Background
Methods
Isolation and identification of aEPEC isolates
Phenotypic antimicrobial susceptibility testing
Screening and confirmation of ESBL producing isolates
Identification of β-lactamase genes
Whole genome sequencing and identification of antimicrobial resistance genes
Statistical analysis
Results
Antimicrobial resistance of aEPEC isolates
Class/antimicrobial | No. of resistant isolates from different sources (%) | Total | P value | |||
---|---|---|---|---|---|---|
Diarrheal patient (151) | Healthy carrier (32) | Animal (51) | Raw meat (33) | |||
Penicillins | ||||||
Ampicillin | 84 (55.6) | 15 (46.9) | 20 (39.2) | 13 (39.4) | 132 (49.4) | 0.1185 |
Piperacillin | 71 (47.0) | 13 (40.6) | 19 (37.3) | 7 (21.2) | 110 (41.2) | 0.0484 |
β-Lactam/β-lactamase inhibitor combinations | ||||||
Amoxicillin–clavulanic acid | 14 (9.3) | 0 | 10 (19.6) | 3 (9.1) | 27 (10.1) | 0.0319 |
Ampicillin–sulbactam | 24 (15.9) | 0 | 11 (21.6) | 9 (27.3) | 44 (16.5) | 0.0177 |
Cephems | ||||||
Cefepime | 14 (9.3) | 3 (9.4) | 0 | 0 | 17 (6.4) | 0.0396 |
Cefotaxime | 39 (25.8) | 5 (15.6) | 1 (2.0) | 4 (12.1) | 49 (18.4) | 0.0013 |
Ceftriaxone | 38 (25.2) | 5 (15.6) | 2 (3.9) | 3 (9.1) | 48 (18.0) | 0.0029 |
Ceftazidime | 7 (4.6) | 1 (3.1) | 0 | 0 | 8 (3.0) | 0.2622 |
Cefuroxime | 39 (25.8) | 5 (15.6) | 2 (3.9) | 6 (18.2) | 52 (19.5) | 0.0071 |
Monobactams | ||||||
Aztreonam | 20 (12.6) | 3 (9.4) | 0 | 1 (3.0) | 23 (8.6) | 0.0202 |
Carbapenems | ||||||
Imipenem | 0 | 0 | 0 | 0 | 0 | – |
Meropenem | 0 | 0 | 0 | 0 | 0 | – |
Aminoglycosides | ||||||
Gentamicin | 57 (37.7) | 3 (9.4) | 11 (21.6) | 6 (18.2) | 77 (28.8) | 0.0019 |
Kanamycin | 22 (14.6) | 1 (3.1) | 9 (17.6) | 7 (21.2) | 39 (14.6) | 0.1782 |
Streptomycin | 78 (51.7) | 9 (28.1) | 20 (39.2) | 16 (48.5) | 123 (46.1) | 0.0692 |
Tetracyclines | ||||||
Tetracycline | 89 (58.9) | 15 (46.9) | 21 (41.2) | 21 (63.6) | 146 (54.7) | 0.0816 |
Quinolones | ||||||
Nalidixic acid | 62 (41.1) | 7 (21.9) | 17 (33.3) | 8 (24.2) | 94 (35.2) | 0.0866 |
Fluoroquinolones | ||||||
Ciprofloxacin | 8 (5.3) | 0 | 4 (7.8) | 1 (3.0) | 13 (4.9) | 0.4053 |
Norfloxacin | 5 (3.3) | 0 | 4 (7.8) | 0 | 9 (3.4) | 0.1447 |
Levofloxacin | 8 (5.3) | 0 | 4 (7.8) | 0 | 12 (4.5) | 0.2020 |
Folate pathway inhibitors | ||||||
Trimethoprim–sulfamethoxazole | 72 (47.7) | 6 (18.8) | 18 (35.3) | 9 (27.3) | 105 (39.3) | 0.0060 |
Phenicols | ||||||
Chloramphenicol | 11 (7.3) | 0 | 9 (17.6) | 8 (24.2) | 28 (10.5) | 0.0020 |
Nitrofurans | ||||||
Nitrofurantoin | 3 (2.0) | 0 | 1 (2.0) | 0 | 4 (1.5) | 0.7275 |
MDR aEPEC isolates
No. of antimicrobial group | No. of resistant isolates from different sources (%) | Total | |||
---|---|---|---|---|---|
Diarrheal patient | Healthy carrier | Animal | Raw meat | ||
0 | 38 (25.2) | 10 (31.3) | 24 (47.1) | 7 (21.2) | 79 (29.6) |
1–2 | 29 (19.2) | 12 (37.5) | 7 (13.7) | 11 (33.3) | 59 (22.1) |
≥ 3 | 84 (55.6) | 10 (31.3) | 19 (37.3) | 15 (45.5) | 128 (47.9) |
Total | 151 (100) | 32 (100) | 51 (100) | 33 (100) | 267 (100) |
ESBL producing aEPEC isolates
Origin (no. of isolates) | Isolates | Antimicrobial resistance pattern |
bla
CTX-M
|
bla
TEM
| |
---|---|---|---|---|---|
CTX-M-1 group | CTX-M-9 group | ||||
Diarrheal patients (38) | EP004 | AM, PRL, SAM, FEP, CTX, CRO, CXM, CAZ, ATM, CN, K, S, TE, NA, SXT | CTX-M-15 | CTX-M-14 | TEM-1 |
EP008 | AM, PRL, SAM, CTX, CRO, CXM, ATM, CN, K, S, TE, NA, SXT | CTX-M-14 | TEM-1 | ||
EP012 | AM, PRL, SAM, CTX, CRO, CXM, ATM, CN, K, S, TE, NA, SXT | CTX-M-14 | TEM-1 | ||
EP013 | AM, PRL, SAM, CTX, CRO, CXM, ATM, CN, K, S, TE, NA, SXT | CTX-M-14 | TEM-1 | ||
EP014 | AM, PRL, SAM, CTX, CRO, CXM, ATM, CN, K, S, TE, NA, SXT | CTX-M-14 | TEM-1 | ||
EP017 | AM, PRL, AMC, SAM, CTX, CRO, CXM, CN, K, S, TE, NA, SXT, C | CTX-M-14 | TEM-1 | ||
EP028 | AM, PRL, FEP, CTX, CRO, CXM, CAZ, ATM, CN, TE, NA, SXT | CTX-M-15 | TEM-1 | ||
EP033 | AM, PRL, CTX, CRO, CXM, CN, S, TE | CTX-M-14 | TEM-1 | ||
EP041 | AM, PRL, CTX, CRO, CXM, CN, S, SXT | CTX-M-3 | TEM-1 | ||
EP043 | AM, PRL, CTX, CRO, CXM, ATM | CTX-M-55 | TEM-1 | ||
EP064 | AM, PRL, CTX, CRO, CXM, CN, NA, SXT | CTX-M-3 | TEM-1 | ||
EP074 | AM, PRL, AMC, SAM, FEP, CTX, CRO, CXM, CAZ, ATM, CN, S, TE, NA, SXT | CTX-M-15 | |||
EP079 | AM, PRL, AMC, SAM, FEP, CTX, CRO, CXM, CAZ, ATM, CN, K, S, TE, NA, SXT | CTX-M-15 | TEM-1 | ||
EP088 | AM, PRL, FEP, CTX, CRO, CXM, CN, S, TE, SXT | CTX-M-3 | |||
EP103 | AM, PRL, SAM, FEP, CTX, CRO, CXM, ATM, CN, K, S, TE, NA, CIP, LEV, C, F | CTX-M-55 | CTX-M-14 | TEM-1 | |
EP105 | AM, PRL, CTX, CRO, CXM, ATM, CN, K, S, TE, NA, CIP, LEV, SXT, F | CTX-M-65 | |||
EP109 | AM, PRL, AMC, CTX, CRO, CXM, ATM, CN, S, NA, SXT | CTX-M-15 | TEM-1 | ||
EP112 | AM, PRL, SAM, CTX, CRO, CXM, CN, S, TE, NA, SXT | CTX-M-14 | |||
EP115 | AM, PRL, AMC, SAM, FEP, CTX, CRO, CXM, ATM, CN, K, S, TE, NA, CIP, LEV, SXT, C, F | CTX-M-15 | TEM-1 | ||
EP116 | AM, PRL, AMC, FEP, CTX, CRO, CXM, CN, S, TE, NA, SXT | CTX-M-14 | TEM-1 | ||
EP136 | AM, PRL, CTX, CRO, CXM, ATM | CTX-M-15 | |||
EP155 | AM, PRL, CTX, CRO, CXM, CN, S, TE, SXT | CTX-M-14 | |||
EP163 | AM, PRL, CTX, CRO, CXM, S, SXT | CTX-M-14 | |||
EP166 | AM, PRL, CTX, CRO, CXM, TE, SXT | CTX-M-14 | TEM-1 | ||
EP171 | AM, PRL, FEP, CTX, CRO, CXM, CAZ, ATM, CN, TE, SXT | CTX-M-55 | TEM-1 | ||
EP176 | AM, PRL, FEP, CTX, CRO, CXM, CN, K, S, TE, NA | CTX-M-14 | TEM-1 | ||
EP179 | AM, PRL, SAM, CTX, CRO, CXM, CN, S, TE, NA, SXT | CTX-M-14 | TEM-1 | ||
EP180 | AM, PRL, FEP, CTX, CRO, CXM, CAZ, ATM, S, TE, NA | CTX-M-15 | CTX-M-14 | ||
EP182 | AM, PRL, SAM, CTX, CRO, CXM, CN, K, S, TE, NA | CTX-M-14 | |||
EP186 | AM, PRL, CTX, CRO, CXM, CN, K, S, TE, NA, CIP, NOR, LEV, SXT, C | CTX-M-14 | TEM-1 | ||
EP187 | AM, PRL, AMC, FEP, CTX, CRO, CXM, CN, S, TE, SXT | CTX-M-3 | TEM-1 | ||
EP191 | AM, PRL, SAM, CTX, CRO, CXM, CN, K, S, TE, SXT | CTX-M-14 | TEM-1 | ||
EP193 | AM, PRL, SAM, FEP, CTX, CRO, CXM, CAZ, ATM, CN, K, S | CTX-M-55 | TEM-1 | ||
EP239 | AM, PRL, AMC, SAM, CTX, CRO, CXM, CN, S, TE, NA, SXT | CTX-M-14 | TEM-1 | ||
EP370 | AM, PRL, FEP, CTX, CRO, CXM, CN, TE, NA, SXT | CTX-M-14 | |||
EP408 | AM, PRL, SAM, CTX, CRO, CXM, ATM, S, TE, NA, SXT | CTX-M-14 | TEM-1 | ||
EP410 | AM, PRL, CTX, CRO, CXM, ATM, CN, NA | CTX-M-15 | |||
EP412 | AM, PRL, CTX, CRO, CXM, TE | CTX-M-13 | |||
Healthy carriers (5) | EP318 | AM, PRL, FEP, CTX, CRO, CXM, CAZ, ATM | CTX-M-15 | ||
EP361 | AM, PRL, FEP, CTX, CRO, CXM, K, S, TE, NA | CTX-M-14 | |||
EP 402 | AM, PRL, FEP, CTX, CRO, CXM, ATM, TE | CTX-M-3 | |||
EP404 | AM, PRL, CTX, CRO, CXM, S | CTX-M-14 | |||
EP415 | AM, PRL, CTX, CRO, CXM, ATM, TE | CTX-M-15 | |||
Animal (1) | EP298 | AM, PRL, CTX, CRO, CXM, K, S, TE, NA, SXT, C | CTX-M-14 | ||
Raw meat (3) | EP244 | AM, PRL, AMC, SAM, CTX, CRO, CXM, ATM, S, TE, NA, SXT, C | CTX-M-14 | ||
EP299 | AM, PRL, CTX, CRO, CXM, K, S, TE, NA, SXT, C | CTX-M-14 | |||
EP344 | AM, PRL, CTX, CRO, CXM, K, S, TE, C | CTX-M-14 |
Molecular characteristics of ESBL genes
Distribution of antimicrobial resistance determinants
Phenotype of resistance (no. of isolates) | Resistance genes | No. of isolates (%) |
---|---|---|
Ampicillin (50) |
bla
TEM-1
| 24 (48.0) |
bla
CTX
| 8 (16.0) | |
bla
OXA
| 3 (6.0) | |
blaTEM-1 + blaCTX | 8 (16.0) | |
blaTEM-1 + blaLEN | 1 (2.0) | |
blaCTX + blaLEN | 2 (4.0) | |
blaCTX + blaOXA | 1 (2.0) | |
Tetracycline (51) |
tetA
| 27 (52.9) |
tetB
| 2 (3.9) | |
tetC
| 1 (2.0) | |
tetA + tetC | 9 (17.6) | |
tetB + tetC | 5 (10.0) | |
Chloramphenicol (8) |
cat
| 3 (37.5) |
cml
| 5 (62.5) | |
Trimethoprim–sulfamethoxazole (40) | sul1 + dfra12/17 | 15 (37.5) |
sul2 + dfra14/17 | 6 (15.0) | |
sul3 + dfra12 | 3 (7.5) | |
sul1 + sul2 + dfra5/12/17 | 14 (35.0) | |
dfra1 | 2 (5.0) | |
dfra17 | 1 (2.5) | |
Gentamicin (33) |
aac3iia
| 23 (69.7) |
aac3iia + ant2ia | 3 (9.1) | |
aac3iia + aph3ia | 2 (6.1) | |
aac3iia + ant2ia + aph3ia | 1 (3.0) | |
Streptomycin (44) |
ant3ia
| 4 (9.1) |
aph33ib
| 2 (4.5) | |
aph33ib + aph6id | 24 (54.5) | |
aph33ib + aph6id + ant3ia | 1 (2.3) | |
Kanamycin (12) |
ant2ia
| 1 (8.3) |
aph3ia
| 3 (25.0) | |
ant2ia + aph3ia | 2 (16.7) |