Background The COVID-19 pandemic has profoundly impacted some of the most vulnerable populations in lowresource settings (LRS) across the globe. These settings tend to have underdeveloped healthcare systems that are exceptionally vulnerable to the strain of an outbreak such as SARS-CoV-2. LRS-based clinicians are in need of effective and contextually appropriate triage and assessment tools that have been purpose-designed to aid in evaluating the severity of potential COVID-19 patients. In the context of the COVID-19 crisis, a low-input severity scoring tool could be a cornerstone of ensuring timely access to appropriate care and justified use of critically limited resources. Aim and objectives The aim of this research was to develop and validate a tool to assist frontline providers in rapidly predicting severe COVID-19 disease in LRS. To achieve this aim, the following objectives were defined: identify existing methods of risk stratification of suspected COVID-19 patients worldwide; establish predictors of severe COVID-19 illness measurable in LRS; derive a risk stratification tool to assist facility-based healthcare providers in LRS in evaluating in-hospital mortality risk; and validate tool SST in the African setting using real-world data. Methods To achieve the aim of this dissertation, quantitative and review methodologies were employed across four studies. First, a scoping review was conducted to identify all studies describing screening, triage, and severity scoring of suspected COVID-19 patients worldwide. These tools were then compared to usability and feasibility standards for LRS emergency units, to determine viable tool options for such settings. Following this, a systematic review and meta-analysis were undertaken to evaluate existing literature for associations between COVID-19 illness severity, and historical characteristics, clinical presentations, and investigations measurable in LRS. Three online databases were searched to identify all studies assessing potential associations between clinical characteristics and investigations, and COVID-19 illness severity. Data for all variables that were statistically analysed in relation to COVID19 disease severity were extracted and a meta-analysis was conducted to generate pooled odds ratios for individual variables' predictive abilities. In the third study, machine learning was used on data from a retrospective cohort of Sudanese COVID-19 patients to derive the AFEM COVID-19 Mortality Score (AFEM-CMS), a contextually appropriate mortality index for COVID-19. Following this, a fourth study was conducted with a more recent Sudanese dataset to validate the tool. Results The scoping review identified COVID-19 risk stratification 23 tools with potential feasibility for use in LRS. Of these, none had been validated in LRS. The systematic review then identified 79 eligible articles, including data from 27713 individual patients with laboratory-confirmed COVID-19. A total of 202 features were studied in relation to COVID-19 severity across these articles, of which 81 were deemed feasible for assessment in LRS. Meta-analysis of two demographic features, 21 comorbidities, and 21 presenting signs and symptoms with appropriate data available identified 19 significant predictors of severe COVID-19, including: past medical history of stroke (pOR: 3.08 (95% CI [1.95, 4.88])), shortness of breath (pOR: 2·78 (95% CI [2·24-3·46])), chronic kidney disease (pOR: 2.55 (95% CI [1.52-4.29])), and presence of any comorbidity (pOR: 2.41 (95% CI [2.01-2.89])). These significant predictors of severe COVID-19 were then considered for inclusion in the AFEM-CMS. Data from 467 COVID-19 patientsin Sudan were used to derive two versions of the tool. Both include age, sex, number of comorbidities, Glasgow Coma Scale, respiratory rate, and systolic blood pressure; in settings with pulse oximetry, oxygen saturation is included and, in settings without access, heart rate is included. The AFEM-CMS showed good discrimination: The model including pulse oximetry had a C-statistic of 0.775 (95% CI: 0.737-0.813) and the model excluding it had a C-statistic of 0.719 (95% CI: 0.678- 0.760). The tool was then validated against a second set of data from Sudan and found to once again have reasonable discriminatory power in identifying those at greatest risk of death from COVID-19: The model including pulse oximetry had a C-statistic of 0.732 (95% CI: 0.687-0.777) and the model excluding pulse oximetry had a C-statistic of 0.696 (0.645-0.747). Conclusions and relevance This dissertation establishes what is, to our knowledge, the first COVID-19 mortality prediction tool intentionally designed for frontline providers in LRS and validated in such a setting. The derivation and validation of the AFEM-CMS highlight the feasibility and potential impact of real-time development of clinical tools to improve patient care, even in times of surge in LRS. This study is just one of hundreds of efforts across all resource levels suggesting that rapid use of machine learning methodologies holds promise in improving responses to pandemics and other emergencies. It is our hope that, in future health crises, LRS-based clinicians and researchers can refer to these techniques to inform contextually and situationally appropriate clinical tools and reduce morbidity and mortality.

Background: Trauma registries are vital to a well-organized trauma system. However, registries are non-existent in most low and middle-income countries, largely due to the difficulty of reliably capturing patient-level data. The aim of this thesis was to develop and implement a context appropriate standardised trauma form incorporating the World Health Organization Data Set for Injury, for both clinical documentation and use in a trauma registry. Methods: This mixed methods participatory action research utilised Susman and Evered's approach to develop and implement a standardised trauma form, using its five steps: diagnosis, action planning, intervention, evaluation and specifying learning. In the diagnosis phase, an assessment of baseline documentation was performed. In the action-planning phase, focus group discussion revealed the barriers and facilitators to completing documentation. Then, in the actiontaking phase, semi structured interviews, training of health care providers, and feedback enabled the development, review, pilot, and implementation of a standardised trauma form. In the evaluation phase, we compared the number and types of variables captured after the form was implemented to the baseline collection. Finally, we specified learning to inform the next steps in the amplification of the observed impact. Results: The diagnosis phase established that many injury variables were not captured routinely at the participating regional hospitals. Analysis of barriers and facilitators and feedback on perceptions of providers toward using standardised documentation informed the development, piloting, modification, training of providers and implementation of a context appropriate standardised trauma documentation form for clinical charting and data capture. Implementation of the standardised trauma form was associated with improved capture of injury variables from baseline pre-implementation (33.6%), during 30-days initial pilot (86.4%) and after seven months post implementation (96.3%). The providers reported the form was user-friendly, resulted in less time documenting, and served as a guide to managing trauma patients. Conclusions: Through participatory action research a contextually appropriate, standardised trauma documentation form was successfully developed and implemented, yielding marked improvement in the capture of essential injury variables. This model can serve as a working guide to other low- and middle-income countries seeking to establish sustainable national injury registries.

Introduction Firearm injuries account for an increasingly significant portion of violence related trauma experienced in South Africa. The related burden on district level emergency care, surgical and inpatient services is poorly described. This research aims to provide epidemiological and health service data on patients sustaining firearm injuries presenting at Mitchells Plain Hospital and Heideveld Emergency Centre. The research also assesses the association of the Triage Early Warning Score with anatomical location of injury, the need for surgical intervention and mortality. A geographical analysis of incident location with respect to home address has also been undertaken. Methods All patients who presented to these emergency centres with a firearm injury over a 12-month period (1 Jan 2019 – 31 Dec 2019) were eligible for inclusion in a retrospective chart review. Results Seven-hundred-and-seventy-six firearm injuries were analysed with those injured having a mean age of 27 years and 91% of those injured being male. Sixty-seven percent of patients self-presented and there were 18 deaths in the emergency centre and a further 23 as an inpatient. The Triage Early Warning Score and Shock Index both showed statistical significance when comparing those not surviving to hospital discharge against those that did survive (p<0.01). Discussion Firearm injuries represented 5.7% of all trauma seen at these two facilities and likely form a higher proportion of the injury profile than at other district services in the City of Cape Town. Although a significant number of those injured are transferred out to tertiary centres that are better capacitated to manage these injuries, many remain at district level for their care. Conclusion Firearm injuries, the immediate surgical needs of those injured and the long-term consequence of those injuries pose a significant burden on limited healthcare resources. Multi-sectoral action, supported by evidence-based primary and secondary preventative strategies, is required to reduce this intentional injury burden, and mitigate the effects.

Background: According to the World Health Organization (WHO), Traumatic Brain Injury (TBI) will become the third largest cause of global disease by the year 2020. Despite its astonishing numbers, TBI remains a silent or even forgotten epidemic with significant paucity in epidemiological data. TBI in developing countries represents a disproportionate burden of disease and data are lacking regarding the unique demographics in South Africa to design and implement focused prevention programmes. A valuable tool to assess the severity of TBI is the use of Computer tomography (CT). CT also is the main imaging modality to provide rapid identification and information for the management of children with TBI. CT scanning utilises ionising radiation and as an imaging modality poses risk to the patient. In order to guide decision protocol/algorithm, various Clinical Decision Rules (CDRs) have been established in High Income Countries. These protocols, including the need for CT scan might differ in a Medium/Low Income setting. Methodology: This is a prospective, single centre cohort study. Data were collected over an 18-month period (1 August 2015 - 31 January 2017). Children under the age of 13 years (n=3007) presenting to RCWCH after sustaining a head injury were included. Various epidemiological data were collected. A Road Safety Questionnaire was also used to evaluate safety knowledge of health care workers. Three different CDRs were compared to the standard of practice in RCWCH. A final analysis of demographics, mechanism of injury, radiology outcome, safety analysis and evaluation of a comparison of local protocol compared to the other CDRs was performed using descriptive statistics. Results: The mean age of paediatric patients presenting after a head injury was 4.6 years. There was a significant male predominance (66%) and almost two thirds of all children were of pre-school age. Falls (53%; n=1601) represented the most common mechanism of injury across all age groups, followed by road traffic related injuries (RTI) (29%; n=864), struck by or against an object (9%; n=279) and injuries as a result of interpersonal violence (8%; n=230). Within the subset of RTI (n=864) only 6 passengers were appropriately restrained, with 142 unrestrained and 56 passengers transported on the back of a goods vehicle. In the under 3-yearold age group, only 1 patient was appropriately transported in a car seat, with 51 unrestrained and 6 transported on the back of a goods vehicle. Pedestrian related injuries were by far the largest group of RTI (70%) with 50% of these under the age of 5 years. Intentional injuries inflicted by an adult were most common (34%) in the pre-verbal (under 2 years old) group. Interpersonal violence among minors (assault with a brick or stone) constituted 52% of intentional injuries. Eight firearm related injuries were recorded. Appliances and iron gates that were not correctly installed were additional causes of injury. CT scans were obtained according to the RCWCH protocol in 59% of cases and 34% showed an abnormal result. The sensitivity (98%) and specificity (93%) while using the standard of practice protocol was better than the 3 CDRs developed in High Income Countries. Analysing our Road Safety Questionnaire there appears great room for improvement regarding awareness of road safety guidelines and legislation. Conclusion: The performance of the current RCWCH CT scan protocol appears appropriate in our setting although there is some room for improvement using the strengths of the other CDRs. Valuable insight regarding the epidemiology of TBI in our setting has been highlighted. Of specific importance is the large proportion of very young children at risk of injury by all mechanisms of injury, particularly pedestrian-related injuries, unrestrained passengers and interpersonal violence among minors. Important gaps in knowledge about current recommendations for road safety were identified by the questionnaire. As long as these issues are not appropriately addressed through enhanced injury prevention programmes, children will continue to carry the heavy burden of TBI morbidity and mortality.

Introduction The Annual Northern Cape Colonoscopy Outreach program provides surveillance colonoscopy to high–risk individuals known with Lynch Syndrome along the west coast and in the Northern Cape Province of South Africa. There are currently over 100 known mutation positive individuals. Surveillance colonoscopies are performed annually in August/September, and are preceded a by a preparation visit approximately 6-8 weeks prior. The aim of the preparation trip has been to directly impart information, regarding preparation and importance of attendance, to individuals required to attend annual surveillance. During the preparation trip an attempt is made to reach all individuals scheduled for surveillance but due to the vastness of the Northern Cape inevitably every year some areas are not visited. It has been noted that over the past few years fewer than 25 % of the total participants obtained 100 % adherence to surveillance. Objectives The primary objective of this study is to determine whether there is a need for a yearly colonoscopy preparation visit to high–risk individuals in the Northern Cape. The study determines if direct interaction with patients prior to surveillance colonoscopy will significantly impact attendance and adequacy of bowel preparation. Methods Seventy-eight individuals known with a genetic mutation for Lynch syndrome were enrolled in this randomised crossover trial spanning two years of surveillance. The control group (Group A) of individuals had bowel preparation and instructions forwarded to their local clinics and distributed to them via clinic or hospital staff. The test group (Group B) of individuals were personally visited and provided with instructions and bowel preparation by the research team. A measurement of attendance at surveillance colonoscopy as well as cleanliness of the colon was recorded. The study spanned two years of colonoscopy surveillance, July 2014 to September 2015, with a crossover of the control and test groups. Results The study cohort consisted of 28 (36%) male and 50 (64%) female participants with a median age of 39.5 years. Groups A and B consisted of 38 and 40 participants respectively. In September 2014 thirty-six (46.2%) participants presented for annual surveillance colonoscopy, 19 (50%) from the control group (Group A) and 17 (42.5%) from the intervention group (Group B). In 2015 there were 41 (53%) compliant individuals; this included 21 (55%) individuals receiving a preparatory direct contact visit (Group A), and 20 (50%) individuals from the 2015 control group B. Following exclusion of carry-over and period effect, the study intervention was found not to significantly impact attendance (p-value = 0.853). Superior attendance was noted in individuals with prior compliance to surveillance (p-value = 0.001). Conclusions Direct interaction with known Lynch syndrome individuals prior to annual surveillance colonoscopy has not shown to positively impact attendance. Interaction and counselling should focus on individuals identified to be defaulting surveillance.

Includes bibliographical references (leaves 43-52). / An immunohistochemical technique is used in this study to detect mismatch repair deficit in young patients with colorectal cancers. Ninety three patients who were 45 years of age or younger at the time of diagnosis of colorectal cancer were studied.

Purpose The Acute Care Surgical Unit at Groote Schuur Hospital was established in 2010 and is the first of its kind in Africa. The aim of this study was to describe the outcomes of emergency surgical cases, as well as determine the logistical factors associated with adverse outcomes following surgery within the unit. Methods This study was a retrospective audit which reviewed the folders of adult patients who underwent an emergency surgical procedure from July 2016 to July 2017. The primary outcome was a major adverse event (AE) which was defined by a Clavien-Dindo score of 3-5. A number of logistical factors related to patient admission and operation were evaluated for association with outcomes. Results A total of 271 patients were included with an mean age of 47 years, with 48% females and 52% males. A major AE was recorded for 13% of patients. The following factors were found to be predictive of a major AE: referral from outside the hospital, urgent booking colour code, reoperation and consultant most senior surgeon present during procedure. Patient admission/surgery performed outside of normal working hours, being booked for surgery on admission, as well as delay to surgery beyond colour code were not associated with a major AE. Conclusion Apart from traditional clinical parameters, factors related to perioperative logistics may contribute to the risk of a major AE after emergency surgery and should be considered for inclusion in more comprehensive predictive models for adverse outcomes within an acute care surgery unit.

Background: Congenital Megaprepuce is a urological condition characterized by a megapreputial reservoir with a long redundant inner prepuce. The condition has been linked to urinary tract infections, lower urinary tract symptoms, and ballooning of the penis during voiding. An impeded urinary stream and resultant ballooning is associated with discomfort and causes parental anxiety due to the unusual appearance of phallus. Surgical correction should improve functionality, but cosmesis is also important. This study took place in a community in which traditional circumcision remains an essential rite of passage. Therefore, early surgical correction of congenital megaprepuce was complicated by the unique requirement that patients remain uncircumcised. Methodology: Here we investigated the functional and cosmetic outcomes of the ventral slit procedure, an uncomplicated technique used to restore urinary flow which, importantly, preserves the foreskin. Parents of 18 paediatric patients were interviewed post-operatively regarding phallic appearance and functionality following surgery. Results: Overall, the ventral slit procedure successfully restored flow, prevented ballooning and alleviated discomfort during voiding in all patients. Parents interviewed were highly satisfied with surgical outcomes, as assessed by the Pediatric Penile Perception score. Conclusion: The ventral slit procedure was found to be a culturally acceptable and simple surgical solution to congenital megaprepuce.

Introduction: Inappropriate dispatch of urgent ambulances by call centre personnel causes an unnecessary drain on existing resources. How often these urgent dispatches are inappropriate has not been evaluated in any lower middle income countries, nor have factors been assessed that contribute to these decisions. Problem: The study aims to establish rates of pre-hospital over-triage in Cape Town, South Africa and to assess the call centre factors around these decision-making processes. Methods: This was a retrospective study examining a single calendar month of all urgent ("lights and sirens") ambulance dispatches made from a large public sector ambulance call centre in Cape Town. On-scene, the ambulance field crew assessed these patients using the South African Triage Score (SATS) and these assessments were correlated with the prioritization of these dispatches by the call centre to determine which patients were 'over-triaged' by the call-taker. Contributory factors were also analysed and included time of day, nature of presenting complaint; and call-taker training and experience - all of which may have affected rates of over-triage. Results: In the course of one month in 2017, 4169 urgent calls were assessed: of these 2701 were over-triaged (58.48%). Over-triage was similar between day (58.02%) and night (59.11%). The most regularly over-triaged complaint was obstetric &amp; gynaecological (84.87%) followed by motor vehicle accidents (65.70%); the lowest rate was for cardiac call-outs (47.12%). We reviewed the 38 highest workload call-takers, and found subtle, but non-statistically significant, trends towards higher over-triage rates with higher levels of training (ILS 62.16%, no medical training 59.42%; p=0.67), more years as a call-taker (< 2 years 59.32%, > 5 years 60.23%; p=0.93) and more years working in the field (0 years 59.36%, > 5 years 63.66%; p=0.31). Conclusion: Rates of pre-hospital over-triage in Cape Town are marginally lower than those described internationally. The nature of the complaint had a strong impact on these rates, notably trauma and gynaecological issues. More experienced call-takers may tend to over-triage more frequently, however the small sample size made these findings uncertain. These findings do however suggest the potential for improvement for better efficiency without compromising patient safety.

Background: Post-hepatectomy liver failure (PHLF) is an important cause of morbidity and mortality following liver resection. Current prognostic models only allow for the detection of PHLF on post-operative day 5. Earlier detection and intervention may improve outcomes. To date, no studies have evaluated serial post-operative lactate and liver function tests (LFT) to predict PHLF. Aim: This study evaluated the prognostic utility of serial lactate concentrations and LFTs to predict PHLF following hepatectomy. Methods: All major liver resections (≥ 3 Couinaud segments) undertaken at Groote Schuur Hospital and UCT Private Academic Hospital from May 2018 to April 2021 were included. Lactate levels were measured 4-hourly for the first 24 hours post hepatectomy and daily LFTs for the first 5 days. Associations between baseline patient characteristics and lactate dynamics in PHLF as well as the predictive value of lactate, INR and bilirubin were determined. Results: Forty-seven patients, mean age 56.5 (±13.2) years, of whom 24 were males were assessed. Five (10.6%) patients had PHLF and were older (67.4 ± 12.2) and were predominantly men (80%)...