Determining Bioaerosol Composition in Swine Production Facilities Through Next Generation Sequencing

PRADEEP KUMAR, Shalini Tiwari, Seyit Uguz, Zonggang Li, Jose Gonzalez, Yuanhui Zhang, Xufei Yang, South Dakota State University

     Abstract Number: 245
     Working Group: Bioaerosols

Abstract
Bioaerosols refer to airborne particles of biological origin, including bacteria, fungal spores, viruses, pollen grains, plant detritus, and insect fragments. Inside swine barns, bioaerosol concentrations can reach exceptionally high levels, posing significant health risks to both humans and animals. Understanding the microbial composition of these aerosols is critical for identifying their sources and developing cost-effective mitigation strategies. Despite rapid advancements in next-generation sequencing (NGS) technologies, no NGS-based studies on microbial composition in U.S. swine facilities have been published since 2014. In this study, air sampling (PM₂.₅ and PM₁₀) was conducted in swine farms located in South Dakota and Illinois using personal cyclones with PTFE-coated glass fiber filters. In addition to air samples, potential source samples including feed, feces, skin, plant detritus, and settled dust were collected. DNA was extracted from all samples, and both 16S rRNA gene sequencing and shotgun metagenomic sequencing were performed using the Oxford Nanopore platform. Bioinformatic analyses were conducted using EPI2ME and other computational tools. The results revealed that Firmicutes was the most abundant bacterial phylum in indoor PM samples, consistent with previous studies. At the genus level, Clostridium and Streptococcus were predominant. 16S rRNA sequencing indicated that PM₂.₅ and PM₁₀ had nearly identical microbial compositions, which differed significantly from any of the potential source samples. Shotgun metagenomic sequencing provided greater taxonomic resolution and also detected the presence of fungi and viruses. Notably, this approach identified antibiotic resistance genes (ARGs) in PM₁₀ samples. Several bacterial species, including members of the genera like Ruminococcus and Clostridium, were identified as potential ARG hosts through gene assembly and annotation. This study enhances our understanding of airborne biohazards in and around swine farms and highlights the potential for airborne transmission of antibiotic resistance. These findings are essential for guiding future source attribution efforts and prioritizing targeted mitigation strategies.