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author = {Joseph Nesme and S{\'{e}}bastien C{\'{e}}cillon and Tom~O. Delmont and Jean-Michel Monier and Timothy~M. Vogel and Pascal Simonet},
title = {Large-Scale Metagenomic-Based Study of Antibiotic Resistance in the Environment},
journal = {Current Biology}
}" data-bib-key="Nesme_2014" contenteditable="false">
Nesme 2014), in which soil metagenomes showed the most diverse pool of ARGs than human feces, ocean, cow and chicken gut and artic snow metagenomes. In relation to glaciar metagenomes, a recent study showed a big diversity of ARGs in samples obtained from glacier from different geographic locations, including Antarctica, Alaska, Himalaya, Greenland and others
( ( class="ltx_cite" data-bib-text="@article{Segawa_2012,
doi = {10.1111/1758-2229.12011},
url = {http://dx.doi.org/10.1111/1758-2229.12011},
year = 2012,
...
author = {Takahiro Segawa and Nozomu Takeuchi and Andres Rivera and Akinori Yamada and Yoshitaka Yoshimura and Gonzalo Barcaza and Kunio Shinbori and Hideaki Motoyama and Shiro Kohshima and Kazunari Ushida},
title = {Distribution of antibiotic resistance genes in glacier environments},
journal = {Environmental Microbiology Reports}
}" data-bib-key="Segawa_2012" contenteditable="false">
Segawa 2012). In addition, this study found important differences in ARG content between Antarctica and Chilean samples (low diversity and closer geographically) and the others glaciar samples (high diversity, closer geographically between them), but this study was based on a PCR approach, masking the real ARG content of those locations.
In the opposite, opposite side, human gut, ocean and cow gut metagenomes, exhibit the lowestdiversity values (19, 17 and 12 different type of b-lactamasegenes respectively). Richness was other important diversity index analyzed, and our results indicate that values, but diversity not alwaysa high level of diversity correlated with richness. Thus, soil metagenomes, glaciers and wastewater metagenomes were the most b-lactamase diverse environments; however the most rich b-lactamase environments wereagricultural soils, human gut, non-agricultural soils and wasterwater (in average 0.0106, 0.0105, 0.0093 gut and 0.0092% of reads identified like b-lactamases from the total number of read per environment). wasterwater. In contrast, glacier metagenomes that exhibited a high b-lactamase diversity, show showed in average an intermediate b-lactamase richness (0.0068% of total number of reads).
Differences richness.
Differences in
b-lactamase content of agricultural close related environments, such soil (agricultural and non-agricultural
soil metagenomes soils) could be attributed to
anthropogenic forces; thus, in the case of soils, have been demonstrated that agricultural practices such as manure amendment, fertilization, irrigation and
more. Thus, more can affect the ARG profile of soils. For instance, class="ltx_cite" data-bib-text="@article{Udikovic_Kolic_2014,
doi = {10.1073/pnas.1409836111},
url = {http://dx.doi.org/10.1073/pnas.1409836111},
year = 2014,
...
author = {Nikolina Udikovic-Kolic and Fabienne Wichmann and Nichole A. Broderick and Jo Handelsman},
title = {Bloom of resident antibiotic-resistant bacteria in soil following manure fertilization},
journal = {Proceedings of the National Academy of Sciences}
}" data-bib-key="Udikovic_Kolic_2014" contenteditable="false">
Udikovic-Kolic 2014 et al. (format) recently demonstrate an increase in ARG (specially in b-lactamase content) in soils amendment with manure compared to the ARG content in soil fertilized with NPK. Interestingly, the cattle that produced the manure had not been treated with antibiotics. The authors concluded that manure application produced a bloom of certain bacterial resistant populations without connection to antibiotic
exposure.
The exposure.
The analysis of the supporting information accompanying the metagenome sequences, clearly indicate that different factor affect the b-lactamase diversity values here obtained. In this context is important indicate that despite that all the metagenomes share the same type of technology used in the sequencing process, differences in methodology can be expected. In the same context, despite that metagenomes can be grouped according different environments, some differences can affect the sequencing results; thus, in the ocean environment, metagenomes related to the Sydney harbour metagenome project (see Table S1) were obtained at 0,3 m in depth, in the estuary of Sydney, and metagenomes related to Amazon continuum metagenomes project were obtained at depths ranged from 3.63 to 4.47 meters, and the samples were obtained at different points, from seawater close to the cost line until seawater far from the cost line (open ocean). For instance, some studies have been show the differences in the AR profile across different water layers in different lake samples (
...
author = {Chu Thi Thanh Binh and Holger Heuer and Martin Kaupenjohann and Kornelia Smalla},
title = {Piggery manure used for soil fertilization is a reservoir for transferable antibiotic resistance plasmids},
journal = {{FEMS} Microbiology Ecology}
}" data-bib-key="Binh_2008" contenteditable="false">Binh 2008 showed that manure is a hot spot of bacteria carrying antibiotic resistance genes in MGEs. Finally, in the case of gut metagenomes, clearly the health situation and/or the drug supply can affect both the microbiological and genomic content. Our analysis take into account those variability, and steps oriented to reduce it were
applied.
Supporting applied.
Supporting the differences in b-lactamase content and diversity, our indicator species analysis show habitat-specificity for some b-lactamase genes. Interestingly, four b-lactamase genes (blaEBR, CfxA, mecA HGI) showed a high faithfulness of occurrence in the human gut environment; those genes have been previously identified only in humans (both health and sick) (
