Gut microbiota composition and Clostridium difficile infection in hospitalized elderly individuals: a metagenomic study

Abstract

The gut microbiota composition of elderly hospitalized patients with Clostridium difficile infection (CDI) exposed to previous antibiotic treatment is still poorly investigated. The aim of this study was to compare the microbiota composition by means of 16S rRNA microbial profiling among three groups of hospitalized elderly patients (age ≥ 65) under standard diet including 25 CDI-positive (CDI group), 29 CDI-negative exposed to antibiotic treatment (AB+ group) and 30 CDI-negative subjects not on antibiotic treatment (AB- group). The functional properties of the gut microbiomes of CDI-positive vs CDI-negative subjects were also assessed by shotgun metagenomics. A significantly lower microbial diversity was detected in CDI samples, whose microbiomes clustered separately from CDI-negative specimens. CDI was associated with a significant under-representation of gut commensals with putative protective functionalities, including Bacteroides, Alistipes, Lachnospira and Barnesiella, and over-representation of opportunistic pathogens. These findings were confirmed by functional shotgun metagenomics analyses, including an in-depth profiling of the Peptostreptococcaceae family. In CDI-negative patients, antibiotic treatment was associated with significant depletion of few commensals like Alistipes, but not with a reduction in species richness. A better understanding of the correlations between CDI and the microbiota in high-risk elderly subjects may contribute to identify therapeutic targets for CDI.

Figure 1. Evaluation of alpha-diversity in AB−, AB+ and CDI samples.

Panel (a) shows the average rarefaction curves representing variation of the Chao1 diversity index at increasing sequencing depth of AB−, AB+ and CDI samples. Panel (b) displays the average rarefaction curves representing variation of the Shannon diversity index at increasing sequencing depth of AB−, AB+ and CDI samples. Panel (c) represents a box plot showing standard deviation of the Chao1 and Shannon indexes calculated by subsampling AB−, AB+ and CDI datasets at 41,870 sequences (representing the highest subsampling performed). Panel (d) depicts a Venn diagram illustrating the total, unique and shared number of OTUs predicted for AB−, AB+ and CDI datasets.

Figure 2. Evaluation of beta-diversity in AB−, AB+ and CDI samples.

The predicted PCoA encompassing all 84 AB−, AB+ and CDI datasets is reported through two three-dimensional images as well as two-dimensional sections. AB−, AB+ and CDI datasets and corresponding clusters are colored in orange, red and blue, respectively.

Figure 3. Impact of antibiotic treatments and CDI on the gut microbiota.

Panel a displays a heat map illustrating bacterial taxa with mean relative abundance >0.1% and showing increase >100% or decrease <−50% in CDI compared to AB− datasets. Panel b shows a heat map illustrating bacterial taxa with mean relative abundance >0.1% and exhibiting an increase >100% or decrease <50% in datasets obtained from AB+ samples as compared to those from AB− samples. Taxa falling outside the cut-offs but being of particular relevance are also reported in the heat maps. Taxa detected in at least 50% of the sample constituting AB−, AB+ and CDI groups are marked.

Figure 4. Role of CDImb in protection from gut microbiota alterations and opportunistic pathogens.

The network representation shows the impact of CDImb (blue dots) on the whole microbiome. Links between the dots represent positive (in green) or negative (in red) correlations based on Kendall tau-rank co-variance analysis. Each link acts as a spring whose attracting or repulsing force as well as line width is proportional to the positive or negative co-variance values, respectively. Taxa with purported health-promoting activities are colored in green while opportunistic pathogens are colored in red.