Development of computational, mathematical and instrumental methods for the analysis of physiological processes in microbial populations

Die Fortschritte der modernen Mikrobiologie und die Verfügbarkeit neuer Hochdurchsatzmethoden liefern eine Fülle von Daten und Informationen. Durch geeignete Methoden und Modelle prozessiert, schaffen diese eine Basis für ein besseres Verstehen physiologischer Prozesse in mikrobiellen Populationen. Im ersten Teil dieser Arbeit wurde die Software eSOMet entwickelt. Sie ist ein Werkzeug zur Untersuchung metabolischer Profile mit dem Ziel diese ähnlichkeitsbasiert zu clustern. Da verschiedene Cluster unterschiedliche physiologische Zustände beschreiben, lassen sich damit diejenigen Metabolite identifizieren, deren Abundanzänderung für den Wechsel zwischen zwei Zuständen charakteristisch ist. Zum hochqualitativen Clustern wurde ein auf einer Hauptkomponentenanalyse basierter Rauschfilter und die Methode der emergenten selbstorganisierenden Karten implementiert. Am Beispiel verschiedener Kultivierungen von Corynbacterium glutamicum über mehrere Wachstumsphasen, konnte die Software erfolgreich evaluiert werden. Im zweiten Teil wurde ein spieltheoretisches Modell zur Untersuchung der Kulturheterogenität in mikrobiellen Populationen entwickelt. Als Heterogenitätskriterium wurde die Anzahl von Distribusomen definiert. Dies sind Zellbestandteile, deren Abundanz einen quantitativen Einfluss auf die Fitness der Subpopulation haben und die durch Zellteilung stochastisch weiterverteilt werden. Unter der Annahme, dass der Photosyntheseapparat von Dinoroseobacter shibae in solchen Distribusomen organisiert ist, konnte theoretisch gezeigt werden, dass sich unter fluktuierenden Umweltbedingungen oszillierend-stabile Subpopulationen ausbilden, die einen evolutionären Vorteil prägen. Um die theoretischen Ergebnisse des zweiten Teils experimentell zu verifizieren, wurde ein Kultivierungsverfahren im Mikrotitermaßstab entwickelt, welches vollautomatisiert durchgeführt eine in vivo Quantifizierung von Bacteriochlorophyll-a unter fluktuierenden Lichtbedingungen zuließ.The progress of modern microbiology and availability of novel high-throughput methods deliver a wealth of data and information. Processed by appropriate methods and models, they provide a basis for a better understanding of physiological processes in microbial populations. In the first part of this work the software eSOMet was developed. It is a tool for the investigation of metabolic profiles aiming to cluster those based on their similarity. Since distinct clusters are descriptors for different physiological states, this method allows the identification of metabolites, which changes of abundance are characteristic for the switch between two states. For high-quality clustering a principle component analysis based noise filter and the method of emergent selforganizing maps were implemented. The software could be successfully evaluated, using the example of different cultivations of Corynebacterium glutamicum over several growth phases. In the second part of this work, a game-theoretical model for the investigation of culture heterogeneity in microbial populations was developed. As heterogeneity criterion the number of distribusomes was defined. These are intracellular particles, which abundance influences the fitness of each subpopulation and which are distributed stochastically during cell division. Under the hypotheses, that the photosynthetic apparatus of Dinoroseobacter shibae is organized in such distribusomes it was shown in theory, that under fluctuating environmental conditions oscillating-stable fractions of subpopulations emerge, exhibiting an evolutionary advantage. In order to verify the theoretical results of the second part experimentally, a cultivation technique was developed at microtiter scale, which can be operated in a fully automated manner and allows for the in vivo quantification of Bchl-a under fluctuating light conditions

Microplastic distributions in a domestic wastewater treatment plant: Removal efficiency, seasonal variation and influence of sampling technique

Wastewater treatment plants (WWTPs) serve as an important route of microplastics (MPs) to the environment. Therefore, more effective MPs sampling and detection methodologies, as well as a better understanding of their influence on MPs occurrence and distributions in WWTP effluents, are needed for better removal and control. In this work, the efficiency of a municipal WWTP to remove MPs was assessed by collecting samples from raw to tertiary effluent during a 12-month sampling campaign (season-based) using different sampling methods (containers, 24-h composite and large grab samples). MPs retrieved from different treatment units within the WWTP were identified and quantified using plastic/non-plastic staining followed by optical microscopy, SEM and μ-Raman microscopy. Overall, the mean removal efficiency of MPs in the WWTP was 97%, with most MPs removed by the secondary stage and a mean effluent concentration of 1.97 MPs L−1 after sand filtration. The relative abundance of particles was lower than fibers in treated effluent compared with the raw wastewater, with MP fibers constituting 74% of the total MPs in raw wastewater and 91% in treated effluent. Taking seasonal variations into account is important as total MPs concentration in the effluent was notably higher in winter compared with the other seasons. Increasing the sampled volume using large samples or 24-h composite samples significantly reduced the variability between replicates. However, MPs concentration post the tertiary stage was significantly lower using morning sampling (9 am) by large grab sampling method (1.2 MPs L−1) compared to 24-h composite sampling (3.2 MPs L−1) possibly due to intra-daily changes. Using a finer mesh size (0.45 μm) to capture MPs beyond the size range typically studied (≥20 μm) effectively doubled the number of MPs detected in the tertiary effluent and highlights the importance of standardizing sampling procedures.acceptedVersio

SYSTOMONAS — an integrated database for systems biology analysis of Pseudomonas

To provide an integrated bioinformatics platform for a systems biology approach to the biology of pseudomonads in infection and biotechnology the database SYSTOMONAS (SYSTems biology of pseudOMONAS) was established. Besides our own experimental metabolome, proteome and transcriptome data, various additional predictions of cellular processes, such as gene-regulatory networks were stored. Reconstruction of metabolic networks in SYSTOMONAS was achieved via comparative genomics. Broad data integration is realized using SOAP interfaces for the well established databases BRENDA, KEGG and PRODORIC. Several tools for the analysis of stored data and for the visualization of the corresponding results are provided, enabling a quick understanding of metabolic pathways, genomic arrangements or promoter structures of interest. The focus of SYSTOMONAS is on pseudomonads and in particular Pseudomonas aeruginosa, an opportunistic human pathogen. With this database we would like to encourage the Pseudomonas community to elucidate cellular processes of interest using an integrated systems biology strategy. The database is accessible at

Freedom of expression, accountability and development in the Arab region

Mechanisms for ensuring government transparency and accountability have yet to become established in the Arab region, where oil rents and security rents have traditionally enabled governments to provide jobs and services without having to rely heavily, if at all, on raising revenue through personal income tax on citizens. Yet various forms of resource mobilisation, which will be needed in future, are likely to require a greater degree of accountability from those responsible for such mobilisation. This paper considers whether a move in this direction is under way. It reviews government approaches to freedom of expression in the media and among non-governmental organisations. It notes changes that have taken place in this sphere since the start of the 1990s, not all of them positive, and concludes that many more steps remain to be taken if media organisations and NGOs are to exert pressure for accountability on behalf of citizens, and especially the disadvantaged

Antimicrobial resistance among migrants in Europe: a systematic review and meta-analysis

BACKGROUND: Rates of antimicrobial resistance (AMR) are rising globally and there is concern that increased migration is contributing to the burden of antibiotic resistance in Europe. However, the effect of migration on the burden of AMR in Europe has not yet been comprehensively examined. Therefore, we did a systematic review and meta-analysis to identify and synthesise data for AMR carriage or infection in migrants to Europe to examine differences in patterns of AMR across migrant groups and in different settings. METHODS: For this systematic review and meta-analysis, we searched MEDLINE, Embase, PubMed, and Scopus with no language restrictions from Jan 1, 2000, to Jan 18, 2017, for primary data from observational studies reporting antibacterial resistance in common bacterial pathogens among migrants to 21 European Union-15 and European Economic Area countries. To be eligible for inclusion, studies had to report data on carriage or infection with laboratory-confirmed antibiotic-resistant organisms in migrant populations. We extracted data from eligible studies and assessed quality using piloted, standardised forms. We did not examine drug resistance in tuberculosis and excluded articles solely reporting on this parameter. We also excluded articles in which migrant status was determined by ethnicity, country of birth of participants' parents, or was not defined, and articles in which data were not disaggregated by migrant status. Outcomes were carriage of or infection with antibiotic-resistant organisms. We used random-effects models to calculate the pooled prevalence of each outcome. The study protocol is registered with PROSPERO, number CRD42016043681. FINDINGS: We identified 2274 articles, of which 23 observational studies reporting on antibiotic resistance in 2319 migrants were included. The pooled prevalence of any AMR carriage or AMR infection in migrants was 25·4% (95% CI 19·1-31·8; I2 =98%), including meticillin-resistant Staphylococcus aureus (7·8%, 4·8-10·7; I2 =92%) and antibiotic-resistant Gram-negative bacteria (27·2%, 17·6-36·8; I2 =94%). The pooled prevalence of any AMR carriage or infection was higher in refugees and asylum seekers (33·0%, 18·3-47·6; I2 =98%) than in other migrant groups (6·6%, 1·8-11·3; I2 =92%). The pooled prevalence of antibiotic-resistant organisms was slightly higher in high-migrant community settings (33·1%, 11·1-55·1; I2 =96%) than in migrants in hospitals (24·3%, 16·1-32·6; I2 =98%). We did not find evidence of high rates of transmission of AMR from migrant to host populations. INTERPRETATION: Migrants are exposed to conditions favouring the emergence of drug resistance during transit and in host countries in Europe. Increased antibiotic resistance among refugees and asylum seekers and in high-migrant community settings (such as refugee camps and detention facilities) highlights the need for improved living conditions, access to health care, and initiatives to facilitate detection of and appropriate high-quality treatment for antibiotic-resistant infections during transit and in host countries. Protocols for the prevention and control of infection and for antibiotic surveillance need to be integrated in all aspects of health care, which should be accessible for all migrant groups, and should target determinants of AMR before, during, and after migration. FUNDING: UK National Institute for Health Research Imperial Biomedical Research Centre, Imperial College Healthcare Charity, the Wellcome Trust, and UK National Institute for Health Research Health Protection Research Unit in Healthcare-associated Infections and Antimictobial Resistance at Imperial College London

Surgical site infection after gastrointestinal surgery in high-income, middle-income, and low-income countries: a prospective, international, multicentre cohort study

Background: Surgical site infection (SSI) is one of the most common infections associated with health care, but its importance as a global health priority is not fully understood. We quantified the burden of SSI after gastrointestinal surgery in countries in all parts of the world. Methods: This international, prospective, multicentre cohort study included consecutive patients undergoing elective or emergency gastrointestinal resection within 2-week time periods at any health-care facility in any country. Countries with participating centres were stratified into high-income, middle-income, and low-income groups according to the UN's Human Development Index (HDI). Data variables from the GlobalSurg 1 study and other studies that have been found to affect the likelihood of SSI were entered into risk adjustment models. The primary outcome measure was the 30-day SSI incidence (defined by US Centers for Disease Control and Prevention criteria for superficial and deep incisional SSI). Relationships with explanatory variables were examined using Bayesian multilevel logistic regression models. This trial is registered with ClinicalTrials.gov, number NCT02662231. Findings: Between Jan 4, 2016, and July 31, 2016, 13 265 records were submitted for analysis. 12 539 patients from 343 hospitals in 66 countries were included. 7339 (58·5%) patient were from high-HDI countries (193 hospitals in 30 countries), 3918 (31·2%) patients were from middle-HDI countries (82 hospitals in 18 countries), and 1282 (10·2%) patients were from low-HDI countries (68 hospitals in 18 countries). In total, 1538 (12·3%) patients had SSI within 30 days of surgery. The incidence of SSI varied between countries with high (691 [9·4%] of 7339 patients), middle (549 [14·0%] of 3918 patients), and low (298 [23·2%] of 1282) HDI (p < 0·001). The highest SSI incidence in each HDI group was after dirty surgery (102 [17·8%] of 574 patients in high-HDI countries; 74 [31·4%] of 236 patients in middle-HDI countries; 72 [39·8%] of 181 patients in low-HDI countries). Following risk factor adjustment, patients in low-HDI countries were at greatest risk of SSI (adjusted odds ratio 1·60, 95% credible interval 1·05–2·37; p=0·030). 132 (21·6%) of 610 patients with an SSI and a microbiology culture result had an infection that was resistant to the prophylactic antibiotic used. Resistant infections were detected in 49 (16·6%) of 295 patients in high-HDI countries, in 37 (19·8%) of 187 patients in middle-HDI countries, and in 46 (35·9%) of 128 patients in low-HDI countries (p < 0·001). Interpretation: Countries with a low HDI carry a disproportionately greater burden of SSI than countries with a middle or high HDI and might have higher rates of antibiotic resistance. In view of WHO recommendations on SSI prevention that highlight the absence of high-quality interventional research, urgent, pragmatic, randomised trials based in LMICs are needed to assess measures aiming to reduce this preventable complication

Reducing the environmental impact of surgery on a global scale: systematic review and co-prioritization with healthcare workers in 132 countries

Abstract Background Healthcare cannot achieve net-zero carbon without addressing operating theatres. The aim of this study was to prioritize feasible interventions to reduce the environmental impact of operating theatres. Methods This study adopted a four-phase Delphi consensus co-prioritization methodology. In phase 1, a systematic review of published interventions and global consultation of perioperative healthcare professionals were used to longlist interventions. In phase 2, iterative thematic analysis consolidated comparable interventions into a shortlist. In phase 3, the shortlist was co-prioritized based on patient and clinician views on acceptability, feasibility, and safety. In phase 4, ranked lists of interventions were presented by their relevance to high-income countries and low–middle-income countries. Results In phase 1, 43 interventions were identified, which had low uptake in practice according to 3042 professionals globally. In phase 2, a shortlist of 15 intervention domains was generated. In phase 3, interventions were deemed acceptable for more than 90 per cent of patients except for reducing general anaesthesia (84 per cent) and re-sterilization of ‘single-use’ consumables (86 per cent). In phase 4, the top three shortlisted interventions for high-income countries were: introducing recycling; reducing use of anaesthetic gases; and appropriate clinical waste processing. In phase 4, the top three shortlisted interventions for low–middle-income countries were: introducing reusable surgical devices; reducing use of consumables; and reducing the use of general anaesthesia. Conclusion This is a step toward environmentally sustainable operating environments with actionable interventions applicable to both high– and low–middle–income countries