Discovery of viruses and bacteria associated with swine respiratory disease on farms at a nationwide scale in China using metatranscriptomic and metagenomic sequencing

作者：Xi Huang, Xinzhi Yao, Wenbo Song, Mengfei Zhao, Zhanwei Zhu, Hanyuan Liu, Xiaorong Song, Jingwen Huang, Yongrun Chen, Zihao Wang, Changjiang Peng, Wenqing Wu, Hao Yang, Lin Hua, Huanchun Chen, Bin Wu, Zhong Peng · 发表于：mSystems · 年份：2025 · DOI：10.1128/msystems.00025-25 · 被引用次数：12 · 研究领域：Microbial infections and disease research、Animal Virus Infections Studies、Bacteriophages and microbial interactions

ABSTRACT Respiratory disease (RD) is a worldwide leading threat to the pig industry, but there is still limited understanding of the pathogens associated with swine RD. In this study, we conducted a nationwide genomic surveillance on identifying viruses, bacteria, and antimicrobial resistance genes (ARGs) from the lungs of pigs with RD in China. By performing metatranscriptomic sequencing combined with metagenomic sequencing, we identified 21 viral species belonging to 12 viral families. Among them, porcine reproductive and respiratory syndrome virus, influenza A virus, herpes virus, adenovirus, and parvovirus were commonly identified. However, emerging viruses, such as Getah virus and porcine respiratory coronaviruses, were also characterized. Apart from viruses, a total of 164 bacterial species were identified, with Streptococcus suis, Mycoplasma hyorhinis , Mycoplasma hyopneumoniae , Glaesserella parasuis , and Pasteurella multocida being frequently detected in high abundances. Notably, Escherichia coli , Enterococcus faecalis , Staphylococcus aureus , and Klebsiella pneumoniae were also highly detected. Our further analysis revealed a complex interaction between the identified pathogens in swine RD. We also conducted retrospectively analyses to demonstrate the prevalent viral genotypes or bacterial serotypes associated with swine RD in China. Finally, we identified 48 ARGs, which conferred resistance to 13 predicted antimicrobial classes, and many of these ARGs were signi...