Introduction Analysis of surveillance data on bacterial respiratory pathogens most commonly causing bacteraemia and meningitis may be useful to measure the impact of vaccination, monitor antimicrobial resistance emergence and document changes in disease epidemiology. Materials and methods Active, laboratory-based, national surveillance for invasive Haemophilus influenzae, meningococcal and pneumococcal disease in South Africa was conducted. Isolates, cultured from normally sterile sites, were submitted for phenotypic and genotypic characterisation. Trends are described and univariate and multivariable models were used to assess differences among groups. Results Following the introduction of H. influenzae serotype b conjugate vaccine (HibCV) in 1999, the number of Hib cases reported for infants <1 year decreased by 65%, from 55 cases in 1999-2000 to 19 cases in 2003-2004. Despite high HibCV coverage, rates of Hib disease in children <5 years then increased from 0.7 per 100,000 population in 2003 to 1.3/100,000 in 2009. Among 263 Hib episodes, 135 (51%) were classified as vaccine failures and 53% of these occurred among children who were not HIV infected. An investigation of meningococcal disease in Gauteng, revealed rates of disease which increased from 0.8/100,000 in 2000 to 4.0/100,000 in 2005; the percentage due to serogroup W135 increased during this time from 7% (4/54) of cases to 75% (221/295). Overall case-fatality ratios doubled from 11% in 2003 to 22% in 2005. Our investigations revealed that the expansion of the Hajj clone explained the emergence of serogroup W135 during this time, as 95% of W135 isolates (285/301) were identified as one clone by pulsed-field gel electrophoresis and seven representative strains belonged to the ST-11/ET-37 complex. Among invasive pneumococcal disease (IPD) cases, 12 levofloxacin-non-susceptible pneumococci were identified in children <15 years, and were found to be associated with a history of tuberculosis (TB) treatment and nosocomial IPD in two treatment centres for multidrug-resistant TB (MDR TB). From 2003 through 2008, prior to pneumococcal conjugate vaccine (PCV) introduction, among IPD cases in children <5 years, 58% (3849/6668), 65% (4314/6668), and 85% (5669/6668) of cases and 61% (455/751), 64% (482/751), 82% (616/751) of deaths were due to serotypes included in 7-valent PCV (PCV-7), PCV-10 and PCV-13, respectively. PCV-13 had significantly higher coverage for isolates from blood culture than for isolates from cerebrospinal fluid: 3882/4531 (86%) vs. 1670/2009 (83%), p=0.009, but only differed by 3%. An analysis of risk factors revealed the relative risk of IPD was 21-fold (95% CI, 19–24) and 34-fold (29–41) greater in HIV-infected compared to HIV-uninfected children in the <1 year and 1–4-year-old age groups, respectively. Discussion and conclusions After initial reductions in Hib disease, vaccine failures, occurring in both HIV-infected and -uninfected children, comprised half of the rise in Hib disease detected 10 years after national introduction of Hib vaccine, given as three doses without a booster. These data contributed to the decision to add a booster dose of Hib vaccine in South Africa in 2009. Continued surveillance of meningococcal serogroup W135 revealed evidence that this serogroup had become endemic in Gauteng causing more severe disease than the previous predominant serogroup A strain. Paediatric fluoroquinolone use for MDR TB led to the emergence and nosocomial spread of levofloxacin-non-susceptible pneumococci. Existing pneumococcal vaccine formulations have the potential to prevent most cases and deaths from IPD among HIV-infected and -uninfected children in South Africa. Surveillance of pneumococcal meningitis may provide representative data for monitoring the impact of PCV.

Degree of Doctor of Philosophy in Medicine by research only A thesis submitted to the Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, in fulfilment of the requirements for the Degree of Doctor of Philosophy in Medicine. Johannesburg, 2014 / Introduction Patients with HIV infection frequently encounter oral candidiasis, caused by Candida species. However, factors responsible for Candida colonisation and development of oral candidiasis in these patients are controversial. This study investigated the effect of social and clinical factors on oral Candida colonisation in HIV positive women. In addition, virulence of these organisms during clinical infection, the role of non-albicans Candida and reinfections with C. albicans were investigated.

Dissertation submitted to the Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, in fulfilment of the requirements for the degree of Master of Science in Medicine. Johannesburg, 2012 / Introduction: Most new HIV-1 infections world-wide are caused by subtype C viruses. The C3V4 region, including the alpha2-helix and V4 loop, has been identified as a major target for autologous neutralising antibodies in subtype C infections. Factors associated with the immunogenicity of this region, and the mechanisms of escape from anti-C3V4 responses have not been described, although charge changes in the alpha2-helix have been proposed to mediate neutralisation escape. Methods: Seventeen HIV-1 subtype C infected individuals were classified as C3V4 responders or nonresponders using chimeric viruses in env-pseudotyped neutralisation assays. Longitudinal sequences obtained from C3V4 responders were used to identify putative neutralisation escape mutations. The role of these mutations in mediating escape was investigated using site-directed mutagenesis. Results: The C3V4 region was confirmed as a major target in HIV-1 subtype C infections. The development of an anti-C3V4 response was associated with shorter V4 loops and fewer potential N-linked glycans (PNGs) in the C3V4 region. Anti-C3V4 responses were associated with higher autologous neutralising titres. Neutralisation escape from an anti-C3V4 response was rarely mediated by charge changes in the alpha2-helix and generally occurred through mutations in other structurally proximal regions of the envelope. This study confirmed the use of glycan shuffling as a predominant escape pathway. In three individuals multiple mechanisms of escape were identified and in two other cases escape mutations within the C3V4 and structurally proximal regions clustered at opposite termini of the alpha2-helix, inconsistent with the surface area of a single epitope. Conclusion: A more exposed and accessible C3V4 region was more likely to elicit an anti-C3V4 response. The highly immunogenic nature of this region may contribute to the higher overall neutralisation titres in subtype C infections. Distinct clusters of mutations may suggest the existence of two “sub-epitopes” within the C3V4 domain that warrant further investigation. These findings emphasise the adaptability and plasticity of the C3V4 region in the context of viral evasion of host defences.

Inter- and intra-host Hey variation was investigated. First. a polymerase chain reactionrestriction fragment length polymorphism procedure was used to assign genotypes and subtypes to Hey infecting 567 individuals (comprising haemophilia patients, blood donors, intravenous drug users, attenders of antenatal and genito-urinary medicine clinics and chronic liver disease patients) from England and Wales. The majority of infections were associated with types 3a, 1 a and 1 b, and genotype distributions were generally similar in different sub-populations. Only 1 % of individuals were identified as being infected with more than one subtype. The intra-host variability of Hey in a selection of haemophilia patients, blood donors and intravenous drug users was then studied. For each individual, peR clones derived from the NS5b and 5' non-coding regions of the Hey genome were screened for sequence differences by denaturing gradient gel electrophoresis (DGGE) and nucleotide sequencing. The complexity and diversity of Hey quasi species, though differing between individuals, could not be correlated with the risk group to which the study patients belonged. Furthermore, no mixed genotype or subtype infections were identified. Thus the hypothesis that multiply exposed individuals are infected with a greater variety of HCY variants could not be substantiated. The DGGE procedure was further used to investigate the hypothesis that HCY genetic evolution occurs uniformly in patients during the acute phase of infection. Changes in diversity in the HCY hypervariable region 1 in individuals undergoing seroconversion were observed to differ between patients, thereby negating that hypothesis. Moreover, in a given individual, Hey could be subjected to either positive or negative selective pressure. Thus, factors other than the acute-phase host response determine the course of Hey genetic evolution.

Jin Yongjie. / Thesis (M.Phil.)--Chinese University of Hong Kong, 2004. / Includes bibliographical references (leaves 138-171). / Abstracts in English and Chinese. / Abstract (in English) --- p.i / Abstract (in Chinese) --- p.iii / Acknowledgments --- p.iv / Table of Contents --- p.v / List of Tables --- p.x / List of Figures --- p.xi / Chapter Chapter 1 --- Introduction --- p.1 / Chapter 1. --- Salmonella --- p.1 / Chapter 1.1 --- Morphology --- p.1 / Chapter 1.2 --- Antigenic structure --- p.1 / Chapter 1.3 --- Identification --- p.2 / Chapter 1.4 --- Nomenclature and classification --- p.2 / Chapter 1.5 --- Pathogenesis and virulence --- p.3 / Chapter 1.6 --- Infections --- p.4 / Chapter 1.6.1 --- Enteric fever --- p.4 / Chapter 1.6.2 --- Gastroenteritis --- p.4 / Chapter 1.7 --- Treatment --- p.5 / Chapter 1.7.1 --- Enteric fever --- p.5 / Chapter 1.7.2 --- Gastroenteritis --- p.5 / Chapter 1.8 --- Epidemiology and control --- p.6 / Chapter 1.8.1 --- Enteric fever --- p.6 / Chapter 1.8.2 --- Salmonella food poisoning --- p.6 / Chapter 2. --- Fluoroquinolones --- p.6 / Chapter 2.1 --- History of fluoroquinolones --- p.8 / Chapter 2.2 --- Mechanisms of action --- p.9 / Chapter 3. --- Antimicrobial resistance --- p.10 / Chapter 3.1 --- Microorganism-mediated resistance --- p.10 / Chapter 3.1.1 --- Intrinsic resistance --- p.11 / Chapter 3.1.2 --- Acquired resistance --- p.11 / Chapter 3.2 --- Resistance due to environmental factors --- p.12 / Chapter 3.3 --- Biological and clinical resistance --- p.12 / Chapter 3.4 --- Breakpoints --- p.13 / Chapter 4. --- Fluoroquinolone-resistance --- p.14 / Chapter 4.1 --- Increasing fluoroquinolone-resistance in bacteria --- p.14 / Chapter 4.2 --- Mechanisms of resistance to fluoroquinolones --- p.16 / Chapter 4.2.1 --- Mutations of target genes --- p.17 / Chapter 4.2.2 --- Active efflux systems and decreased membrane permeability --- p.20 / Chapter 5. --- Fluoroquinolone-resistance in Salmonella --- p.21 / Chapter 5.1 --- Prevalence of fluoroquinolone-resistant salmonellae in man and Animals --- p.21 / Chapter 5.1.1 --- Prevalence in the world --- p.21 / Chapter 5.1.2 --- Increasing resistance trend in Hong Kong --- p.24 / Chapter 5.2 --- Clinical outcome --- p.25 / Chapter 5.3 --- Mechanisms of fluoroquinolone-resistance in Salmonella --- p.25 / Chapter 5.3.1 --- Target gene mutations --- p.25 / Chapter 5.3.2 --- Other resistance mechanisms --- p.28 / Chapter 5.3.3 --- In vitro development of Salmonella resistant mutants --- p.29 / Chapter 6. --- Restricting the development of resistant mutants --- p.31 / Chapter 6.1 --- Mutant prevention concentration (MPC) --- p.31 / Chapter 6.1.1 --- Definition --- p.31 / Chapter 6.1.2 --- Development of MPC concept --- p.31 / Chapter 6.1.3 --- Significance --- p.34 / Chapter 6.2 --- Mutant selection window (MSW) --- p.35 / Chapter 6.2.1 --- The concept of mutant selection window (MSW) --- p.35 / Chapter 6.2.2 --- Significance --- p.36 / Chapter 7. --- Detection of gene mutations --- p.37 / Chapter 8. --- Objectives --- p.37 / Chapter Chapter 2 --- Materails and Methods --- p.39 / Chapter 1. --- Materials --- p.39 / Chapter 1.1 --- Bacterial strains --- p.39 / Chapter 1.1.1 --- Bacterial strains used for this study --- p.39 / Chapter 1.1.2 --- Storage of bacterial strains --- p.39 / Chapter 1.2 --- Materials --- p.40 / Chapter 2. --- Methods --- p.40 / Chapter 2.1 --- Identification --- p.40 / Chapter 2.2 --- Microbiological methods --- p.40 / Chapter 2.2.1 --- Determination of minimal inhibitory concentration (MIC) --- p.40 / Chapter 2.2.1.1 --- Preparation of antibiotic plates --- p.40 / Chapter 2.2.1.2 --- Preparation of inoculum --- p.43 / Chapter 2.2.1.3 --- Inoculation of antibiotic plates --- p.43 / Chapter 2.2.2 --- Determination of mutant prevention concentration (MPC) --- p.43 / Chapter 2.2.2.1 --- Preparation of bacterial suspension --- p.43 / Chapter 2.2.2.2 --- Inoculation of bacterial suspension --- p.43 / Chapter 2.2.2.3 --- Determination of the size of the inoculum --- p.43 / Chapter 2.2.2.4 --- Reading of results --- p.45 / Chapter 2.3 --- Molecular methods --- p.45 / Chapter 2.3.1 --- Polymerase chain reaction (PCR) --- p.45 / Chapter 2.3.2 --- Agarose gel electrophoresis --- p.47 / Chapter 2.3.3 --- Multiplex PCR amplimer conformation (MPAC) analysis --- p.47 / Chapter 2.3.3.1 --- Preparation of samples --- p.47 / Chapter 2.3.3.2 --- Electrophoresis --- p.49 / Chapter 2.3.3.3 --- Silver staining --- p.49 / Chapter 2.3.4 --- DNA Sequencing --- p.50 / Chapter 2.3.4.1 --- Purification of PCR products --- p.50 / Chapter 2.3.4.2 --- Sequencing reactions --- p.50 / Chapter 2.3.4.3 --- Electrophoresis --- p.50 / Chapter 2.3.4.4 --- Silver staining --- p.52 / Chapter 2.4 --- Stepwise selection and characterization of mutants --- p.53 / Chapter 2.4.1 --- In vitro selection of first-step strains --- p.53 / Chapter 2.4.2 --- Characterization of selected strains --- p.53 / Chapter 2.4.3 --- Subsequent selection of stepwise mutants --- p.54 / Chapter 3. --- Research plan --- p.54 / Chapter Chapter 3 --- Results --- p.55 / Chapter 1. --- Identification and fluoroquinolone MICs of Salmonella strains --- p.55 / Chapter 1.1 --- Identification of Salmonella strains --- p.55 / Chapter 1.2 --- Fluoroquinolone MICs for Salmonella strains --- p.55 / Chapter 1.2.1 --- Salmonella Typhimurium --- p.55 / Chapter 1.2.2 --- Salmonella Hadar --- p.57 / Chapter 2. --- Mutant prevention concentration (MPC) --- p.57 / Chapter 2.1 --- Salmonella Typhimurium --- p.57 / Chapter 2.1.1 --- MPC value --- p.57 / Chapter 2.1.2 --- MPC/MIC ratio --- p.57 / Chapter 2.1.3 --- Cmax/MPC ratio --- p.60 / Chapter 2.1.4 --- Frequencies of development of resistant strains --- p.60 / Chapter 2.2 --- Salmonella Hadar --- p.63 / Chapter 2.2.1 --- MPC value --- p.63 / Chapter 2.2.2 --- MPC/MIC ratio --- p.63 / Chapter 2.2.3 --- Cmax/MPC ratio --- p.63 / Chapter 2.2.4 --- Frequencies of development of resistant strains --- p.65 / Chapter 3. --- Stepwise selection of resistant mutants --- p.65 / Chapter 3.1 --- Salmonella Typhimurium --- p.70 / Chapter 3.1.1 --- Characterization of 1 St-step strains --- p.70 / Chapter 3.1.1.1 --- Antimicrobial susceptibilities --- p.70 / Chapter 3.1.1.2 --- Characterization of gene mutations --- p.75 / Chapter 3.1.1.3 --- Mutations and fluoroquinolone susceptibilities --- p.80 / Chapter 3.1.1.4 --- Mutations and nalidixic acid susceptibilities --- p.81 / Chapter 3.1.2 --- Characterization of 2nd-step mutants --- p.81 / Chapter 3.1.2.1 --- Antimicrobial susceptibilities --- p.82 / Chapter 3.1.2.2 --- Characterization of gene mutations --- p.85 / Chapter 3.1.2.3 --- Mutations and fluoroquinolone susceptibilities --- p.87 / Chapter 3.1.2.4 --- Nalidixic acid susceptibilities --- p.87 / Chapter 3.1.3 --- Characterization of 3rd-step mutants --- p.88 / Chapter 3.1.3.1 --- Antimicrobial susceptibilities --- p.88 / Chapter 3.1.3.2 --- Characterization of gene mutations --- p.92 / Chapter 3.1.3.3 --- Mutations and fluoroquinolone susceptibilities --- p.94 / Chapter 3.1.3.4 --- Nalidixic acid susceptibilities --- p.95 / Chapter 3.1.4 --- Characterization of 4th-step mutants --- p.95 / Chapter 3.1.4.1 --- Antimicrobial susceptibilities --- p.95 / Chapter 3.1.4.2 --- Characterization of gene mutations --- p.98 / Chapter 3.1.4.3 --- Nalidixic acid susceptibilities --- p.98 / Chapter 3.2 --- Salmonella Hadar --- p.98 / Chapter 3.2.1 --- Characterization of 1 St-step strains --- p.98 / Chapter 3.2.1.1 --- Antimicrobial susceptibilities --- p.99 / Chapter 3.2.1.2 --- Characterization of gene mutations --- p.102 / Chapter 3.2.1.3 --- Mutations and fluoroquinolone susceptibilities --- p.107 / Chapter 3.2.1.4 --- Mutations and nalidixic acid susceptibilities --- p.108 / Chapter 3.2.2 --- Characterization of 2nd-step mutants --- p.109 / Chapter 3.2.2.1 --- Antimicrobial susceptibilities --- p.109 / Chapter 3.2.2.2 --- Characterization of gene mutations --- p.112 / Chapter 3.2.2.3 --- Mutations and fluoroquinolone susceptibilities --- p.112 / Chapter 3.2.2.4 --- Nalidixic acid susceptibilities --- p.113 / Chapter Chapter 4 --- Discussion --- p.114 / Chapter 1. --- Susceptibility of salmonellae to fluoroquinolones --- p.114 / Chapter 2. --- The potential of fluoroquinolones to restrict the development of Salmonella resistant strains --- p.114 / Chapter 2.1 --- MPC and MPC/MIC of fluoroquinolones --- p.115 / Chapter 2.2 --- Cmax/MPC of fluoroquinolones --- p.117 / Chapter 2.3 --- Selection frequency of fluoroquinolones --- p.118 / Chapter 2.4 --- Effects of fluoroquinolones on the development of resistancein Salmonella Typhimurium and Salmonella Hadar --- p.119 / Chapter 3. --- Characterization of in vitro fluoroquinolone-resistant Salmonella mutants --- p.120 / Chapter 3.1 --- Development of resistance phenotype --- p.120 / Chapter 3.1.1 --- Microbiology --- p.120 / Chapter 3.1.2 --- Antimicrobial susceptibilities --- p.120 / Chapter 3.1.2.1 --- First-step strains --- p.120 / Chapter 3.1.2.2 --- Second-step mutants --- p.121 / Chapter 3.1.2.3 --- Third-step mutants --- p.121 / Chapter 3.1.2.4 --- Fourth-step mutants --- p.122 / Chapter 3.2 --- Contribution of target gene mutations to resistance development --- p.122 / Chapter 3.2.1 --- First-step mutants --- p.122 / Chapter 3.2.2 --- Second-step mutants --- p.125 / Chapter 3.2.3 --- Third-step mutants --- p.126 / Chapter 3.2.4 --- Fourth-step mutants --- p.128 / Chapter 3.3 --- The sequential development of gene mutations --- p.129 / Chapter 3.4 --- Other fluoroquinolone-resistance mechanisms --- p.130 / Chapter 4. --- Mutations and susceptibilities to fluoroquinolones and nalidixic acid --- p.132 / Chapter 4.1 --- Nalidixic acid - a marker for resistance to fluoroquinolones --- p.132 / Chapter 4.2 --- Breakpoint and clinical efficiency --- p.133 / Chapter 5. --- Strategies to reduce development of fluoroquinolone-resistance --- p.134 / Chapter 6. --- Conclusion --- p.136 / Chapter 7. --- Areas for future research --- p.136 / References --- p.138

Research report submitted in partial fulfilment of the requirements for the degree of Master of Medicine in Paediatrics. Johannesburg, 2015. / Urinary tract infections (UTIs) are an important cause of morbidity in children in developing countries and increasing antimicrobial resistance is reported in many countries. This retrospective study describes the performance of urine dipsticks, the aetiology and the antimicrobial susceptibility of paediatric UTIs at Rahima Moosa Mother and Child Hospital, Johannesburg. METHODS: We conducted a retrospective study of results from patients investigated for UTI over a four year period between January 2009 and December 2012 in the Department of Paediatrics & Child Health at Rahima Moosa Mother and Child Hospital. RESULTS: Escherichia coli was the commonest isolated uropathogen. Dipsticks sensitivity to identify UTI was 40% for leucocyte esterase and 34% for nitrites. The specificity was 94.6% for leucocyte esterase and 96% for nitrites. Malnutrition was associated with greater risk of having a UTI, with odds ratio of 2.06 (95% Confidence interval 1.4-2.9). In addition malnourished children tended to present with more resistant uropathogens. Resistance to sulphamethoxasole/trimethoprim and cephalexin has been progressively increasing between 2009 and 2012. From 64% to 79% for sulphamethoxasole/trimethoprim and from 24% to 63% for cephalexin. CONCLUSION: Positive urine dipsticks results allow immediate patient treatment but negative results need to be interpreted within the clinical context due to a high rate of false negatives. Malnourished children are significantly predisposed to urinary tract infections and tend to have more resistant uropathogens. Resistance to cephalexin is rising and studies to assess patient outcomes are needed to determine whether cephalexin still has a role in the treatment of paediatric UTI.

M.Med.(Paediatrics), Faculty of Health Sciences, University of the Witwatersrand, 2011 / Medium and large vessel vasculopathy in HIV-infected patients is an uncommon but important cause of mortality and morbidity in both adult and paediatric patients. The estimated frequency in children from the current literature is 1-2%. The overall HIV prevalence among children 18 years of age and younger in South Africa is currently 2.9%. This series reports on medium and large vessel vasculopathy in children with HIV. Six HIV infected children seen at three Johannesburg hospitals between 2000 -2006, are described, all presenting with complications arising from medium and/or large vessel involvement. Additional cases are reviewed from the literature. A description of the clinical presentation, radiological investigations, the possible aetiology, pathophysiology and management of these patients is presented. The case series and literature review compares HIV vasculopathy and Takayasu’s arteritis. Both entities can present with multiple aneurysms and a diagnosis of tuberculosis, thus a possible link in the pathogenesis is explored. Most patients with HIV vasculopathy present while severely immunosuppressed. However, some patients in the case series and literature review present despite adequate viral suppression, suggesting the possibility of an immune-reconstitution inflammatory syndrome in the pathogenesis of this vascular complication. Medical management and in selected cases, surgery, has been used in the management of patients with HIV vasculopathy. The outcomes thus far are good.

Thesis (MPH)--University of Limpopo (Medunsa Campus), 2011. / Background: South Africa hosts the largest number of pregnant HIV-positive women, accounting for almost 15% of the global total. Many amongst these HIV-positive pregnancies are unplanned and may be related to reproductive unmet needs, sexual risky behaviours, and/or community, contextual and individual factors that may determine and/or make these HIV-infected women to fall pregnant. The occurrence of an HIV-positive pregnancy in our region implies however the practice of unprotected sex, and is associated with the risk of reinfection with a different strain of HIV as well as with the risk of HIV transmission to an uninfected male partner and to the offspring. Knowing the demographic profile of HIV-infected women who become pregnant and experience parenthood as well as the circumstances of occurrence of their pregnancies is necessary for developing policies and interventions aimed at addressing the reproductive needs of this subpopulation, thus preventing HIV-positive unintended pregnancies as well as the horizontal and vertical transmission of HIV. Objectives: This study had three objectives. The first objective was to describe the demographic profile of pregnant HIV-positive women attending antenatal care (ANC) in public sector clinics in Postmasburg, South Africa. The second study objective was to determine the proportion of these pregnant HIV-infected women who were aware of their HIV-positive status prior to the occurrence of their current pregnancy. Lastly, the third objective sought to describe the circumstances of occurrence of their current pregnancy. Methodology: We used a quantitative descriptive design to collect data on 41 consecutive pregnant HIV-positive women who attended ANC at three public sector clinics in Postmasburg, from September to December 2010. Participants were administered a structured pre-tested questionnaire in their home language by trained interviewers. The study instrument was designed to collect data related to participants‘ socio-demographic characteristics, the time-period of HIV- v positive diagnosis relative to their current pregnancy, and the circumstances of occurrence of their current pregnancy. Results: The analyses of the study results showed that pregnant HIV-positive women attending ANC in Postmasburg were likely to be young (mean age, 27.71 ± 5.72 years), never married (56.10%), Afrikans (65.9%) and Setswana speakers (58.52%) of low socioeconomic status, with no or one child (65.85%). The majority of participants (63.4%) were from a predominantly informal settlement; 78% were unemployed while 61% were either devoid of any income or were living with Rands 500 or less. Sex mixing was common in the 15-19 years-old, involving 80% of respondents of this age category. Most of respondents (78.05%) became aware of their HIV-positive diagnosis during their current pregnancy that was unplanned in 73.17%. The study findings also revealed low levels of pregnancy intendedness (31.71%), hormonal contraceptives use (24.9%) and condoms uptake (34.15%), with high rates of condoms failure among users (87.12%). Respondents also reported other circumstances of occurrence of their current pregnancy, including, irregular condoms use (14.29% of condom users), partner refusal to use condom (10%), stopping contraceptives use because of side effects (50% of users), partner‘s pressure (12% of participants), coerced sex (2.4%) and having had sex under the influence of alcohol (2.4%). Conclusion: These results highlight the need for improving the reproductive health services that are offered to HIV-positive individuals. Integrating PMTCT and Family planning services, training health workers in issues related to the reproductive rights and reproductive health of HIV-infected individuals, systematically offering HIV counseling and testing to women of childbearing age who come into contact with health facilities for any reason and adequately informing HIV-positive women of childbearing age about available reproductive options, planned conception and safer motherhood, are necessary for preventing unintended HIV-positive pregnancies as well as the horizontal and vertical transmission of HIV.

Thesis (PhD (Medical Virology))-- University of Limpopo, 2010. / Background: Rotavirus infection remains a significant clinical problem throughout the world, infecting almost every child younger than 5 years of age, despite socio-economic status or environmental conditions. Rotavirus is the most common cause of severe dehydrating gastroenteritis in infants and young children. Implementation of an effective vaccine programme could reduce the incidence and severity of rotavirus disease. Decisions about new candidate rotavirus vaccines require reliable data on disease impact in both developed and developing countries. The aim of this study was to assess the burden of rotavirus associated disease at the tertiary care Dr George Mukhari Hospital, Ga-Rankuwa and the secondary care hospital Brits Hospital, Madibeng and to describe the genetic diversity of rotavirus strains circulating in Ga-Rankuwa and Brits communities over a similar time period as the testing of Rotarix@ vaccine. The broad objectives included; to perform a hospital-based burden of rotavirus disease in two different hospitals in the North West of Pretoria area, to conduct molecular characterization of rotaviruses circulating in the Pretoria region and lastly to devise an alternative molecular typing method to detect rotavirus VP6 subgroups. Materials and Method: To investigate the hospital-based burden of rotavirus disease, diarrhoeal stool samples were collected at Dr George Mukhari and Brits Hospitals from children less than 5 years of age. Group A rotavirus antigen was detected from the samples using commercially available rotavirus enzyme immunoassay IDEIA TM Rotavirus test (DAKO, Dakocytomation, Denmark). Genetic analyses of rotavirus strains were determined by polyacrylamide gel electrophoresis (PAGE) to characterize the electrophoretic patterns followed by analysis of the P and G genotypes by RT -PCR and multiplex PCR amplification of specific sequences of VP7 and VP4 genes. To devise an alternative molecular typing method to detect rotavirus VP6 subgroups, with subgroup specificities determined by both VP6 monoclonal antibodies and restriction fragment length polymorphism using restriction endonuclease Acil, Odel and Rsa I. Selected PCR amplicons (VP7 and VP6 genes) were purified, cloned and sequenced. Consensus sequences of the VP7 and VP6 genes were aligned and analysed manually with Chromaslite and BioEdit software packages. Multiple sequence alignment was implemented by Mafft software packages. The nucleotide and deduced amino acid sequences of the VP7 and VP6 genes were compared with reference strains available from GenBank. Multiple methods were used to construct phylogenetic trees and included neighbor¬ joining, maximum parsimony analysis and maximum likelihood distance. Bootstrap values were computed using 1000 replicates with Phylip and the MEGA softwares. The graphic representation of each phylogenetic tree was displayed with the Treeview program. Results: Between 2003 and 2005, a total of 2 514 diarrhoeal stool samples were collected. Of these, 527 (21%) were positive for group A rotavirus and the majority of children hospitalized were less than 2 years of age. The annual peak prevalences of group A rotavirus were 56%, 59% and 56% for 2003, 2004 and 2005, respectively and were observed during the autumn and winter months. The estimated incidence of gastroenteritis associated with rotavirus indicates that one in every 50 to 70 children in the area is likely to be hospitalized with rotavirus diarrhoea between birth and 2 years of age. During the three-year study period, ten, six and seven different RNA electrophoretic patterns were identified in 2003, 2004 and 2005, respectively. The VP6 genes of the representative strains (G1, G2, G3, G9, G8 and G12) were ana lysed with restriction endonuclease Acil, Ode! and Rsa!. The restriction endonucleases produced 11 unique restriction profiles (A-K). The VP6 RFLP results correlated well with strains displaying long RNA electropherotypes and VP6 subgroup 1/ specificity and also with strains displaying short RNA electropherotypes and exhibiting VP6 subgroup I specificity as determined with VP6 monoclonal antibodies. The genotypic distribution varied remarkably and major rotavirus strains detected in circulation during the study period included G2P[4] in 2003, G1 P[8] in 2004 and G3P[8]/ G3P[6] in 2005. Rotavirus strains carrying G8P[8] specificities and unusual G 12P[6] strains were also detected at low frequency The consensus VP7 nucleotide sequences, exhibited the greatest homology and identity (97-99%), when compared against corresponding international reference strains. The nucleotide sequence datasets were closely related to strains from South Africa, Vietnam, Bangladesh, East India, Republic of Congo, China, Russia, Thailand and Japan. The phylogenetic tree revealed the South African strains (G1-G3, G8-G9 and G12) clustered with international strains whereas the G1 strains clustered into two different lineages. Phylogenetic analysis of the VP6 gene revealed four lineages with international reference strains. The VP6 gene showed 97-99% identity at the deduced amino acids level with strains from Taiwan, Bangladesh, the United States and Brazil. Conclusion: This is the first study to estimate the disease burden associated with rotavirus diarrhoea in South Africa. The overall results confirm that rotavirus is the most common cause of severe diarrhoea. The epidemiology of rotavirus diarrhoea in South Africa correlates well with what has been reported in other countries. The proportion of hospitalization of rotavirus infection in children less than 5 years was estimated to an annual prevalence of 22.8% (95%CI 21.2%, 24.5%) at Dr George Mukhari Hospital, while at Brits Hospital was estimated at 18.2% (95%CI 14.9%, 22.1 %). Rotavirus genotypes circulating at Dr George Mukhari Hospital showed a high degree of diversity and the emergence of uncommon rotavirus strains such as G12. The emergence of novel rotaviruses in the region needs to be taken into account where vaccine efficacy is concerned. It is, thus, important to continue with such studies to monitor the rotavirus strains associated with severe gastroenteritis in a hospital setting before and after the introduction of a rotavirus vaccine. Results also indicated that RFLP analysis of VP6 amplicons might be a simple and reliable, alternative to MAb subgrouping. The sequence analysis of the partial length VP6 gene confirmed the location and the recognition sites of the restriction enzymes The RFLP analysis proved to have more potential to accurately detect different rotavirus subgroups.

Thesis (MSc (Clinical Psychology)) -- University of Limpopo, 2012. / Recent literature on childbearing and HIV has indicated a plethora of evidence suggesting that many women living with HIV continue to desire children, become pregnant and give birth after knowing their HIV status. This desire to have children has been associated with the availability of HAART and PMTC interventions and its improvement in the quality of life for HIV-positive women. This study aimed at exploring the emotional experiences of HIV-positive married women wanting to bear children. A qualitative research design was used to explore the above mentioned aim. Through the use of semi-structured interviews a sample of 12 HIV-positive married women were purposefully selected. The participants were chosen from Tshepang clinic at Dr. George Mukhari Hospital situated in the township of Ga-Rankuwa using a purposive sampling design. Semi-structured interviews using interview guide were conducted to explore their unique and subjective emotional experiences of being HIV, married and in need of a child. The process of data analysis in the current study was guided by phenomenological approach in order to allow the inherent meaning of the data to emerge without being distorted. The findings of these study revealed that the experiences surrounding HIV positive diagnosis, marriage and childbearing proves to be associated with overwhelming emotional experiences for women in the current study. Most of the participants in this study viewed motherhood as a unique, subjective and a personal fulfilment for all women irrespective of their HIV status. Participants felt that children stabilise a marriage by giving it meaning. A decision to conceive for some participants is influenced by pressure as a result of their marital, social and situational context