Huang Xi, Yao Xinzhi, Song Wenbo, Zhao Mengfei, Zhu Zhanwei, Liu Hanyuan, Song Xiaorong, Huang Jingwen, Chen Yongrun, Wang Zihao, Peng Changjiang, Wu Wenqing, Yang Hao, Hua Lin, Chen Huanchun, Wu Bin, Peng Zhong
National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.
Hubei Hongshan Laboratory, Wuhan, China.
mSystems. 2025 Feb 18;10(2):e0002525. doi: 10.1128/msystems.00025-25. Epub 2025 Jan 30.
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 suis, , , , and being frequently detected in high abundances. Notably, , , , and 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 significantly associated with a substantial number of mobile genetic elements, including transposons (e.g., AIS1, A1353, 3, and Cau1) and plasmids (e.g., Col(BS512), Col(YC)]. These findings will contribute to further understanding the etiology, epidemiology, and microbial interactions in swine RD, and may also shed a light on the development of effective vaccines.IMPORTANCEIn this study, we identified viruses and bacteria from the lungs of pigs with RD in China at a nationwide farm scale by performing metatranscriptomic sequencing combined with metagenomic sequencing. We also demonstrated the complex interactions between different viral and/or bacterial species in swine RD. Our work provides a comprehensive knowledge about the etiology, epidemiology, and microbial interactions in swine RD and data reference for the research and development of effective vaccines against the disease.
呼吸道疾病（RD）是全球养猪业面临的主要威胁，但对与猪呼吸道疾病相关的病原体仍了解有限。在本研究中，我们在中国开展了一项全国性的基因组监测，以鉴定患有呼吸道疾病的猪肺中的病毒、细菌和抗菌抗性基因（ARG）。通过进行宏转录组测序并结合宏基因组测序，我们鉴定出属于12个病毒科的21种病毒。其中，猪繁殖与呼吸综合征病毒、甲型流感病毒、疱疹病毒、腺病毒和细小病毒较为常见。然而，新兴病毒，如盖塔病毒和猪呼吸道冠状病毒也得到了表征。除病毒外，共鉴定出164种细菌，其中猪链球菌、[此处原文缺失部分细菌名称]等经常被高丰度检测到。值得注意的是，[此处原文缺失部分细菌名称]也被高度检测到。我们的进一步分析揭示了猪呼吸道疾病中已鉴定病原体之间的复杂相互作用。我们还进行了回顾性分析，以证明中国与猪呼吸道疾病相关的流行病毒基因型或细菌血清型。最后，我们鉴定出48个ARG，它们对13种预测的抗菌类别具有抗性，其中许多ARG与大量移动遗传元件显著相关，包括转座子（如AIS1、A1353、3和Cau1）和质粒（如Col(BS512)、Col(YC)）。这些发现将有助于进一步了解猪呼吸道疾病的病因、流行病学和微生物相互作用，也可能为有效疫苗的开发提供线索。重要性在本研究中，我们通过进行宏转录组测序并结合宏基因组测序，在全国农场规模上从患有呼吸道疾病的猪肺中鉴定出病毒和细菌。我们还证明了猪呼吸道疾病中不同病毒和/或细菌物种之间的复杂相互作用。我们的工作提供了关于猪呼吸道疾病的病因、流行病学和微生物相互作用的全面知识，以及针对该疾病的有效疫苗研发的数据参考。
