Insecticide susceptibility analysis of Anopheles gambiae complex in Vlakbult, Mpumalanga 2012/13

South Africa is one of the 34 malaria endemic countries that are currently targeting malaria elimination. Although South Africa is also listed as malaria endemic, malaria in South Africa is limited to the North-eastern three provinces of KwaZulu-Natal (KZN), Mpumalanga and Limpopo. Anopheles arabiensis is the major malaria transmitting vector and the causative agent in over 90% of the malaria infections in South Africa had been and remains Plasmodiumfalciparum. Many species of malaria vectors are known to belong to a 'species complex' and therefore look identical morphologically. Such species need to be identified further through the use of modern molecular methods such as Polymerase Chain Reaction (PCR). One such group is the An. gambiae complex, which comprises of eight members: An. gambiae, An. coluzzii and An. arabiensis (major malaria vectors), An. merus, An. melas and An .bwambae (minor or localized vectors) and An. quadriannulatus and An. amharicus are not known to transmit malaria. This study focused on a new vector breeding site identified in Mpumalanga (Vlakbult) m 2011. The aims of this study were to: Obtain data on malaria vector prevalence in Vlakbult, Mpumalanga province (November 2012-January 2013), determine insecticide susceptibility status of An. arabiensis from Vlakbult and to determine sporozoite infectivity rate in wild caught An.arabiensis mosquitoes collected in Vlakbult from November 2012 -January 2013. The study found that the breeding site in Vlakbult had An. arabiensis that were found in this breeding site are susceptible to 4% DDT and 0.05% deltamethrin and that the wild caught Anopheles arabiensis found in this area (Vlakbult) were not infected with P. falciparum parasites. For the Mpumalanga malaria control program, these findings mean that there is a need for continuing entomological and vector susceptibility surveillance in order to inform malaria control and elimination efforts. Mpumalanga malaria control also needs to review their vector control activities in Vlakbult to ensure that the presence of An. arabiensis is addressed appropriately since the presence of the malaria transmitting vector in Vlakbult poses a potential risk for an outbreak of malaria.Mini Dissertation (MPh (Public Health))--University of Pretoria, 2013.School of Health Systems and Public Health (SHSPH)MPh (Public Health)Unrestricte

Salmonella Enteritidis clades in South Africa: why we should be paying more attention

Salmonella Enteritidis is the most reported non-typhoidal Salmonella serovar and is implicated in both gastroenteritis and invasive non-typhoidal disease. Whole-genome sequence comparison of Salmonella Enteritidis isolates from across the world identified four definitive clades: Outlier, Global Epidemic, East African and West African. Three of these clades were implicated in epidemics: the Global Epidemic clade was linked to poultry-associated gastroenteritis, while the two African clades were related to invasive disease. Despite the recognition of different Salmonella Enteritidis clades, the distribution and epidemiology of these clades across Africa is poorly understood. In our proof-of-concept study, we classified 618 Salmonella Enteritidis isolates originating from four South African provinces over a period of two years (2012 – 2013) into clades using a clade-typing real-time PCR assay. Associations between clades and province of collection, antimicrobial resistance and HIV status were explored using statistical analysis. Majority of the South African isolates were classified within the Outlier clade (61.00%), with fewer classified within the Global Epidemic clade (38.83%) and only one isolate classified within the West African Clade (0.16%). Of note, were the isolates within the Global clade, which were strongly associated with ciprofloxacin resistance (15.42%, OR: 7.45, CI: 3.526 – 15.751) and invasive disease (58.33%, OR: 1.57, CI: 1.13 – 2.17) in humans. The increase in poultry consumption and importation in South Africa has placed the country at risk of a Salmonella Enteritidis epidemic. Thus, there is a necessity for routine monitoring of S. Enteritidis along the farm-to-fork continuum to implement preventative measures

Emergence of <i>Vibrio cholerae</i> O1 Sequence Type 75, South Africa, 2018–2020

International audienceWe describe the molecular epidemiology of cholera in South Africa during 2018-2020. Vibrio cholerae O1 sequence type (ST) 75 recently emerged and became more prevalent than the V. cholerae O1 biotype El Tor pandemic clone. ST75 isolates were found across large spatial and temporal distances, suggesting local ST75 spread

Outbreak of Listeriosis in South Africa Associated with Processed Meat

International audienceBackgroundAn outbreak of listeriosis was identified in South Africa in 2017. The source was unknown.MethodsWe conducted epidemiologic, trace-back, and environmental investigations and used whole-genome sequencing to type Listeria monocytogenes isolates. A case was defined as laboratory-confirmed L. monocytogenes infection during the period from June 11, 2017, to April 7, 2018.ResultsA total of 937 cases were identified, of which 465 (50%) were associated with pregnancy; 406 of the pregnancy-associated cases (87%) occurred in neonates. Of the 937 cases, 229 (24%) occurred in patients 15 to 49 years of age (excluding those who were pregnant). Among the patients in whom human immunodeficiency virus (HIV) status was known, 38% of those with pregnancy-associated cases (77 of 204) and 46% of the remaining patients (97 of 211) were infected with HIV. Among 728 patients with a known outcome, 193 (27%) died. Clinical isolates from 609 patients were sequenced, and 567 (93%) were identified as sequence type 6 (ST6). In a case–control analysis, patients with ST6 infections were more likely to have eaten polony (a ready-to-eat processed meat) than those with non-ST6 infections (odds ratio, 8.55; 95% confidence interval, 1.66 to 43.35). Polony and environmental samples also yielded ST6 isolates, which, together with the isolates from the patients, belonged to the same core-genome multilocus sequence typing cluster with no more than 4 allelic differences; these findings showed that polony produced at a single facility was the outbreak source. A recall of ready-to-eat processed meat products from this facility was associated with a rapid decline in the incidence of L. monocytogenes ST6 infections.ConclusionsThis investigation showed that in a middle-income country with a high prevalence of HIV infection, L. monocytogenes caused disproportionate illness among pregnant girls and women and HIV-infected persons. Whole-genome sequencing facilitated the detection of the outbreak and guided the trace-back investigations that led to the identification of the source

The African Network for Improved Diagnostics, Epidemiology and Management of common infectious Agents

Background!#!In sub-Saharan Africa, acute respiratory infections (ARI), acute gastrointestinal infections (GI) and acute febrile disease of unknown cause (AFDUC) have a large disease burden, especially among children, while respective aetiologies often remain unresolved. The need for robust infectious disease surveillance to detect emerging pathogens along with common human pathogens has been highlighted by the ongoing novel coronavirus disease 2019 (COVID-19) pandemic. The African Network for Improved Diagnostics, Epidemiology and Management of Common Infectious Agents (ANDEMIA) is a sentinel surveillance study on the aetiology and clinical characteristics of ARI, GI and AFDUC in sub-Saharan Africa.!##!Methods!#!ANDEMIA includes 12 urban and rural health care facilities in four African countries (Côte d'Ivoire, Burkina Faso, Democratic Republic of the Congo and Republic of South Africa). It was piloted in 2018 in Côte d'Ivoire and the initial phase will run from 2019 to 2021. Case definitions for ARI, GI and AFDUC were established, as well as syndrome-specific sampling algorithms including the collection of blood, naso- and oropharyngeal swabs and stool. Samples are tested using comprehensive diagnostic protocols, ranging from classic bacteriology and antimicrobial resistance screening to multiplex real-time polymerase chain reaction (PCR) systems and High Throughput Sequencing. In March 2020, PCR testing for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and analysis of full genomic information was included in the study. Standardised questionnaires collect relevant clinical, demographic, socio-economic and behavioural data for epidemiologic analyses. Controls are enrolled over a 12-month period for a nested case-control study. Data will be assessed descriptively and aetiologies will be evaluated using a latent class analysis among cases. Among cases and controls, an integrated analytic approach using logistic regression and Bayesian estimation will be employed to improve the assessment of aetiology and associated risk factors.!##!Discussion!#!ANDEMIA aims to expand our understanding of ARI, GI and AFDUC aetiologies in sub-Saharan Africa using a comprehensive laboratory diagnostics strategy. It will foster early detection of emerging threats and continued monitoring of important common pathogens. The network collaboration will be strengthened and site diagnostic capacities will be reinforced to improve quality management and patient care