Whole-genome sequencing-based typing methods for Clostridium butyricum strains from clinical, animal, plant, and environmental sources
Rattachement africain : fr, Burkina Faso, Maroc. Niveau de preuve : code pays fourni par la source.
Le résumé fourni par la source
ABSTRACT Clostridium butyricum exhibits a dual role, acting not only as a probiotic but also as an opportunistic pathogen associated with neonatal necrotizing enterocolitis (NEC) and infant botulism. We aimed to establish high-resolution genotyping frameworks to improve molecular surveillance and outbreak investigations. We analyzed 297 C. butyricum genomes, including 200 isolates from preterm neonates across 13 French neonatal intensive care units over a 20-year period and 97 publicly available genomes. A core-genome multilocus sequence typing (cgMLST) scheme was developed using chewBBACA, defining 2,621 loci, and applied to genomes with ≥95% locus presence. Core-genome single-nucleotide polymorphism (cgSNP) analysis was performed for complementary resolution. Phylogenetic cgMLST classified isolates into nine major clades. Some clinical strains displayed clonal relationships, whereas others were geographically and temporally unrelated. All botulinum neurotoxin type E-producing strains were grouped within a single clade. NEC-associated isolates showed geographic and temporal clustering, but no clade was uniquely linked to NEC. cgSNP analysis identified 11 clusters with overall discriminatory power similar to cgMLST while providing finer resolution for NEC-related strains. We propose robust cgMLST and cgSNP schemes for C. butyricum , enabling high-resolution genotyping and supporting epidemiological surveillance and outbreak investigation of this emerging opportunistic pathogen in neonatal settings. IMPORTANCE Clostridium butyricum has been identified in fecal samples from both asymptomatic neonates and cases of necrotizing enterocolitis (NEC). Using a large collection of strains from different origins and spatiotemporal contexts, we developed and established a cgMLST scheme for the molecular typing of C. butyricum . Our results show that most C. butyricum strains cluster independently of origin and spatiotemporal context factors. However, specific cgMLST clades of C. butyricum were found for plant and botulinum neurotoxin type E strains. Clonal strains were also identified. No specific cgMLST clade was found to be genetically associated with NEC. cgSNP showed higher discriminatory power compared to cgMLST. Importantly, cgSNP provided better discriminatory power for strain relatedness with respect to strains isolated from NEC patients.
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Le contrôle bibliographique ouvert
DOI retrouvé dans Crossref DOI retrouvé, mais le titre doit être comparé manuellement.
- Titre Crossref
- Whole-genome sequencing-based typing methods for <i>Clostridium butyricum</i> strains from clinical, animal, plant, and environmental sources
- Date Crossref
- 03/02/2026
- Éditeur
- American Society for Microbiology
- Type
- journal-article
Ce recoupement confirme des métadonnées liées au DOI. Il ne confirme ni la méthode ni les conclusions de l’étude, et il ne compte pas comme une seconde source scientifique indépendante.
Où se fait cette recherche
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Inserm pays non établi dans la noticeOrganisme public
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Université Paris Cité pays non établi dans la noticeUniversité ou école supérieure
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Méditerranée Infection Foundation pays non établi dans la noticeInstitution
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Assistance Publique Hôpitaux de Marseille pays non établi dans la noticeÉtablissement de santé
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Sorbonne Paris Cité pays non établi dans la noticeInstitution
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Institut de Recherche Pour le Développement Burkina Faso (code pays fourni par la source)Organisme public
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Physiopathologie et pharmacotoxicologie placentaire humaine : Microbiote pré & post natal pays non établi dans la noticeStructure de recherche
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Institut Pasteur pays non établi dans la noticeOrganisation à but non lucratif
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Laboratoire National de Référence Maroc (code pays fourni par la source)Structure de recherche
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IHU Méditerranée Infection pays non établi dans la noticeInstitution
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Aix-Marseille Université Microbes Evolution Phylogeny and Infection (MEPHI) pays non établi dans la noticeUniversité ou école supérieure
Inserm, Université Paris Cité et Méditerranée Infection Foundation, avec 8 autres affiliations. Pays d’affiliation : Burkina Faso, Maroc.
Une affiliation ne permet pas de déduire la nationalité d’un auteur.