Plasmids conferring resistance to extended-spectrum beta-lactamases including a rare IncN+IncR multireplicon carrying blaCTX-M-1 in Escherichia coli recovered from migrating barnacle geese (Branta leucopsis)

Increasing antimicrobial resistance (AMR) is a global threat and wild migratory birds may act as mediators of resistant bacteria over country borders. Barnacle geese are breeding in increasing numbers and roam in urban, densely human-populated areas, such as near housing and recreational parks. The population size of barnacle geese has grown drastically during the past decades, and their breeding habits have changed. Abundance of geese breeding in and migrating through new areas has resulted in conflicts with people, crop damages, and public health concerns of potential spread of AMR via geese feces and potentially zoonotic infectious diseases. Of particular concern are plasmid-mediated extended-spectrum beta-lactamase (ESBL) and AmpC-producing Enterobacteriaceae. Plasmids harboring resistance genes have been essential in the fast-paced spread of resistance genes worldwide and are able to transmit between different bacterial cells and even species. Our objective was to study ESBL/pAmpC-producing Escherichia coli in barnacle geese using whole genome sequencing to help assess the role of migratory birds as a source of AMR, and to conduct genomic comparison and identify plasmids associated with ESBL/AmpC genes by hybrid assembly combining short- and long-read sequencing.