Bacterial contamination of platelet concentrates (PCs) poses the major transfusion-associated infectious risk. Coagulase negative staphylococci (CoNS), the predominant platelet contaminants, are recognized as one of the leading causes of hospital-acquired infections due to their ability to form biofilms (surface-attached aggregates). In this study, 29 CoNS strains were characterized for their growth and biofilm formation abilities in media and PCs. Twenty-five strains were aerobic including Staphylococcus epidermidis, S. capitis, and S. chromogenes, while four were identified as the anaerobe S. saccharolyticus. Biofilm-associated icaA and icaD genes were amplified from eight strains. Interestingly, only six of those strains were biofilm-positive. Sequencing of S. capitis icaD revealed no mutations that could explain differences in biofilm phenotypes. Growth of CoNS in PCs varied significantly between strains. This study provides preliminary evidence that slow-growing biofilm-positive S. epidermidis are more likely to be missed during platelet culture, highlighting the need for improved screening methods.

Aim: Microbial biofilm matrix contains polysaccharides and proteins and can require extracellular nucleic acids for initial formation. Experiments were designed to identify infectious pathogens in human aneurysms and to characterize biofilm formed by calcified human arterial-derived nanoparticles. Materials & method: A total of 26 different microbial pathogens were isolated from 48 inflammatory aneurysms. Consistent amounts (0.49 McFarland units) of nanoparticles derived from similar tissue were seeded into 24-well plates and cultured for 21 days in the absence (control) or presence of RNase, tetracycline or gentamicin. Results: Control biofilm developed within 14 days, as detected by concanavalin A and BacLight™ Green staining. The formation of biofilm in wells treated with RNase was not different from the control; however, gentamicin partially inhibited and tetracycline completely inhibited biofilm formation. Therefore, nanoparticle biofilm retains some characteristics of conventional bacterial biofilm and requires protein-calcium interactions, although extracellular RNA is not required. Conclusion: This model system may also allow study of nanosized vesicles derived from donor tissue, including any microbes present, and could provide a useful tool for in vitro investigation of nanoparticle biofilm formation.

The new Canadian federal wastewater regulations, which restricts the release of ammonia from treated wastewaters, has resulted in upgrade initiatives at many water resource recovery facilities across the country to reduce the discharge of ammonia into our natural waters. The objective of this dissertation is therefore to investigate and optimize the performance of two attached growth technologies for rural and peri-urban/urban municipal ammonia removal. In particular, the first specific objective of this dissertation is to investigate the performance and microbial response of the BioCord technology as an upgrade system for the post-carbon removal nitrification of rural wastewaters. The second specific objective is to study the start-up of an attached growth anammox technology to enhance current knowledge pertaining to anammox biofilm attachment, growth and maturation. The results pertaining to the first specific objective of this research, a study of the design and optimization of the BioCord technology, demonstrates a recommended design rate for the post-carbon removal, nitrifying BioCord system of a surface area loading rate (SALR) of 1.6 NH4⁺-N/m²·d and up to 1.8 NH4⁺-N/m²·d with steady ammonia-nitrogen removal efficiencies greater than 90% and steady and low solids production rate up to 0.26 g TSS/d. A loss of system stability and biofilm sloughing, identified as fluctuating ammonia removal rates and solids production rates, were observed at elevated SALRs of 2.1 and 2.4 g -N/m²·d. The microbial results indicate that the meso-scale structure of the biofilm and the micro-animal population are directly affected by operational conditions. Enhanced air scouring configuration is shown to be a potential optimization strategy to prevent the clogging of biofilm pores and improve the system stability in terms of solids production rate in the BioCord technology. The results pertaining to the second specific objective of this research, the study of inoculation and carrier modification strategies for the rapid start-up of attached growth anammox technology, demonstrates significantly higher kinetics, faster biofilm growth and greater anammox bacteria enrichment on the silica-functionalized carriers and pre-seeded denitrifying carriers in a system inoculated with detached anammox biofilm mass during the early stages of attachment and growth of start-up. The study suggests that the use of the silica-functionalized and pre-seeded denitrifying carriers along with detached anammox biofilm inoculation has the potential to accelerate the anammox biofilm attachment, growth and maturation.

Indiana University-Purdue University Indianapolis (IUPUI) / Dental biofilm is a main contributing factor in the initiation and progression of dental caries. The maturation of dental biofilms is expected to alter the anti-caries efficacy of fluoride compounds. In the first aim, we conducted a series of modeldevelopment experiments to test different variables to standardize a reproducible in-vitro microbial caries model. We evaluated: surface conditioning using saliva; sucrose concentrations and caries lesion severity; growth media conditions and mineral saturation; dental substrate types; pH cycling protocol characteristics. In the second aim, we used the developed model to evaluate the changes in the anti-caries efficacy of three fluoride compounds (Sodium fluoride (NaF); Stannous fluoride (SnF2); Amine fluoride (AmF); and deionized water (DIW- negative control)) at increasing maturation of a microcosm biofilm. We continued the pH cycling protocol for 4 days, 8 days, and 12 days. We tested biofilm cariogenicity and carious lesion severity at each maturation stage. In the third aim, we used the developed model to test the effect of different exposure periods (early vs. late exposure) of the biofilm to three fluoride compounds (NaF, SnF2, AmF, DIW) in comparison to DIW. We also evaluated the recovery of biofilm cariogenicity with each exposure period. We evaluated, for each exposure period and recovery stage, biofilm cariogenicity and carious lesion severity. We analyzed the relationships between different variables (biofilm age, fluoride compound type, exposure period) using ANOVA models. In conclusion: 1. The present model allows testing the effect of biofilm maturation on the anti-caries efficacy of fluoride compounds. 2. Biofilm maturation plays an important role in increasing biofilm tolerance against fluoride treatment; it could also influence the selection of fluoride compounds to achieve optimum cariostatic effect. 3. Exposure period, and type of fluoride compound, both influence the biofilm tolerance to fluoride anti-caries effect; they may also result in a sustainable release of fluoride over time. / 2021-08-21

Diese Arbeit befasst sich mit der Untersuchung von aus Patientenisolaten gewonnenen S. aureus Kulturen und deren Biofilmbildung auf implantatähnlichen Titan-Oberflächen. Ziel war es, den zeitlichen Ablauf bakterieller periprothetischer Infektionen über einen Zeitraum von 21 Tagen zu beschreiben und besser zu verstehen. Dazu sollte überprüft werden, ob ein fluoreszenzspektrometrisch ausgewertetes LIVE/DEAD Assay eine zusätzliche Aussage zum Status der im Biofilm befindlichen Zellen liefern kann. Zudem wurde die Biofilmentwicklung anhand etablierter fluoreszenzspektrometrischer Methoden (Concanavalin-A-Markierung extrazellulärer Polymerer Substanzen, DNA-Markierung mit Hoechst 33342) untersucht. Es konnte ein reproduzierbarer Verlauf der Entwicklung des Biofilms, sowie der DNA-Menge aufgezeigt werden. Das LIVE/DEAD Assay lieferte keine signifikanten Ergebnisse in Bezug auf das Verhältnis lebender zu toter S. aureus Zellen im Biofilm. Weiter wurde die Angreifbarkeit des frühen, am Titan adhärenten Biofilms (Alter 1-5 Tage) durch das in der Orthopädie gängig eingesetzte Antibiotikum Gentamicin untersucht. Die Wirksamkeit konnte zu jedem getesteten Zeitpunkt der ersten fünf Tage durch Anzucht von Kolonien bestätigt werden. Auch wurde die Wirksamkeit über das LIVE/DEAD Assay überprüft, jedoch konnten hier keine aussagekräftigen Daten gewonnen werden, die diese Methode zur Überprüfung der Antibiotikawirksamkeit empfehlen könnten. / This thesis deals with the investigation of S. aureus cultures obtained from patient isolates and their biofilm formation on implant-like titanium surfaces. The aim was to describe and better understand the chronological sequence of bacterial periprosthetic infections over a period of 21 days. For this purpose, it should be checked whether a LIVE/DEAD assay evaluated by fluorescence spectrometry can provide additional information on the status of the cells in the biofilm. In addition, the development of biofilms was investigated using established fluorescence spectrometric methods (Concanavalin-A labelling of extracellular polymer substances, DNA labelling with Hoechst 33342). A reproducible course of the development of the biofilm and the amount of DNA could be shown. The LIVE/DEAD assay did not provide any significant results with regarding the ratio of live to dead S. aureus cells in the biofilm. The vulnerability of the early biofilm adhering to titanium (age 1-5 days) was also examined by using the antibiotic gentamicin, which is commonly used in orthopedics. By cultivating colonies it could be shown, that the antibiotic was effective at every tested time during the first five days. The effectiveness was also checked using the LIVE / DEAD assay, but no meaningful data could be obtained here that could recommend this method for checking the effectiveness of antibiotics against adherent Biofilms.

Pseudomonas aeruginosa is a Gram-negative pathogen that forms biofilms, which increase tolerance to antibiotics. Biofilms are dense, surfaceassociated communities of bacteria that grow in a self-produced matrix of polysaccharides, proteins, and extracellular DNA (eDNA). Sub-minimal inhibitory concentration (sub-MIC) levels of antibiotics induce the formation of biofilms, indicating a potential role in response to antibiotic stress. However, the mechanisms behind sub-MIC antibiotic-induced biofilm formation are unknown. We show that treatment with sub-MIC levels of cefixime (cephalosporin), carbenicillin (β-lactam), tobramycin (aminoglycoside), chloramphenicol (chloramphenicol), thiostrepton (thiopeptide), novobiocin (aminocoumarin), ciprofloxacin (fluoroquinolone), or trimethoprim (antifolate) induces biofilm formation, with maximal induction at ~ ¼ to ½ MIC. We demonstrate that addition of exogenous eDNA or cell lysate does not stimulate biofilm formation to the same extent as antibiotics, suggesting that the release of common goods by antibiotic action does not solely drive the biofilm response. We show that increased biofilm formation upon antibiotic exposure requires the outer membrane porin OprF and the extracytoplasmic function sigma factor SigX. Through transposon mutant screening and deletion studies, we found that OprF is important for biofilm induction, as mutants lacking this protein did not form increased biofilm when exposed to sub-MIC antibiotics. OprF expression is v controlled by SigX, and its loss increases SigX activity. Loss of SigX also prevents biofilm induction by sub-MIC antibiotics. Together, these results show that antibiotic-induced biofilm formation may constitute a type of stress response. This response may be useful to screen for new antibiotics due to its ability to reveal antibiotic activity at concentrations below the MIC. Further study of this response may also provide targets for adjuvant therapies that reduce biofilm formation in P. aeruginosa infections and increase the efficacy of current antibiotics. / Thesis / Master of Science (MSc) / Pseudomonas aeruginosa is a bacterium that causes illness in patients with compromised immune systems, like patients with cystic fibrosis. This bacterium forms biofilms, which are dense groups that stick to surfaces within a protective slime that contains proteins, sugars, and DNA. Biofilms make the bacteria harder to treat with antibiotics. If the bacteria are treated with low levels of antibiotics, they respond by forming more biofilm but how this happens is unknown. We showed that adding DNA does not increase biofilm formation, while adding dead cell debris only causes a small increase. By testing a library of mutant bacteria, we found that they need two genes, oprF and sigX, to form more biofilm when they are treated with low levels of antibiotic. By studying how bacteria respond to low levels of antibiotics, we can find ways to identify new antibiotics and to make our current antibiotics work better.

This study uses scanning electron microscopy (SEM) to examine the occurrence of bacteria and their exopolysaccharide slime layer in microbial enhanced oil recovery experiments. A test of SEM preservation techniques showed that air drying and 10% glutaraldehyde fixation preserved the slime layer but distorted and flattened bacteria. Techniques with ethanol dehydration preserved the bacterial textures but fragmented the slime layer. In sandstones that had been plugged during microbial enhanced oil recovery experiments, bacteria are sparsely distributed. An irregular, confluent slime sheet covers grains and coats pore spaces and is responsible for permeability modification in microbial enhanced oil recovery. The development of the slime layer over time involves several steps: growth of ultramicrobacteria into full-sized bacteria; creation of a slime capsule; growth of globular masses, ropy masses, webs, thin sheets; and growth of a thicker, poreilling mass of slime associated with large balls of slime.

Biofilm communities host complex biogeochemical processes and play a role in the formation of many carbonate rocks by influencing both carbonate precipitation and dissolution. In this study, the biogeochemistry of microbial mats from a hypersaline pond and biofilm from a coral reef are described using SEM, microelectrode profiling, Biolog, fatty acid methyl ester (FAME) and carbon nitrogen analysis. Results show that the microbial mats are distinctly layered, having an oxic upper portion and an H2S-rich lower portion. The most significant conclusions are that the mats have exceptionally high TOC values and display significant differences in microbial communities present, both between layers and between cores. Additionally, organic matter is abundant in microbial mat and biofilm samples, but evidence of precipitation is surprisingly lacking.

No description available.

Microbial biofilms are defined as clusters of microbial cells living in self-produced extracellular polymeric substances (EPS), which always attached to various kinds of surfaces. In this thesis, we studied several mathematical models of biofilm in the human body and marble environment. Some related background of biofilm growth and some basic existing numerical models were introduced in the first chapter. In the first project, we introduced how biofilm affects the local oxygen concentration near the neutrophil cells in the human body with three one-dimensional reaction-diffusion models from different geometries. In nature, microbial biofilm development can be observed on almost all kinds of stone monuments and can also be associated with the problem of monument conservation. In the second part of my research, we built the deliquescence models for biofilm growth environment in the first model and added biomass into consideration in the second one. Also, we analyzed the stability of the equilibria. In the third part, we applied the weather data collected from the weather station on the roof of the Jefferson Memorial to the deliquescence model with biofilm. Furthermore, compared the simulation result for biofilm growth in cold and warm weathers. In the last part of this thesis, we analyzed the biofilm activity with support vector regression. The machine learning model we obtained can be used to find the growth trends of biofilm for any pair of temperature and relative humidity data. / Mathematics