Decreased Fecal Bacterial Diversity and Altered Microbiome in Children Colonized With Clostridium difficile

Lea Ann Chen, Suchitra K. Hourigan, Zoya Grigoryan, Zhan Gao, Jose C. Clemente, Jai Ram Rideout, Sankar Chirumamilla, Shervin Rabidazeh, Shehzad Saeed, Charles O. Elson, Maria Oliva-Hemker, Martin Blaser, Cynthia L. Sears

Research output: Contribution to journalArticle

1 Citation (Scopus)

Abstract

OBJECTIVES: The gut microbiome is believed to play a role in the susceptibility to and treatment of Clostridium difficile infections (CDIs). It is, however, unknown whether the gut microbiome is also affected by asymptomatic C difficile colonization. Our study aimed to evaluate the fecal microbiome of children based on C difficile colonization, and CDI risk factors, including antibiotic use and comorbid inflammatory bowel disease (IBD). METHODS: Subjects with IBD and non-IBD controls were prospectively enrolled from pediatric clinics for a biobanking project (n = 113). A fecal sample was collected from each subject for research purposes only and was evaluated for asymptomatic toxigenic C difficile colonization. Fecal microbiome composition was determined by 16S rRNA sequencing. RESULTS: We found reduced bacterial diversity and altered microbiome composition in subjects with C difficile colonization, concurrent antibiotic use, and/or concomitant IBD (all P < 0.05). Accounting for antibiotic use and IBD status, children colonized with C difficile had significant enrichment in taxa from the genera Ruminococcus, Eggerthella, and Clostridium. Children without C difficile had increased relative abundances of Faecalibacterium and Rikenellaceae. Imputed metagenomic functions of those colonized were enriched for genes in oxidative phosphorylation and beta-lactam resistance, whereas in the subjects without C difficile, several functions in translation and metabolism were over-represented. CONCLUSIONS: In children, C difficile colonization, or factors that predispose to colonization such as antibiotic use and IBD status were associated with decreased gut bacterial diversity and altered microbiome composition. Averting such microbiome alterations may be a method to prevent or treat CDI.

Original languageEnglish (US)
Pages (from-to)502-508
Number of pages7
JournalJournal of pediatric gastroenterology and nutrition
Volume68
Issue number4
DOIs
StatePublished - Apr 1 2019
Externally publishedYes

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Clostridium difficile
Microbiota
Inflammatory Bowel Diseases
Clostridium Infections
Anti-Bacterial Agents
Ruminococcus
beta-Lactam Resistance
Metagenomics
Clostridium
Oxidative Phosphorylation
Pediatrics
Research
Genes

All Science Journal Classification (ASJC) codes

  • Pediatrics, Perinatology, and Child Health
  • Gastroenterology

Cite this

Chen, Lea Ann ; Hourigan, Suchitra K. ; Grigoryan, Zoya ; Gao, Zhan ; Clemente, Jose C. ; Rideout, Jai Ram ; Chirumamilla, Sankar ; Rabidazeh, Shervin ; Saeed, Shehzad ; Elson, Charles O. ; Oliva-Hemker, Maria ; Blaser, Martin ; Sears, Cynthia L. / Decreased Fecal Bacterial Diversity and Altered Microbiome in Children Colonized With Clostridium difficile. In: Journal of pediatric gastroenterology and nutrition. 2019 ; Vol. 68, No. 4. pp. 502-508.
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abstract = "OBJECTIVES: The gut microbiome is believed to play a role in the susceptibility to and treatment of Clostridium difficile infections (CDIs). It is, however, unknown whether the gut microbiome is also affected by asymptomatic C difficile colonization. Our study aimed to evaluate the fecal microbiome of children based on C difficile colonization, and CDI risk factors, including antibiotic use and comorbid inflammatory bowel disease (IBD). METHODS: Subjects with IBD and non-IBD controls were prospectively enrolled from pediatric clinics for a biobanking project (n = 113). A fecal sample was collected from each subject for research purposes only and was evaluated for asymptomatic toxigenic C difficile colonization. Fecal microbiome composition was determined by 16S rRNA sequencing. RESULTS: We found reduced bacterial diversity and altered microbiome composition in subjects with C difficile colonization, concurrent antibiotic use, and/or concomitant IBD (all P < 0.05). Accounting for antibiotic use and IBD status, children colonized with C difficile had significant enrichment in taxa from the genera Ruminococcus, Eggerthella, and Clostridium. Children without C difficile had increased relative abundances of Faecalibacterium and Rikenellaceae. Imputed metagenomic functions of those colonized were enriched for genes in oxidative phosphorylation and beta-lactam resistance, whereas in the subjects without C difficile, several functions in translation and metabolism were over-represented. CONCLUSIONS: In children, C difficile colonization, or factors that predispose to colonization such as antibiotic use and IBD status were associated with decreased gut bacterial diversity and altered microbiome composition. Averting such microbiome alterations may be a method to prevent or treat CDI.",
author = "Chen, {Lea Ann} and Hourigan, {Suchitra K.} and Zoya Grigoryan and Zhan Gao and Clemente, {Jose C.} and Rideout, {Jai Ram} and Sankar Chirumamilla and Shervin Rabidazeh and Shehzad Saeed and Elson, {Charles O.} and Maria Oliva-Hemker and Martin Blaser and Sears, {Cynthia L.}",
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Chen, LA, Hourigan, SK, Grigoryan, Z, Gao, Z, Clemente, JC, Rideout, JR, Chirumamilla, S, Rabidazeh, S, Saeed, S, Elson, CO, Oliva-Hemker, M, Blaser, M & Sears, CL 2019, 'Decreased Fecal Bacterial Diversity and Altered Microbiome in Children Colonized With Clostridium difficile', Journal of pediatric gastroenterology and nutrition, vol. 68, no. 4, pp. 502-508. https://doi.org/10.1097/MPG.0000000000002210

Decreased Fecal Bacterial Diversity and Altered Microbiome in Children Colonized With Clostridium difficile. / Chen, Lea Ann; Hourigan, Suchitra K.; Grigoryan, Zoya; Gao, Zhan; Clemente, Jose C.; Rideout, Jai Ram; Chirumamilla, Sankar; Rabidazeh, Shervin; Saeed, Shehzad; Elson, Charles O.; Oliva-Hemker, Maria; Blaser, Martin; Sears, Cynthia L.

In: Journal of pediatric gastroenterology and nutrition, Vol. 68, No. 4, 01.04.2019, p. 502-508.

Research output: Contribution to journalArticle

TY - JOUR

T1 - Decreased Fecal Bacterial Diversity and Altered Microbiome in Children Colonized With Clostridium difficile

AU - Chen, Lea Ann

AU - Hourigan, Suchitra K.

AU - Grigoryan, Zoya

AU - Gao, Zhan

AU - Clemente, Jose C.

AU - Rideout, Jai Ram

AU - Chirumamilla, Sankar

AU - Rabidazeh, Shervin

AU - Saeed, Shehzad

AU - Elson, Charles O.

AU - Oliva-Hemker, Maria

AU - Blaser, Martin

AU - Sears, Cynthia L.

PY - 2019/4/1

Y1 - 2019/4/1

N2 - OBJECTIVES: The gut microbiome is believed to play a role in the susceptibility to and treatment of Clostridium difficile infections (CDIs). It is, however, unknown whether the gut microbiome is also affected by asymptomatic C difficile colonization. Our study aimed to evaluate the fecal microbiome of children based on C difficile colonization, and CDI risk factors, including antibiotic use and comorbid inflammatory bowel disease (IBD). METHODS: Subjects with IBD and non-IBD controls were prospectively enrolled from pediatric clinics for a biobanking project (n = 113). A fecal sample was collected from each subject for research purposes only and was evaluated for asymptomatic toxigenic C difficile colonization. Fecal microbiome composition was determined by 16S rRNA sequencing. RESULTS: We found reduced bacterial diversity and altered microbiome composition in subjects with C difficile colonization, concurrent antibiotic use, and/or concomitant IBD (all P < 0.05). Accounting for antibiotic use and IBD status, children colonized with C difficile had significant enrichment in taxa from the genera Ruminococcus, Eggerthella, and Clostridium. Children without C difficile had increased relative abundances of Faecalibacterium and Rikenellaceae. Imputed metagenomic functions of those colonized were enriched for genes in oxidative phosphorylation and beta-lactam resistance, whereas in the subjects without C difficile, several functions in translation and metabolism were over-represented. CONCLUSIONS: In children, C difficile colonization, or factors that predispose to colonization such as antibiotic use and IBD status were associated with decreased gut bacterial diversity and altered microbiome composition. Averting such microbiome alterations may be a method to prevent or treat CDI.

AB - OBJECTIVES: The gut microbiome is believed to play a role in the susceptibility to and treatment of Clostridium difficile infections (CDIs). It is, however, unknown whether the gut microbiome is also affected by asymptomatic C difficile colonization. Our study aimed to evaluate the fecal microbiome of children based on C difficile colonization, and CDI risk factors, including antibiotic use and comorbid inflammatory bowel disease (IBD). METHODS: Subjects with IBD and non-IBD controls were prospectively enrolled from pediatric clinics for a biobanking project (n = 113). A fecal sample was collected from each subject for research purposes only and was evaluated for asymptomatic toxigenic C difficile colonization. Fecal microbiome composition was determined by 16S rRNA sequencing. RESULTS: We found reduced bacterial diversity and altered microbiome composition in subjects with C difficile colonization, concurrent antibiotic use, and/or concomitant IBD (all P < 0.05). Accounting for antibiotic use and IBD status, children colonized with C difficile had significant enrichment in taxa from the genera Ruminococcus, Eggerthella, and Clostridium. Children without C difficile had increased relative abundances of Faecalibacterium and Rikenellaceae. Imputed metagenomic functions of those colonized were enriched for genes in oxidative phosphorylation and beta-lactam resistance, whereas in the subjects without C difficile, several functions in translation and metabolism were over-represented. CONCLUSIONS: In children, C difficile colonization, or factors that predispose to colonization such as antibiotic use and IBD status were associated with decreased gut bacterial diversity and altered microbiome composition. Averting such microbiome alterations may be a method to prevent or treat CDI.

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