Application of molecular epidemiological methods to investigate strains of salmonella enterica serovar enteritidis in South Africa

A dissertation submitted to the Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa, in fulfillment of the requirements for the degree of Master of Science in Medicine Johannesburg, 2017In South Africa, Salmonella Enteritidis has become a significant pathogen and the numbers of cases reported to the Centre for Enteric Diseases (CED) have increased. Pulsed-field gel electrophoresis (PFGE) is a primary for molecular subtyping of Salmonella. However, this technique has poor discrimination for serotypes with high homogeneity such as Salmonella Enteritidis. Multi-locus variable-number tandem-repeats analysis (MLVA) has shown higher discriminatory power for Salmonella Enteritidis compared to PFGE. In this study, MLVA was used to investigate the molecular epidemiology and relatedness of human Salmonella Enteritidis strains from Gauteng and Western Cape, South Africa. Furthermore, MLVA was also used to investigate the relatedness of human and non-human Salmonella Enteritidis strains. MLVA included analysis of five VNTR loci, with varying degrees of diversity. A total of 1221 human isolates and 43 non-human isolates were included in the study. Eighty-six MLVA profiles were obtained; MLVA profiles 7, 21, 22 and 28 were the predominant MLVA profiles. MLVA profile 28 was the most common MLVA profile amongst both the human and non-human isolates. Isolates had low prevalence of antimicrobial resistance, however sulfamethoxazole resistance was notable amongst both the human (348; 29%) and non-human (10; 23%) isolates. During the study period, seven Salmonella Enteritidis outbreaks were investigated from six provinces and isolates from each individual outbreak showed an identical MLVA profile. MLVA was shown to be a successful molecular subtyping tool for Salmonella Enteritidis, for both surveillance purposes and outbreak investigations. Salmonella Enteritidis strains circulating within the human and non-human population were clonal. The study emphasizes the need for the one health approach, in order to curb the spread of Salmonella Enteritidis in South Africa.MT201

Disease Severity and Comorbidities among Healthcare Worker COVID-19 Admissions in South Africa: A Retrospective Analysis

Healthcare workers (HCWs) are among the most vulnerable in regard to contracting severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. Comorbidities are reported to increase the risk for more severe COVID-19 outcomes, often requiring hospitalization. However, the evidence on disease severity and comorbidities among South African HCWs is lacking. This retrospective study analyzed the prevalence of comorbidities among HCW hospitalized with COVID-19 and its association with the severity of outcomes. Data from public and private hospitals in nine provinces of South Africa were extracted from the national hospital surveillance database for COVID-19 admissions. A total of 10,149 COVID-19 HCWs admissions were reported from 5 March 2020 to 31 December 2021. The risk of disease severity among HCWs increased with age, with those older (≥60 years) having seven times the odds of disease severity (aOR 7.0; 95% CI 4.2–11.8) compared to HCWs in the younger age (20–29 years) group. The most commonly reported comorbidity was hypertension (36.3%), followed by diabetes (23.3%) and obesity (16.7%). Hypertension (aOR 1.3; 95% CI 1.0–1.6), diabetes (aOR 1.6; 95% CI 1.3–2.0), and HIV (aOR 1.6; 95% CI 1.2–2.1) were significantly associated with disease severity. In conclusion, age, gender, and existing comorbidities were strong predictors of the prognosis of severe COVID-19 among HCWs in South Africa. The information is important in the development of occupational health policies and vulnerability risk assessments for HCWs in light of future COVID-19 waves or similar outbreaks