3.6. Clusters, scatters, and composite correlation index analysis of ESBL-producing E. coli
At this step, with the support of the MATLAB program, the unique spectra, which are the fingerprints of each bacterium, were compared with each other and analyzed (II. Phyloproteomic study) and the data are given separately in Figure 3. First, the dendrogram (Fig. 3A) and 2D scattering profiles (Fig. 3B) generated for 35 CFEC-ESBLs together with a total of 10 variance values are shown (Fig. 3A).
As a result of the dendrogram analysis with of isolates showing only ESBL characteristics, only CFEC-ESBL-38 (CFEC-38) took its place on a separate line on the far right (Figure 3A), and it was located farthest (yellow dot) in the 2D scattering profile. It was found that this isolate differed from 34 CFEC-ESBLs with a variance of 41%. On the other hand, the second isolate, which is separated from the large cluster (n=33) with a 15% variance value, was also CFEC-ESBL-90.
Composite for calculating the distance and proximity indices of CFEC-ESBL CCI were also calculated automatically with the MATLAB program (data not shown). In the graphic given in Figure 3C, the total value of CCI % of 34 isolates with itself, calculated for 35 CFEC-ESBL and each isolate, is on the y-axis, and each isolate itself is on the x-axis. As the closeness to the isolates within the group increases, the total %CCI value on the y-axis increases for each isolate. On the other hand, as the proximity value decreases, the total %CCI value also decreases. In this respect, when Figure 3C is examined, it is seen that the lowest total CCI percentage value belongs to CFEC-ESBL-38. Also, it was found that the total %CCI value of CFEC-ESBL-90 was lower than the other group members. It is a result that is highly compatible with dendrogram, variance, and 2D results. According to 33 isolates of CFEC-ESBL, CFEC-ESBL38 is very different and CFEC-ESBL-90 is different.
Another isolate that drew attention in 3C in the figure is CFEC-ESBL-93. It is seen that the total percent CCI value of this isolate is low. However, the variance value is 1% and is nested in the main cluster with 32 other CFEC-ESBLs in the dendrogram and scattering profile.
The CCI color matrix of all ESBL-CFEC isolates is presented in Figure 3D. In this color matrix, the dark red color represents the highest CCI% value (each isolate has 100% similarity to itself and this color is dark red), and the dark blue color corresponds to the lowest (0-1%) CCI value. If we take an overview of this, green tiles in the CCI color matrix correspond to 40% to 59%, and yellow to dark red tiles correspond to a CCI index of 60% to 100%. It indicates that the boxes from light blue to dark blue also have a CCI index from 39% to 0%.
The color matrices of two isolates with low affinity (CFEC-ESBL-38, CFEC-ESBL-90) and an isolate with the highest affinity (CFEC-ESBL-68) among 35 CFEC-ESBL are given in Figure 3E by matching their CCI% values. In this respect, it was found that the boxes corresponding to CFEC-ESBL-38 in the color matrix were mostly in blue tones and the %CCI values were low in proportion to this. In contrast, the box corresponding to CFEC-ESBL-90 appears to be light red (87% CCI). Also, the closeness of this isolate to CFEC-ESBL-41 and CFEC-ESBL-69 isolates, which are members of the large cluster, was determined to be 60% and 54%, respectively, in the dendrogram. On the other hand, it was reported to have the lowest affinity value (1%) against CFEC-ESBL-9, CFEC-ESBL-106, and CFEC-ESBL-110 isolates among other isolates (Figure 3 E). It is seen that CFEC-ESBL-38 has the lowest overall CCI % value since it has the lowest affinity values to other CFEC-ESBLs except for a few isolates.
It was found that the second different isolate, CFEC-ESBL-90, has the highest affinity (87%) against CFEC-ESBL-38 isolate. Similar to CFEC-ESBL-38, the affinity index to CFEC-ESBL-41 and CFEC-ESBL-69 isolates is 64% and 62%, respectively. Also, the affinity index values for some isolates (n=6) in the large cluster are over 50%, while the affinity indexes for 14 group members are between 30%-40%. This explains the relatively lower variance value compared to CFEC-ESBL-38 (Fig. 3 E).
As expected, the presence of mostly yellow to dark red colored boxes in the CCI color matrix of CFEC-ESBL-68, which has the highest percentage of closeness in total, draws attention. When we look at the color matrix in general, most of the CFEC-ESBL isolates that have a low variance value (≤5%) in the large cluster in the dendrogram (Figure 3A) and are very close to each other in the scattering profile (Figure 3B) have plenty of colored boxes from yellow to red on the color scale (Figure 3D).