(Meta)Genomics-Based Pathogen Identification Center for Animal and Plant Disease Diagnostics, Biosecurity, and Pandemic Prevention

By integrating advanced sequencing technologies and bioinformatics, we provide comprehensive services and conduct cutting-edge research to enhance pathogen detection and identification, ultimately contributing to public health, agriculture, and environmental sustainability.

Available Services

• Comprehensive and Rapid Pathogen Screening:
  Using metagenomic sequencing, we provide thorough screening of samples to identify a wide range of plant and animal pathogens, including bacteria, viruses, and fungi. Our services enable timely intervention in clinical diagnostics, environmental monitoring, disease outbreak management, and pathogen surveillance.

• Custom Metagenomic Analysis:
  Tailored metagenomic analysis services allow for the detection and characterization of specific pathogens of interest. This includes the design of bespoke bioinformatics pipelines to meet unique research or clinical needs.

Sample Submission

We are currently in the process of establishing our service. For more details on sample submission and expected turnaround time, please contact:

• For plant sample submission: Please contact Dr. Boris Vinatzer at vinatzer@vt.edu.
• For animal sample submission: Please contact Dr. Kevin Lahmers at klahmers@vt.edu.

Research & Collaboration

We are eager to partner with researchers who share our commitment to advancing the field of pathogen identification and surveillance. If you are interested in collaborating, please contact us to discuss potential opportunities.

We are currently using Oxford Nanopore technology (ONT) for whole genome sequencing and metagenomics-based pathogen identification. 

Sample Requirements

Sample Mass and Concentration:

Sample Purity:

DNA samples should have a 260/280 ratio between 1.8 and 2.0 and a 260/230 ratio between 2.0 and 2.2.

Library Integrity:

To QC the sequencing libraries before loading for sequencing, we run a TapeStation analysis. TapeStation data verifies successful library construction and determines the average fragment size of the sequencing library, which is required to calculate the molar concentration before loading.

Other things to keep in mind while handling the samples:

High molecular weight (HMW) genomic DNA samples require careful handling. During isolation and subsequent handling, do not vortex HMW DNA, and always use wide bore pipette tips for any pipetting. Perform all pipetting actions slowly to prevent shearing. Additionally, to preserve the integrity of HMW DNA, it is recommended to use low DNA binding microfuge tubes. 

Selected Publications

1. A Survey of Xylella fastidiosa in the U.S. State of Virginia Reveals Wide Distribution of Both Subspecies fastidiosa and multiplex in Grapevine, S. Abdelrazek, E. Bush, C. Oliver, H. Liu, P. Sharma, M.A. Johnson, M.A. Donegan, R.P.P. Almeida, M. Nita, B.A. Vinatzer, Phytopathology, 2024;114:35–46.
2. Metagenomic sequencing for detection and identification of the boxwood blight pathogen Calonectria pseudonaviculata, S. Yang, M.A. Johnson, M.A. Hansen, E. Bush, S. Li, B.A. Vinatzer, Sci. Rep., 2022;12:1399.
3. Metagenomics and long-read nanopore sequencing for rapid and culture-free plant pathogen surveillance, M. Aguilera, P. Sharma, S. Yang, H. Liu, R. Mazloom, L. Heath, S. Li, B.A. Vinatzer, Phytopathology, AMER PHYTOPATHOLOGICAL SOC 3340 PILOT KNOB ROAD, ST PAUL, MN 55121 USA, 2021: pp. 160–160.
4. Detecting the boxwood blight pathogen, Calonectria pseudonaviculata (Cps), using the Oxford Nanopore MinION sequencing device, S. Yang, M. Aguilera, M.A. Hansen, E.A. Bush, S. Li, B.A. Vinatzer, Phytopathology, AMER PHYTOPATHOLOGICAL SOC 3340 PILOT KNOB ROAD, ST PAUL, MN 55121 USA, 2020: pp. 39–39.
5. Strain-Level Identification of Bacterial Tomato Pathogens Directly from Metagenomic Sequences, M.E. Mechan Llontop, P. Sharma, M. Aguilera Flores, S. Yang, J. Pollok, L. Tian, C. Huang, S. Rideout, L.S. Heath, S. Li, B.A. Vinatzer, Phytopathology, 2020;110:768–779.
6. Investigating plant disease outbreaks with long-read metagenomics: sensitive detection and highly resolved phylogenetic reconstruction applied to Xylella fastidiosa, M.A. Johnson, H. Liu, E. Bush, P. Sharma, S. Yang, R. Mazloom, L.S. Heath, M. Nita, S. Li, B.A. Vinatzer, Microb Genom, 2022;8.
7. Fusobacterium Genomics Using MinION and Illumina Sequencing Enables Genome Completion and Correction, S.M. Todd, R.E. Settlage, K.K. Lahmers, D.J. Slade, mSphere, 2018;3.
8. Rapid virulence prediction and identification of Newcastle disease virus genotypes using third-generation sequencing, S.L. Butt, T.L. Taylor, J.D. Volkening, K.M. Dimitrov, D. Williams-Coplin, K.K. Lahmers, P.J. Miller, A.M. Rana, D.L. Suarez, C.L. Afonso, J.B. Stanton, Virol. J., 2018;15:179.
9. Randomly primed, strand-switching, MinION-based sequencing for the detection and characterization of cultured RNA viruses, K.T. Young, K.K. Lahmers, H.S. Sellers, D.E. Stallknecht, R.L. Poulson, J.T. Saliki, S.M. Tompkins, I. Padykula, C. Siepker, E.W. Howerth, M. Todd, J.B. Stanton, J. Vet. Diagn. Invest., 2021;33:202–215.
10. Detection of atypical porcine pestivirus genome in newborn piglets affected by congenital tremor and high preweaning mortality, K.M. Sutton, K.K. Lahmers, S.P. Harris, H.R. Wijesena, B.E. Mote, S.D. Kachman, T. Borza, D.C. Ciobanu, J. Anim. Sci., 2019;97:4093–4100.
11. Multi-laboratory evaluation of the Illumina iSeq platform for whole genome sequencing of Salmonella, Escherichia coli and Listeria, P.K. Mitchell, L. Wang, B.J. Stanhope, B.D. Cronk, R. Anderson, S. Mohan, L. Zhou, S. Sanchez, P. Bartlett, C. Maddox, V. DeShambo, R. Mani, L.M. Hengesbach, S. Gresch, K. Wright, S. Mor, S. Zhang, Z. Shen, L. Yan, R. Mackey, R. Franklin-Guild, Y. Zhang, M. Prarat, K. Shiplett, A. Ramachandran, S. Narayanan, J. Sanders, A.A. Hunkapiller, K. Lahmers, A.A. Carbonello, N. Aulik, A. Lim, J. Cooper, A. Jones, J. Guag, S.M. Nemser, G.H. Tyson, R. Timme, E. Strain, R. Reimschuessel, O. Ceric, L.B. Goodman, Microb Genom, 2022;8.
12. Complete Genome Sequence of Curtobacterium sp. Isolated from Surface-Sterilized Germinating Alfalfa Seeds, K.K. Compton, R.V. Jensen, K. Lahmers, B.E. Scharf, Microbiol Resour Announc, 2022;11

Useful Resources

For DNA extraction protocols, contaminants, and DNA stability/storage, please refer to the Nanopore documentation.

Are you looking to:

• Master the fundamentals of nanopore sequencing and data analysis?
• Discover how to effectively plan your experiments and begin using the technology?
• Acquire practical, hands-on experience in conducting experiments with our equipment?
• Obtain the tools needed to successfully perform nanopore sequencing experiments on the MinION, GridION, and PromethION?

We are always looking for undergraduate and graduate students who are interested in learning essential or advanced metagenomic sequencing skills.

Please contact us at abdelrazek@vt.edu for more information.