1,721,545 research outputs found
Real-time PCR based quantitative microbial source tracking : method characteristics and applicability
No full textRecent years have brought huge advances in methods for the identification of the sources of faecal pollution. However the use of quantitative real-time PCR (qPCR) for quantitative microbial source tracking (QMST) is facing challenges on the levels of methodology and applied study design. In terms of methodology this study aimed at defining some key issues for the quality assurance of QMST results. These include necessary definitions of the limit of detection (LOD) and the limit of quantification (LOQ) in qPCR methods based on the characteristics of the acquired data. Important factors influencing these key figures are the stochastic and truncated distribution of qPCR data at low concentrations and the heteroscedasticity of the measurement variability. In the light of the recovered results, further investigations should concentrate on the development of flexible confidence intervals, which take negative results into consideration or a probabilistic approach to determine the probability of a correct measurement, given a certain amount of target.In addition DNA extraction efficiencies were determined for QMST markers in various environmental water samples which help in determining sample limits of detection (SLODs). To assess the applicability of the ruminant-specific QMST BacR and the human-specific BacH methods beyond the catchment area they were originally developed in LKAS2, BacR/H were tested on water samples from alpine karstic spring LKAS8 situated on the Eastern verges of the Austrian calcareous alps. During a period of 17 months QMST markers, classical faecal indicators, hydrological and chemo-physical parameters were investigated. Taking into account the hydrological and water quality characteristics of the spring an innovative nested sampling design with three tiers was applied: (i) a three-weekly basic monitoring, (ii) a high frequency monitoring with 2 samplings per week during summer months, and (iii) an investigation of a late summer flood event. Statistical analysis of the results revealed the strong role of ruminant sources in faecal pollution of the spring while human sources seem to have a negligible impact on the spring water quality. This was especially evident in samples taken during the summer months and the flood event. In addition the nested sampling design proved to be a faesible and comprehensive approach for QMST investigations.The results from this study are in strong accordance with those from a previous study on the karstic spring LKAS2, emphasising the usefulness of the applied QMST approach
Exploring the full information content of genetic faecal markers for next generation water safety management
Full text linkDie fäkale Verunreinigung von Wasser ist die Hauptursache für wasserübertragbare Krankheiten, und wird seit über einem Jahrhundert durch die kultivierungsbasierte Detektion von bakteriellen Fäkalindikatoren nachgewiesen. Genetische Methoden bieten nun neue Möglichkeiten zur Analyse der fäkalen Verunreinigung von Wasser. Das Hauptziel dieser Arbeit bestand darin, zu untersuchen, wie genetische Fäkalmarker zukunftsweisendes Wassersicherheitsmanagement unterstützen können, und insbesondere darin, wie sie in die Einschätzung von Gesundheitsrisiken einbezogen werden können. Dieses Ziel wurde durch eine systematische Literaturanalyse und zwei Fallstudien verfolgt. Der Review Artikel stellt eine systematische Analyse der Anwendungsbereiche sowie der wichtigsten Forschungsfragen und Studiendesigns auf dem Gebiet der genetischen Fäkalmarker dar. Grundlage dieses Artikels ist die Analyse von über 1000 wissenschaftlichen Veröffentlichungen auf diesem Gebiet, wobei der Nachweis von Fäkalkontamination und deren Herkunftsbestimmung als die derzeitigen Hauptanwendungsbereiche ermittelt wurden. Bei der ersten Fallstudie handelt es sich um eine umfassende mikrobielle Herkunftsbestimmung, bei der die Donau und ihre Augebiete in Wien untersucht wurden. Die Ergebnisse der wirtsassoziierten genetischen Fäkalmarker deuten darauf hin, dass die Donau in erster Linie durch menschliche Abwässer belastet ist, während die Auen von mehreren Fäkalverschmutzungsquellen betroffen sind. Basierend auf diesen Ergebnissen wurde in der zweiten Fallstudie eine Szenarioanalyse durchgeführt. Hierbei wurden die Auswirkungen von Veränderungen im Einzugsgebiet einerseits auf die mikrobiologische Wasserqualität der Donau bei Wien sowie andererseits auf die daraus resultierenden mikrobiologischen Behandlungsanforderungen für eine sichere Trinkwasserversorgung untersucht. In dieser Studie wurden genetische Fäkalienmarker für das Setup und für die Kalibrierung eines kombinierten Modells, das aus ein mikrobiologisches Transportmodell für das Einzugsgebiet und ein gesundheitliches Risikoabschätzungsmodell (QMRA) besteht, verwendet. Das zweite Ziel der Arbeit bestand darin, die Einsetzbarkeit von Enzymaktivitätsmessungen (z. B. β-D-Glucuronidase, GLUC) zum Nachweis fäkaler Verunreinigungen sowie deren Anwendbarkeit für die Online-Überwachung von Fäkalkontamination zu bewerten. Die Analyse der veröffentlichten Literatur ergab, dass derartige Schnelltestverfahren bereits etabliert sind, die Aussagekraft so gewonnener Daten allerdings noch diskutiert wird.Faecal contamination of water is the primary origin of waterborne diseases and has been tested for using cultivation-based faecal indicator organisms for over a century. Genetic methods now allow new opportunities to analyse faecal contamination in water. The first, main objective of the thesis was to explore how genetic faecal markers may support next generation water safety management, and in particular, how they may be incorporated into health risk assessment. This objective was addressed through a systematic literature review and two case studies. The literature review provides a systematic analysis of application areas, key research questions and study designs in the scientific field of genetic faecal markers based on over 1000 publications. Faecal pollution detection and microbial source tracking, i.e., the tracking of the biological source of faecal pollution, were found to be the current core application areas. The first case study is comprehensive microbial source tracking investigation that assessed the Danube River and its floodplains at Vienna. The host-associated genetic faecal marker results indicate that the Danube is primarily impacted by human wastewater, while the floodplains are affected by mixed sources of faecal pollution. Based on these findings, the second case study was a scenario analysis of catchment changes and their impacts on the microbiological river water quality of the Danube River at Vienna, and the on the microbiological treatment requirements for safe drinking water supply. In this study, genetic faecal markers were employed to guide the setup and to calibrate a combined catchment microbial fate and transport and QMRA model. The second objective of the thesis was to assess the faecal indication capacity and field applicability of enzyme activity measurements (such as β-D-glucuronidase, GLUC) for online faecal pollution detection. The analysis of the published literature found that this method of rapid microbiology is an established method but open questions remain regarding its interpretation
Untersuchung von Antibiotikaresistenzmustern in niederösterreichischen Flüssen entlang von fäkalen Verschmutzungsgradienten
Full text linkAntibiotic resistance (AR) is increasing worldwide causing several hundred thousands of deaths per year. The clinical environment has been demonstrated to be a hot-spot of development, transmission and spread of AR in developed countries such as Austria. However, in the past years, there have been increasing discussions about the role of the natural environment in the transmission, evolution and spread of AR, and therefore environmental AR surveillance and monitoring is recommended. Antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARGs) predominantly enter surface waters such as lakes and rivers through faecal pollution via the wastewater pathway but also diffuse pollution sources such as agricultural run-offs. The aim of the thesis is to evaluate the AR and faecal pollution situation in Lower Austrian rivers in water and submerged biofilms with strong focus on the human wastewater pathway and also whether clinical resistance situation is reflected in the environment. The first chapter presents a large-scale screening of AR in three tributaries and a small stretch of the Danube River in Lower Austria over a one-year cycle. Beside river water samples, submerged biofilms were investigated to find out whether in these habitats is an accumulation of AR and if clinically relevant ARB and ARGs are likely to establish in the environment. All samples were investigated with a harmonised toolbox and study design to elucidate potential driving factors of the resistome in these rivers. For a quantitative assessment, the abundance of nine ARGs and the resistance ratios of 5197 Escherichia coli (E. coli) isolates were linked to quantitative faecal pollution data and environmental, chemical and hydrological parameters. The key parameter influencing AR abundance in the investigated catchment was anthropogenic faecal pollution and strongly connected to wastewater discharges. In all rivers the faecal pollution levels were clearly higher in the water compared to biofilm indicating that faecal bacteria do not establish in the riverine biofilm communities. However, for ARB and ARGs neither water nor biofilm could be identified as generally more important AR habitat with partly contrasting results for the individual rivers and at the sampling sites. This clearly indicates that general conclusions about the prevalence and potential driving factors of ARGs or phenotypic resistances in rivers and the role of biofilms should be drawn with caution, specifically when investigations were done at small spatial scales and with different methods. In the second chapter, the main results from first chapter concerning the occurrence and abundances of ARB and ARG in the four investigated rivers were summarized for the national water management sector and water authorities. This chapter also contains a detailed comparison of the measured ARB and ARG concentrations in river water with results from other countries with focus on Europe and shows that the investigated rivers in Austria display a comparably moderate pollution status concerning ARB and ARG.The third chapter represents a comparison of environmental E. coli isolates sampled in the Danube River upstream and downstream of a wastewater treatment plant receiving wastewater from a hospital with isolates obtained in the same hospital from urine of patients suffering from urinary tract infections or colonised urethral catheters. Patient isolates had significantly higher resistance ratios than the environmental ones and higher resistance ratios were found in biofilm compared to water. Seven extended-spectrum beta-lactamase (ESBL) producing isolates were isolated from the patients, two ESBL-E.coli were obtained from biofilm. In addition, one multi-drug resistant isolate carrying a tigecycline resistance, slightly higher imipenem and significantly higher amoxicillin/clavulanic acid resistance levels were detected in the biofilm isolates compared to the patient isolates.The fourth chapter evaluated the impact of a short-term cultural event on the faecal pollution status of the Traisen River. Enterococci and E. coli were quantified as standard faecal indicators before, during and after the music festival. During the event a massive increase in enterococci was observed, while the E. coli concentrations did not show such clear elevation. The difference of the two indicators may be explained by different persistence to many of the substances of personal care products which were found in high levels water. The different sensitivity may have been additionally supported by the high water temperatures and solar radiation during the festival period. In concern of human health, for upcoming festivals a more effective management, i.e., improved sanitation infrastructure and better waste management, is recommended to prevent such massive faecal pollution in the Traisen River.Although this thesis has a strong focus on rivers in Lower Austria, the developed investigation strategy including study design and quantitative methodology allows comparing AR prevalences internationally. In addition to the investigation strategy which can be applied on different environmental waters, the thesis provides suggestions for future management strategies, e.g., application of more efficient wastewater treatment and creation of awareness for AR, to prevent dissemination and mitigation of AR and faecal pollution in the riverine environment
Development of graphene-based materials as antimicrobial additives for 3D polymers
No full textThe goal of the diploma thesis was to achieve antibacterial properties by graphene materials themselves, enhancement due doping of graphene materials by Ag(I) and Cu(I)-ions, or enhancement due deposition of Ag-NP, Cu-NP, Cu/Cu2O-NP, Cu2(OH)3Cl-NP (copper oxychloride) on graphene oxide and integration into different kind of resins that could be polymerised using 3D printing. Materials with antibacteral properties could be used as alternative medical devices such as dental aerosol exhausters, plastic masks, or different kind of prothesis and implants. The main purpose is to achieve good antimicrobial properties while mechanical and printing properties of polymers would not deteriorate due modification and graphene material additions. Graphene oxide was produced via electrochemical exfoliation of graphite rods. The graphene oxide was reduced and modified by the materials mentioned above. The versatile graphene modifications were mixed with two different resins that are commonly used in 3D printing for medical devices namely the LT Dental and the Standard Grey resins. Rectangular and cubic formations were 3D printed under well-defined conditions. The produced graphene oxide modifications were characterised via several methods such as Raman spectroscopy, SEM/EDX, XRD spectroscopy. Furthermore, on the polymer composites different kinds of antimicrobial property analysis were carried out such as OD600 measurements for screening, subsequent well plate analysis, LDH cytotoxicity assay, Cellular ROS assay and Presto Blue Cell Viability Reaction, respectively. The characterization of the novel graphene oxide modifications was very promising, and the composites were stable over a longer period. However, after the application to polymers the antibacterial property analysis was not showing so high effectiveness than the one in the literature [1], so the process of the additive manufacturing needs to be improved and changed in order to achieve better results
Ein Vergleich von Antibiotikaresistenzen aus klinischen E. coli Isolaten mit Isolaten aus der Donau
No full textEvaluation des E. coli Effektorproteins EspG und seiner Rolle in chronisch entzündlichen Darmerkrankungen
No full textChronisch entzündliche Darmerkrankungen (CED) zeichnen sich durch Entzündungen des gastrointestinalen (GI) Traktes aus. Die zwei häufigsten CED sind Morbus Crohn (MC) und Colitis Ulcerosa. (CU) CED breiten sich in den letzten Jahrzehnten immer schneller aus und mittlerweile sind über 3.6 Millionen Menschen davon betroffen. Die Pathogenese von CEDs beinhaltet drei Faktoren: genetische Suszeptibilität, Umweltfaktoren und das Mikrobiom des GI-Traktes. Es wurde gezeigt, dass das Effektorprotein EspG, welches in pathogenen Enterobacteriacea-Spezies vorkommt, humane p21-aktivierte Kinasen (PAKs) binden und aktivieren kann. PAKs aktivieren proinflammatorische Signalkaskaden und sind in CED sowohl überexprimiert als auch aktiviert. Die zugrunde liegenden biochemischen Ursachen verbleiben jedoch unklar. Das Ziel dieser Diplomarbeit war es die Inzidenz von EspG und in CED Patienten zu evaluieren. Die Untersuchung von DNS aus Stuhlproben (152 CU, 210 MC, 100 Kontrollen) mittels Polymerase Kettenreaktion (PCR) ergab, dass 20 % der CED Patienten detektierbare Mengen von EspG in ihrem Stuhl haben, im Vergleich zu 10 % in der Kontrollgruppe. Das Vorhandensein von EspG ist mit entzündlichen Prozessen assoziiert, da der Median der EspG-positiven CU Proben mit 468 mg/kg deutlich über dem EspG-negativer Proben (155 mg/kg) liegt. Neun aus dreizehn CED-Patienten zeigen eine Assoziation von EspG mit Spitzen in Calprotektin-Werten im longitudinalen Verlauf. Quantitative PCR Analysen ergaben, dass eine metagenomische Rekonstruktion der EspG-tragenden Bakteriengenome in 11 MC Proben möglich ist. Das Vorhandensein der EspG-tragenden bakteriellen Pathogenitätsinsel wurde bei ausgewählten Proben weiters mittels Multiplex-PCR bestätigt. Des Weiteren wurde beim Sequenzieren der EspG-PCR-Produkte bisher unbeschriebene DNS Codes entdeckt, was auf unbekannte bakterielle Spezies hinweist. Zusammengenommen zeigen diese Ergebnisse eine Assoziation von EspG mit CED und weisen damit in Richtung eines neuen biochemischen Weges, welcher für die Entwicklung personalisierte Behandlungen genutzt werden könnte.Inflammatory bowel diseases (IBD) are chronic diseases with inflammation of the gastrointestinal tract and comprise ulcerative colitis (UC) and Crohn's disease (CD).The pathogenesis of IBD involves three major, intertwined denominators: genetic susceptibility, environmental factors and the gut microbiota. The pathogenic Enterobacteriacea effector protein EspG has been shown to bind and activate human p21-activated kinases (PAK). PAKs drive proinflammatory pathways and are overexpressed and activated in IBD, although the underlying biological processes are not understood. The aim of this thesis was to evaluate the incidence of EspG in IBD patients. Polymerase chain reaction (PCR) screening of DNA extracted out of stool samples (152 UC, 210 CD, 100 controls) revealed that 20 % of IBD patients have traceable amounts of EspG in their feces compared to 10 % in the control group. EspG positivity is associated with inflammation, as median calprotectin value of EspG-positive UC patients was more than three times as high (468 mg/kg) than in the EspG-negative UC population (155 mg/kg). Longitudinal analysis revealed that 9 out of 13 IBD-patients displayed a distinct association of EspG-positivity with spikes in calprotectin-values. Quantitative PCR suggested metagenomic reconstruction of the EspG-carrying bacterial genomes being feasible in 11 CD-samples. Presence of the bacterial EspG-carrying pathogenicity islands was further confirmed with a multiplex-PCR in selected samples. Sequencing of EspG-PCR amplifications hints to undescribed bacterial species being involved in these observations. Taken together these results validate an association of EspG with IBD, thereby pointing in the direction of a novel pathway that can be harnessed for personalized treatment
Going Beyond Counting First Authors in Author Co-citation Analysis
Full text linkThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Effect of scale and configuration on partial nitritation and anammox process
Full text linkDie ständige Neigung der Menschen, sich in städtischen Gebieten zu konzentrieren hat zu neuen Herausforderungen in Bezug auf das eingeleitete Abwasser und seine Behandlung geführt. Die Kombination der partiellen Nitritation und des Anammox Prozesses ist eine kosteneffiziente Methode, um kommunale Abwässer reich an Ammonium zu behandeln. Im Rahmen dieser Arbeit wurde der Einfluss von Maßstab und Konfiguration auf die partielle Nitritation und Anammox während einer Alkalinitätsreduzierung untersucht. Zur Durchführung der Untersuchung wurden zwei halbtechnische Reaktoren und ein 3 L Labor Reaktor zum Einsatz gebracht. Ammonium und andere Parameter wurden konstant gehalten, während dessen wurde die Alkalinität schrittweise reduziert. In einen der halbtechnischen Reaktoren wurde durch ein Sieb ein Reaktor mit zwei Kammern geschaffen. Eine Partikelmessung wurde durchgeführt, um zu sehen, in welchem Reaktor mehr Anammox Granulen mit größerem Durchmesser enthalten. Die Partikelmessung hat gezeigt, dass das Einkammersystem prozentual 40% Partikel in der Größe 50-150 μm und 43% in der Größe 10-50 μm beinhaltet, wohingegen im Zweikammersystem 34% Partikel in der Größe von 50-150 μm und 27% in der Größe von 10-50 μm wuchsen. Das kontinuierlich betriebene Zweikammersystem mit dem eingesetzten Sieb konnte größere Anammox Granulen zurückhalten. Die Auswertung der Stickstoffverbindungen zeigte, dass die Strategie für die Regulierung der im Reaktor vorhandenen Mikroorganismen gut funktionierte. Die durchschnittliche Stickstoffentfernung nach künstlicher Alkalinitätszufuhr im Einkammersystem erreichte 73 % und im Zweikammersystem 69 %. Dennoch war sowohl in den halbtechnischen Reaktoren als auch im kleintechnischen Reaktor eine Ansammlung von Nitrat vorhanden. Die durchschnittliche Stickstoffentfernung für einen m3 Belüftungsvolumen, während der Alkalinitätsuntersuchung war 0.0125 kg N im Einkammersystem (SBR) und 0.0180 kg im Zweikammersystem (kontinuierlich). Der 3 L Reaktor hatte mit 0.0024 kg vergleichbare Ergebnisse. Der 3 L Reaktor zeigte die geringste Sensibilität bezüglich Alkalinitätslimitierung, während das Einkammersystem am meisten davon betroffen war, indem die Abbauleistung schneller zurückging. Eine weitere Optimierung von Ammonium oxidierenden Bakterien könnte die Leistung der partiellen Nitritation und des Anammox Prozesses verbessern, besonders in dem kontinuierlichen Zweikammersystem mit dem Potential geringerer Lachgasemissionen.The continuous disposition of people to concentrate in urban areas has risen challenges regarding the discharged wastewater and its treatment. Partial nitritation and anammox is a cost-effective method for treating municipal wastewater rich in ammonia. In the frame of this study, the influence of scale and configuration on the partial nitritation and anammox was assessed, while alkalinity was reduced. Two semi-scale reactors (375 L) and a 3 L lab reactor were set up to carry out the experiment. Ammonium and other parameters were kept constant while the alkalinity was reduced gradually. Furthermore, a mesh was integrated into one of the semi-scale reactors, to create two compartments. A particle measurement was undertaken to see which reactor had larger anammox granules. Particle measurement showed that the one-compartment system had 40% of size 50-150μm and 43% were of size 10-50μm, whereas the two-compartment system had 34% particles in the range of 50-150μm and 27% of 10-50μm. The integrated mesh did assist in retaining larger anammox granules in the two-compartment system. N-compound evaluation showed that the control strategy to regulate the microorganism consortia in the bioreactor worked well. The average nitrogen removal efficiency after supplemental alkalinity reached up to 76% for the one-compartment system and 69% for the two-compartment system. However, an accumulation of nitrates was present in both semi-scale reactors and the small-scale reactor. In one-compartment system (SBR) and two-compartment system (continuous) the average nitrogen removal efficiency during the alkalinity limitation experiment was 0.0125 and 0.0180 kg N removal per m3 aeration. Also, the small-scale reactor was comparable in this regard with 0.0024 kg N removal per m3 aeration. The 3 L reactor showed the least sensibility with respect to the alkalinity limitation, while the one-compartment bioreactor was the most affected by a faster reduction of removal rate. Further optimization of the ammonium oxidizing bacteria could possibly improve the performance of partial nitritation and anammox process, especially in the two-compartment system (continuous) with the potential of lower nitrous oxide emissions
Elucidating the potential of high-throughput sequencing for microbiological water quality monitoring
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