Humans In South Africa Research Articles

Whole Genome Sequence Analysis of Brucella spp. from Human, Livestock, and Wildlife in South Africa

Brucellosis is an economically important zoonotic disease affecting humans, livestock, and wildlife health globally and especially in Africa. Brucella abortus and B. melitensis have been isolated from human, livestock (cattle and goat), and wildlife (sable) in South Africa (SA) but with little knowledge of the population genomic structure of this pathogen in SA. As whole genome sequencing can assist to differentiate and trace the origin of outbreaks of Brucella spp. strains, the whole genomes of retrospective isolates (n = 19) from previous studies were sequenced. Sequences were analysed using average nucleotide identity (ANI), pangenomics, and whole genome single nucleotide polymorphism (wgSNP) to trace the geographical origin of cases of brucellosis circulating in human, cattle, goats, and sable from different provinces in SA. Pangenomics analysis of B. melitensis (n = 69) and B. abortus (n = 56) was conducted with 19 strains that included B. abortus from cattle (n = 3) and B. melitensis from a human (n = 1), cattle (n = 1), goat (n = 1), Rev1 vaccine strain (n = 1), and sable (n = 12). Pangenomics analysis of B. melitensis genomes, highlighted shared genes, that include 10 hypothetical proteins and genes that encodes for acetyl-coenzyme A synthetase (acs), and acylamidase (aam) amongst the sable genomes. The wgSNP analysis confirmed the B. melitensis isolated from human was more closely related to the goat from the Western Cape Province from the same outbreak than the B. melitensis cattle sample from different cases in the Gauteng Province. The B. melitensis sable strains could be distinguished from the African lineage, constituting their own African sub-clade. The sequenced B. abortus strains clustered in the C2 lineage that is closely related to the isolates from Mozambique and Zimbabwe. This study identified genetically diverse Brucella spp. among various hosts in SA. This study expands the limited known knowledge regarding the presence of B. melitensis in livestock and humans in SA, further building a foundation for future research on the distribution of the Brucella spp. worldwide and its evolutionary background.

Can ‘life writing’ be therapeutic in response to trauma? An exploratory research project in Medical Humanities in South Africa

The therapeutic benefit of expressive writing has been well researched in the Global North but there is no literature from the Global South. Potentially healing interventions need to be investigated...

Molecular Characterization of Lyssaviruses Originating from Domestic and Wild Cats Provides an Insight on the Diversity of Lyssaviruses and a Risk of Rabies Transmission to Other Susceptible Mammals and Humans in South Africa.

Rabies is one of the most significant public and veterinary health problems, causing approximately 59,000 human deaths annually in the developing countries of Asia and Africa. The aetiologic agent, a viral species of the Lyssavirus genus, is highly neurotropic and has a wide host range, including terrestrial mammals and several Chiropteran species. The Lyssavirus mokola (MOKV) was first isolated in the late 1960s from organ pools of shrews (Crocidura flavescens manni) in the Mokola forest (Nigeria). To date, at least 30 MOKV isolations have been confirmed, all exclusively from Africa, with 73% from southern Africa. There is limited knowledge about the epidemiology of MOKV, and the reservoir host species is unknown. Here, we report on the molecular characterization of rabies viruses originating from both domestic and African wild cats. A partial region of the lyssavirus genome, encoding the nucleoprotein, was amplified and sequenced. Nucleotide sequence analysis demonstrated that 98% of cats were infected with both the canid and mongoose rabies virus variants, as well as a rare lyssavirus, Lyssavirus mokola, from a domestic cat from Eswatini. Furthermore, the nucleotide sequence divergence between the recently identified MOKV isolate and the historical Lyssavirus mokola isolates ranged from 6.8% to 8.3%. This study further highlights the association between the potential host species of Lyssavirus mokola and the domestic cat as an incidental host, and the important role cats may play in rabies transmission dynamics in the country. Therefore, continuous vaccination of domestic cats against rabies is crucial, even after the elimination of dog-mediated rabies, as spillover related to sylvatic rabies cycles is likely to occur.

SARS-CoV-2 Reverse Zoonoses to Pumas and Lions, South Africa.

Reverse-zoonotic infections of severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2) from humans to wildlife species internationally raise concern over the emergence of new variants in animals. A better understanding of the transmission dynamics and pathogenesis in susceptible species will mitigate the risk to humans and wildlife occurring in Africa. Here we report infection of an exotic puma (July 2020) and three African lions (July 2021) in the same private zoo in Johannesburg, South Africa. One Health genomic surveillance identified transmission of a Delta variant from a zookeeper to the three lions, similar to those circulating in humans in South Africa. One lion developed pneumonia while the other cases had mild infection. Both the puma and lions remained positive for SARS-CoV-2 RNA for up to 7 weeks.

Prevalence of Antibiotic Resistance in Salmonella Serotypes Concurrently Isolated from the Environment, Animals, and Humans in South Africa: A Systematic Review and Meta-Analysis.

One of the main global concerns is the usage and spread of antibiotic resistant Salmonella serovars. The animals, humans, and environmental components interact and contribute to the rapid emergence and spread of antimicrobial resistance, directly or indirectly. Therefore, this study aimed to determine antibiotic resistance (AR) profiles of Salmonella serotypes isolated from the environment, animals, and humans in South Africa by a systematic review and meta-analysis. The preferred reporting items for systematic reviews and meta-analyses (PRISMA) guidelines were followed to search four databases for studies published from 1980 to 2021, that reported the antibiotic resistance profiles of Salmonella serotypes isolated in South Africa. The AR was screened from 2930 Salmonella serotypes which were isolated from 6842 samples. The Western Cape province had high pooled prevalence estimates (PPE) of Salmonella isolates with AR profiles followed by North West, Gauteng, and Eastern Cape with 94.3%, 75.4%, 59.4%, and 46.2%, respectively. The high PPE and heterogeneity were observed from environmental samples [69.6 (95% CI: 41.7−88.3), Q = 303.643, I2 = 98.353, Q-P = 0.045], animals [41.9 (95% CI: 18.5–69.5), Q = 637.355, I2 = 98.745, Q-P = 0.577], as well as animals/environment [95.9 (95% CI: 5.4−100), Q = 55.253, I2 = 96.380, Q-P = 0.300]. The majority of the salmonella isolates were resistant to sulphonamides (92.0%), enrofloxacin and erythromycin (89.3%), oxytetracycline (77.4%), imipenem (72.6%), tetracycline (67.4%), as well as trimethoprim (52.2%), among the environment, animals, and humans. The level of multidrug-resistance recorded for Salmonella isolates was 28.5% in this review. This study has highlighted the occurrence of AR by Salmonella isolates from animals, humans, and environmental samples in South Africa and this calls for a consolidated “One Health” approach for antimicrobial resistance epidemiological research, as well as the formulation of necessary intervention measures to prevent further spread.

Genomic Characterization of Endemic and Ecdemic Non-typhoidal Salmonella enterica Lineages Circulating Among Animals and Animal Products in South Africa.

In Africa, the burden of illness caused by non-typhoidal Salmonella enterica is disproportionally high; however, whole-genome sequencing (WGS) efforts are overwhelmingly concentrated in world regions with lower burdens. While WGS is being increasingly employed in South Africa to characterize Salmonella enterica, the bulk of these efforts have centered on characterizing human clinical strains. Thus, very little is known about lineages circulating among animals in the country on a genomic scale. Here, we used WGS to characterize 63 Salmonella enterica strains isolated from livestock, companion animals, wildlife, and animal products in South Africa over a 60-year period. Genomes were assigned to serotypes Dublin, Hadar, Enteritidis, and Typhimurium (n = 18, 8, 13, and 24 strains, respectively) and sequence types (STs) ST10 (all S. Dublin), ST33 (all S. Hadar), ST11/ST366 (n = 12 and 1 S. Enteritidis, respectively), and ST19/ST34 (n = 23 and 1 S. Typhimurium, respectively; via seven-gene multi-locus sequence typing). Within-ST phylogenies were constructed using genomes sequenced in this study, plus publicly available genomes representative of each ST’s (i) global (n = 2,802 and 1,569 S. Dublin and Hadar genomes, respectively) and (ii) African (n = 716 and 343 S. Enteritidis and Typhimurium genomes, respectively) population. For S. Dublin ST10, a largely antimicrobial-susceptible, endemic lineage circulating among humans, animals, and food in South Africa was identified, as well as a lineage that was likely recently introduced from the United States. For S. Hadar ST33, multiple South African lineages harboring streptomycin and tetracycline resistance-conferring genes were identified. African S. Enteritidis ST11 could be primarily partitioned into one largely antimicrobial-susceptible and one largely multidrug-resistant (MDR) clade, with South African isolates confined to the largely antimicrobial-susceptible clade. S. Typhimurium ST19/ST34 strains sequenced here were distributed across the African S. Typhimurium ST19/ST34 phylogeny, representing a diverse range of lineages, including numerous MDR lineages. Overall, this study provides critical insights into endemic and ecdemic non-typhoidal Salmonella enterica lineages circulating among animals, foods, and humans in South Africa and showcases the utility of WGS in characterizing animal-associated strains from a world region with a high salmonellosis burden.

Beautiful places and recreating humanity in South Africa

The article investigates the connection between beauty and justice, by exploring everyday aesthetics through ordinary life, specifically the very concrete reality of contemporary urban South Africa. On the one hand, it delves beneath the statement that apartheid is ugly, by exploring the ugly spaces apartheid created, the devastation of an aesthetic built on segregation, and the distortions of whiteness. It also seeks to explore a theological aesthetic that starts from the ordinary life lived in particular places, arguing that beauty in particular places must be interwoven with humanness in all places, and proposing a theological aesthetic that gives priority to the voices silenced in particular places. Through this, beauty and justice are intimately interwoven in the ongoing work of disruption and transformation of a white racist place.

Digitizing Humanities in South Africa: Computational linguistic resources, training, and community building

South Africa has eleven official languages. However, not all have received similar amounts of attention. In particular, for many of the languages, only a limited number of digital language resources (data sets and computational tools) exist. This scarcity hinders (computational) research in the fields of humanities and social sciences for these languages. Additionally, using existing computational linguistics tools in a practical setting requires expert knowledge on the usage of these tools. In South Africa, only a small number of people currently have this expertise, further limiting the type of research that relies on computational linguistic tools. The South African Centre for Digital Language Resources (SADiLaR) aims to enable and enhance research in the area of language technology by focusing on the development, management, and distribution of digital language resources for all South African languages. Additionally, it aims to build research capacity, specifically in the field of digital humanities. This requires several challenges to be resolved that we cluster under resources, training, and community building. SADiLaR hosts a repository of existing digital language resources and supports the development of new resources. Additionally, it provides training on the use of these resources, specifically for (but not limited to) researchers in the fields of humanities and social sciences. Through this training, SADiLaR tries to build a community of practice to boost information sharing in the area of digital humanities.

West Nile Virus in Wildlife and Nonequine Domestic Animals, South Africa, 2010-2018.

West Nile virus (WNV) lineage 2 is associated with neurologic disease in horses and humans in South Africa. Surveillance in wildlife and nonequine domestic species during 2010–2018 identified WNV in 11 (1.8%) of 608 animals with severe neurologic and fatal infections, highlighting susceptible hosts and risk for WNV epizootics in Africa.

Virulence Characteristics and Antimicrobial Resistance Profiles of Shiga Toxin-Producing Escherichia coli Isolates from Humans in South Africa: 2006-2013.

Shiga toxin-producing Escherichia coli (STEC) isolates (N = 38) that were incriminated in human disease from 2006 to 2013 in South Africa were characterized by serotype, virulence-associated genes, antimicrobial resistance and pulsed-field gel electrophoresis (PFGE). The isolates belonged to 11 O:H serotypes. STEC O26:H11 (24%) was the most frequent serotype associated with human disease, followed by O111:H8 (16%), O157:H7 (13%) and O117:H7 (13%). The majority of isolates were positive for key virulence-associated genes including stx1 (84%), eaeA (61%), ehxA (68.4%) and espP (55%), but lacked stx2 (29%), katP (42%), etpD (16%), saa (16%) and subA (3%). stx2 positive isolates carried stx2c (26%) and/or stx2d (26%) subtypes. All pathogenicity island encoded virulence marker genes were detected in all (100%) isolates except nleA (47%), nleC (84%) and nleD (76%). Multidrug resistance was observed in 89% of isolates. PFGE revealed 34 profiles with eight distinct clusters that shared ≥80% intra-serotype similarity, regardless of the year of isolation. In conclusion, STEC isolates that were implicated in human disease between 2006 and 2013 in South Africa were mainly non-O157 strains which possessed virulence genes and markers commonly associated with STEC strains that have been incriminated in mild to severe human disease worldwide. Improved STEC monitoring and surveillance programs are needed in South Africa to control and prevent STEC disease in humans.

Fatal Tuberculosis in a Free-Ranging African Elephant and One Health Implications of Human Pathogens in Wildlife.

Tuberculosis (TB) in humans is a global public health concern and the discovery of animal cases of Mycobacterium tuberculosis (Mtb) infection and disease, especially in multi-host settings, also has significant implications for public health, veterinary disease control, and conservation endeavors. This paper describes a fatal case of Mtb disease in a free-ranging African elephant (Loxodonta africana) in a high human TB burden region. Necropsy revealed extensive granulomatous pneumonia, from which Mtb was isolated and identified as a member of LAM3/F11 lineage; a common lineage found in humans in South Africa. These findings are contextualized within a framework of emerging Mtb disease in wildlife globally and highlights the importance of the One Health paradigm in addressing this anthroponotic threat to wildlife and the zoonotic implications.

Arboviruses in South Africa, Known and Unknown

The emergence of novel arboviruses of zoonotic potential in South Africa (SA) threatens human health and animal welfare, and affects economic growth and development. These viruses cause severe infections in animals and humans, including neurological diseases, such as encephalitis, resulting in high morbidities, mortalities and economic losses. With increasing reports of Middelburg, Shuni, Sindbis, West Nile and Wesselsbron virus infections in animals and humans in SA, this article reviews and discusses known and currently emerging arboviruses in the country. These reports underscore the need for increased surveillance, vector control management, public health preparedness, focused research, community awareness programs, and the development of rapid and sensitive diagnostic approaches. Furthermore, appropriate medical personnel training and strengthening initiatives for a one-health approach are required to understand and mitigate the emerging arboviral threat to public health.

Ambiguities of a decolonising press culture: On South Africa’s Imvo Zabantsundu (Native Opinion)

Decolonising roles of African language-based print media remain an elusive research subject in South Africa. Largely, this is as a result of the ahistorical understanding of media platforms in current research and decolonial discourses of the country. Focusing on the ambiguous and conflicting roles of the founding ‘owner’ and editor of Imvo Zabantsundu (Native Opinion), this article asserts that this African language-based newspaper fell short of the decolonising quest it set to achieve when it was started in 1884. The article further asserts that while the use of African languages provided an important impetus towards decolonisation of the press, the newspaper’s reliance on white capital during South Africa’s early colonial era compromised the ambitions of the journal’s founding editor. It argues that this compromised role of the editor was demonstrated when the newspaper was later used by its funders to campaign for the colonial parliament candidates that had presided over the desecration of African humanity in South Africa. The conclusion reached by this article is that while African languages play an important role in the decolonisation process, this role was compromised in the case of Imvo ZabaNtsundu (Native Opinion) by its founder and editor.

Practices and discourses of ubuntu: Implications for an African model of disability?

BackgroundSouthern African scholars and activists working in disability studies have argued that ubuntu or unhu is a part of their world view.ObjectivesThinking seriously about ubuntu, as a shared collective humanness or social ethics, means to examine how Africans have framed a struggle for this shared humanity in terms of decolonisation and activism.MethodThree examples of applications of ubuntu are given, with two mainly linked to making explicit umaka. Firstly, ubuntu is linked to making visible the invisible inequalities for a common humanity in South Africa. Secondly, it becomes correlated to the expression of environmental justice in West and East African countries.ResultsAn African model of disability that encapsulates ubuntu is correlated to how Africans have illustrated a social ethics of a common humanity in their grassroots struggles against oppression and disablement in the 20th century. Ubuntu also locates disability politically within the wider environment and practices of sustainability which are now important to the post-2105 agenda, Convention on the Rights of Persons with Disabilities (CRPD) and the (UN) Sustainable Development Goals linked to climate change.ConclusionA different kind of political action linked to social justice seems to be evolving in line with ubuntu. This has implications for the future of disability studies.

Practices and discourses of ubuntu: Implications for an African model of disability?

Background: Southern African scholars and activists working in disability studies have argued that ubuntu or unhu is a part of their world view. Objectives: Thinking seriously about ubuntu, as a shared collective humanness or social ethics, means to examine how Africans have framed a struggle for this shared humanity in terms of decolonisation and activism. Method: Three examples of applications of ubuntu are given, with two mainly linked to making explicit umaka. Firstly, ubuntu is linked to making visible the invisible inequalities for a common humanity in South Africa. Secondly, it becomes correlated to the expression of environmental justice in West and East African countries. Results: An African model of disability that encapsulates ubuntu is correlated to how Africans have illustrated a social ethics of a common humanity in their grassroots struggles against oppression and disablement in the 20th century. Ubuntu also locates disability politically within the wider environment and practices of sustainability which are now important to the post-2105 agenda, Convention on the Rights of Persons with Disabilities (CRPD) and the (UN) Sustainable Development Goals linked to climate change. Conclusion: A different kind of political action linked to social justice seems to be evolving in line with ubuntu. This has implications for the future of disability studies.

Calling for the punishment to fit the crime: Genocide, war crimes and crimes against humanity in South Africa

A person found guilty of genocide, war crimes or crimes against humanity is liable to be sentenced to life imprisonment. However, in terms of the Criminal Law Amendment Act, a person guilty of murder or rape in certain circumstances has to be sentenced to life imprisonment unless there are substantial and compelling circumstances in which case the court has to impose a lesser sentence. This article argues, inter alia, that there is a need to amend South Africa's Implementation of the Rome Statute Act so that courts are obliged to impose life imprisonment on a person found guilty of genocide, war crimes and crimes against humanity unless there are strong reasons to impose a lesser sentence. This would show South Africa's commitment to punish severely those convicted of such international crimes.

A New Field:History of Humanities

A New Field:<i>History of Humanities</i>

State of urgency

William Faulkner’s appalled recognition – ‘The past is never dead. It’s not even past.’ – sets the scene for many of the animating concerns of this Special Issue. This is focused on work in and debates around the humanities in South Africa, where many artists and academics appear to be wrestling with a particularly strong version of Faulkner’s dilemma. For just over 20 years after the formal dismantling of apartheid embodied in the adoption of South Africa’s new Constitution, what we are witnessing is a living on of the past, a startled recognition that the past is not even past. For the structural persistence of forms of racialized inequality at every level of society and of the economy is now becoming increasingly expressed and articulated in and through the deeply polarising debates around higher education which are largely taking place within the humanities. This persistence of the past, combined with the dictates of a national higher education policy cloned from a global template indifferent or even hostile to the humanities and the qualitative social sciences, exerts both globally familiar and locally specific pressures on the possibilities and potentials for humanist study and critical reflection. In these pages we cannot pretend to cover or fully represent the totality of work in the arts and humanities in South Africa. However, we hope that this assemblage of snapshots, glimpses and fragments of work will nonetheless work to yield some insight into the South African academy, and offer some sense of its uneasy relation to the larger forces and conflicts of the nation and the state. All of these conflicts are now rapidly coming to a head in the university system, where as we write, campuses across the country are closed due to student protests. #FeesMustFall follows on the #RhodesMustFall protests at the University of Cape Town (UCT) in March 2015. Here, a student in a well-publicized demonstration stirred up students across the country (and beyond) by throwing a bottle of human waste over the statue – centrally placed at UCT – of the great symbol of colonialism, Cecil John Rhodes, resulting in the at least temporary and perhaps

Hopeless Entanglement: The Short History of the Academic Humanities in South Africa

Hopeless Entanglement: The Short History of the Academic Humanities in South Africa

The ‘medical humanities’ in health sciences education in South Africa

A new masters-level course, 'Medicine and the Arts" will be offered in 2014 at the University of Cape Town, setting a precedent for interdisciplinary education in the field of medical humanities in South Africa. The humanities and social sciences have always been an implicit part of undergraduate and postgraduate education in the health sciences, but increasingly they are becoming an explicit and essential component of the curriculum, as the importance of graduate attributes and outcomes in the workplace is acknowledged. Traditionally, the medical humanities have included medical ethics, history, literature and anthropology. Less prominent in the literature has been the engagement with medicine of the disciplines of sociology, politics, philosophy, linguistics, education, and law, as well as the creative and expressive arts. The development of the medical humanities in education and research in South Africa is set to expand over the next few years, and it looks as if it will be an exciting inter-disciplinary journey.