Characterisation of penA and tetM resistance genes of Neisseria gonorrhoeae isolated in southern Africa - epidemiological monitoring and resistance development

Objective. To investigate penA and tetM resistance gene variation of Neisseria gonorrhoeae in order to define gene types for epidemiological monitoring and resistance development. Design. Isolates of N. gonorrhoeae which were susceptible and resistant to penicillin and/or tetracycline were selected. Strains comprised South African isolates (22 from Bloemfontein, 13 from Transvaal, 20 from the Cape) and 15 Botswana and 4 Namibia isolates. The penA genes (2 kb) of all strains and tetM genes (765 bp) of 11 high-level tetracycline-resistant strains were amplified and restricted with Hpall. Results and conclusions. Twelve different Hpall fingerprint patterns were obtained from the 74 isolates analysed for penicillin-binding protein (PBP) 2 gene (penA) alterations. Focusing on the transpeptidase domain, 25 isolates (3 whole gene patterns, minimal inhibitory concentrations (MICs) ~ 0,03 - 0,125 ug/ml) had restriction sites equivalent to those previously described for a susceptible strain. Of the remaining 9 PBP 2 'gene groups, 25 strains fell into a designated group E. Penicillin/ penicillin + clavulanic acid MICs determined on these group E isolates gave a range of 0,125 - 2,0 ug/ml, although MICs against 4 strains were ~ 0,03 ug/ml. MICs of penicillin/penicillin + c1avulanic acid for the 24 isolates that contained altered PBP 2 transpeptidase gene regions not designated group E were only ~ 0,03 - 0,125 ug/ml. The lack of a Hpall restriction site at nucleotide 1934 in the PBP 2 gene of group E strains was indicative of a small terminal region of N. cinerea DNA. This gene block, which was found in all the southern African areas studied, appears to predispose isolates to increased penicillin resistance. The 25,2 MDa conjugative plasmid carrying the tetM resistance determinant was readily demonstrated in 11 Botswana Namibia isolates exhibiting high-level resistance to tetracycline (MICs > 16 ug/ml). The tetM gene was shown to be of the American type

Modeling the Effects of Future Growing Demand for Charcoal in the Tropics

Global demand for charcoal is increasing mainly due to urban population in developing countries. More than half the global population now lives in cities, and urban-dwellers are restricted to charcoal use because of easiness of production, access, transport, and tradition. Increasing demand for charcoal, however, may lead to increasing impacts on forests, food, and water resources, and may even create additional pressures on the climate system. Here we assess how different charcoal scenarios based on the Shared Socio-economic Pathways (SSP) relate to potential biomass supply. For this, we use the energy model TIMER to project the demand for fuelwood and charcoal for different socio-economic pathways for urban and rural populations, globally, and for four tropical regions (Central America, South America, Africa and Indonesia). Second, we assess whether the biomass demands for each scenario can be met with current and projected forest biomass estimated with remote sensing and modeled Net Primary Productivity (NPP) using a Dynamic Global Vegetation Model (LPJ-GUESS). Currently one third of residential energy use is based on traditional bioenergy, including charcoal. Globally, biomass needs by urban households by 2100 under the most sustainable scenario, SSP1, are of 14.4 mi ton biomass for charcoal plus 17.1 mi ton biomass for fuelwood (31.5 mi ton biomass in total). Under SSP3, the least sustainable scenario, we project a need of 205 mi tons biomass for charcoal plus 243.8 mi ton biomass for fuelwood by 2100 (total of 450 mi ton biomass). Africa and South America contribute the most for this biomass demand, however, all areas are able to meet the demand. We find that the future of the charcoal sector is not dire. Charcoal represents a small fraction of the energy requirements, but its biomass demands are disproportionate and in some regions require a large fraction of forest. This could be because of large growing populations moving to urban areas, conversion rates, production inefficiencies, and regions that despite available alternative energy sources still use a substantial amount of charcoal. We present a framework that combines Integrated Assessment Models and local conditions to assess whether a sustainable sector can be achieved

The role of peatland degradation, protection and restoration for climate change mitigation in the SSP scenarios

Peatlands only cover a small fraction of the global land surface (∼3%) but store large amounts of carbon (∼600 GtC). Drainage of peatlands for agriculture results in the decomposition of organic matter, leading to greenhouse gas (GHG) emissions. As a result, degraded peatlands are currently responsible for 2%–3% of global anthropogenic emissions. Preventing further degradation of peatlands and restoration (i.e. rewetting) are therefore important for climate change mitigation. In this study, we show that land-use change in three SSP scenarios with optimistic, recent trends, and pessimistic assumptions leads to peatland degradation between 2020 and 2100 ranging from −7 to +10 Mha (−23% to +32%), and a continuation or even an increase in annual GHG emissions (−0.1 to +0.4 GtCO2-eq yr−1). In default mitigation scenarios without a specific focus on peatlands, peatland degradation is reduced due to synergies with forest protection and afforestation policies. However, this still leaves large amounts of GHG emissions from degraded peatlands unabated, causing cumulative CO2 emissions from 2020 to 2100 in an SSP2-1.5 °C scenario of 73 GtCO2. In a mitigation scenario with dedicated peatland restoration policy, GHG emissions from degraded peatlands can be reduced to nearly zero without major effects on projected land-use dynamics. This underlines the opportunity of peatland protection and restoration for climate change mitigation and the need to synergistically combine different land-based mitigation measures. Peatland location and extent estimates vary widely in the literature; a sensitivity analysis implementing various spatial estimates shows that especially in tropical regions degraded peatland area and peatland emissions are highly uncertain. The required protection and mitigation efforts are geographically unequally distributed, with large concentrations of peatlands in Russia, Europe, North America and Indonesia (33% of emission reductions are located in Indonesia). This indicates an important role for only a few countries that have the opportunity to protect and restore peatlands with global benefits for climate change mitigation

Development of chemical emission scenarios using the Shared Socio-economic Pathways

The widespread use of chemicals has led to significant water quality concerns, and their use is still increasing. Hence, there is an urgent need to understand the possible future trends in chemical emissions to water systems. This paper proposes a general framework for developing emission scenarios for chemicals to water using the Shared Socio-economic Pathways (SSPs) based on an emission-factor approach. The proposed approach involves three steps: (i) identification of the main drivers of emissions, (ii) quantification of emission factors based on analysis of publicly available data, and (iii) projection of emissions based on projected changes in the drivers and emission factors. The approach was tested in Europe for five chemical groups and on a national scale for five specific chemicals representing pharmaceuticals, pesticides, and industrial chemicals. The resulting emission scenarios show widely diverging trends of increased emissions by 240% for ibuprofen in SSP3 (regional rivalry) to a 68% decrease for diclofenac in SSP1 (sustainable development) by 2050. While emissions typically decrease in SSP1, they follow the historical trend in SSP2 (middle-of-the-road scenario) and show an increase in the regional rivalry scenario SSP3 for most selected chemicals. Overall, the framework allows understanding of future chemical emissions trends as a function of the socio-economic trends as captured in the SSPs. Our scenarios for chemical emissions can thus be used to model future aqueous emissions to support risk assessment. While the framework can be easily extended to other pharmaceuticals and pesticides, it heavily leans on the availability and quality of historical emission data and a detailed understanding of emission sources for industrial chemicals

Origin and putative colonization routes for invasive rodent taxa in the democratic Republic of Congo

The threat posed by biological invasions is well established. An important consideration in preventing the spread of invasives and also subsequent introductions lies in understanding introduction pathways. The Democratic Republic of the Congo (DRC) houses a large percentage of the world's biodiversity, yet no national strategy exists to deal with the growing number of invasive alien species. Amongst these are the house mouse and ship and Norwegian rats. By comparing our result to published data, we show that species were possibly introduced into the DRC via two routes. The first is via the western seaport at Kinshasa where specimens of M. m. domesticus and R. rattus on the western and northwestern side of the DRC show ties with European haplotypes. The second is via the east where specimens of R. rattus appear linked to Arab and southeast Asian haplotypes. Future work should consider more comprehensive sampling throughout the DRC to more accurately investigate the occurrence of invasive species throughout the country as well as extend sampling to other African countries

The use of non-invasive stool tests for verification of Helicobacter pylori eradication and clarithromycin resistance

Background: Clarithromycin resistance of Helicobacter pylori (H. pylori) represents a major challenge in eradication therapy. In this study, we assessed if non-invasive stool tests can be used to verify successful H. pylori eradication and determine clarithromycin resistance. Materials and methods:In this prospective study, patients undergoing urea breath testing (UBT) for confirmation of H. pylori eradication were asked to collect the stool as both a dry fecal sample and fecal immunochemical test (FIT). Stool H. pylori antigen testing (SAT) was performed on these samples and assessed for its accuracy in eradication verification. Type and duration of antibiotic treatment were retrospectively collected from patient records and compared with clarithromycin resistance determined by PCR of stool samples. Results: H. pylori eradication information was available for a total of 145 patients (42.7% male, median age: 51.2). Successful eradication was achieved in 68.1% of patients. SAT on FIT samples had similar accuracy for eradication assessment compared to dry fecal samples, 72.1% [95% CI 61.4–81.2] versus 72.2% [95% CI 60.9–81.7]. Clarithromycin resistance rate was 13.4%. Conclusion: H. pylori antigen testing on FIT stool samples to verify H. pylori eradication is feasible and has similar accuracy as H. pylori antigen testing on dry stool samples. Dry stool, but not FIT, was suitable for non-invasive identification of H. pylori clarithromycin resistance by rt-PCR personalizing antibiotic treatment strategies without the need for invasive diagnostics is desirable, as the cure rate of first-line empirical H. pylori treatment remains low.</p

The Scenario Model Intercomparison Project (ScenarioMIP) for CMIP6

Model experiment description paperProjections of future climate change play a fundamental role in improving understanding of the climate system as well as characterizing societal risks and response options. The Scenario Model Intercomparison Project (ScenarioMIP) is the primary activity within Phase 6 of the Coupled Model Intercomparison Project (CMIP6) that will provide multi-model climate projections based on alternative scenarios of future emissions and land use changes produced with integrated assessment models. In this paper, we describe ScenarioMIP's objectives, experimental design, and its relation to other activities within CMIP6. The ScenarioMIP design is one component of a larger scenario process that aims to facilitate a wide range of integrated studies across the climate science, integrated assessment modeling, and impacts, adaptation, and vulnerability communities, and will form an important part of the evidence base in the forthcoming Intergovernmental Panel on Climate Change (IPCC) assessments. At the same time, it will provide the basis for investigating a number of targeted science and policy questions that are especially relevant to scenario-based analysis, including the role of specific forcings such as land use and aerosols, the effect of a peak and decline in forcing, the consequences of scenarios that limit warming to below 2 °C, the relative contributions to uncertainty from scenarios, climate models, and internal variability, and long-term climate system outcomes beyond the 21st century. To serve this wide range of scientific communities and address these questions, a design has been identified consisting of eight alternative 21st century scenarios plus one large initial condition ensemble and a set of long-term extensions, divided into two tiers defined by relative priority. Some of these scenarios will also provide a basis for variants planned to be run in other CMIP6-Endorsed MIPs to investigate questions related to specific forcings. Harmonized, spatially explicit emissions and land use scenarios generated with integrated assessment models will be provided to participating climate modeling groups by late 2016, with the climate model simulations run within the 2017-2018 time frame, and output from the climate model projections made available and analyses performed over the 2018-2020 period.CRESCENDO project members (V. Eyring, P. Friedlingstein, E. Kriegler, R. Knutti, J. Lowe, K. Riahi, D. van Vuuren) acknowledge funding received from the Horizon 2020 European Union’s Framework Programme for Research and Innovation under grant agreement no. 641816. C. Tebaldi, G. A. Meehl and B. M. Sanderson acknowledge the support of the Regional and Global Climate Modeling Program (RGCM) of the U.S. Department of Energy’s, Office of Science (BER), Cooperative Agreement DE-FC02-97ER6240

Extending shared socio-economic pathways for pesticide use in Europe: Pest-Agri-SSPs

While pesticides are essential to agriculture and food systems to sustain current production levels, they also lead to significant environmental impacts. The use of pesticides is constantly increasing globally, driven mainly by a further intensification of agriculture, despite stricter regulations and higher pesticide effectiveness. To further the understanding of future pesticide use and make informed farm-to-policy decisions, we developed Pesticide Agricultural Shared Socio-economic Pathways (Pest-AgriSSPs) in six steps. The Pest-Agri-SSPs are developed based on an extensive literature review and expert feedback approach considering significant climate and socio-economic drivers from farm to continental scale in combination with multiple actors impacting them. In literature, pesticide use is associated with farmer behaviour and practices, pest damage, technique and efficiency of pesticide application, agricultural policy and agriculture demand and production. Here, we developed PestAgri-SSPs upon this understanding of pesticide use drivers and relating them to possible agriculture development as described by the Shared Socio-economic Pathways for European agriculture and food systems (Eur-Agri-SSPs).The Pest-AgriSSPs are developed to explore European pesticide use in five scenarios representing low to high challenges to mitigation and adaptation up to 2050. The most sustainable scenario (Pest-Agri-SSP1) shows a decrease in pesticide use owing to sustainable agricultural practices, technological advances and better implementation of agricultural policies. On the contrary, the Pest-Agri-SSP3 and Pest-Agri-SSP4 show a higher increase in pesticide use resulting from higher challenges from pest pressure, resource depletion and relaxed agricultural policies. Pest-Agri-SSP2 presents a stabilised pesticide use resulting from stricter policies and slow transitions by farmers to sustainable agricultural practices. At the same time, pest pressure, climate change and food demand pose serious challenges. Pest-Agri-SSP5 shows a decrease in pesticide use for most drivers, influenced mainly by rapid technological development and sustainable agricultural practices. However, Pest-Agri-SSP5 also presents a relatively low rise in pesticide use driven by agricultural demand, production, and climate change. Our results highlight the need for a holistic approach to tackle pesticide use, considering the identified drivers and future developments. The storylines and qualitative assessment provide a platform to make quantitative assumptions for numerical modelling and evaluating policy targets

Impacts of climate change on agricultural production in arid areas (ICCAP) -The possible effect of climatic changes on the irrigated agriculture of Seyhan Basin-

We present a new framework for modelling the complexities of food and water security under globalisation. The framework sets out a method to capture regional and sectoral interdependencies and cross-scale feedbacks within the global food system that contribute to emergent water use patterns. The framework integrates aspects of existing models and approaches in the fields of hydrology and integrated assessment modelling. The core of the framework is a multi-agent network of city agents connected by infrastructural trade networks. Agents receive socio-economic and environmental constraint information from integrated assessment models and hydrological models respectively and simulate complex, socio-environmental dynamics that operate within those constraints. The emergent changes in food and water resources are aggregated and fed back to the original models with minimal modification of the structure of those models. It is our conviction that the framework presented can form the basis for a new wave of decision tools that capture complex socio-environmental change within our globalised world. In doing so they will contribute to illuminating pathways towards a sustainable future for humans, ecosystems and the water they share