Development and validation of novel methods for microbial source tracking based on Escherichia coli as an indicator of water quality

Microbial pollution in water periodically affects human health in Australia, particularly in times of drought and flood. There is an increasing need for the control of waterborn microbial pathogens. Methods, allowing the determination of the origin of faecal contamination in water, are generally referred to as Microbial Source Tracking (MST). Various approaches have been evaluated as indicatorsof microbial pathogens in water samples, including detection of different microorganisms and various host-specific markers. However, until today there have been no universal MST methods that could reliably determine the source (human or animal) of faecal contamination. Therefore, the use of multiple approaches is frequently advised. MST is currently recognised as a research tool, rather than something to be included in routine practices. The main focus of this research was to develop novel and universally applicable methods to meet the demands for MST methods in routine testing of water samples. Escherichia coli was chosen initially as the object organism for our studies as, historically and globally, it is the standard indicator of microbial contamination in water. In this thesis, three approaches are described: single nucleotide polymorphism (SNP) genotyping, clustered regularly interspaced short palindromic repeats (CRISPR) screening using high resolution melt analysis (HRMA) methods and phage detection development based on CRISPR types. The advantage of the combination SNP genotyping and CRISPR genes has been discussed in this study. For the first time, a highly discriminatory single nucleotide polymorphism interrogation of E. coli population was applied to identify the host-specific cluster. Six human and one animal-specific SNP profile were revealed. SNP genotyping was successfully applied in the field investigations of the Coomera watershed, South-East Queensland, Australia. Four human profiles [11], [29], [32] and [45] and animal specific SNP profile [7] were detected in water. Two human-specific profiles [29] and [11] were found to be prevalent in the samples over a time period of years. The rainfall (24 and 72 hours), tide height and time, general land use (rural, suburban), seasons, distance from the river mouth and salinity show a lack of relashionship with the diversity of SNP profiles present in the Coomera watershed (p values > 0.05). Nevertheless, SNP genotyping method is able to identify and distinquish between human- and non-human specific E. coli isolates in water sources within one day. In some samples, only mixed profiles were detected. To further investigate host-specificity in these mixed profiles CRISPR screening protocol was developed, to be used on the set of E. coli, previously analysed for SNP profiles. CRISPR loci, which are the pattern of previous DNA coliphages attacks, were considered to be a promising tool for detecting host-specific markers in E. coli. Spacers in CRISPR loci could also reveal the dynamics of virulence in E. coli as well in other pathogens in water. Despite the fact that host-specificity was not observed in the set of E. coli analysed, CRISPR alleles were shown to be useful in detection of the geographical site of sources. HRMA allows determination of ‘different’ and ‘same’ CRISPR alleles and can be introduced in water monitoring as a cost-effective and rapid method. Overall, we show that the identified human specific SNP profiles [11], [29], [32] and [45] can be useful as marker genotypes globally for identification of human faecal contamination in water. Developed in the current study, the SNP typing approach can be used in water monitoring laboratories as an inexpensive, high-throughput and easy adapted protocol. The unique approach based on E. coli spacers for the search for unknown phage was developed to examine the host-specifity in phage sequences. Preliminary experiments on the recombinant plasmids showed the possibility of using this method for recovering phage sequences. Future studies will determine the host-specificity of DNA phage genotyping as soon as first reliable sequences can be acquired. No doubt, only implication of multiple approaches in MST will allow identification of the character of microbial contamination with higher confidence and readability.

Development and Validation of an UV-Derivative Spectrophotometric Method for Determination of Glimepiride in Tablets

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

Validation of Two Methods of Data Collection of Self-Reported Medicine Use Among the Elderly

The accuracy of medicine use information was compared for a telephone interview and mail questionnaire, using an in-home medicine check as the standard of assessment The validity of medicine use information varied by data source, level of specificity of data, and respondent characteristics. The mail questionnaire was the more valid source of overall medicine use information. Implications for both service providers and researchers are provided.

Analytical Validation of Quantitative High-Performance Liquid Chromatographic Methods in Pharmaceutical Analysis: A Practical Approach

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

Thermal analysis and validation of UV and visible spectrophotometric methods for the determination of new antibiotic tigecycline in pharmaceutical product

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

Validation of Thin Layer Chromatographic Methods

Thin-layer and high-performance thin-layer chromatography (TLC/HPTLC) methods for assaying compound(s) in a sample must be validated to ensure that they are fit for their intended purpose and, where applicable, meet the strict regulatory requirements for controlled products. Two validation approaches are identified in the literature, i.e. the classic and the alternative, which is using accuracy profiles.Detailed procedures of the two approaches are discussed based on the validation of methods for pharmaceutical analysis, which is an area considered having more strict requirements. Estimation of the measurement uncertainty from the validation approach using accuracy profiles is also described.Examples of HPTLC methods, developed and validated to assay sulfamethoxazole and trimethoprim on the one hand and lamivudine, stavudine, and nevirapine on the other, in their fixed-dose combination tablets, are further elaborated.

Development and validation of an analytical method by RP-HPLC for quantification of sibutramine hydrochloride in pharmaceutical capsules

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

Validation of UV spectrophotometric method for determination of lomefloxacin in pharmaceutical dosage form

A simple and reproducible method was developed for the assay of lomefloxacin in tablets. The excipients in the commercial tablet preparation did not interfere with the assay. Beer's law is obeyed in the range 2.0-9.0 μg.mL-1 at λmax 280 nm. The molar absorptivity was calculated. Six triplicate analyses of solutions containing six different concentrations of the examined drug were carried out and gave a mean correlation coefficient 0.9997. The proposed method was applied to the determination of the examined drug in coated tablet and the results demonstrated that the method is equally accurate, precise and reproducible as the official methods.

Comparison of sample preparation methods, validation of an UPLC-MS/MS procedure for the quantification of tetrodotoxin present in marine gastropods and analysis of pufferfish

Tetrodotoxin (TTX) is one of the most potent marine neurotoxins reported. The global distribution of this toxin is spreading with the European Atlantic coastline now being affected. Climate change and increasing pollution have been suggested as underlying causes for this. In the present study, two different sample preparation techniques were used to extract TTX from Trumpet shells and pufferfish samples. Both extraction procedures (accelerated solvent extraction (ASE) and a simple solvent extraction) were shown to provide good recoveries (80-92%). A UPLC-MS/MS method was developed for the analysis of TTX and validated following the guidelines contained in the Commission Decision 2002/657/EC for chemical contaminant analysis. The performance of this procedure was demonstrated to be fit for purpose. This study is the first report on the use of ASE as a mean for TTX extraction, the use of UPLC-MS/MS for TTX analysis, and the validation of this method for TTX in gastropods.

Development and validation of Fluid Structure Interaction Methods for an Oscillating Wave Surge Converter

The term fatigue loads on the Oyster Oscillating Wave Surge Converter (OWSC) is used to describe hydrostatic loads due to water surface elevation with quasi-static changes of state. Therefore a procedure to implement hydrostatic pressure distributions into finite element analysis of the structure is desired. Currently available experimental methods enable one to measure time variant water surface elevation at discrete locations either on or around the body of the scale model during tank tests. This paper discusses the development of a finite element analysis procedure to implement time variant, spatially distributed hydrostatic pressure derived from discretely measured water surface elevation. The developed method can process differently resolved (temporal and spatial) input data and approximate the elevation over the flap faces with user defined properties. The structural loads, namely the forces and moments on the body can then be investigated by post processing the numerical results. This method offers the possibility to process surface elevation or hydrostatic pressure data from computational fluid dynamics simulations and can thus be seen as a first step to a fluid-structure interaction model.