Sessions

Small carnivores are among the wildlife species frequently found in urbanised environments, even inside buildings, and are also encountered by people on hiking trails. These species are able to transmit several pathogens to humans and domestic animals, making surveillance of the pathogens they carry relevant for both human and veterinary health perspectives. Their diet includes arthropods, molluscs, plants and vertebrates, and they drink from natural water sources. Their faeces therefore also provide information about their diet and environmental exposures, in addition to their relevance to One Health. We aimed to investigate this information through metagenomic analysis.

We collected seven small carnivore faecal samples along hiking trails near human settlements in two mountain regions of Hungary and analysed them using metagenomic methods. In addition to identifying the host species and animal and plant components of the diet, we detected sequences assigned to potentially pathogenic bacteria (e.g. Escherichia coli, Klebsiella pneumoniae) and fungi (e.g. Pichia kudriavzevii, Mucor spp.).

From the results of the sequencing data, we assembled two complete and two nearly complete mitochondrial genomes of the beech marten (Martes foina) and one complete mitochondrial genome of the red fox (Vulpes vulpes). To our knowledge, no such data have previously been available from Hungary.

Among the antimicrobial resistance genes (ARGs) identified, E. coli and Citrobacter sp. carried genes associated with influencing the effect of carbapenems, monobactams, rifamycins and glycylcyclines. Genes associated with fosfomycin resistance were found in Buttiauxella ferragutiae, Escherichia albertii, E. coli and Pantoea agglomerans. All four E. coli genomes recovered by metagenomic assembly can be classified to the ExPEC- associated filogroup (B2, D, F), while none belonged to the commensal-associated phylogroups A or B1. The bacterial genomes also carried a range of virulence factor genes (VFGs) potentially contributing to pathogenicity, e.g. Ibes factors, Type 1 fimbirae and TTSS.

Additionaly, short, fragmented seqeunces of Erannis ankeraria nucleopolyhedrovirus were detected in samples from both mountain regions, which may indicate the presence of E. ankeraria.

Based on these results, we think that the equipped stress-free, non-invasive sample-collection based method is applicable as a part of a One Health and ecology oriented monitoring system. Furter studies are recommended to establish the hosts full genome, gender, for the the more precise description of the digested food's components and the intestinal micro- and macro parasites, by using a sequencing with a greater depth than ours (e.g. 10M clusters).