Innovation – Open view page
General information
| Innovation ID | 606 |
| Version ID | 183 |
| Innovation Title | Rapid pathogen sequencing (Rappseq): a cloud platform for identifying aquaculture bacterial pathogens from long-read DNA sequence data |
| Innovation description | The Nanopore MinION DNA sequencer offers a cost-effective solution for identifying bacterial pathogens in real time. However, the data it produces is inherently noisy, making accurate pathogen typing a challenge. This new developed cloud platform employs a learning and classification approach to accurately and rapidly identify bacterial pathogens to serotype and sequence type (ST) level. This tool will enable farmers to make timely and effective decisions around treatment and vaccination when pathogen outbreaks occur. |
| Reporting Staff | Jerome Delamare-Deboutteville (WF) |
| Year (Reporting) | 2020 |
| Reporting status | Approved |
| Innovation Type | Research and Communication Methodologies and Tools |
Stage reached
| Stage of Innovation | Stage 1: discovery/proof of concept |
| Year (Stage) | 2020 |
| Stage Description | We have collected two types of genomic data from 25 bacterial isolates: 1) highly accurate sequence data derived from long and short read sequencing that will be used for building the reference training database for machine learning algorithms 2) raw nanopore read data from the same pathogens for model development. |
| Has a lead organization | yes |
| Lead Organization | WorldFish |
| Top 5 contributors | University of Queensland; Wilderlab NZ Ltd; Mahidol University, Faculty of science, Center of Excellence for Shrimp Molecular Biology and Biotechnology |
Contributions and mapping
| All partners | University of Exeter-Academic Institutions (universities, colleges, etc.); Centre for Environment, Fisheries and Aquaculture Science-Government |
| Main CRP | CGIAR Research Program on Fish Agri-Food Systems |
| Flagship project | FP1-Sustainable aquaculture |
| Cluster | FP1-2-Fish health, nutrition and feeds |
| Other CRPs-Flagships-Clusters |
Scope
| Geographic scope | Global |
| Regions | |
| Countries |
Targeted outcomes
| Main Sub-IDO | Reduced livestock and fish disease risks associated with intensification and climate change |
| Other Sub-IDO | Increased capacity for innovation in partner development organizations and in poor and vulnerable communities |
| Other Sub-IDO | Reduced production risk |
Evidences
| Evidences | Delamare-Deboutteville, Jerome; Barnes, Andrew, 2019, "Fish bacterial pathogen genomic data", https://doi.org/10.7910/DVN/GA0NTB, Harvard Dataverse, V3 [https://doi.org/10.7910/DVN/GA0NTB] WorldFish blog. Lab-in-a-backpack: Rapid Genomic Detection to revolutionize control of disease outbreaks in fish farming. March 2020. [http://blog.worldfishcenter.org/2020/03/lab-in-a-backpack-rapid-genomic-detection-to-revolutionize-control-of-disease-outbreaks-in-fish-farming/] FISH CRP website. Lab-in-a-backpack: Rapid Genomic Detection to revolutionize control of disease outbreaks in fish farming. March 2020. [https://fish.cgiar.org/impact/stories-of-change/lab-backpack-rapid-genomic-detection-revolutionize-control-disease] 2019 WINNER Rapid genomic detection of aquaculture pathogens [https://bigdata.cgiar.org/inspire/inspire-challenge-2019/rapid-genomic-detection-of-aquaculture-pathogens/] Delamare-Deboutteville, Jerome, 2020, "ONT bacterial samples metadata, DNA quantification, sequencing info run002+run007+run008", https://doi.org/10.7910/DVN/DBZ7IV, Harvard Dataverse, V1, UNF:6:RZjy50B29/4hhUMxG5CURQ== [fileUNF] [ https://doi.org/10.7910/DVN/DBZ7IV] Jerome Delamare-Deboutteville, Andrew Barnes. (10/10/2019). Rapid genomic detection of aquaculture pathogens. Malaysia: WorldFish (WF). [https://hdl.handle.net/20.500.12348/3826] Delamare-Deboutteville, Jerome, 2020, "ONT samples metadata, DNA quantification, sequencing info run003+run004", https://doi.org/10.7910/DVN/7UFTV6, Harvard Dataverse, V1, UNF:6:laYvepACx6Bds9cy4kPSeQ== [fileUNF] [https://doi.org/10.7910/DVN/7UFTV6] |
Linked Elements
| Milestones |
| Outcome Impact Case |
| Policy |