Table 5 Primers used in the present study
Panel | Primer pair | Sequence (5′ to 3′) | Annealing temp (°C) | Product size (bp) | Ref. |
|---|---|---|---|---|---|
Phylogenetic grouping | |||||
 Quadruplex | chuA | F: ATGGTACCGGACGAACCAAC R: TGCCGCCAGTACCAAAGACA | 59 | 288 | [23] |
yjaA | F: CAAACGTGAAGTGTCAGGAG R: AATGCGTTCCTCAACCTGTG | 211 | |||
TspE4.C2 | F: CACTATTCGTAAGGTCATCC R: AGTTTATCGCTGCGGGTCGC | 152 | |||
arpA | F: AACGCTATTCGCCAGCTTGC R: TCTCCCCATACCGTACGCTA | 400 | |||
 Group E | arpA | F: GATTCCATCTTGTCAAAATATGCC R: GAAAAGAAAAAGAATTCCCAAGAG | 57 | 219 | |
 Group C | trpA | F: AGTTTTATGCCCAGTGCGAG R: TCTGCGCCGGTCACGCCC | 59 | 489 | |
β- Lactamase/ESBL genes | |||||
 Triplex | BlaTEM | F: CATTTCCGTGTCGCCCTTATTC R: CGTTCATCCATAGTTGCCTGAC | 57 | 800 | [50] |
BlaSHV | F: AGCCGCTTGAGCAAATTAAAC R: ATCCCGCAGATAAATCACCAC | 713 | |||
BlaOXA | F: GGCACCAGATTCAACTTTCAAG R: GACCCCAAGTTTCCTGTAAGTG | 564 | |||
 Uniplex | BlaCTX-M | F: ATGTGCAGYACCAGTAARGTKATGGC R: TGGGTRAARTARGTSACCAGAAYCAGCGG | 61 | 593 | [51] |
APEC virulence genotyping | |||||
 iroN | F: AATCCGGCAAAGAGACGAACCGCCT R: GTTCGGGCAACCCCTGCTTTGACTTT | 60 | 553 | [5] | |
 ompT | F: TCATCCCGGAAGCCTCCCTCACTACTAT R: TAGCGTTTGCTGCACTGGCTTCTGATAC | 496 | |||
 hlyF | F: GGCCACAGTCGTTTAGGGTGCTTACC R: GGCGGTTTAGGCATTCCGATACTCAG | 450 | |||
 iss | F: CAGCAACCCGAACCACTTGATG R: AGCATTGCCAGAGCGGCAGAA | 323 | |||
 iutA | F: GGCTGGACATCATGGGAACTGG R: CGTCGGGAACGGGTAGAATCG | 302 | |||
Plasmid replicon typing | |||||
 1 | B/O | F: GCGGTCCGGAAAGCCAGAAAAC R: TCTGCGTTCCGCCAAGTTCGA | 60 | 159 | [35] |
FIC | F: GTGAACTGGCAGATGAGGAAGG R: TTCTCCTCGTCGCCAAACTAGAT | 262 | |||
A/C | F: GAGAACCAAAGACAAAGACCTGGA R: ACGACAAACCTGAATTGCCTCCTT | 465 | |||
P | F: CTATGGCCCTGCAAACGCGCCAGAAA R: TCACGCGCCAGGGCGCAGCC | 534 | |||
T | F: TTGGCCTGTTTGTGCCTAAACCAT R: CGTTGATTACACTTAGCTTTGGAC | 750 | |||
 2 | K/B | F: GCGGTCCGGAAAGCCAGAAAAC R: TCTTTCACGAGCCCGCCAAA | 60 | 160 | |
W | F: CCTAAGAACAACAAAGCCCCCG R: GGTGCGCGGCATAGAACCGT | 242 | |||
FIIA | F: CTGTCGTAAGCTGATGGC R: CTCTGCCACAAACTTCAGC | 270 | |||
FIA | F: CCATGCTGGTTCTAGAGAAGGTG R: GTATATCCTTACTGGCTTCCGCAG | 462 | |||
FIB | F: GGAGTTCTGACACACGATTTTCTG R: CTCCCGTCGCTTCAGGGCATT | 702 | |||
Y | F: AATTCAAACAACACTGTGCAGCCTG R: GCGAGAATGGACGATTACAAAACTTT | 765 | |||
 3 | I1 | F: CGAAAGCCGGACGGCAGAA R: TCGTCGTTCCGCCAAGTTCGT | 60 | 139 | |
Frep | F: TGATCGTTTAAGGAATTTTG R: GAAGATCAGTCACACCATCC | 270 | |||
X | F: AACCTTAGAGGCTATTTAAGTTGCTGAT R: TGAGAGTCAATTTTTATCTCATGTTTTAGC | 376 | |||
HI1 | F: GGAGCGATGGATTACTTCAGTAC R: TGCCGTTTCACCTCGTGAGTA | 471 | |||
N | F: GTCTAACGAGCTTACCGAAG R: GTTTCAACTCTGCCAAGTTC | 559 | |||
HI2 | F: TTTCTCCTGAGTCACCTGTTAACAC R: GGCTCACTACCGTTGTCATCCT | 644 | |||
L/M | F: GGATGAAAACTATCAGCATCTGAAG R: CTGCAGGGGCGATTCTTTAGG | 785 | |||