3.3. The use of PCA in MALDI-TOF MS for chicken feces E.
coli
A general PCA analysis (I. Phyloproteomic study) of 122 CFEC isolates
was performed, and a dendrogram profile and a 2D scattering profile was
formed (Figure 1). Also, the variance values were automatically
calculated and shown on the dendrogram in Figure 1A. With these three
analyses (dendrogram, scattering profile, and variance), rough
preliminary information was obtained according to the cluster formation
of the most distant and the farthest and closest ones among 35 isolates
among 122 CFECs and the scattering of these isolates. These two profiles
and variance values were evaluated together. As seen in Figures 1A and
1B, seven CFEC isolates that are far from the main cluster as they have
some differences are separated from other CFECs in the dendrogram
profile and settled into separate clusters. For example, CFEC-38
(CFEC-ESBL-38), CFEC-90 (CFEC-ESBL-90), and CFEC-19 isolates with the
highest variance (PC1) of 31% in this analysis were placed on the far
right in a separate cluster. Also, three E.coli CFEC-108,
CFEC-69, and CFEC-35 are separated by a separate line although they
appear to be part of the larger cluster by the second variance value
(PC2: 14%) (Fig. 1A and B). Consistent with the results in the
dendrogram, the scattering profile in Figure 1C also shows that these
seven isolates scatter far from the large cluster.