The role of gut microbiota in Clostridium difficile infection

Samarkos, Michael; Mastrogianni, Elpida; Kampouropoulou, Olga

doi:10.1016/j.ejim.2018.02.006

Cited by 60 publications

(45 citation statements)

References 65 publications

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“…C. difficile is an opportunistic bacterium that can infect the gut, result ing in the production of toxins that can cause diarrhoea, dehydration, sepsis and death. C. difficile infection occurs only in the setting of a microbiome that is altered by factors such as exposure to broad spectrum anti biotics or recent gastrointestinal surgery 61 . The importance of the microbiome in C. difficile infection is underscored by the 80-90% effectiveness of faecal stool transplan tation in treating and potentially curing the disease 62,63 .…”

Section: Clinical Microbiome Analysesmentioning

confidence: 99%

Clinical metagenomics

2019

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| Clinical metagenomic next-generation sequencing (mNGS), the comprehensive analysis of microbial and host genetic material (DNA and RNA) in samples from patients, is rapidly moving from research to clinical laboratories. This emerging approach is changing how physicians diagnose and treat infectious disease, with applications spanning a wide range of areas, including antimicrobial resistance, the microbiome, human host gene expression (transcriptomics) and oncology. Here, we focus on the challenges of implementing mNGS in the clinical laboratory and address potential solutions for maximizing its impact on patient care and public health.

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Section: Clinical Microbiome Analysesmentioning

confidence: 99%

Clinical metagenomics

2019

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“…However, it is important to consider the influence of symbiotic bacteria on host defenses. For example, Clostridium difficile infection is associated with shifts in symbiotic bacteria diversity (Samarkos et al, 2018) and a decrease in the abundance of Firmicutes and Bacteroidetes alongside an expansion of Enterobacteriaceae (Peterfreund et al, 2012).…”

Section: Introductionmentioning

confidence: 99%

Vibrio cholerae-Symbiont Interactions Inhibit Intestinal Repair in Drosophila

et al. 2020

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“…Under normal conditions, the healthy intestinal microbiota exists in homeostasis with the host, whereby the population growth (and toxigenicity) of LCCM including pathobionts remains controlled. However, in a state of dysbiosis (i.e., intestinal microbial imbalance), these LCCM can multiply and cause serious problems in clinical settings (Gorkiewicz, 2009 ; Litvak et al, 2017 ; Samarkos et al, 2018 ). Therefore, to comprehensively assess the intestinal microbiota—a diverse microbial ecosystem with a wide dynamic range—it is essential that we precisely understand not only the relative abundance, but also the microbial cell counts of the predominant bacterial groups and the LCCM—including facultative anaerobes and indigenous pathobionts.…”

Section: Introductionmentioning

confidence: 99%

Counting the Countless: Bacterial Quantification by Targeting rRNA Molecules to Explore the Human Gut Microbiota in Health and Disease

Tsuji

Matsuda²,

Nomoto

2018

Front. Microbiol.

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Over the past decade, the advent of next-generation-sequencing tools has revolutionized our approach to understanding the human gut microbiota. However, numerical data on the gut bacterial groups—particularly low-cell-count microbiota, such as indigenous pathobionts, that are otherwise important components of the microbiota—are relatively limited and disparate. As a result, the comprehensive quantitative structure of the human gut microbiota still needs to be fully defined and standardized. With the aim of filling this knowledge gap, we have established a highly sensitive quantitative analytical system that is based on reverse transcription—quantitative PCR and targets microbial rRNA molecules. The system has already been validated in the precise, sensitive, and absolute quantification of more than 70 target bacterial groups belonging to various human gut bacterial clades, including predominant obligate and facultative anaerobes. The system demonstrates sensitivity several hundred times greater than that of other rRNA-gene-targeting methods. It is thus an efficient and valuable tool for exhaustive analysis of gut microbiota over a wide dynamic range. Using this system, we have to date quantified the gut microbiota of about 2,000 healthy Japanese subjects ranging in age from 1 day to over 80 years. By integrating and analyzing this large database, we came across several novel and interesting features of the gut microbiota, which we discuss here. For instance, we demonstrated for the first time that the fecal counts of not only the predominant bacterial groups but also those at lower cell counts conform to a logarithmically normal distribution. In addition, we revealed several interesting quantitative differences in the gut microbiota of people from different age groups and countries and with different diseases. Because of its high analytic sensitivity, the system has also been applied successfully to other body niches, such as in characterizing the vaginal microbiota, detecting septicemia, and monitoring bacterial translocation. Here, we present a quantitative perspective on the human gut microbiota and review some of the novel microbial insights revealed by employing this promising analytical approach.

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The role of gut microbiota in Clostridium difficile infection

Cited by 60 publications

References 65 publications

Clinical metagenomics

Clinical metagenomics

Vibrio cholerae-Symbiont Interactions Inhibit Intestinal Repair in Drosophila

Counting the Countless: Bacterial Quantification by Targeting rRNA Molecules to Explore the Human Gut Microbiota in Health and Disease

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