Wild mammals in Portugal: gut microbiota as a source of pathogenic bacteria and antibacterial resistance ; Mamíferos selvagens em Portugal: microbiota intestinal como fonte de bactérias patogénicas e resistência antibacteriana

As the human population increases and expands, the natural habitats become more fragmented, and wildlife comes into contact with humans and their livestock, increasing the possibility of transmission of pathogens between populations. Antimicrobial resistance (AMR) is a major problem that threats global health security. Several studies investigated AMR in wildlife microbiota, and it has been suggested that the proximity to human populations and their activities impacts wildlife resistome. This raises the possibility of AMR bacteria to spread through the food chain or other routes and disseminate into the environment. The transmission of AMR is a complex, dynamic and multi-layered process, that involves humans, animals, and the environment, being an One Health issue. Little is known about the abundance and diversity of ARGs and MGEs in wildlife. The aim of the present thesis was to characterize the AMR and the shiga toxinproducing Escherichia coli (STEC) linked to the faecal microbiota of four wild mammal species in Portugal: wild boar (Sus scrofa), red deer (Cervus elaphus), Eurasian otter (Lutra lutra) and red fox (Vulpes vulpes). Faecal samples from wild boar (n=56), red deer (n=101), Eurasian otter (n=92) and red fox (n=37) were collected from Montesinho Natural Park, Lousã Mountain, Tapada Nacional de Mafra, Baixo Vouga Lagunar, and Freita, Arada and Montemuro Mountains. The general levels of AMR in two bacterial indicators, E. coli and Enterococcus spp., were determined by antibiotic susceptibility testing, and the faecal resistome of each mammal species was characterized regarding diversity and abundance using qPCR arrays. In general, the E. coli isolates were mainly resistant to β-lactams, aminoglycosides and tetracycline, and had a non-wildtype phenotype mainly for quinolones, β- lactams and tetracycline. The Enterococcus spp. isolates were mostly resistant to glycylcycline, streptogramin, and tetracycline classes, having a non-wildtype phenotype mainly associated with aminoglycoside, tetracycline and ...