Juanita Bezuidenhout

Localisation of mycobacterial DNA and mRNA in human tuberculous granulomas

In situ hybridisation was used to detect the presence of Mycobacterium tuberculosis in paraffin-embedded lung tissue of nine patients diagnosed with tuberculosis (TB). Mycobacterial DNA was found in all nine patients and in 175 out of 191 granulomas examined. A combination of in situ hybridisation and immunohistochemistry techniques demonstrated that mycobacterial DNA was associated with CD68-positive cells with the morphology of macrophages and giant cells. Mycobacterial DNA was also found within the necrotic regions of some granulomas. mRNA for the mycobacterial RNA polymerase beta subunit (rpoB) was detected by RNA: RNA in situ hybridisation. The rpoB mRNA was also localised to CD68-positive cells with the morphology of macrophages and to giant cells of certain necrotic granulomas. No rpoB mRNA was found in the necrotic regions of granulomas. Mycobacterial DNA was detected in 92% of patient granulomas of which 8% were positive for rpoB mRNA. The ability to identify mycobacterial RNA transcripts within human tuberculous granulomas affords us the opportunity to analyse the interplay between pathogen gene expression and the human immune response and should provide valuable insight into the mechanisms used by M. tuberculosis to persist within the human host.

Genomic medicine and risk prediction across the disease spectrum

Abstract Genomic medicine is based on the knowledge that virtually every medical condition, disease susceptibility or response to treatment is caused, regulated or influenced by genes. Genetic testing may therefore add value across the disease spectrum, ranging from single-gene disorders with a Mendelian inheritance pattern to complex multi-factorial diseases. The critical factors for genomic risk prediction are to determine: (1) where the genomic footprint of a particular susceptibility or dysfunction resides within this continuum, and (2) to what extent the genetic determinants are modified by environmental exposures. Regarding the small subset of highly penetrant monogenic disorders, a positive family history and early disease onset are mostly sufficient to determine the appropriateness of genetic testing in the index case and to inform pre-symptomatic diagnosis in at-risk family members. In more prevalent polygenic non-communicable diseases (NCDs), the use of appropriate eligibility criteria is required to ensure a balance between benefit and risk. An additional screening step may therefore be necessary to identify individuals most likely to benefit from genetic testing. This need provided the stimulus for the development of a pathology-supported genetic testing (PSGT) service as a new model for the translational implementation of genomic medicine in clinical practice. PSGT is linked to the establishment of a research database proven to be an invaluable resource for the validation of novel and previously described gene-disease associations replicated in the South African population for a broad range of NCDs associated with increased cardio-metabolic risk. The clinical importance of inquiry concerning family history in determining eligibility for personalized genotyping was supported beyond its current limited role in diagnosing or screening for monogenic subtypes of NCDs. With the recent introduction of advanced microarray-based breast cancer subtyping, genetic testing has extended beyond the genome of the host to also include tumor gene expression profiling for chemotherapy selection. The decreasing cost of next generation sequencing over recent years, together with improvement of both laboratory and computational protocols, enables the mapping of rare genetic disorders and discovery of shared genetic risk factors as novel therapeutic targets across diagnostic boundaries. This article reviews the challenges, successes, increasing inter-disciplinary integration and evolving strategies for extending PSGT towards exome and whole genome sequencing (WGS) within a dynamic framework. Specific points of overlap are highlighted between the application of PSGT and exome or WGS, as the next logical step in genetically uncharacterized patients for whom a particular disease pattern and/or therapeutic failure are not adequately accounted for during the PSGT pre-screen. Discrepancies between different next generation sequencing platforms and low concordance among variant-calling pipelines caution against offering exome or WGS as a stand-alone diagnostic approach. The public reference human genome sequence (hg19) contains minor alleles at more than 1 million loci and variant calling using an advanced major allele reference genome sequence is crucial to ensure data integrity. Understanding that genomic risk prediction is not deterministic but rather probabilistic provides the opportunity for disease prevention and targeted treatment in a way that is unique to each individual patient.

Developing an educational research framework for evaluating rural training of health professionals: A case for innovation

Background: World-wide, rural clinical training of undergraduate medical students is looking to transform learning experiences, calling for the adoption of innovative approaches that create spaces for curriculum renewal and new ways of thinking. In order for these teaching models to gain acceptance and credibility among the relevant academic communities, it is critical that they be studied and evaluated. Aim: This article describes an innovative rural education intervention and a concomitant, intentional process that was adopted to establish a research framework within which the intervention will be evaluated. Methods: Key role-players participated in a one-day workshop aimed at developing the framework. A collaborative, structured process that moved through three phases of deliberation and reflection was followed. Results: The documentation and raw data generated during the workshop was used to generate the framework that will serve as a blueprint for ensuring the study and evaluation of the educational innovation. Conclusion: Establishing an educational research framework, by adopting a consultative and collaborative process, provides a vehicle for encouraging a culture of critical accountability that seeks to discern evidence of good practice in the training of health care workers in a rural context.

Understanding rural clinical learning spaces: Being and becoming a doctor.

Abstract Context: Calls for health professions education that can foster transformative educational experiences have been voiced. Studies suggest that extended clinical training at rural sites potentially provides transformative learning spaces. This article explores ‘being and becoming’ as a construct for understanding the student experience at a rural clinical school (RCS). Methods: Sixty-two in-depth interviews were conducted over a three-year period with RCS students, graduates (as interns) and intern supervisors. Thematically analysed data were mapped according to the adapted Kirkpatrick model for appraising educational interventions. Drawing on realist perspectives, findings were further analysed to discern the mechanisms influencing the being and becoming of junior doctors. Results: Responses provided evidence of changed attitudes and behaviour, and the adoption of professional practice that was seen to influence patient outcomes. Analysis highlighted sharing of values through role modelling, engagement with preceptors, being respected as part of a team, and being trusted to assume responsibility for a patient as key mechanisms. The outcome was confident, competent and caring interns. Discussion: Rural clinical learning spaces influence the ‘being and becoming’ of a junior doctor. Understanding this process in the context of place (rural platform), participation (community of practice) and person can inform expanded agendas for students’ clinical learning.

The impact of a faculty development programme for health professions educators in sub-Saharan Africa: an archival study

BackgroundIn 2008 the sub-Saharan FAIMER Regional Institute launched a faculty development programme aimed at enhancing the academic and research capacity of health professions educators working in sub-Saharan Africa. This two-year programme, a combination of residential and distance learning activities, focuses on developing the leadership, project management and programme evaluation skills of participants as well as teaching the key principles of health professions education-curriculum design, teaching and learning and assessment. Participants also gain first-hand research experience by designing and conducting an education innovation project in their home institutions. This study was conducted to determine the perceptions of participants regarding the personal and professional impact of the SAFRI programme.MethodsA retrospective document review, which included data about fellows who completed the programme between 2008 and 2011, was performed. Data included fellows’ descriptions of their expectations, reflections on achievements and information shared on an online discussion forum. Data were analysed using Kirkpatrick’s evaluation framework.ResultsParticipants (n=61) came from 10 African countries and included a wide range of health professions educators. Five key themes about the impact of the SAFRI programme were identified: (1) belonging to a community of practice, (2) personal development, (3) professional development, (4) capacity development, and (5) tools/strategies for project management and/or advancement.ConclusionThe SAFRI programme has a positive developmental impact on both participants and their respective institutions.

Necrotizing Enterocolitis in HIV-Exposed and Nonexposed Infants: Clinical Presentation and Histopathological Features

Necrotizing enterocolitis (NEC) is the most common gastrointestinal emergency in neonates and is associated with significant morbidity and mortality. An association between HIV-positive maternal status and increased risk of NEC in preterm infants has been described, and antiretroviral therapy has been proposed as an independent risk factor. Our aim was to compare the clinical presentation and histopathological features of necrotizing enterocolitis in HIV-exposed and unexposed infants. A retrospective study of archival material from the National Health Laboratory Services Histopathology Laboratory in Tygerberg Hospital/Stellenbosch University from 1992 to 2008 was conducted. All surgical specimens from infants who presented to pediatric surgery for a laparotomy and bowel resection for NEC and in whom the HIV status was known were included in the study. In the 37 cases that fulfilled these criteria, male gender was overrepresented in the study population (67%). Nonsteroidal anti-inflammatory drugs appeared to play a significant role in the development of surgical NEC in infants who were not exposed to HIV, but HIV-exposed infants had a significantly poorer survival rate. There was no significant difference in the histopathology between HIV-exposed and nonexposed infants, and Cytomegalovirus infection was not identified in any of the cases studied.

Alienation and engagement in postgraduate training at a South African medical school

Background: The importance of contextual factors, such as the learning environment and sociocultural characteristics of the student, are becoming increasingly evident. Mann [2001. Alternative perspectives on the student experience: Alienation and engagement. Stud High Educ 26(1):7–19.] proposed that all learning experiences can be viewed as either alienating or engaging and Case expanded on this work. Aim: The purpose of this study was to explore perceptions of alienation or engagement as experienced by residents in anatomical pathology at one South African university. Method: A cross-sectional case study, with 16 semi-structured interviews was conducted. Residents were categorised as either alienated or engaged, based mainly on workplace experiences. Results: Four relevant dimensions were identified; individual, home, workplace and institution. The personal attributes, strategies for coping and reasons for choosing pathology of alienated residents differed from those with engaged experiences. Poor socioeconomic background and schooling did not lead to predominantly alienating experiences, but this group still lacked some generic skills. In the workplace, two main factors resulting in alienated experiences were the interaction between residents and consultants and residents’ comprehension of workplace-based learning. Conclusions: We present a simple model which may be used to identify factors that engage and alienate students in the learning experience in the workplace-based setting. Addressing these factors can contribute towards a more engaging experience for all residents.

Tuberculosis and phrenic nerve destruction

Phrenic nerve palsy (PNP) is often associated with Mycobacterium tuberculosis -related expansile pneumonia, possibly because of nerve entrapment by healing fibrosis. Mohan and Jayaswal 1 postulated that pressure on the left phrenic nerve by an enlarged hilar lymph node caused unilateral diaphragmatic paralysis in a 6-year-old boy who developed PNP during the course of pulmonary tuberculosis (PTB). Gie et al. 2 described 6 childhood cases of PTB complicated by unilateral PNP. The children did not recover on antituberculosis drugs and steroids, or in 1 case, after surgical decompression. Therefore the theory of glandular compression alone does not adequately account for PNP as a complication of PTB. Our case, in which the fate of the phrenic nerve was confirmed, provides strong evidence that destruction of the phrenic nerve by the tuberculous inflammatory process is involved in the pathogenesis of diaphragmatic paralysis, which may influence the clinical management of these children. South African Medical Journal Vol. 97 (8) 2007: pp. 572-573

Exome Sequencing in a Family with Luminal-Type Breast Cancer Underpinned by Variation in the Methylation Pathway

Panel-based next generation sequencing (NGS) is currently preferred over whole exome sequencing (WES) for diagnosis of familial breast cancer, due to interpretation challenges caused by variants of uncertain clinical significance (VUS). There is also no consensus on the selection criteria for WES. In this study, a pathology-supported genetic testing (PSGT) approach was used to select two BRCA1/2 mutation-negative breast cancer patients from the same family for WES. Homozygosity for the MTHFR 677 C>T mutation detected during this PSGT pre-screen step was considered insufficient to cause bilateral breast cancer in the index case and her daughter diagnosed with early-onset breast cancer (<30 years). Extended genetic testing using WES identified the RAD50 R385C missense mutation in both cases. This rare variant with a minor allele frequency (MAF) of <0.001 was classified as a VUS after exclusion in an affected cousin and extended genotyping in 164 unrelated breast cancer patients and 160 controls. Detection of functional polymorphisms (MAF > 5%) in the folate pathway in all three affected family members is consistent with inheritance of the luminal-type breast cancer in the family. PSGT assisted with the decision to pursue extended genetic testing and facilitated clinical interpretation of WES aimed at reduction of recurrence risk.

Clinical teaching with minimal and indirect supervision

What problems were addressed? In medical education, the adequate supervision of medical students is known to result in improved patient outcomes. However, this presents a challenge in clinical clerkships, in which faculty supervisors need to balance their time and resources. As such, the ability to provide indirect supervision to students – particularly in a setting in which the faculty member is not directly managing the student–patient encounter – is an important skill. Although minimal supervision of students presents a feasible solution to challenges in faculty supervision, it is unclear how such practices are perceived by patients and how they affect the learning experiences of students. To investigate this issue, this study examined patient and medical student perceptions of clinical teaching in a setting with minimal faculty supervision. What was tried? We performed a cross-sectional study with a sequential sample of obstetrics patients at an antenatal out-patient clinic. Questionnaires focusing on perceptions of students’ performance during the consultation were administered preand post-student consultation. In addition, patients were asked to write three words representing what they felt before and after the consultation. Students’ selfperceptions of their performance while consulting with patients were obtained through a questionnaire administered at the end of the process. An openended question requested students to write five words representing what they felt after consulting with patients with minimal clinical supervision. What lessons were learned? Of the 95 pregnant women studied, 95% knew that the student would perform routine antenatal care and would receive feedback from the supervisor following the consultation. They acknowledged that it was important for students to perform prenatal care as part of their training (85%). Before the consultation, 22% were not sure if they felt comfortable being examined by a medical student and 20% were unsure whether they could trust a student. After the consultation, 97% of patients felt comfortable about the examination and 99% felt they trusted the students. Of the pre-consultation descriptor words, ‘anxiety’ was the most frequently used word. ‘Calm’ and ‘satisfaction’ were the most frequently used post-consultation descriptors. Of the 77 students, 56% were in Year 5 of medical school and 44% were in Year 6. Students agreed that the ambulatory format with minimal faculty supervision encouraged their participation and engagement (82%). They felt that case discussions with faculty staff were useful (90%) and contributed to their learning (88%). The words ‘trust’, ‘secure’, ‘responsibility’ and ‘autonomy’ were the most representative of those used by students to express their feelings about meeting patients by themselves, supported by the outside supervision of the preceptor. Students expressed interest in knowing the opinions of the pregnant women about their performance in providing supportive medical care (92%) and confirmed that they would feel comfortable about being assessed by patients (84%). We observed positive patient feedback, and the perceptions of finalyear students regarding this out-patient clinical teaching method with minimal faculty supervision reinforced the potential to expand their autonomy. These findings may support additional assessments that incorporate patient perspectives into the overall clinical evaluation of students, which may improve the validity of the clinical assessment system.