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 blaCTX-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 blaCTX-M-15. Poultry-associated blaCMY-2 was identified from the widely distributed IncI1 and IncK plasmids from four different isolates. One isolate harbored an IncI1 plasmid with blaCTX-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.

Wastewater Surveillance Detected Carbapenemase Enzymes in Clinically Relevant Gram-Negative Bacteria in Helsinki, Finland; 2011–2012

“…Nutrient-rich wastewater containing varying levels of biocidal chemicals might assert varying selection pressure on its bacterial content ( Fahrenfeld and Bisceglia, 2016 ). Additionally, the possible contribution of carbapenemase genes from zoonotic sources related to domestic pets (dogs and cats), human food, commercial farm animals, and runoff from agricultural areas cannot be ruled out ( Grönthal et al, 2018 ; Kurittu et al, 2021a , b ). However, our study site was an urban area without significant commercial farms, so there might be no significant contribution from commercial farms.…”

Prevalence, Risk Factors, and Genetic Characterization of Extended-Spectrum Beta-Lactamase Escherichia coli Isolated From Healthy Pregnant Women in Madagascar

“…To our knowledge, this is the first report of such a high prevalence of an IncY plasmid in ESBL-E. coli isolates. The extremely high sequence identity shared with an IncY plasmid in an E. coli strain isolated in Finland from Branta leucopsis (Kurittu et al, 2021) indicates that migratory birds could represent a powerful means of resistance spread even if a direct link to E. coli isolates from Madagascar is unlikely, due to the Northern Hemisphere habitat of this bird species (Owen and Black, 1989).…”

Climate Change Impacts on Microbiota in Beach Sand and Water: Looking Ahead

“…Bird population increase in beach settings is expected to lead to a potential increase in human exposure risk to pathogens such as Salmonella, Campylobacter and Chlamydia if populations continue growing in response to climate change [79]. These pathogens, in addition to other zoonotic disease-associated microbiota such as West Nile Virus, Aspergillus, Staphylococcus, and a variety of antimicrobial-resistant bacteria have been documented in gulls, terns, and barnacle geese [80][81][82]. These microbiota may be transmitted directly via deposition from the birds to coastal environments (sand and water), where they may accumulate and present human health risks.…”