Table 1.
Phenotypic/molecular characteristics of ESβL/carbapenemases-producing E. coli and Klebsiella spp. isolates recovered from the 18 sampling sites.
| Sample name a | Feature b | Phylogroup | MLST e | Antimicrobial Resistance c | Resistance genes for d | ||
|---|---|---|---|---|---|---|---|
| β-lactams | Quinolones | Aminoglycosides | |||||
| C1 E. coli | ESβL + | B2 | NT | AMP, AMC, PIP, ATM, FEP, CTX, CAZ, CXM, CIP, LEV, GEN, TOB, TET, TMS | blaCTX-M-type | aac(6′)-Ib-cr | aac(6′)-Ib-cr |
| C1 K. pneumoniae | ESβL + Carba R+ | / | ST258 | AMP, AMC, PIP, ATM, CLO, FEP, CTX, CAZ, CXM, CIP, LEV, AK, GEN, TOB, ERT, IMI, MER, TZP, TET | blaKPC-2 blaCTX-M-type | aac(6′)-Ib-cr | aac(6′)-Ib-cr |
| C2 E. coli | ESβL + | B2 | NT | AMP, AMC, PIP, ATM, FEP, CTX, CAZ, CXM, CIP, LEV, AK(I) TET | blaCTX-M-27 | aac(6′-)Ib-cr | aac(6′)-Ib-cr |
| C6 E. coli | ESβL + | B2 | NT | AMP, PIP, ATM, FEP, CTX, CAZ, CXM, CIP, LEV, TET, TMS | blaCTX-M-type | aac(6′)-Ib-cr | – |
| C7 E. coli (WGS) | ESβL + | B2 | ST131 | AMP, AMC, PIP, ATM, FEP, CTX, CAZ, CXM, CIP, LEV, TZP |
blaOXA-244 blaCTX-M-15 |
Chromosomal Mutations |
aadA5 |
| C7-2 E. coli | ESβL + | Unknown | NT | AMP, PIP, ATM, FEP, CTX, CAZ, CXM, TET | blaCTX-M-type | – | – |
| C9 K. oxytoca | ESβL – | / | NT | AMP, AMC, PIP, ATM, CTX, CAZ, CXM, TZP, TOB, TET, TMS | not detected | – | – |
| C9-1 E. coli | ESβL + | D | NT | AMP, PIP, ATM, FEP, CTX, CAZ, TET, AK(I), GEN(I) | blaCTX-M-type | – | – |
| C9-2 E. coli | ESβL + | B2 | ST131 | AMP, PIP, ATM, FEP, CTX, CAZ, TET |
blaOXA-244 blaCTX-M-type |
– | – |
| C9-3 E. coli (WGS) | ESβL + | B2 | ST131 | AMP, AMC, PIP, ATM, FEP, CTX, CAZ, CLO, CIP, LEV, TZP, TET, TMS |
blaOXA-244 blaCTX-M-15 |
Chromosomal Mutations |
aadA5 |
| C9-4 E. coli | ESβL + | B2 | ST131 | AMP, AMC, PIP, ATM, FEP, CTX, CAZ, CIP, LEV, TZP, TET, TMS |
blaOXA-244 blaCTX-M-type |
– | – |
| C10-1 E. coli | ESβL + | A | NT | AMP, AMC, PIP, ATM, FEP, CTX, CAZ, CXM, CIP, LEV, AK(I), TZP(I), GEN, TOB, TET, TMS | blaCTX-M-type | aac(6′)-Ib-cr | aac(6′)-Ib-cr |
| C10-2 E. coli | ESβL + | D | ST648 | AMP, AMC, PIP, ATM, FEP, CTX, CAZ, CXM, COL, CIP, LEV, AK(I), GEN, TOB, TET | blaCTX-M-type | aac(6′)-Ib-cr | aac(6′)-Ib-cr |
| C10-3 E. coli | ESβL + | D | ST648 | AMP, AMC, PIP, ATM, FEP, CTX, CAZ, CXM, COL, CIP, LEV, AK(I), GEN, TOB, TET | blaCTX-M-type | aac(6′)-Ib-cr | aac(6′)-Ib-cr |
| C11-1 E. coli | ESβL + | A | ST23 | AMP, PIP, ATM, FEP, CTX, CAZ(I), COL, TET | blaCTX-M-1 | – | – |
| C11-2 E. coli | ESβL + | A | ST23 | AMP, PIP, ATM, FEP, CTX, CXM, CAZ(I), TET | blaCTX-M-1 | – | – |
| C17 K. pneumoniae | ESβL + | / | NT | AMP, PIP, ATM, FEP, CTX, CAZ(I), CXM, CIP, TET | blaCTX-M-type | qnrS | – |
| C17 E. coli | ESβL + | A | NT | AMP, PIP, ATM, FEP, CTX, CXM, CIP, LEV, TET, TMS | blaCTX-M-type | qnrS | – |
| C17-2 K. pneumoniae | ESβL + | / | NT | AMP, PIP, ATM, FEP, CTX, CAZ, CXM, CIP, TET, TMS | blaCTX-M-type | qnrS | – |
| C21 E. coli | ESβL + | B2 | ST131 | AMP, PIP, ATM, FEP, CTX, CAZ, CXM, CIP, LEV, TET | blaCTX-M-14 | – | – |
| C21-2 E. coli | ESβL + | B1 | NT | AMP, PIP, ATM, FEP, CTX, CAZ, CXM, TET, AK(I), TOB, TMS | blaCTX-M-type | aac(6′)-Ib-cr | aac(6′)-Ib-cr |
| C21-3 E. coli | ESβL + | B2 | ST131 | AMP, PIP, ATM, FEP, CTX, CAZ, CIP, LEV, TET, TMS(I) | blaCTX-M-type | – | – |
| C21-4 E. coli | ESβL + | D | NT | AMP, AMC, PIP, ATM, FEP, CTX, CAZ(I), CXM, CIP, LEV, TET | blaCTX-M-gr9 | – | – |
| C22 K. aerogenes | ESβL – | / | NT | AMP, PIP, ATM, FEP, CTX, CAZ, CLO, TZP, TET | blaCTX-M neg | – | – |
| C22 E. coli | ESβL + | Negative for all | NT | AMP, PIP, ATM, FEP, CTX, CAZ, CXM, TET | blaCTX-M-type | – | – |
| C22-2 E. coli | ESβL + | D | NT | AMP, PIP, ATM, FEP, CTX, CAZ, CXM, CIP, LEV, TET |
blaVEB-1 blaMOX-2 |
– | – |
a
Sample was subjected to whole-genome sequencing.
b
ESβL, Extended spectrum β-lactamase; CARBA R, carbapenem-resistant; LAC-, lactose non-fermenter.
c
AMC, amoxicillin/clavulanic acid; AMP, ampicillin; PIP, piperacillin; ATM, aztreonam; FEP, cefepime; CTX, cefotaxime; CAZ, ceftazidime; CXM, cefuroxime; CIP, ciprofloxacin; LEV, levofloxacin; TZP, piperacillin-tazobactam, AK, amikacin; GM, gentamicin; TOB, tobramycin; ERT, ertapenem; IMI, imipenem; MEM, meropenem; TET, tetracycline; TMS, trimethoprim/sulfamethoxazole.
d
-, isolate was not checked for the presence of resistance genes due to phenotypic susceptibility.
e
NT, not tested.