Acquisition and dissemination of cephalosporin-resistant E. coli in migratory birds sampled at an Alaska landfill as inferred through genomic analysis

Ahlstrom, Christina A.; Bonnedahl, Jonas; Woksepp, Hanna; Hernández, Jorge; Olsén, Björn; Ramey, Andrew M.

doi:10.1038/s41598-018-25474-w

Cited by 67 publications

(47 citation statements)

References 89 publications

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“…First, 9 of the 10 E. coli isolates we sequenced carried at least one acquired ARG, and all of these ARGs have been previously identified in E. coli from both humans and domestic cattle in East Africa (48)(49)(50)(51)(52). Further, prior research on AMR at human-livestock-wildlife interfaces suggests that the presence of these ARGs in wild animals is closely associated with anthropogenic land usage (27,47,(53)(54)(55). Second, although the dominant B1 phylogroup of our sequenced isolates is typical for E. coli in both domestic and wild herbivorous animals (36,56), two other isolates belonged to phylogroups A and B2, the dominant phylogroups of human populations (36,57).…”

Section: Discussionmentioning

confidence: 99%

“…Average read depth and genome coverage were determined by mapping reads to the E. coli K-12 strain MG1655 chromosome (NCBI reference sequence NC_000913.3) using the Burrows-Wheeler Aligner v 0.7.17 (106) and SAMtools v 1.5 (107). De novo genome assemblies of high-quality reads were performed with SPAdes v 3.10.0 (108) following the assembly selection procedure of Ahlstrom et al (47).…”

Section: Methodsmentioning

confidence: 99%

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Assessing Transmission of Antimicrobial-Resistant Escherichia coli in Wild Giraffe Contact Networks

Miller

Johnson

Paul

et al. 2019

Appl Environ Microbiol

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There is growing evidence that anthropogenic sources of antibiotics and antimicrobial-resistant bacteria can spill over into natural ecosystems, raising questions about the role wild animals play in the emergence, maintenance, and dispersal of antibiotic resistance genes. In particular, we lack an understanding of how resistance genes circulate within wild animal populations, including whether specific host characteristics, such as social associations, promote interhost transmission of these genes. In this study, we used social network analysis to explore the forces shaping population-level patterns of resistantEscherichia coliin wild giraffe (Giraffa camelopardalis) and assess the relative importance of social contact for the dissemination of resistantE. colibetween giraffe. Of 195 giraffe sampled, only 5.1% harboredE. coliisolates resistant to one or more tested antibiotics. Whole-genome sequencing on a subset of resistant isolates revealed a number of acquired resistance genes with linkages to mobile genetic elements. However, we found no evidence that the spread of resistance genes among giraffe was facilitated by interhost associations. Giraffe with lower social degree were more likely to harbor resistantE. coli, but this relationship was likely driven by a correlation between an individual’s social connectedness and age. Indeed, resistantE. coliwas most frequently detected in socially isolated neonates, indicating that resistantE. colimay have a selective advantage in the gastrointestinal tracts of neonates compared to other age classes. Taken together, these results suggest that the maintenance of antimicrobial-resistant bacteria in wild populations may, in part, be determined by host traits and microbial competition dynamics within the host.IMPORTANCEAntimicrobial resistance represents a significant threat to human health, food security, and the global economy. To fully understand the evolution and dissemination of resistance genes, a complete picture of antimicrobial resistance in all biological compartments, including natural ecosystems, is required. The environment and wild animals may act as reservoirs for anthropogenically derived resistance genes that could be transferrable to clinically relevant bacteria of humans and domestic animals. Our study investigated the possible transmission mechanisms for antimicrobial-resistant bacteria within a wild animal population and, more broadly, contributes to our understanding of how resistance genes are spread and maintained in natural ecosystems.

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Section: Discussionmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Assessing Transmission of Antimicrobial-Resistant Escherichia coli in Wild Giraffe Contact Networks

Miller

Johnson

Paul

et al. 2019

Appl Environ Microbiol

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“…The authors made an interesting observation that the bla OXA-48positive isolates were obtained from temporally and spatially separated samples, suggesting the resistant strain was maintained in the gull population or in an environmental source often visited by gulls. Whether the gulls obtained CPE locally from anthropogenic sources, such as the nearby landfill, or brought them via migration remained a question that the authors may answer in their ongoing research in Alaska (6,7).…”

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confidence: 99%

“…While research in areas with lower and well-defined anthropogenic sources as those studies being conducted by Ahlstrom and colleagues in Alaska may answer many essential questions. In the One Health concept, technologies such as whole-genome sequencing based on selectively obtained AMR bacterial isolates are highly useful for identifying shared bacterial strains, their similarity on the level of SNPs, antibiotic resistance genes, and mobile genetic elements (6). Nevertheless, the genotyping of selected AMR bacteria enables us to see only a small portion of the problem.…”

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confidence: 99%

Wildlife Is Overlooked in the Epidemiology of Medically Important Antibiotic-Resistant Bacteria

Dolejská

Literák

2019

Antimicrob Agents Chemother

129

103

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Wild animals foraging in the human-influenced environment are colonized by bacteria with clinically important antibiotic resistance. The occurrence of such bacteria in wildlife is influenced by various biological, ecological, and geographical factors which have not yet been fully understood. More research focusing on the human-animal-environmental interface and using novel approaches is required to understand the role of wild animals in the transmission of antibiotic resistance and to assess potential risks for the public health.

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“…Finally, integrating movement analysis also allows the identification of source areas for contaminants, plastics, pathogens, or alien species likely to be imported to lakes such as FP (Figure S4). Gulls using landfills may transport harmful bacteria such as Salmonella or E. coli including strains resistant to antibiotics (Ahlstrom et al., ; Dolejska, Bierošová, Kohoutova, Literak, & Čížek, ), as well as a range of contaminants (Belant, ).…”

Section: Discussionmentioning

confidence: 99%

Quantifying nutrient inputs by gulls to a fluctuating lake, aided by movement ecology methods

et al. 2019

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Eutrophication of aquatic ecosystems is a global problem with major ecological and economic impacts. In many lakes and reservoirs, guanotrophication occurs when roosting waterbirds import nutrients (nitrogen and phosphorus) from surrounding terrestrial habitats. To date, nutrient loading by waterbirds has been estimated based on censuses in the absence of detailed information on their movements. We quantified nutrient importation by the lesser black‐backed gull (Larus fuscus) to Fuente de Piedra (1,350 ha) in Andalusia (south‐west Spain), where an average of 36,288 individuals are counted in January. During seven winters from 2010 to 2017, we used movement data from 20 individual gulls tagged with Global Positioning System trackers that foraged in four landfills. Together with monthly bird counts and measurements of total N and P content in faeces and pellet samples, movement data were used to quantify the total external loading effect for different winters. Movement data allowed us to quantify the proportion of time spent in the lake and the time spent at different foraging sites and enabled correction of censuses. According to tracking data, on average 69% of the birds had already left the lake to head for feeding sites when waterbird counts were carried out. Nutrient inputs to the lake depend partly on the proportion of the day that gulls spend there, which was higher in late winters and was reduced when lake depth went below or above 20–35 cm. An estimated average of 10.17 kg N ha−1 year−1 and 2.07 kg P ha−1 year−1 were imported to this closed‐basin lake by gulls each winter, with highest values recorded in winter 2016–2017. Gull guano is the most important winter source of nutrients to the lake. Regurgitated pellets have been ignored as a source of nutrients in other guanotrophy studies, but we found them to be a more important source of P than faeces. A movement ecology approach complements traditional censuses and facilitates the study of guanotrophication in multiple ways, including identification of sources of nutrients, correction of censuses, and measuring time spent at roost sites.

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Acquisition and dissemination of cephalosporin-resistant E. coli in migratory birds sampled at an Alaska landfill as inferred through genomic analysis

Cited by 67 publications

References 89 publications

Assessing Transmission of Antimicrobial-Resistant Escherichia coli in Wild Giraffe Contact Networks

Assessing Transmission of Antimicrobial-Resistant Escherichia coli in Wild Giraffe Contact Networks

Wildlife Is Overlooked in the Epidemiology of Medically Important Antibiotic-Resistant Bacteria

Quantifying nutrient inputs by gulls to a fluctuating lake, aided by movement ecology methods

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