Abstract
BackgroundAntibiotic resistance is rendering common bacterial infections untreatable. Wildlife can incorporate and disperse antibiotic-resistant bacteria in the environment, such as water systems, which in turn serve as reservoirs of resistance genes for human pathogens. Anthropogenic activity may contribute to the spread of bacterial resistance cycling through natural environments, including through the release of human waste, as sewage treatment only partially removes antibiotic-resistant bacteria. However, empirical data supporting these effects are currently limited. Here we used bulk RNA-sequencing (meta-transcriptomics) to assess the diversity and expression levels of functionally viable resistance genes in the gut microbiome of birds with aquatic habits in diverse locations.ResultsWe found antibiotic resistance genes in birds from all localities, from penguins in Antarctica to ducks in a wastewater treatment plant in Australia. Comparative analysis revealed that birds feeding at the wastewater treatment plant carried the greatest resistance gene burden, including genes typically associated with multidrug resistance plasmids as the aac(6)-Ib-cr gene. Differences in resistance gene burden also reflected aspects of bird ecology, taxonomy, and microbial function. Notably, ducks, which feed by dabbling, carried a higher abundance and diversity of resistance genes than turnstones, avocets, and penguins, which usually prey on more pristine waters.ConclusionsThese transcriptome data suggest that human waste, even if it undergoes treatment, might contribute to the spread of antibiotic resistance genes to the wild. Differences in microbiome functioning across different bird lineages may also play a role in the antibiotic resistance burden carried by wild birds. In summary, we reveal the complex factors explaining the distribution of resistance genes and their exchange routes between humans and wildlife, and show that meta-transcriptomics is a valuable tool to access functional resistance genes in whole microbial communities.
Highlights
Antibiotic resistance is rendering common bacterial infections untreatable
Microbiome samples from 110 birds, grouped into 11 libraries (Additional file 1: Table S1), contained transcripts corresponding to 81 unique antibiotic resistance genes associated with phenotypic resistance to nine classes of antibiotics (Fig. 1, Additional file 1: Table S2)
This study shows that clinically important and functional antibiotic resistance genes are widespread, even in birds from areas as remote as Antarctica, and that the resistance gene load is significantly higher in birds living in the lagoons of a wastewater treatment facility
Summary
Antibiotic resistance is rendering common bacterial infections untreatable. Wildlife can incorporate and disperse antibiotic-resistant bacteria in the environment, such as water systems, which in turn serve as reservoirs of resistance genes for human pathogens. Anthropogenic activity may contribute to the spread of bacterial resistance cycling through natural environments, including through the release of human waste, as sewage treatment only partially removes antibiotic-resistant bacteria. Multiple resistance genes can be present in a single mobile element, and the spread of plasmid-borne resistance has jeopardized the efficacy of many antibiotics, including β-lactam drugs used as a last resort [6, 7]. Both the environment and wildlife are major sources and reservoirs of resistance gene diversity [8, 9]. Birds in contact with wastewater treatment influents or effluents could be at increased risk of acquiring these genes, empirical data to support this idea are scarce [8]
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