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


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Article Info

DATE

2022-05-10

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

ABSTRACT

BackgroundThe global pork industry is continuously affected by infectious diseases that can result in large-scale mortality, trade restrictions, and major reductions in production. Nevertheless, the cause of many infectious diseases in pigs remains unclear, largely because commonly used diagnostic tools fail to capture the full diversity of potential pathogens and because pathogen co-infection is common.ResultsWe used a meta-transcriptomic approach to systematically characterize the pathogens in 136 clinical cases representing different disease syndromes in pigs, as well as in 12 non-diseased controls. This enabled us to simultaneously determine the diversity, abundance, genomic information, and detailed epidemiological history of a wide range of potential pathogens. We identified 34 species of RNA viruses, nine species of DNA viruses, seven species of bacteria, and three species of fungi, including two novel divergent members of the genus Pneumocystis. While most of these pathogens were only apparent in diseased animals or were at higher abundance in diseased animals than in healthy animals, others were present in healthy controls, suggesting opportunistic infections. Importantly, most of the cases examined here were characterized by co-infection with more than two species of viral, bacterial, or fungal pathogens, some with highly correlated occurrence and abundance levels. Examination of clinical signs and necropsy results in the context of relevant pathogens revealed that a multiple-pathogen model was better associated with the data than a single-pathogen model was.ConclusionsOur data demonstrate that most of the pig diseases examined were better explained by the presence of multiple rather than single pathogens and that infection with one pathogen can facilitate infection or increase the prevalence/abundance of another. Consequently, it is generally preferable to consider the cause of a disease based on a panel of co-infecting pathogens rather than on individual infectious agents.-CFtrnVrpn8o8P42pZ9u6vVideo abstract More... »

PAGES

73

References to SciGraph publications

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    http://scigraph.springernature.com/pub.10.1186/s40168-022-01265-4

    DOI

    http://dx.doi.org/10.1186/s40168-022-01265-4

    DIMENSIONS

    https://app.dimensions.ai/details/publication/pub.1147759092

    PUBMED

    https://www.ncbi.nlm.nih.gov/pubmed/35538563


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    26 schema:description BackgroundThe global pork industry is continuously affected by infectious diseases that can result in large-scale mortality, trade restrictions, and major reductions in production. Nevertheless, the cause of many infectious diseases in pigs remains unclear, largely because commonly used diagnostic tools fail to capture the full diversity of potential pathogens and because pathogen co-infection is common.ResultsWe used a meta-transcriptomic approach to systematically characterize the pathogens in 136 clinical cases representing different disease syndromes in pigs, as well as in 12 non-diseased controls. This enabled us to simultaneously determine the diversity, abundance, genomic information, and detailed epidemiological history of a wide range of potential pathogens. We identified 34 species of RNA viruses, nine species of DNA viruses, seven species of bacteria, and three species of fungi, including two novel divergent members of the genus Pneumocystis. While most of these pathogens were only apparent in diseased animals or were at higher abundance in diseased animals than in healthy animals, others were present in healthy controls, suggesting opportunistic infections. Importantly, most of the cases examined here were characterized by co-infection with more than two species of viral, bacterial, or fungal pathogens, some with highly correlated occurrence and abundance levels. Examination of clinical signs and necropsy results in the context of relevant pathogens revealed that a multiple-pathogen model was better associated with the data than a single-pathogen model was.ConclusionsOur data demonstrate that most of the pig diseases examined were better explained by the presence of multiple rather than single pathogens and that infection with one pathogen can facilitate infection or increase the prevalence/abundance of another. Consequently, it is generally preferable to consider the cause of a disease based on a panel of co-infecting pathogens rather than on individual infectious agents.-CFtrnVrpn8o8P42pZ9u6vVideo abstract
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