Development of biomarkers for bacterial infections to reduce the overuse of antibiotics

Antibiotic resistance is a global challenge, largely driven by excessive (mis)use of antibiotics in animals, humans, and crops.

There is a major focus on reducing antibiotic use in food systems to preserve the efficacy of existing antibiotics and reduce resistance development. However, it is difficult to distinguish between bacterial and viral infections, leading to improper antibiotic use.

We will therefore develop a test that can differentiate between viral and bacterial infections by measuring the expression of specific host genes in blood.

Pig immune cells exposed to bacterial and viral pathogens and blood samples from experimental infections will be screened by RNA sequencing to identify differentially expressed genes.

These candidates, genes identified from the literature, and previously identified putative genes will be evaluated and validated by qPCR on the generated sample material.

A robust in-field method for RNA extraction will be developed and each qPCR assay redesigned as loop-mediated isothermal amplification assays and visualized with a portable reading device.

LAMP assays will be evaluated on blind tests and field cases where the infectious agent has been identified by metagenomic sequencing.

This new assay will differentiate porcine infections with bacteria from viral, identify herds with high infection pressure and sub-clinically infected pigs, aiding in the decision to use antibiotics or choose other control measures e.g. vaccination, isolation or culling.