Genotypic and Phenotypic Characterization of Pathogenic Escherichia coli, Salmonella spp., and Campylobacter spp., in Free-Living Birds in Mainland Portugal

Abstract

Birds are potential carriers of pathogens affecting humans and agriculture. Aiming to evaluate the occurrence of the top three most important foodborne pathogens in free-living birds in Portugal, we investigated 108 individual fecal samples from free-living birds and one pooled sample of gull feces (<i>n</i> = 50) for the presence of <i>Escherichia coli</i> (pathogenic and non-pathogenic), <i>Salmonella</i> spp. and <i>Campylobacter</i> spp. Virulence- and antimicrobial resistance- (AMR) associated genes were detected by PCR and Whole-Genome Sequencing (WGS), and phenotypic (serotyping and AMR profiles) characterization was performed. Overall, 8.9% of samples tested positive for pathogenic <i>E. coli</i>, 2.8% for <i>Salmonella</i> spp., and 9.9% for <i>Campylobacter</i> spp. AMR was performed on all pathogenic isolates and in a fraction of non-pathogenic <i>E. coli</i>, being detected in 25.9% of them. Ten of the tested <i>E. coli</i> isolates were multidrug-resistant (MDR), and seven of them were Extended-spectrum β-lactamase (ESBL) producers. Among <i>Salmonella</i> (<i>n</i> = 3) and <i>Campylobacter</i> (<i>n</i> = 9), only one strain of <i>C. jejuni</i> was identified as MDR. Most of the identified serotypes/sequence types had already been found to be associated with human disease. These results show that free-living birds in Portugal may act as carriers of foodborne pathogens linked to human disease, some of them resistant to critically important antimicrobials.