How did probiotic use contribute to the A. clausii outbreak in South African hospitals?
Alkalihalobacillus clausii (A. clausii), formerly known as Bacillus clausii, is a spore-forming gram-positive bacillus widely used in probiotic formulations. It has demonstrated therapeutic potential in managing antibiotic-associated diarrhoea by reducing inflammation, protecting intestinal integrity, and restoring gut microbiota balance.
Although generally considered safe, A. clausii probiotics have been implicated in bacteraemia among both immunocompromised and immunocompetent patients. Documented cases include infants and adults, with genetic evidence linking A. clausii bacteraemia directly to probiotic use. Large-scale outbreaks have also been reported globally, often associated with contaminated medical products.
In South Africa, a suspected outbreak of A. clausii bacteraemia was reported to the National Institute for Communicable Diseases (NICD) on 11 June 2024, involving private-sector hospitals in Gauteng and later North West province. The infections were suspected to be linked to the use of A. clausii-containing probiotics widely administered in these facilities.
This report summarises the outbreak investigation conducted between February and October 2024 to determine its scope, confirm the source, and guide public health response.
Materials and Methods
Following the outbreak notification, a retrospective review of laboratory-confirmed A. clausii bacteraemia cases was conducted. A line list of patients with A. clausii isolated from blood cultures between February and October 2024 was obtained from the reporting private sector laboratory. A case was defined as any patient with A. clausii isolated from a blood culture from February to October 2024.
Clinical isolates and two opened A. clausii-containing probiotic packets used by affected patients were sent to the Centre for Healthcare Associated Infections, Antimicrobial Resistance and Mycoses (CHARM) at the NICD for testing. Bacterial isolates were obtained from culture on blood agar, and identification was conducted using Matrix-Assisted Laser Desorption/Ionisation Time-of-Flight Mass Spectrometry (MALDI-TOF MS) (Microflex, Bruker Daltonics, USA).
Results
From February 2024 to October 2024, 11 cases (patients) were reported across eight private-sector hospitals (Figure 1) in the Gauteng (n=10) and North West (n=1) provinces. Seven patients had more than one positive culture during their hospital stay. The median age was seven years (IQR: 2–55 years), and 55% (6/11) were female.
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