Hair has, over recent years, become widely recognised as an alternate or complementary matrix to blood and urine for drug analysis. Hair analysis offers a wider detection window after drug exposure than blood or urine testing and can provide a long-term history of an individual’s drug use. There are several practical applications of hair analysis for drugs including workplace drug testing, doping control, driving licence re-granting, drug-related deaths and drug-facilitated crimes. As a result hair analysis is currently being performed within various toxicological fields in laboratories around the world. However, before the start of this study no hair analysis for drugs was being performed in South Africa. Therefore, the main aim of this study, as stated in Chapter 1, was to develop a method for the detection and quantification of drugs of abuse, specifically methamphetamine and amphetamine, in hair using High Performance Liquid Chromatography coupled to Mass Spectrometry.

Violence and resulting injuries are critical health burdens worldwide, accounting for the death of millions of individuals annually. The literature reports an association between drug use and violence, providing data indicating that the use of psychoactive substances increases the risk of morbidity and mortality due to violent acts. South Africa has a long history of violence, with one of the highest rates of recorded violence- and injury-related deaths in the world. This is complicated by an increase in illicit substance use and abuse, particularly in the Cape Town Metropole, located within the Western Cape Province. The use of toxicological findings from victims of violent death (homicides, suicides, and accidents) to examine community-specific drug-related violence is slowly increasing in different parts of the world. In South Africa, however, monitoring drug trends in violent fatalities using toxicological analysis is uncommon, and hence drug toxicology of violent-related fatalities is limited. Divided into three contextual sections, this research study focuses on the post-mortem toxicology of violent deaths in a South African setting. The first section provides a general idea of the research problem and an initial development of the investigation process. The second section provides a theoretical basis for performing routine toxicological analyses in deaths due to violence, reports important research work conducted in the field worldwide, and emphasizes the need to monitor toxicological data derived from violent fatalities in Cape Town, South Africa. The last section, in the form of a manuscript, presents the overall research study including the methodology, outcomes, and concluding findings in a concise and illustrative manner. The primary aim of this pilot study was to investigate the prevalence and characteristics of illicit substances in violent fatalities (homicides, suicides, and accidents) of the Salt River mortuary in Cape Town, South Africa. The objectives were to conduct a comprehensive drug toxicology analysis to generate qualitative and comparative data from the aforementioned cases. In addition, this study investigated the dynamics between psychoactive substance use and violent deaths in terms of toxicological trends, and the demographics and circumstances of death of the victim. Lastly, the author discusses potential qualitative associations between illicit substances and violence-related deaths in a South African setting, and provide suggestions for future toxicological analyses in these fatalities.

Drug usage, both of a recreational or pharmaceutical nature, is common, however the abuse of such substances is an international problem. In the Western cape, South Africa, the burden of drug-related fatalities is high compared to the rest of the country. The provincial Forensic Pathology Service may encounter cases where drug-related fatalities are unclear whether death was accidental or suicidal, or drug toxicity is inconsistent with the medical/social history. This may be due to genetic alterations with drug metabolism and it has been suggested that genetic analyses may be the next step in these cases. However, toxicology results from the National Forensic Chemistry Laboratory in the Western Cape may be delayed by months to years, meaning that upon interpretation of toxicology results, there is no chance to obtain another blood sample from the deceased individual for genetic analysis. It was therefore important to determine the suitability of blood samples collected and handled in toxicology environments for subsequent genetic tests. Previously, blood samples from 30 post-mortem cases were collected into two red-top (no additives), two grey-top (sodium fluoride/potassium oxalate) and one purple-top (EDTA) tubes. Samples from one red-top and one grey-top tube underwent toxicological analysis, followed by DNA analysis, while the remaining tubes (controls) underwent DNA analysis immediately. All samples were then stored for approximately one year, prior to this study. The DNA analysis was repeated on all blood samples (n = 150) and results were assessed in terms of storage time and tube type. DNA was not significantly degraded in any of the samples; however, DNA from red-top tubes had significantly lower concentrations compared to that from grey-top tubes (p < 0.001), regardless of whether the sample had undergone toxicological analysis. The very low yields of DNA from red-top tubes posed substantial challenges for PCR-based analysis, resulting in poor quality Sanger sequencing results. Some DNA from grey-top tubes, passed the quality assessments and hence further work is required to provide an informed decision on which tube type is better suited for genetic analyses.

Introduction: Road traffic accidents (RTAs) and associated morbidity and mortality are a global public health burden. Literature reports on an association between drugs and/or alcohol intoxication and traffic collisions. In South Africa (SA), where drug use and abuse are prevalent, annual RTAs rates are higher than the average global burden. Toxicological analyses in cases of RTA fatalities are not performed routinely in SA (apart from alcohol analysis), thus understanding the burden of other drug impairment on road traffic deaths is limited. Aim: A prospective toxicological analysis was performed in a cohort of road traffic fatality cases (drivers, passengers, pedestrians, motorcyclists and cyclists) from Salt River Mortuary in Cape Town, SA. The objectives were to perform drug screening in these cases to preliminary investigate detected substances as well as to evaluate the demographics and circumstances of death of the aforementioned cases. Methods: A systematic review was first performed to investigate the prevalence of drugs in internationally reported RTA fatalities. For the prospective study, post-mortem specimens including blood, vitreous humor, urine and bile were collected from cases in which next-of-kin consent was obtained. All samples were analysed using liquid chromatography-quadrupole time-of -flight mass spectrometry (LC/QTOF-MS). Results: Thirty cases were analysed over 3 months, of which most were male, pedestrians and between the age group of 31-40 years. The most prevalent cause of death was multiple blunt force injuries to the body. Single vehicle crashes were predominant particularly among the pedestrians and motorcyclists whereas drivers were mostly involved in multiple vehicle crashes. Substances (other than ethanol) were detected in 90% (n=27) of the cases. A broad range of drug groups were detected, and the most prevalent specific legal substances were caffeine (66.7%) and nicotinamide (53.3%) and illegal substances were methaqualone (10.0%) and methamphetamine (6.67%). Multiple cases indicated the detection of impairing substances even if consumed therapeutically, such as codeine, chlorpheniramine, diphenhydramine and zopiclone. Discussion: This study was the first to the author’s knowledge to report on prospective toxicological findings in road traffic accident cases in Cape Town. Although this was a pilot study, the results were in line with findings from other international studies, together with findings of prominent abused drugs within Western Cape (e.g. methaqualone and methamphetamine). While this study made no inferences of drug intoxication to cause of death, it has set a basis for future research in this topic and the development of a standardised protocol for the routine analyses of such cases in SA.

Includes abstract. Includes bibliographical references.

Extracting forensically useable DNA from human remains recovered from an open marine environment is problematic, and in some cases, impossible. The reason is unclear given the lack of research on marine decomposition, DNA survival in seawater, and possible methods to optimise the DNA extraction workflow. Compounding this problem is the fact that South Africa experiences a high number of unidentified human bodies entering its mortuaries each year, and these individuals often remain unidentified. The aim of the study was to extract forensically useable DNA from pig (Sus scrofa) teeth submerged in-situ in an open marine environment, by a process of optimisation and implementation. Detailed environmental information was available for this study. A DNA extraction technique was developed and optimised on “fresh” control pig teeth (n = 13). The developed methods for decontamination, tooth sampling, and the optimised DNA extraction protocol were successfully performed on these, with forensically useable DNA obtained. However, this was not the case for the subsample of experimental pig teeth (n = 6) tested. Implementation of the developed method on a larger sample of experimental teeth (n = 28) was warranted to assess the recovery of nDNA and mtDNA. Amplification of nDNA by qPCR was successful in 60% (17/28) of samples for a 96 bp fragment, and in 46% (13/28) for 200 bp. By comparison, mtDNA showed a detection rate of 57% (16/28) for a 486 bp fragment via PCR amplification. In seven samples mtDNA was detected where nDNA was not, demonstrating improved survivability in seawater. Colder and more stable seawater temperatures is hypothesised to have preserved molecular elements. DNA hydrolysis and the possibility of DNAase activity from marine bacteria, may have contributed to poor DNA preservation in the other samples. Recovery of DNA from teeth submerged in an open marine environment is complex and requires further investigation in human samples to improve the identification process for individuals who have died at sea.

In forensic entomology, determining species identity is a crucial step towards estimating post mortem interval. DNA barcoding can aid in the identification of unknown forensically relevant species, and this requires the comparison of DNA barcodes to reference data from known species. However, there is a lack of DNA barcode reference data of forensically relevant Calliphoridae species in the Western Cape (South Africa). DNA barcodes were generated for the COI and ITS2 markers for 41 forensically relevant Calliphoridae specimens, representing seven species from six localities in the Western Cape: Chrysomya albiceps (n = 3), Chrysomya chloropyga (n = 8), Chrysomya marginalis (n = 5), Chrysomya megacephala (n = 7), Hemipyrellia fernandica (n = 1), Lucilia cuprina (n = 8) and Lucilia sericata (n = 9). This data was combined with that from Cooke et al. (2018) (n = 40), and subjected to rigorous statistical and phylogenetic analyses. Phylogenetic analysis which combined data for both COI and ITS2 barcodes returned monophyletic clades for each species with increased support when compared to using each barcode individually. This combined dataset was able to discriminate between L. cuprina and L. sericata with full support (100% pP), which was not achieved previously. DNA barcodes were evaluated for intra- and inter-specific variance as well as haplotype patterning. No haplotype patterning was observed for either barcodes across sampled localities. Lastly, a single-blinded approach was used to assess the dataset, whereby DNA barcodes from ‘unknown’ specimens were correctly identified using this reference data. These identifications were more accurate than those using GenBank® or BOLD, highlighting the importance of using locally relevant reference data. This study has contributed new data pertaining to DNA barcodes for seven Calliphoridae species, which was previously scarce for the Western Cape, and this has directly contributed to an improvement in the accuracy of local species identification.

Death due to cranial blunt force trauma is a major issue not just in South Africa but worldwide. The vast majority of studies conducted on cranial blunt force trauma have analysed trauma to the frontal portion of the head. This is due to the involvement of the frontal portion of the head in automotive accidents. The lateral portion of the head is however no less important and is often impacted during homicidal assault. In cases involving cranial blunt force trauma, a common question asked of experts relates to the amount of force involved with a particular trauma. The goal of forensic science in general is to provide objective, repeatable results. At present, however, answering this question relies on a subjective rating scale of mild, moderate or severe force. Determining the severity of the force is also subjective, in that it relies heavily on the experience of the expert. Forensic anthropology by its nature is often subjective; however there is a need to move away from conducting analyses based predominantly on the experience of the investigator. With this in mind, this dissertation offers background information on fracture mechanics and impact biomechanics and provides a current review of the literature surrounding lateral impact to the skull. The research conducted as part of this dissertation attempts to quantify the force and energy involved with lateral impact to the skull due to a blow by a hammer, as well as describes the wound morphology associated with such impacts. Human tissue for experimentation is becoming increasingly difficult to acquire. There is therefore a need to determine suitable models for use in such testing. In the current study whole porcine heads were impacted on the fronto-parietal portion of the cranium. Half of the specimens were impacted with an implement resembling the shape and weight of a hammer. These hammer tests were conducted primarily to determine the type of trauma associated with such impacts and determine if a correlation exists between velocity or energy of impact and the level of trauma sustained. The remaining specimens were impacted with a Hopkinson pressure bar of the same diameter as the striker in the hammer tests. The Hopkinson pressure bar apparatus allows for the determination of the force of impact. The use of the Hopkinson pressure bar to determine fracture forces in whole specimens is novel. The fracture forces obtained in the current study agree considerably with the literature previously published on lateral, cranial blunt force trauma to both human and porcine specimens. The fractures produced, however, are atypical and may indicate a need to conduct further tests on other animal models.

Introduction: In South Africa (SA), the forensic sector faces significant challenges including how to meet increasing public expectations for high quality, reliable and valid scientific and medico legal results, whilst dealing with increasing caseloads and restricted resources in a developing country. Internationally, lean six-sigma and/or business-based frameworks have been developed to define, measure and analyse the efficiency, effectiveness and output of forensic laboratories, so as to assess performance to meet such challenges. Aim: This pilot project aimed to investigate the effectiveness and efficiency of forensic pathology practice at Salt River Mortuary (SRM) by applying lean six sigma principles (define, measure, analyse and improve) and FORESIGHT metric analyses to retrospective case and staffing data, as well as prospective observational analyses. Methods: A retrospective analysis of cases admitted to Salt River Mortuary in 2015 was conducted to define and measure a snapshot of forensic pathology practice in Cape Town. In addition, observations of autopsy processes were conducted to identify bottlenecks in the system and provide suggestions for improvement. Results: An analysis of post-mortem report turn-around for 3567 cases admitted to SRM in 2015 showed that approximately 10% of cases were closed (cause of death was determined) on the day of the post-mortem, 65% within 14 days and 80% closed within a 30 day period. Certain requested ancillary investigations delayed the finalisation of cause of death; for example, only 8.33% of carbon monoxide testing and 30.31% of histological examinations were completed within the year. A process map outlining autopsy practices at SRM was generated through observational data, which also identified key bottlenecks in the process (e.g.: equipment issues). Preliminary financial data suggested that it cost on average R16 155.03 per case. Staff data demonstrated a lack of pathologists compared to other staff categories and high case load requirements. Discussion: This pilot study investigates the utilization of metrics and strategic frameworks to assess forensic pathology processes in Cape Town. This study offers a cross-sectional insight into financial performance, efficiency and effectiveness of post-mortem investigations at SRM, highlighting bottlenecks and inefficiencies, and providing suggestions for improvement. The findings will assist in forming a basis for future work into the development of a framework for monitoring performance and progress, and developing benchmark standards for the death investigation system in South Africa

Introduction: Pesticides offer great benefits in the agricultural sector, but exposure may pose both acute and chronic health risks to humans. In developing countries, morbidity and mortality rates related to pesticide exposure are high and in certain areas (such as in rural, lower socioeconomic and/or agricultural-dependent communities), pesticides may be stored in and around homes, which may increase the risk of accidental exposure as well as intentional poisoning. In Cape Town, South Africa, this public health issue is exacerbated by the informal selling of street pesticides. These are pesticides that usually comprise of a mixture of these chemicals, sold unregistered as liquids or granules in bottles or packages without clear identification labels, for domestic use. While cheap and widely available in informal settlements; these pesticide formulations are not regulated and extremely toxic. Data illustrating the extent and nature of fatalities related to acute and chronic pesticide exposure in Cape Town, particularly as related to street pesticides, is limited. This dissertation provides an overview of the literature associated with pesticide toxicity and related mortality, paying particular attention to available South African research. This is followed by a study investigating pesticide deaths at Salt-River Mortuary over a period of five years. Aim: The aim of this study was to determine the prevalence and characteristics of deaths associated with suspected acute pesticide toxicity, to broaden the spectrum of knowledge concerning pesticide-related deaths in Cape Town, South Africa. Methods: A retrospective analysis of cases admitted to Salt River Mortuary (SRM) from 2011 to 2015 (inclusive) was conducted. Demographic, autopsy, investigative and toxicological data (where available) were collected from post-mortem and other investigative reports. Results: Of the total of 16,453 cases admitted to SRM over a five-year period from January 2011 until December 2015, 104 (0.63%) were deemed to be acutely pesticide-related based on available autopsy data. There was an equal number of male (n=52; 50%) and female (n=52; 50%) victims. Most deaths (n=74; 71%) occurred at medical centres following exposure, and Terbufos was found to be the common pesticide detected analytically (n=42, 61%) in toxicology reports available (76%). Results revealed that (60%) of acute pesticide toxicity cases were suspected suicides, while (6%) of cases were suspected accidents and (3%) cases were suspected homicides, while the remainder were still undetermined pending toxicological investigations. Conclusion: A history of ingestion, autopsy findings and toxicological results (if available) assisted in identification of these cases, most of which came from lower socio-economic communities. While the number of overall cases is low, it is evident that these deaths are a public health burden, and may be preventable through improved notification and policy development. Challenges with this study involved the inability to distinguish mortality associated with chronic pesticide exposure, the lack of toxicological results available, limited scene investigation information to identify street pesticide contributions, and that the study was limited to one mortuary in Western Cape. An extension of this research to other mortuaries in Western Cape as well as collaborative work with community and public health sectors on availability and toxicity of street pesticides will assist in strategic intervention methods and policy reform to reduce accidental and suicidal mortality associated with acute pesticide exposure.