Meta-transcriptomics reveals a diverse antibiotic resistance gene pool in avian microbiomes.

Authors:
Vanessa R Marcelino
Vanessa R Marcelino
School of BioSciences
Kansas City | United States
Aeron C Hurt
Aeron C Hurt
School of Applied Sciences
Australia
Marcel Klaassen
Marcel Klaassen
Netherlands Institute of Ecology (NIOO-KNAW)
Netherlands
Timothy E Schlub
Timothy E Schlub
University of New South Wales
Australia
John-Sebastian Eden
John-Sebastian Eden
University of New South Wales
Australia
Mang Shi
Mang Shi
State Key Laboratory for Infectious Disease Prevention and Control
Hong Kong

BMC Biol 2019 Apr 8;17(1):31. Epub 2019 Apr 8.

Marie Bashir Institute for Infectious Diseases and Biosecurity and Sydney Medical School, The University of Sydney, Sydney, NSW, 2006, Australia.

Background: 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. 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.

Results: We 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.

Conclusions: These 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.

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Source
https://bmcbiol.biomedcentral.com/articles/10.1186/s12915-01
Publisher Site
http://dx.doi.org/10.1186/s12915-019-0649-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6454771PMC
April 2019
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