Table 1.
Source, antibiograms, sequence types (STs), phylogroups, resistance genes, virulence genes and plasmids found in the Escherichia coli isolates
| ID | Source | Resistance pattern | Sequence Type | Phylogroup | ABR genes | Virulence genes | Plasmid replicon | Pmlst | |
|---|---|---|---|---|---|---|---|---|---|
| β-lactamases | Others | ||||||||
| P51B | Patient | AMP-CXM-CAZ-CRO-FEP-AMC-TZP-GEN-TOB-CIP-SXT | ST648 | F | blaTEM−1B, blaCTX−M−15, blaOXA−1 | sul2, dfrA17, tet(B), tet(M), mph(A), aac(3)-IIa, aac(6’)-Ib-cr | air, astA, chuA, eilA, fyuA, gad, hlye, hra, irp2, kpsM, kpsE, lpfA, papA, papC, terC, traT, yfcv | Col(BS512), IncFIA, IncFIB(pB171), IncFII, IncI1-I(Alpha), IncQ1, IncX1 | IncF[F2:A1:B32] |
| E53 |
Environment (Bed) |
AMP-CXM-CAZ-CRO-FEP-AMC-TZP-GEN-TOB-CIP-SXT | ST648 | F | blaOXA−1, blaTEM−169, blaCTX−M−15, blaTEM−33, | sul2, dfrA17,aac(6’)-Ib-cr, aac(3)-IId, mph(A), erm(B), tet(M), tet(B) | terC, ipfA, papC, yfcV, papa_F43, eilA, hra, chuA, irp2, fyuA, astA, gad, kpsMIII_K98, traT, kpsE | Col(BS512), IncFIA, IncFIB(pB171), IncFII, IncQ1, IncX1 | IncF[F2:A1:B32] |
| P2R | Patient | AMP-CXM-CAZ-CRO-FEP-AMC-TZP-SXT | ST940 | B1 | blaTEM−35, blaOXA−181 | sul2, dfrA12, dfrA1, aph(6)-Id, aadA2, aph(3’’)-Ib, qnrS1,erm(B), tet(B) | lpfA, gad, hlyE, traT, capU, terC | IncFIA, IncFIB, IncFIC(II), ColKP3 | IncF [F-:A-:B12] |
| P73 | Patient | AMP-CXM-CAZ-CRO-FEP-MEM-AMC | ST940 | B1 | blaOXA−1, blaOXA−181, blaTEM−35 | sul2, aph(3’’)-Ib, aph(6)-Id, aadA1,qnrS1, tet(B) | lpfA, gad, traT, hlyE, iss, capU, terC | ColKP3, IncFIA, IncFIB, IncFII | IncF[F36:A1:B1] |
| P128 | Patient | AMP-CAZ-CRO-FEP-AMC-TZP-SXT | ST13846 | D | blaTEM−1B, blaCTX−M−15 | sul2, dfrA14, aph(6)-Id, aph(3’’)-Ib, qnrS1, tet(A) | ipfA, eilA, irp2, chuA, sitA, fyuA, gad, kpsMIII_K96, ompT, iss, kpsE, terC | IncY | |
| P166 | Patient | AMP-CXM-CAZ-CRO-FEP-AMC-TZP-SXT | ST13846 | D | blaTEM−1B, blaCTX−M−15 | sul2, dfrA14, aph(6)-Id, aph(3’’)-Ib, qnrS1, tet(A) | ipfA, air, eilA, sitABCD, irp2, chuA, fyuA, gad, kpsMIII_K96, ompT, kpsE, terC | IncY | |
| P49 | Patient | AMP-CXM-CAZ-CRO-FEP-AMC-TZP-ERT-SXT | ST73 | B2 | bla TEM−1B | sul1, sul2, dfrA1, dfrA17, dfrG, aadA5, aadA1, aph(3’’)-Ib, aph(6)-Id, erm(B), tet(B), tet(M), tet(L), qacE | ccI, cea, clbB, cnf1, focc, focG, hlyA, hra, ibeA, ireA, iroN, iss, iucC, iutA, kpsE, kpsM, mchB, mchf, mchC, mcmA, neuc, ompT, papA, papC, pic, senB, sfaD, sitA, tcpC, terC, traT, usp, vat | Col(MG828), Col156, ColRNAI, IncFIA, IncFIB, IncFII, IncQ1 | IncF[F36:A1:B1] |
| P142 | Patient | AMP-CXM-CAZ-CRO-FEP-AMC-TZP-DOR-MEM-SXT | ST5614 | B1 | blaTEM−104, blaTEM−1B, blaTEM−198, blaCTX−M−15, blaTEM−217, blaTEM−234 | sul1, sul2, dfrA1, dfrA17,aph(3’’)-Ib, aadA5, aph(6)-Id, qnrS1, mph(A), tet(A), tet(B), qacE | iha, ipfA, sigA, iucC, iutA, cib, gad, traT, iss, capU, terC, hlyE | IncB/O/K/Z, IncFII, IncQ1 | IncF [F-:A-:B] *FII |
| P17 | Patient | AMP-CXM-CAZ-CRO-FEP-AMC-TZP-TOB-CIP-SXT | ST224 | B1 | blaCTX−M−22, blaCTX−M−216, blaCTX−M−103, blaCTX−M−176, blaCTX−M−15, blaCTX−M−156, blaCTX−M−3, blaCTX−M−202, blaCTX−M−88, blaCTX−M−203, blaCTX−M−71, blaCTX−M−167, blaOXA−1, | sul1, sul3, dfrA12, dfrA17, aadA1, aadA2, aadA5, aac(6’)-Ib-cr, mph(A), erm(B), tet(A), qacE | ipfA, sitABCD, iucC, sitA, iutA, gad, traT, terC | IncFIA, IncFIB, IncFII, IncI1-I(Alpha), IncY | IncF[F2:A4:B1] |
| P60R | Patient | AMP-CXM-CAZ-CRO-FEP-AMC-TZP-SXT | ST1722 | F | blaCTX−M−15, blaTEM−1B | sul2, dfrA14, aph(6)-Id, aph(3’’)-Ib, qnrS1, tet(A) | IpfA, afaA, afaB, afaC, afaD, air, eilA, cia, chuA, gad, traT, iss, kpsE, terC | IncB/O/K/Z, IncI2(Delta), IncY, pXuzhou21 | |
| P165 | Patient | AMP-CXM-CAZ-CRO-FEP-AMC-TZP-GEN-TOB-CIP-SXT | ST3489 | A | - | neuC, gad, ompT, terC | IncFIB(K), IncL, IncY | ||
| P105 | Patient | AMP-CXM-CAZ-CRO-FEP-AMC-TZP-GEN-TOB-CIP-SXT | ST10 | A | blaOXA−1, blaCTX−M−15 | sul1, dfrA17, aadA5,aac(3)-IIa, aac(6’)-Ib-cr, mph(A), tet(B), qacE | hra, senB, sitABCD, iucC, irp2, sitA, iutA, fyuA, mchF, traT, terC | IncFIA, IncFIB, IncFII | IncF[F36:A4:B1] |
| P159 | Patient | AMP-CXM-CAZ-CRO-FEP-AMC-TZP-GEN-TOB -CIP-SXT | ST617 | A | blaOXA−1, blaCTX−M−15 | sul1, sul2, dfrA17, aadA5, aph(6)-Id, aac(6’)-Ib-cr, aph(3’’)-Ib, mph(A), tet(B), qacE | sitABCD, iucC, irp2, sitA, iutA, fyuA, traT, iss, terC | IncFIA, IncFIB | IncF[F-:A4:B1] |
| P72 | Patient | AMP-CXM-CRO-CAZ-FEP-AMC-TZP-CIP-SXT | ST167 | A | bla CTX−M−27 | sul1, sul2, dfrA12, aph(6)-Id, aph(3’’)-Ib, aadA2, qepA4, mph(A), tet(A), tet(B) | irp2, fyuA, traT, terC | IncFIA, IncFIB, IncFII | IncF[F48:A1:B49] |
| E56 |
Environment (Bed) |
AMP-CXM-CAZ-CRO-FEP-AMC-TZP-GEN-TZP-CIP-SXT | ST638 | A | blaTEM−1B, blaOXA−1 | aac(3)-IIa, tet(A) | ipfA, yfcv, terC | Col(BS512), IncFIB(K), IncR | |
| E37 |
Environment (Tap) |
AMP-CXM-CAZ-CRO-FEP-AMC-TZP-GEN-TOB-CIP-SXT | ST410 | C | blaCTX−M−15, blaOXA−1 | sul2, dfrA14,mph(A), aac(3)-IIa, aac(6’)-Ib-cr, tet(B) | cba, cma, cnf1, fyuA, hlya, hlyE, hra, irp2, iucC, iutA, lpfA, papA, papC, sitA, terC, traT | IncFIA, IncFIB, IncFII, IncQ1 | IncF [F104:A1:B1] |
| E29 |
Environment (Tap) |
AMP-CXM-CAZ-CRO-FEP-AMC-TZP-GEN-TOB-CIP-SXT | ST450 | A | blaCTX−M−3, blaTEM−1B | sul2, dfrA17,mph(A), aac(3)-IId, tet(A) | fyuA, gad, hlyE, iha, irp2, iucC, iutA, kpsE, mchf, ompT, papA, papc, sat, senb, terC, traT | Col(BS512), Col156, IncFIA, IncFIB, IncFII, IncI1-I(Alpha), IncI2(Delta) | IncF [F4:A2:B20] |
| E25B |
Environment (Bed) |
AMP-CXM-CAZ-CRO-FEP-AMC-TZP | ST127 | B2 | bla TEM−1D | sul1, dfrA7,tet(B) | papC, sfaD, sfaE, sfaS, yfcv, papA, hra, vat, clbB, cnf1, tcpC, chuA, iroN, irp2, sitA, fyuA, usp, mcmA, gad, iss, kpsE, kpsMII_F48, ompT, traT, TerC | IncFIA, IncFIB, IncFII | IncF[F1:A1:B20] |
| E50-1 |
Environment (Dripstand) |
AMP-TZP-DOR-MEM-SXT | ST155 | B1 | - | sul2, dfrA17, aadA5, tet(A) | ipfA, gad, ompT, iss, terC | - | |
| E55-2 |
Environment (Bed) |
AMP-DOR-MEM-SXT- | ST58 | B1 | bla TEM−1B | sul1, sul2, dfrA17, aadA5, aph(3’’)-Ib, aph(6)-Id, qnrB19, mph(A), tet(A), qacE | iha, ipfA, papA_F43,sat, senB, iucC, sitABCD, iutA, cea, gad, traT, kpsMII_K52, iss, capU, terC | Col(pHAD28), Col156, IncFIB, IncFI1(29) | IncF[F29:A-:B10] |
| P115 | Patient | AMP-CXM-CAZ-CRO-FEP-AMC-TZP-SXT | Unknown | E | blaCTX−M−15, blaTEM−35, blaOXA−1 | sul2, dfrA1, drfA17, aadA1, aadA5, qnrS1, mph(A), tet(B) | IpfA, papA_F19, papA_F20, eilA, V, terC | Col(BS512), IncFIA, IncFIB, IncFII, IncFHI2, IncFHI2A | IncF[F36:A1:B20] |
| P143 | Patient | AMP-CXM-CAZ-CRO-FEP-AMC-TZP-SXT | Unknown | Unknown | bla OXA−1 | sul2, dfrA14, tet(B) | eatA, irp2, fyuA, terC | IncFII, IncL, IncN | IncF[[F-:A-:B-] FII_84* |
| P63 | Patient | AMP-CXM-CAZ-CRO-FEP-AMC-TZP-GEN-TOB-CIP-SXT | Unknown | E | blaTEM−1B, blaOXA−1, blaCTX−M−15, blaDHA−1 | sul1, sul3, dfrA1, dfrA12, dfrA17, aac(6’)-Ib-cr, aac(3)-IIa, aadA2, aadA5, aadA1, qnrB4, mph(A), erm(B), tet(A), tet(B) | ipfA, yfcv, iucC, irp2, sitABCD, iutA, fyuA, terC | Col(BS512), IncFIA, IncFIB, IncFII, IncR | IncF[F36:A4:B1] |
ampicillin (AMP), cefuroxime (CXM), ceftazidime (CAZ), ceftriaxone (CRO), cefepime (FEP), gentamicin (GEN), tobramycin (TOB), amikacin (AMK), amoxicillin/clavulanic (AMC), piperacillin/tazobactam (TZP), imipenem (IPM), doripenem (DOR), meropenem (MEM), ertapenem (ERT), ciprofloxacin (CIP), trimethoprim-sulphamethoxazole (SXT) and tigecycline (TGC)