Orientador: Marcos Antonio Machado / Resumo: A morte súbita dos citros (MSC) causou a morte ou erradicação de aproximadamente quatro milhões de plantas de laranja doce na principal região citrícola do Brasil. Embora sua etiologia ainda não esteja completamente resolvida, seus sintomas e distribuição (especial e temporal) indicam uma provável doença viral. Trabalhos anteriores associaram a MSC ao vírus da tristeza dos citros (CTV) e ao CSDaV (Citrus sudden death-associated virus), no entanto, os resultados obtidos destes trabalhos não são conclusivos. Afim de estudar as populações de vírus presentes em plantas de citros afetadas pela MSC, este trabalho realizou uma análise comparativa, através do sequenciamento de alta performance do transcriptoma e dos pequenos RNAs de plantas sintomáticas e assintomáticas para MSC. Os dados revelaram uma infecção viral mista, incluindo o CTV como vírus mais predominante, seguido do CSDaV, um pararetrovírus endógeno de citros (CitPRV) e dois possíveis novos vírus, putativamente denominados de Citrus jingmen-like virus (CJLV) e Citrus virga-like virus (CVLV). As análises de correlação com a MSC indicaram uma provável associação de plantas sintomáticas com o CitPRV, enquanto que os dois novos vírus mostraram estar mais associados com plantas assintomáticas. A associação mais evidente foi observada entre plantas sintomáticas e um genótipo específico de CSDaV, o que nos conduziu a um estudo mais específico de variabilidade genética de 31 isolados de CSDaV, obtidos de plantas MSC-sintomática... (Resumo completo, clicar acesso eletrônico abaixo) / Doutor

Please read the abstract in the 00front part of this document / Dissertation (MSc Agric (Microbiology))--University of Pretoria, 2007. / Microbiology and Plant Pathology / unrestricted

Please read the abstract in the section 00front of this document / Dissertation (Magister Istitutiones Agrariae)--University of Pretoria, 2006. / Plant Production and Soil Science / unrestricted

Please read the abstract in the section 00front of this document / Dissertation (MSc (Agric): Genetics)--University of Pretoria, 2005. / Genetics / unrestricted

The increasing incidence of infections due to antibiotic resistant bacteria has led to renewed interest in bacteriophages (= phages) and phage therapy. Although phage therapy has been applied to control bacterial diseases in plants, poultry, livestock and humans, its application in aquaculture is still relatively limited. The emergence of phage-resistant bacterial mutants has been considered to be one of the major limitations of phage therapy. This study aimed to (i) isolate and characterise phages; (ii) select phages and their bacterial hosts to set up in vivo phage therapy models with aquaculture animals, and estimate the efficiency of phage therapy; (iii) investigate the generation and characteristics of phage-resistant mutants, and thus estimate the consequence of applying phage therapy when phage-resistant mutants emerge; and (iv) discuss the prospects for application of phages in aquaculture. Two Vibrio isolates and their phages were isolated from a Scottish marine fish farm. Based on the results of conventional phenotype testing and 16S rRNA gene sequencing analysis, the two vibrios, V9 and V13, were identified as Vibrio splendidus and Vibrio cyclitrophicus, respectively. The bacterial characteristics including morphology, temperature and salinity range of growth, production of extracellular enzymes, and the possession of virulence genes were examined. According to the morphological characteristics observed using transmission electron microscopy by negative staining, phage PVS9 of V. splendidus V9 was identified as a myophage, while phage PVC13 of V. cyclitrophicus V13 was identified as a siphophage. The phages could only lyse one bacterial host strain and their genomic DNA was double stranded with a size of ~46 kb. The two Vibrio isolates were found to be non- or of low virulence to rainbow trout, goldsinny wrasse and Artemia in pathogenicity experiments. Thus an in vivo phage therapy model could not be set up using these Vibrio isolates and their phages. Two phages pAS-3 and pAS-6 were isolated using the Aeromonas salmonicida subsp. salmonicida Hooke strain as the host. Phages pAS-3 and pAS-6 had a similar genome size of ~50 kb, and the same relatively narrow host range within A. salmonicida subsp. salmonicida strains. The siphophage pAS-3 formed clear plaques and inhibited A. salmonicida Hooke growth in vitro completely for at least 18 hours when using MOI = 1,000, whereas the podophage pAS-6 formed turbid plaques and weakly inhibited Hooke growth. Rainbow trout exposed by intraperitoneal injection with 0.1 mL of the raw phage preparations at a concentration of 108 PUF mL-1 showed no adverse effects over 14 days. In the phage therapy trial, fish were firstly injected with 1 x 102 CFU fish-1 of A. salmonicida Hooke, then immediately injected with phage preparations of pAS-3 and pAS-6, respectively, using MOI = 10,000. Compared with the control group (which did not receive phage treatment), phage treated groups showed a delay in the time to death, and lower mortalities. However, the mortalities and time to death between phage treated and non-treated groups were not significantly different. Phage-resistant mutants of pathogenic A. salmonicida strain Hooke were induced by repeatedly challenging with phage pAS-3. One of the mutants, termed HM, was chosen to compare the characteristics with the parental wild-type strain Hooke. Test results including the formation of ‘smooth’ colonies on TSA, autoagglutination negative, the formation of creamy colonies on Coomassie Brilliant Blue agar, and the degradation of a thick/furry layered structure on the cell surface indicated a deficiency of the A-layer in the phage-resistant mutant HM. Therefore, it was deduced that the A-layer either directly acted as the receptor of A. salmonicida phage pAS-3, or was affected indirectly by the change of an unknown phage receptor. The greater wax moth larvae model was used to compare the virulence of the phage-resistant mutant HM and the parental wild-type strain Hooke, as it is an ethically acceptable animal model, which has the advantages of being low cost and convenient for injection, and is also a recognised alternative model for bacterial pathogens of fish. The results showed that virulence of the phage-resistant mutant HM did not decline in the greater wax moth larvae model compared with that of the parental wild-type strain Hooke. In conclusion, different approaches were used to isolate and characterise phages from different aquaculture environments for potential use in phage therapy. A rainbow trout model was set up using pathogenic A. salmonicida strain Hooke and two A. salmonicida phages pAS-3 and pAS-6. The use of phage treatment led to lower cumulative mortalities and delay to the time of death, although the differences between the groups were not significant, futher work is required to determine if these phages have potential in phage therapy. The consequence of applying phage therapy when phage-resistant mutants emerge was estimated based on their characteristics and virulence, and no decline in virulence of the phage-resistant mutant from this study indicates the importance of fully testing the virulence of phage-resistant mutants before carrying out large scale field trials of phage therapy. It appears feasible to use phage therapy as an alternative approach to control bacterial infections in aquaculture, but further studies are required to focus on improving effectiveness, and also to overcome the concrete limitations and hurdles in application and commercialisation. Moreover, a broader range of applications of phages in aquaculture should be explored.

The effect of the inclusion of sexual behaviour, particularly three sexual orientation classes, on the transmission dynamics of HPV and cervical cancer incidence was investigated. A comprehensive literature review of mathematical models of HPV transmission and the natural history of cervical cancer was concluded. A mathematical model using ordinary differential equations was developed, which incorporated the three sexual orientation classes, and a sexual mixing algorithm for modelling the transmission dynamics. Reproduction numbers, determined through a simplified version of the developed model, indicated that the bisexual population could form a bridge between the heterosexual and homosexual population. The level of interaction is determined by the selection preferences of a bisexual individual to form a partnership with an individual of the same or opposite sex. The model was simulated, with parameters based on a South African population and HPV type 16/18, to investigate the effects of HIV status, sexual orientation and various vaccination strategies on HPV transmission and cervical cancer incidence. The results indicated that HIV status is a significant factor when determining cervical cancer incidence. The results regarding vaccination strategies agreed with results from the literature review with a two sex before sexual debut and catch up program the most effective, noting that with increased vaccination coverage of females the marginal impact on cervical cancer incidence of this approach diminished.

No description available.

Adult immunizations effectively reduce morbidity, mortality, and transmission rates of multiple diseases; however, outpatient providers often a struggle to convince patients to accept vaccinations. This project’s aim is to address vaccination rates in our adult population, focusing first on the influenza vaccine in year one (2016), and then on pneumococcal vaccine in year two (2017), by 1) using a strong quality improvement strategy (known as a Champion Team) and 2) implementing a clinic program consisting of provider training, improved documentation, and informative posters targeted at patients. A quality improvement strategy known as a “Champion Team” provided a strong mechanism through which we developed and implemented the interventions across both years. Specifically, the Champion Team consisted of key stakeholders (nurses, residents, physician faculty, and informatics expert) who identified, developed, and evaluated the program. Programming included an annual health care professional training session for each vaccine (early fall of 2016 and 2017 for flu, spring 2017 for pneumococcal), improved documentation strategies and nursing uptake, and informative posters in the clinic. We assayed data from our patient electronic health record to evaluate: the percentage of our patient population for whom an immunization was documented relative to the number of unique patients seen in our clinic during that time frame. This approach in year one showed a marked increase in influenza vaccination rates in our clinic. During the 2014/2015 and 2015/2016 flu seasons our clinic vaccination rates were 39.98% and 42.05% respectively. After implementation of our champion team and clinic wide program to increase rates in 2016 our vaccination rates for the 2016/2017 flu seasons was 50.88%. Pneumonia data for a full year are under analyses and will be included in this presentation. We anticipate a similar increase in rates for our pneumococcal vaccinations. Our Champion Team and clinic wide program were perceived as relatively low-effort interventions yet appeared to increase vaccinations over the course of this study. The replication of these findings across pneumonia data (pending) and, in future work, with the herpes zoster vaccine (planned for Year 3), will increase our confidence that increases in rates were attributable to these very accessible interventions.

ABSTRACT: Hepatitis C virus (HCV) is associated with various glomerulopathies and nephrotic syndrome. However nephrotic syndrome following treatment is rare. Ledipasvir/sofosbuvir (L/S) has recently come into favor in treating HCV due to its relatively mild side effects compared to the more traditional interferon therapy. To the best of our knowledge, there are no reported cases of nephrotic syndrome following treatment with L/S. We present a case of nephrotic syndrome suspected secondary to L/S in a patient with chronic kidney disease. Increased vigilance when assessing therapeutic options in HCV patients with renal comorbidities can improve patient outcomes. A 63 year-old male patient presented to the hospital with shortness of breath, and a two-week history of bilateral lower extremity edema. Past medical history was significant for liver cirrhosis secondary to Hepatitis C genotype Ia, hepatocellular carcinoma status post liver transplantation 6 months prior to admission and Stage 3b chronic kidney disease with baseline creatinine (Cr) approximately 1.5 mg/dl. Medications included L/S for HCV and tacrolimus and prednisone for post-transplant treatment. Patient’s vitals were stable and physical exam was remarkable for facial swelling, mainly on the eyelids, decreased breath sounds bilaterally, distended abdomen with a fluid wave, and 2-3+ pitting edema up to the knees on lower extremities bilaterally. Laboratory work-up was remarkable for low albumin of 3.0 g/dl, and total protein of 5.6 g/ dl. Creatinine of 1.8 mg/dl was elevated from patient’s baseline. HCV viral load was undetectable and electrolytes, transaminases and the complete blood count were within normal limits. Subsequently, urine protein to creatinine ratio was measured because of generalized swelling and hypoproteinemia, which was found to be significantly high at 8.80, compared to 0.04 one year prior. 24-hour total urine protein was found to be 2065 mg/day. Renal ultrasonography showed no hydronephrosis and was otherwise unremarkable. Renal biopsy however, revealed changes suggestive of membranoproliferative glomerulonephritis (MPGN] most likely secondary to HCV. No immune complexes, lambda/kappa light chains, or cryogloblin were appreciated. Nephrotoxic agents such as diuretics and corticosteroids were held. Tacrolimus trough was appropriate to dose level and was continued along with L/S. As admission progressed the patient’s creatinine continued to get worse and rose up to 4.3 mg/dl with persistent proteinuria. With tacrolimus trough levels within normal limits and given L/S was the most recently initiated drug, L/S was thought to be the culprit and was thus held. The renal function began to improve gradually, and the patient was discharged in stable condition with close follow up. Follow up one month later found creatinine and renal function return to baseline and proteinuria resolved. Our case shows that Ledipasvir/sofosbuvir may possibly be related to nephrotic syndrome in HCV patients. Although further studies are needed to prove the causality our case seeks to raise clinical suspicion and increase vigilance when assessing therapeutic options in HCV patients with renal comorbidities such as chronic kidney disease.

Bibliography: pages 175-184. / The occurrence of maize dwarf mosaic virus (MDMV) in field grown maize was investigated. For this purpose, maize showing mosiac symptoms was collected from different maize growing areas in South Africa by Prof. M.B. von Wechmar. These samples from Transvaal, Orange Free State and Natal were then investigated for the presence of MDMV and possible strains of this virus. Three virus isolates were purified and partially characterised. These isolates were serologically compared together with a fourth isolate SCMV 4975, obtained from the U.S., to establish strain relationships.