Fecal Microbiota of Toxigenic Clostridioides difficile-Associated Diarrhea

Abstract

Clostridioides difficile infection (CDI) is currently one of the most important causes of infectious diarrhea in developed countries and the main cause in healthcare settings. Here, we characterized the gut microbiota from the feces of 57 patients with diarrhea from nosocomial and community-acquired CDI. We performed an ecological analysis by high-throughput sequencing of the V3-V4 region of 16S rRNA amplicons and evaluated the association of the various ecological profiles with CDI risk factors. Among all samples Bacteroidaceae 31.01%, Enterobacteriaceae 9.82%, Lachnospiraceae 9.33%, Tannerellaceae 6,16%, and Ruminococcaceae 5.64%, were the most abundant families. A reduced abundance of Bacteroides was associated with a poor CDI prognosis, with severe diarrhea and a high incidence of recurrence. This reduction was associated with a weakened host immune system and previous aggressive antibiotherapy. Peptostreptococcaceae family was 1.56% overall and within the family the only identified member was the genus Clostridioides, positively correlated with the presence of Akkermansia that may be predictive of the presence of a CDI. Finally, a relevant aspect that must be considered in clinical practice is the misdiagnosis of CDI, as patients with a stool sample that tests positive for C. difficile are usually diagnosed with CDI and subsequently treated as such. However, co-infection with other pathogenic agents often plays an important role in the development of diarrhea, and must be considered when prescribing antibiotic treatment.

Keywords: 16S rRNA; CDI; Clostridioides difficile; bacterial; diarrhea; microbiota.

FIGURE 1

Metadata of the 57 patients studied. (A) Distribution of the patients according to age (y, years and , average age), sex (female and male), and community-, healthcare in a nursing home-, and nosocomial-acquired diarrhea. (B) Distribution of the patients according to the number of previous hospital admissions (1, 2, or more than 3 previous hospital admissions). The inner ring indicates a community origin (there were two patients with no previous admission not shown in the figure) and the outer ring, nosocomial or healthcare-in-a-nursing home origin of the infection.

FIGURE 2

Principal Coordinates Analysis (PCoA), representing the total microbiota of the samples plotted according to the origin of the infection: blue, community; red, nosocomial; and green, nursing home. Two clusters A (full black) and B (dot lane) were observed. Different samples from the same individual are indicated by the shapes MS0217, MS1502, and MS1193; MS0209, MS0222, and MS0214; MS0155 and MS0147; MS01508 and MS1506; MS0144 and MS0150; and MS1746 and MS1496.

FIGURE 3

Relative abundance (%) of the 15 most abundant families found in the samples plotted in the A or B cluster of the PCoA: (A,B), respectively.

FIGURE 4

Abundance of taxa within the order Clostridiales.

FIGURE 5

Heat map showing the distribution and relative abundance of members of the Peptostreptococcaceae family grouped (in rows) within the different samples (in columns). C. difficile was absent from nine samples: asterisks indicate the negative samples of cluster A and black dots the negative samples of cluster B.

FIGURE 6

Correlation matrix of the relative abundance of genera above 1% abundance (significance level = 0.05). The average percentage of each genus among all samples is shown to the left of the name of the genus. A positive correlation was observed between the Akkermansia and Clostridioides genera (C. difficile).