Search

We present CAMELS-CH (Catchment Attributes and MEteorology for Large-sample Studies – Switzerland), a large-sample hydro-meteorological data set for hydrologic Switzerland in central Europe. This domain covers 331 basins within Switzerland and neighboring countries. About one-third of the catchments are located in Austria, France, Germany and Italy. As an Alpine country, Switzerland covers a vast diversity of landscapes, including mountainous environments, karstic regions, and several strongly cultivated regions, along with a wide range of hydrological regimes, i.e., catchments that are glacier-, snow- or rain dominated. Similar to existing data sets, CAMELS-CH comprises dynamic hydro-meteorological variables and static catchment attributes. CAMELS-CH (Höge et al., 2023; available at https://doi.org/10.5281/zenodo.7784632) encompasses 40 years of data between 1 January 1981 and 31 December 2020, including daily time series of stream flow and water levels, and of meteorological data such as precipitation and air temperature. It also includes daily snow water equivalent data for each catchment starting from 2 September 1998. Additionally, we provide annual time series of land cover change and glacier evolution per catchment. The static catchment attributes cover location and topography, climate, hydrology, soil, hydrogeology, geology, land use, human impact and glaciers. This Swiss data set complements comparable publicly accessible data sets, providing data from the “water tower of Europe”.

Assessments of climate change impacts on runoff regimes are essential to climate change adaptation and mitigation planning. Changing runoff regimes and thus changing seasonal patterns of water availability strongly influence various economic sectors such as agriculture, energy production, and fishery and also affect river ecology. In this study, we use new transient hydrological scenarios driven by the most up-to-date local climate projections for Switzerland, the Swiss Climate Change Scenarios. These provide detailed information on changes in runoff regimes and their time of emergence for 93 rivers in Switzerland under three Representative Concentration Pathways (RCPs): RCP2.6, RCP4.5, and RCP8.5. These transient scenarios also allow changes to be framed as a function of global mean temperature. The new projections for seasonal runoff changes largely confirm the sign of changes in runoff from previous hydrological scenarios with increasing winter runoff and decreasing summer and autumn runoff. Spring runoff is projected to increase in high-elevation catchments and to decrease in lower-lying catchments. Despite the increases in winter and some increases in spring, the annual mean runoff is projected to decrease in most catchments. Compared to lower-lying catchments, runoff changes in high-elevation catchments (above 1500 m a.s.l.) are larger in winter, spring, and summer due to the large influence of reduced snow accumulation and earlier snowmelt and glacier melt. The changes in runoff and the agreement between climate models on the sign of change both increase with increasing global mean temperatures and higher-emission scenarios. This amplification highlights the importance of climate change mitigation. The time of emergence is the time when the climate signal emerges significantly from natural variability. Under RCP8.5, times of emergence were found early, before the period 2036–2065, in winter and summer for catchments with mean altitudes above 1500 m a.s.l. Significant changes in catchments below 1500 m a.s.l. emerge later in the century. Not all catchments show significant changes in the distribution of seasonal means; thus, no time of emergence could be determined in these catchments. Furthermore, the significant changes of seasonal mean runoff are not persistent over time in some catchments due to nonlinear changes in runoff.

Future changes in river runoff will impact many sectors such as agriculture, energy production, or ecosystems. Here, we study changes in the seasonality, frequency, and magnitude of moderate low and high flows and their time of emergence. The time of emergence indicates the timing of significant changes in the flow magnitudes. Daily runoff is simulated for 93 Swiss catchments for the period 1981–2099 under Representative Concentration Pathway 8.5 with 20 climate model chains from the most recent transient Swiss Climate Change Scenarios. In the present climate, annual low flows typically occur in the summer half-year in lower-lying catchments ( m a.s.l.) and in the winter half-year in Alpine catchments (>1500 m a.s.l.). By the end of the 21st century, annual low flows are projected to occur in late summer and early autumn in most catchments. This indicates that decreasing precipitation and increasing evapotranspiration in summer and autumn exceed the water contributions from other processes such as snowmelt and glacier melt. In lower-lying catchments, the frequency of annual low flows increases, but their magnitude decreases and becomes more severe. In Alpine catchments, annual low flows occur less often and their magnitude increases. The magnitude of seasonal low flows is projected to decrease in the summer half-year in most catchments and to increase in the winter half-year in Alpine catchments. Early time of emergence is found for annual low flows in Alpine catchments in the 21st century due to early changes in low flows in the winter half-year. In lower-lying catchments, significant changes in low flows emerge later in the century. Annual high flows occur today in lower-lying catchments in the winter half-year and in Alpine catchments in the summer half-year. Climate change will change this seasonality mainly in Alpine catchments with a shift towards earlier seasonality in summer due to the reduced contribution of snowmelt and glacier melt in summer. Annual high flows tend to occur more frequent, and their magnitude increases in most catchments except some Alpine catchments. The magnitude of seasonal high flows in most catchments is projected to increase in the winter half-year and to decrease in the summer half-year. However, the climate model agreement on the sign of change in moderate high flows is weak.

Determining the role of different precipitation periods for peak discharge generation is crucial for both projecting future changes in flood probability and for short- and medium-range flood forecasting. In this study, catchment-averaged daily precipitation time series are analyzed prior to annual peak discharge events (floods) in Switzerland. The high number of floods considered – more than 4000 events from 101 catchments have been analyzed – allows to derive significant information about the role of antecedent precipitation for peak discharge generation. Based on the analysis of precipitation times series, a new separation of flood-related precipitation periods is proposed: (i) the period 0 to 1 day before flood days, when the maximum flood-triggering precipitation rates are generally observed, (ii) the period 2 to 3 days before flood days, when longer-lasting synoptic situations generate "significantly higher than normal" precipitation amounts, and (iii) the period from 4 days to 1 month before flood days when previous wet episodes may have already preconditioned the catchment. The novelty of this study lies in the separation of antecedent precipitation into the precursor antecedent precipitation (4 days before floods or earlier, called PRE-AP) and the short range precipitation (0 to 3 days before floods, a period when precipitation is often driven by one persistent weather situation like e.g., a stationary low-pressure system). A precise separation of "antecedent" and "peak-triggering" precipitation is not attempted. Instead, the strict definition of antecedent precipitation periods permits a direct comparison of all catchments. The precipitation accumulating 0 to 3 days before an event is the most relevant for floods in Switzerland. PRE-AP precipitation has only a weak and region-specific influence on flood probability. Floods were significantly more frequent after wet PRE-AP periods only in the Jura Mountains, in the western and eastern Swiss plateau, and at the outlet of large lakes. As a general rule, wet PRE-AP periods enhance the flood probability in catchments with gentle topography, high infiltration rates, and large storage capacity (karstic cavities, deep soils, large reservoirs). In contrast, floods were significantly less frequent after wet PRE-AP periods in glacial catchments because of reduced melt. For the majority of catchments however, no significant correlation between precipitation amounts and flood occurrences is found when the last 3 days before floods are omitted in the precipitation amounts. Moreover, the PRE-AP was not higher for extreme floods than for annual floods with a high frequency and was very close to climatology for all floods. The fact that floods are not significantly more frequent nor more intense after wet PRE-AP is a clear indicator of a short discharge memory of Pre-Alpine, Alpine and South Alpine Swiss catchments. Our study poses the question whether the impact of long-term precursory precipitation for floods in such catchments is not overestimated in the general perception. The results suggest that the consideration of a 3–4 days precipitation period should be sufficient to represent (understand, reconstruct, model, project) Swiss Alpine floods.

This work aimed to investigate interactions between antibody-opsonized SARS-CoV-2 and monocytes enriched from human peripheral blood mononuclear cells (PBMC) to determine whether antibody dependent enhancement might contribute to the pathophysiology of COVID-19. Pre-incubation of SARS-CoV-2 with sera from hospitalized COVID-19 patients led to significantly increased virus uptake and viral replication in monocytes. Remarkably, SARS-CoV-2 pre-incubated with sera from patients with severe COVID-19 but not those with mild disease or post vaccination strongly increased IL-6 secretion by monocytes. Antibody dependent viral uptake was partially inhibited by monoclonal anti-FcγRIIa antibody whereas IL-6 secretion was completely abolished. FcγRIIa preferentially binds IgG2, and sera from patients with severe COVID-19 contained lower IgG2 levels as compared to mild COVID-19 cases whereas IgG1 levels were increased. These data suggests that FcγRIIa-mediated binding of antibody-opsonized SARS-CoV-2 critically impacts monocytic inflammatory cytokine release and COVID-19 pathophysiology.

As many gastro-intestinal pathogens, the majority of Clostridioides difficile strains express flagella together with a complete chemotaxis system. The resulting swimming motility is likely contributing to the colonization success of this important pathogen. In contrast to the well investigated general energy metabolism of C. difficile , little is known about the metabolic requirements for maintaining the ion motive force across the membrane, which in turn powers the flagellar motor. We studied here systematically the effect of various amino acids and carbohydrates on the swimming velocity of C. difficile using video microscopy in conjunction with a software based quantification of the swimming speed. Removal of individual amino acids from the medium identified proline and cysteine as the most important amino acids that power swimming motility. Glycine, which is as proline one of the few amino acids that are reduced in Stickland reactions, was not critical for swimming motility. This suggests that the ion motive force that powers the flagellar motor, is critically depending on proline reduction. A maximal and stable swimming motility was achieved with only four compounds, including the amino acids proline, cysteine and isoleucine together with a single, but interchangeable carbohydrate source such as glucose, succinate, mannose, ribose, pyruvate, trehalose, or ethanolamine. We expect that the identified "minimal motility medium" will be useful in future investigations on the flagellar motility and chemotactic behavior in C. difficile , particularly for the unambiguous identification of chemoattractants., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2023 Schwanbeck, Oehmig, Groß and Bohne.)

Introduction: Chronic activation of the mineralocorticoid receptor (MR) leads to pathological processes like inflammation and fibrosis during cardiorenal disease. Modulation of immunological processes in the heart or kidney may serve as a mechanistic and therapeutic interface in cardiorenal pathologies. In this study, we investigated anti-inflammatory/-fibrotic and immunological effects of the selective nonsteroidal MR antagonists finerenone (FIN) in the deoxycorticosterone acetate (DOCA)-salt model., Methods: Male C57BL6/J mice were uninephrectomized and received a DOCA pellet implantation (2.4 mg/day) plus 0.9% NaCl in drinking water (DOCA-salt) or received a sham operation and were orally treated with FIN (10 mg/kg/day) or vehicle in a preventive study design. Five weeks after the procedure, blood pressure (BP), urinary albumin/creatinine ratio (UACR), glomerular and tubulointerstitial damage, echocardiographic cardiac function, as well as cardiac/renal inflammatory cell content by FACS analysis were assessed., Results: BP was significantly reduced by FIN. FACS analysis revealed a notable immune response due to DOCA-salt exposure. Especially, infiltrating renal RORγt γδ-positive T cells were upregulated, which was significantly ameliorated by FIN treatment. This was accompanied by a significant reduction of UACR in FIN-treated mice. In the heart, FIN reduced DOCA-salt-induced cardiac hypertrophy, cardiac fibrosis and led to an improvement of the global longitudinal strain. Cardiac actions of FIN were not associated with a regulation of cardiac RORγt γδ-positive T cells., Discussion/conclusion: The present study shows cardiac and renal protective effects of FIN in a DOCA-salt model. The cardiorenal protection was accompanied by a reduction of renal RORγt γδ T cells. The observed actions of FIN may provide a potential mechanism of its efficacy recently observed in clinical trials., (© 2022 S. Karger AG, Basel.)

Flagellar motility is important for the pathogenesis of many intestinal pathogens, allowing bacteria to move to their preferred ecological niche. Clostridioides difficile is currently the major cause for bacterial health care-associated intestinal infections in the western world. Most clinical strains produce peritrichous flagella and are motile in soft-agar. However, little knowledge exists on the C. difficile swimming behaviour and its regulation at the level of individual cells. We report here on the swimming strategy of C. difficile at the single cell level and its dependency on environmental parameters. A comprehensive analysis of motility parameters from several thousand bacteria was achieved with the aid of a recently developed bacterial tracking programme. C. difficile motility was found to be strongly dependent on the matrix elasticity of the medium. Long run phases of all four motile C. difficile clades were only observed in the presence of high molecular weight molecules such as polyvinylpyrrolidone (PVP) and mucin, which suggests an adaptation of the motility apparatus to the mucin-rich intestinal environment. Increasing mucin or PVP concentrations lead to longer and straighter runs with increased travelled distance per run and fewer turnarounds that result in a higher net displacement of the bacteria. The observed C. difficile swimming pattern under these conditions is characterised by bidirectional, alternating back and forth run phases, interrupted by a short stop without an apparent reorientation or tumbling phase. This motility type was not described before for peritrichous bacteria and is more similar to some previously described polar monotrichous bacteria., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2021 Schwanbeck, Oehmig, Groß, Zautner and Bohne.)

This study was performed as a head-to-head comparison of the performance characteristics of (1) two SARS-CoV-2-specific rapid antigen assays with real-time PCR as gold standard as well as (2) a fully automated high-throughput transcription-mediated amplification (TMA) assay and real-time PCR in a latent class analysis-based test comparison without a gold standard with several hundred samples in a low prevalence "real world" setting. Recorded sensitivity and specificity of the NADAL and the LumiraDx antigen assays and the Hologic Aptima SARS-CoV-2 TMA assay were 0.1429 (0.0194, 0.5835), 0.7644 (0.7016, 0.8174), and 0.7157 (0, 1) as well as 0.4545 (0.2022, 0.7326), 0.9954 (0.9817, 0.9988), and 0.9997 (not estimable), respectively. Agreement kappa between the positive results of the two antigen-based assays was 0.060 (0.002, 0.167) and 0.659 (0.492, 0.825) for TMA and real-time PCR. Samples with low viral load as indicated by cycle threshold (Ct) values > 30 were generally missed by both antigen assays, while 1:10 pooling suggested higher sensitivity of TMA compared to real-time PCR. In conclusion, both sensitivity and specificity speak in favor of the use of the LumiraDx rather than the NADAL antigen assay, while TMA results are comparably as accurate as PCR, when applied in a low prevalence setting.

Mobile genetic elements, such as plasmids, facilitate the spread of antibiotic resistance genes in Enterobacterales. In line with this, we investigated the plasmid-resistome of seven bla OXA-48 gene-carrying Klebsiella pneumoniae isolates, which were isolated between 2013 and 2014 at the University Medical Center in Göttingen, Germany. All isolates were subjected to complete genome sequencing including the reconstruction of entire plasmid sequences. In addition, phenotypic resistance testing was conducted. The seven isolates comprised both disease-associated isolates and colonizers isolated from five patients. They fell into two clusters of three sequence type (ST)101 and two ST11 isolates, respectively; and ST15 and ST23 singletons. The seven isolates harbored various plasmids of the incompatibility (Inc) groups IncF, IncL/M, IncN, IncR, and a novel plasmid chimera. All bla OXA-48 genes were encoded on the IncL/M plasmids. Of note, distinct phenotypical resistance patterns associated with different sets of resistance genes encoded by IncL/M and IncR plasmids were observed among isolates of the ST101 cluster in spite of high phylogenetic relatedness of the bacterial chromosomes, suggesting nosocomial transmission. This highlights the importance of plasmid uptake and plasmid recombination events for the fast generation of resistance variability after clonal transmission. In conclusion, this study contributes a piece in the puzzle of molecular epidemiology of resistance gene-carrying plasmids in K. pneumoniae in Germany.

Due to the beginning of vaccination against COVID-19, serological discrimination between vaccine-associated humoral response and serology-based surveillance of natural SARS-CoV-2 infections as well as breakthrough infections becomes an issue of relevance. Here, we assessed the differentiated effects of the application of an RNA vaccine using SARS-CoV-2 spike protein epitopes on the results of both anti-spike protein-based serology (EUROIMMUN) and anti-nucleocapsid-based serology (VIROTECH). A total of 80 serum samples from vaccinees acquired at different time points after vaccination was assessed. While positive or borderline serological response in the anti-spike protein assay was observed for all samples (90% both IgG and IgA, 6.3% IgA only, 3.8% borderline IgG only), only a single case of a falsely positive IgM was observed for the anti-nucleocapsid assay as expected due to this assay's specificity. Positive anti-spike protein antibodies were already detectable in the second week after the first dose of vaccination, with higher titers after the second dose of the vaccine. In conclusion, the combined application of anti-spike protein-based serology and anti-nucleocapsid-based serology will provide a useful option for the discrimination of vaccination response and natural infection.

Serological assays can contribute to the estimation of population proportions with previous immunologically relevant contact with the Severe Acute Respiratory Syndrome Corona Virus 2 (SARS-CoV-2) virus. In this study, we compared five commercially available diagnostic assays for the diagnostic identification of SARS-CoV-2-specific antibodies. Depending on the assessed immunoglobulin subclass, recorded sensitivity ranged from 17.0% to 81.9% with best results for immunoglobulin G. Specificity with blood donor sera ranged from 90.2% to 100%, with sera from EBV patients it ranged from 84.3% to 100%. Agreement from fair to nearly perfect was recorded depending on the immunoglobulin class between the assays, the with best results being found for immunoglobulin G. Only for this immunoglobulin class was the association between later sample acquisition times (about three weeks after first positive PCR results) and positive serological results in COVID-19 patients confirmed. In conclusion, acceptable and comparable reliability for the assessed immunoglobulin G-specific assays could be shown, while there is still room for improvement regarding the reliability of the assays targeting the other immunoglobulin classes.

Introduction: To efficiently monitor the COVID-19 pandemic for surveillance purposes, reliable serological rapid diagnostic tests (RDTs) are desirable for settings where well-established high-throughput bench-top solutions are not available. Here, we have evaluated such an RDT., Methods: We have assessed the Xiamen AmonMed Biotechnology COVID-19 IgM/IgG test kit (Colloidal gold) and the EUROIMMUN benchtop assay with serum samples from patients with polymerase chain reaction (PCR)-confirmed COVID-19 disease. Samples from patients with Epstein-Barr-virus (EBV) infection and blood donors were used for specificity testing., Results: For the colloid gold rapid test and the EUROIMMUN assay, the study indicated overall sensitivity of 15.2% and 67.4%, respectively, while specificity of 99.0% and 97.9% with the blood donor sera, as well as 100% and 96.8% with the EBV-patients, were observed, respectively. An association of the time period between positive PCR results and serum acquisition with serological test positivity could be observed for the immunologlobulin G subclass of the EUROIMMUN assay only., Conclusions: In spite of acceptable specificity of the assessed RDT, the detected poor sensitivity leaves room for improvement. The test results remain difficult to interpret and therefore the RDT can currently not be recommended for routine diagnostic or surveillance use.

Young children are frequently colonized with Clostridioides ( C. ) difficile . Depending on their resistance patterns, antibiotic treatment can facilitate gastrointestinal spreading in colonized individuals, potentially leading to transmission to others. C. difficile was isolated from stool samples from infants born in two hospitals in Göttingen and Darmstadt, Germany. All isolates were subjected to phenotypic antimicrobial resistance testing, PCR-based screening for toxin genes and mass spectrometry-based exclusion of ribotypes 027 and 176. Within an initial cohort of 324 neonates with a longitudinal survey of C. difficile , 137 strains were isolated from 48 individuals. Antimicrobial resistance was recorded against metronidazole in one (0.7%), erythromycin in 16 (11.7%) and moxifloxacin in 2 (1.5%) of the strains, whereas no resistance was observed against vancomycin (0.0%) or rifampicin (0.0%). Newly observed resistance against erythromycin in children with detection of previously completely sensitive isolates was reported for C. difficile isolates from 2 out of 48 children. In 20 children (42%), non-toxigenic strains were detected, and from 27 children (56%), toxigenic strains were isolated, while both toxigenic and non-toxigenic strains were recorded for 1 child (2%). Ribotypes 027 or 176 were not observed. In conclusion, the German C. difficile strains isolated from the children showed mild to moderate resistance with predominance of macrolide resistance, a substance class which is frequently applied in children. The observed switches to the dominance of macrolide-resistant isolates suggests likely selection of resistant C. difficile strains already in children.

Background: Motility in bacteria forms the basis for taxis and is in some pathogenic bacteria important for virulence. Video tracking of motile bacteria allows the monitoring of bacterial swimming behaviour and taxis on the level of individual cells, which is a prerequisite to study the underlying molecular mechanisms., Results: The open-source python program YSMR (Your Software for Motility Recognition) was designed to simultaneously track a large number of bacterial cells on standard computers from video files in various formats. In order to cope with the high number of tracked objects, we use a simple detection and tracking approach based on grey-value and position, followed by stringent selection against suspicious data points. The generated data can be used for statistical analyses either directly with YSMR or with external programs., Conclusion: In contrast to existing video tracking software, which either requires expensive computer hardware or only tracks a limited number of bacteria for a few seconds, YSMR is an open-source program which allows the 2-D tracking of several hundred objects over at least 5 minutes on standard computer hardware. The code is freely available at https://github.com/schwanbeck/YSMR.

Objectives: The identification and characterization of clinical Clostridioides difficile isolates with reduced fidaxomicin susceptibility., Methods: Agar dilution assays were used to determine fidaxomicin MICs. Genome sequence data were obtained by single-molecule real-time (SMRT) sequencing in addition to amplicon sequencing of rpoB and rpoC alleles. Allelic exchange was used to introduce the identified mutation into C. difficile 630Δerm. Replication rates, toxin A/B production and spore formation were determined from the strain with reduced fidaxomicin susceptibility., Results: Out of 50 clinical C. difficile isolates, isolate Goe-91 revealed markedly reduced fidaxomicin susceptibility (MIC >64 mg/L). A V1143D mutation was identified in rpoB of Goe-91. When introduced into C. difficile 630Δerm, this mutation decreased fidaxomicin susceptibility (MIC >64 mg/L), but was also associated with a reduced replication rate, low toxin A/B production and markedly reduced spore formation. In contrast, Goe-91, although also reduced in toxin production, showed normal growth rates and only moderately reduced spore formation capacities. This indicates that the rpoBV1143D allele-associated fitness defect is less pronounced in the clinical isolate., Conclusions: To the best of our knowledge, this is the first description of a pathogenic clinical C. difficile isolate with markedly reduced fidaxomicin susceptibility. The lower-than-expected fitness burden of the resistance-mediating rpoBV1143D allele might be an indication for compensatory mechanisms that take place during in vivo selection of mutants.