Molecular Characterization of Multidrug-Resistant Escherichia coli Isolated from Beef and Chicken Meat Products in Samsun, Türkiye
Abstract
1. Introduction
2. Results
2.1. Prevalence and Virulence Gene Profiles of E. coli Isolates
2.2. Antimicrobial Resistance and Multidrug Resistance Profiles of E. coli Isolates




3. Discussion
3.1. E. coli Prevalence in Red Meat and Poultry
3.2. Virulence Gene Profiles of E. coli Isolates
3.3. Antimicrobial Resistance
4. Materials and Methods
4.1. Sample Collection
4.2. Isolation and Characterization of E. coli
4.3. DNA Extraction
4.4. PCR Confirmation of E. coli Isolates Using the uspA Gene
4.5. Detection of Virulence Genes in E. coli Isolates by PCR
4.6. Agarose Gel Electrophoresis
4.7. Antimicrobial Susceptibility Testing
4.8. Multidrug Resistance (MDR) and Multiple Antibiotic Resistance (MAR) Index
4.9. Statistical Analysis
5. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
Abbreviations
| AMR | Antimicrobial Resistance |
| ATCC | American Type Culture Collection |
| CFU | Colony-Forming Unit |
| CLSI | Clinical and Laboratory Standards Institute |
| EHEC | Enterohemorrhagic Escherichia coli |
| EMB | Eosin Methylene Blue Agar |
| HUS | Hemolytic Uremic Syndrome |
| MDR | Multidrug-Resistant |
| MAR | Multiple Antibiotic Resistance |
| MHA | Mueller–Hinton Agar |
| MHB | Mueller–Hinton Broth |
| STEC | Shiga Toxin-Producing Escherichia coli |
| TSA | Tryptic Soy Agar |
| TSB | Tryptic Soy Broth |
| VRBA | Violet Red Bile Agar |
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| Type of Sample | No. of Samples Examined (n) | Positive Sample n (%) | No. of E. coli (+) Isolates |
|---|---|---|---|
| Beef meat products | |||
| Diced beef | 20 | 3 (15%) | 11 |
| Minced beef | 20 | 11 (55%) | 21 |
| Meatball | 20 | 8 (40%) | 20 |
| Hamburger | 20 | 13 (65%) | 34 |
| Sausage | 20 | 3 (15%) | 7 |
| Total beef | 100 | 38 (38%) | 93 |
| Chicken meat products | |||
| Breast | 20 | 15 (75%) | 30 |
| Drumstick | 20 | 13 (65%) | 33 |
| Wing | 20 | 11 (55%) | 26 |
| Sausage | 20 | 3 (15%) | 3 |
| Burger | 20 | ND | ND |
| Total chicken | 100 | 42 (42%) | 92 |
| Overall total | 200 | 80 (40%) | 185 |
| Type of Sample | No. of E. coli uspA (+) Isolates | stx1 n (%) | stx2 n (%) | eae n (%) | hlyA n (%) |
|---|---|---|---|---|---|
| Beef meat products | |||||
| Diced beef | 11 | 0 (0.0%) | 3 (27.3%) | 3 (27.3%) | 1 (9.1%) |
| Minced beef | 21 | 5 (23.8%) | 10 (47.6%) | 7 (33.3%) | 6 (28.6%) |
| Meatball | 20 | 1 (5.0%) | 15 (75.0%) | 7 (35.0%) | 6 (30.0%) |
| Hamburger | 34 | 2 (5.9%) | 12 (35.3%) | 14 (41.2%) | 1 (2.9%) |
| Sausage | 7 | 1 (14.3%) | 7 (100.0%) | 0 (0.0%) | 6 (85.7%) |
| Total beef | 93 | 9 (9.7%) | 47 (50.5%) | 31 (33.3%) | 20 (21.5%) |
| Chicken meat products | |||||
| Breast | 30 | 0 (0.0%) | 16 (53.3%) | 14 (46.7%) | 1 (3.3%) |
| Drumstick | 33 | 1 (3.0%) | 16 (48.5%) | 12 (36.4%) | 1 (3.0%) |
| Wing | 26 | 2 (7.7%) | 14 (53.8%) | 9 (34.6%) | 2 (7.7%) |
| Sausage | 3 | 0 (0.0%) | 2 (66.7%) | 3 (100.0%) | 0 (0.0%) |
| Burger | ND | ND | ND | ND | ND |
| Total chicken | 92 | 3 (3.3%) | 48 (52.2%) | 38 (41.3%) | 4 (4.3%) |
| Overall total | 185 | 12 (6.5%) | 95 (51.4%) | 69 (37.3%) | 24 (13.0%) |
| Virulence Gene Combination | Beef Meat Products n (%) (n = 93) | Chicken Meat Products n (%) (n = 92) | Total Sample n (%) (n = 185) |
|---|---|---|---|
| stx2 + eae | 24 (25.8%) | 19 (20.7%) | 43 (23.2%) |
| stx2 + eae + hlyA | 4 (4.3%) | 0 (0%) | 4 (2.2%) |
| stx2 + hlyA | 15 (16.1%) | 3 (3.3%) | 18 (9.7%) |
| stx1 + stx2 | 8 (8.6%) | 2 (2.2%) | 10 (5.4%) |
| stx1 + stx2 + eae + hlyA | 2 (2.1%) | 0 (0%) | 2 (1.1%) |
| stx1 + stx2 + eae | 4 (4.3%) | 1 (1.1%) | 5 (2.7%) |
| eae + hlyA | 4 (4.3%) | 1 (1.1%) | 5 (2.7%) |
| Virulence Gene | Beef Meat Products | Chicken Meat Products | Total | |||
|---|---|---|---|---|---|---|
| MDR (+) | MDR (−) | MDR (+) | MDR (−) | MDR (+) | MDR (−) | |
| stx1 (n = 12) | 5 (55.6%) | 4 (44.4%) | 2 (66.7%) | 1 (33.3%) | 7 (58.3%) | 5 (41.7%) |
| stx2 (n = 95) | 22 (46.8%) | 25 (53.2%) | 45 (93.8%) | 3 (6.3%) | 67 (70.5%) | 28 (29.5%) |
| eae (n = 69) | 12 (38.7%) | 19 (61.3%) | 35 (92.1%) | 3 (7.9%) | 47 (68.1%) | 22 (31.9%) |
| hlyA (n = 24) | 10 (50.0%) | 10 (50.0%) | 4 (100.0%) | 0 (0.0%) | 14 (58.3%) | 10 (41.7%) |
| No. (%) of E. coli Isolates | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| Antibiotics | Beef Samples (n = 93) | Chicken Samples (n = 92) | Total Samples (n = 185) | |||||||
| (Disk Content) | R | I | S | R | I | S | R | I | S | p-Value |
| AK (30 µg) | 11 (11.8%) | 1 (1.1%) | 81 (87.1%) | 3 (3.3%) | 0 (0.0%) | 89 (96.7%) | 14 (7.6%) | 1 (0.5%) | 170 (91.9%) | 0.051 |
| AM (10 µg) | 28 (30.1%) | 10 (10.8%) | 55 (59.1%) | 80 (87.0%) | 4 (4.3%) | 8 (8.7%) | 108 (58.4%) | 14 (7.6%) | 63 (34.1%) | <0.001 |
| AMC (20 + 10 μg) | 3 (3.2%) | 10 (10.8%) | 80 (86.0%) | 6 (6.5%) | 18 (19.6%) | 68 (73.9%) | 9 (4.9%) | 28 (15.1%) | 148 (80.0%) | 0.119 |
| AZM (15 µg) | 2 (2.2%) | 12 (12.9%) | 79 (84.9%) | 23 (25.0%) | 6 (6.5%) | 63 (68.5%) | 25 (13.5%) | 18 (9.7%) | 142 (76.8%) | <0.001 |
| CAZ (30 µg) | 10 (10.8%) | 8 (8.6%) | 75 (80.6%) | 9 (9.8%) | 24 (26.1%) | 59 (64.1%) | 19 (10.3%) | 32 (17.3%) | 134 (72.4%) | 0.007 |
| FOX (30 µg) | 16 (17.2%) | 2 (2.2%) | 75 (80.6%) | 5 (5.4%) | 6 (6.5%) | 81 (88.0%) | 21 (11.4%) | 8 (4.3%) | 156 (84.3%) | 0.018 |
| CTX (30 µg) | 15 (16.1%) | 2 (2.2%) | 76 (81.7%) | 46 (50.0%) | 6 (6.5%) | 40 (43.4%) | 61 (33.0%) | 8 (4.3%) | 116 (62.7%) | <0.001 |
| CIP (5 µg) | 14 (15.1%) | 23 (24.7%) | 56 (60.2%) | 49 (53.3%) | 34 (37.0%) | 9 (9.8%) | 63 (34.1%) | 57 (30.8%) | 65 (35.1%) | <0.001 |
| C (30 µg) | 22 (23.7%) | 3 (3.2%) | 68 (73.1%) | 52 (56.5%) | 16 (17.4%) | 24 (26.1%) | 74 (40.0%) | 19 (10.3%) | 92 (49.7%) | <0.001 |
| CN (10 µg) | 12 (12.9%) | 0 (0.0%) | 81 (87.1%) | 32 (34.8%) | 4 (4.3%) | 56 (60.9%) | 44 (23.8%) | 4 (2.2%) | 137 (74.1%) | <0.001 |
| IPM (10 µg) | 1 (1.1%) | 2 (2.2%) | 90 (96.8%) | 3 (3.3%) | 2 (2.2%) | 87 (94.6%) | 4 (2.2%) | 4 (2.2%) | 177 (95.7%) | 0.593 |
| NA (30 µg) | 17 (18.3%) | 0 (0.0%) | 76 (81.7%) | 57 (62.0%) | 19 (20.7%) | 16 (17.4%) | 74 (40.0%) | 19 (10.3%) | 92 (49.7%) | <0.001 |
| F (300 µg) | 13 (14.0%) | 5 (5.4%) | 75 (80.6%) | 30 (32.6%) | 8 (8.7%) | 54 (58.7%) | 43 (23.2%) | 13 (7.0%) | 129 (69.7%) | 0.005 |
| TE (30 µg) | 47 (50.5%) | 0 (0.0%) | 46 (49.5%) | 82 (89.1%) | 2 (2.2%) | 10 (10.9%) | 129 (69.7%) | 2 (1.1%) | 56 (30.3%) | <0.001 |
| SXT (1.25/23.75 µg) | 19 (20.4%) | 1 (1.1%) | 73 (78.5%) | 70 (76.1%) | 5 (5.4%) | 17 (18.5%) | 89 (48.1%) | 6 (3.2%) | 90 (48.6%) | <0.001 |
| S (10 µg) | 20 (21.5%) | 15 (16.1%) | 58 (62.4%) | 55 (59.8%) | 4 (4.3%) | 33 (35.9%) | 75 (40.5%) | 19 (10.3%) | 91 (49.2%) | <0.001 |
| Number of Antibiotics | Beef Isolates n (%) (n = 93) | Chicken Isolates n (%) (n = 92) | Total Isolates n (%) (n = 185) | MAR Index |
|---|---|---|---|---|
| 1 | 17 (18.3%) | 1 (1.1%) | 18 (9.7%) | 0.06 |
| 2 | 8 (8.6%) | 1 (1.1%) | 9 (4.8%) | 0.12 |
| 3 | 8 (8.6%) | 5 (5.4%) | 13 (7.0%) | 0.18 |
| 4 | 7 (7.5%) | 10 (10.9%) | 17 (9.1%) | 0.25 |
| 5 | 11 (11.8%) | 17 (18.5%) | 28 (15.1%) | 0.31 |
| 6 | 1 (1.1%) | 14 (15.2%) | 15 (8.1%) | 0.37 |
| 7 | 6 (6.5%) | 5 (5.4%) | 11 (5.9%) | 0.43 |
| 8 | 2 (2.2%) | 8 (8.7%) | 10 (5.4%) | 0.50 |
| 9 | 0 (0%) | 14 (15.2%) | 14 (7.5%) | 0.56 |
| 10 | 3 (3.2%) | 6 (6.5%) | 9 (4.8%) | 0.62 |
| 11 | 0 (0%) | 6 (6.5%) | 6 (3.2%) | 0.68 |
| 12 | 0 (0%) | 2 (2.2%) | 2 (1.1%) | 0.75 |
| ≥13 | 1 (1.1%) | 0 (0%) | 1 (0.5%) | 1.00 |
| Mean ± SD | 0.165 ± 0.19 | 0.406 ± 0.18 | 0.285 ± 0.22 |
| Primer | Primer Sequences (5′–3′) | Product Size (bp) | Annealing (°C) | Reference |
|---|---|---|---|---|
| uspA-F uspA-R | 5′-CCGATACGCTGCCAATCAGT-3′ 5′-ACGCAGACCGTAGGCCAGAT-3′ | 884 | 63 | Chen & Griffiths [40] |
| stx1-F stx1-R | 5′-AGTTAATGTGGTGGCGAAGG-3′ 5′-CACCAGACAATGTAACCGC-3′ | 347 | 57 | Fujioka et al. [41] |
| stx2-F stx2-R | 5′-TTCGGTATCCTATTCCCGG-3′ 5′-CGTCATCGTATACACAGGAG-3′ | 589 | 57 | Fujioka et al. [41] |
| eae-F eae-R | 5′-GTGGCGAATACTGGCGAGACT-3′ 5′-CCCCATTCTTTTTCACCGTCG-3′ | 890 | 55 | Gannon et al. [42] |
| hlyA-F hlyA-R | 5′-ACGATGTGGTTTATTCTGGA-3′ 5′-CTTCACGTGACCATACATAT-3′ | 165 | 55 | Fratamico et al. [43] |
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Terzi Gulel, G.; Kanat, S.; Ekizceli, E. Molecular Characterization of Multidrug-Resistant Escherichia coli Isolated from Beef and Chicken Meat Products in Samsun, Türkiye. Antibiotics 2026, 15, 668. https://doi.org/10.3390/antibiotics15070668
Terzi Gulel G, Kanat S, Ekizceli E. Molecular Characterization of Multidrug-Resistant Escherichia coli Isolated from Beef and Chicken Meat Products in Samsun, Türkiye. Antibiotics. 2026; 15(7):668. https://doi.org/10.3390/antibiotics15070668
Chicago/Turabian StyleTerzi Gulel, Goknur, Sibel Kanat, and Esra Ekizceli. 2026. "Molecular Characterization of Multidrug-Resistant Escherichia coli Isolated from Beef and Chicken Meat Products in Samsun, Türkiye" Antibiotics 15, no. 7: 668. https://doi.org/10.3390/antibiotics15070668
APA StyleTerzi Gulel, G., Kanat, S., & Ekizceli, E. (2026). Molecular Characterization of Multidrug-Resistant Escherichia coli Isolated from Beef and Chicken Meat Products in Samsun, Türkiye. Antibiotics, 15(7), 668. https://doi.org/10.3390/antibiotics15070668

