Metagenomic sequencing of garden dormouse
This sequencing project was a part of a larger study investigating pathogens in garden dormouse. Wild rodents are key reservoirs for zoonotic pathogens, but their impact on declining wildlife species remains unclear. The garden dormouse (Eliomys quercinus), a nocturnal European rodent experiencing widespread population loss, may be affected by infectious agents. To investigate this, we reviewed 73 years of literature and screened dead dormice from Germany using microbiological and metagenomic methods. In addition to conventional testing, seven kidney-derived DNA samples and three pools of 66 samples were sequenced using Illumina Nextera XT and NovaSeq Xplus 10B at the NIH/NCI Sequencing Facility. Staphylococcus aureus was the most prevalent pathogen (29%), and Leptospira borgpetersenii was identified for the first time in dormice (1.1%). While DNA viruses including Parvoviridae and Polyomaviridae were detected, no widespread infection by zoonotic agents was observed. Overall, pathogens are unlikely to be a major factor in the species decline; however, our identification of previously unknown viruses highlights the importance of metagenomic screening for novel pathogens that may evade detection by conventional methods.