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Characterization of Gut Microbiota in Hospitalized Patients with Clostridioides difficile Infection


Clostridioides difficile infection (CDI) is one of the most common causes of nosocomial diarrhea in developed countries and the main cause in healthcare settings. This case–control study was designed to evaluate the composition of the gut microbiota dominant bacterial groups in patients with CDI compared to the healthy control subjects. A total of 100 adult subjects involving 50 inpatients with CDI and 50 healthy persons were enrolled in the study. C. difficile isolates were characterized according to the anaerobic culture and presence of toxin genes with multiplex PCR. An ecological analysis was performed real-time quantitative PCR for bacterial elements. The abundances of Enterococcus spp., Lactobacillus spp., Escherichia coli, C. difficile, and Akkermansia muciniphila were higher in group CDI compared with group HC (P < 0.05). The abundances of Bacteroides spp., Bifidobacterium spp., and Faecalibacterium prausnitzii were lower in group CDI than in group HC (P < 0.05). No significant difference was observed in the copy number of Prevotella genus between the CDI and HC subjects (P-value = 0.087). We observed that economic status and income levels were reduced at patients with CDI, however, there was no significant difference between CDI and HC group results and other variables, such as age, BMI, and educational level. These findings showed a reduction in butyrate-producing bacteria and increase in lactic acid-producing bacteria was seen in CDI status. Overrepresentation of Akkermansia may be a predictive marker for the development of nosocomial diarrhea can result in a worse CDI prognosis.

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The authors would like to express their gratitude to Dr. Parisa Shoaei and Dr. Bahram Bagherpour for their special cooperation in our study. We are thankful to the staff of Isfahan University Training Hospitals and Infectious Disease Research center, Isfahan, University of medical sciences, Isfahan, Iran for their great help in performing tests.


A part of this article (PCR analysis and sample collection) is performed from research (Grant No. 291235) that performed in the Infectious Disease Research center, Isfahan University of medical sciences, Isfahan, Iran.

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Correspondence to Seyed Davar Siadat.

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The Ethics Committee on Clinical Investigation of the Isfahan University of Medical Sciences, Isfahan, Iran, approved this presented research.

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Vakili, B., Fateh, A., Asadzadeh Aghdaei, H. et al. Characterization of Gut Microbiota in Hospitalized Patients with Clostridioides difficile Infection. Curr Microbiol 77, 1673–1680 (2020).

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