Developing a Conceptual Model for Sustainable water Resource Management and Agricultural Development: the Case of the Breede River Catchment Area, South Africa.

The complex relationship that exists between water resources and agricultural production has been increasing constantly globally. Several factors are interacting to influence the management of water resources making the system complex and dynamic. To increase the understanding of these complex and dynamic systems, relevant tools are needed to identify the causal relationships that exist between the drivers and their influences on the system. Participatory modelling based on the system dynamics approach provides a simplistic and visualisation tool that can improve the understanding of the functioning of a complex and dynamic system. A multi-stage participatory approach was used in this study involving relevant stakeholders in the development of an integrated conceptual system dynamic model using causal loop diagrams. This approach was used because it captures the thought process and mental model of relevant stakeholders in the development of the model, making it a valuable tool for policy and decision making at government and individual levels. The integrated model built in this study used causal loop diagrams to address problems of water management and agricultural sustainability in the Breede River Catchment. The model shows major causal-relationships and feedback loops that determine the functioning of the overall system. The model demonstrates the usefulness of the participatory approach in solving problems related to water management and agricultural development in the catchment.

Bacterial Genotyping of Central Nervous System Tuberculosis in South Africa: Heterogenic Mycobacterium tuberculosis Infection and Predominance of Lineage 4.

Tuberculous meningitis (TBM), the most severe extrapulmonary manifestation of tuberculosis, is caused by the pathogen Mycobacterium tuberculosis The M. tuberculosis complex includes seven lineages, all described to harbor a unique geographical dissemination pattern and clinical presentation. In this study, we set out to determine whether a certain M. tuberculosis lineage demonstrated tropism to cause TBM in patients from Cape Town, South Africa. DNA was extracted from formalin-fixed paraffin-embedded central nervous system (CNS) tissue from a unique neuropathological cohort of 83 TBM patients, collected between 1975 and 2012. M. tuberculosis lineages 1, 2, 3, and 4 were determined using an allele-specific PCR and Sanger sequencing. Of the 83 patient specimens tested, bacterial characterization could be performed on 46 specimens (55%). M. tuberculosis lineage 4 was present in 26 patient specimens (56%), and non-lineage 4 was identified in 10 cases (22%). Moreover, genomic heterogeneity was detected in the CNS specimens of 7 adults and 3 children. We could show that infection of the CNS is not restricted to a single M. tuberculosis lineage and that even young children with rapid progression of disease can harbor more than one M. tuberculosis lineage in the CNS.

In vitro permeation of platinum and rhodium through Caucasian skin.

During platinum group metals (PGMs) refining the possibility exists for dermal exposure to PGM salts. The dermal route has been questioned as an alternative route of exposure that could contribute to employee sensitisation, even though literature has been focused on respiratory exposure. This study aimed to investigate the in vitro permeation of platinum and rhodium through intact Caucasian skin. A donor solution of 0.3mg/ml of metal, K2PtCl4 and RhCl3 respectively, was applied to the vertical Franz diffusion cells with full thickness abdominal skin. The receptor solution was removed at various intervals during the 24h experiment, and analysed with high resolution ICP-MS. Skin was digested and analysed by ICP-OES. Results indicated cumulative permeation with prolonged exposure, with a significantly higher mass of platinum permeating after 24h when compared to rhodium. The mass of platinum retained inside the skin and the flux of platinum across the skin was significantly higher than that of rhodium. Permeated and skin retained platinum and rhodium may therefore contribute to sensitisation and indicates a health risk associated with dermal exposure in the workplace.

Critical appraisal of volumetric-modulated arc therapy compared with electrons for the radiotherapy of cutaneous Kaposi's sarcoma of lower extremities with bone sparing.

OBJECTIVE: To evaluate the use of volumetric-modulated arc therapy [VMAT, RapidArc® (RA); Varian Medical Systems, Palo Alto, CA] for the treatment of cutaneous Kaposi's sarcoma (KS) of lower extremities with adequate target coverage and high bone sparing, and to compare VMAT with electron beam therapy. METHODS: 10 patients were planned with either RA or electron beams. The dose was prescribed to 30 Gy, 10 fractions, to mean the planning target volume (PTV), and significant maximum dose to bone was limited to 30 Gy. Plans were designed for 6-MV photon beams for RA and 6 MeV for electrons. Dose distributions were computed with AcurosXB® (Varian Medical Systems) for photons and with a Monte Carlo algorithm for electrons. RESULTS: V(90%) was 97.3±1.2 for RA plans and 78.2±2.6 for electrons; similarly, V(107%) was 2.5±2.2 and 37.7±3.4, respectively. RA met coverage criteria. Concerning bone sparing, D(2%) was 29.6±1.1 for RA and 31.0±2.4 for electrons. Although acceptable for bone involvement, pronounced target coverage violations were obtained for electron plans. Monitor units were similar for electrons and RA, although for the latter they increased when superior bone sparing was imposed. Delivery times were 12.1±4.0 min for electrons and 4.8±1.3 min for the most modulated RA plans. CONCLUSION: High plan quality was shown for KS in the lower extremities using VMAT, and this might simplify their management in comparison with the more conventional usage of electrons, particularly in institutes with limited staff resources and heavy workloads. ADVANCES IN KNOWLEDGE: VMAT is also dosimetrically extremely advantageous in a typology of treatments where electron beam therapy is mainly considered to be effective owing to the limited penetration of the beams.

Attitude of Lesotho health care workers towards HIV/AIDS and impact of HIV/AIDS on the population structure.

BACKGROUND: The impact and management of HIV/AIDS in Lesotho in the context of disaster management was investigated. OBJECTIVES: Lesotho health care workers' perception on HIV/AIDS progression, whether HIV/AIDS was managed as a disaster, and the impact on the demographic profile was investigated. METHODS: The empirical investigation included a literature study, and primary and secondary data analyses. Questionnaires (n=116) determined health care workers' perception of HIV/AIDS. Interviews with officers of Lesotho Disaster Management determined how HIV/AIDS was managed as a disaster. National population censuses and data from surveys were summarised to describe the impact of HIV/AIDS on the population structure. RESULTS: Respondents' modal age group was 25 to 39 years, 28.4% viewed HIV/AIDS related deaths as very high and perceived that HIV/AIDS changed the age composition, sex and dependency ratio of the population. Although HIV/AIDS was declared a disaster, the Lesotho Disaster Management Authority only aided the National AIDS Commission. There was evidence that HIV/AIDS caused the population pyramid base to shrink, and an indentation in the active population. CONCLUSION: Health care workers attributed HIV/AIDS to changing the demographic profile of Lesotho, also reflected in the population pyramid. Lesotho Disaster Management Authority played a supporting role in HIV/AIDS disaster management.

The evolving epidemic of drug-resistant tuberculosis among children in Cape Town, South Africa.

SETTING: Tygerberg Children's Hospital, Cape Town, South Africa. OBJECTIVE: To determine the prevalence and trend of drug resistance and human immunodeficiency virus (HIV) co-infection among children with culture-confirmed tuberculosis (TB). METHOD: Prospective surveillance from March 2007 to February 2009, compared to three previous surveys (1994-1998, 2003-2005, 2005-2007). Drug susceptibility testing (DST) against isoniazid (INH) and rifampicin (RMP) was performed using genotypic and phenotypic testing. If multidrug-resistant TB (MDR-TB) was detected, further DST against ethambutol (EMB) and second-line drugs was performed. RESULTS: A total of 294 children with a median age of 26 months (range 3 days-13 years) were diagnosed with culture-confirmed TB. DST results were available for 292 (99.3%); 41 (14%) were INH-resistant, including 26 (8.9%) with MDR-TB. Four children (1.4%) had RMP monoresistance. EMB resistance was present in 12/24 (50%) MDR-TB cases tested. Two isolates were resistant to ofloxacin; none had extensively drug-resistant TB. Of those tested, 29% (63/217) were HIV-infected. Any resistance to RMP increased between 1994 and 2009 (P < 0.001), as did RMP monoresistance (P = 0.009) and MDR-TB (P < 0.001). Sensitivity was 87.5% and specificity 100% for genotypic compared to phenotypic testing for INH resistance. CONCLUSIONS: RMP, and consequently multidrug, resistance is increasing among children with TB in this setting. EMB resistance is common among children with resistance to RMP and INH.

Genetic mixed-stock analysis of Atlantic sturgeon Acipenser oxyrinchus oxyrinchus in a heavily exploited marine habitat indicates the need for routine genetic monitoring.

Although a previous genetic mixed-stock analysis (gMSA) conducted in the early 1990s showed that marine-captured New York Bight Atlantic sturgeon Acipenser oxyrinchus oxyrinchus almost exclusively originated from the Hudson River, fish from southern U.S. rivers were well represented within this contemporary sample (n = 364 fish), at least during the autumn. Widely distributed spawning stocks are therefore exposed to heavy fishing activity and habitat degradation in this relatively small area, illustrating the need for spatial management across multiple management jurisdictions and routine gMSA to account for temporal change.

Rifampicin-monoresistant Mycobacterium tuberculosis disease among children in Cape Town, South Africa.

SETTING: Tygerberg Children's Hospital (TCH) and Brooklyn Chest Hospital (BCH), South Africa. OBJECTIVES: To describe paediatric cases of rifampicin (RMP) monoresistant tuberculosis (RMR-TB) disease. DESIGN: Records of children with culture-confirmed RMR-TB between 1 March 2003 and 28 February 2009 were identified from a prospectively recorded database of drug-resistant TB at TCH and BCH. Mutation analysis was performed on available specimens. RESULTS: Eighteen children with a median age of 6.9 years (range 2 months-12.8 years) were identified. Nine (50%) were human immunodeficiency virus (HIV) infected and four (22%) were HIV-exposed but non-infected. Eleven (61%) had had previous TB treatment or prophylaxis. Nine children (50%) had cavitary disease and five children (22%) had extra-pulmonary disease. Twelve (67%) had adult TB source cases, including five (42%) adults with known RMR-TB. Primary transmission occurred among 11 children (61%) and acquisition of RMR-TB was possible in seven (39%) with prior RMP exposure. Median delay to specific RMR-TB treatment was 70 days (range 23-188). One child died from RMR-TB meningitis. Gene mutations consistent with RMR-TB were confirmed in five available samples. CONCLUSION: RMR-TB disease is increasingly encountered, particularly among HIV-infected and HIV-exposed non-infected children. Delay in commencing appropriate treatment for RMR-TB and high rates of cavitary disease could be a source of RMR-TB transmission.

Ethionamide cross- and co-resistance in children with isoniazid-resistant tuberculosis.

BACKGROUND: Ethionamide (ETH) is a structural analogue of isoniazid (INH). Both are pro-drugs requiring activation by separate and common enzyme pathways, which could lead to co- and/or cross-resistance. OBJECTIVE: To characterise paediatric INH-resistant mycobacterial isolates to investigate the presence of ETH resistance and mutations in the katG gene and the inhA promoter region. METHODS: Forty-five INH-resistant and 19 INH-susceptible Mycobacterium tuberculosis control isolates from children from the Western Cape Province, South Africa, were analysed to quantify INH minimal inhibitory concentration, test for ETH resistance and investigate mutations in the katG gene and/or inhA promoter region. RESULTS: Among 45 INH-resistant children, ETH resistance was present in 19 of 39 (49%). An inhA promoter mutation was identified in 15 (33.3%); 12/14 (86%) of these isolates were also ETH-resistant. Of the 21 isolates with a katG mutation, six (29%) were ETH-resistant. No isolate had both katG and inhA promoter mutations. Nine (20%) isolates had neither inhA promoter nor katG mutations. Of 15 isolates with inhA promoter mutation, 14 (93%) displayed low- or intermediate-level INH resistance. Among the 19 INH-susceptible isolates, ETH resistance was present in 1/18 (6%) and none showed inhA or katG gene mutations. CONCLUSION: We found a high level of cross- and co-resistance with ETH among INH-resistant M. tuberculosis isolates from children in this geographic area.

Molecular characterisation of rifampicin-resistant Mycobacterium tuberculosis strains from Morocco.

Mutations in the rpoB gene associated with rifampicin (RMP) resistance were studied in 47 RMP-resistant and 147 RMP-susceptible clinical strains of Mycobacterium tuberculosis from Morocco using probe-based assay and DNA sequencing. RMP-resistant mutations were identified in 85% of RMP-resistant isolates. No mutations were observed among the 147 RMP-susceptible strains. Sequence analysis identified 10 alleles, including two deletions not previously reported. Nucleotide changes at codons 531, 526 and 516 were the most prominent, accounting for 74.4% of our RMP-resistant strains. These results demonstrate that resistance genotyping at these codons would be a good marker for the rapid detection of RMP resistance.

Discordance between mycobacterial interspersed repetitive-unit-variable-number tandem-repeat typing and IS6110 restriction fragment length polymorphism genotyping for analysis of Mycobacterium tuberculosis Beijing strains in a setting of high incidence of tuberculosis.

IS6110 restriction fragment length polymorphism (RFLP) genotyping is the most widely used genotyping method to study the epidemiology of Mycobacterium tuberculosis. However, due to the complexity of the IS6110 RFLP genotyping technique, and the interpretation of RFLP data, mycobacterial interspersed repetitive-unit-variable-number tandem-repeat (MIRU-VNTR) genotyping has been proposed as the new genotyping standard. This study aimed to determine the discriminatory power of different MIRU-VNTR locus combinations relative to IS6110 RFLP genotyping, using a collection of Beijing genotype M. tuberculosis strains with a well-established phylogenetic history. Clustering, diversity index, clustering concordance, concordance among unique genotypes, and divergent and convergent evolution were calculated for seven combinations of 27 different MIRU-VNTR loci and compared to IS6110 RFLP results. Our results confirmed previous findings that MIRU-VNTR genotyping can be used to estimate the extent of recent or ongoing transmission. However, molecular epidemiological linking of cases varied significantly depending on the genotyping method used. We conclude that IS6110 RFLP and MIRU-VNTR loci evolve independently and at different rates, which leads to discordance between transmission chains predicted by the respective genotyping methods. Concordance between the two genotyping methods could be improved by the inclusion of genetic distance (GD) into the clustering formulae for some of the MIRU-VNTR loci combinations. In summary, our findings differ from previous reports, which may be explained by the fact that in settings of low tuberculosis incidence, the genetic distance between epidemiologically unrelated isolates was sufficient to define a strain using either marker, whereas in settings of high incidence, continuous evolution and persistence of strains revealed the weaknesses inherent to these markers.

Fluorometric assay for testing rifampin susceptibility of Mycobacterium tuberculosis complex.

The emergence and transmission of multidrug-resistant tuberculosis (MDR-TB) and extensively drug-resistant tuberculosis (XDR-TB) have raised concern about diagnostic delay associated with culture-based drug susceptibility testing methods. The association between rifampin resistance and MDR-TB or XDR-TB makes it an important genetic marker for genotypic drug susceptibility testing. In this article, we describe the analysis of the physical properties of the rifampin resistance-determining region (RRDR) in the rpoB gene by high-resolution thermal melt analysis as a method for detecting rifampin resistance in Mycobacterium tuberculosis complex. The RRDR from the M. tuberculosis complex was amplified by PCR from DNA templates extracted from sputum cultures of M. tuberculosis or the laboratory strain (H37Rv) in the presence of a fluorescent DNA binding dye. Subsequent mixing of the amplification products from the respective sputum cultures and the laboratory strain and thermocycling allowed the formation of DNA duplexes. The thermal denaturation properties of these DNA duplexes were determined by measuring the derivative of the intensity of fluorescence at different temperatures. Analysis of DNA extracted from 153 sputum cultures showed a sensitivity of 98% and a specificity of 100% for the detection of rifampin resistance compared to the "gold standard" culture-based phenotyping method. No statistical difference was detected in the performance of the method when applied to crude DNA from 134 boiled cultures. This method, named "FAST-Rif" ("fluorometric assay for susceptibility testing of rifampin"), allowed the rapid, reliable, and easy detection of genotypic rifampin resistance as a marker for MDR-TB and XDR-TB.

Spread of a low-fitness drug-resistant Mycobacterium tuberculosis strain in a setting of high human immunodeficiency virus prevalence.

The fitness cost associated with the evolution of resistance to rifampin in Mycobacterium tuberculosis may be different in clinical isolates compared to in vitro-generated mutants. An atypical Beijing strain (attenuated phenotype) demonstrated the ability to spread despite acquiring resistance to rifampin. Transmission was linked to human immunodeficiency virus coinfection (P = 0.029), raising concern for the spread of drug resistance in vulnerable populations.

Evaluation of a rapid screening test for rifampicin resistance in re-treatment tuberculosis patients in the Eastern Cape.

BACKGROUND AND OBJECTIVES: Patients with multidrug-resistant (MDR) tuberculosis (TB) are at high risk of treatment failure. It is anticipated that early identification of MDR-TB and appropriate treatment will improve patient outcome and disease control. We evaluated the rapid detection of rifampicin resistance in previously treated TB patients, directly from acidfast bacilli (AFB)-positive sputum using a phage-based test, FASTPlaque-Response (Biotec Laboratories Ltd, Ipswich, UK). The ability of rifampicin resistance to predict MDR-TB was also determined. DESIGN: A prospective study was done comparing performance of the rapid phage test with conventional culture and drug susceptibility testing (DST) in AFB-positive TB patients. SETTING: Five primary health clinics and one TB referral centre in the Port Elizabeth Metropolitan area, Eastern Cape. OUTCOME MEASURES: Sensitivity, specificity and overall accuracy of the phage test were determined compared with gold standard culture and DST. Discrepant results were resolved by molecular detection of mutations conferring rifampicin resistance. The proportion of rifampicin-resistant strains that were MDR was also determined. RESULTS: Previously treated patients were at a high risk of MDRTB (35.7%). Sensitivity, specificity and overall accuracy of FASTPlaque-Response for rifampicin resistance determination were 95.4% (95% confidence interval (CI): 91.0 - 99.8%), 97.2% (95% CI: 94.5 - 99.9%) and 96.5% (95% CI: 94.1 - 98.9%) respectively compared with conventional DST (unresolved), calculated for specimens that had both FASTPlaque-Response and conventional DST results available. FASTPlaque-Response results were available in 2 days instead of 28 - 85 days with conventional DST. However, only 70.6% of FASTPlaque-Response results were interpretable compared with 86.3% of conventional DST results. The majority (95.5%) of rifampicinresistant strains were MDR-TB. CONCLUSIONS: Rapid detection of rifampicin resistance using FASTPlaque-Response could contribute to improved management of patients at risk of MDR-TB, such as previously treated patients. However, improvement in control of specimen-related contamination is needed to ensure that a higher proportion of FASTPlaque-Response results are interpretable. Where indicated, early modification of therapy could improve patient prognosis and reduce disease transmission.

Spread of an emerging Mycobacterium tuberculosis drug-resistant strain in the western Cape of South Africa.

BACKGROUND: South Africa has a high burden of drug-resistant tuberculosis (TB). METHODS: Routine drug susceptibility testing was performed prospectively over a 2-year period on Mycobacterium tuberculosis isolates in two health districts of the Western Province, South Africa. A cluster of drug-resistant strains that shared a rare mutation in katG315 was found in 64 of the 450 cases identified as having been infected with drug-resistant TB. Isolates belonging to this cluster were phenotypically and genotypically characterised. Epidemiological and clinical characteristics were used to identify mechanisms leading to the acquisition and spread of this drug-resistant strain. RESULTS: An outbreak of an emerging non-Beijing drug-resistant strain infecting 64 pulmonary tuberculosis (PTB) cases was identified. This previously undetected genotype (now designated DRF150) is characterised by five IS6110 insertions, specific spoligotypes and high levels of resistance to the first-line TB medications isoniazid, streptomycin and rifampicin. In 45% of the cases it is also resistant to ethambutol and pyrazinamide. Key factors leading to the development and spread of this drug-resistant genotype were inappropriate chemotherapy, poor adherence to treatment and prolonged periods of infectiousness due to delays in susceptibility testing. CONCLUSIONS: Molecular markers allowed early identification of an emerging non-Beijing drug-resistant strain.

An outbreak of drug-resistant tuberculosis caused by a Beijing strain in the western Cape, South Africa.

During October 2005, four children in a school in Cape Town were identified with multidrug-resistant tuberculosis (MDR-TB). Genetic analysis confirmed that these isolates belonged to a single cluster (Beijing cluster 220) and that all harboured a -15 inhA(C-T) promoter mutation demonstrating transmission. Genetic analysis of isolates cultured from patients from the Boland-Overberg-South Cape-Karoo and Cape Town regions showed that 28% (58/209) of patients infected with a Beijing strain had the cluster 220 genotypes and that all harboured the same -15 inhA(C-T) promoter mutation. The presence of these transmissible MDR-TB strains may pose a threat to the community, and rigorous infection control measures are needed to ensure the safety of those exposed.

Ethambutol resistance testing by mutation detection.

OBJECTIVE: To identify chromosomal mutations that confer resistance to ethambutol (EMB) in Mycobacterium tuberculosis. DESIGN: Drug-resistant (n = 235) and drug-susceptible (n = 117) M. tuberculosis isolates collected from the Western Cape in South Africa were subjected to embB gene analysis and the results were compared to phenotypic EMB testing. RESULTS: Genotypic analysis identified mutations at codon 306 of the embB gene in 20% (47/235) of the resistant isolates in comparison to only 1.7% (4/235) of those that were phenotypically resistant to EMB by the agar diffusion method. No gene mutations were detected in susceptible isolates. Phenotypic retesting in BACTEC demonstrated that the 47 genotypically resistant isolates were phenotypically resistant to EMB. This implies that 91.4% (43/47) of EMB resistance had been phenotypically missed by routine laboratory procedures. EMB resistance was closely linked to multidrug resistance (MDR); 87.2% (41/47) of the EMB-resistant isolates were resistant to both isoniazid and rifampicin. A newly developed one-step amplification refractory mutation system polymerase chain reaction (ARMS-PCR) method correctly detected the EMB-resistant genotype. CONCLUSION: Implementation of more accurate diagnosis of EMB resistance may enhance patient management in South Africa, as standardised treatment of MDR-TB with second-line drugs is currently dependent on the outcome of the EMB resistance test.

Ewing's sarcoma of the vulva--a case report.

Extraosseous Ewing's sarcoma of the vulva is extremely rare with only three such cases described. A 26-year-old woman presented with Ewing's sarcoma of the vulva. She received chemotherapy to shrink the lesion. However, the response was suboptimal and she subsequently received radiotherapy. Although resection was planned, she developed chest metastases within a short period of time and subsequently died.