The Impact of the Evolving Human Immunodeficiency Virus Response on the Epidemiology of Tuberculosis in South African Children and Adolescents.

BACKGROUND: Few studies have evaluated tuberculosis control in children and adolescents. We used routine tuberculosis surveillance data to quantify age- and human immunodeficiency virus (HIV)-stratified trends over time and investigate the relationship between tuberculosis, HIV, age, and sex. METHODS: All children and adolescents (0-19 years) routinely treated for drug-susceptible tuberculosis in South Africa and recorded in a de-duplicated national electronic tuberculosis treatment register (2004-2016) were included. Age- and HIV-stratified tuberculosis case notification rates (CNRs) were calculated in four age bands: 0-4, 5-9, 10-14, and 15-19 years. The association between HIV infection, age, and sex in children and adolescents with tuberculosis was evaluated using multivariable logistic regression. RESULTS: Of 719 400 children and adolescents included, 339 112 (47%) were 0-4 year olds. The overall tuberculosis CNR for 0-19 year olds declined by 54% between 2009 and 2016 (incidence rate ratio [IRR] = 0.46; 95% confidence interval [CI], .45-.47). Trends varied by age and HIV, with the smallest reductions (2013-2016) in HIV-positive 0-4 year olds (IRR = 0.90; 95% CI, .85-.95) and both HIV-positive (IRR = .84; 95% CI, .80-.88) and HIV-negative (IRR = 0.89; 95% CI, .86-.92) 15-19 year olds. Compared with 0- to 4-year-old males, odds of HIV coinfection among 15-19 year olds were nearly twice as high in females (adjusted odds ratio [aOR] = 2.49; 95% CI, 2.38-2.60) than in males (aOR = 1.35; 95% CI, 1.29-1.42). CONCLUSIONS: South Africa's national response to the HIV epidemic has made a substantial contribution to the observed declining trends in tuberculosis CNRs in children and adolescents. The slow decline of tuberculosis CNRs in adolescents and young HIV-positive children is concerning. Understanding how tuberculosis affects children and adolescents beyond conventional age bands and by sex can inform targeted tuberculosis control strategies.

Future land cover change scenarios in South African grasslands - implications of altered biophysical drivers on land management.

Future land cover changes may result in adjustments to biophysical drivers impacting on net ecosystem carbon exchange (NEE), catchment water use through evapotranspiration (ET), and the surface energy balance through a change in albedo. The Land Change Modeller (Idrisi Terrset 18.08) and land cover for 2000 and 2014 are used to create a future scenario of land cover for two catchment with different land management systems in the Eastern Cape Province for the year 2030. In the S50E catchment, a dualistic farming system, the trend shows that grasslands represented 57% of the total catchment area in 2014 decreasing to 52% by 2030 with losses likely to favour a gain in woody plants and cultivated land. In T35B, a commercial system, persistence of grasslands is modelled with approximately 80% coverage in both years, representing a more stable system. Finally, for S50E, NEE and ET will increase under this land cover change scenario leading to increased carbon sequestration but less water availability and corresponding surface temperature increases. This implies that rehabilitation and land management initiatives should be targeted in catchments under a dualistic farming system, rather than those which are predominantly commercial systems.

Using remote sensing in support of environmental management: A framework for selecting products, algorithms and methods.

Traditionally, to map environmental features using remote sensing, practitioners will use training data to develop models on various satellite data sets using a number of classification approaches and use test data to select a single 'best performer' from which the final map is made. We use a combination of an omission/commission plot to evaluate various results and compile a probability map based on consistently strong performing models across a range of standard accuracy measures. We suggest that this easy-to-use approach can be applied in any study using remote sensing to map natural features for management action. We demonstrate this approach using optical remote sensing products of different spatial and spectral resolution to map the endemic and threatened flora of quartz patches in the Knersvlakte, South Africa. Quartz patches can be mapped using either SPOT 5 (used due to its relatively fine spatial resolution) or Landsat8 imagery (used because it is freely accessible and has higher spectral resolution). Of the variety of classification algorithms available, we tested maximum likelihood and support vector machine, and applied these to raw spectral data, the first three PCA summaries of the data, and the standard normalised difference vegetation index. We found that there is no 'one size fits all' solution to the choice of a 'best fit' model (i.e. combination of classification algorithm or data sets), which is in agreement with the literature that classifier performance will vary with data properties. We feel this lends support to our suggestion that rather than the identification of a 'single best' model and a map based on this result alone, a probability map based on the range of consistently top performing models provides a rigorous solution to environmental mapping.

Transmission of tuberculosis in a high incidence urban community in South Africa.

BACKGROUND: The objective of this study was to identify risk factors for ongoing community transmission of tuberculosis (TB) in two densely populated urban communities with a high incidence rate of TB in Cape Town, South Africa. METHODS: Between 1993 and 1998 DNA fingerprints of mycobacterial isolates from TB patients were determined by restriction fragment length polymorphism (RFLP). Cases whose isolates shared identical fingerprint patterns were considered to belong to the same cluster and to be attributable to ongoing community transmission. RESULTS: The average annual notification rate of new smear positive TB was 238/100000. In all, 1023/1526 reported patients were culture positive, and RFLP was available for 768 (75%) of the isolates from these patients. Since some patients experienced more than one infection during the study period, 797 cases were included in the analysis. Of the cases, 575/797 (72%) were clustered. Smear-positive cases and those who were retreated after default were more likely to be clustered than smear-negative and new cases, respectively. Patients from Uitsig were more often part of large clusters than were patients from Ravensmead. Age, sex, year of diagnosis, and outcome of disease were not risk factors for clustering, nor for being the first case in a cluster, although various analytical approaches were used. CONCLUSIONS: The incidence and proportion of cases that are clustered in this area are higher than reported elsewhere. An overwhelming majority of TB cases in this area is attributed to ongoing community transmission, and only very few to reactivation. This may explain the lack of demographic risk factors for clustering.

Proportion of tuberculosis transmission that takes place in households in a high-incidence area.

The prevalence of infection among household contacts of people with tuberculosis is high. This information frequently guides active case finding. We analysed DNA fingerprints of Mycobacterium tuberculosis from 765 tuberculosis patients in Ravensmead and Uitsig, adjacent suburbs of Cape Town, South Africa. In 129 households in which DNA fingerprints were available for more than one patient, we identified 313 patients, of whom 145 (46%) had a fingerprint pattern matching that of another member of the household. The proportion of transmission in the community that took place in the household was 19%, and therefore, in this high-incidence area, tuberculosis transmission occurs mainly outside the household.

Multiple Mycobacterium tuberculosis strains in early cultures from patients in a high-incidence community setting.

In an ongoing molecular epidemiology study, human immunodeficiency virus-negative patients with first-time pulmonary tuberculosis from a high-incidence community were enrolled. Mycobacterium tuberculosis strains were identified by restriction fragment length polymorphism analysis with two fingerprinting probes. Of 131 patients, 3 (2.3%) were shown to have a mixture of strains in one or two of their serial cultures. This study further investigated these cases with disease caused by multiple M. tuberculosis strains in the context of the molecular epidemiology of the study setting.