A total infectome approach to understand the etiology of infectious disease in pigs

• DOI: 10.1186/s40168-022-01265-4
• Publication Date: 2022-05-10T05:02:41Z
• Authors: Xinyi Huang; Weichen Wu; Xiaoxiao Tian; Xin Hou; Xingyang Cui; Yihong Xiao; Qiulin Jiao; Pei Zhou; Liqiang Liu; Weilin Shi; Ligong Chen; Yue Sun; Yongbo Yang; Jianxin Chen; Guihong Zhang; Jinling Liu; Edward C. Holmes; Xuehui Cai; Tongqing An; Mang Shi
• Keywords: Medical microbiology; Etiology

Abstract Background The global pork industry is continuously affected by infectious diseases that can result in large-scale mortality, trade restrictions, and major reductions production. Nevertheless, the cause of many pigs remains unclear, largely because commonly used diagnostic tools fail to capture full diversity potential pathogens pathogen co-infection common. Results We a meta-transcriptomic approach systematically characterize 136 clinical cases representing different disease syndromes pigs, as well 12 non-diseased controls. This enabled us simultaneously determine diversity, abundance, genomic information, detailed epidemiological history wide range pathogens. identified 34 species RNA viruses, nine DNA seven bacteria, three fungi, including two novel divergent members genus Pneumocystis . While most these were only apparent diseased animals or at higher abundance than healthy animals, others present controls, suggesting opportunistic infections. Importantly, examined here characterized with more viral, bacterial, fungal pathogens, some highly correlated occurrence levels. Examination signs necropsy results context relevant revealed multiple-pathogen model was better associated data single-pathogen was. Conclusions Our demonstrate pig explained presence multiple rather single infection one facilitate increase prevalence/abundance another. Consequently, it generally preferable consider based on panel co-infecting individual agents.