0043-FI
- 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, Volume 72, Issue 6: 001720. DOI: 10.1099/jmm.0.001720
- 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®, Volume 112, Issue 9: 1859–1866. DOI: 10.1094/PHYTO-11-21-0454-R
- Proaño-Cuenca, F., Espindola, A.S., Garzon, C.D. 2023. Detection of Phytophthora, Pythium, Globisporangium, Hyaloperonospora, and Plasmopara species in high-throughput sequencing data by in silico and in vitro analysis using Microbe Finder (MiFi). PhytoFrontiers™, Volume 3, Issue 1: 124–136. DOI: 10.1094/PHYTOFR-04-22-0039-FI
- 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. Springer US, New York, NY. DOI: 10.1007/978-1-0716-1464-8_23
- 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, Volume 13, Issue 7: 1223. DOI: 10.3390/v13071223
- Espindola, A.S., Cardwell, K.F. 2021. Microbe Finder (MiFi®): Implementation of an Interactive Pathogen Detection Tool in Metagenomic Sequence Data. Plants, Volume 10, Issue 2: 250. DOI: 10.3390/plants10020250
- Carter, S.D., Cardwell, K., Espindola Camacho, A., Silva Lara, I. 2020. Electronic probes for assessment of changes in gastrointestinal microbiome in nursery pigs. Journal of Animal Science, Volume 98, Supplement 3: 25–26. DOI: 10.1093/jas/skaa054.045
- Espindola, A.S., Schneider, W., Cardwell, K.F., Carrillo, Y., Hoyt, P.R., Marek, S.M., Melouk, H.A., Garzon, C.D. 2018. Inferring the presence of aflatoxin-producing Aspergillus flavus strains using RNA sequencing and electronic probes as a transcriptomic screening tool. PLOS ONE, Volume 13, Issue 10: e0198575. DOI: 10.1371/journal.pone.0198575
- Espindola, A., Schneider, W., Hoyt, P.R., Marek, S.M., Garzon, C. 2015. A new approach for detecting fungal and oomycete plant pathogens in next generation sequencing metagenome data utilising electronic probes. International Journal of Data Mining and Bioinformatics, Volume 12, Issue 2: 115–128. DOI: 10.1504/IJDMB.2015.069422
- Stobbe, A.H., Daniels, J., Espindola, A.S., Verma, R., Melcher, U., Ochoa-Corona, F., Garzon, C., Fletcher, J., Schneider, W. 2013. E-probe Diagnostic Nucleic acid Analysis (EDNA): a theoretical approach for handling of next generation sequencing data for diagnostics. Journal of Microbiological Methods, Volume 94, Issue 3: 356–366. DOI: 10.1016/j.mimet.2013.07.002
The Process
MiFi.tech is the customer-facing cloud-based host for developed and validated e-probes to be used by diagnostic laboratory licensees. For access to the MiFi library of E-Probes Sign in and Register.
The lab user extracts DNA/RNA from their sample, sequences the extract, and uploads the raw, unassembled, metagenomic sample sequence data into MiFi.tech, then selects relevant e-probes to scan the data. The site currently has validated e-probes for 220 pathogens of plants, animals and humans. Users include:
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Extract DNA / RNA
Extract nucleic acids from your sample using standard laboratory protocols.
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Sequence the Extract
Sequence using any platform; portable long-read sequencers are recommended for field use.
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Upload Raw Metagenomic Data
Upload raw, unassembled, sequencing data directly to MiFi.tech. No preprocessing required.
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Select E-Probes
Choose the relevant pathogen e-probes from the MiFi library to scan against your data.
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Run Analysis & Receive Results
The cloud pipeline runs automatically. Receive a Positive/Negative diagnostic result with statistical confidence.
Currently Available E-Probe Products
- Citrus regulatory germplasm testing to prove ‘Free From’ up to 47 exotic pathogens for imports
- Blueberry differentiation of Ralstonia strains
- Sugar cane regulatory testing to prove ‘Free From’ up to 15 exotic pathogens for imports
- Rose virus diagnostic panel
- Bovine respiratory and gastrointestinal causal agent differentiation for Veterinary Medicine
- Human respiratory pathogens for childhood diseases
- Zoonotic pathogens: tick-borne infectious diseases; mosquito-borne parasites (Proof of Concept)
- Researchers: Microbiome and Ecology studies, Epidemiological tracking, gene function
Initial Target Markets
- Plant disease diagnostic laboratories for regulatory testing (Citrus Clonal Protection Program, US Sugar)
- Veterinary medicine infectious disease diagnostic testing (livestock, wildlife, companion animals); IDEXX, NAHLN
- Human disease diagnostics – for preliminary screening and public health monitoring (State Health Depts, CDC, WHO)
E-Probe Development Services
E-probes are unique identifier 30–120 nucleotide-long sequences derived from along the genome of a target disease-causing pathogen. Each probe is designed to be highly specific, capable of detecting a pathogen’s unique genomic signature even in the presence of closely related species or strains.
MiFi is also a bioinformatic software platform with a graphic user interface to develop, curate, and conduct in silico validation of e-probes for any microbe of interest. MiFi partners with external subject matter experts to custom-build and validate libraries of e-probes of interest to the industry.
E-probe developer partners have royalty options if and when the e-probes are released for general use by diagnostic laboratories in MiFi.tech.
MiFi seeks partners with infectious disease Subject Matter Experts to build the next suite of e-probes for your industry. Industry partners participate in testing and validation of target-specific e-probes in de-identified known positive and negative sample nucleic acid.
Target Partner Industries
We are actively seeking partners in the following sectors.
- Food safety laboratories (IEH, retail food chains, FDA, FSIS, HACCP managers)
- Water testing laboratories
Platform Access
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Contact UsThe Team
Dr. Kitty Cardwell
MiFi, Inc — Founder, President and Chief Technical Officer
Dr. Marcos Ribeiro-Junior
MiFi, Inc — Chief Scientist
Dr. Andres Espindola
Assistant Professor, Institute of Biosecurity and Microbial Forensics
Dr. Akhilesh Ramachandran
Associate Professor, Center for Veterinary Medicine and Pathologist, Oklahoma Animal Disease Diagnostic Laboratory
Dr. Josh Habiger
Associate Professor, Statistics (OSU Stillwater)
Dr. Donna Tyungu
Collaborator
Dr. Georgios Vidalakis
Collaborator
Dr. William Schneider
Original Founding Member — CSO, F1K9, LLC, Frederick MD
Dr. Ulrich Melcher
In Memoriam — Professor Emeritus, Biochemistry and Molecular Biology
Partners & Collaborating Institutions
Cowboy Technologies, LLC
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Institute for Biosecurity & Microbial Forensics (IBMF)
Oklahoma State University | Primary research home of the MiFi bioinformatics team.
Contact Us
For inquiries regarding MiFi®, e-probe development, HTS pipeline development, collaborations, or technical support, please reach out to our team.
contact@mifi.tech