bacterial and viral microbial profiles in endemic influenza A virus infected swine herds using nanopore metagenomic sequencing on tracheobronchial swabs

Swine influenza A virus (swIAV) plays an important role in porcine respiratory infections. Next to its ability to cause severe disease by itself, it is important in the multi-etiological porcine respiratory disease complex (PRDC). Still, to date no comprehensive diagnostics are offered to study polymicrobial infections in detail. Hence, veterinary practitioners rely on monospecific and costly diagnostics, such as RT-qPCR, antigen detection, and serology. This prevents proper understanding of the entire disease context, hampering effective preventive and therapeutic actions. A new nanopore-based metagenomic diagnostic platform was applied to study respiratory co-infections across four age groups on 25 endemic swIAV infected German farms with respiratory distress in the nursery. Farms were screened for swIAV using RT-qPCR on nasal and tracheobronchial swabs (TBS). TBS samples were pooled per age group prior to metagenomic characterization. Resulting data showed a correlation between swIAV viral loads and normalized sequencing reads, supporting a (semi-)quantitative interpretation of the metagenomic data. Interestingly, in-depth characterization using beta diversity and PERMANOVA analyses revealed the age-dependent interplay of known viral and bacterial agents. Also, lesser-known microbes, such as porcine polyoma-, parainfluenza-, and hemagglutinating encephalomyelitis viruses were identified. Analyses of swIAV incidence and clinical signs established differing microbial communities for the age groups, highlighting age-specific contribution of various microbes in porcine respiratory disease. In conclusion, nanopore metagenomics was shown to enable a panoramic view on co-infections and pathogen dynamics in endemic swIAV infected herds. The results also highlighted the need for better insights into lesser studied agents potentially associated with porcine respiratory disease.