Quantitative multitarget diagnostics to identify infections for acute or preventive treatments in livestock and aquaculture

Project objectives

• Task 1-1 Develop, validate and inter-laboratory test at least five multiplex diagnostic assays for Cattle, Sheep and Goat pathogens, inclusive of strain identification and ARG diagnostics as appropriate.

• Task 1-2 Provision of validated multiplex diagnostic assays for Pig, Rabbit and Poultry pathogens, inclusive of strain identification and ARG diagnostics as appropriate.

• Task 1-3 Provision of validated multiplex diagnostic assays for Salmon, Trout, oyster and carp pathogens, inclusive of strain identification and ARG diagnostics as appropriate.

• Task 1-4 Provision of validated multiplex diagnostic assays for extensive Reindeer herds and for wildlife that carrying farm-animal pathogens.

• Task 1-5 Establishment and validation of at least four unbiased and untargeted diagnostic tools for sampling animal matrices

• Task 2-1 Demonstration of complete environmental sampling protocols

• Task 2-2 Validation of multiple animal matrices as indirect routes to diagnose multiple pathogens.

• Task 2-3 Field demonstration of nanopore sequencing.

• Task 3-1 Annual technical reporting on the emerging threat to European farm animal production.

• Task 3-2 Provision of training opportunity for dPCR and aerosol sampling and field-based nanopore sequencing

• Task 3-3 Sharing of validation materials between partners

Outcomes and impacts

The primary overarching outcome for JIP OO3-A4 is the provision of sensitive, specific, verified multitarget diagnostic tools and platforms for a whole range of important common, rare and emerging enzootic microorganisms of livestock, including aquaculture, that require active treatment and prevention.

The impact of this is more accurate, rapid and cost-effective diagnostic capacity to enable efficient direction of treatments, assisting decision making for primary care givers from veterinarians through to farmers. An additional outcome, which has the potential to dramatically increase impact, this JIP will also provide methods to allow differentiation of pathogen strains and antimicrobial sensitivities, where this is deemed important for directing treatment strategies.

This consortium will bring together a broad expertise on diverse methods for pathogen detection. This expertise will increase our overall readiness to define the most suitable detection methods in case of future disease outbreaks of known or unknown pathogens