Bacillus clausii genome decoded from rare human bacteremia case

An eight-year-old girl in Ecuador has become the focus of a landmark genomic investigation after a probiotic drink sold over the counter to support gut health was linked—through whole-genome sequencing—to the bloodstream infection that nearly claimed her life. In a case report published in New Microbes and New Infections, researchers led by Santiago Campos-Miño of the Hospital Metropolitano describe how Bacillus clausii, the active ingredient in the widely used probiotic Enterogermina, was isolated from the blood of a critically ill child who had been receiving the probiotic as part of her treatment. Using a battery of high-resolution genomic techniques, the team found that the blood isolate and the commercial probiotic strain were so closely related that a common origin was the most likely explanation—a conclusion no previous study of probiotic-associated bacteremia had reached with this level of genomic rigor.

The story begins in March 2024, when the girl was admitted to the pediatric intensive care unit with sepsis and respiratory failure caused by nosocomial pneumonia. Her medical history made her exceptionally vulnerable: she suffered from severe malnutrition, cerebral palsy, and epilepsy, and had recently recovered from SARS-CoV-2 pneumonia. Bronchial secretions yielded extended-spectrum β-lactamase–producing Klebsiella pneumoniae, a multidrug-resistant pathogen that was successfully treated with a combination of meropenem and amikacin. Alongside these intravenous antibiotics, the clinical team administered oral Bacillus clausii, the spore-forming probiotic commonly dispensed to support gastrointestinal health and to prevent antibiotic-associated diarrhea.

One week later, the girl developed diarrhea. Five days after that, she developed fever, and blood cultures were drawn. To the surprise of the clinical team, the cultures yielded Bacillus clausii—an organism better known as a friendly gut supplement than as a bloodstream pathogen. Identification was confirmed by 16S rRNA sequencing, the gold-standard method for bacterial species determination. The patient was treated with fourteen days of intravenous ciprofloxacin and made a full recovery. But the case raised an uncomfortable question: had the very probiotic being given to protect her gut actually caused her bloodstream infection?

To answer that question, the researchers turned to whole-genome sequencing. Both the bloodstream isolate, designated B. clausii 2082, and the commercial probiotic strain, B. clausii 4771, were sequenced on the Oxford Nanopore MinION Mk1B platform using R10.4.1 flow cells, generating complete or near-complete genome assemblies for direct comparison. The team then deployed a suite of independent analytical approaches, each offering a different window into the relationship between the two bacteria: assembly-based single nucleotide polymorphism analysis, read-based variant calling with the Clair3 algorithm, average nucleotide identity (ANI) calculations, core genome multilocus sequence typing (cgMLST), and full phylogenomic reconstruction.

The results were striking in their concordance. Assembly-based analysis identified 60 SNPs between the two genomes—suggesting some divergence—but when the team used read-based variant calling with Clair3, a method that avoids errors introduced during genome assembly, no SNPs or indels were detected at all. This indicated that the 60 apparent differences were artifacts of the assembly process rather than genuine genetic variation. ANI, a measure of overall genomic similarity, reached 99.5299 percent—a value indicating exceptionally high nucleotide identity, though remaining just below the 99.99 percent threshold conventionally accepted for declaring strict strain identity. Meanwhile, cgMLST identified 220 shared loci with complete allelic concordance, meaning that at every one of those 220 core genomic positions, the two isolates carried identical alleles.

Phylogenomic reconstruction added further weight to the picture. When placed on a phylogenetic tree alongside reference genomes, both the blood isolate and the probiotic strain clustered together with B. clausii B106 and B. clausii ENTPro, the probiotic reference strains, supporting a common evolutionary origin. Taken together, the convergence of these independent genomic methods provides robust evidence of an exceptionally close relationship between the administered probiotic and the organism recovered from the child’s blood. Genome assemblies and raw sequencing reads have been deposited in public databases under BioProject accession PRJNA1413925, allowing other researchers to verify and extend the findings.

How does a probiotic end up in the bloodstream? The most likely route, the authors argue, is bacterial translocation—the passage of intestinal bacteria across the gut lining and into the blood. This phenomenon is well documented in patients with compromised intestinal barriers, and Bacillus clausii may be particularly well suited to making the journey. The probiotic’s spores are thermostable and remarkably resistant to nutrient deprivation, dehydration, and low pH, allowing the organism to persist in the gastrointestinal tract long after ingestion. Prior research has shown that B. clausii survives intestinal transit and maintains a considerable intestinal titer for up to twelve days after a single oral administration—a long window of opportunity for a determined microbe in a compromised host.

In this case, several factors conspired to create exactly such a host. Severe chronic malnutrition impairs immune function, reducing the body’s ability to clear exogenous bacteria and increasing the risk of probiotic-associated sepsis. In pediatric patients, malnutrition also causes direct damage to the intestinal epithelium, weakening the physical barrier that normally keeps gut bacteria where they belong. On top of this, gastrointestinal dysfunction linked to COVID-19 has been associated with increased microbial translocation and elevated risk of bacteremia, adding a further layer of vulnerability. The close temporal association between probiotic administration and the onset of bacteremia, combined with the girl’s immune and intestinal impairment, led the authors to conclude that intestinal translocation of the probiotic strain is the most likely source of the infection.

The case marks a significant advance over previous reports. Although several pediatric cases of B. clausii bacteremia have been described in the literature, evidence linking commercial probiotic preparations to bloodstream isolates has until now relied exclusively on phenotypic identification methods such as MALDI-TOF mass spectrometry or conventional microbiological techniques. These approaches can confirm that the same species was involved, but they cannot distinguish between individual strains within a species—leaving open the possibility that the blood isolate came from an environmental source or the patient’s own microbiota rather than the administered probiotic. By integrating whole-genome approaches, including read-based SNP validation, ANI, cgMLST, and phylogenomic reconstruction, the Ecuadorian team has provided the most convincing genomic evidence to date that a commercial probiotic strain can cross from the gut into the blood. The researchers are careful to note that the evidence does not establish strict strain identity, but the complementary analyses strongly support an exceptionally close genomic relationship between the two isolates.

The findings arrive at a moment of growing scrutiny for the probiotic industry. Probiotic consumption is generally considered safe, and millions of doses of B. clausii preparations are administered worldwide each year without incident. But safety concerns have long been raised for vulnerable populations, particularly strains selected for strong mucosal adhesion—the very property that allows probiotics to colonize the gut effectively. Strong adherence may also promote translocation across the intestinal barrier, increasing the risk of sepsis in immunocompromised individuals. Previous reviews of probiotic safety have documented rare but real cases of fungemia and bacteremia attributable to probiotic organisms, and clinical guidelines in several countries advise against giving live microbial supplements to severely immunocompromised patients, including those with central venous catheters or critical illness.

The authors emphasize that their findings should prompt caution rather than alarm. Probiotic strains such as B. clausii could, in susceptible hosts, cause bacteremia and potentially adapt within the body, and this possibility underscores the need for individualized decisions about probiotic use in vulnerable pediatric populations. Therapeutic decisions, they argue, should weigh the patient’s immune status and the severity of any underlying infection against the anticipated benefits of probiotic therapy. For a child with severe malnutrition, cerebral palsy, recent COVID-19, and an immature or damaged intestinal barrier, the calculus may look very different than it does for a healthy adult taking probiotics for everyday digestive complaints.

The research also highlights a broader lesson about the power of modern genomics to resolve questions that traditional microbiology cannot. Where phenotypic identification stops at the species level, whole-genome sequencing can trace the ancestry of individual isolates and reveal whether two organisms recovered from different sources share a recent common origin. As sequencing costs continue to fall, the researchers suggest that similar genomic surveillance could become a routine component of investigations into suspected probiotic-associated infections, providing the evidence base needed to define safety boundaries for live microbial therapeutics. The team calls for continued research and close clinical monitoring to better define probiotic safety, particularly as live biotherapeutic products move from the supplement shelf into mainstream clinical practice. For now, the case of one eight-year-old girl stands as a sobering reminder that even organisms marketed as beneficial can turn opportunist when the defenses that separate gut from bloodstream fall away.