| 1. |
- Feldbauer, Johannes, et al.
(author)
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Ensemble of models shows coherent response of a reservoir's stratification and ice cover to climate warming
- 2022
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In: Aquatic Sciences. - : Springer Nature. - 1015-1621 .- 1420-9055. ; 84:4
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Journal article (peer-reviewed)abstract
- Water temperature, ice cover, and lake stratification are important physical properties of lakes and reservoirs that control mixing as well as bio-geo-chemical processes and thus influence the water quality. We used an ensemble of vertical one-dimensional hydrodynamic lake models driven with regional climate projections to calculate water temperature, stratification, and ice cover under the A1B emission scenario for the German drinking water reservoir Lichtenberg. We used an analysis of variance method to estimate the contributions of the considered sources of uncertainty on the ensemble output. For all simulated variables, epistemic uncertainty, which is related to the model structure, is the dominant source throughout the simulation period. Nonetheless, the calculated trends are coherent among the five models and in line with historical observations. The ensemble predicts an increase in surface water temperature of 0.34 K per decade, a lengthening of the summer stratification of 3.2 days per decade, as well as decreased probabilities of the occurrence of ice cover and winter inverse stratification by 2100. These expected changes are likely to influence the water quality of the reservoir. Similar trends are to be expected in other reservoirs and lakes in comparable regions.
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| 2. |
- Abramova, Anna, 1990, et al.
(author)
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A global baseline for qPCR-determined antimicrobial resistance gene prevalence across environments
- 2023
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In: Environment International. - 0160-4120 .- 1873-6750. ; 178
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Journal article (peer-reviewed)abstract
- The environment is an important component in the emergence and transmission of antimicrobial resistance (AMR). Despite that, little effort has been made to monitor AMR outside of clinical and veterinary settings. Partially, this is caused by a lack of comprehensive reference data for the vast majority of environments. To enable monitoring to detect deviations from the normal background resistance levels in the environment, it is necessary to establish a baseline of AMR in a variety of settings. In an attempt to establish this baseline level, we here performed a comprehensive literature survey, identifying 150 scientific papers containing relevant qPCR data on antimicrobial resistance genes (ARGs) in environments associated with potential routes for AMR dissemination. The collected data included 1594 samples distributed across 30 different countries and 12 sample types, in a time span from 2001 to 2020. We found that for most ARGs, the typically reported abundances in human impacted environments fell in an interval from 10-5 to 10-3 copies per 16S rRNA, roughly corresponding to one ARG copy in a thousand bacteria. Altogether these data represent a comprehensive overview of the occurrence and levels of ARGs in different environments, providing background data for risk assessment models within current and future AMR monitoring frameworks.
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| 3. |
- Abramova, Anna, 1990, et al.
(author)
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Meta-analysis reveals the global picture of antibiotic resistance gene prevalence across environments
- 2022
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In: bioRXIV. - : Cold Spring Harbor Laboratory.
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Journal article (other academic/artistic)abstract
- The environment is an important component in the emergence and transmission of antimicrobial resistance (AMR). Despite that, current AMR monitoring initiatives lack comprehensive reference data for the vast majority of environments. To enable monitoring to detect deviations from the normal background resistance levels in the environment, it is necessary to establish the typical baseline of AMR in a variety of settings. In an attempt to establish this baseline level, we here performed a comprehensive literature survey across 2516 scientific papers, 150 of which contained relevant qPCR data on antibiotic resistance genes (ARGs) in environments associated with potential routes of AMR dissemination. The collected data include 1487 samples distributed across 30 different countries and 17 environmental types, in a time span from 2005 to 2018. More than 330 different genes were identified from the collected studies. Most surveyed environments contained a diverse set of ARGs, but generally at low abundances. We used linear mixed models and overrepresentation analysis to identify time trends and associations between ARGs and specific environments. Altogether these data represent a comprehensive overview of the occurrence and levels of ARGs in different environments, providing background data for risk assessment models within current and future AMR monitoring frameworks.
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| 4. |
- Anjum, Muna F, et al.
(author)
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The potential of using E. coli as an indicator for the surveillance of antimicrobial resistance (AMR) in the environment
- 2021
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In: Current Opinion in Microbiology. - : Elsevier. - 1369-5274 .- 1879-0364. ; 64, s. 152-158
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Research review (peer-reviewed)abstract
- To understand the dynamics of antimicrobial resistance (AMR), in a One-Health perspective, surveillance play an important role. Monitoring systems already exist in the human health and livestock sectors, but there are no environmental monitoring programs. Therefore there is an urgent need to initiate environmental AMR monitoring programs nationally and globally, which will complement existing systems in different sectors. However, environmental programs should not only identify anthropogenic influences and levels of AMR, but they should also allow for identification of transmissions to and from human and animal populations. In the current review we therefore propose using antimicrobial resistant Escherichia coli as indicators for monitoring occurrence and levels of AMR in the environment, including wildlife.
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| 5. |
- Eckert, EM, et al.
(author)
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Every fifth published metagenome is not available to science.
- 2020
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In: PLoS biology. - : Public Library of Science (PLoS). - 1545-7885. ; 18:4
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Journal article (peer-reviewed)abstract
- Have you ever sought to use metagenomic DNA sequences reported in scientific publications? Were you successful? Here, we reveal that metagenomes from no fewer than 20% of the papers found in our literature search, published between 2016 and 2019, were not deposited in a repository or were simply inaccessible. The proportion of inaccessible data within the literature has been increasing year-on-year. Noncompliance with Open Data is best predicted by the scientific discipline of the journal. The number of citations, journal type (e.g., Open Access or subscription journals), and publisher are not good predictors of data accessibility. However, many publications in high-impact factor journals do display a higher likelihood of accessible metagenomic data sets. Twenty-first century science demands compliance with the ethical standard of data sharing of metagenomes and DNA sequence data more broadly. Data accessibility must become one of the routine and mandatory components of manuscript submissions-a requirement that should be applicable across the increasing number of disciplines using metagenomics. Compliance must be ensured and reinforced by funders, publishers, editors, reviewers, and, ultimately, the authors.
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| 6. |
- Heß, Stefanie, et al.
(author)
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Sewage from Airplanes Exhibits High Abundance and Diversity of Antibiotic Resistance Genes
- 2019
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In: Environmental Science & Technology. - : American Chemical Society (ACS). - 0013-936X .- 1520-5851. ; 53:23, s. 13898-13905
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Journal article (peer-reviewed)abstract
- Airplane sanitary facilities are shared by an international audience. We hypothesized the corresponding sewage to be an extraordinary source of antibiotic-resistant bacteria (ARB) and resistance genes (ARG) in terms of diversity and quantity. Accordingly, we analyzed ARG and ARB in airplane-borne sewage using complementary approaches: Metagenomics, quantitative polymerase chain reaction (qPCR), and cultivation. For the purpose of comparison, we also quantified ARG and ARB in the inlets of municipal treatment plants with and without connection to airports. As expected, airplane sewage contained an extraordinarily rich set of mobile ARG, and the relative abundances of genes were mostly increased compared to typical raw sewage of municipal origin. Moreover, combined resistance against third-generation cephalosporins, fluorochinolones, and aminoglycosides was unusually common (28.9%) among Escherichia coli isolated from airplane sewage. This percentage exceeds the one reported for German clinical isolates by a factor of 8. Our findings suggest that airplane-borne sewage can effectively contribute to the fast and global spread of antibiotic resistance.
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| 7. |
- Kampouris, Ioannis D, et al.
(author)
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The global groundwater resistome: core ARGs and their dynamics – an in silico re-analysis of publicly available groundwater metagenomes
- 2022
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Journal article (other academic/artistic)abstract
- Despite the importance of groundwater environments as drinking water resources, there is currently no comprehensive picture of the global levels of antibiotic resistance genes in groundwater. Moreover, the biotic and abiotic factors that might shape the groundwater resistome remain to be explored on a global scale. Herein, we attempted to fill this knowledge gap by in silico re-analysis of publicly available global groundwater metagenomes. We first investigated the occurrence of antibiotic resistance genes (ARGs) to define the core groundwater resistome. We further tested whether the ARG dissemination in the pristine groundwater environments could be explained by natural ecological processes such as competition between fungal and bacterial taxa. Six ARGs encoding resistance to aminoglycosides (aph3'), aph3''), sulfonamides (sul1, sul2), and beta-lactams (blaOXA, blaTEM) occurred in at least 50% of samples at high abundance, thereby constituting the core groundwater resistome. ARG abundances differed significantly between countries and only weakly correlated with bacterial community composition. While only limited effects of anthropogenic impacts could be observed, ecological interactions played a significant role in shaping the abundance patterns of at least a number of the core ARGs. Fungal abundance positively correlated with blaTEM and blaOXA abundance, ARGs that confer resistance to beta-lactams, regularly produced by fungi. However, no direct correlation was determined for the remainder of the core ARGs. Still, using co-occurrence network analysis we identified that the fungal abundance acted as a hub-node that included blaOXA and blaTEM, but also indirectly contributed to the abundance of aminoglycoside ARG aph3'). Hence, interactions between bacteria and fungi including potential antibiotic production can contribute to the dissemination of ARGs in groundwater environments. Consequently, fungal/bacterial SSU ratio could serve as an indicator for the abundance of certain ARGs in the pristine groundwater environments.
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