Abstract
Effective porcine health management relies majorly on diagnostic tests, vaccination, treatment strategies, and a proper biosecurity management plan. However, understanding the link between circulating microbes and biosecurity measures on a pig farm is not evident. Substantial progress has been made in recent years with the availability of new diagnostic tools (e.g., sequencing‐based diagnostics) and extensive biosecurity management questionnaires. However, the interpretation and correlation of these results are hampered by the abundance of gained (meta)data. Therefore, we aimed to cross‐correlate viral and bacterial pathogens with respiratory tropism detected by third‐generation nanopore metagenomic sequencing with biosecurity measures assessed by Biocheck.UGent™. The study was conducted on 25 sow farms with attached nurseries in Germany with known respiratory distress. The biosecurity level of the study farms complied with the European averages. Interestingly, the farms with the highest biosecurity score showed the lowest overall prevalence of porcine reproductive and respiratory syndrome virus (PRRSV) and Actinobacillus sp.; the circulation of well‐studied pathogenic viruses, such as PRRSV, was correlated with overall lower biosecurity scores, a higher number of stillborn piglets, and cocirculation of porcine parvovirus type 7. Moreover, potential risk factors for lesser‐known agents (e.g., porcine hemagglutinating and encephalomyelitis virus, porcine respiratory coronavirus, and porcine polyomavirus) could also be addressed. For the bacterial pathogen Glaesserella sp., a correlation with increased clinical signs was observed, whereas Lactobacillus sp. and Moraxella sp. are putative biomarkers for pig farms with better biosecurity scores. In conclusion, in‐depth cross‐correlation of (meta)data from new diagnostic platforms with biosecurity measures on pig farms may contribute to a better understanding of new actions in adapting biosecurity measures. This will not only contribute to improved animal welfare and economic productivity but also helping to address (new) zoonotic disease threats and potential treatments.