Table 3.
Specifications of primers used in the study.
| Target (Subtype) | Primer Name | Sequence (5′ to 3′ Direction) a | Natural (N) or Acquired (A)/Phenotype | Amplicon Size (bp) | Tm (°C) | Reference |
|---|---|---|---|---|---|---|
| ACI (1) | ACI-F/R | CCGTTGACATGGAGAATGG, GCGTGTCGGTTATGGAATT | N/ESBL | 507 | 54 | This study |
| ADC (178) | ADC-F1/R1 | MAACCTAAAAACYCAATCGGTG, YGGATAAGMAAACTCTTCCCA | N/AmpC, ESBL or CARBA | 417–420 | 58 | [34] |
| ADC (29) | ADC-F2/R2 | RGGTTTCTAYCAAGTCGGYA, GCGTTCTTCATTBGGAATACGT | 268 | 59 | ||
| ADC (5) | ADC-F3/R3 | TGGTCTACAATCCGTTCAAGA, GCCGGGGTTAACTCGAAT | 517 | 54 | ||
| ADC (7) | ADC-F4/R4 | TATRATGTGCCGGGTATGG, RTCTGTTTGTACTTCAYCTGG | 318 | 54 | This study | |
| BEL (4) | BEL-F/R | CGTTCCTTGAAGAGTACGC, ACCCGTTACCCATGAATCA | A/ESBL | 401 | 53 | This study |
| BES (1) | BES-F/R | ATAAGCGGGTGCATTATGC, CTTTAAGCCAGCTCACCAG | A/ESBL | 363 | 53 | This study |
| BPS (11) | BPS-F/R | GCTYCAGTACAGCGACAAC, GTCKTGTTGCCGAGCATCCA | N/cephalosporinase or ESBL | 270 | 57 | This study |
| BPU (1) | BPU-F/R | AAGAAAAGTCCCCATGGGT, CGAACTTGTTCGATGGGAG | N/ESBL | 364 | 55 | This study |
| CARB (8) | CARB-F2/R2 | GGGAAAACGTTGGGAACAT, TAATAGCACGCGACCCATA | N or A/BSBL or ESBL | 578 | 54 | |
| CDD (2) | CDD-F/R | AACAAGTGCAAACAATGGC, TTCCTTTACCTTTGGCCCT | N/ESBL | 266 | 52 | This study |
| CdiA (2) | CdiA-F/R | CGTGCTCGCTTTCTTTACT, CACCTGCTCCGGTTTTATC | N/penicillinase or ESBL | 692 | 53 | This study |
| CepA (6) | CepA-F/R | AGTGACAATAATGCCTGCG, TGCTTCGGAATCTTTCACG | N/ESBL | 438 | 52 | This study |
| CfxA (13) | CfxA-F/R | GAAATTGGTGTGGCGGTTA, CAGCACCAAGAGGAGATGT | N or A/BSBL or ESBL | 442 | 53 | This study |
| CGA (1) | CGA-F/R | AGCTACAGTCGGTGTTTCT, TTCATTTTCTGCGCCTGTT | N/ESBL | 640 | 53 | This study |
| CIA (4) | CIA-F/R | GATGGTTTCTGCCTTTGCT, CTTCCGGAAATTTTTCGCG | N/ESBL | 299 | 53 | This study |
| CME (3) | CME-F/R | CCAAAGTGACAACAACGGA, TCCTGAATCGTTCTCAGCA | N/ESBL | 376 | 53 | This study |
| CSP (1) | CSP-F/R | TCTGCTGAGGTTGATTGGA, TCCCACATCATTGGTAGCA | N/ESBL | 346 | 53 | This study |
| CTX-M (208), KLUB (2), KLUG (5), KLUY (5) | CTX-M-F1/R1 | ATGTGCAGYACCAGTAARGT, TGGGTRAARTARGTSACCAGA | N or A/ESBL or CARBA | 593 | 55 | [37] |
| CTX-M (7) | CTX-M-F2/R2 | ATGTGCAGYACCAGYAAAG, GGCCARATCACCGCRATAT | 551 | 56 | [34] | |
| CumA (3) | CumA-F/R | ATCTCCAATGCTATGGGCT, TCACGAGGATCACCATGAA | N/BSBL or ESBL | 483 | 53 | This study |
| DES (1) | DES-F/R | GTTCCAGTTATTCCAGGCG, TGCCAGCACTTTAAAGGTG | N/ESBL | 269 | 53 | This study |
| ERP (1) | ERP-F/R | GTATCGGGCTGTCTCTGAT, GCTGTGCTGTCTGTAATCC | N/ESBL | 477 | 54 | This study |
| FAR (1) | FAR-F/R | CTGAAGAAATCTGGTCGCC, AGCAGTTTCAGGATCTGGT | N/ESBL | 473 | 53 | This study |
| FONA (8) | FONA-F/R | CCGATCTGGTCAACTACAAC, CCCTTCATCCATTCAACCAG | N/ESBL | 340 | 55 | This study |
| GES (45) | GES-F1/R1 | ACGTTCAAGTTTCCGCTAG, GGCAACTAATTCGTCACGT | N or A/ESBL or CARBA | 624 | 53 | [25] |
| GES (1) | GES-F2/R2 | ATGATCGTGGAGTGGAGCCC, AAGAAGCCGATGTCGTTGCG | 448 | 58 | This study | |
| HMB (1), KHM (1) | HMB, KHM-F/R | AAATCGAAGCYTTTTATCCGGG, TTTCCAGCAGCGATGCRTCG | N or A/ESBL or CARBA | 237 | 60 | This study |
| KLUA (12) | KLUA-F/R | CGCTCAATGTTAACGGTGA, TTCATGGCAGTATTGTCGC | N/ESBL | 395 | 52 | This study |
| KLUC (6) | KLUC-F/R | CGATTGCGGAAAAACATGT, CGCCGAGGCTAAWACATC | N or A/ESBL | 521 | 53 | This study |
| KPC (52) | KPC-F/R | CGCTAAACTCGAACAGGAC, CGGTCGTGTTTCCCTTTAG | N or A/ESBL or CARBA | 548 | 54 | [34] |
| LUT (6) | LUT-F/R | TGCTCATGAAAAAGCTGGG, ACCTGTCTTATCGCCTACC | N/BSBL or ESBL | 299 | 54 | This study |
| L2 (18) | L2-F1/R1 | TTCCCGATGTGCAGCAC, TTGCTGCCGGTCTTGTC | N/ESBL | 518 | 53 | [34] |
| OHIO (1) | OHIO-F/R | CTTTCCCATGATGAGCACC, CCCGCAGATAAATCACCAC | A/ESBL | 599 | 54 | This study |
| OXA-1-like (11) | OXA(1)-F/R | TCTGTTGTTTGGGTTTCGC, TCTATGGTGTTTTCTATGGCTG | N or A/NSBL, BSBL or ESBL | 245 | 53 | [27] |
| OXA-2-like (22) | OXA(2)-F/R | GATAGTTGTGGCAGACGAAC, TCCATYCTGTTTGGCGTATC | N or A/ESBL | 603 | 55 | This study |
| OXA-10-like (38) | OXA(3)-F/R | ACAAAGAGTTCTCTGCCGAA, TCCACTTGATTAACTGCGGA | N or A/ESBL | 418 | 53 | This study |
| OXA-18 | OXA(4)-F/R | ACCATCTGGCTGAAGGATT, CAGAAGTTTTCCGACAGGG | A/ESBL | 506 | 54 | This study |
| OXA-23-like (41) | OXA(5)-F/R | ACTAGGAGAAGCCATGAAGC, ATTTTTCCATCTGGCTGCTC | N or A/ESBL or CARBA | 369 | 55 | [34] |
| OXA-45 | OXA(6)-F/R | GCGGTAAACACACTGTCAT, GGGTCAATTGCTGCGAATA | A/ESBL | 333 | 52 | This study |
| OXA-48-like (38) | OXA(7)-F/R | ACCARGCATTTTTACCCGCA, GGCATATCCATATTCATCGC | N or A/ESBL or CARBA | 538 | 55 | This study |
| OXY (28) | OXY-F1/R1 | TAAAGTGATGGCYGCCGC, RTTGGTGGTGCCGTAATC | N/ESBL | 517 | 54 | This study |
| OXY (20) | OXY-F2/R2 | CCCTGCCTTTATTGCTCTG, TTTATCTCCCACGACCCAG | 665 | 54 | ||
| PER (12) | PER-F1/R1 | CTCGACGCTACTGATGGTA, TTCATTGGTTCGGCTTGAC | N or A/ESBL | 820 | 54 | This study |
| PER (3) | PER-F2/R2 | CTGTTAATCGTGCTGCAGT, GACAAATACCGCCACCAAT | 530 | 53 | ||
| PME (1) | PME-F/R | GATCCACTTCAGCGATGAC, GACATCGTGGGTCTTGTTC | A/ESBL | 478 | 54 | This study |
| RAHN (2) | RAHN-F/R | ATGACGTCAGTTCAGCAAC, CATCCATTCCACCAGTTGC | N/ESBL | 555 | 54 | This study |
| RSA1 (1) | RSA-F1/R1 | TCGACGATCCTCACTGTTT, GTTGGTGTTCAAATCGGGT | N or A/ESBL or CARBA | 483 | 53 | This study |
| RSA2 (1) | RSA-F2/R2 | TGTGGACCTTTCCGAAGAA, CGCGATCAGATTACGAGTG | 475 | 55 | ||
| SGM (7) | SGM-F/R | CATGTGCTCGACCTTCAAG, ATCGGCAGCARCAGRTTGG | N/ESBL | 225 | 58 | This study |
| SHV (199) | SHV-F/R | TGGATGCCGNTGACNAACAGC, NTATCGGCGATAAACCAGNCC | N or A/BSBL, ESBL or CARBA | 451 | 59 | [34] |
| SMO (1) | SMO-F/R | CTCACAGACCGTATACCGT, GAATGTCTCATCGCCGATC | N/ESBL | 316 | 54 | This study |
| TEM (199) | TEM-F/R | CACCAGTCACAGAAAAGCA, AGGGCTTACCATCTGGC | N or A/BSBL or ESBL | 450 | 54 | [34] |
| SFO (1) | SFO-F/R | CTCGAGAAAAACTCCGGTG, GTTAGGGTTTGCAGGCTTT | A/ESBL | 473 | 54 | This study |
| TLA (2) | TLA-F/R | GCTAAAGGTACGGATTCGC, CTTAACGCCAAGCTTGCTA | A/ESBL | 417 | 54 | This study |
| TLA2 (1) | TLA2-F/R | ATCGTGCTTGCTGTTTTGA, TCATTTGCCGCATTGTTCT | A/ESBL | 623 | 52 | This study |
| VEB (27) | VEB-F/R | TTTCCGATTGCTTTAGCCG, CCCCAACATCATTAGTGGC | N or A/ESBL | 553 | 54 | [34] |
| YOC (1) | YOC-F/R | CCGGCATCAGAAGAGAAAAA, GGATTCGGGTAGCTTTTGTT | N/ESBL | 467 | 54 | This study |
a For degenerate primers: B = C or G or T; K = G or T; M = A or C; N = any base; R = A or G; S = G or C; W= A or T; Y = C or T. Abbreviations: AmpC—AmpC, ampicillin chromosomal cephalosporinase; BSBL—broad-spectrum β-lactamase; CARBA—carbapenemase; CTX-M, cefotaxime-hydrolyzing β-lactamase–Munich; ESBL—extended-spectrum β-lactamase; GES, Guiana extended-spectrum β-lactamase; KPC, Klebsiella pneumoniae carbapenemase; NDM, New Delhi metallo-β-lactamase; NSBL—narrow-spectrum β-lactamase; OXA, oxacillin carbapenemase/oxacillinase; SHV, sulfhydryl variant of the TEM enzyme; TEM, Temoneira class A extended-spectrum β-lactamase.