ETD Collection

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    Analysing the national notifiable diseases surveillance system in South Africa
    (2018) Benson, Frew Gerald
    Background Outbreaks of infectious diseases contribute to premature mortality and underscore the importance of effective disease surveillance and response systems. There is limited knowledge on the performance of the South African notifiable disease surveillance system (NDSS). Objective The aim of this PhD study was to analyse the NDSS of South Africa. The specific objectives were to: analyse key informants’ perspectives on system attributes of the National NDSS; analyse the NDSS attributes through comparing notifications with laboratory surveillance; determine the factors influencing provider compliance with the NDSS; and make policy recommendations to improve the effectiveness of the NDSS. Methods This thesis combined a novel comparative analysis of laboratory and notification records for three tracer conditions of measles, meningococcal meningitis, and typhoid with two cross-sectional, analytical studies among NDSS key stakeholders (n=169) and health care providers (n=1050) respectively. STATA® 14 was used to conduct quantitative, statistical analyses. Results The key stakeholders’ survey had an 84% response rate: 25% perceived the system to be acceptable; 51%, flexible; 45%, timely; 61%, useful; and 74%, simple. Stakeholders with more experience were less likely to perceive the NDSS as acceptable (OR 0.91, 95 % CI: 0.84–1.00, p = 0.041); those in disease detection were less likely to perceive it as timely (OR 0.10, 95 % CI: 0.01–0.96, p = 0.046) and those participating in National Outbreak Response Team were less likely to perceive it as useful (OR 0.38, 95 % CI: 0.16–0.93, p = 0.034). vii For all three diseases, fewer cases were notified than laboratory confirmed. Completeness for the laboratory system was higher for measles (63% vs. 47%, p<0.001) and meningococcal meningitis (63% vs. 57%, p<0.001), but not for typhoid (60% vs. 63%, p=0.082). Stability was higher for the laboratory (all 100%) compared to notified measles (24%, p<0.001), meningococcal meningitis (74%, p<0.001), and typhoid (36%, p<0.001). Representativeness was also higher for the laboratory (all 100%) than for notified measles (67%, p=0.058), meningococcal meningitis (56%, p=0.023), and typhoid (44%, p=0.009). The sensitivity of the NDSS was 50%, 98%, and 93%, and the PPV was 20%, 57%, and 81% for measles, meningococcal meningitis, and typhoid, respectively. The response rate for the health care provider (HCP) survey was 90%. In the year preceding the survey, 58% diagnosed a notifiable disease; 92% of these HCPs reported the disease, but only 51% notified correctly to the Department of Health. Factors influencing notification were HCPs perceptions of workload (OR 0.84, 95% CI 0.70 - 0.99, p=0.043) and that notification data are not useful (OR 0.84, 95% CI 0.71 - 0.99, p=0.040). Conclusion The NDSS in South Africa performed poorly on most of the system attributes. In addition, HCP compliance with the NDSS was suboptimal. The study generated new knowledge on the performance of the NDSS in South Africa, which should inform the revitalisation and reforms of the system.
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    The role of planned relook laparotomy in the management of severe intra-abdominal infection in an experimental rat model
    (1991) Browning, Neil
    Severe intra-abdominal infection (IAI) carries a high mortality. Methods of treatment such as radical peritonaal debridement, continuos post-operative lavage and local intra-peritonaal instillation of anti-biotics have not improved. [Abbreviated Abstract. Open document to view full version]
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    Studies on bacterial respiratory pathogens causing bacteraemia and meningitis in South Africa
    (2014-03-28) Gottberg, Anna Margareta, von
    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.
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    Factors associated with bacterial vaginosis in sexually active women enrolled in the Microbicide Development Program 301 Study.
    (2014-03-27) Manyema, Mercy
    Introduction Bacterial vaginosis (BV) is a highly prevalent vaginal infection which poses a significant public health burden in Sub-Saharan Africa (SSA) due to its association with HIV, other STIs and several gynaecological and obstetrical complications. The aim of this study was to explore the underlying and proximate factors associated with BV and the relationships between them. Materials and Methods This study was a cross-sectional secondary analysis of the data collected during the Microbial Development Program (MDP) 301 trial. Logistic regression and structural equation modelling were used to test for the associations between BV and the explanatory variables and to test for the direct, indirect and total effects of the variables on BV. Results A total of 2 470 women were included in the analysis and of these 2 203 were aged 40 and below. The majority of them were unemployed at 72% and 51,8% were in the lowest socio-economic level. The baseline prevalence of BV was 40.5%. In the logistic regression, high socio-economic level (AOR=1.66; 95% CI 1.04-2.64) and using a condom during their last sexual encounter (AOR 0.82; 95% CI 0.69-0.97) were associated with BV infection. The STIs significantly associated with BV infection were: Herpes Simplex Virus 2 (HSV2) (AOR=1.31; 95% CI 1.10-1.56), trichomoniasis (AOR=2.68; 95% CI 1.97-3.64) and chlamydia infection (AOR 2.02; 95% CI 1.61-2.62). In the structural equation modelling (SEM) high socio-economic status had a positive direct effect on BV infection (beta=0.12, OR=1.14).Condom use during the last sex act had a negative direct effect on BV (beta=-0.043, OR=0.96). The presence of T.vaginalis, HSV2 or chlamydia infection had significant positive effects on BV infection. Conclusions Sexual behavioural factors and the presence of STIs were significantly associated with BV. The SEM analysis showed the interaction of contraceptive use and sexual behavioural factors. No interaction between the STIs and sexual behaviour could be demonstrated in this study.
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    The detection of Burkholderia spp. and pathogenic Leptospira spp. in South Africa
    (2013-03-18) Saif, Adrienne N.
    Leptospirosis is a zoonosis of ubiquitous distribution and causes a wide spectrum of disease. Burkholderia species are important plant and human pathogens. Little or no investigation has been performed on any clinically-relevant Burkholderia or Leptospira species in Johannesburg. Environmental samples were taken from different sites in Johannesburg along the Jukskei River. These were subjected to culturing for Burkholderia spp. and polymerase chain reaction (PCR) for Burkholderia and Leptospira spp. Human serum, animal serum and kidney samples were also subjected to PCR for both organisms. A Leptospira IgM ELISA was also performed on human serum samples. More Burkholderia spp. were isolated by culture from soil samples than water samples. The PCR yielded a significantly higher PCR positive from soil samples (p = 0.015). There was a high prevalence of pathogenic Leptospira spp. in soil samples. The ELISA yielded only 7.8% (26/332) positive samples. There were no human or animal positive PCR results for either organism. There is an environmental presence of both leptospires and Burkholderia in the area sampled. More studies are needed to establish how both organisms might affect patients with compromised immune systems, and how often both infections are incorrectly or under-diagnosed.