Background
Methods
Isolation and characterization of bacterial strains
Governorate | Total | |||||
---|---|---|---|---|---|---|
Dakahlia | Sharkiya | Gharbiya | Damietta | Kafr El-Sheikh | ||
No. of farms | 20 | 5 | 4 | 9 | 10 | 48 |
No. of birds | 58,000 | 18,000 | 12,000 | 28,000 | 28,000 | 144,000 |
No. of samples | 232 | 72 | 48 | 112 | 112 | 576 |
Identification by MALDI-TOF MS
DNA extraction and purification
Identification of E. coli isolates using PCR
Genoserotyping of E. coli isolates using microarray assay
Phenotypic antibiotic susceptibility testing
Antibiotic | Class | S | I | R | Resistance rate (%) |
---|---|---|---|---|---|
Penicillin (PEN) | β-Lactam | 0 | 1 | 55 | 98.2 |
Erythromycin (ERY) | Macrolide | 1 | 1 | 54 | 96.4 |
Rifampicin (RAM) | Ansamycin | 1 | 1 | 54 | 96.4 |
Trimethoprim/sulfamethoxazole (T/S) | Diaminopyrimidine/sulfonamide | 19 | 1 | 36 | 64.3 |
Streptomycin (STR) | Aminoglycoside | 12 | 14 | 30 | 53.6 |
Tetracycline (TET) | Tetracycline | 24 | 4 | 28 | 50.0 |
Ceftazidime (CAZ) | β-Lactam (cephalosporin) | 24 | 9 | 23 | 41.1 |
Amoxicillin/clavulanic acid (AMC) | β-Lactam/β-lactamase inhibitor | 29 | 12 | 15 | 26.8 |
Chloramphenicol (CMP) | Non-classified | 41 | 2 | 13 | 23.2 |
Ciprofloxacin (CIP) | Fluoroquinolone | 38 | 6 | 12 | 21.4 |
Gentamicin (GEN) | Aminoglycoside | 38 | 7 | 11 | 19.6 |
Levofloxacin (LEV) | Fluoroquinolone | 35 | 13 | 8 | 14.3 |
Amikacin (AMK) | Aminoglycoside | 43 | 7 | 6 | 10.7 |
Imipenem (IMP) | β-Lactam (carbapenem) | 48 | 7 | 1 | 1.8 |
Antibiotic | Enterobacter cloacae (n = 5) | Resistance rate (%) | Citrobacter spp. (n = 2) | Resistance rate (%) | Klebsiella pneumoniae (n = 2) | Resistance rate (%) | ||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|
S | I | R | S | I | R | S | I | R | ||||
Penicillin (PEN) | 0 | 0 | 5 | 100 | 0 | 0 | 2 | 100 | 0 | 0 | 2 | 100 |
Erythromycin (ERY) | 0 | 0 | 5 | 100 | 1 | 0 | 1 | 50.0 | 0 | 0 | 2 | 100 |
Rifampicin (RAM) | 0 | 0 | 5 | 100 | 0 | 0 | 2 | 100 | 0 | 0 | 2 | 100 |
Trimethoprim/sulfamethoxazole (T/S) | 2 | 0 | 3 | 60.0 | 0 | 1 | 1 | 50.0 | 0 | 0 | 2 | 100 |
Streptomycin (STR) | 1 | 0 | 4 | 80.0 | 0 | 0 | 2 | 100 | 0 | 0 | 2 | 100 |
Tetracycline (TET) | 4 | 0 | 1 | 20.0 | 1 | 0 | 1 | 50.0 | 0 | 0 | 2 | 100 |
Ceftazidime (CAZ) | 3 | 1 | 1 | 20.0 | 0 | 0 | 2 | 100 | 0 | 0 | 2 | 100 |
Amoxicillin/clavulanic acid (AMC) | 1 | 0 | 4 | 80.0 | 1 | 1 | 0 | 0.0 | 0 | 0 | 2 | 100 |
Chloramphenicol (CMP) | 4 | 0 | 1 | 20.0 | 2 | 0 | 0 | 0.0 | 0 | 0 | 2 | 100 |
Ciprofloxacin (CIP) | 4 | 0 | 1 | 20.0 | 2 | 0 | 0 | 0.0 | 0 | 0 | 2 | 100 |
Gentamicin (GEN) | 4 | 0 | 1 | 20.0 | 2 | 0 | 0 | 0.0 | 0 | 0 | 2 | 100 |
Levofloxacin (LEV) | 4 | 0 | 1 | 20.0 | 2 | 0 | 0 | 0.0 | 0 | 0 | 2 | 100 |
Amikacin (AMK) | 5 | 0 | 0 | 0.0 | 1 | 0 | 1 | 50.0 | 2 | 0 | 0 | 0.0 |
Imipenem (IMP) | 4 | 1 | 0 | 0.0 | 2 | 0 | 0 | 0.0 | 1 | 1 | 0 | 0.0 |
Vitek-2 system
Detection of antibiotic resistance and virulence-associated genes of E. coli isolates by microarray analysis
Determination of colistin resistance
Results
Isolation and identification of Enterobacteriaceae
Antimicrobial susceptibility testing
Genoserotyping of E. coli isolates using microarray analysis
Detection of antibiotic resistance determinants in E. coli by microarray analysis
District | Isolate | O-type | H-type | Virulence genes | Resistance genes | Phenotypic resistance | ESBL |
---|---|---|---|---|---|---|---|
Dakahliya (n = 7) | 16CS0049 | – | 5 | hemL | qnrS, tetA, blaTEM | TET, RAM, ERY, PEN | |
16CS0070 | – | 51 | ipfA, cma, hemL, intl1, iroN, iss | sul3, cmlA1, floR, aadA1, aphA, strB, mphA, mrx, blaTEM | CIP, TET, CMP, RAM, GEN, STR, ERY, PEN | ||
16CS0071 | – | 21 | ipfA, cma, intl1, iroN, iss | sul1, sul2, dfrA12, tetA, floR, aadA1, mphA, mrx, blaCMY, blaTEM | CIP, LEV, T/S, TET, CMP, RAM, GEN, STR, ERY, PEN, AMP, CAZ | + | |
16CS0078 | – | 4 | hemL, intl1, iss | sul2, dfrA14, tetA, strB | T/S, TET, RAM, STR, ERY, PEN | ||
16CS0740 | – | 26 | cif, espA, espF_O103H2, espJ, nleA, nleB, O157:H7, tccP, astA, hemL, intl1, tir, eae | sul1, sul2, sul3, dfrA14, tetA, cmlA1, floR, arr, aadA1, aadB, ant2, aphA, strB, mphA, mrx, blaOXA-7 | CIP, T/S, TET, CMP, RAM, GEN, STR, ERY, PEN, AMP | + | |
16CS0744 | – | 51 | cma, hemL, intl1, iroN | sul3, dfrA1, dfrA14, tetA, cmlA1, aadA1, aphA, mphA, mrx, blaCMY, blaTEM | CIP, T/S, TET, RAM, GEN, STR, ERY, PEN, AMP, CAZ | ||
16CS0772 | – | 51 | ipfA, mchF, hemL, intl1, iroN, iss | qnrS, sul2, dfrA17, tetB, catA1, floR, aadA1, aadA4, strB, blaTEM, blaCTX-M9 | CIP, T/S, TET, CMP, RAM, GEN, STR, ERY, PEN, AMP, CAZ | + | |
Damietta (n = 3) | 16CS0069 | – | 51 | cma, intl1, iroN, iss | sul3, dfrA12, cmlA1, aadA1, mphA, mrx | CIP, LEV, T/S, CMP, RAM, STR, ERY, PEN, AMP | |
16CS0743 | – | 51 | mchF, hemL, intl1, iroN, iss | sul2, dfrA17, tetB, catA1, aadA4, blaTEM | CIP, T/S, TET, CMP, RAM, STR, ERY, PEN | ||
16CS0752 | – | 6 | iha, prfB, sat, hemL, intl1 | sul1, sul3, dfrA12, cmlA1, floR, aac6, aac6 lb, aadA1, aadA2, aphA, mphA, mrx, blaCTX-M1/blaCTX-M15, blaOXA-1, blaTEM | not determined | ||
Gharbiya (n = 3) | 16CS0747 | – | 32 | hemL, intl1, ireA | qnrS, sul3, tetA, cmlA1, floR, arr, aadA1, blaOXA-7, blaSHV, blaTEM | T/S, TET, CMP, RAM, GEN, STR, ERY, PEN AMP, CAZ | + |
16CS0761 | – | 51 | hemL, intl1, iroN, iss | qnrS, sul2, dfrA1, dfrA17, tetA, tetC, catA1, floR, aadA1, aadA4, aphA, strB, ereA, blaTEM, blaLAP-1 | CIP, LEV, T/S, TET, CMP, RAM, GEN, STR, ERY, PEN, AMP | + | |
16CS0762 | – | 51 | ipfA, mchF, hemL, intl1, intl2, iroN, iss | sul2, dfrA1, dfrA17, tetA, tetB, tetC, catA1, floR, aadA1, aadA4, aphA, strB, ereA, blaTEM | not determined | ||
Kafr El-sheikh (n = 4) | 16CS0067 | 15 | 1 | prfB, senB, hemL, iss | qnrS, sul1, sul2, dfrA7, dfrA17, dfrA19, tetA, aadA4, strA, strB, mphA, mrx, blaTEM | T/S, TET, RAM, GEN, STR, ERY, PEN | |
16CS0075 | – | 51 | ipfA, cma, hemL, intl1, iroN, iss | sul3, cmlA1, floR, aadA1, aphA, mphA, blaTEM | CIP, TET, CMP, RAM, GEN, STR, ERY, PEN | ||
16CS0755 | – | 10 | prfB, cme, intel1, iroN, iss | sul2, sul3, dfrA1, cmlA1, floR, aadA1, aphA, ereA, blaTEM | CIP, LEV, T/S, TET, CMP, RAM, GEN, STR, ERY, PEN, AMP, CAZ | + | |
16CS0774 | – | 1 | ipfA, prfB, tsh, mchF, hemL, ireA, iroN, iss | qnrB, sul1, sul2, dfrA7, dfrA17, dfrA19, tetB, aphA, blaDHA-1 | T/S, TET, RAM, STR, ERY, PEN, AMP, CAZ | + |
Isolate | PIP | TZP | CTX | CAZ | FEB | ATM | IMP | MEM | AMK | GEN | TOB | CIP | MXF | TGC | FOS | CT | T/S | |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
16CS0049 | R | I | S | S | S | S | S | S | S | S | S | I | R | S | S | S | S | No ESBL |
16CS0070 | R | I | S | S | S | S | S | S | S | R | R | R | R | S | S | S | S | No ESBL |
16CS0071 | R | I | R | R | I | R | S | S | S | R | R | R | R | S | S | S | R | ESBL |
16CS0075 | R | I | S | S | S | S | S | S | S | R | R | R | R | S | S | R | S | No ESBL |
16CS0743 | R | I | S | S | S | S | S | S | S | S | S | R | R | S | S | S | R | No ESBL |
16CS0744 | R | I | R | R | I | R | S | S | S | R | R | R | R | S | S | R | R | ESBL |
16CS0747 | R | R | R | R | I | R | I | I | S | R | R | I | R | S | S | S | S | ESBL/Carba |
16CS0761 | R | I | R | I | I | I | S | S | S | R | R | R | R | S | S | S | R | ESBL |
16CS0772 | R | R | R | R | I | R | S | S | S | R | R | R | R | S | S | S | R | ESBL |
16CS0774 | R | I | I | R | I | R | S | S | S | S | S | S | S | S | S | S | R | ESBL |
16CS0067 | R | I | S | S | S | S | S | S | I | R | R | S | R | S | S | S | R | No ESBL |
16CS0740 | R | I | S | S | S | S | S | S | S | R | R | R | R | S | S | S | R | No ESBL |
16CS0755 | R | I | R | R | I | R | S | S | S | R | R | R | R | I | S | S | R | ESBL |
Genotypic and phenotypic identification of resistance to colistin
Isolate | Governorate | Farm | O-antigen | H-antigen | Resistance genes | Virulence genes | Phenotypic resistance | mcr-1 | MIC value | ESBL | Carbapenemase |
---|---|---|---|---|---|---|---|---|---|---|---|
16CS0744 | Dakahliya | 9 | – | 51 | sul3, dfrA1, dfrA14, tetA, cmlA1, aadA1, aphA, mphA, mrx, blaCMY, blaTEM | cma, hemL, intl1, iroN | CIP, T/S, TET, RAM, GEN, STR, ERY, PEN, AMP, CAZ | + | ≥ 4 | Positive | Negative |
16CS0078 | Dakahliya | 16/2 | – | 4 | sul2, dfrA14, tetA, strB | hemL, intl1, iss | T/S, TET, RAM, STR, ERY, PEN | + | ≥ 6 | nd by VITEK | nd by VITEK |
16CS0075 | Kafr El-Sheikh | 9 | – | 51 | sul3, cmlA1, floR, aadA1, aphA, mphA, blaTEM | cma, hemL, intl1, iroN, iss | CIP, TET, CMP, RAM, GEN, STR, ERY, PEN | + | ≥ 32 | Negative | Negative |
16CS0775 | Damietta | 4 | – | 4 | – | pic, vat, cma, hlyE, mchF, hemL, ireA, iroN, iss | TET, RAM, ERY, PEN | + | ≥ 6 | nd by VITEK | nd by VITEK |
16CS0036 | Damietta | 6 | – | 21 | – | hemL | RAM, ERY, PEN, AMC | + | ≥ 4 | nd by VITEK | nd by VITEK |
16CS0747 | Gharbiya | 4 | – | 32 | qnrS, sul3, tetA, cmlA1, floR, arr, aadA1, blaOXA-7, blaSHV, blaTEM | hemL, intl1, ireA | T/S, TET, CMP, RAM, GEN, STR, ERY, PEN AMP, CAZ | − | nd | Positive | Positive |