Many infectious pathogens, and in particular viruses, have an extremely high rate of mutation. This can lead to rapid evolution driven by selection pressures operating at both the within- and between-host levels, as strains compete for resources within their chosen host while also competing to effectively transmit to new hosts. In the case of chronic viral infections, such as the human immunodeficiency virus (HIV) or hepatitis C, substantial viral evolution may take place within a single infected host. The fitness of a pathogen has been studied at the between-host level and at the within-host level, but linking the two levels of selection pressure is a difficult problem that has yet to be studied satisfactorily. We modify a simple model describing the within host dynamics of HIV infection by including multiple pathogen strains with different properties and allowing these strains to mutate. Within the host we observe different strategies for pathogen success during different stages of infection, which often leads to different strains predominating within the host over the course of infection. We then embed our within-host model into a Monte Carlo simulation that models the interactions between infected individuals. This approach allows us to combine selective pressure at the within-host level with pressures at the between-host level and helps us to predict which strains are most likely to be present within the population. We show that under our model assumptions the co-existence of multiple strains is possible and we explore the factors leading to the success of a pathogen.

Thesis (Ph.D.)--Murdoch University, 1999. / Thesis submitted to the Division of Science. Bibliography: leaves 190-217.

In order to study the behaviour of pathogenic viruses in groundwater, several tracer experiments were performed at chalk aquifer sites using three different bacteriophage. Laboratory experiments were performed in parallel to investigate the efficacy of the bacteriophage as models of pathogenic virus behaviour. The high titres per ml of bacteriophage available for the initial inoculum and the simplicity of the assay permitted the detection of a pattern of bacteriophage recovery from three different groundwater sites. The greatest percentage of original inoculum recovered was 1.9 percent. Bacteriophage were observed to migrate 1km over a five month period and 366m within just over 3.5 hours. The laboratory experiments explored: i) decay rates of viruses suspended within chalk groundwater; ii) adsorption of viruses to chalk in batch studies and; iii) virus behaviour in chalk columns representing natural aquifer conditions. Three human enteric viruses were used: poliovirus 1, echovirus 1 and coxsackievirus B5. In addition the simian rotavirus (SA-11), and a group of bacteriophage were tested. The laboratory experiments indicated that the bacteriophage included in this study survived longer than the animal viruses in groundwater and that all viruses adsorbed well to chalk. In the simulated aquifer conditions all viruses investigated percolated through a chalk column at a similar rate and with a similar pattern. No differences in behaviour between the viruses, whether in laboratory or field experiments, was found which could be directly attributed to their size or shape. A mathematical model was used which included coefficients for adsorption and decay observed in the laboratory experiments and certain other parameters found in one of the field sites under investigation. Those factors considered and included in the model were shown to be sufficient to produce the same behaviour pattern as that observed in the field. This confirmed that the main factors influencing viral migration in natural conditions have been considered in this investigation. Bacteriophage were found to be good tracers for determining certain properties of chalk aquifers and a potential model of the behaviour of human enteric viruses in groundwater.

The current research relates to a system driven by renewable energy and chemical energy contained in the feed, which will eliminate and reduce pathogens found in human excreta. A project in the form of an experiment for demonstration will be designed and built to operate in the local waste water treatment plant. Data will be analyzed and recorded, including fecal coliforms and E.coli levels, chemical oxygen demand (COD) and total solids removal (TS). The effectiveness of the system will depend upon results obtained and weather conditions. The principal objective of the research is to test and demonstrate that the "Small Decentralized ATAD" is successful in removing/eliminating enteric pathogens found in human excreta. Most importantly, the Bill and Melinda Gates Charity Foundation is providing financial support (Grants) for new sanitation ideas to help developing countries overcome diseases, specifically water borne diseases and also diseases related to hygiene and sanitation. Moreover, the "Water, Sanitation & Hygiene: Grand Challenges Explorations" granted a $100,000 Grant to Professor James Blackburn from Southern Illinois University at Carbondale in the Mechanical Engineering and Energy Processes Department. Consequently, the "Decentralized Next Generation for Diarrheal Pathogens" project will be tested using the ATAD (Autothermal Thermophilic Aerobic Digestion) to demonstrate its effectiveness in pathogen reduction and elimination.

No description available.

No description available.

A rapid increase in the amount of available pathogen genetic data, which is ongoing and likely to continue for the foreseeable future, presents new opportunities and challenges in molecular epidemiology, and in the emerging field of “phylodynamics”, which seeks to unify the study of the evolutionary and epidemiological dynamics of pathogen populations. This thesis explores some of these challenges and opportunities, with a focus on pathogens infecting livestock and poultry. I conducted analyses of sequences from two serotypes of foot-and-mouth-disease virus (FMDV) in order to investigate the global population dynamics of the virus. For serotype SAT 2, the amount of publicly available genomic data is still small enough that all of it could be included in a single analysis. A particular focus was the origins of historical outbreaks occurring in North Africa and the Middle East, outside the endemic area for the serotype. The results suggested sources for these in countries just south of the Sahara, and that the viruses responsible for three outbreaks occurring in 2012 were the result of separate introductions. For serotype O, including every available sequence was not feasible and the data had to be sub-sampled. Little research has been conducted on how to design a sampling strategy for sequence analysis of pathogens, an issue of increasing importance, so a simulation study was conducted to identify one. This suggested that, when reconstructing the temporal and spatial dynamics of a structured population of pathogens or infected individuals, it is preferable to stratify by subpopulation and by time period. The type O analysis itself showed that the south-east Asian topotype moves between countries according to cattle trade networks, but that geographic proximity is also important for strains from southern Asia and the Middle East. With genetic data available at an epidemiological resolution that was previously inconceivable, there are opportunities for new types of inference. For example, if we can acquire a sequence from all or most infected cases in an epidemic, they can inform inference of who infected who, complementing traditional contact-tracing approaches. I introduce a novel phylodynamic method for the simultaneous reconstruction of phylogeny and transmission tree for an epidemic in a situation where every infected host or premises can be identified and a sequence acquired from most of them. The performance of this method was demonstrated using simulated data, and then it was applied to reconstruct both trees from the 2003 H7N7 avian influenza outbreak in the Netherlands.

Brucella ovis is a sexually transmitted, facultatively anaerobic, intracellular bacterial pathogen of sheep (Ovis aries) and red deer (Cervus elaphus). Brucella spp. infect primarily by penetrating the mucosa and are phagocytized by host macrophages, where survival and replication occurs. At least in some species, it has been shown that entry into stationary phase is necessary for successful infection. Brucella, like other alphaproteobacteria, lack the canonical stationary phase sigma factor ?s. Research on diverse members of this large phylogenetic group indicate the widespread presence of a conserved four-gene set including an alternative ECF sigma factor, an anti-sigma factor, a response regulator (RR), and a histidine kinase (HK). The first description of the system was made in Methylobacterium extorquens where the RR, named PhyR, was found to regulate the sigma factor activity by sequestering the anti-sigma factor in a process termed "sigma factor mimicry." These systems have been associated with various types of extracellular stress responses in a number of environmental bacteria. I hypothesized that homologous genetic sequences (Bov_1604-1607), which are similarly found among all Brucella species, may regulate survival functions during pathogenesis. To further explore the involvement of this system to conditions analogous to those occurring during infection, pure cultures of B. ovis cells were subjected to environments of pH (5 and 7) for 15, 30, and 45 minutes and oxidative (50mM H2O2) stress, or Spermine NONOate for 60 minutes. RNA was extracted and converted to cDNA andchanges in transcript levels of the sigma factor Bov1605 were measured using qPCR. Preliminary results indicate that under the exposure to Spermine NONOate there was little change in expression, but under oxidative stress expression of the sigma factor Bov1605 was 4.68-fold higher than that expressed under normal conditions. These results suggest that the sigma factor Bov1605 may be involved in oxidative stress defense during infection. Under acid stress (pH5), Bov1605 was found to be upregulated at 15 and 30 minutes, but after 45 and 60 minutes the time decreased.

No description available.

The detection and identification of bio-threat agents and study of host-pathogen interactions require a high-resolution detection platform capable of discerning closely related species. This dissertation addresses the completion of the development of an array based platform and provides a robust pipeline for the discovery of unique bio-signatures for pathogens and their host. Our collection (library) of host and pathogen signatures has been greatly expanded to improve robustness and identification accuracy of an 'unknown' sample. The library containing measured bio-signatures for each species/isolate is complemented with computational methodologies to resolve the identity of the unknown sample as well as a mixture of organisms or a pathogen in a host background. Current approaches for pathogen detection rely on prior genomic sequence information. This research targets use of a broad based platform for identification of pathogens from field or laboratory samples on a high density Universal Bio-signature Detection Array (UBDA). This array is genome independent and contains all possible (49 combinations) 9-mer probes which are mathematically computed and genome independent. It works by comparing signal intensity readout to a library of readouts established by interrogating a wide spectrum of organisms. Each genome has a unique pattern of signal intensities corresponding to each of these probes. These signal intensities were used to generate un-biased cluster analysis patterns that can easily distinguish organisms into accepted and known phylogenomic relationships. Classification methods such as hierarchical clustering, Pearson's correlation matrix, principal component analysis and curve fitting regression methods were tested for pathogen specific use cases. Hierarchical clustering and Pearson's correlation matrix methods can establish phylogenomic relationships between highly diverse genomes. However, in order to assign a given sample to one or more groups, such as a pure isolate of a single species or composite mixture of multiple species, principal component analysis (PCA) was used. The test cases included identification of mixed samples, case study of field samples from state diagnostic labs and finally a surveillance method for viral and parasite carrying insect host vectors. Completion of these application challenges is meant to demonstrate the power and confirm confidence in the Universal Bio-signature Detection Array. / Ph. D.