scholarly journals Shotgun metagenomics reveals differences in antibiotic resistance genes among bacterial communities in Western Balkans glacial lakes sediments

2020 ◽  
Vol 18 (3) ◽  
pp. 383-397
Author(s):  
Brankica Filipic ◽  
Katarina Novovic ◽  
David J. Studholme ◽  
Milka Malesevic ◽  
Nemanja Mirkovic ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Resistance Genes ◽  
Bacterial Communities ◽  
Human Population ◽  
Antibiotic Resistance Genes ◽  
Efflux Pumps ◽  
Mobile Genetic Elements ◽  
Glacial Lakes ◽  
Western Balkans ◽  
Shotgun Metagenomics

Abstract Long-term overuse of antibiotics has driven the propagation and spreading of antibiotic resistance genes (ARGs) such as efflux pumps in the environment, which can be transferred to clinically relevant pathogens. This study explored the abundance and diversity of ARGs and mobile genetic elements within bacterial communities from sediments of three Western Balkans glacial lakes: Plav Lake (high impact of human population), Black Lake (medium impact of human population) and Donje Bare Lake (remote lake, minimal impact of human population) via shotgun metagenomics. Assembled metagenomic sequences revealed that Resistance-Nodulation-Division (RND) efflux pumps genes were most abundant in metagenome from the Plav Lake. The Integron Finder bioinformatics tool detected 38 clusters of attC sites lacking integron-integrases (CALIN) elements: 20 from Plav Lake, four from Black Lake and 14 from Donje Bare Lake. A complete integron sequence was recovered only from the assembled metagenome from Plav Lake. Plasmid contents within the metagenomes were similar, with proportions of contigs being plasmid-related: 1.73% for Plav Lake, 1.59% for Black Lake and 1.64% for Donje Bare Lake. The investigation showed that RNDs and mobile genetic elements content correlated with human population impact.

scholarly journals A glyphosate-based herbicide cross-selects for antibiotic resistance genes in bacterioplankton communities

2021 ◽  
Author(s):  
Naíla Barbosa da Costa ◽  
Marie-Pier Hébert ◽  
Vincent Fugère ◽  
Yves Terrat ◽  
Gregor Fussmann ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Resistance Genes ◽  
Bacterial Communities ◽  
Antibiotic Resistance Genes ◽  
Efflux Pumps ◽  
Cross Resistance ◽  
Resistant Bacteria ◽  
Metagenomic Sequencing ◽  
Resistance Mutations ◽  
Variation Explained

Agrochemicals often contaminate freshwater bodies, affecting microbial communities that underlie aquatic food webs. For example, Roundup, a widely-used glyphosate-based herbicide (GBH), has the potential to indirectly select for antibiotic resistant bacteria. Such cross-selection could occur, for example, if the same genes (e.g. encoding efflux pumps) confer resistance to both glyphosate and antibiotics. To test for cross-resistance in natural aquatic bacterial communities, we added Roundup to 1,000-L mesocosms filled with water from a pristine lake. Over 57 days, we tracked changes in bacterial communities with shotgun metagenomic sequencing, and annotated metagenome-assembled genomes (MAGs) for the presence of known antibiotic resistance genes (ARGs), plasmids, and resistance mutations in the enzyme targeted by glyphosate (enolpyruvyl-shikimate-3-phosphate synthase; EPSPS). We found that high doses of GBH significantly increased ARG frequency and selected for multidrug efflux pumps in particular. The relative abundance of MAGs after a high dose of GBH was predictable based on the number of ARGs encoded in their genomes (17% of variation explained) and, to a lesser extent, by resistance mutations in EPSPS (2% of variation explained). Together, these results indicate that GBHs have the potential to cross-select for antibiotic resistance in natural freshwater bacteria.

scholarly journals Antibiotic Resistance Genes in Phage Particles from Antarctic and Mediterranean Seawater Ecosystems

2020 ◽  
Vol 8 (9) ◽  
pp. 1293
Author(s):  
Pedro Blanco-Picazo ◽  
Gabriel Roscales ◽  
Daniel Toribio-Avedillo ◽  
Clara Gómez-Gómez ◽  
Conxita Avila ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Resistance Genes ◽  
Bacterial Communities ◽  
Anthropogenic Activities ◽  
Antibiotic Resistance Genes ◽  
Mediterranean Area ◽  
Mediterranean Coast ◽  
Anthropogenic Pressure ◽  
The Mediterranean ◽  
The Antarctic

Anthropogenic activities are a key factor in the development of antibiotic resistance in bacteria, a growing problem worldwide. Nevertheless, antibiotics and resistances were being generated by bacterial communities long before their discovery by humankind, and might occur in areas without human influence. Bacteriophages are known to play a relevant role in the dissemination of antibiotic resistance genes (ARGs) in aquatic environments. In this study, five ARGs (blaTEM, blaCTX-M-1, blaCTX-M-9, sul1 and tetW) were monitored in phage particles isolated from seawater of two different locations: (i) the Mediterranean coast, subjected to high anthropogenic pressure, and (ii) the Antarctic coast, where the anthropogenic impact is low. Although found in lower quantities, ARG-containing phage particles were more prevalent among the Antarctic than the Mediterranean seawater samples and Antarctic bacterial communities were confirmed as their source. In the Mediterranean area, ARG-containing phages from anthropogenic fecal pollution might allow ARG transmission through the food chain. ARGs were detected in phage particles isolated from fish (Mediterranean, Atlantic, farmed, and frozen), the most abundant being β-lactamases. Some of these particles were infectious in cultures of the fecal bacteria Escherichia coli. By serving as ARG reservoirs in marine environments, including those with low human activity, such as the Antarctic, phages could contribute to ARG transmission between bacterial communities.

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