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...
author = {Andrea Di Cesare and Ester M. Eckert and Alessia Teruggi and Diego Fontaneto and Roberto Bertoni and Cristiana Callieri and Gianluca Corno},
title = {Constitutive presence of antibiotic resistance genes within the bacterial community of a large subalpine lake},
journal = {Molecular Ecology}
}" data-bib-key="Di_Cesare_2015" contenteditable="false">
Cesare 2015). In relation to soil metagenomes,
the agricultural metagenomes
here analyzed were exposed to different agricultural practices that can affect the microbiological content on soil and therefor, affect the genomic content on soil. Illustrating the last point,
...
editor = {Zhi Zhou},
title = {Antimicrobial-Resistant Bacterial Populations and Antimicrobial Resistance Genes Obtained from Environments Impacted by Livestock and Municipal Waste},
journal = {{PLOS} {ONE}}
}" data-bib-key="Agga_2015" contenteditable="false">Agga 2015 (formato) demonstrated that manure applications to agricultural soils affect the bacterial community and the profile of ARGs in
soils. Finally, soils, and 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 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) (
...
author = {B. Ballhausen and A. Kriegeskorte and N. Schleimer and G. Peters and K. Becker},
title = {The {mecA} Homolog {mecC} Confers Resistance against ~-Lactams in Staphylococcus aureus Irrespective of the Genetic Strain Background},
journal = {Antimicrobial Agents and Chemotherapy}
}" data-bib-key="Ballhausen_2014" contenteditable="false">Ballhausen 2014)
2014, Hu 2013) or in hospital and municipal wastewater systems (
...
title = {Detection of antibiotic-resistant bacteria and their resistance genes in wastewater,
surface water, and drinking water biofilms},
journal = {{FEMS} Microbiology Ecology}
}" data-bib-key="Schwartz_2003" contenteditable="false">Schwartz 2003), but there are no reports of their occurrence in natural environments. In addition, this analysis was performed when environments were categorized according degrees of human impact (see results); thus, the four previous genes that shown a high probability of be present in human gut metagenomes, exhibit again the same trend, this mean show the same high probability to be present in the category of higher anthropogenic
impact, but more interesting is that impact. Interestingly, in the category of the lowest anthropogenic impact, that include glacier and non-agricultural soil metagenomes,
49 a high number of b-lactamase genes
(49) show a high faithfulness of
occurrence. occurrence.
On the whole, our results suggest that highly anthropogenic impacted environments select for only few specific b-lactamases, b-lactamase genes, while less impacted environments, probably with a lower level of selective pressure, may content lower levels of b-lactamases but with a high b-lactamase diversity.
Our gene network results show a high number of connections between nodes from the same type of environment, but only few connections between nodes of two different environments; suggesting that b-lactamase genes show a high intra-habitat mobility, but a limited inter-habitat transferability. Our findings are in concordance with metagenomic (Fondi et al. 2016 and
...
editor = {Zhi Zhou},
title = {Antimicrobial-Resistant Bacterial Populations and Antimicrobial Resistance Genes Obtained from Environments Impacted by Livestock and Municipal Waste},
journal = {{PLOS} {ONE}}
}" data-bib-key="Agga_2015" contenteditable="false">Agga 2015,
Munck 2015) and more classical approaches (Forsberg 2014,
...
title = {Cytoscape: A Software Environment for Integrated Models of Biomolecular Interaction Networks},
journal = {Genome Research}
}" data-bib-key="Shannon_2003" contenteditable="false">Shannon 2003). Statistical analysis included betweenness, clustering coefficient, closeness and assortativity. In addition cluster identification was performed with NetworkAnalyzer and AutoAnnottate tools in cytoscape.
Supplemental material
Acknowledgments
Funding information
References
McCune, B. and M. J. Mefford. 2011. PC-ORD. Multivariate Analysis of
Ecological Data. Version 6. MjM Software, Gleneden Beach, Oregon, U.S.A.
