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)

Abstract

Background: Increasing antimicrobial resistance (AMR) is a global threat and wild migratory birds may act as mediators of resistant bacteria across country borders. Our objective was to study extended-spectrum beta-lactamase (ESBL) and plasmid-encoded AmpC (pAmpC) producing Escherichia coli in barnacle geese using whole genome sequencing (WGS) and to identify plasmids harboring bla genes. Methods: Barnacle geese feces (n=200) were collected during fall 2017 and spring 2018 from an urban area in Helsinki, Finland. ESBL/AmpC-producing E. coli were recovered from nine samples (4.5%) and isolates were subjected to WGS on both short- and long-read sequencers, enabling hybrid assembly and determination of the genomic location of bla genes. Results: A rare multireplicon IncN+IncR was recovered from one isolate carrying bla CTX-M-1 in addition to aadA2b, lnu(F), and qnrS1. Moreover, rarely detected IncY plasmids in two isolates were found to harbor multiple resistance genes in addition to the human-associated bla CTX-M-15. Poultry-associated bla CMY-2 was identified from the widely distributed IncI1 and IncK plasmids from four different isolates. One isolate harbored an IncI1 plasmid with bla CTX-M-1 and flor. A chromosomal point mutation in the AmpC promoter was identified in one of the isolates. WGS analysis showed isolates carried multiple resistance and virulence genes and harbored multiple different plasmid replicons in addition to bla-carrying plasmids. Conclusions: Our findings suggest that wild migratory birds serve as a limited source of ESBL/AmpC-producing E. coli and may act as disseminators of the epidemic plasmid types IncI1 and IncK but also rarely detected plasmid types carrying multidrug resistance. Human and livestock-associated ESBL enzyme types were recovered from samples, suggesting a potential for interspecies transmission. WGS offers a thorough method for studying AMR from different sources and should be implemented more widely in the future for AMR surveillance and detection. Understanding plasmid epidemiology is vital for efforts to mitigate global AMR spread.