Table 1.
Comparison of routine C. difficile negative samples (set of samples with formed stool and set with unformed stool) vs. healthy donors by logistic regression model.
Table 2.
Comparison of different sets of routine C. difficile positive samples vs. healthy donors by logistic regression model.
Table 3.
Comparisons of all routine C. difficile positive vs. all routine C. difficile negative samples by logistic regression model.
Figure 1.
Representative DHPLC profiles of faecal microbiota.
The profiles show archaeal (a), fungal (b) and bacterial (c) faecal microbiota. The faecal profiles of healthy volunteers are in the upper row and the profiles from the diarrhoeal patients colonised by Clostridium difficile 027 ribotypes are in the lower row. The selected profiles show typical chromatograms of the three studied microbial groups. The chromatograms show increasing complexities from archaeal to fungal and bacterial microbiota, respectively.
Figure 2.
Fungal DHPLC profiles of all seven sets of samples.
The samples were distributed into sets according to consistency, source (healthy/routine) and C. difficile presence. The peaks with different retention times (x - axis) represents different fungal groups.Fungal microbiota in healthy volunteers and C. difficile positive samples differs in the composition (position of the peaks) but not in diversity (number of the peaks).
Figure 3.
Bacterial DHPLC profiles of all seven sets of samples.
Bacterial microbiota in healthy individuals is composed of a large number of species, hence the peaks are numerous but the area below each peak is small. The presence of C. difficile correlates with decreased diversity reflected by a lower number of peaks which are, however, more prominent.
Figure 4.
Principal component analysis of DHPLC profiles of dominant bacterial, fungal and archaeal species.
Individual samples (represented by black dots) were clustered into sets according to C. difficile presence and type, origin and consistency (elipses) and the centre of gravity computed for each set of samples. All sets of samples show large dispersion and overlap (elipses). Figure 4a compares the samples sent for routine C.difficile testing (pat) and healthy donors (hea). Particularly the former set shows a great dispersion. Figures 4b, c and d compare different sets of samples from the patients. Figure 4b shows comparison of six different sets of routine samples; a greater shift in the centre of gravity between the formed and the diarrhoeal C. difficile negative samples (FNP/DNP), compared to the C. difficile positive samples (FOS/DOS, F027/D027). Fig 4c shows only the subset of different routine diarrheic samples. Fig 4d shows only the subset of different routine formed samples DNP - diarrhoeal/C. difficile negative samples, D27 - diarrhoeal/C. difficile ribotype 027 positive samples, DOS–diarrhoeal/C. difficile other ribotypes positive samples, FNP - formed stool/C. difficile negative samples, F27 - formed stool/C. difficile ribotype 027 positive samples, FOS - formed stool/C. difficile other ribotypes positive samples, pat - samples sent for routine C. difficile testing, hea - healthy donors).
Figure 5.
Average numbers of bacterial and fungal groups in different sets of faecal samples.
The average numbers of present bacterial and fungal groups within each sample set are presented as means with confidence bars plot. 027/F: C. difficile 027 ribotype/formed stool; 027/D: C. difficile 027 ribotype/diarrhoea; NEG/F: C. difficile negative/formed stool; NEG/D: C. difficile negative/diarrhoea; OTHER/F: C. difficile non 027 ribotype/formed stool; OTHER/D: C. difficile non 027 ribotype; HEALTHY: healthy donors.
Table 4.
Differences in microbial groups between healthy donors and routine samples as detected by the PCT model.
Table 5.
Differences in microbial groups present between different types of C. difficile colonisation as predicted by the PCT model.
Figure 6.
J48 decision tree describing the patterns of colonisation associated with presence or absence of C. difficile.
Decision tree is showing only routine sample sets. The decision tree shows combinations of microbial groups that predict the outcome regarding C. difficile colonisation. The numbers in parentheses show the total number of samples and the number of incorrectly cassified instances, respectively.