Table 1.
Primers sets and multiplex PCRs used in analysis of APEC.
| Gene | Amplicon size (bp) | Primer sequence (5′-3′) | Description | References |
|---|---|---|---|---|
| MULTIPLEX 1 | ||||
| malX | 925 | GGACATCCTGTTACAGCGCGCA | ||
| TCGCCACCAATCACAGCCGAAC | ||||
| papA | 717 | ATGGCAGTGGTGTTTTGGTG | Pap operon | (16) |
| CGTCCCACCATACGTGCTCTTC | ||||
| fimH | 508 | TCGAGAACGGATAAGCCGTGG | Type 1 fimbriae | (16) |
| GCAGTCACCTGCCCTCCGGTA | ||||
| kpsIII | 392 | TCCTCTTGCTACTATTCCCCCT | Capsule | (16) |
| AGGCGTATCCATCCCTCCTAAC | ||||
| papEF | 326 | GCAACAGCAACGCTGGTTGCATCAT | Pap operon | (16) |
| AGAGAGAGCCACTCTTATACGGACA | ||||
| ireA | 254 | GATGACTCAGCCACGGGTAA | Iron acquisition | (15) |
| CCAGGACTCACCTCACGAAT | ||||
| ibeA | 171 | AGGCAGGTGTGCGCCGCGTAC | Invasin | (16) |
| TGGTGCTCCGGCAAACCATGC | ||||
| MULTIPLEX 2 | ||||
| cnf-1 | 1,105 | ATCTTATACTGGATGGGATCATCTTGG | Cytotoxic necrotizing factor | (16) |
| GCAGAACGACGTTCTTCATAAGTATC | ||||
| fyuA | 787 | TGATTAACCCCGCGACGGGAA | Iron acquisition | (16) |
| CGCAGTAGGCACGATGTTGTA | ||||
| ironEC | 667 | AAGTCAAAGCAGGGGTTGCCCG | Salmochelin | (15) |
| GACGCCGACATTAAGACGCAG | ||||
| bmaE | 507 | ATGGCGCTAACTTGCCATGCTG | Heme-agglutinin | (16) |
| AGGGGGACATATAGCCCCCTTC | ||||
| sfa-foc | 410 | CTCCGGAGAACTGGGTGCATCTTAC | Fimbriae | (16) |
| CGGAGGAGTAATTACAAACCTGGCA | ||||
| aerJ | 302 | GGCTGGACATCATGGGAACTGG | Aerobactin | (16) |
| CGTCGGGAACGGGTAGAATCG | ||||
| papGIII | 258 | GGCCTGCAATGGATTTACCTGG | Pap operon | (16) |
| CCACCAAATGACCATGCCAGAC | ||||
| MULTIPLEX 3 | ||||
| hlyD | 904 | CTCCGGTACGTGAAAAGGAC | Hemolysin D | (15) |
| GCCCTGATTACTGAAGCCTG | ||||
| rfc | 788 | ATCCATCAGGAGGGGACTGGA | O antigen polymerase | |
| AACCATACCAACCAATGCGAG | ||||
| ompT | 559 | ATCTAGCCGAAGAAGGAGGC | OM protein | (15) |
| CCCGGGTCATAGTGTTCATC | ||||
| papGI' | 479 | CTACTATAGTTCATGCTCAGGTC | Pap operon | (16) |
| CCTGCATCCTCCACCATTATCGA | ||||
| papGI | 461 | TCGTGCTCAGGTCCGGAATTT | Pap operon | (16) |
| TGGCATCCCCCAACATTATCG | ||||
| kpsII | 272 | GCGCATTTGCTGATACTGTTG | Capsule | (16) |
| CATCCAGACGATAAGCATGAGCA | ||||
| papC | 205 | GTGGCAGTATGAGTAATGACCGTTA | Pap operon | (16) |
| ATATCCTTTCTGCAGGGATGCAATA | ||||
| MULTIPLEX 4 | ||||
| gafD | 952 | TGTTGGACCGTCTCAGGGCTC | Fimbria | (16) |
| TCCCGGAACTCGCTGTTACT | ||||
| cvaC | 679 | CACACACAAACGGGAGCTGTT | colIV operon | (16) |
| CTTCCCGCAGCATAGTTCCAT | ||||
| fliC | 547 | ACGATGCAGGCAACTTGACG | Flagellar gene | (15) |
| GGGTTGGTCGTTGCAGAACC | ||||
| cdtS | 430 | GAAAATAAATGGAACACACATGTCCG | Toxin | (16) |
| GAAAGTAAATGGAATATAAATGTCCG | ||||
| focG | 364 | CAGCACAGGCAGTGGATACGA | Fimbrial subunit | (16) |
| GAATGTCGCCTGCCCATTGCT | ||||
| traT | 290 | GGTGTGGTGCGATGAGCACAG | Complement resistance | (16) |
| CACGGTTCAGCCATCCCTGAG | ||||
| papGII | 190 | GGGATGAGCGGGCCTTTGAT | Pap operon | (16) |
| CGGGCCCCCAAGTAACTCG | ||||
| MULTIPLEX 5 | ||||
| papGI | 1,140 | CTGTAATTACGGAAGTGATTTCTG | Pap operon | |
| TTCCAGAAATAGCTCATGTAACCCG | ||||
| papGII&III | 1,070 | CTGTAATTACGGAAGTGATTTCTG | Pap operon | |
| ACTATCCGGCTCCGGATAAACCAT | ||||
| iha | 829 | CTGGCGGAGGCTCTGAGATCA | UPEC island | |
| TCCTTAAGCTCCCGCGGCTGA | ||||
| afa | 594 | GGCAGAGGGCCGGCAACAGGC | Adhesin Afa | |
| CCCGTAACGCGCCAGCATCTC | ||||
| iss | 323 | CAGCAACCCGAACCACTTGATG | Increased serum survival | (17) |
| AGCATTGCCAGAGCGGCAGAA | ||||
| sfaS | 244 | GTGGATACGACGATTACTGTG | Fimbrial minor subunit | (16) |
| CCGCCAGCATTCCCTGTATTC | ||||
| K1 | 153 | TAGCAAACGTTCTATTGGTGC | Capsule | (16) |
| CATCCAGACGATAAGCATGAGCA | ||||
| MULTIPLEX 6 | ||||
| hlyF | 599 | GGCGATTTAGGCATTCCGATACTC | Hemolysin F | |
| ACGGGGTCGCTAGTTAAGGAG | ||||
| etsB | 537 | CAGCAGCGCTTCGGACAAAATCTCCT | E. coli transport system | |
| TTCCCCACCACTCTCCGTTCTCAAAC | ||||
| colM | 498 | CAGCGCCATTACCCCATAAATAGTGA | Colicin M | |
| GGTTCGTTCGCCGGTGTAAGCGTTAG | ||||
| etsA | 450 | CAACTGGGCGGGAACGAAATCAGGA | E. coli transport system | |
| TCAGTTCCGCGCTGGCAACAACCTAC | ||||
| colB | 430 | ACAAGACAGCACCAGTTATGGGTATT | Colicin B | |
| GTTGTTGGTTTTGTTGGCGTAGTTAT | ||||
| eitB | 380 | TGATGCCCCGCCAAACTCAAGA | Iron transport system | |
| ATGCGCCGGCCTGACATAAGTGCTAA | ||||
| eitA | 284 | ACGCCGGGTTAATAGTTGGGAGATAG | Iron transport system | |
| ATCGATAGCGTCAGCCCGGAAGTTAG | ||||
| MULTIPLEX 8 | ||||
| blaTEM | 558 | ATGTGCGCGGAACCCCTATTTGTTTA | Ampicillin resistance | |
| AAAAAGCGGTTAGCTCCTTCGGTCCT | ||||
| aac3VI | 502 | GGCACCCGCGACGCCCTGGTCCAAAAG | Gentamicin resistance | |
| GGGCCCGGCGCCGATCGACAGGATTT | ||||
| tetB | 446 | AACGCGTGAAGTGGTTCGGTTGGT | Tetracycline resistance | |
| TTCGCCCCATTTAGTGGCTATTCTTC | ||||
| tetA | 372 | CGGGGCGACTGGGGCGGTAGC | Tetracycline resistance | |
| CAAAGCGCGGCCGGCACCTGT | ||||
| groEL | 318 | CGCCGGCATGAACCCGATGGACCTCA | Chaperone | |
| TCGGCCTGCATCGACTGCGGGTTGTTG | ||||
| aph(3)IA | 278 | TCGGGCAATCAGGTGCGACAATCTA | Gentamicin resistance | |
| TGCCAGCGCATCAACAATATTTTCACC | ||||
| drf17 | 243 | ATATCCCGTGGTCAGTAAAAGGTG | Trimethoprim resistance | |
| GACCCCCGCCAGAGACATA | ||||
| MULTIPLEX 12 | ||||
| terX | 576 | ATGCGCCGCCTGCCTGTTTACCTTGTTA | Tellurite resistance | |
| CGCGCTTGTGCTGCCGGAAGACA | ||||
| pcoA | 507 | ATCCGGAAGGTCAGCACCGTCCATAGAC | Copper resistance | |
| GACCTCGCGGATGTCAGTGGCTACACCT | ||||
| terF | 428 | CCGACAAACTTCCAGAAGATGGGGTAGT | Tellurite resistance | |
| GAGGCAGCGGTTGCATTTGTACTTGACG | ||||
| pcoE | 385 | GTGGGGCAGCTTTTGCTCAGTCCAGTGA | Copper resistance | |
| CGAAGCTTTCTTGCCTGCGTCTGATGTG | ||||
| terY3 | 302 | CCTGGGGCCGTCAGCGGACCTG | Tellurite resistance | |
| TCCTTGCTGGTGGCCGTTCATACTTCAT | ||||
| terD | 231 | CCACTGCGCGGAATTTCCACTCACCAT | Tellurite resistance | |
| ACGCCGTCCCGTCTGATGTTGACAAG | ||||
| arsC | 153 | CCAGCCTGCGGCACCTCGCGTAATAC | Arsenic resistance | |
| ACGCAGCAGCGCTCGTACTGAAATACCC | ||||
| MULTIPLEX 17 | ||||
| silP | 603 | ACACCCCGGCCTGGGCTCCTT | Silver resistance | |
| TGCGGGCACGGGAACAAACCTC | ||||
| intl1 | 545 | CACTCCGGCACCGCCAACTTTC | Integrase | |
| GAACGGGCATGCGGATCAGTGAG | ||||
| pcoD | 502 | GGCGCCCAGAATGATAATCGCAACA | Copper resistance | |
| GGGCGTGGCGCTGGCTACACTT | ||||
| sulI | 462 | CGCCGCTCTTAGACGCCCTGTCC | Sulfa resistance | |
| CAACGGTGGCGCCCAAGAAGGAT | ||||
| iseC12 | 404 | CGCGGCCACGTAAACCGAAAGATAAA | Transposase | |
| GCGCGGGTGCACAGCAACCTC | ||||
| aadA | 365 | TAACGGCGCAGTGGCGGTTTTCA | Aminoglycoside resistance | |
| AAGCTCGCCGCGTTGTTTCATCAAG | ||||
| aac3VI | 302 | GGGCAAGCGCCGCGTCACTTATT | Gentamicin resistance | |
| CGCGGCGTTGTTTCGGCTTCA | ||||
| qacEdelta1 | 246 | TCGGCCTCCGCAGCGACTTCC | Ammonium resistance | |
| CTTGCCCCTTCCGCCGTTGTCTAAT | ||||
| PHYLOGENETIC TYPING | ||||
| chuA | 288 | ATGGTACCGGACGAACCAAC | (18) | |
| TGCCGCCAGTACCAAAGACA | (19) | |||
| yjaA | 211 | CAAACGTGAAGTGTCAGGAG | (18) | |
| AATGCGTTCCTCAACCTGTG | Quadruplex PCR | (18) | ||
| TspE4.C2 | 152 | CACTATTCGTAAGGTCATCC | (18) | |
| AGTTTATCGCTGCGGGTCGC | (18) | |||
| arpA | 400 | AACGCTATTCGCCAGCTTGC | (18) | |
| TCTCCCCATACCGTACGCTA | (20) | |||
| arpA1 | 301 | GATTCCATCTTGTCAAAATATGCC | Group E | (21) |
| GAAAAGAAAAAGAATTCCCAAGAG | (21) | |||
| trpA | 219 | AGTTTTATGCCCAGTGCGAG | Group C | (21) |
| TCTGCGCCGGTCACGCCC | (21) | |||