Table 2.
Phenotypic antimicrobial resistance (AMR) profile, resistance genes, and gene mutations for AMR of ESBL- and ESBL-/AmpC-producing Escherichia spp. isolates from clams.
| Isolate No. | β-lactamase profile | Phenotypic AMR | Resistance genes and/or mutations | |||||||
|---|---|---|---|---|---|---|---|---|---|---|
| β-lactams | Quinolone and Fluoroquinolone | Tetracycline | Aminoglycoside | Sulf | Phenicol and trimethoprim | Spec | MLS | |||
| AN2 | ESBL | AMP AZI (NS) FOT NAL TET SMX TMP (MDR) | bla CTX-M-27 | gyrA (p.S83L) | tet(A) | aph (3′′)-Ib aph(6)-Id aadA5 | sul1 sul2 | dfrA17 | aadA5 | mph(A) |
| AN9 | ESBL | AMP FOT FEP (SSD) TAZ (I) SMX | bla CTX-M-15 | |||||||
| AN1 | ESBL | AMP FOT TAZ CHL NAL TET SMX (MDR) | bla SHV12 | gyrA (p.D87N) | tet(A) tet(B) | aadA1 aadA2b | sul3 | cmlA1 | aadA1 aadA2b | |
| AN 5 | ESBL | AMP FOT | bla CTX-M-1 | |||||||
| AN6 | ESBL/AmpC | AMP FOT TAZ NAL TET FOX CIP (MDR) | blaCMY-2 blaOXA-1 blaTEM-126/blaTEM-106blaTEM-1B | aac(6′)-Ib-cr parC (p.S80I) gyrA (p.D87N) gyrA (p.S83L) | tet(A) | aac(6′)-Ib-cr | ||||
| AN8 | ESBL | AMP AZI (NS) FOT FEP (SSD) | bla CTX-M-14 | aac(6′)-Ib-cr | aac(6′)-Ib-cr aac(6′)-Ib3 | cmlA1 | mph(A) | |||
| AN3 | ESBL | AMP FOT TMP TET SMX FEP (SSD) (MDR) | blaCTX-M-1 blaTEM-1B | qnrS1 | tet(A) | aph(3″)-Ib aph(6)-Id aadA2b | sul2 | dfrA5 | aadA2b | mph(A) |
| AN4 | ESBL/AmpC | AMP FOT TAZ (I), NAL FOX FEP (SSD) | blaCTX-M-14 blaCMY-2 blaTEM-1B | gyrA (p.S83L) | ||||||
| AN13 | ESBL/AmpC* | AMP FOT SMX FOX FEP (SSD) (MDR) | bla CTX-M-1 | sul2 | ||||||
| AN7 | ESBL | AMP FOT CIP TAZ (I) CHL NAL TMP TET SMX FEP (SSD) (MDR) | bla CTX-M-55 blaTEM-1B | gyrA (p.D87Y) gyrA (p.S83L) parE (p.S458A) parC (p.S80I) | tet(A) | aph(3′)-Ia aph(3″)-Ib aph(6)-Id | sul2 | catA2 dfrA14 | ||
| AN10 | ESBL | AMP FOT TAZ (I) FEP SMX | blaCTX-M-15 blaTEM-35 | gyrA (p.S83A) | ||||||
| AN11 | ESBL/AmpC** | AMP FOT CIP TAZ NAL GEN SMX FOX (I) FEP (MDR) | blaCTX-M-15 blaOXA-1 blaTEM-1B | aac(6′)-Ib-cr gyrA (p.D87N) gyrA (p.S83L) parC (p.S80I) parC (p.E84V) parE (p.I529L) | aac(6′)-Ib-cr aac(3)-IIa | |||||
| AN12 | ESBL | AMP FOT CHL TMP TET GEN SMX FEP (SSD) (MDR) | blaCTX-M-15 blaTEM-1B | qnrS1 | tet(M) tet(A) | aph(3′)-Ia aph(3′′)-Ib aph(6)-Id aadA1 aac(3)-IId | sul2 sul3 | cmlA1 dfrA14 dfrA12 | aadA1 | lnu(F) |
*Mutations in the ampC-promoter: ampC-promoter: p.L9R, ampC-promoter:p.R8C, ampC-promoter:p.R11Q. **Mutation in the ampC-promoter: ampC-promoter:g.-28G > A. Genes indicated in black and bold were identified with 100% length coverage and 100% sequence identity. Genes indicated in black were identified with 100% length coverage and identity ≥ 95%. In brackets: SDD, susceptible dose-dependent; I, intermediate; NS, non-susceptible; Sulf, Sulfonamide; Spec, spectinomycin; MLS, macrolides–lincosamides–streptogramins.