NICD links over-the-counter probiotic to bacteraemia outbreak in Gauteng and North West

The National Institute For Communicable Diseases (NICD) has declared an outbreak of Alkalihalobacillus clausii (A. clausii) bacteraemia cases in private-sector hospitals in Gauteng and North West, reportedly linked to use of the Enterogermina probiotic.

Alkalihalobacillus clausii is typically a non-pathogenic bacterium that does not cause invasive infections in humans, which is why it’s used in probiotics, according to Dr Caroline Maluleka, senior pathologist from the Centre for Healthcare-Associated Infections, Antimicrobial Resistance and Mycoses at the NICD. The outbreak marks the first documented cases of bacteraemia due to this bacterium in South Africa.

In three of the 11 cases identified by the NICD, the patients have died. However, Maluleka noted that “the patients who were severely ill… had some comorbidities, which are underlying conditions. It is actually unknown whether the deaths were directly due to the use of a probiotic, or if it was just coincidental timing.”

Microbiological investigation

Bacteraemia is the presence of bacteria in the bloodstream. According to the NICD, it was first alerted to an increase in bacteraemia cases of Alkalihalobacillus clausii by a pathologist in a private laboratory in June 2024.

“Following the notification, an investigation was conducted, collecting microbiological records of A. clausii-positive blood cultures from the reporting laboratory from January 2024 to October 2024. Over this period, 11 cases of A. clausii bacteraemia were identified in eight different hospitals across [the] Gauteng and North West provinces. Most of the patients had reported using Enterogermina probiotics prior to the bacteraemia onset,” said the NICD.

“Isolates from four cases and two open packets of Enterogermina probiotic used by the patients were sent to the NICD for whole genome sequencing. The investigation determined Enterogermina probiotic as the likely source for A. clausii bacteraemia.”

Whole genome sequencing involves the DNA sequencing of the entirety of an organism’s genome. It can be used to determine the genetic relatedness of microbial isolates in an outbreak.

Maluleka said that the NICD was unable to disclose the names of the eight hospitals where A. clausii bacteraemia cases were identified. However, she explained that the patients varied in that some ended up at a hospital after consuming the probiotic elsewhere, while others had received the probiotic at a hospital.

The NICD’s initial investigation did not include hospitals in the public sector. Maluleka said further work would be done to determine if the same problem was occurring in state facilities.

Symptoms and path to care

According to Maluleka, the symptoms of A. clausii bacteraemia can include:

• fever;


• increased heart rate;


• sweating; and


• general body weakness or malaise

In severe cases, the infection can progress to sepsis, which presents with an altered mental state and multi-organ dysfunction.

“When you see a doctor, you will definitely explain the signs and symptoms, and it’s important to mention the use of Enterogermina as a probiotic, so that the doctor will then know which direction to take… Not all signs and symptoms that patients have will definitely be due to the probiotic, so the clinician will know how to deal with this, to exclude other causes,” said Maluleka.

Populations who might be more vulnerable to A. clausii bacteraemia include:

• patients with comorbidities;


• patients who are immunocompromised, such as those with cancer, organ transplants or HIV/Aids;


• patients who’ve been in the hospital for a long time;


• patients in ICUs; and


• newborn babies.

Managing the outbreak

Alkalihalobacillus clausii has been shown to have probiotic properties and “significant therapeutic potential”, according to the NICD. The institute stated that the bacterium was commonly prescribed to manage gut dysbiosis and diarrhoea, including antibiotic-associated diarrhoea.

The Enterogermina probiotic is an oral bacteriotherapy product. It’s marketed as a ready-to-drink vial containing Alkalihalobacillus clausii spores, which assist in “protecting the gut from side effects such as diarrhoea and abdominal cramps”, according to the product description on the Enterogermina website.






The NICD has shared a detailed report with the reporting laboratory recommending that all pharmacists at hospitals with A. clausii bacteraemia cases notify the South African Health Products Regulatory Authority (Sahpra) for further investigation.

“Hospitals with cases clustering by time and place should conduct further investigations to rule out a healthcare-associated source. Healthcare professionals and patients should be informed of this outbreak and educated on the safe use of probiotics including consideration of patients’ immune status, contraindications and side effects,” stated the NICD.

Daily Maverick contacted Sahpra about the outbreak but had not received a response at the time of publishing. DM

This article was updated on 28 November to include comment from Opella Healthcare South Africa, the company that owns the Enterogermina probiotic .