Metaviromic and metagenomic study of the pathogens in unexplained pneumonia cases in goats

Goats are an economically important livestock species in China. However, the high mortality rate due to pneumonia represents a significant challenge to the development of intensive goat farms. 10 goat lung tissue samples were collected in this study, and all samples exhibited pneumonia of different severity as determined by lung lesion scoring and histopathological examination. Subsequently, this study employed qRT-PCR to measure the relative expression level of pro-inflammatory cytokines in lung tissue, and conducted metaviromic and metagenomic analyses to elucidate the structure and composition of the pulmonary microbiota, the correlation between the abundance of specific microbes and inflammatory factors, and between microbial abundance and the expression of virulence genes. Metaviromic results indicated that Ungulate tetraparvovirus 4 (83.3 %) had the highest relative abundance in the viral composition. Metagenomic data showed that Mycoplasma (28.2 %) and Streptococcus (24.8 %) are the primary dominant genus in goat pneumonia. Notably, a total of 8 pathogens associated with pneumonia in humans or animals were identified across all samples, including Mycoplasma ovipneumoniae, Streptococcus agalactiae, Streptococcus pneumoniae, Escherichia coli, Bordetella hinzii, Bibersteinia trehalosi, Bordetella pertussis, and Pasteurella multocida, with mixed infections with multiple pathogens are very common in this study. Correlation analysis indicates a significant association between the degree of pathogen co-infection and the severity of pulmonary lesions. Furthermore, Pasteurella multocida showed a significant positive correlation with the expression of IL-6 (P< 0.01). The pneumonia samples also revealed a multitude of virulence factors associated with bacterial pathogenicity including those related to biofilm formation, endotoxin production, bacterial invasion and evasion of host immunity. In conclusion, the present study can provide a reference for clinical pathogen diagnosis of unexplained pneumonia in goats.