Meta-transcriptomics reveals a diverse antibiotic resistance gene pool in avian microbiomes
Abstract 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 acti...
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ftdatacite:10.6084/m9.figshare.c.4463822 2023-05-15T13:30:53+02:00 Meta-transcriptomics reveals a diverse antibiotic resistance gene pool in avian microbiomes Marcelino, Vanessa Wille, Michelle Hurt, Aeron GonzĂĄlez-AcuĂąa, Daniel Klaassen, Marcel Schlub, Timothy John-Sebastian Eden Shi, Mang Iredell, Jonathan Sorrell, Tania Holmes, Edward 2019 https://dx.doi.org/10.6084/m9.figshare.c.4463822 https://springernature.figshare.com/collections/Meta-transcriptomics_reveals_a_diverse_antibiotic_resistance_gene_pool_in_avian_microbiomes/4463822 unknown Figshare https://dx.doi.org/10.1186/s12915-019-0649-1 CC BY 4.0 https://creativecommons.org/licenses/by/4.0 CC-BY Microbiology FOS Biological sciences Genetics Evolutionary Biology 59999 Environmental Sciences not elsewhere classified FOS Earth and related environmental sciences Ecology Cancer Hematology 110309 Infectious Diseases FOS Health sciences 60506 Virology Collection article 2019 ftdatacite https://doi.org/10.6084/m9.figshare.c.4463822 https://doi.org/10.1186/s12915-019-0649-1 2021-11-05T12:55:41Z Abstract 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. Article in Journal/Newspaper Antarc* Antarctica DataCite Metadata Store (German National Library of Science and Technology) |
institution |
Open Polar |
collection |
DataCite Metadata Store (German National Library of Science and Technology) |
op_collection_id |
ftdatacite |
language |
unknown |
topic |
Microbiology FOS Biological sciences Genetics Evolutionary Biology 59999 Environmental Sciences not elsewhere classified FOS Earth and related environmental sciences Ecology Cancer Hematology 110309 Infectious Diseases FOS Health sciences 60506 Virology |
spellingShingle |
Microbiology FOS Biological sciences Genetics Evolutionary Biology 59999 Environmental Sciences not elsewhere classified FOS Earth and related environmental sciences Ecology Cancer Hematology 110309 Infectious Diseases FOS Health sciences 60506 Virology Marcelino, Vanessa Wille, Michelle Hurt, Aeron GonzĂĄlez-AcuĂąa, Daniel Klaassen, Marcel Schlub, Timothy John-Sebastian Eden Shi, Mang Iredell, Jonathan Sorrell, Tania Holmes, Edward Meta-transcriptomics reveals a diverse antibiotic resistance gene pool in avian microbiomes |
topic_facet |
Microbiology FOS Biological sciences Genetics Evolutionary Biology 59999 Environmental Sciences not elsewhere classified FOS Earth and related environmental sciences Ecology Cancer Hematology 110309 Infectious Diseases FOS Health sciences 60506 Virology |
description |
Abstract 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. |
format |
Article in Journal/Newspaper |
author |
Marcelino, Vanessa Wille, Michelle Hurt, Aeron GonzĂĄlez-AcuĂąa, Daniel Klaassen, Marcel Schlub, Timothy John-Sebastian Eden Shi, Mang Iredell, Jonathan Sorrell, Tania Holmes, Edward |
author_facet |
Marcelino, Vanessa Wille, Michelle Hurt, Aeron GonzĂĄlez-AcuĂąa, Daniel Klaassen, Marcel Schlub, Timothy John-Sebastian Eden Shi, Mang Iredell, Jonathan Sorrell, Tania Holmes, Edward |
author_sort |
Marcelino, Vanessa |
title |
Meta-transcriptomics reveals a diverse antibiotic resistance gene pool in avian microbiomes |
title_short |
Meta-transcriptomics reveals a diverse antibiotic resistance gene pool in avian microbiomes |
title_full |
Meta-transcriptomics reveals a diverse antibiotic resistance gene pool in avian microbiomes |
title_fullStr |
Meta-transcriptomics reveals a diverse antibiotic resistance gene pool in avian microbiomes |
title_full_unstemmed |
Meta-transcriptomics reveals a diverse antibiotic resistance gene pool in avian microbiomes |
title_sort |
meta-transcriptomics reveals a diverse antibiotic resistance gene pool in avian microbiomes |
publisher |
Figshare |
publishDate |
2019 |
url |
https://dx.doi.org/10.6084/m9.figshare.c.4463822 https://springernature.figshare.com/collections/Meta-transcriptomics_reveals_a_diverse_antibiotic_resistance_gene_pool_in_avian_microbiomes/4463822 |
genre |
Antarc* Antarctica |
genre_facet |
Antarc* Antarctica |
op_relation |
https://dx.doi.org/10.1186/s12915-019-0649-1 |
op_rights |
CC BY 4.0 https://creativecommons.org/licenses/by/4.0 |
op_rightsnorm |
CC-BY |
op_doi |
https://doi.org/10.6084/m9.figshare.c.4463822 https://doi.org/10.1186/s12915-019-0649-1 |
_version_ |
1766013493818949632 |