Features: Community engagement for biobanking research: perspectives from Africa

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Data mining and biological sample exportation from South Africa: a new wave of bioexploitation under the guise of clinical care?

Discovery Health, one of the leading healthcare funders in South Africa (SA), will offer genetic testing to its members for USD250 (approximately ZAR3 400) per test from 2016. On the surface, this appears to be innovative and futuristic. However, a deeper look at this announcement reveals considerable problems in the exportation of biological samples and data out of SA, and brings into sharp focus the lack of protection in place for potential donors. In return for a reduced-cost genetic test, which will nevertheless be billed to a member’s savings plan, data from the patient’s results and probably the sample itself Author: OK? will be sent to the USA for storage, research purposes and possible commercialisation, Author ‘commercial use’? with no further benefit for the patient. This development has demonstrated the need for more stringent protection of the movement of biological samples and data out of SA, particularly with reference to consenting procedures, material transfer agreements, and the export of biological data themselves

Maternal serum fructosamine values after delivery of macrosomic babies and unexplained stillbirths

Measurement of serum fructosamine and haemoglobin A, levels and glucose tolerance tests were performed in 75 women in the immediate postpartum period. None had predisposing factors to gestational diabetes. They were divided into three groups: group I consisted of 15 women who delivered an unexplained stillbirth; group 11 of 30 women who gave birth to babies weighing between 2500 g and 3900 g at term; and group III of 30 women who delivered babies weighing≥ 4000 g. There was a significant difference in the mean level of serum fructosamine between the unexplained stillbirth and control groups (P < 0,001). Although the HbA, values varied in the three groups, there was a significant difference between the unexplained stillbirth group and the macrosomic infant group (P < 0,05). All patients had normal glucose tolerance tests

The implications of Methylphenidate use by healthy medical students and doctors in South Africa

Background: The use of medical stimulants to sustain attention, augment memory and enhance intellectual capacity is increasing in society. The use of Methylphenidate for cognitive enhancement is a subject that has received much attention in the literature and academic circles in recent times globally. Medical doctors and medical students appear to be equally involved in the off-label use of Methylphenidate. This presents a potential harm to society and the individual as the long-term side effect profile of this medication is unknown. Discussion: The implication of the use of Methylphenidate by medical students and doctors has not been fully explored. This article considers the impact of this use on the traditional role of medicine, society, the patient and suggests a way forward. We discuss the salient philosophy surrounding the use of cognitive enhancement. We query whether there are cognitive benefits to the use of Methylphenidate in healthy students and doctors and whether these benefits would outweigh the risks in taking the medication. Could these benefits lead to tangible outcomes for society and could the off label-use of Methylphenidate potentially undermine the medical profession and the treatment of patients? If cognitive benefits are proven then doctors may be coerced explicitly or implicitly to use the drug which may undermine their autonomy. The increased appeal of cognitive enhancement challenges the traditional role of medicine in society, and calls into question the role of a virtuous life as a contributing factor for achievement. In countries with vast economic disparity such as South Africa an enhancement of personal utility that can be bought may lead to greater inequities. Summary: Under the status quo the distribution of methylphenidate is unjust. Regulatory governmental policy must seek to remedy this while minimising the potential for competitive advantage for the enhanced. Public debate on the use of cognitive enhancement is long overdue and must be stimulated. The use of Methylphenidate for cognitive enhancement is philosophically defendable if long-term research can prove that the risks are negligible and the outcomes tangible

ClassTR: Classifying Within-Host Heterogeneity Based on Tandem Repeats with Application to Mycobacterium tuberculosis Infections.

Genomic tools have revealed genetically diverse pathogens within some hosts. Within-host pathogen diversity, which we refer to as "complex infection", is increasingly recognized as a determinant of treatment outcome for infections like tuberculosis. Complex infection arises through two mechanisms: within-host mutation (which results in clonal heterogeneity) and reinfection (which results in mixed infections). Estimates of the frequency of within-host mutation and reinfection in populations are critical for understanding the natural history of disease. These estimates influence projections of disease trends and effects of interventions. The genotyping technique MLVA (multiple loci variable-number tandem repeats analysis) can identify complex infections, but the current method to distinguish clonal heterogeneity from mixed infections is based on a rather simple rule. Here we describe ClassTR, a method which leverages MLVA information from isolates collected in a population to distinguish mixed infections from clonal heterogeneity. We formulate the resolution of complex infections into their constituent strains as an optimization problem, and show its NP-completeness. We solve it efficiently by using mixed integer linear programming and graph decomposition. Once the complex infections are resolved into their constituent strains, ClassTR probabilistically classifies isolates as clonally heterogeneous or mixed by using a model of tandem repeat evolution. We first compare ClassTR with the standard rule-based classification on 100 simulated datasets. ClassTR outperforms the standard method, improving classification accuracy from 48% to 80%. We then apply ClassTR to a sample of 436 strains collected from tuberculosis patients in a South African community, of which 92 had complex infections. We find that ClassTR assigns an alternate classification to 18 of the 92 complex infections, suggesting important differences in practice. By explicitly modeling tandem repeat evolution, ClassTR helps to improve our understanding of the mechanisms driving within-host diversity of pathogens like Mycobacterium tuberculosis

Sedation for paediatric auditory electrophysiology in South Africa

Background: The sedation of children in the medical and allied professional fields has been a topic of controversy and debate internationally. Limited information is available on the use of sedation for auditory electrophysiology testing in South Africa.Objectives: The aim of this study was to determine how sedation information is recorded in electrophysiology audiology reports where diagnostic electrophysiology testing was used, and to obtain baseline information on sedation procedures and medications used during diagnostic electrophysiology testing.Methods: Audiology reports of 169 children undergoing auditory electrophysiology testing were reviewed for sedation information.Conclusion: Sedation data is not clearly documented and the use of medical or anaesthetist monitoring during sedation is not routinely included in reports. Sedation medication is varied and does not always include medications listed as safe for use with the paediatric population. This places doubt on procedures and protocols as well as the safety mechanisms in place for auditory diagnostic testing of children in South Africa.Keywords: auditory electrophysiology, diagnostic audiology, sedatio

Synergies, tensions and challenges in HIV prevention, treatment and cure research: exploratory conversations with HIV experts in South Africa

Background: The ethical concerns associated with HIV prevention and treatment research have been widely explored in South Africa over the past 3 decades. However, HIV cure research is relatively new to the region and significant ethical and social challenges are anticipated. There has been no published empirical enquiry in Africa into key informant perspectives on HIV cure research. Consequently, this study was conducted to gain preliminary data from South African HIV clinicians, researchers and activists. Methods: In-depth interviews were conducted on a purposive sample of fourteen key informants in South Africa. Audiotaped interviews were transcribed verbatim with concurrent thematic analysis. The perspectives of HIV clinicians, researchers and activists were captured. Analyst triangulation occurred as the data were analysed by three authors independently. Results: The rapid evolution of HIV cure research agendas was prominent with participants expressing some concern that the global North was driving the cure agenda. Participants described a symbiotic relationship between cure, treatment and prevention research necessitating collaboration. Assessing and managing knowledge and expectations around HIV cure research emerged as a central theme related to challenges to constructing ‘cure’ - how patients understand the idea of cure is important in explaining the complexity of cure research especially in the South African context where understanding of science is often challenging. Managing expectations and avoiding curative misconception will have implications for consent processes. Unique strategies in cure research could include treatment interruption, which has the potential to create therapeutic and ethical conflict and will be perceived as a significant risk. Ethical challenges in cure research will impact on informed consent and community engagement. Conclusions: It was encouraging to note the desire for synergy amongst researchers and clinicians working in the fields of prevention, treatment and cure. Translation of complex HIV cure science into lay language is critical. Moving forward, RECs must be adequately constituted with scientific expertise and community representation when reviewing cure protocols. It is hoped that knowledge and resource sharing in the context of collaboration between research scientists working in cure and those working in treatment and prevention will accelerate progress towards cur

Comparative host specificity of human- and pig- associated Staphylococcus aureus clonal lineages.

Bacterial adhesion is a crucial step in colonization of the skin. In this study, we investigated the differential adherence to human and pig corneocytes of six Staphylococcus aureus strains belonging to three human-associated [ST8 (CC8), ST22 (CC22) and ST36(CC30)] and two pig-associated [ST398 (CC398) and ST433(CC30)] clonal lineages, and their colonization potential in the pig host was assessed by in vivo competition experiments. Corneocytes were collected from 11 humans and 21 pigs using D-squame® adhesive discs, and bacterial adherence to corneocytes was quantified by a standardized light microscopy assay. A previously described porcine colonization model was used to assess the potential of the six strains to colonize the pig host. Three pregnant, S. aureus-free sows were inoculated intravaginally shortly before farrowing with different strain mixes [mix 1) human and porcine ST398; mix 2) human ST36 and porcine ST433; and mix 3) human ST8, ST22, ST36 and porcine ST398] and the ability of individual strains to colonize the nasal cavity of newborn piglets was evaluated for 28 days after birth by strain-specific antibiotic selective culture. In the corneocyte assay, the pig-associated ST433 strain and the human-associated ST22 and ST36 strains showed significantly greater adhesion to porcine and human corneocytes, respectively (p<0.0001). In contrast, ST8 and ST398 did not display preferential host binding patterns. In the in vivo competition experiment, ST8 was a better colonizer compared to ST22, ST36, and ST433 prevailed over ST36 in colonizing the newborn piglets. These results are partly in agreement with previous genetic and epidemiological studies indicating the host specificity of ST22, ST36 and ST433 and the broad-host range of ST398. However, our in vitro and in vivo experiments revealed an unexpected ability of ST8 to adhere to porcine corneocytes and persist in the nasal cavity of pigs

Negotiating requests for reimbursement for community engagement: challenges in developing an educational video for genomic biobanking research in South Africa

Genomic research and the biobanking capacity it requires are experiencing considerable growth on the continent of Africa. However genomic research and biobanking raise a range of legal, ethical, social, and cultural issues, including concerns about broad consent, confidentiality, community stigmatization, discrimination, indefinite storage, and long-term use. There is a need to establish governance frameworks that address these issues, and many international health research ethics and biobanking guidelines now recommend that the best way to do so is by involving potential research participants and key community stakeholders in the research development and the process of acquiring samples and data through active community engagement (CE). This article describes the experience and challenges in developing an educational tool as part of a CE initiative in South Africa and the commentaries reflect on how this process may be improved going forward