Figure 1. Flowchart showing the scheme of phylogroup determination proposed by Clermont et al. based on the presence and absence of chuA, yjaA, and DNA fragment TSPE4.C2.

Figure 1. Flowchart showing the scheme of phylogroup determination proposed by Clermont et al. based on the presence and absence of chuA, yjaA, and DNA fragment TSPE4.C2.

Figure 2. Pie chart showing the distribution of the bovine fecal E. coli isolates according to their isolation locations.

Figure 2. Pie chart showing the distribution of the bovine fecal E. coli isolates according to their isolation locations.

Figure 3. In vitro antibiotic-susceptibility pattern of isolates; a stacked-bar chart showing the percentage resistance and sensitivity of bovine fecal E. coli isolates towards tested antibiotics. The antibiotics used in AST profiling include (1) amoxicillin (AML, 10 µg), (2) Ampicillin (AMP, 10 µg), (3) amoxicillin-clavulanate (AMC, 20/10 µg), (4) doxycycline (DO, 30 µg), (5) tetracycline doxycycline (TE, 30 µg), (6) piperacillin-tazobactam (TZP, 100/10 µg), (7) eratapenem (ETP, 10 µg), (8) meropenem (MEM, 10 µg), (9) imipenem (IPM, 10 µg), (10) gentamicin (CN, 10 µg), (11) tobramycin (TOB, 10 µg), (12) streptomycin (S, 10 µg), (13) amikacin (AK, 30 µg), (14) ciprofloxacin (CIP, 5 µg), (15) norfloxacin (NOR, 10 µg), (16) ofloxacin (OFX, 5 µg), (17) levofloxacin (LEV, 5 µg), (18) trimethoprim-sulfamethoxazole (SXT, 25 µg), (19) cefepime (FEP, 30 µg), (20) cefoxitin (FOX, 30 µg), (21) ceftriaxone (CRO, 30 µg), (22) cefotaxime (CTX, 30 µg), (23) ceftazidime (CAZ, 30 µg), (24) nitrofurantoin (F, 300 µg), (25) chloramphenicol (C, 30 µg), (26) erythromycin (E, 15 µg), and (27) colistin sulfate.

Figure 3. In vitro antibiotic-susceptibility pattern of isolates; a stacked-bar chart showing the percentage resistance and sensitivity of bovine fecal E. coli isolates towards tested antibiotics. The antibiotics used in AST profiling include (1) amoxicillin (AML, 10 µg), (2) Ampicillin (AMP, 10 µg), (3) amoxicillin-clavulanate (AMC, 20/10 µg), (4) doxycycline (DO, 30 µg), (5) tetracycline doxycycline (TE, 30 µg), (6) piperacillin-tazobactam (TZP, 100/10 µg), (7) eratapenem (ETP, 10 µg), (8) meropenem (MEM, 10 µg), (9) imipenem (IPM, 10 µg), (10) gentamicin (CN, 10 µg), (11) tobramycin (TOB, 10 µg), (12) streptomycin (S, 10 µg), (13) amikacin (AK, 30 µg), (14) ciprofloxacin (CIP, 5 µg), (15) norfloxacin (NOR, 10 µg), (16) ofloxacin (OFX, 5 µg), (17) levofloxacin (LEV, 5 µg), (18) trimethoprim-sulfamethoxazole (SXT, 25 µg), (19) cefepime (FEP, 30 µg), (20) cefoxitin (FOX, 30 µg), (21) ceftriaxone (CRO, 30 µg), (22) cefotaxime (CTX, 30 µg), (23) ceftazidime (CAZ, 30 µg), (24) nitrofurantoin (F, 300 µg), (25) chloramphenicol (C, 30 µg), (26) erythromycin (E, 15 µg), and (27) colistin sulfate.

Figure 4. Bar chart showing the number of E. coli isolates resistant to different antibiotic classes tested. The x-axis shows the number of antibiotic classes, while y-axis shows the percentage of E. coli isolates resistant to specific number of antibiotic classes. The antibiotic classes that were used for antibiotic-susceptibility profiling include: (I) penicillin, (II) tetracycline, (III) penicillin β-lactamase inhibitor, (IV) carbapenem, (V) fluoroquinolone, (VI) aminoglycoside, (VII) cephalosporin, (VIII) nitrofuran, (IX) phenicol, (X) macrolide, (XI) Colistin, and (XII) sulfonamide.

Figure 4. Bar chart showing the number of E. coli isolates resistant to different antibiotic classes tested. The x-axis shows the number of antibiotic classes, while y-axis shows the percentage of E. coli isolates resistant to specific number of antibiotic classes. The antibiotic classes that were used for antibiotic-susceptibility profiling include: (I) penicillin, (II) tetracycline, (III) penicillin β-lactamase inhibitor, (IV) carbapenem, (V) fluoroquinolone, (VI) aminoglycoside, (VII) cephalosporin, (VIII) nitrofuran, (IX) phenicol, (X) macrolide, (XI) Colistin, and (XII) sulfonamide.

Figure 5. Phenotypic associations. (A) Scatter plot showing the MAR index of bovine fecal E. coli isolates. Dots representing each isolate’s response show the variability and distribution of data. The isolates above the red line are considered highly resistant, (B) scatter plot showing the R-Score of E. coli isolates. Dots representing each isolate’s response show the variability and distribution of data, (C) box plot showing the comparison of the MAR index of various locations from which the bovine fecal E. coli isolates were collected, and (D) box plot showing the comparison of R-Scores of various locations from which the E. coli isolates were collected.

Figure 5. Phenotypic associations. (A) Scatter plot showing the MAR index of bovine fecal E. coli isolates. Dots representing each isolate’s response show the variability and distribution of data. The isolates above the red line are considered highly resistant, (B) scatter plot showing the R-Score of E. coli isolates. Dots representing each isolate’s response show the variability and distribution of data, (C) box plot showing the comparison of the MAR index of various locations from which the bovine fecal E. coli isolates were collected, and (D) box plot showing the comparison of R-Scores of various locations from which the E. coli isolates were collected.

Figure 6. Phenotypic associations: (A) box plot showing the comparison of the MAR indexes of various phylogenetic groups, and (B) box plot showing the comparison of the R-Scores of various phylogenetic groups.

Figure 6. Phenotypic associations: (A) box plot showing the comparison of the MAR indexes of various phylogenetic groups, and (B) box plot showing the comparison of the R-Scores of various phylogenetic groups.

Figure 7. Biofilm formation assay (A) scatter plot showing the biofilm formation by bovine fecal E. coli isolates. Dots represent each isolate’s biofilm value. (B) Pie chart showing the percentage of biofilm formation by bovine fecal E. coli isolates.

Figure 7. Biofilm formation assay (A) scatter plot showing the biofilm formation by bovine fecal E. coli isolates. Dots represent each isolate’s biofilm value. (B) Pie chart showing the percentage of biofilm formation by bovine fecal E. coli isolates.

Figure 8. Phenotypic associations: (A) stacked bar chart showing the comparison of biofilm formation by E. coli strains isolated from various locations, and(B) stacked bar chart showing the comparison of biofilm formation by E. coli strains from different phylogenetic groups.

Figure 8. Phenotypic associations: (A) stacked bar chart showing the comparison of biofilm formation by E. coli strains isolated from various locations, and(B) stacked bar chart showing the comparison of biofilm formation by E. coli strains from different phylogenetic groups.

Figure 9. Scatter plot showing the growth in human urine by bovine fecal E. coli strains isolated from healthy cows. Dots represent each isolate’s optical-density value and the red line represents the standard O.D value required by the strains to be determined positive for growth in human urine; the strains at or above the red lines are positive for growth in human urine.

Figure 9. Scatter plot showing the growth in human urine by bovine fecal E. coli strains isolated from healthy cows. Dots represent each isolate’s optical-density value and the red line represents the standard O.D value required by the strains to be determined positive for growth in human urine; the strains at or above the red lines are positive for growth in human urine.

Figure 10. Motility assays by bovine fecal E. coli isolates. Dots in scatter plots represent each isolate’s motility in its respective media, and the red line represents the standard cutoff value required by the strains to be determined motile; the strains at or above the red lines are motile. (A) Scatter plot showing swimming motility by bovine fecal E. coli isolates, (B) pie chart showing the percentage of isolates that were positive and negative for swimming motility, (C) scatter plot showing swarming motility by bovine fecal E. coli isolates, (D) pie chart showing the percentage of isolates that were positive and negative for swarming motility, (E) scatter plot showing twitching motility bovine fecal E. coli isolates, and (F) pie chart showing the percentage of isolates that were positive and negative for twitching motility.

Figure 10. Motility assays by bovine fecal E. coli isolates. Dots in scatter plots represent each isolate’s motility in its respective media, and the red line represents the standard cutoff value required by the strains to be determined motile; the strains at or above the red lines are motile. (A) Scatter plot showing swimming motility by bovine fecal E. coli isolates, (B) pie chart showing the percentage of isolates that were positive and negative for swimming motility, (C) scatter plot showing swarming motility by bovine fecal E. coli isolates, (D) pie chart showing the percentage of isolates that were positive and negative for swarming motility, (E) scatter plot showing twitching motility bovine fecal E. coli isolates, and (F) pie chart showing the percentage of isolates that were positive and negative for twitching motility.

Figure 11. Pie chart showing the relative distribution of phylogenetic groups among bovine fecal E. coli isolates.

Figure 11. Pie chart showing the relative distribution of phylogenetic groups among bovine fecal E. coli isolates.

Figure 12. Bar graph showing the percentage prevalence of virulence-associated genes in bovine fecal E. coli isolates.

Figure 12. Bar graph showing the percentage prevalence of virulence-associated genes in bovine fecal E. coli isolates.

Table 1. Table representing the DEC pathotypes along with their detection marker.

Table 1. Table representing the DEC pathotypes along with their detection marker.

Sr. NoDEC PathotypeDetection Marker1Typical EPECeaeA, bfpB2Atypical EPECeaeA3EHECstx1, stx24EAECaggR5EIECinvE6ETECIt, stp, sth

Table 2. Table presenting the percentage of enzymatic activities shown by bovine fecal E. coli isolates.

Table 2. Table presenting the percentage of enzymatic activities shown by bovine fecal E. coli isolates.

Enzymatic ActivityConfirmatory TestNo. of IsolatesPercentage %ESBL8241MBL1608AmpC β-lactamase0603Carbapenamase0201