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

Marcelino, Vanessa R., Wille, Michelle, Hurt, Aeron C., González-Acuña, Daniel, Klaassen, Marcel, Schlub, Timothy E., Eden, John-Sebastian, Shi, Mang, Iredell, Jonathan R., Sorrell, Tania C. and Holmes, Edward C. 2019, Meta-transcriptomics reveals a diverse antibiotic resistance gene pool in avian microbiomes, BMC biology, vol. 17, no. 1, doi: 10.1186/s12915-019-0649-1.

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Title Meta-transcriptomics reveals a diverse antibiotic resistance gene pool in avian microbiomes
Author(s) Marcelino, Vanessa R.
Wille, Michelle
Hurt, Aeron C.
González-Acuña, Daniel
Klaassen, MarcelORCID iD for Klaassen, Marcel orcid.org/0000-0003-3907-9599
Schlub, Timothy E.
Eden, John-Sebastian
Shi, Mang
Iredell, Jonathan R.
Sorrell, Tania C.
Holmes, Edward C.
Journal name BMC biology
Volume number 17
Issue number 1
Article ID 31
Total pages 11
Publisher BioMed Central
Place of publication London, Eng.
Publication date 2019-04-08
ISSN 1741-7007
Keyword(s) Antimicrobial resistance
Birds
Meta-transcriptomics
Microbiome
Resistome
Wastewater
Science & Technology
Life Sciences & Biomedicine
Biology
Life Sciences & Biomedicine - Other Topics
ESCHERICHIA-COLI
GUT MICROBIOTA
BETA-LACTAMASES
WILD BIRDS
BACTERIA
EVOLUTION
GULLS
PREVALENCE
ADAPTATION
Summary 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.
Language eng
DOI 10.1186/s12915-019-0649-1
Field of Research 06 Biological Sciences
HERDC Research category C1 Refereed article in a scholarly journal
Copyright notice ©2019, The Authors
Persistent URL http://hdl.handle.net/10536/DRO/DU:30120992

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