A Prolonged Outbreak of Enteric Fever Associated With Illegal Miners in the City of Matlosana, South Africa, November 2020–September 2022

Abstract

Background In South Africa, the annual incidence of enteric fever averaged 0.1 per 100 000 persons between 2003 and 2018. During 2021 an increase in the number of enteric fever cases was observed. An outbreak investigation was conducted to determine the magnitude and source of the outbreak. Methods We performed a cross-sectional descriptive study. Data were collected through telephonic or face-to-face interviews with cases or proxies using a standardized case investigation form. Whole Genome Sequencing (WGS) was performed on all Salmonella Typhi isolates. Drinking water samples were collected, tested and analysed. Descriptive analysis was performed using Microsoft Excel. Results Between January 2020 and September 2022, a cluster of 53 genetically highly related Salmonella Typhi isolates were identified from five different provinces in South Africa. Isolates associated with the cluster showed ≤5 allelic differences as determined following core-genome multilocus sequence typing analysis. Most (60%; 32/53) of the cases were in the North West Province. Males comprised 68% (36/53). Of these, 72% (26/36) were within age group 15-49 years with median age of 31 years. And where occupation was known within this age group 78% (14/18) were illegal gold miners. Illegal miners reported illness onset while working underground. Five municipal tap water samples were tested and showed no evidence of fecal contamination. Conclusion This outbreak predominantly affected illegal gold miners, likely due to the consumption of contaminated groundwater while working in a gold mine shaft. In addition, this investigation highlights the value of WGS to detect clusters and support epidemiological investigation of enteric fever outbreaks.