Resilience of swine nasal microbiota to influenza A virus challenge in a longitudinal study

Authors: Hau, Samantha; NIELSEN, DANIEL - Oak Ridge Institute For Science And Education (ORISE); MOU, KATHY - Oak Ridge Institute For Science And Education (ORISE); ALT, DAVID - Retired ARS Employee; KELLNER, STEVEN - Thermo Fisher Scientific; Brockmeier, Susan

Submitted to: BMC Veterinary Research
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/24/2023
Publication Date: 5/2/2023
Citation: Hau, S.J., Nielsen, D.W., Mou, K.T., Alt, D.P., Kellner, S., Brockmeier, S. 2023. Resilience of swine nasal microbiota to influenza A virus challenge in a longitudinal study. BMC Veterinary Research. 54:Article 38. https://doi.org/10.1186/s13567-023-01167-9.
DOI: https://doi.org/10.1186/s13567-023-01167-9

Interpretive Summary: Respiratory disease in pigs is often a mixed infection. It is caused by multiple viruses and bacteria. Respiratory disease costs the swine industry millions of dollars annually and is one of the largest contributors to antibiotic use. Influenza virus is a common cause of respiratory disease in pigs. Influenza infections are often complicated by bacterial secondary infections. How bacteria cause secondary infections is not well understood. Changes in the bacterial community of the nose after viral infection may increase the risk of bacterial infection. To determine if bacterial community changes contribute to bacterial infections, we compared the bacteria in the nose of pigs after influenza infection to non-infected animals. The bacterial community of infected animals became different from controls after the infection was cleared However, we found no difference in the bacterial communities during influenza infection. This showed bacterial infection after influenza virus is not caused by changes in the bacterial community in the pig nose. Instead, bacterial infection may be enhanced by damage from viral infection and/or immune suppression. This work is an important first step to understanding complex respiratory infections in pigs. This work helps direct future research that will limit the economic impact of respiratory disease and antibiotic usage in the swine industry.

Technical Abstract: Influenza A virus (IAV) is an important contributing pathogen of porcine respiratory disease complex (PRDC) infections. Evidence in humans has shown that IAV can disturb the nasal microbiota and increase host susceptibility to bacterial secondary infections. Few, small-scale studies have examined the impact of IAV infection on the swine nasal microbiota. To better understand the effects of IAV infection on the nasal microbiota and its potential indirect impacts on the respiratory health of the host, a larger, longitudinal study was undertaken to characterize the diversity and community composition of the nasal microbiota of pigs challenged with an H3N2 IAV. The microbiome of challenged pigs was compared with non-challenged animals over a 6-week period using 16S rRNA gene sequencing and analysis workflows to characterize the microbiota. Minimal changes to microbial diversity and community structure were seen between the IAV infected and control animals the first 10 days post-IAV infection. However, from day 14 through day 28, the microbial populations were significantly different between the two groups. There were several genera showing significant increases in abundance following IAV infection, such as Actinobacillus and Streptococcus at different time points post-challenge. The results here highlight areas for future investigation, including the implications of these changes post-infection on host susceptibility to subsequent respiratory infections.