TABLE 3.
Profiles of genes conferring resistance to β-lactam antibiotics identified in silico in 17 ESBL-negative MDR isolates of NTS.
| Profile no. | Number of isolates (%) | Isolate ID | Serotype | Year of isolation | MLST | Antimicrobial resistance phenotype | Antimicrobial resistance genes identified by WGS |
||
| Resistance to β-lactams | Resistance to quinolones/fluoroquinolones | Resistance to other classes of antimicrobials | |||||||
| 1 | 9 (52.94%) | A_1153 | S. Typhimurium | 2016 | 328 | AMP, AUG, AZI, IMI* | ftsI (S357N, D350N) | gyrA (D87N) | aac(6′)-Iaa |
| A_4649 | S. Derby | 2016 | 40 | CIP, NAL, SM, S3, TE | ftsI (S357N, D350N) | qnrB10 | aac(6′)-Iy, aadA2, sul1, tet(A) | ||
| A_4970 | S. Derby | 2016 | 40 | CIP, NAL, SM, S3, TE | ftsI (S357N, D350N) | qnrB10 | aac(6′)-Iy, aadA2, sul1, tet(A) | ||
| A_5064 | S. Typhimurium | 2016 | 19 | SM, S3, TE | ftsI (S357N, D350N) | NI** | aac(6′)-Iaa, aph(3′′)-Ib, aph(6)-Id, sul2, tet(A) | ||
| A_6059 | S. Enteritidis | 2016 | 11 | AMP, NAL, C | ftsI (S357N, D350N) | gyrA (D87N) | aac(6′)-Iaa, catII, tet(D) | ||
| A_6187 | S. Enteritidis | 2016 | 11 | AMP*, C, TE | ftsI (S357N, D350N) | NI | aac(6′)-Iaa, catI, tet(A) | ||
| A_7187 | S. Newport | 2013 | 31 | AMP*, NAL, SM*, S3, T/S, TE | ftsI (S357N, D350N) | aac(6′)-Ib-cr | aac(6′)-Iy, aadA16, arr3, dfrA27, tet(A), sul1 | ||
| A_8239 | S. Typhimurium | 2016 | 19 | SM, S3, TE | ftsI (S357N, D350N) | NI | aac(6′)-Iaa, aph(3′′)-Ib, aph(6)-Id, sul2, tet(A) | ||
| G_311 | S. Typhimurium | 2016 | 36 | AMP, AUG*, NAL, C, S3 | ftsI (S357N, D350N) | NI | aac(6′)-Iaa, aph(3′′)-Ib, floR, sul2 | ||
| 2 | 3 (17.65%) | A_1722 | S. Typhimurium | 2012 | 328 | AMP, AUG, CIP*, NAL, C, SM*, TE, S3, T/S | blaOXA–1, ftsI (S357N, D350N) | gyrA (D87N) | aac(6′)-Iaa, aadA, aph(3′)-Ia, catI, sul1, tet(B), tetR |
| A_3889 | S. Typhimurium | 2012 | 328 | AMP, AUG, CRO, TZ*, CIP*, NAL, C, SM*, S3, TE | blaOXA–1, ftsI (S357N, D350N) | gyrA (D87N) | aac(6′)-Iaa, aadA, aph(3′)-Ia, catI, sul1, tet(B), tetR | ||
| A_5923 | S. Typhimurium | 2011 | 328 | AMP, AUG, AZI, CIP*, NAL, C, SM, S3, T/S | blaOXA–1, ftsI (S357N, D350N) | gyrA (D87N) | aac(6′)-Iaa, aadA, aph(3′)-Ia, dfrA19, sul1 | ||
| 3 | 3 (17.65%) | A_478 | S. Kentucky | 2016 | 198 | AMP, AUG*, CIP*, NAL | blaTEM–1, ftsI (S357N, D350N) | gyrA (S83F), parC (S80I) | aac(6′)-Iy |
| A_588 | S. Enteritidis | 2016 | 11 | AMP, CIP*, NAL, SM*, S3, T/S | blaTEM–1, ftsI (S357N, D350N) | gyrA (D87N) | aac(6′)-Iy, aadA5, dfrA17 | ||
| G_1150 | S. Typhimurium | 2016 | 19 | AMP, AUG*, SM, S3, T/S | blaTEM–1, ftsI (S357N, D350N) | NI | aac(6′)-Iaa, aph(3′)-Ia, aph(3′′)-Ib, aph(6)-Id, dfrA5, sul2 | ||
| 4 | 1 (5.88%) | A_7201 | S. Enteritidis | 2016 | 11 | AMP, CRO*, CIP, NAL | blaCTX–M–3, ftsI (S357N, D350N) | NI | aac(6′)-Iaa, rpoB |
| 5 | 1 (5.88%) | G_104 | S. Enteritidis | 2016 | 11 | AMP, AUG*, CRO, TZ, S3 | blaCTX–M–15, ftsI (S357N, D350N) | qnrS1 | aac(6′)-Iaa |
ESBL, extended-spectrum beta-lactamase; MDR, multidrug-resistant; NTS, non-typhoidal Salmonella; MLST, multi locus sequence type; WGS, whole genome sequencing; AMP, ampicillin; AUG, amoxicillin-clavulanic acid; AZI, azithromycin; C, chloramphenicol; CIP, ciprofloxacin; CRO, ceftriaxone; TZ, ceftazidime; IMI, imipenem; NAL, nalidixic acid; SM, streptomycin; TE, tetracycline; T/S, trimethoprim-sulfamethoxazole; S3, sulfonamides. *Intermediate susceptibility to antimicrobial agent. **Not identified (NI).