Rafael R C Cuadrat1, Maria Sorokina2, Bruno G Andrade3, Tobias Goris4, Alberto M R Dávila5,6. 1. Department of Molecular Epidemiology, German Institute of Human Nutrition Potsdam-Rehbruecke - DIfE, Arthur-Scheunert-Allee 114-116, 14558 Nuthetal, Germany. 2. Institute for Inorganic and Analytical Chemistry, Friedrich-Schiller University, Lessingstrasse 8, 07743 Jena, Germany. 3. Animal Biotechnology Laboratory, Embrapa Southeast Livestock, EMBRAPA, Rodovia Washington Luiz, Km 234 s/n°, 13560-970 São Carlos, SP, Brazil. 4. Department of Molecular Toxicology, Research Group Intestinal Microbiology, German Institute of Human Nutrition Potsdam-Rehbruecke - DIfE, Arthur-Scheunert-Allee 114-116, 14558 Nuthetal, Germany. 5. Computational and Systems Biology Laboratory, Oswaldo Cruz Institute, FIOCRUZ, Av Brasil 4365, 21040-900 Rio de Janeiro, RJ, Brazil. 6. Graduate Program in Biodiversity and Health, Oswaldo Cruz Institute, FIOCRUZ, Av. Brasil 4365, 21040-900 Rio de Janeiro, RJ, Brazil.
Abstract
BACKGROUND: The rise of antibiotic resistance (AR) in clinical settings is of great concern. Therefore, the understanding of AR mechanisms, evolution, and global distribution is a priority for patient survival. Despite all efforts in the elucidation of AR mechanisms in clinical strains, little is known about its prevalence and evolution in environmental microorganisms. We used 293 metagenomic samples from the TARA Oceans project to detect and quantify environmental antibiotic resistance genes (ARGs) using machine learning tools. RESULTS: After manual curation of ARGs, their abundance and distribution in the global ocean are presented. Additionally, the potential of horizontal ARG transfer by plasmids and their correlation with environmental and geographical parameters is shown. A total of 99,205 environmental open reading frames (ORFs) were classified as 1 of 560 different ARGs conferring resistance to 26 antibiotic classes. We found 24,567 ORFs in putative plasmid sequences, suggesting the importance of mobile genetic elements in the dynamics of environmental ARG transmission. Moreover, 4,804 contigs with >=2 putative ARGs were found, including 2 plasmid-like contigs with 5 different ARGs, highlighting the potential presence of multi-resistant microorganisms in the natural ocean environment. Finally, we identified ARGs conferring resistance to some of the most relevant clinical antibiotics, revealing the presence of 15 ARGs similar to mobilized colistin resistance genes (mcr) with high abundance on polar biomes. Of these, 5 are assigned to Psychrobacter, a genus including opportunistic human pathogens. CONCLUSIONS: This study uncovers the diversity and abundance of ARGs in the global ocean metagenome. Our results are available on Zenodo in MySQL database dump format, and all the code used for the analyses, including a Jupyter notebook js avaliable on Github. We also developed a dashboard web application (http://www.resistomedb.com) for data visualization.
BACKGROUND: The rise of antibiotic resistance (AR) in clinical settings is of great concern. Therefore, the understanding of AR mechanisms, evolution, and global distribution is a priority for patient survival. Despite all efforts in the elucidation of AR mechanisms in clinical strains, little is known about its prevalence and evolution in environmental microorganisms. We used 293 metagenomic samples from the TARA Oceans project to detect and quantify environmental antibiotic resistance genes (ARGs) using machine learning tools. RESULTS: After manual curation of ARGs, their abundance and distribution in the global ocean are presented. Additionally, the potential of horizontal ARG transfer by plasmids and their correlation with environmental and geographical parameters is shown. A total of 99,205 environmental open reading frames (ORFs) were classified as 1 of 560 different ARGs conferring resistance to 26 antibiotic classes. We found 24,567 ORFs in putative plasmid sequences, suggesting the importance of mobile genetic elements in the dynamics of environmentalARG transmission. Moreover, 4,804 contigs with >=2 putative ARGs were found, including 2 plasmid-like contigs with 5 different ARGs, highlighting the potential presence of multi-resistant microorganisms in the natural ocean environment. Finally, we identified ARGs conferring resistance to some of the most relevant clinical antibiotics, revealing the presence of 15 ARGs similar to mobilized colistin resistance genes (mcr) with high abundance on polar biomes. Of these, 5 are assigned to Psychrobacter, a genus including opportunistic human pathogens. CONCLUSIONS: This study uncovers the diversity and abundance of ARGs in the global ocean metagenome. Our results are available on Zenodo in MySQL database dump format, and all the code used for the analyses, including a Jupyter notebook js avaliable on Github. We also developed a dashboard web application (http://www.resistomedb.com) for data visualization.
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