Abstract
Background Lacticaseibacillus (formerly Lactobacillus) rhamnosus is widely used in probiotics or food supplements to promote microbiome health and may also be part of the normal microbiota of the human gastrointestinal tract. However, it rarely also causes invasive or severe infections in patients. It has been postulated that these infections may originate from probiotics or from endogenous commensal reservoirs. In this report, we examine the population structure of Lacticaseibacillus rhamnosus and investigate the utility of using bacterial genomics to identify the source of invasive Lacticaseibacillus infections. Methods Core genome phylogenetic analysis was performed on 602 L. rhamnosus genome sequences from the National Center for Biotechnology public database. This information was then used along with newly generated sequences of L. rhamnosus isolates from yogurt to investigate a fatal case of L. rhamnosus endocarditis. Results Phylogenetic analysis demonstrated substantial genetic overlap of L. rhamnosus isolates cultured from food, probiotics, infected patients, and colonized individuals. This was applied to a patient who had both consumed yogurt and developed L. rhamnosus endocarditis to attempt to identify the source of his infection. The sequence of the isolate from the patient’s bloodstream differed at only one nucleotide position from one of the yogurt isolates. Both isolates belonged to a clade, identified here as clade YC, composed of mostly gastrointestinal isolates from healthy individuals, some of which also differed by only a single nucleotide change from the patient’s isolate. Conclusions As illustrated by this case, whole genome sequencing may be insufficient to reliably determine the source of invasive infections caused by L. rhamnosus.
Original language | English (US) |
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Article number | e0300843 |
Journal | PloS one |
Volume | 19 |
Issue number | 8 |
DOIs | |
State | Published - Aug 2024 |
Funding
The work was supported by the National Institute of Allergy and Infectious Diseases at the National Institutes of Health, URL: https://www. niaid.nih.gov/ (grant U19AI135964 to E.A.O. and A. R.H and grants R01AI118257, K24AI104831, R21AI153953, and R21AI164254 to A.R.H.) and the American Cancer Society, URL: https://www. cancer.org/ (Clinician Scientist Development Grant #134251-CSDG-20-053-01-MPC to K.E.R.B). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. This work was supported by the Northwestern University NUSeq Core Facility and the Robert H. Lurie Comprehensive Cancer Center. This work was also supported in part through the computational resources and staff contributions provided by the Genomics Compute Cluster, which is jointly supported by the Feinberg School of Medicine, the Center for Genetic Medicine, and Feinberg\u2019s Department of Biochemistry and Molecular Genetics, the Office of the Provost, the Office for Research, and Northwestern Information Technology. The Genomics Compute Cluster is part of Quest, Northwestern University\u2019s high-performance computing facility, with the purpose to advance research in genomics. We would like to thank members of the Center for Structural Genomics of Infectious Diseases (CSGID) and the Hauser laboratory for their valuable comments during numerous discussions of this work. We would also like to thank Ramon Lorenzo-Redondo for his advice and guidance on clustering analysis.
ASJC Scopus subject areas
- General