Epidemiology of Clostridioides difficile in South Africa

De Jager, Pieter
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Background: Clostridioides difficile (CD) is the most common healthcare associated enteric infection. Based on evidence from high income countries, the burden of CD Infection (CDI) is growing and associated with significant morbidity and mortality. However, there is currently very limited epidemiological evidence on CDI incidence in South Africa. Aim: To describe the epidemiology of CDI in the South African public sector for the period 1 July 2016 to 30 June 2017. Methods: A secondary data analysis utilizing two primary data sources was conducted to describe the epidemiology of CDI in South Africa. Patient level data (age, sex, province, district, facility name, date of specimen taken, CD testing method and result) were obtained from the National Health Laboratory Service (NHLS) for all patients referred for a stool CD test between 1 July 2016 and 30 June 2017. Facility level admission data were obtained from the District Health Barometer (DHB). We assessed the patient-level association between variables of interest, CDI and CDI recurrence, by undertaking both univariate and multivariate analysis. Adjusted odds ratios (aOR) were calculated utilizing multivariate logistic regression. The incidence of CDI, CDI recurrence and CD testing was estimated by Poisson regression for various levels of care and provinces. Results: A total of 14 023 samples were tested for CD during the study period. After applying exclusion criteria (<18 years of age, missing data, private sector patients), we were left with a sample of 9 282 of which 1 730 (18.64%) had CDI. A positive and significant association between CDI and level of care is found, with patients treated in a specialised tuberculosis (TB) hospital having a more than 11 fold increased risk for CDI (aOR 11.17, CI95% 8.50 –14.69) compared to those managed in primary care. Patients receiving care at a secondary, tertiary or central hospital had 40%, 83% and 44% increased risk of CDI compared to those managed in primary care, respectively. National incidence of CDI is estimated at 53.89 cases per 100000 hospitalisations (CI95% 51.58 –56.29), the incidence of recurrence at 21.39 (CI95% 15.06 –29.48) cases per 1 000 cases and a recurrence rate of 2.14% (CI95% 1.51 –2.94). There is significant variability in the incidence of CD testing and CDI across provinces and levels of care. Conclusion: This is the first study in South Africa to estimate the national burden of CDI. Compared to European countries, we found a comparable incidence of CDI. However, our estimates are lower than those for the United States. This study found a significantly lower CDI recurrence in the South African public sector, compared to high income countries
A research report submitted to the Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, in partial fulfilment of the requirements for the degree Master of Medicine in the branch of Anaesthesiology, 2021