Three experiments were conducted to characterize the concentration of microorganisms in biosolids, the plume of aerosols created during land application of biosolids and the occupational risk of infection due to pathogens aerosolized during land application of biosolids in the United States. In all, more than three-hundred air samples were collected immediately downwind of biosolids applications throughout the United States using liquid impingers, and more than one-hundred air samples were collected downwind of microbially seeded, land applied water, which served as a conservative model system of aerosol generation. The novel model system made it possible to calculate the flux of microorganisms through a virtual plane defined by air samplers in vertical and horizontal arrays, located immediately downwind of a passing spray applicator. The rate of aerosolization during land application of biosolids near Tucson, Arizona, was calculated to be less than 33 plaque forming units (PFU) of coliphage and 10 colony forming units (CFU) of coliform bacteria per meter traveled by the spray applicator. Rates of aerosolization from the model system were shown to be much greater. To assess the risk to occupational health from bioaerosols generated during land application of biosolids, coliform bacteria, coliphages, and heterotrophic plate count (HPC) bacteria were enumerated from air and biosolids at 10 land application sites throughout the nation. The method of land application strongly influenced aerosolization, while relative humidity, temperature and wind speed showed limited correlation to concentrations of fecal indicator microorganisms in air. Occupational risks of infection and illness from aerosolized Salmonella and enteroviruses were calculated for a variety of land application scenarios. Realistic exposure scenarios carried occupational risks of Salmonella infection ranging from of 0.0001% to 0.013% per year. The corresponding occupational risk of infection from enteroviruses, using coxsackievirus A-21 as a model, ranged from 0.78% to 2.1% per year, depending on the type of activity performed by the worker. In addition, samples of biosolids from the Southwestern United States were characterized to provide up-to-date information about pathogens in biosolids for environmental regulators, biosolids producers, researchers, and public health agencies.

Chronic viral infection is a significant burden on healthcare systems worldwide. Robust anti-viral immune responses are essential for viral clearance. Persistent viruses use a variety of mechanisms to evade immune surveillance including the upregulation of host immunesuppressive factors. Secreted fibrinogen-like protein 2 (FGL2) has been identified as an inhibitory effector molecule in suppressing immune responses in patients with chronic hepatitis C virus (HCV) and hepatitis B virus (HBV) disease. In a murine model of chronic infection caused by Lymphocytic choriomeningitis virus (LCMV) clone 13, we demonstrate that mice deficient in Fgl2 have increased numbers of mature antigen-presenting cells (APC), improved virus-specific cytotoxic T cell immunity and enhanced viral clearance when compared to wild-type mice. These results highlight the importance of the FGL2 inhibitory pathway in immune evasion and provide a rationale to investigate the effects of blocking FGL2 as a novel immune therapeutic in patients suffering from persistent infections.

Chronic viral infection is a significant burden on healthcare systems worldwide. Robust anti-viral immune responses are essential for viral clearance. Persistent viruses use a variety of mechanisms to evade immune surveillance including the upregulation of host immunesuppressive factors. Secreted fibrinogen-like protein 2 (FGL2) has been identified as an inhibitory effector molecule in suppressing immune responses in patients with chronic hepatitis C virus (HCV) and hepatitis B virus (HBV) disease. In a murine model of chronic infection caused by Lymphocytic choriomeningitis virus (LCMV) clone 13, we demonstrate that mice deficient in Fgl2 have increased numbers of mature antigen-presenting cells (APC), improved virus-specific cytotoxic T cell immunity and enhanced viral clearance when compared to wild-type mice. These results highlight the importance of the FGL2 inhibitory pathway in immune evasion and provide a rationale to investigate the effects of blocking FGL2 as a novel immune therapeutic in patients suffering from persistent infections.

Background: Street-involved youth are known to be at a greatly increased risk of HIV and sexually transmitted infections (STIs); however, the role that environmental and structural factors play in driving disease transmission risk among this population has not been thoroughly examined. Methods: The At Risk Youth Study (ARYS) is a prospective cohort of homeless and street-involved youth between the ages of 14 and 26. From September 2005 to October 2006, participants completed a baseline questionnaire which elicited information regarding sexual activity, injection and non-injection drug use, addiction treatment experience, encounters with police and security guards, and health service utilization. Environmental and structural correlates of number of recent sex partners were identified using quasi-Poisson regression. Factors independently associated with consistent condom use were also examined using logistic regression. Results: Among 529 participants, 415 (78.4%) were sexually active during the past six months, of whom 253 (61.0%) reported multiple sex partners and 288 (69.6%) reported inconsistent condom use during this time period. In multivariate logistic regression, homelessness and self-reported structural barriers to accessing health services were inversely associated with consistent condom use. In multivariate analysis, living in a shelter, hostel, or single room occupancy hotel was positively associated with greater numbers of recent sex partners. Structural factors that were associated with number of sex partners included having a warrant or area restriction that affects access to health services, and for males, being accosted by the police. Conclusions: Unstable housing, homelessness, and structural factors related to the criminalization and displacement of street-involved youth were associated with an increased risk of HIV and STI transmission, even after extensive adjustment for sociodemographic and individual level characteristics. These findings suggest that both environmental and structural factors influence the spread of HIV and STIs, and point to the need for environmental-structural interventions to reduce the burden of these diseases among this population.

Išanalizuoti 100 hemodialize gydomų pacientų duomenys per 2007 metus. Išskirti pacientai, kuriems tiriamuoju laikotarpiu buvo skirta antibiotikoterapija. Darbo tikslas- apžvelgti racionalios antibiotikoterapijos principus ir įvertinti racionalumo lygį bei jo pokytį po intervencijos KMUK nefrologijos skyriuje 2007 metais. Kiekvienam pacientui, gydytam antimikrobiniais vaistais, užpildytas tam tikras protokolas. Antimikrobinio vaisto skyrimo racionalumas vertintas pagal atitikimą 2004 metais išleistoms „Racionalaus antimikrobinių vaistų vartojimo“ metodinėms rekomendacijoms. Gauti rezultatai parodė, kad 2006 metų pabaigoje atlikta intervencija dėl racionalaus antimikrobinių vaistų vartojimo nefrologijos skyriuje pasiteisino - neatitinkančių rekomendacijų antibiotikų skyrimo atvejų sumažėjo beveik dvigubai (2006 metais – 17,4 proc., 2007 metais – 9,9 proc.). Pagal Pirsono χ2 kriterijų, skirtumas yra statistiškai patikimas (χ2 > 9,488; p < 0,05). Racionalumo lygis padidėjo dėl racionaliau gydomų šlapimo takų ir kvėpavimo takų infekcijų bei dažniau atliekant bakteriologinius testus. / We analyzed data of 100 hemodialysis patients during 2007 year and excluded cases of antibioticotherapy. The aim of the study was to review the principles of rational antibioticotherapy and to investigate level of non-adherence of the prescribed antimicrobial drugs to nationally available guidelines and its change after intervention in nephrology department in 2007. The evaluation of adherence to national recommendation was estimated using “Rational use of antimicrobial preparations: recommendations for microbiological diagnostics, treatment, and propylaxis of infectious diseases” (Vilnius, 2004). The results showed, that the level of non - rationality in using antimicrobials decreased from 17.4% in 2006 till 9.9% in 2007. This is statistically significant (χ2 > 9.488; p < 0.05).

Le virus de l’hépatite C (VHC) est un problème mondial. La majorité des personnes infectées (70-85%) développent une infection chronique qui cause des complications hépatiques. Le seul régime thérapeutique approuvé pour le VHC est l'interféron alpha (IFN-α). Ce traitement a un taux de réussite de 50-80% selon le génotype de virus et le moment de l'initiation de la thérapie. Les facteurs régissant la réponse au traitement ne sont pas bien définis. Des études antérieures ont suggéré un rôle potentiel de la réponse immunitaire de l'hôte au succès de la thérapie, toutefois, ces résultats sont controversés. Nous avons émis l'hypothèse que la réponse immunitaire de l’hôte sera plus efficace chez les patients qui commencent la thérapie tôt pendant la phase aiguë de l'infection. En revanche, la réponse immunitaire sera épuisée lorsque le traitement est initié pendant la phase chronique. L'objectif principal de ce mémoire est d’étudier les facteurs immunologiques qui régissent la réponse à la thérapie, et de déterminer si la contribution de la réponse immunitaire de l'hôte peut être influencée par la période de l'infection. Nos résultats démontrent l'efficacité de la restauration de la réponse immunitaire spécifique au VHC lorsque la thérapie par l'interféron est initiée tôt. Ceci est démontré par le sauvetage des cellules T efficaces spécifiques au VHC efficace similaires à celles observées chez les individus qui ont résolu spontanément, suggérant ainsi qu'elles jouent un rôle actif dans la réponse au traitement. Toutefois, cette réponse n'a pas été restaurée chez les patients traités au cours de la phase chronique. Ces résultats ont des implications importantes dans la compréhension des mécanismes sous-jacents à la réponse aux traitements actuels et au développement des nouvelles thérapies. / Hepatitis C virus (HCV) is a major public health problem worldwide. Only 15-30% of infected individuals clear the virus spontaneously, while the majority develops chronic infection that causes liver complications. The only approved therapy for HCV is interferon alpha (IFN-α) based. This therapy has a 50-80% success rate depending on the infecting virus genotype and the timing of initiation of therapy. Factors governing the response to therapy are not well defined. Previous studies have suggested a role for the host immune response in the success of therapy. However, these results were controversial. We hypothesized that host immunity has an effective role in the success of IFN-α therapy when initiated early during the acute phase of HCV infection, while late initiation during the chronic phase minimizes this role. The main objective of this thesis was to dissect the immunological factors governing the differential response to IFN-α therapy, and to determine if the contribution of the immune response to success of therapy might be influenced by the period of infection. Our results demonstrate restoration of efficient HCV-specific immune responses when therapy is initiated early during the acute phase. This is demonstrated by the rescue of functional HCV-specific T cells similar to those observed in spontaneously resolved individuals, suggesting that they may play an active role in response to therapy. However, such responses were not restored following late therapy suggesting irreversible damage to the host’s defence system with chronicity. These findings have important implications in understanding the mechanisms underlying response to current treatments and development of novel therapies.

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Submitted in partial fulfillment of the academic requirements for the degree of Master of Technology: Biotechnology, 2009. / Production of numerous biotechnologically-important products such as threonine is based on cultivation of bacterial cultures. Infection of these bacterial cultures by bacteriophages has a detrimental effect in the production of these bioproducts. Despite this, most people controlling these bioprocesses do not recognize the early signs of bacteriophage infection. SA Bioproducts (Ply) Ltd was no exception and has suffered tremendous loss of production time after bacteriophages infected threonine producing E. coli strain B. This study was aimed at developing assays to control and prevent bacteriophage infection at this company. These included determining the source of phages by monitoring the process plant environment, optimising the detection and enumeration methods so as to monitor the levels of bacteriophages in the environment, identification of bacteriophages in order to determine the number of bacteriophages capable of infection threonine producing E. coli strain B, treatment and of phages, and possible prevention of phage infection. Adam's DAL method was very efficient at detecting phages in the samples collected at various areas (sumps, odour scrubber, process water, and soil) around the plant for 16 weeks. High levels of phages were found in the sumps and this was identified as the source of infection. Samples collected were grouped together according to their source. The samples were enriched and purified in order to characterise them. The prevalent phage in all samples was identified as a T1-like phage. Bacterial strains that grew on the plate in the presence of phages were assumed to be resistant to phages or contained lysogenic phages which would explain the new lytic cycles that were observed whenever these resistant strains were used for production. UV light, green v indicator plates, and a mutagen (Mitomycin C) were used to detect Iysogens. Mitomycin C at 1 IJg/ml was found to be most effective in detecting lysogenic phages. This was shown by new plaque forming units that were visible on the DAL plates. Temperature (heat), chemicals, and inhibitors (vitamins) were investigated as strategies for prevention and treatment of bacteriophage infection. Bacteriophage samples were exposed to 70, 80, 100, and 120°C. At these temperatures pfu counts in the samples were reduced significantly. At 120°C there was a complete inactivation of bacteriophages within 30 minutes. Chemicals investigated such as sodium hydroxide and Albrom 100T were capable of complete deactivation of bacteriophages at a very low concentration (0.1%). Therefore, these chemicals can be used to clean the plant area and sumps. Vitamins C, K and E solutions were investigated to determine their inhibitory effect on bacteriophages. Vitamin C, K and E reduced pfu counts by 3, 2, and 4 logs, respectively. Therefore vitamin C and E solutions were mixed and to determine if mixing them would enhance their inactivation capabilities. This resulted in a reduction greater than 9 logs of phage in the sample (from 7.7 x 109 to 3 pfu/ml). The host bacterium was also exposed to this mixture to determine effect of the vitamin mixture on its growth. It was found that there was no effect exerted by this mixture on the host bacteria. This proved to be an ideal mixture for combating phages during fermentation. However, vitamin E is not cost effective for co-feeding in 200 m' fermenters, and therefore vitamin C solution was a cost-effective alternative. It was concluded that bacteriophage contaminated bioprocessing plant should be properly cleaned using a combination of heat and chemicals. Bacteriophage infection should be prevented by employing inhibitors.