Table 2.
Antimicrobial resistance genes detected in ESBL E. coli isolates from livestock and in-contact humans in Southeast Nigeria.
| Antimicrobial class | Antimicrobial resistance gene | Overall number of isolates harbouring gene (N = 157) | Distribution of AMR genes among species | |||||
|---|---|---|---|---|---|---|---|---|
| Human (n = 18) | Cattle (n = 27) | Chicken (n = 23) | Goat (n = 29) | Pig (n = 28) | Sheep (n = 30) | |||
| Aminoglycoside | strB | 104 (66.2)* | 12 (66.7) | 22 (81.5) ** | 10 (43.5) | 18 (62.1) | 21 (75.0) | 21 (70.0) |
| strA | 97 (61.8) | 11 (61.1) | 22 (81.5) | 8 (34.8) | 16 (55.2) | 20 (71.4) | 20 (66.7) | |
| aac3-IId | 27 (17.2) | 3(16.7) | 2 (7.4) | 13 (56.5) | 3 (10.3) | 4 (14.3) | 2 (6.7) | |
| aac6-Ib-cr | 18 (11.5) | 5 (27.8) | 1 (3.7) | 2 (8.7) | 2 (6.9) | 4 (14.3) | 4 (13.3) | |
| aadA5 | 16 (10.2) | 5 (27.8) | 0 | 3 (13.0) | 2 (6.9) | 4 (14.3) | 2 (6.7) | |
| aadA2 | 13 (8.3) | 1 (5.6) | 3 (11.1) | 3 (13.0) | 5 (17.2) | 0 | 1 (3.3) | |
| ant3-Ia | 12 (7.6) | 2 (11.1) | 2 (7.4) | 3 (13.0) | 2 (6.9) | 1 (3.6) | 2 (6.7) | |
| ant3-1a | 10 (6.4) | 1 (5.6) | 2 (7.4) | 0 | 5 (17.2) | 0 | 2 (6.7) | |
| aadA6 | 8 (5.1) | 2 (11.1) | 1 (3.7) | 1 (4.3) | 0 | 0 | 4 (13.3) | |
| aac3-pEK516 | 7 (4.5) | 2 (11.1) | 0 | 0 | 1 (3.4) | 0 | 4 (13.3) | |
| aph3-Ia | 6 (3.8) | 1 (5.6) | 0 | 2 (8.7) | 2 (6.9) | 1 (3.6) | 0 | |
| aadA22_b | 5 (3.2) | 1 (5.6) | 2 (7.4) | 0 | 0 | 0 | 2 (6.7) | |
| aac6-Ib4 | 3 (1.9) | 0 | 0 | 1 (4.3) | 0 | 0 | 2 (6.7) | |
| aac6-Ib9 | 3 (1.9) | 0 | 0 | 1 (4.3) | 0 | 0 | 2 (6.7) | |
| aac6-Ib_a | 3 (1.9) | 0 | 0 | 1 (4.3) | 0 | 0 | 2 (6.7) | |
| aadA15 | 3 (1.9) | 0 | 1 (3.7) | 0 | 1 (3.4) | 1 (3.6) | 0 | |
| aadA12 | 1 (0.6) | 0 | 0 | 0 | 1 (3.4) | 0 | 0 | |
| aadA24 | 1 (0.6) | 1 (5.6) | 0 | 0 | 0 | 0 | 0 | |
| aac6-Ib3 | 1 (0.6) | 1 (5.6) | 0 | 0 | 0 | 0 | 0 | |
| Extended-spectrum Cephalosporin | CTX-M-15 | 138 (87.9) | 18 (100) | 26 (96.3) | 11 (47.8) | 29 (100) | 26 (92.9) | 28 (93.3) |
| OXA-1 | 15 (9.6) | 5 (27.8) | 1 (3.7) | 2 (8.7) | 2 (6.9) | 3 (10.7) | 2 (6.7) | |
| CTX-M-55 | 12 (7.6) | 1 (5.6) | 1 (3.7) | 8 (34.8) | 0 | 1 (3.6) | 1 (3.3) | |
| CTX-M-65 | 2 (1.3) | 0 | 0 | 2 (8.7) | 0 | 0 | 0 | |
| ACT-25 | 2 (1.3) | 1 (5.6) | 0 | 0 | 0 | 0 | 1 (3.3) | |
| CTX-M-64 | 1 (0.6) | 0 | 0 | 1 (4.3) | 0 | 0 | 0 | |
| SHV-28 | 1 (0.6) | 0 | 0 | 0 | 1 (3.4) | 0 | 0 | |
| Penicillin | TEM-1b | 101 (64.3) | 12 (66.7) | 20 (74.1) | 10 (43.5) | 21 (72.4) | 18 (64.3) | 20 (66.7) |
| TEM-1c | 2 (1.3) | 0 | 0 | 1 (4.3) | 0 | 0 | 1 (3.3) | |
| TEM-1 | 1 (0.6) | 0 | 0 | 1 (4.3) | 0 | 0 | 0 | |
| TEM-191 | 1 (0.6) | 0 | 0 | 0 | 1 (3.4) | 0 | 0 | |
| TEM-1a | 1 (0.6) | 0 | 0 | 1 (4.3) | 0 | 0 | 0 | |
| Fluoroquinolone | qnrS1 | 106 (67.5) | 10 (55.6) | 21 (77.8) | 17 (73.9) | 17 (58.6) | 23 (82.1) | 18 (60.0) |
| qnrS4 | 4 (2.5) | 0 | 0 | 0 | 2 (6.9) | 0 | 2 (6.7) | |
| qepA | 4 (2.5) | 0 | 0 | 0 | 4 (13.8) | 0 | 0 | |
| qnrS3 | 2 (1.3) | 0 | 0 | 0 | 0 | 0 | 2 (6.7) | |
| qepA4 | 2 (1.3) | 1 (5.6) | 1 (3.7) | 0 | 0 | 0 | 0 | |
| qnrB1 | 2 (1.3) | 1 (5.6) | 0 | 0 | 0 | 0 | 1 (3.3) | |
| oqxA10 | 1 (0.6) | 0 | 0 | 0 | 1 (3.4) | 0 | 0 | |
| oqxA8 | 1 (0.6) | 0 | 0 | 0 | 1 (3.4) | 0 | 0 | |
| oqxB17 | 1 (0.6) | 0 | 0 | 0 | 1 (3.4) | 0 | 0 | |
| qepA2 | 1 (0.6) | 0 | 0 | 0 | 1 (3.4) | 0 | 0 | |
| Tetracycline | tet-A-v2 | 97 (61.8) | 9 (50.0) | 18 (66.7) | 17 (73.9) | 17 (58.6) | 21 (75) | 15 (50) |
| tet-AB | 24 (15.3) | 6 (33.3) | 2 (7.4) | 2 (8.7) | 5 (17.2) | 4 (14.3) | 5 (16.7) | |
| tet-A | 4 (2.5) | 1 (5.6) | 2 (7.4) | 0 | 1 (3.4) | 0 | 0 | |
| tet-D | 2 (1.3) | 0 | 2 (7.4) | 0 | 0 | 0 | 0 | |
| Sulfamethoxazole | sul2 | 115 (73.2) | 14 (77.8) | 23 (85.2) | 18 (78.3) | 18 (62.1) | 21 (75.0) | 21 (70.0) |
| sul1 | 21 (13.4) | 7 (38.9) | 1 (3.7) | 3 (13.0) | 3 (10.3) | 4 (14.3) | 3 (10.0) | |
| sul3-v1 | 12 (7.6) | 1 (5.6) | 1 (3.7) | 2 (8.7) | 6 (20.7) | 1 (3.6) | 1 (3.3) | |
| Trimethoprim | dfrA14 | 84 (53.5) | 10 (55.6) | 19 (70.4) | 12 (52.2) | 10 (34.5) | 17 (60.7) | 16 (53.3) |
| dfrA17 | 20 (12.7) | 5 (27.8) | 0 | 4 (17.4) | 6 (20.7) | 4 (14.3) | 1 (3.3) | |
| dfrA12 | 15 (9.6) | 1 (5.6) | 4 (14.8) | 4 (17.4) | 5 (17.2) | 0 | 1 (3.3) | |
| dfrA1 | 13 (8.3) | 1 (5.6) | 2 (7.4) | 3 (13.0) | 2 (6.9) | 1 (3.6) | 4 (13.3) | |
| dfr2d | 2 (1.3) | 1 (5.6) | 0 | 0 | 1 (3.4) | 0 | 0 | |
| dfrA8 | 2 (1.3) | 0 | 1 (3.7) | 0 | 0 | 1 (3.6) | 0 | |
| dfrB4 | 2 (1.3) | 1 (5.6) | 0 | 0 | 1 (3.4) | 0 | 0 | |
| dfrA8 | 1 (0.6) | 0 | 1 (3.7) | 0 | 0 | 0 | 0 | |
| dfrA21 | 1 (0.6) | 0 | 1 (3.7) | 0 | 0 | 0 | 0 | |
| dfrA22 | 1 (0.6) | 0 | 1 (3.7) | 0 | 0 | 0 | 0 | |
| Phenicol | catA1 | 15 (9.6) | 4 (22.2) | 3 (11.1) | 1 (4.3) | 1 (3.4) | 2 (7.1) | 4 (13.3) |
| cml_ | 10 (6.4) | 1 (5.6) | 2 (7.4) | 1 (4.3) | 5 (17.2) | 0 | 1 (3.3) | |
| catB3 | 3 (1.9) | 0 | 0 | 1 (4.3) | 0 | 0 | 2 (6.7) | |
| floR | 2 (1.3) | 0 | 0 | 2 (8.7) | 0 | 0 | 0 | |
| Phosphonic (Fosfomycin) | fosA | 2 (1.3) | 1 (5.6) | 0 | 0 | 0 | 0 | 1 (3.3) |
| fosA_v3 | 1 (0.6) | 0 | 0 | 0 | 1 (3.4) | 0 | 0 | |
| Macrolide | mphA | 24 (15.3) | 6 (33.3) | 2 (7.4) | 4 (17.4) | 4 (13.8) | 4 (14.3) | 4 (13.3) |
| mefB | 5 (3.2) | 0 | 0 | 2 (8.7) | 2 (6.9) | 1 (3.6) | 0 | |
| ermB | 1 (0.6) | 1 (5.6) | 0 | 0 | 0 | 0 | 0 | |
| mphB | 1 (0.6) | 0 | 0 | 1 (4.3) | 0 | 0 | 0 | |
| Nucleoside | sat2A | 10 (6.4) | 1(5.6) | 2 (7.4) | 2 (8.7) | 2 (6.9) | 1 (3.6) | 2 (6.7) |
*
Figures in brackets represent % of each cell.
**
Figures in bold signifies the host species with highest percentage number of resistances.