Clostridioides difficile concentration-dependant alterations in gut microbiota of asymptomatic infants

Mahnič, Aleksander (author), Lozar Krivec, Jana (author), Paro Panjan, Darja (author), Valcl, Andreja (author), Obermajer, Tanja (author), Bogovič Matijašić, Bojana (author), Benedik, Evgen (author), Bratina, Petra (author), Rupnik, Maja (author)

Background: Asymptomatic carriage of Clostridioides difficile is highly prevalent in early infancy, affecting approximately 40% of infants. This phenomenon offers a unique opportunity to study its impact on the gut microbiota without the confounding effects of disease. In this study, we analysed C. difficile-associated gut microbiome alterations in 76 asymptomatic infants, one year after receiving antibiotic treatment during early infancy. The presence and concentration of C. difficile were assessed in relation to gut microbiota structure and an extensive set of metadata. Results: Bacterial gut community structure was characterized using 16 S rRNA amplicon sequencing, while C. difficile concentration and the presence of the tcdB gene were quantified via digital PCR. C. difficile was detected in 36.8% of infants, with 10.5% testing positive for the tcdB gene. Significant alterations in gut microbiota were observed in relation to C. difficile concentration. Specifically, higher C. difficile loads were associated with reduced microbial diversity, greater deviations from average community structure, and co-occurrence with the genus Escherichia. Conversely, C. difficile colonization alone or the presence of the tcdB gene did not result in significant gut microbiota alterations. Additionally, no host-specific factors were significantly linked to C. difficile prevalence or concentration. Conclusions: Asymptomatic carriage of C. difficile in neonates is not associated with significant gut microbiota alterations unless pathogen concentration is considered. Our findings suggest that elevated C. difficile proliferation occurs in dysbiotic infant gut microbiota, characterized by reduced alpha diversity and an increase in Escherichia.

• Language: English
• Keywords: gut microbiota, clostridioides difficile, infant, asymptomatic, aysbiosis
• Work type: Article
• Typology: 1.01 - Original Scientific Article
• Organization: MF - Faculty of Medicine; BF - Biotechnical Faculty
• Publication status: Published
• Publication version: Version of Record
• Year: 2025
• Number of pages: 6 str.
• Numbering: Vol. 7, art. 17
• PID: 20.500.12556/RUL-176648
• UDC: 579.852.13:616.3
• ISSN on article: 1757-4749
• DOI: 10.1186/s13099-025-00687-3
• COBISS.SI-ID: 236974851
• Publication date in RUL: 23.12.2025

Record is a part of a journal

• Title: Gut pathogens
• Shortened title: Gut pathog.
• Publisher: BioMed Central
• ISSN: 1757-4749
• COBISS.SI-ID: 517534489

Licences

• License: CC BY-NC 4.0, Creative Commons Attribution-NonCommercial 4.0 International
• Link: http://creativecommons.org/licenses/by-nc/4.0/
• Description: A creative commons license that bans commercial use, but the users don’t have to license their derivative works on the same terms.

Secondary language

• Language: Slovenian
• Keywords: clostridium difficile, črevesna mikrobiota, disbioza