ArticleMicrobiome2022
A total infectome approach to understand the etiology of infectious disease in pigs.
Article in Microbiome, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed.
- Divergent coronaviruses discovered in the virome of lamprey with reddening syndrome.Journal of virology · 2026Article
- A total infectome framework for resolving complex disease etiology in aquaculture.Advanced biotechnology · 2026Article
- Infectome Landscape of Rodents and Shrews in Guangdong Province Reveals Diverse Pathogens with Zoonotic Potential in Wildlife.Viruses · 2026Article
- Infectome analysis of small mammals in Southern China reveals pathogen ecology and emerging risks.Nature communications · 2025Article
- Age-dependent patterns of the gut microbiome, antibiotic resistome, and pathogenicity in captive koalas (Phascolarctos cinereus).Communications biology · 2025Article
- Metatranscriptomic characterization of the canine fecal virome from pooled samples in Gansu, China.Virus research · 2025Article
- Meta-transcriptomics characterization of individualMicrobiology spectrum · 2025Article
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- Evolving spectrum of Pneumocystis host specificity, genetic diversity, and evolution.FEMS microbiology reviews · 2025Review
- Profiling the composition of resistome and bacteriome in the upper respiratory tract of domestic cats with respiratory signs in China.Microbiome research reports · 2025Article
- Recombinant characterization and pathogenicity of a novel L1C RFLP-1-4-4 variant of porcine reproductive and respiratory syndrome virus in China.Veterinary research · 2024Article
- Demographic and zoological drivers of infectome diversity in companion cats with ascites.mSystems · 2024Article
- Article
- Meta-Transcriptomic Analysis Reveals Novel RNA Viruses in PolychaetesVeterinary sciences · 2024Article
- Development of Highly Efficient UniversalJournal of fungi (Basel, Switzerland) · 2024Article
- Natural co-infection of pigs with African swine fever virus and porcine reproductive and respiratory syndrome virus in India.Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology] · 2024Article
- Article
- Meta-Analysis and Systematic Literature Review of the GenusJournal of fungi (Basel, Switzerland) · 2023Article
- Detection of porcine circovirus 2, porcine parvovirus 1, and torque teno sus virus k2a in wild boars from northeastern Patagonia, Argentina.Archives of virology · 2023Article
- Commentary: Identification of pulmonary infections with porcine Rotavirus A in pigs with respiratory disease.Frontiers in veterinary science · 2023Article
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Authors and funding
20 authors.
Funding
No grant is acknowledged in the PubMed record.
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. Video abstract.
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