A robust, scalable, and cost-efficient approach to whole genome sequencing of RSV directly from clinical samples

Respiratory syncytial virus (RSV) is a leading cause of acute lower respiratory tract infections causing significant morbidity and mortality among children and the elderly; two RSV vaccines and a monoclonal antibody have recently been approved. Thus, there is an increasing need for a detailed and continuous genomic surveillance of RSV circulating in resource-rich and resource-limited settings worldwide. However, robust, cost-effective methods for whole genome sequencing of RSV from clinical samples that are amenable to high-throughput are still scarce. We developed Next-RSV-SEQ, an experimental and computational pipeline to generate whole genome sequences of historic and current RSV genotypes by in-solution hybridization capture-based next generation sequencing. We optimized this workflow by automating library preparation and pooling libraries prior to enrichment in order to reduce hands-on time and cost, thereby augmenting scalability. Next-RSV-SEQ yielded near-complete to complete genome sequences for 98% of specimens with Cp values ≤31, at median on-target reads >93%, and mean coverage depths between ~1,000 and >5,000, depending on viral load. Whole genomes were successfully recovered from samples with viral loads as low as 230 copies per microliter RNA. We demonstrate that the method can be expanded to other respiratory viruses like parainfluenza virus and human metapneumovirus. Next-RSV-SEQ produces high-quality RSV genomes directly from culture isolates and, more importantly, clinical specimens of all genotypes in circulation. It is cost-efficient, scalable, and can be extended to other respiratory viruses, thereby opening new perspectives for a future effective and broad genomic surveillance of respiratory viruses.

IMPORTANCE

Respiratory syncytial virus (RSV) is a leading cause of severe acute respiratory tract infections in children and the elderly, and its prevention has become an increasing priority. Recently, vaccines and a long-acting monoclonal antibody to protect effectively against severe disease have been approved for the first time. Hence, there is an urgent need for genomic surveillance of RSV at the global scale to monitor virus evolution, especially with an eye toward immune evasion. However, robust, cost-effective methods for RSV whole genome sequencing that are suitable for high-throughput of clinical samples are currently scarce. Therefore, we have developed Next-RSV-SEQ, an experimental and computational pipeline that produces reliably high-quality RSV genomes directly from clinical specimens and isolates.

Who Benefited the Most? Effectiveness of a Lifestyle Intervention Against Cognitive Decline in Older Women and Men - Secondary Analysis of the AgeWell.de-trial

INTRODUCTION

Differences between women and men matter in the prevalence and risk factors of dementia. We aimed to examine potential sex differences regarding the effectiveness by running a secondary analysis of the AgeWell.de trial, a cluster-randomized multicenter multi-domain lifestyle intervention to reduce cognitive decline.

METHODS

Intention-to-treat analyses of women (n=433) and men (n=386) aged 60 to 77 years were used for models including interactions between intervention group allocation and sex followed by subgroup analysis stratified by sex on primary and secondary outcomes. Further, the same procedure was repeated for age groups (60-69 vs. 70-77) within sex-specific subgroups to assess the effectiveness in different age groups.

TRIAL REGISTRATION

German Clinical Trials Register (ref. number: DRKS00013555).

RESULTS

No differences were found between women and men in the effectiveness of the intervention on cognitive performance. However, women benefitted from the intervention regarding depressive symptoms while men did not. Health-related quality of life was enhanced for younger intervention participants (60-69 years) in both women and men.

CONCLUSION

The AgeWell.de intervention was able to improve depressive symptoms in women and health-related quality of life in younger participants. Female participants between 60 and 69 years benefited the most. Results support the need of better individually targeted lifestyle interventions for older adults.

Neighbourhood watch: genomic epidemiology of SARS-CoV-2 variants circulating in a German federal state, Mecklenburg-Western Pomerania, in 2020-2022

ABSTRACTGlobal and even national genome surveillance approaches do not provide the resolution necessary for rapid and accurate direct response by local public health authorities. Hence, a regional network of microbiological laboratories in collaboration with the health departments of all districts of the German federal state of Mecklenburg-Western Pomerania (M-V) was formed to investigate the regional molecular epidemiology of circulating SARS-CoV-2 lineages between 11/2020 and 03/2022. More than 4750 samples from all M-V counties were sequenced using Illumina and Nanopore technologies. Overall, 3493 (73.5%) sequences fulfilled quality criteria for time-resolved and/or spatially-resolved maximum likelihood phylogenic analyses and k-mean/ median clustering (KMC). We identified 116 different Pangolin virus lineages that can be assigned to 16 Nextstrain clades. The ten most frequently detected virus lineages belonged to B.1.1.7, AY.122, AY.43, BA.1, B.1.617.2, BA.1.1, AY.9.2, AY.4, P.1 and AY.126. Time-resolved phylogenetic analyses showed the occurrence of virus clades as determined worldwide, but with a substantial delay of one to two months. Further spatio-temporal phylogenetic analyses revealed a regional outbreak of a Gamma variant limited to western M-V counties. Finally, KMC elucidated a successive introduction of the various virus lineages into M-V, possibly triggered by vacation periods with increased (inter-) national travel activities. The COVID-19 pandemic in M-V was shaped by a combination of several SARS-CoV-2 introductions, lockdown measures, restrictive quarantine of patients and the lineage specific replication rate. Complementing global and national surveillance, regional surveillance adds value by providing a higher level of surveillance resolution tailored to local health authorities.

Small proteins in bacteria - Big challenges in prediction and identification

Proteins with up to 100 amino acids have been largely overlooked due to the challenges associated with predicting and identifying them using traditional methods. Recent advances in bioinformatics and machine learning, DNA sequencing, RNA and Ribo-seq technologies, and mass spectrometry (MS) have greatly facilitated the detection and characterisation of these elusive proteins in recent years. This has revealed their crucial role in various cellular processes including regulation, signalling and transport, as toxins and as folding helpers for protein complexes. Consequently, the systematic identification and characterisation of these proteins in bacteria have emerged as a prominent field of interest within the microbial research community. This review provides an overview of different strategies for predicting and identifying these proteins on a large scale, leveraging the power of these advanced technologies. Furthermore, the review offers insights into the future developments that may be expected in this field.

The role of stormwater infrastructure in regional methane emissions

Stormwater infrastructure has been recently indicated as a potential hotspot for methane (CH4) emissions. Although local assessments based on direct CH4 measurements are increasingly available, there is currently no standardized approach for evaluating CH4 emissions from different types of stormwater infrastructure, including permanently impounded or fast-draining structures in Urban Drainage Systems (UDS). Therefore, a comparative analysis with wastewater infrastructure systems, such as wastewater treatment plants (WWTPs), is not yet possible. Here, we present a conceptual framework for the first-order quantification and upscaling of CH4 emissions from stormwater infrastructure at local and national scales. We combined in-situ and ex-situ measurements of CH4 emissions with purposely acquired data from selected stormwater facilities to provide initial estimates of CH4 emissions and emission factors for stormwater infrastructure in Germany. The results show that while stormwater infrastructure might emit comparable amounts of CH4 per area as natural and anthropogenically impacted inland waters, it may exhibit higher mean emission factors (up to 7 times) than conventional WWTPs, indicating less efficiency in limiting CH4 emissions than WWTPs. This is particularly true for permanently impounded facilities, which showed substantially higher mean surface CH4 emissions (up to 632 mg m-2 d-1) than fast-draining infrastructure (0.5-1.28 mg m-2 d-1). Permanently impounded sedimentation basins for stormwater management alone may reach up to 60% of the total CH4 emissions originating from WWTPs in Germany. These results are in conflict with the ongoing trend towards increasing implementation of impounded stormwater infrastructure systems, highlighting the urgent need for more extensive assessments of their impact on CH4 dynamics.

MpoxRadar: a worldwide MPXV genomic surveillance dashboard

The mpox virus (MPXV) is mutating at an exceptional rate for a DNA virus and its global spread is concerning, making genomic surveillance a necessity. With MpoxRadar, we provide an interactive dashboard to track virus variants on mutation level worldwide. MpoxRadar allows users to select among different genomes as reference for comparison. The occurrence of mutation profiles based on the selected reference is indicated on an interactive world map that shows the respective geographic sampling site in customizable time ranges to easily follow the frequency or trend of defined mutations. Furthermore, the user can filter for specific mutations, genes, countries, genome types, and sequencing protocols and download the filtered data directly from MpoxRadar. On the server, we automatically download all MPXV genomes and metadata from the National Center for Biotechnology Information (NCBI) on a daily basis, align them to the different reference genomes, generate mutation profiles, which are stored and linked to the available metainformation in a database. This makes MpoxRadar a practical tool for the genomic survaillance of MPXV, supporting users with limited computational resources. MpoxRadar is open-source and freely accessible at https://MpoxRadar.net.

Vibrationally Resolved Inner-Shell Photoexcitation of the Molecular Anion C2. Chemphyschem 2023:e202300061. [PMID: 36815408 DOI: 10.1002/cphc.202300061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0]

Carbon 1s core-hole excitation of the molecular anion C₂ ^- has been experimentally studied at high resolution by employing the photon-ion merged-beams technique at a synchrotron light source. The experimental cross section for photo-double-detachment shows a pronounced vibrational structure associated with 1 σ u → 3 σ g ${1\sigma _u \to 3\sigma _g }$ and 1 σ g → 1 π u ${1\sigma _g \to 1\pi _u }$ core excitations of the C₂ ^- ground level and first excited level, respectively. A detailed Franck-Condon analysis reveals a strong contraction of the C₂ ^- molecular anion by 0.2 Å upon this core photoexcitation. The associated change of the molecule's moment of inertia leads to a noticeable rotational broadening of the observed vibrational spectral features. This broadening is accounted for in the present analysis which provides the spectroscopic parameters of the C₂ ^- 1 σ u - 1 3 σ g 2 2 Σ u + ${1\sigma _u^{ - 1} \,3\sigma _g^2 \;^2 \Sigma _u^ + }$ and 1 σ g - 1 3 σ g 2 2 Σ g + ${1\sigma _g^{ - 1} \,3\sigma _g^2 \;^2 \Sigma _g^ + }$ core-excited levels.

1358. Establishing Genomic SARS-CoV-2 Surveillance at the National Level: Germany, 2021

Background

The COVID-19 pandemic has demonstrated the importance of pathogen genomic surveillance. At RKI, the German National Institute of Public Health, we established the Integrated Molecular Surveillance for SARS-CoV-2 (IMS-SC2) network to perform SARS-CoV-2 genomic surveillance.

Methods

SARS-CoV-2 positive samples from laboratories distributed across Germany regularly undergo whole-genome sequencing at RKI. This surveillance instrument enables (i) almost-real-time monitoring of SARS-CoV-2 genomic diversity and evolution, (ii) in vitro assessment of vaccine coverage against emerging variants and (iii) genome-based estimates of SARS-CoV-2-incidences.

Results

We report the results of our analyses of 3623 SARS-CoV-2 genomes collected between 12/1/2020 and 12/31/2021. All variants of concern were identified, at ratios equivalent to those in the 100-fold larger German GISAID sequence dataset from the same time period. Lineage distributions fluctuated over time, covering the rise of the Alpha and Delta, as well as the emergence of Omicron. Phylogenetic analysis confirmed variant assignments. Multiple mutations of concern emerged during the observation period. To model vaccine effectiveness in vitro, we employed authentic-virus neutralization assays, confirming that both the Beta and Zeta variants are capable of immune evasion. The IMS-SC2 sequence dataset facilitated an estimate of the SARS-CoV-2 incidence based on genetic evolution rates. Together with modelled vaccine efficacies, Delta-specific incidence estimation indicated that the German vaccination campaign contributed substantially to a deceleration of the nascent German Delta wave.

Conclusion

This example illustrates that pathogen genomics enables a proactive approach to controlling a pandemic as the virus evolves. Molecular and genomic SARS-CoV-2 surveillance will be crucial during the post-pandemic future, informing public health policies including vaccination strategies. Of note, the IMS-SC2 infrastructure can be adapted to many other pathogens, serving as a blueprint for future efforts to increase genomic pathogen surveillance.

Disclosures

All Authors: No reported disclosures.

Listeria monocytogenes genes supporting growth under standard laboratory cultivation conditions and during macrophage infection

The Gram-positive bacterium Listeria monocytogenes occurs widespread in the environment and infects humans when ingested along with contaminated food. Such infections are particularly dangerous for risk group patients, for whom they represent a life-threatening disease. To invent novel strategies to control contamination and disease, it is important to identify those cellular processes that maintain pathogen growth inside and outside the host. Here, we have applied transposon insertion sequencing (Tn-Seq) to L. monocytogenes for the identification of such processes on a genome-wide scale. Our approach identified 394 open reading frames that are required for growth under standard laboratory conditions and 42 further genes, which become necessary during intracellular growth in macrophages. Most of these genes encode components of the translation machinery and act in chromosome-related processes, cell division, and biosynthesis of the cellular envelope. Several cofactor biosynthesis pathways and 29 genes with unknown functions are also required for growth, suggesting novel options for the development of antilisterial drugs. Among the genes specifically required during intracellular growth are known virulence factors, genes compensating intracellular auxotrophies, and several cell division genes. Our experiments also highlight the importance of PASTA kinase signaling for general viability and of glycine metabolism and chromosome segregation for efficient intracellular growth of L. monocytogenes.

Costs and benefits of combined sewer overflow management strategies at the European scale

Combined sewer overflows (CSOs) may represent a significant source of pollution, but they are difficult to quantify at a large scale (e.g. regional or national), due to a lack of accessible data. In the present study, we use a large scale, 6-parameter, lumped hydrological model to perform a screening level assessment of different CSO management scenarios for the European Union and United Kingdom, considering prevention and treatment strategies. For each scenario we quantify the potential reduction of CSO volumes and duration, and estimate costs and benefits. A comparison of scenarios shows that treating CSOs before discharge in the receiving water body (e.g. by constructed wetlands) is more cost-effective than preventing CSOs. Among prevention strategies, urban greening has a benefit/cost ratio one order of magnitude higher than grey solutions, due to the several additional benefits it entails. We also estimate that real time control may bring on average a CSO volume reduction of just above 20%. In general, the design of appropriate CSO management strategies requires consideration of context-specific conditions, and is best made in the context of an integrated urban water management plan taking into account factors such as other ongoing initiatives in urban greening, the possibility to disconnect impervious surfaces from combined drainage systems, and the availability of space for grey or nature-based solutions.

CovRadar: continuously tracking and filtering SARS-CoV-2 mutations for genomic surveillance

SUMMARY

The ongoing pandemic caused by SARS-CoV-2 emphasizes the importance of genomic surveillance to understand the evolution of the virus, to monitor the viral population, and plan epidemiological responses. Detailed analysis, easy visualization and intuitive filtering of the latest viral sequences are powerful for this purpose. We present CovRadar, a tool for genomic surveillance of the SARS-CoV-2 Spike protein. CovRadar consists of an analytical pipeline and a web application that enable the analysis and visualization of hundreds of thousand sequences. First, CovRadar extracts the regions of interest using local alignment, then builds a multiple sequence alignment, infers variants and consensus and finally presents the results in an interactive app, making accessing and reporting simple, flexible and fast.

AVAILABILITY AND IMPLEMENTATION

CovRadar is freely accessible at https://covradar.net, its open-source code is available at https://gitlab.com/dacs-hpi/covradar.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

A decade of monitoring micropollutants in urban wet-weather flows: What did we learn?

Urban wet-weather discharges from combined sewer overflows (CSO) and stormwater outlets (SWO) are a potential pathway for micropollutants (trace contaminants) to surface waters, posing a threat to the environment and possible water reuse applications. Despite large efforts to monitor micropollutants in the last decade, the gained information is still limited and scattered. In a metastudy we performed a data-driven analysis of measurements collected at 77 sites (683 events, 297 detected micropollutants) over the last decade to investigate which micropollutants are most relevant in terms of 1) occurrence and 2) potential risk for the aquatic environment, 3) estimate the minimum number of data to be collected in monitoring studies to reliably obtain concentration estimates, and 4) provide recommendations for future monitoring campaigns. We highlight micropollutants to be prioritized due to their high occurrence and critical concentration levels compared to environmental quality standards. These top-listed micropollutants include contaminants from all chemical classes (pesticides, heavy metals, polycyclic aromatic hydrocarbons, personal care products, pharmaceuticals, and industrial and household chemicals). Analysis of over 30,000 event mean concentrations shows a large fraction of measurements (> 50%) were below the limit of quantification, stressing the need for reliable, standard monitoring procedures. High variability was observed among events and sites, with differences between micropollutant classes. The number of events required for a reliable estimate of site mean concentrations (error bandwidth of 1 around the "true" value) depends on the individual micropollutant. The median minimum number of events is 7 for CSO (2 to 31, 80%-interquantile) and 6 for SWO (1 to 25 events, 80%-interquantile). Our analysis indicates the minimum number of sites needed to assess global pollution levels and our data collection and analysis can be used to estimate the required number of sites for an urban catchment. Our data-driven analysis demonstrates how future wet-weather monitoring programs will be more effective if the consequences of high variability inherent in urban wet-weather discharges are considered.

[Removal of a bent femoral nail : Case report: treatment strategy of a complex femoral deformity with a bent femoral nail in situ since 36 years]

To remove a bent femoral nail is always a challenging task for a surgeon. In the last 20 years several case reports and descriptions of techniques are to be found in literature, the goal being to weaken the nail at the apex and then straightening it in situ in most cases. Those reports all have one parameter in common: the necessity to remove the nail relates to a refracture of the femur.We report the case of a patient who presented with the explicit wish to have a bent femoral nail removed and a femoral angulation corrected because of pain in the ipsilateral hip. A femoral fracture had been treated by a Küntscher nail in 1982. A refracture with severe bending of the nail had occurred a short time later, which was treated conservatively without a second surgical procedure.We can show that a planned removal of a bent and well-osseointegrated Küntscher nail can be achieved without complications and that thereby a multiplane angulation in the femur can be corrected, paving the way for a future arthroplasty in this specific case.

Advancing Precision Vaccinology by Molecular and Genomic Surveillance of Severe Acute Respiratory Syndrome Coronavirus 2 in Germany, 2021

BACKGROUND

Comprehensive pathogen genomic surveillance represents a powerful tool to complement and advance precision vaccinology. The emergence of the Alpha variant in December 2020 and the resulting efforts to track the spread of this and other severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern led to an expansion of genomic sequencing activities in Germany.

METHODS

At Robert Koch Institute (RKI), the German National Institute of Public Health, we established the Integrated Molecular Surveillance for SARS-CoV-2 (IMS-SC2) network to perform SARS-CoV-2 genomic surveillance at the national scale, SARS-CoV-2-positive samples from laboratories distributed across Germany regularly undergo whole-genome sequencing at RKI.

RESULTS

We report analyses of 3623 SARS-CoV-2 genomes collected between December 2020 and December 2021, of which 3282 were randomly sampled. All variants of concern were identified in the sequenced sample set, at ratios equivalent to those in the 100-fold larger German GISAID sequence dataset from the same time period. Phylogenetic analysis confirmed variant assignments. Multiple mutations of concern emerged during the observation period. To model vaccine effectiveness in vitro, we employed authentic-virus neutralization assays, confirming that both the Beta and Zeta variants are capable of immune evasion. The IMS-SC2 sequence dataset facilitated an estimate of the SARS-CoV-2 incidence based on genetic evolution rates. Together with modeled vaccine efficacies, Delta-specific incidence estimation indicated that the German vaccination campaign contributed substantially to a deceleration of the nascent German Delta wave.

CONCLUSIONS

SARS-CoV-2 molecular and genomic surveillance may inform public health policies including vaccination strategies and enable a proactive approach to controlling coronavirus disease 2019 spread as the virus evolves.

SARS-CoV-2 Omicron variants BA.1 and BA.2 both show similarly reduced disease severity of COVID-19 compared to Delta, Germany, 2021 to 2022

German national surveillance data analysis shows that hospitalisation odds associated with Omicron lineage BA.1 or BA.2 infections are up to 80% lower than with Delta infection, primarily in ≥ 35-year-olds. Hospitalised vaccinated Omicron cases' proportions (2.3% for both lineages) seemed lower than those of the unvaccinated (4.4% for both lineages). Independent of vaccination status, the hospitalisation frequency among cases with Delta seemed nearly threefold higher (8.3%) than with Omicron (3.0% for both lineages), suggesting that Omicron inherently causes less severe disease.

Repetitive transcranial magnetic stimulation (rTMS) for catatonia– a case report

Introduction

Catatonia is one of the most common severe motor syndromes, with an estimated prevalence among psychiatric inpatients of about 15 %. Benzodiazepines and electroconvulsive therapy (ECT) are the most widely studied treatment methods recommended as first-line therapy. We present the case of a 55-year-old female patient with paranoid schizophrenia and severe life-threatening catatonia who remitted under a short series of rTMS.

Objectives

s. Introduction

Methods

The point of resting motor threshold (RMT) for the musculus rectus femoris was determined for the left hemisphere. A straight line 3 cm anterior and parasagittal from that point defined the SMA. A total of three sessions, each with 1000 pulses at intensity 66 % of the RMT, were performed within 24 and 120 hours apart. Stimulation protocol was set to 1Hz in the area of the left SMA with 25 series of 40 pulses, pulse width 25 ms, angle of attack 45°. Hardware: MagVenture, 8-coil “cool-B65 butterfly-shaped coil from Medtronic.

Results

Within 24 hours after the first session, a marked improvement of catatonic symptoms like independent locomotion and verbal communication was recognized. One week after the whole rTMS treatment, a food intake without a gastric tube was possible.

Conclusions

The present case demonstrates that pronounced catatonia may be successfully treated with inhibitory rTMS. Our results underline the importance of non-invasive brain stimulation as a valuable addition to the existing treatment spectrum for catatonia. Future research is empowered to path the way for a significant expansion of treatment.

Disclosure

No significant relationships.

A wildfire vulnerability index for buildings

Recent wildfire events (e.g. Mediterranean region, USA, and Australia) showed that this hazard poses a serious threat for wildland–urban interface (WUI) areas around the globe. Furthermore, recent events in regions where wildfire does not constitute a frequent hazard (e.g. Siberia, Scandinavia) indicated that the spatial pattern of wildfire risk might have significantly changed. To prepare for upcoming extreme events, it is critical for decision-makers to have a thorough understanding of the vulnerability of the built environment to wildfire. Building quality and design standards are important not only because building loss is costly but also because robust buildings may offer shelter when evacuation is not possible. However, studies aiming at the analysis of wildfire vulnerability for the built environment are limited. This paper presents an innovative solution for the vulnerability assessment to wildfires, making use of an all-relevant feature selection algorithm established on statistical relationships to develop a physical vulnerability index for buildings subject to wildfire. Data from a recent and systematically documented wildfire event in Greece (Mati, 2018) are used to select and weight the relevant indicators using a permutation-based automated feature selection based on random forests. Building characteristics including the structural type, the roof type, material and shape, the inclination of the ground, the surrounding vegetation, the material of the shutters and the ground covering were selected and formed into the index. The index may be used in other places in Europe and beyond, especially where no empirical data are available supporting decision-making and risk reduction of an emerging hazard amplified by climate change.

The association of sleep patterns and depressive symptoms in medical students: a cross-sectional study

Objective

Mental health is a fundamental aspect in ensuring the stable and successful professional life of future physicians. Depressive symptoms can negatively affect the work-life-balance and efficiency at work of medical students.

To date, there have been very few studies involving medical students that examine the association between single sleep characteristics and the outcome of the Beck Depression Inventory-II score. Therefore, the aim of the present study is to investigate this possible association. A classroom survey using socio-demographic characteristics, the Beck Depression Inventory-II, and the Pittsburgh Sleep Quality Index was conducted amongst students at a German medical school from December 2017 to September 2018. Data analysis was performed with descriptive statistics and binary logistic regression.

Results

Of the students surveyed, 19% showed depressive symptoms with a Beck Depression Inventory-II score over 13 and 42% of these cases were moderate or severe. The occurrence of relevant depressive symptoms was associated with lower sleep quality, higher sleep latency, and the consumption of sleeping pills. In general, female students and students from abroad had a higher risk of depressive symptoms. Addressing these relevant findings in medical school can increase awareness of mental health.

Prevalence and predictive factors for depressive symptoms among medical students in Germany - a cross-sectional study

Background: Elevated levels of depressive symptoms among medical students have been the subject of international and national research before, yet associated risk factors and protective factors are to be determined. This study aims to show the burdens of depression at different stages of academic medical education with a special emphasis on correlated risk factors and protective factors. Methods: A total number of n=1103 medical students of a middle-sized German university were sampled and surveyed regarding depressive symptoms and correlating factors. The assessment of potential depressive symptoms was based on the BDI-II. Correlating factors were surveyed through a self-designed questionnaire consisting of possible cofactors for depressive symptoms based on established scientific literature. Results: Survey response rate was 90.2% (1103/1223). The prevalence of depressive symptoms was 11% for mild, 5.6% for moderate and 2.4% for severe symptoms. The sample's most prevalent risk factors were feeling unable to confide one's own worries to someone else (88%); and experiencing a lack of time for partner, friends and family (77%) or hobbies (76%). Significant predictors for depressive symptoms were neuroticism above all, insufficient emotional support, eating irregular meals, use of medication or drugs to calm down, and mental overload. Factors associated with less depressive symptoms could be identified as: spending time with partner, friends, family, hobbies and exercise; and confiding worries to classmates. Conclusions: Every fifth medical student surveyed reported at least mild depressive symptoms. The majority of the surveyed medical students felt unable to confide their worries to someone else and lamented not having enough time for social interaction with peers, family and hobbies. Certain personality traits - such as neuroticism - and insufficient emotional support showed to play important roles in making medical students more prone to developing depressive symptoms. Based on this research, control of the surveyed cofactors associated with depressive symptoms and possible intervention programs targeted to these are proposed to be a key subject of further research.

Critical Assessment of MetaProteome Investigation (CAMPI): a multi-laboratory comparison of established workflows

Metaproteomics has matured into a powerful tool to assess functional interactions in microbial communities. While many metaproteomic workflows are available, the impact of method choice on results remains unclear. Here, we carry out a community-driven, multi-laboratory comparison in metaproteomics: the critical assessment of metaproteome investigation study (CAMPI). Based on well-established workflows, we evaluate the effect of sample preparation, mass spectrometry, and bioinformatic analysis using two samples: a simplified, laboratory-assembled human intestinal model and a human fecal sample. We observe that variability at the peptide level is predominantly due to sample processing workflows, with a smaller contribution of bioinformatic pipelines. These peptide-level differences largely disappear at the protein group level. While differences are observed for predicted community composition, similar functional profiles are obtained across workflows. CAMPI demonstrates the robustness of present-day metaproteomics research, serves as a template for multi-laboratory studies in metaproteomics, and provides publicly available data sets for benchmarking future developments.

Critical Assessment of MetaProteome Investigation (CAMPI): a multi-laboratory comparison of established workflows

Metaproteomics has matured into a powerful tool to assess functional interactions in microbial communities. While many metaproteomic workflows are available, the impact of method choice on results remains unclear. Here, we carry out a community-driven, multi-laboratory comparison in metaproteomics: the critical assessment of metaproteome investigation study (CAMPI). Based on well-established workflows, we evaluate the effect of sample preparation, mass spectrometry, and bioinformatic analysis using two samples: a simplified, laboratory-assembled human intestinal model and a human fecal sample. We observe that variability at the peptide level is predominantly due to sample processing workflows, with a smaller contribution of bioinformatic pipelines. These peptide-level differences largely disappear at the protein group level. While differences are observed for predicted community composition, similar functional profiles are obtained across workflows. CAMPI demonstrates the robustness of present-day metaproteomics research, serves as a template for multi-laboratory studies in metaproteomics, and provides publicly available data sets for benchmarking future developments.

Modelling copper emissions from antifouling paints applied on leisure boats into German water bodies

Copper-containing antifouling paints (AFP) are widely used for leisure boat maintenance. Cu emitted from AFP into German surface water bodies has been suggested to be a significant source of heavy metal pollution, threatening water quality. We developed two scenarios to model Cu emissions from AFP applied on leisure boats on national scale, which allow identifying regional hotspots. The top-down approach (scenario A) was based on a previous study on national AFP consumption, while in the bottom-up approach (scenario B), median and interquartile range of Cu release rates depending on salinity conditions were considered for emission estimation. Both scenarios clearly highlighted the locally high emission pressure on inland waters in popular watersport regions, identifying these as requiring intense protection. Scenario B generally predicted lower Cu emissions (sea: 11.05-25.53 t a^-1, inland: 14.15-34.59 t a^-1) than scenario A (sea: 22.53 t a^-1, inland: 47.97 t a^-1). To evaluate their relevance, scenario results were compared to emissions modelled with MoRE (Modelling of Regionalized Emissions), which is used as reporting tool on substance emissions by Germany. According to scenarios A and B, the emission from AFP accounted for 13 % and 4-9 % of the total Cu emissions into inland waters in 2016, respectively. Scenario results were similar or higher than other emission pathways such as industrial direct dischargers. Thus, we consider Cu emissions from AFP as a significant pathway to be included in the MoRE emission inventory. We recommend scenario B for implementation as it allows a more flexible adaptation for future modelling.

Protein expression profiling of Staphylococcus aureus in response to the bacteriocin bovicin HC5

Alternative strategies to antibiotic treatment are required to inhibit pathogens, including Staphylococcus aureus. Bacteriocins, such as the lantibiotic bovicin HC5, have shown potential to control pathogens. This study aims to evaluate the stress response of S. aureus to bovicin HC5 using a proteomic approach. Sublethal concentrations of the bacteriocin repressed the synthesis of 62 cytoplasmic proteins, whereas 42 proteins were induced in S. aureus COL. Specifically, synthesis of several proteins involved in amino acid biosynthesis, mainly products of ilv-leu operon, and DNA metabolism, such as DNA polymerase I, decreased following bovicin treatment while proteins involved in catabolism, mainly tricarboxylic acid cycle metabolism, and chaperones were over-expressed. The levels of CodY and CcpA, important regulators involved in the stationary phase adaptation and catabolite repression, respectively, also increased in the presence of the bacteriocin. These results indicate that stress caused by the sublethal concentration of bovicin HC5 in the cell membrane results in growth reduction, reduced protein synthesis, and, at the same time, enhanced the levels of chaperones and enzymes involved in energy-efficient catabolism in an attempt to restore energy and cell homeostasis. These results bring relevant information to amplify the knowledge concerning the bacterial physiological changes in response to the stress caused by the cell exposition to bovicin HC5. New potential targets for controlling this pathogen can also be determined from the new protein expression pattern presented. KEY POINTS: • Bovicin HC5 changed the synthesis of cytoplasmic proteins of S. aureus. • Bovicin HC5 interfered in the synthesis of proteins of amino acids biosynthesis. • Synthesis of chaperones enhanced in the presence of sublethal dosage of bovicin HC5.

Mutations in the gdpP gene are a clinically relevant mechanism for β-lactam resistance in meticillin-resistant Staphylococcus aureus lacking mec determinants

In Staphylococcus aureus, resistance to β-lactamase stable β-lactam antibiotics is mediated by the penicillinbinding protein 2a, encoded by mecA or by its homologues mecB or mecC. However, a substantial number of meticillin-resistant isolates lack known mec genes and, thus, are called meticillin resistant lacking mec (MRLM). This study aims to identify the genetic mechanisms underlying the MRLM phenotype. A total of 141 MRLM isolates and 142 meticillin-susceptible controls were included in this study. Oxacillin and cefoxitin minimum inhibitory concentrations were determined by broth microdilution and the presence of mec genes was excluded by PCR. Comparative genomics and a genome-wide association study (GWAS) approach were applied to identify genetic polymorphisms associated with the MRLM phenotype. The potential impact of such mutations on the expression of PBP4, as well as on cell morphology and biofilm formation, was investigated. GWAS revealed that mutations in gdpP were significantly associated with the MRLM phenotype. GdpP is a phosphodiesterase enzyme involved in the degradation of the second messenger cyclic-di-AMP in S. aureus. A total of 131 MRLM isolates carried truncations, insertions or deletions as well as amino acid substitutions, mainly located in the functional DHH-domain of GdpP. We experimentally verified the contribution of these gdpP mutations to the MRLM phenotype by heterologous complementation experiments. The mutations in gdpP had no effect on transcription levels of pbp4; however, cell sizes of MRLM strains were reduced. The impact on biofilm formation was highly strain dependent. We report mutations in gdpP as a clinically relevant mechanism for β-lactam resistance in MRLM isolates. This observation is of particular clinical relevance, since MRLM are easily misclassified as MSSA (meticillin-susceptible S. aureus), which may lead to unnoticed spread of β-lactam-resistant isolates and subsequent treatment failure.

Up-to-date monitoring data of wastewater and stormwater quality in Germany

A comprehensive dataset of pollutant concentrations in German urban wastewater systems is available from recently completed monitoring projects. It contains up to 1000 concentration values for each of 79 substances in wastewater treatment plant (WWTP) effluents from 49 sites, and up to 157 values for each of 95 substances in combined sewer overflows (CSOs) from 12 sites. WWTP influents and stormwater outfalls were sampled to a lesser extent. All sampling methods were harmonised and aimed at collecting event or multi-day composite samples over periods of ≥1 year. Among the substances analysed were biocides and pesticides, polycyclic aromatic hydrocarbons, perfluorinated alkyl substances, metals, pharmaceuticals, benzotriazoles, phenols, acesulfame, di-(2-ethylhexyl)phthalate, and hexabromocyclododecanes. Occurrence, concentration ranges, and removal rates of selected WWTPs are presented. CSOs can be confirmed as an important pathway of metals and PAH to receiving waters when compared to WWTPs on the basis of annual per capita loads. The derived volume-weighted site mean concentrations are qualified to be used as representative input data for estimation of average substance emissions in large areas, e.g. on river basin scale, if no site-specific data are available. As such, they will contribute to the development of strategies to reduce substance emissions, taking into account not only WWTPs but also stormwater-related discharges.

Interlaboratory evaluation of Mucorales PCR assays for testing serum specimens: A study by the fungal PCR Initiative and the Modimucor study group

Interlaboratory evaluations of Mucorales qPCR assays were developed to assess the reproducibility and performance of methods currently used. The participants comprised 12 laboratories from French university hospitals (nine of them participating in the Modimucor study) and 11 laboratories participating in the Fungal PCR Initiative. For panel 1, three sera were each spiked with DNA from three different species (Rhizomucor pusillus, Lichtheimia corymbifera, Rhizopus oryzae). For panel 2, six sera with three concentrations of R. pusillus and L. corymbifera (1, 10, and 100 genomes/ml) were prepared. Each panel included a blind negative-control serum. A form was distributed with each panel to collect results and required technical information, including DNA extraction method, sample volume used, DNA elution volume, qPCR method, qPCR template input volume, qPCR total reaction volume, qPCR platform, and qPCR reagents used. For panel 1, assessing 18 different protocols, qualitative results (positive or negative) were correct in 97% of cases (70/72). A very low interlaboratory variability in Cq values (SD = 1.89 cycles) were observed. For panel 2 assessing 26 different protocols, the detection rates were high (77-100%) for 5/6 of spiked serum. There was a significant association between the qPCR platform and performance. However, certain technical steps and optimal combinations of factors may also impact performance. The good reproducibility and performance demonstrated in this study support the use of Mucorales qPCR as part of the diagnostic strategy for mucormycosis.

smORFer: a modular algorithm to detect small ORFs in prokaryotes

Emerging evidence places small proteins (≤50 amino acids) more centrally in physiological processes. Yet, their functional identification and the systematic genome annotation of their cognate small open-reading frames (smORFs) remains challenging both experimentally and computationally. Ribosome profiling or Ribo-Seq (that is a deep sequencing of ribosome-protected fragments) enables detecting of actively translated open-reading frames (ORFs) and empirical annotation of coding sequences (CDSs) using the in-register translation pattern that is characteristic for genuinely translating ribosomes. Multiple identifiers of ORFs that use the 3-nt periodicity in Ribo-Seq data sets have been successful in eukaryotic smORF annotation. They have difficulties evaluating prokaryotic genomes due to the unique architecture (e.g. polycistronic messages, overlapping ORFs, leaderless translation, non-canonical initiation etc.). Here, we present a new algorithm, smORFer, which performs with high accuracy in prokaryotic organisms in detecting putative smORFs. The unique feature of smORFer is that it uses an integrated approach and considers structural features of the genetic sequence along with in-frame translation and uses Fourier transform to convert these parameters into a measurable score to faithfully select smORFs. The algorithm is executed in a modular way, and dependent on the data available for a particular organism, different modules can be selected for smORF search.

Implementation of comparative detection approaches for the accurate assessment of sediment thickness and sediment volume in the Passaúna Reservoir

Siltation has significant economic and social impacts as it directly reduces the useable amount of water in reservoirs. Giving a solution to the issue of sedimentation is a complicated task and maybe one of the most important engineering and environmental challenges of the 21^st century. The deposited volume and the distribution pattern of the sediment are often unknown and not easy to assess. The sedimentation process is highly dynamic, initially due to the hydrological conditions of the incoming rivers, but also due to common internal phenomena like resuspension or density currents. Sediment remediation measures such as mechanical sediment removal or flushing are planned based on the sediment thickness distribution and the overall sediment volume/mass. Often, the sediment thickness is calculated through topographic differencing between the pre-impoundment reservoir lake bottom and the actual lake bottom. However, it is common that the previous depth distribution map is not available or in insufficient quality. In this regard, alternative measurement techniques have to be taken into consideration. In this study, we assessed the best possible approach depending on the characteristics of the sediment and of the reservoir. We combined three different acoustic systems (a multibeam, a sub-bottom profiler, and a single beam dual frequency system) with sediment coring and dynamic free fall penetrometer measurements for an improved assessment of sediment stock and sediment distribution in the Passaúna Reservoir. Our results showed that topographic differencing could not be applied, as the data for the pre-impoundment lake bottom was insufficiently accurate. The parametric sub-bottom profiler could detect the sediment thickness in high accuracy, but significant limitations were recorded in areas with high gas contents. The dual-frequency echosounder derived the sediment thickness with a normalized mean absolute error of 56% due to the high volumetric gas content in the sediment. The dynamic free-fall penetrometer showed satisfying results compared to the other systems. The normalized mean absolute error was 22%, and sediment thickness could be detected in areas with up to 1.8 m of sediment. Sediment coring is also a reliable technique for sediment thickness determination. However, the results showed that if only traditional coring devices are used (gravity corer), the limited penetration depth of the equipment combined with sampling disturbances often prevent a correct assessment of the sediment thickness. The overall results of this study can help for an improved decision-making regarding reservoir management. The accurate assessment of sediment volume and distribution can reduce costs for sediment removal and assist in having a precise overview of the reservoir lifetime.

Towards the characterization of the hidden world of small proteins in Staphylococcus aureus, a proteogenomics approach

Small proteins play essential roles in bacterial physiology and virulence, however, automated algorithms for genome annotation are often not yet able to accurately predict the corresponding genes. The accuracy and reliability of genome annotations, particularly for small open reading frames (sORFs), can be significantly improved by integrating protein evidence from experimental approaches. Here we present a highly optimized and flexible bioinformatics workflow for bacterial proteogenomics covering all steps from (i) generation of protein databases, (ii) database searches and (iii) peptide-to-genome mapping to (iv) visualization of results. We used the workflow to identify high quality peptide spectrum matches (PSMs) for small proteins (≤ 100 aa, SP100) in Staphylococcus aureus Newman. Protein extracts from S. aureus were subjected to different experimental workflows for protein digestion and prefractionation and measured with highly sensitive mass spectrometers. In total, 175 proteins with up to 100 aa (SP100) were identified. Out of these 24 (ranging from 9 to 99 aa) were novel and not contained in the used genome annotation.144 SP100 are highly conserved and were found in at least 50% of the publicly available S. aureus genomes, while 127 are additionally conserved in other staphylococci. Almost half of the identified SP100 were basic, suggesting a role in binding to more acidic molecules such as nucleic acids or phospholipids.

Determination of antibiotic resistance genes in a WWTP-impacted river in surface water, sediment, and biofilm: Influence of seasonality and water quality

Many pathogenic bacteria are adapted to live in aquatic habitats, which makes rivers possible sources and spread pathways of antibiotic resistance, since they usually receive effluents from wastewater treatment plants (WWTP), possibly containing antibiotic residues and also antibiotic-resistant bacteria. This study investigates different monitoring strategies to identify the occurrence of antibiotic-resistant bacteria in rivers. We analyzed the presence of 13 antibiotic resistance genes (ARGs) and seven gene markers for facultative pathogenic bacteria (FPB) with qPCR in sampling sites upstream and downstream of a small WWTP in Southern Germany. Five sampling campaigns were conducted from February to June 2019. Surface water, sediment, and biofilm samples were analyzed. The biofilm was collected from an artificial sampler placed in the river. bla_TEM, ermB, tetM, and sul1 genes were detected in all samples analyzed. The results showed there was a previous background in the river, but the WWTP and the water quality of the river influenced the concentration and occurrence of ARGs and FPB. Genes representing resistance against strong or last-resort antibiotics, such as mecA, bla_CMY-2, bla_KPC-3, and mcr-1, and multidrug resistance were also detected, mainly in samples collected downstream of the WWTP. Downstream of the WWTP, the occurrence of ARG and FPB correlated with ammoniacal nitrogen, while upstream of the WWTP correlated with turbidity, suspended solids, and seasonal factors such as UVA radiation and the presence of macrophytes. Biofilm samples presented higher abundances of ARGs and FPB. The biofilm sampler was efficient and allowed to collect biofilms from specific periods, which helped to identify seasonal patterns.

Comparison of novel approaches for expedited pathogen identification and antimicrobial susceptibility testing against routine blood culture diagnostics

Blood stream infections pose a major challenge for clinicians as the immediate application of an appropriate antibiotic treatment is the vital factor to safe the patients' lives. This preliminary study compares three different systems promising fast pathogen identification and susceptibility testing in comparison to conventional blood culture (BC): (i) the rapid antimicrobial susceptibility testing protocol according to EUCAST in combination with the Sepsityper^® kit (sRAST), (ii) the direct inoculation method on the VITEK^®2 system (dVIT) and (iii) testing with the Accelerate Pheno^® system (AccPh). All methods were assessed in terms of accuracy, time to result and usability. Twenty‐three BC samples obtained from patients suffering from proven sepsis were analysed in detail. Pathogen identification was successful in 95·6, 91·3 and 91·3% in sRAST, dVIT and AccPh, respectively. Categorical agreement in antimicrobial susceptibility testing was 89·5, 96 and 96·6%, respectively. Time to result from sample entry to reporting ranged from an average of 4·6 h for sRAST and 6·9 h for AccPh to 10·6 h for dVIT. These results imply a significant shortening of reporting times at considerably high agreement rates for these new diagnostic approaches.

RegAB Homolog of Burkholderia pseudomallei is the Master Regulator of Redox Control and involved in Virulence

Burkholderia pseudomallei, the etiological agent of melioidosis in humans and animals, often occupies environmental niches and infection sites characterized by limited concentrations of oxygen. Versatile genomic features enable this pathogen to maintain its physiology and virulence under hypoxia, but the crucial regulatory networks employed to switch from oxygen dependent respiration to alternative terminal electron acceptors (TEA) like nitrate, remains poorly understood. Here, we combined a Tn5 transposon mutagenesis screen and an anaerobic growth screen to identify a two-component signal transduction system with homology to RegAB. We show that RegAB is not only essential for anaerobic growth, but also for full virulence in cell lines and a mouse infection model. Further investigations of the RegAB regulon, using a global transcriptomic approach, identified 20 additional regulators under transcriptional control of RegAB, indicating a superordinate role of RegAB in the B. pseudomallei anaerobiosis regulatory network. Of the 20 identified regulators, NarX/L and a FNR homolog were selected for further analyses and a role in adaptation to anaerobic conditions was demonstrated. Growth experiments identified nitrate and intermediates of the denitrification process as the likely signal activateing RegAB, NarX/L, and probably of the downstream regulators Dnr or NsrR homologs. While deletions of individual genes involved in the denitrification process demonstrated their important role in anaerobic fitness, they showed no effect on virulence. This further highlights the central role of RegAB as the master regulator of anaerobic metabolism in B. pseudomallei and that the complete RegAB-mediated response is required to achieve full virulence. In summary, our analysis of the RegAB-dependent modulon and its interconnected regulons revealed a key role for RegAB of B. pseudomallei in the coordination of the response to hypoxic conditions and virulence, in the environment and the host.

Adaptation of Dinoroseobacter shibae to oxidative stress and the specific role of RirA

Dinoroseobacter shibae living in the photic zone of marine ecosystems is frequently exposed to oxygen that forms highly reactive species. Here, we analysed the adaptation of D. shibae to different kinds of oxidative stress using a GeLC-MS/MS approach. D. shibae was grown in artificial seawater medium in the dark with succinate as sole carbon source and exposed to hydrogen peroxide, paraquat or diamide. We quantified 2580 D. shibae proteins. 75 proteins changed significantly in response to peroxide stress, while 220 and 207 proteins were differently regulated by superoxide stress and thiol stress. As expected, proteins like thioredoxin and peroxiredoxin were among these proteins. In addition, proteins involved in bacteriochlophyll biosynthesis were repressed under disulfide and superoxide stress but not under peroxide stress. In contrast, proteins associated with iron transport accumulated in response to peroxide and superoxide stress. Interestingly, the iron-responsive regulator RirA in D. shibae was downregulated by all stressors. A rirA deletion mutant showed an improved adaptation to peroxide stress suggesting that RirA dependent proteins are associated with oxidative stress resistance. Altogether, 139 proteins were upregulated in the mutant strain. Among them are proteins associated with protection and repair of DNA and proteins (e. g. ClpB, Hsp20, RecA, and a thioredoxin like protein). Strikingly, most of the proteins involved in iron metabolism such as iron binding proteins and transporters were not part of the upregulated proteins. In fact, rirA deficient cells were lacking a peroxide dependent induction of these proteins that may also contribute to a higher cell viability under these conditions.

Computational strategies to combat COVID-19: useful tools to accelerate SARS-CoV-2 and coronavirus research

SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) is a novel virus of the family Coronaviridae. The virus causes the infectious disease COVID-19. The biology of coronaviruses has been studied for many years. However, bioinformatics tools designed explicitly for SARS-CoV-2 have only recently been developed as a rapid reaction to the need for fast detection, understanding and treatment of COVID-19. To control the ongoing COVID-19 pandemic, it is of utmost importance to get insight into the evolution and pathogenesis of the virus. In this review, we cover bioinformatics workflows and tools for the routine detection of SARS-CoV-2 infection, the reliable analysis of sequencing data, the tracking of the COVID-19 pandemic and evaluation of containment measures, the study of coronavirus evolution, the discovery of potential drug targets and development of therapeutic strategies. For each tool, we briefly describe its use case and how it advances research specifically for SARS-CoV-2. All tools are free to use and available online, either through web applications or public code repositories. Contact:evbc@unj-jena.de.

Effective treatment of the wastewater from ceramic industry using ceramic membranes

Emissions of organic compounds, heavy metals and chemicals used in the ceramic industry cause significant organic and inorganic pollution of water. The effluent must be treated before it is discharged into a water body. International and EU laws control the chemical oxygen demand (COD) of the wastewater. Conventional technologies, such as sedimentation, flocculation and biological treatment, have lots of drawbacks, whereas membrane technologies give many benefits, as they are chemical-free and allow a reduction of the treatment steps. One-step wastewater nanofiltration with ceramic membranes of 450 Da cut-off is able to reduce the COD of ceramic wastewater to a sufficient level. However, the working time without cleaning is limited and the rejection of membranes can be significantly reduced due to fouling. Multistage filtration can be the solution. Filtration experiments with various combinations (MF, UF and NF) of ceramic membranes were performed at a laboratory scale with single-channel membranes and at pilot scale with 7-, 19- and 151-channel membranes in order to permanently reach the limit value of a COD below 80 mg/L and to increase the operating time. Four types of membranes were sequentially tested in the cross-flow mode: MF (200 nm pore size), UF (2,000 Da), NF (450 Da) and NF (200 Da). 5-day Biological Oxygen Demand (BOD) tests were performed in order to examine the wastewater biodegradability. The test results with single-channel membranes showed that in terms of the highest COD rejection and the highest permeability, the best combination was that of MF and UF membranes. Here, UF membranes were sufficient to reach the limit values. As for the multi-channel membranes, the combination of MF and NF (450 Da) was the best and the final COD concentration ranged from 11 to 48 mg/L. 5-day BOD bottle tests showed a COD/BOD ratio of 3.8, which opened up possibilities for combined treatment.

Genome-Wide Association Studies for the Detection of Genetic Variants Associated With Daptomycin and Ceftaroline Resistance in Staphylococcus aureus

Background

As next generation sequencing (NGS) technologies have experienced a rapid development over the last decade, the investigation of the bacterial genetic architecture reveals a high potential to dissect causal loci of antibiotic resistance phenotypes. Although genome-wide association studies (GWAS) have been successfully applied for investigating the basis of resistance traits, complex resistance phenotypes have been omitted so far. For S. aureus this especially refers to antibiotics of last resort like daptomycin and ceftaroline. Therefore, we aimed to perform GWAS for the identification of genetic variants associated with DAP and CPT resistance in clinical S. aureus isolates.

Materials/methods

To conduct microbial GWAS, we selected cases and controls according to their clonal background, date of isolation, and geographical origin. Association testing was performed with PLINK and SEER analysis. By using in silico analysis, we also searched for rare genetic variants in candidate loci that have previously been described to be involved in the development of corresponding resistance phenotypes.

Results

GWAS revealed MprF P314L and L826F to be significantly associated with DAP resistance. These mutations were found to be homogenously distributed among clonal lineages suggesting convergent evolution. Additionally, rare and yet undescribed single nucleotide polymorphisms could be identified within mprF and putative candidate genes. Finally, we could show that each DAP resistant isolate exhibited at least one amino acid substitution within the open reading frame of mprF. Due to the presence of strong population stratification, no genetic variants could be associated with CPT resistance. However, the investigation of the staphylococcal cassette chromosome mec (SCCmec) revealed various mecA SNPs to be putatively linked with CPT resistance. Additionally, some CPT resistant isolates revealed no mecA mutations, supporting the hypothesis that further and still unknown resistance determinants are crucial for the development of CPT resistance in S. aureus.

Conclusion

We hereby confirmed the potential of GWAS to identify genetic variants that are associated with antibiotic resistance traits in S. aureus. However, precautions need to be taken to prevent the detection of spurious associations. In addition, the implementation of different approaches is still essential to detect multiple forms of variations and mutations that occur with a low frequency.

[Obesity and eating disorders]

Obesity is a chronic disease that is difficult to manage and is often punctuated by treatment failure. Screening for eating disorders, the prevalence of which is high in overweight patients, is essential in order to minimize the risk of relapse and the «yoyo» phenomenon. As the reason for consulting obese subjects is rare to be eating disorders from the outset, it is necessary to assess this behaviour from the first consultations, in order to propose a specific therapeutic approach aimed at stable weight loss in the long term.

Genome-Based Analyses of Fitness Effects and Compensatory Changes Associated with Acquisition of bla CMY-, bla CTX-M-, and bla OXA-48/VIM-1-Containing Plasmids in Escherichia coli

(1) Background: Resistance plasmids are under selective conditions beneficial for the bacterial host, but in the absence of selective pressure, this carriage may cause fitness costs. Compensation of this fitness burden is important to obtain competitive ability under antibiotic-free conditions. In this study, we investigated fitness effects after a conjugative transfer of plasmids containing various beta-lactamase genes transferred into Escherichia coli. (2) Methods: Fourteen beta-lactamase-encoding plasmids were transferred from clinical donor strains to E. coli J53. Growth rates were compared for all transconjugants and the recipient. Selected transconjugants were challenged in long-term growth experiments. Growth rates were assessed at different time points during growth for 500 generations. Whole-genome sequencing (WGS) of initial and evolved transconjugants was determined. Results: Most plasmid acquisitions resulted in growth differences, ranging from -4.5% to 7.2%. Transfer of a single bla _CMY-16-carrying plasmid resulted in a growth burden and a growth benefit in independent mating. Long-term growth led to a compensation of fitness burdens and benefits. Analyzing WGS revealed genomic changes caused by Single Nucleotide Polymorphisms (SNPs) and insertion sequences over time. Conclusions: Fitness effects associated with plasmid acquisitions were variable. Potential compensatory mutations identified in transconjugants' genomes after 500 generations give interesting insights into aspects of plasmid-host adaptations.

Asking future doctors: what support options do medical students want to cope with medical school?

Aim

Medical school is demanding, and research aimed at improving the mental health of medical students is scarce. No quantitative study about which specific measures students actually prefer to reinforce their health has been performed yet. The aim of this survey is to find out which types of support should be given to medical students according to students’ own perspectives.

Subject and methods

A classroom survey of medical students (N = 1108, years 1–5) was carried out regarding various support options and depressive symptoms. The statistical analysis was finalized using chi-square tests, t-tests, and the Kolmogorov–Smirnov test.

Results

The support options with the highest average scores were accessible sports classes, desire for free water/fruit during lectures, and a clear study structure. Groups to exchange experiences with, including social media groups, were favored less. Depressive symptoms in students correlated with a higher level of applicability of support options.

Conclusion

Medical students require supportive study conditions. Specific subgroups of medical students could not be correlated to a particular support program. Thus, we need a support program that addresses students’ wishes, not a program based on feasibility, staff interests or passions.

High protein prescription in methylmalonic and propionic acidemia patients and its negative association with long-term outcome

BACKGROUND AND OBJECTIVE

Methylmalonic acidemia (MMA) and propionic acidemia (PA) are inborn errors of metabolism. While survival of MMA and PA patients has improved in recent decades, long-term outcome is still unsatisfactory. A protein restricted diet is the mainstay for treatment. Additional amino acid mixtures (AAM) can be prescribed if natural protein is insufficient. It is unknown if dietary treatment can have an impact on outcome.

DESIGN

We performed a nationwide retrospective cohort study and evaluated both longitudinal dietary treatment and clinical course of Dutch MMA and PA patients. Protein prescription was compared to the recommended daily allowances (RDA); the safe level of protein intake as provided by the World Health Organization. The association of longitudinal dietary treatment with long-term outcome was evaluated.

RESULTS

The cohort included 76 patients with a median retrospective follow-up period of 15 years (min-max: 0-48 years) and a total of 1063 patient years on a protein restricted diet. Natural protein prescription exceeded the RDA in 37% (470/1287) of all prescriptions and due to AAM prescription, the total protein prescription exceeded RDA in 84% (1070/1277). Higher protein prescriptions were associated with adverse outcomes in severely affected patients. In PA early onset patients a higher natural protein prescription was associated with more frequent AMD. In MMA vitamin B12 unresponsive patients, both a higher total protein prescription and AAM protein prescription were associated with more mitochondrial complications. A higher AAM protein prescription was associated with an increased frequency of cognitive impairment in the entire.

CONCLUSION

Protein intake in excess of recommendations is frequent and is associated with poor outcome.

A Multi-Omics Protocol for Swine Feces to Elucidate Longitudinal Dynamics in Microbiome Structure and Function

Swine are regarded as promising biomedical models, but the dynamics of their gastrointestinal microbiome have been much less investigated than that of humans or mice. The aim of this study was to establish an integrated multi-omics protocol to investigate the fecal microbiome of healthy swine. To this end, a preparation and analysis protocol including integrated sample preparation for meta-omics analyses of deep-frozen feces was developed. Subsequent data integration linked microbiome composition with function, and metabolic activity with protein inventories, i.e., 16S rRNA data and expressed proteins, and identified proteins with corresponding metabolites. 16S rRNA gene amplicon and metaproteomics analyses revealed a fecal microbiome dominated by Prevotellaceae, Lactobacillaceae, Lachnospiraceae, Ruminococcaceae and Clostridiaceae. Similar microbiome compositions in feces and colon, but not ileum samples, were observed, showing that feces can serve as minimal-invasive proxy for porcine colon microbiomes. Longitudinal dynamics in composition, e.g., temporal decreased abundance of Lactobacillaceae and Streptococcaceae during the experiment, were not reflected in microbiome function. Instead, metaproteomics and metabolomics showed a rather stable functional state, as evident from short-chain fatty acids (SCFA) profiles and associated metaproteome functions, pointing towards functional redundancy among microbiome constituents. In conclusion, our pipeline generates congruent data from different omics approaches on the taxonomy and functionality of the intestinal microbiome of swine.

Survey of metaproteomics software tools for functional microbiome analysis

To gain a thorough appreciation of microbiome dynamics, researchers characterize the functional relevance of expressed microbial genes or proteins. This can be accomplished through metaproteomics, which characterizes the protein expression of microbiomes. Several software tools exist for analyzing microbiomes at the functional level by measuring their combined proteome-level response to environmental perturbations. In this survey, we explore the performance of six available tools, to enable researchers to make informed decisions regarding software choice based on their research goals. Tandem mass spectrometry-based proteomic data obtained from dental caries plaque samples grown with and without sucrose in paired biofilm reactors were used as representative data for this evaluation. Microbial peptides from one sample pair were identified by the X! tandem search algorithm via SearchGUI and subjected to functional analysis using software tools including eggNOG-mapper, MEGAN5, MetaGOmics, MetaProteomeAnalyzer (MPA), ProPHAnE, and Unipept to generate functional annotation through Gene Ontology (GO) terms. Among these software tools, notable differences in functional annotation were detected after comparing differentially expressed protein functional groups. Based on the generated GO terms of these tools we performed a peptide-level comparison to evaluate the quality of their functional annotations. A BLAST analysis against the NCBI non-redundant database revealed that the sensitivity and specificity of functional annotation varied between tools. For example, eggNOG-mapper mapped to the most number of GO terms, while Unipept generated more accurate GO terms. Based on our evaluation, metaproteomics researchers can choose the software according to their analytical needs and developers can use the resulting feedback to further optimize their algorithms. To make more of these tools accessible via scalable metaproteomics workflows, eggNOG-mapper and Unipept 4.0 were incorporated into the Galaxy platform.

A complete and flexible workflow for metaproteomics data analysis based on MetaProteomeAnalyzer and Prophane

Metaproteomics, the study of the collective protein composition of multi-organism systems, provides deep insights into the biodiversity of microbial communities and the complex functional interplay between microbes and their hosts or environment. Thus, metaproteomics has become an indispensable tool in various fields such as microbiology and related medical applications. The computational challenges in the analysis of corresponding datasets differ from those of pure-culture proteomics, e.g., due to the higher complexity of the samples and the larger reference databases demanding specific computing pipelines. Corresponding data analyses usually consist of numerous manual steps that must be closely synchronized. With MetaProteomeAnalyzer and Prophane, we have established two open-source software solutions specifically developed and optimized for metaproteomics. Among other features, peptide-spectrum matching is improved by combining different search engines and, compared to similar tools, metaproteome annotation benefits from the most comprehensive set of available databases (such as NCBI, UniProt, EggNOG, PFAM, and CAZy). The workflow described in this protocol combines both tools and leads the user through the entire data analysis process, including protein database creation, database search, protein grouping and annotation, and results visualization. To the best of our knowledge, this protocol presents the most comprehensive, detailed and flexible guide to metaproteomics data analysis to date. While beginners are provided with robust, easy-to-use, state-of-the-art data analysis in a reasonable time (a few hours, depending on, among other factors, the protein database size and the number of identified peptides and inferred proteins), advanced users benefit from the flexibility and adaptability of the workflow.

Cluedo - Source identification in a case of septicemia fatality caused by Capnocytophaga canimorsus

The Gram negative pathogen Capnocytophaga canimorsus is a frequent commensal in the oral cavity of cats and dogs. Although the bacterium is generally considered harmless, infections in humans can occur displaying a broad spectrum of clinical syndromes. This makes a clinical diagnosis difficult. The patient in the present case was 67 years old and presented to the emergency room (ER) with pain in the upper right abdomen and clinical signs of a feverish infection. The only noticeable record in the patient´s medical history was a splenectomy in childhood. The anamnesis revealed that the patient was the owner of two dogs. After a suspected diagnosis of sepsis the patient was transferred to the intensive care unit (ICU), where his medical condition deteriorated rapidly. Despite intensive care measures as well as the fast initialization of a broad-spectrum antibiotic therapy, the patient died 37 h after his presentation in the ER. The search for the causative pathogen turned out to be challenging. Eventually, molecular biological methods assisted in solving the puzzle. It could be demonstrated that the pathogen, found in the patient´s blood, was also present in one of his dogs' oral cavity.

Comprehensive integrated NGS-based surveillance and contact-network modeling unravels transmission dynamics of vancomycin-resistant enterococci in a high-risk population within a tertiary care hospital

Vancomycin-resistant E. faecium (VRE) are an important cause of nosocomial infections, which are rapidly transmitted in hospitals. To identify possible transmission routes, we applied combined genomics and contact-network modeling to retrospectively evaluate routine VRE screening data generated by the infection control program of a hemato-oncology unit. Over 1 year, a total of 111 VRE isolates from 111 patients were collected by anal swabs in a tertiary care hospital in Southern Germany. All isolated VRE were whole-genome sequenced, followed by different in-depth bioinformatics analyses including genotyping and determination of phylogenetic relations, aiming to evaluate a standardized workflow. Patient movement data were used to overlay sequencing data to infer transmission events and strain dynamics over time. A predominant clone harboring vanB and exhibiting genotype ST117/CT469 (n = 67) was identified. Our comprehensive combined analyses suggested intra-hospital spread, especially of clone ST117/CT469, despite of extensive screening, single room placement, and contact isolation. A new interactive tool to visualize these complex data was designed. Furthermore, a patient-contact network-modeling approach was developed, which indicates both the periodic import of the clone into the hospital and its spread within the hospital due to patient movements. The analyzed spread of VRE was most likely due to placement of patients in the same room prior to positivity of screening. We successfully demonstrated the added value for this combined strategy to extract well-founded knowledge from interdisciplinary data sources. The combination of patient-contact modeling and high-resolution typing unraveled the transmission dynamics within the hospital department and, additionally, a constant VRE influx over time.

IS26-Mediated Transfer of bla NDM-1 as the Main Route of Resistance Transmission During a Polyclonal, Multispecies Outbreak in a German Hospital

One of the most demanding challenges in infection control is the worldwide dissemination of multidrug-resistant (MDR) bacteria in clinical settings. Especially the increasing prevalence of carbapenemase producing Gram-negative pathogens poses an urgent threat to public health, as these enzymes confer resistance to almost all β-lactam antibiotics including carbapenems. In this study, we report a prolonged nosocomial outbreak of various NDM-1-producing Enterobacterales species due to clonal spread and cross-species exchange of plasmids and possibly transposons. Between July 2015 and September 2017, a total of 51 carbapenemase-positive isolates were collected from 38 patients and three environmental sources in a single German hospital. Combining molecular typing methods and whole genome sequencing, the metallo-β-lactamase gene bla _NDM-1 was found to be present in 35 isolates of which seven additionally carried the carbapenemase gene bla _KPC-2. Core genome MLST (cgMLST) revealed different clusters of closely related isolates of Escherichia coli, Klebsiella pneumoniae, Citrobacter freundii, Morganella morganii or Enterobacter cloacae indicating clonal spread. The detailed reconstruction of the plasmid sequences revealed that in all outbreak-associated isolates bla_NDM-1 was located on similar composite transposons, which were also very similar to Tn125 previously described for Acinetobacter baumannii. In contrast to Tn125, these structures were flanked by IS26 elements, which could facilitate horizontal gene transfer. Moreover, the identical plasmid was found to be shared by E. coli and M. morganii isolates. Our results highlight the importance of detailed genome-based analyses for complex nosocomial outbreaks, allowing the identification of causal genetic determinants and providing insights into potential mechanisms involved in the dissemination of antibiotic resistances between different bacterial species.

Emerging contaminants and antibiotic resistance in the different environmental matrices of Latin America

This review aims to gather and summarize information about the occurrence of emerging contaminants and antibiotic resistance genes in environmental matrices in Latin America. We aim to contribute to future research by compiling a list of priority pollutants adjusted to the needs and characteristics of Latin America, according to the data presented in this study. In order to perform a comprehensive research and secure a representative and unbiased amount of quality data concerning emerging contaminants in Latin America, the research was performed within the Scopus® database in a time frame from 2000 to July 2019. The countries with higher numbers of published articles were Brazil and México, while most studies were performed in the surroundings of Mexico City and in Southern and Southeastern Brazil. The main investigated environmental matrices were drinking water and surface water. The presence of antibiotic resistance was frequently reported, mainly in Brazil. Monitoring efforts should be performed in other countries in Latin America, as well as in other regions of Brazil and México. The suggested priority list for monitoring of emerging contaminants in Latin America covers: di(2-ethylhexyl) phthalate (DEHP), bisphenol-A (BP-A), 4-nonylphenol (4-NP), triclosan (TCS), estrone (E1), estradiol (E2), ethinylestradiol (EE2), tetracycline (TC), amoxicillin (AMOX), norfloxacin (NOR), ampicillin (AMP) and imipenem (IMP). We hope this list serves as a basis for the orientation of the future research and monitoring projects to better understand the distribution and concentration of the listed emerging substances.