Purdue-led study enhances swine respiratory disease testing

A Swine Health Information Center-funded study aimed to improve detection of common and emerging swine pathogens using a next generation sequencing panel. Led by Rebecca Wilkes at Purdue University, the study sought to develop and validate a targeted next-generation sequencing respiratory panel capable of detecting multiple viral and bacterial swine respiratory pathogens in a single test. Swine respiratory disease is often caused by multiple pathogen infections occurring simultaneously, making diagnosis and control difficult when relying on single-pathogen tests. Results from this study showed strong agreement between tNGS and PCR, high specificity, and robust sensitivity across clinically relevant pathogen loads. Moreover, the panel successfully identified mixed infections and detected pathogens that may be missed by targeted PCR testing alone.  

Infectious disease syndromes in swine are frequently multifactorial and can be challenging to determine the causative pathogen(s) by clinical signs alone. Co-infections with viral and bacterial pathogens often occur, making accurate diagnoses challenging. Many diagnostic tests utilized in swine are single pathogen assays. Consequently, there is a critical need within the swine industry for comprehensive diagnostic approaches capable of simultaneously detecting co-infections and identifying emerging or unexpected pathogens. This comprehensive approach can help support more informed treatment decisions, guide targeted interventions, and reduce reliance on sequential or repeated testing.  

Objectives of the study described herein include 1) develop and optimize primers targeting swine respiratory pathogens, 2) validate specificity and sequencing performance with characterized strains, 3) determine analytical sensitivity in comparison with qPCR and 4) validate diagnostic performance using clinical samples. An array of primers targeting multiple regions across the genomes of common and emerging swine respiratory pathogens was designed in collaboration with the AgriSeq Bioinformatics team (Thermo Fisher Scientific). The panel was developed to enable simultaneous detection of viral, bacterial and selected virulence-associated targets relevant to swine disease syndromes. Primer design focused on highly conserved genomic regions to ensure broad detection, while selected targets included regions enabling genotyping or lineage assignment for specific pathogens, such as porcine reproductive and respiratory syndrome virus and porcine circovirus type 2.