Use of culture and molecular analysis to determine the effect of antibiotic treatment on microbial community diversity and abundance during exacerbation in patients with cystic fibrosis

Background: Anaerobic bacteria are increasingly regarded as important in cystic fibrosis (CF) pulmonary infection. The aim of this study was to determine the effect of antibiotic treatment on aerobic and anaerobic microbial community diversity and abundance during exacerbations in patients with CF.

Methods: Sputum was collected at the start and completion of antibiotic treatment of exacerbations and when clinically stable. Bacteria were quantified and identified following culture, and community composition was also examined using culture-independent methods.

Results: Pseudomonas aeruginosa or Burkholderia cepacia complex were detected by culture in 24/26 samples at the start of treatment, 22/26 samples at completion of treatment and 11/13 stable samples. Anaerobic bacteria were detected in all start of treatment and stable samples and in 23/26 completion of treatment samples. Molecular analysis showed greater bacterial diversity within sputum samples than was detected by culture; there was reasonably good agreement between the methods for the presence or absence of aerobic bacteria such as P aeruginosa (kappa=0.74) and B cepacia complex (kappa=0.92), but agreement was poorer for anaerobes. Both methods showed that the composition of the bacterial community varied between patients but remained relatively stable in most individuals despite treatment. Bacterial abundance decreased transiently following treatment, with this effect more evident for aerobes (median decrease in total viable count 2.3 x 10(7) cfu/g, p=0.005) than for anaerobes (median decrease in total viable count 3 x 10(6) cfu/g, p=0.046).

Conclusion: Antibiotic treatment targeted against aerobes had a minimal effect on abundance of anaerobes and community composition, with both culture and molecular detection methods required for comprehensive characterisation of the microbial community in the CF lung. Further studies are required to determine the clinical significance of and optimal treatment for these newly identified bacteria.

Alternative method for producing organic fertiliser from anaerobic digestion liquor and limestone powder:High Shear wet granulation

Generally, the solid and liquid fractions (digestate) from Anaerobic Digestion (AD) energy production are considered as waste. This has a negative impact on the sustainability of AD processes because of the financial outlay required to treat digestate before being discharged into municipal water treatment plants or natural water bodies. The main aim of this research was to investigate feasibility of producing an organic fertiliser using anaerobic digestate and limestone powders as the raw materials employing a high shear granulation process. Two-level factorial experimental design was used to determine the influence of granulation process variables on, the strength, resistance to attrition and yield of the granules. It was concluded from the study that it is technically feasible to produce organic fertiliser granules of acceptable strength and product yield. Increasing the liquid-to-solid ratio during granulation leads to increased granule strength and better product yield. Although the strength of the granules produced was lower than typical strength of commercial synthetic fertiliser granules (about 5 to 7. MPa), this could be improved by mixing the digestate with a polymeric binder or coating the particles post granulation. © 2012 Elsevier B.V.

Resistance Development of Cystic Fibrosis Respiratory Pathogens When Exposed to Fosfomycin and Tobramycin Alone and in Combination under Aerobic and Anaerobic Conditions

Although antibiotics from different classes are frequently prescribed in combination to prevent the development of resistance amongst Cystic Fibrosis (CF) respiratory pathogens, there is a lack of data as to the efficacy of this approach. We have previously shown that a 4:1 (w/w) combination of fosfomycin and tobramycin (F:T) has excellent activity against CF pathogens with increased activity under physiologically relevant anaerobic conditions. Therefore, the aim of this study was to determine whether F:T could delay or prevent the onset of resistance compared to either fosfomycin or tobramycin alone under aerobic and anaerobic conditions. The frequency of spontaneous mutants arising following exposure to fosfomycin, tobramycin and F:T was determined for clinical Pseudomonas aeruginosa and MRSA isolates under aerobic and anaerobic conditions. The effect of sub-inhibitory concentrations of fosfomycin, tobramycin and F:T on the induction of resistance was also investigated, with the stability of resistance and fitness cost associated with resistance assessed if it developed. P. aeruginosa and MRSA isolates had a lower frequency of spontaneous mutants to F:T compared to fosfomycin and tobramycin under both aerobic and anaerobic conditions. There was a maximum two-fold increase in F:T MICs when P. aeruginosa and MRSA isolates were passaged in sub-inhibitory F:T for 12 days. In contrast, sequential resistance to fosfomycin and tobramycin developed quickly (n = 3 days for both) after passage in sub-inhibitory concentrations. Once developed, both fosfomycin and tobramycin resistance was stable and not associated with a biological fitness cost to either P. aeruginosa or MRSA isolates. The results of this study suggest that F:T may prevent the development of resistance compared to fosfomycin or tobramycin alone under aerobic and physiologically relevant anaerobic conditions. F:T may be a potential treatment option in CF patients chronically colonised by MRSA and/or P. aeruginosa.

Fosfomycin and tobramycin in combination downregulate nitrate reductase genes narG and narH, resulting in increased activity against Pseudomonas aeruginosa under anaerobic conditions

The activity of aminoglycosides, used to treat Pseudomonas aeruginosa respiratory infection in cystic fibrosis (CF) patients, is reduced under the anaerobic conditions that reflect the CF lung in vivo. In contrast, a 4:1 (w/w) combination of fosfomycin and tobramycin (F:T), under investigation for use in the treatment of CF lung infection, has increased activity against P. aeruginosa under anaerobic conditions. The aim of this study was to elucidate the mechanisms underlying the increased activity of F:T under anaerobic conditions. Microarray analysis was used to identify the transcriptional basis of increased F:T activity under anaerobic conditions, and key findings were confirmed by microbiological tests including nitrate utilization assays, growth curves and susceptibility testing. Notably, growth in sub-inhibitory concentrations of F:T, but not tobramycin or fosfomycin alone, significantly downregulated (p <0.05) nitrate reductase genes narG and narH, essential for normal anaerobic growth of P. aeruginosa. Under anaerobic conditions, F:T significantly decreased (p

Bio-removal of toxic metals by metal resistant anaerobic bacteria: molecular characterization and performance studies

Tese de dout., Ciências Biotecnológicas (Biotecnologia Ambiental), Faculdade de Ciências e Tecnologia, Univ. do Algarve, 2010

A Study of Single Stage Semi‐Dry Anaerobic Digestion of Organic Fraction of Municipal Solid Waste

Solid waste generation is a natural consequence of human activity and is increasing along with population growth, urbanization and industrialization. Improper disposal of the huge amount of solid waste seriously affects the environment and contributes to climate change by the release of greenhouse gases. Practicing anaerobic digestion (AD) for the organic fraction of municipal solid waste (OFMSW) can reduce emissions to environment and thereby alleviate the environmental problems together with production of biogas, an energy source, and digestate, a soil amendment. The amenability of substrate for biogasification varies from substrate to substrate and different environmental and operating conditions such as pH, temperature, type and quality of substrate, mixing, retention time etc. Therefore, the purpose of this research work is to develop feasible semi-dry anaerobic digestion process for the treatment of OFMSW from Kerala, India for potential energy recovery and sustainable waste management. This study was carried out in three phases in order to reach the research purpose. In the first phase, batch study of anaerobic digestion of OFMSW was carried out for 100 days at 32°C (mesophilic digestion) for varying substrate concentrations. The aim of this study was to obtain the optimal conditions for biogas production using response surface methodology (RSM). The parameters studied were initial pH, substrate concentration and total organic carbon (TOC). The experimental results showed that the linear model terms of initial pH and substrate concentration and the quadratic model terms of the substrate concentration and TOC had significant individual effect (p < 0.05) on biogas yield. However, there was no interactive effect between these variables (p > 0.05). The optimum conditions for maximizing the biogas yield were a substrate concentration of 99 g/l, an initial pH of 6.5 and TOC of 20.32 g/l. AD of OFMSW with optimized substrate concentration of 99 g/l [Total Solid (TS)-10.5%] is a semi-dry digestion system .Under the optimized condition, the maximum biogas yield was 53.4 L/kg VS (volatile solid).. In the second phase, semi-dry anaerobic digestion of organic solid wastes was conducted for 45 days in a lab-scale batch experiment for substrate concentration of 100 g/l (TS-11.2%) for investigating the start-up performances under thermophilic condition (50°C). The performance of the reactor was evaluated by measuring the daily biogas production and calculating the degradation of total solids and the total volatile solids. The biogas yield at the end of the digestion was 52.9 L/kg VS for the substrate concentration of 100 g/l. About 66.7% of volatile solid degradation was obtained during the digestion. A first order model based on the availability of substrate as the limiting factor was used to perform the kinetic studies of batch anaerobic digestion system. The value of reaction rate constant, k, obtained was 0.0249 day-1. A laboratory bench scale reactor with a capacity of 36.8 litres was designed and fabricated to carry out the continuous anaerobic digestion of OFMSW in the third phase. The purpose of this study was to evaluate the performance of the digester at total solid concentration of 12% (semi-dry) under mesophlic condition (32°C). The digester was operated with different organic loading rates (OLRs) and constant retention time. The performance of the reactor was evaluated using parameters such as pH, volatile fatty acid (VFA), alkalinity, chemical oxygen demand (COD), TOC and ammonia-N as well as biogas yield. During the reactor’s start-up period, the process is stable and there is no inhibition occurred and the average biogas production was 14.7 L/day. The reactor was fed in continuous mode with different OLRs (3.1,4.2 and 5.65 kg VS/m3/d) at constant retention time of 30 days. The highest volatile solid degradation of 65.9%, with specific biogas production of 368 L/kg VS fed was achieved with OLR of 3.1 kg VS/m3/d. Modelling and simulation of anaerobic digestion of OFMSW in continuous operation is done using adapted Anaerobic Digestion Model No 1 (ADM1).The proposed model, which has 34 dynamic state variables, considers both biochemical and physicochemical processes and contains several inhibition factors including three gas components. The number of processes considered is 28. The model is implemented in Matlab® version 7.11.0.584(R2010b). The model based on adapted ADM1 was tested to simulate the behaviour of a bioreactor for the mesophilic anaerobic digestion of OFMSW at OLR of 3.1 kg VS/m3/d. ADM1 showed acceptable simulating results.

Knowledge-based modelling and simulation of operational problems of microbiological origin in wastewater treatment plants

The activated sludge and anaerobic digestion processes have been modelled in widely accepted models. Nevertheless, these models still have limitations when describing operational problems of microbiological origin. The aim of this thesis is to develop a knowledge-based model to simulate risk of plant-wide operational problems of microbiological origin.For the risk model heuristic knowledge from experts and literature was implemented in a rule-based system. Using fuzzy logic, the system can infer a risk index for the main operational problems of microbiological origin (i.e. filamentous bulking, biological foaming, rising sludge and deflocculation). To show the results of the risk model, it was implemented in the Benchmark Simulation Models. This allowed to study the risk model's response in different scenarios and control strategies. The risk model has shown to be really useful providing a third criterion to evaluate control strategies apart from the economical and environmental criteria.

Treatment of mature urban landfill leachates by anammox process

This thesis results from the collaborative projects between the LEQUIA-UdG group and Cespa (a company in charge of several landfill sites in Spain). The aim of the work was the development of a suitable alternative treatment for nitrogen removal from mature landfill leachates. The thesis presents the application of the anammox (anaerobic ammonium oxidation process) process to treat ammonium rich leachates as the second step of the PANAMMOX® process. The work deals with preliminary studies about the characteristics of the anammox process in a SBR, with special focus on the response of the biomass to nitrite exposure. The application of the anammox process with leachate was first studied in a lab-scale reactor, to test the effect of the leachate matrix on anammox biomass and its progressive adaptation. Finally, a start-up strategy is developed and applied for the successful start-up of a 400L anammox SBR in less than 6 months.

Dynamics of Aeromonas species isolated from wastewater treatment system

Aeromonas are widely distributed in the aquatic environment, and are considered to be emerging organisms that can produce a series of virulence factors. The present study was carried out in a sanitary sewage stabilization pond treatment system, located in Lins, State of Sao Paulo, Brazil. Most probable number was applied for estimation of the genus Aeromonas. Colony isolation was carried out on blood agar ampicillin and confirmed by biochemical characterization. Aeromonas species were isolated in 72.4% of influent samples, and in 55.2 and 48.3% of effluent from anaerobic and facultative lagoons, respectively. Thirteen Aeromonas species were isolated, representing most of the recognized species of these organisms. Even though it was possible to observe a tendency of decrease, total elimination of these organisms from the studied system was not achieved. Understanding of the pathogenic organism`s dynamics in wastewater treatment systems with a reuse potential is especially important because of the risk it represents.

Anaerobic degradation of organic materials - significance of the substrate surface area

In anaerobic degradation of substrates containing mainly particulate organic matter, solids hydrolysis is rate-limiting. In these investigations, the particle size of various substrates was reduced by comminution to support hydrolysis. Two positive effects of comminution were observed. For substrates with high fibre content, which are particularly resistant to biodegradation, a significant improvement of the degradation degree was observed as a result of comminution. Secondly, for all substrates tested, and particularly for those rich in fibres, the degradation rate of comminuted samples was significantly higher. The first reason for both effects is an increase of the sample surface area. Several methods for measuring the specific surface area of organic materials, including particle size analysis, Nitrogen-adsorption and enzyme adsorption, were used and compared for the purpose of this study, where the surface area accessible to microbial enzymes is critical. The significance of the surface area in anaerobic degradation of particulate substrates was investigated through a kinetic model where the hydrolysis rate was based on the sample surface area. Good agreements were obtained between model and experiments carried out with samples of various specific surface areas. These results reinforced the significance of the sample surface area in anaerobic degradation processes. However, other effects of comminution responsible for the increased degradation degree and degradation rate were identified and discussed. These include: the increase of dissolved compounds due to cell rupture, exposition of surface areas previously inaccessible for microbial degradation, and alteration of the sample structure such as the lignin-cellulose arrangements.

Use of anaerobic cecal microflora, lactose and acetic acid for the protection of broiler chicks against experimental infection with Salmonella Typhimurium and Salmonella enteritidis

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Effects of caffeine on time to exhaustion in exercise performed below and above the anaerobic threshold

Controversy still exists concerning the potential ergogenic benefit of caffeine (CAF) for exercise performance. The purpose of this study was to compare the effects of CAF ingestion on endurance performance during exercise on a bicycle ergometer at two different intensities, i.e., approximately 10% below and 10% above the anaerobic threshold (AT). Eight untrained males, non-regular consumers of CAF, participated in this study. AT, defined as the intensity (watts) corresponding to a lactate concentration of 4 mM, was determined during an incremental exercise test from rest to exhaustion on an electrically braked cycle ergometer. on the basis of these measurements, the subjects were asked to cycle until exhaustion at two different intensities, i.e., approximately 10% below and 10% above AT. Each intensity was performed twice in a double-blind randomized order by ingesting either CAF (5 mg/kg) or a placebo (PLA) 60 min prior to the test. Venous blood was analyzed for free fatty acid, glucose, and lactate, before, during, and immediately after exercise. Rating of perceived exertion and time to exhaustion were also measured during each trial. There were no differences in free fatty acids or lactate levels between CAF and PLA during and immediately after exercise for either intensity. Immediately after exercise glucose increased in the CAF trial at both intensities. Rating of perceived exertion was significantly lower (CAF = 14.1 ± 2.5 vs PLA = 16.6 ± 2.4) and time to exhaustion was significantly higher (CAF = 46.54 ± 8.05 min vs PLA = 32.42 ± 14.81 min) during exercise below AT with CAF. However, there was no effect of CAF treatment on rating of perceived exertion (CAF = 18.0 ± 2.7 vs PLA = 17.6 ± 2.3) and time to exhaustion (CAF = 18.45 ± 7.28 min vs PLA = 19.17 ± 4.37 min) during exercise above AT. We conclude that in untrained subjects caffeine can improve endurance performance during prolonged exercise performed below AT and that the decrease of perceived exertion can be involved in this process

Start-up adjustment of a plug-flow digester for cassava wastewater (manipueira) treatment

Um dos resíduos gerados no processamento da mandioca (Manihot esculenta) é a manipueira, passível de tratamento por biodigestão anaeróbia. Este trabalho objetivou estudar o processo de partida de um biodigestor tipo plug-flow, tratando manipueira de duas maneiras: diminuindo-se gradativamente o tempo de retenção hidráulica (TRH) até se chegar ao tempo pré-estabelecido, quatro dias; ou mantendo-se o TRH fixo em quatro dias e aumentando-se gradativamente a concentração do afluente. O biodigestor, com capacidade 1980 mL, foi mantido a temperatura de 32ºC ± 1. Empregou-se como substrato manipueira e ajustou-se o pH entre 5,5 e 6,0. A primeira etapa foi caracterizada empregando-se TRH de 16,6; 13,6; 11,6 e 9,6 dias e 3,1; 2,0; 2,3 e 2,9 g DQO L-1 d-1 de carga orgânica, respectivamente. Na segunda etapa manteve-se TRH fixo, 4 dias, porém cargas orgânicas de 0,48, 0,86, 1,65 e 2,46 g DQO L-1 d-1. Determinaram-se no afluente e efluente, sólidos totais (ST) e sólidos voláteis (SV), demanda química de oxigênio (DQO), alcalinidade e acidez volátil. Na primeira etapa, melhores resultados foram observados trabalhando com TRH 9,6 dias e carga orgânica 2,9 g DQO L-1 d-1, quando houve redução de DQO, ST e SV de 60%, 44% e 60%, respectivamente. Na segunda etapa o TRH de 4 dias apresentou melhores resultados empregando-se carga orgânica de 0,86 g DQO L-1 d-1, houve redução de 71%, 58% e 79% de DQO, ST e SV, respectivamente. A partida do biodigestor plug-flow tratando manipueira, pode ser realizada tanto diminuindo-se o TRH, quanto mantendo-o fixo e aumentado-se a concentração do afluente.

Comparison of hexamethyidisilazane and critical point drying treatments for SEM analysis of anaerobic biofilms and granular sludge

We present a fast procedure for scanning electron microscopy (SEM) analysis in which hexamethyldisilazane (HMDS) solvent, instead of the critical point drying, is used to remove liquids from a microbiological specimen. The results indicate that the HMDS solvent is suitable for drying samples of anaerobic cells for examination by SEM and does not cause cell structure disruption.

Lethal photosensitization in microbiological treatment of ligature-induced peri-implantitis: a preliminary study in dogs

This pilot study evaluated, by culture testing, the effectiveness of lethal photosensitization for the microbiological treatment of peri-implantitis in dogs. Experimental peri-implantitis was induced by ligature placement for 2 months. Following ligature removal, plaque control was instituted by scrubbing with 0.12% chlorhexidine daily for 12 months. Subsequently, mucoperiosteal flaps were elevated for scaling the implant surface. Microbial samples were obtained with paper points before and after treatment of implant surfaces by means of 100 microg/ml toluidine blue O (TBO,) and were exposed, for 80 s, to light with a wavelength of 685 nm from a 50 mW GaAlAs diode laser. The mean initial and final bacterial counts were 7.22 +/- 0.20 and 6.84 +/- 0.44 CFU/ml, respectively for TVC (P < 0.0001); 6.19 +/- 0.45 and 3.14 +/- 3.29 CFU/ml for P. intermedia/nigrescens (P = 0.001); 5.98 +/- 0.38 and 1.69 +/- 2.90 CFU/ml for Fusobacterium spp. (P = 0.001); and 6.07 +/- 0.22 to 1.69 +/- 2.94 CFU/ml for beta-hemolytic Streptococcus (P = 0.0039). It may be concluded that lethal photosensitization resulted in a reduction of the bacterial count. Complete elimination of bacteria was achieved in some samples.