Table A1.
Target genes, calculated detection limits and oligonucleotides used for the resistance-gene-specific and pathogen-specific real-time PCR assays. Hyphens in the oligonucleotide sequences have been inserted to increase the readability, not to delineate codon triplets.
| PCR Target | CTX-M-Type Beta-Lactamase (Groups I–V) |
|---|---|
| Target gene | bla CTX-M |
| Detection limit | <102 copies/µL |
| Forward primer I | 5′-GCT-GGA-CTG-CCT-GCT-TCC-T-3′ |
| Forward primer II | 5′-TGC-CGA-AAT-CAT-GGG-TAG-TG-3′ |
| Forward primer III | 5′-CTA-CCC-ACA-TCG-TGG-GTT-GTC-3′ |
| Forward primer IV/V | 5′-ATT-CGG-GCC-GGC-TTA-CC-3′ |
| Reverse primer I | 5′-CGT-TGG-TGG-TGC-CAT-AGY-CA-3′ |
| Reverse primer II | 5′-TCG-TTG-GTG-GTG-CCA-TAA-TCT-3′ |
| Reverse primer III | 5′-GAT-GTC-ATT-CGT-CGT-ACC-ATA-ATC-A-3′ |
| Reverse primer IV | 5′-ATC-ATT-GGT-GGT-GCC-GTA-GYC-3′ |
| Reverse primer V | 5′-GCG-ATA-TCA-TTC-GTC-GTA-CCA-TAA-3′ |
| Probe and modifications | 5‘-VIC-CCG-CTG-CCG-GTC-TTA-TC-MGB-NFQ-3‘ |
| Positive control plasmid insert | 5′-CGC-AGC-CAG-CAT-TCG-GGC-CGG-CTT-ACC-GAC-GTC-GTG-GAC-TGT-GGG-TGA-TAA-GAC-CGG-CAG-CGG-CGA-CTA-CGG-CAC-CAC-CAA-TGA-TAT-TGC-GGT-GA-3′ |
| GenBank accession number of the insert | OM355481.1 |
| Reference | [59] |
| PCR target | VIM-type beta-lactamase |
| Target gene | bla VIM |
| Detection limit | <102 copies/µL |
| Forward primer | 5′-GAG-ATT-CCC-ACG-CAY-TCT-CTA-GA-3′ |
| Reverse primer | 5′-AAT-GCG-CAG-CAC-CAG-GAT-AG-3′ |
| Probe and modifications | 5′-JOE-ACG-CAG-TGC-GCT-TCG-GTC-CAG-T-BHQ1-3′ |
| Positive control plasmid insert | 5′-AGA-GGG-GAG-CGA-GAT-TCC-CAC-GCA-CTC-TCT-AGA-AGG-ACT-CTC-ATC-GAG-CGG-GGA-CGC-AGT-GCG-CTT-CGG-TCC-AGT-AGA-ACT-CTT-CTA-TCC-TGG-TGC-TGC-GCA-TTC-GAC-CGA-CAA-3′ |
| GenBank accession number of the insert | NG_050338.1 |
| Reference | [59] |
| PCR target | IMP-type beta-lactamase |
| Target gene | bla IMP |
| Detection limit | <102 copies/µL |
| Forward primer | 5′-GGC-GGA-ATA-GAG-TGG-CTT-AAT-TCT-C-3′ |
| Reverse primer I | 5′-GAA-TTT-TTA-GCT-TGT-ACT-TTA-CCG-TCT-TT-3′ |
| Reverse primer II | 5′-ATT-TTT-AGC-TTG-TAC-CTT-ACC-GTA-TT-3′ |
| Reverse primer III | 5′-TTT-GTA-GCT-TGC-ACC-TTA-TTG-TCT-TT-3′ |
| Probe I and modifications | 5′-FAM-ATG-CAT-CTG-AAT-TAA-C-MGB-TAMRA-3′ |
| Probe II and modifications | 5‘-FAM-TAT-*GCA-TCT-*GAA-T*TA-A*CA-AAT-*GA-TAMRA-3‘ |
| Positive control plasmid insert | 5′-CGA-CAG-CAC-GGG-CGG-AAT-AGA-GTG-GCT-TAA-TTC-TCA-ATC-TAT-CCC-CAC-GTA-TGC-ATC-TGA-ATT-AAC-AAA-TGA-ACT-TCT-TAA-AAA-AGA-CGG-TAA-AGT-ACA-AGC-TAA-AAA-TTC-ATT-TAG-CGG-AG-3′ |
| GenBank accession number of the insert | NG_049212.1 |
| Reference | [59] |
| PCR target | NDM-type beta-lactamase |
| Target gene | bla NDM |
| Detection limit | <102 copies/µL |
| Forward primer | 5′-CAT-TAG-CCG-CTG-CAT-TGA-TG-3′ |
| Reverse primer | 5′-GTC-GCC-AGT-TTC-CAT-TTG-CT-3′ |
| Probe and modifications | 5′-ROX-CAT-GCC-CGG-TGA-AAT-CCG-CC-BHQ2-3′ |
| Positive control plasmid insert | 5′-CTG-AGC-ACC-GCA-TTA-GCC-GCT-GCA-TTG-ATG-CTG-AGC-GGG-TGC-ATG-CCC-GGT-GAA-ATC-CGC-CCG-ACG-ATT-GGC-CAG-CAA-ATG-GAA-ACT-GGC-GAC-CAA-CGG-TTT-GGC-3′ |
| GenBank accession number of the insert | NG_088409.1 |
| Reference | [59] |
| PCR target | KPC-type beta-lactamase |
| Target gene | bla KPC |
| Detection limit | <102 copies/µL |
| Forward primer | 5′-TGC-AGA-GCC-CAG-TGT-CAG-TTT-3′ |
| Reverse primer | 5′-CGC-TCT-ATC-GGC-GAT-ACC-A-3′ |
| Probe and modifications | 5′-Cy5-TTC-CGT-CAC-GGC-GCG-CG-BHQ2-3′ |
| Positive control plasmid insert | 5′-GGC-CTT-CAT-GCG-CTC-TAT-CGG-CGA-TAC-CAC-GTT-CCG-TCT-GGA-CCG-CTG-GGA-GCT-GGA-GCT-GAA-CTC-CGC-CAT-CCC-AGG-CGA-TGC-GCG-CTA-TAC-CTC-ATC-GCC-GCG-CGC-CGT-GAC-GGA-AAG-CTT-ACA-AAA-ACT-GAC-ACT-GGG-CTC-TGC-ACT-GGC-TGC-GC-3′ |
| GenBank accession number of the insert | NG_067225.1 |
| Reference | [59] |
| PCR target | OXA-23-like-type beta-lactamase |
| Target gene | blaOXA-23-like |
| Detection limit | <102 copies/µL |
| Forward primer | 5′-TAA-ATG-GAA-GGG-CGA-GAA-3′ |
| Reverse primer | 5′-ACC-TGC-TGT-CCA-ATT-TCA-G-3′ |
| Probe and modifications | 5′-FAM-CCA-TGA-AGC-TTT-CTG-CAG-TCC-CAG-TC-TAMRA-3′ |
| Positive control plasmid insert | 5′-ATG-AAA-TAT-TTA-AAT-GGA-AGG-GCG-AGA-AAA-GGT-CAT-TTA-CCG-CTT-GGG-AAA-AAG-ACA-TGA-CAC-TAG-GAG-AAG-CCA-TGA-AGC-TTT-CTG-CAG-TCC-CAG-TCT-ATC-AGG-AAC-TTG-CGC-GAC-GTA-TCG-GTC-TTG-ATC-TCA-TGC-AAA-AAG-AAG-TAA-AAC-GTAT-TGG-TTT-CGG-TAA-TGC-TGA-AAT-TGG-ACA-GCA-GGT-TGA-TAA-TTT-C-3′ |
| GenBank accession number of the insert | OM310935.1 |
| Reference | [60] |
| PCR target | OXA-40/24-like-type beta-lactamase |
| Target gene | blaOXA-40/24-like |
| Detection limit | <102 copies/µL |
| Forward primer | 5′-TGA-CTT-TAG-GTG-AGG-CAA-TG-3′ |
| Reverse primer | 5′-GTT-ATG-TGC-AAG-GTC-ATC-GG-3′ |
| Probe and modifications | 5′-Cy5-TGC-AAG-ACG-GAC-TGG-CCT-AGA-GCT-AAT-BHQ2-3′ |
| Positive control plasmid insert | 5′-GAG-AAA-GAT-ATG-ACT-TTA-GGT-GAG-GCA-ATG-GCA-TTG-TCA-GCA-GTT-CCA-GTA-TAT-CAA-GAG-CTT-GCA-AGA-CGG-ACT-GGC-CTA-GAG-CTA-ATG-CAG-AAA-GAA-GTA-AAG-CGG-GTT-AAT-TTT-GGA-AAT-ACA-AAT-ATT-GGA-ACA-CAG-GTC-GAT-AAT-TTT-TGG-TTA-GTT-GGC-CCC-CTT-AAA-ATT-ACA-CCA-GTA-CAA-GAA-GTT-AAT-TTT-GCC-GAT-GAC-CTT-GCA-CAT-AAC-CGA-TTA-CCT-T-3′ |
| GenBank accession number of the insert | NG_078047.1 |
| Reference | [60] |
| PCR target | OXA-48-like-type beta-lactamase |
| Target gene | blaOXA-48-like |
| Detection limit | <102 copies/µL |
| Forward primer | 5′-AGG-GCG-TAG-TTG-TGC-TC-3′ |
| Reverse primer | 5′-GTG-TTC-ATC-CTT-AAC-CAC-GC-3′ |
| Probe and modifications | 5′-ROX-TCT-TAA-ACG-GGC-GAA-CCA-AGC-AT-BHQ2-3′ |
| Positive control plasmid insert | 5′-CAT-AAA-TCA-CAG-GGC-GTA-GTT-GTG-CTC-TGG-AAT-GAG-AAT-AAG-CAG-CAA-GGA-TTT-ACC-AAT-AAT-CTT-AAA-CGG-GCG-AAC-CAA-GCA-TTT-TTA-CCC-GCA-TCT-ACC-TTT-AAA-ATT-CCC-AAT-AGC-TTG-ATC-GCC-CTC-GAT-TTG-GGC-GTG-GTT-AAG-GAT-GAA-CAC-CAA-GTC-TTT-A-3′ |
| GenBank accession number of the insert | ON651448.1 |
| Reference | [60] |
| PCR target | OXA-58-like-type beta-lactamase |
| Target gene | blaOXA-58-like |
| Detection limit | <102 copies/µL |
| Forward primer | 5′-ATT-GGC-ACG-TCG-TAT-TGG-3′ |
| Reverse primer | 5′-CCC-CTC-TGC-GCT-CTA-CAT-A-3′ |
| Probe and modifications | 5′-JOE-AGT-GAA-TTG-CAA-CGT-ATT-GGT-TAT-GGC-A-BHQ1-3′ |
| Positive control plasmid insert | 5′-TAT-ATC-AAG-AAT-TGG-CAC-GTC-GTA-TTG-GTC-CAA-GCT-TAA-TGC-AAA-GTG-AAT-TGC-AAC-GTA-TTG-GTT-ATG-GCA-ATA-TGC-AAA-TAG-GCA-CGG-AAG-TTG-ATC-AAT-TTT-GGT-TGA-AAG-GGC-CTT-TGA-CAA-TTA-CAC-CTA-TAC-AAG-AAG-TAA-AGT-TTG-TGT-ATG-ATT-TAG-CCC-AAG-GGC-AAT-TGC-CTT-TTA-AAC-CTG-AAG-TTC-AGC-AAC-AAG-TGA-AAG-AGA-TGT-TGT-ATG-TAG-AGC-GCA-GAG-GGG-AGA-ATC-GTC-T-3′ |
| GenBank accession number of the insert | KY660721.1 |
| Reference | [60] |
| PCR target | GES-type beta-lactamase |
| Target gene | bla GES |
| Detection limit | <102 copies/µL |
| Forward primer | 5′-TGG-CTA-AAG-TCC-TCT-ATG-3′ |
| Reverse primer | 5′-CAA-CCC-AAT-CTT-TAG-GAA-A-3′ |
| Probe and modifications | 5′-FAM-CGT-CTC-CCG-TTT-GGT-TTC-CG-TAMRA-3′ |
| Positive control plasmid insert | 5′-GCA-CGT-ACT-GTG-GCT-AAA-GTC-CTC-TAT-GGC-GGC-GCA-CTG-ACG-TCC-ACC-TCG-ACC-CAC-ACC-ATT-GAG-AGG-TGG-CTG-ATC-GGA-AAC-CAA-ACG-GGA-GAC-GCG-ACA-CTA-CGA-GCG-GGT-TTT-CCT-AAA-GAT-TGG-GTT-GTT-GGA-GAG-AA-3′ |
| GenBank accession number of the insert | NG_080773.1 |
| Reference | [61] |
| PCR target | NMC-A/IMI-type beta-lactamase |
| Target gene | bla NMC-A/IMI |
| Detection limit | <102 copies/µL |
| Forward primer | 5′-GTC-ACT-TAA-TGT-AAA-ACC-AA-3′ |
| Reverse primer | 5′-CTA-CCA-TTG-AAA-TCT-GTT-TC-3′ |
| Probe and modifications | 5′-Cy5-AGC-CAT-CTT-GTT-TAG-CTC-TTG-TTT-AGT-BHQ2-3′ |
| Positive control plasmid insert | 5′-ATG-TCA-CTT-AAT-GTA-AAA-CCA-AGC-AGA-ATA-GCC-ATC-TTG-TTT-AGC-TCT-TGT-TTA-GTT-TCA-ATA-TCA-TTT-TTC-TCA-CAG-GCC-AAT-ACA-AAG-GGC-ATC-GAT-GAT-ATT-AAA-AAC-CTT-GAA-ACA-GAT-TTC-AAT-GGT-AGA-ATT-GGT-GTC-3′ |
| GenBank accession number of the insert | NG_065426.1 |
| Reference | [61] |
| PCR target | BIC-type beta-lactamase |
| Target gene | bla BIC |
| Detection limit | <102 copies/µL |
| Forward primer | 5′-GGA-GAA-ACG-TAT-CGA-CTA-TA-3′ |
| Reverse primer | 5′-TCC-AGA-AGC-AAA-TTT-GTC-3′ |
| Probe and modifications | 5′-JOE-CAC-CGT-TGT-CGC-TGT-ACT-GC-BHQ1-3′ |
| Positive control plasmid insert | 5′-AAG-GCT-TAC-TGG-AGA-AAC-GTA-TCG-ACT-ATA-AGA-ATC-GGG-TGA-TGG-AAC-CTC-ACT-CTC-CCA-TCA-GCG-CAC-AAC-ATA-GTT-CGA-CGG-GTA-TGA-CCG-TGG-CGC-AAT-TAG-CGG-CAG-CGG-CGC-TGC-AGT-ACA-GCG-ACA-ACG-GTG-CGA-CAA-ATT-TGC-TTC-TGG-AAA-ACG-TTC-TG-3′ |
| GenBank accession number of the insert | NG_048708.1 |
| Reference | [61] |
| PCR target | SME-type beta-lactamase |
| Target gene | bla SME |
| Detection limit | <102 copies/µL |
| Forward primer | 5′-GGC-TCA-GGT-ATG-ACA-TTA-3′ |
| Reverse primer | 5′-TCT-CCA-ATA-GAA-CGC-ATA-A-3′ |
| Probe and modifications | 5′-ROX-CTC-AGG-ACC-GCC-AAG-AAA-TCG-BHQ2-3′ |
| Positive control plasmid insert | 5′-AAA-ATA-TAA-AGG-CTC-AGG-TAT-GAC-ATT-AGG-TGA-TAT-GGC-TTC-TGC-TGC-ATT-GCA-ATA-TAG-CGA-CAA-TGG-GGC-AAC-AAA-TAT-AAT-TAT-GGA-ACG-ATT-TCT-TGG-CGG-TCC-TGA-GGG-GAT-GAC-TAA-ATT-TAT-GCG-TTC-TAT-TGG-AGA-TAA-TGA-GTT-T-3′ |
| GenBank accession number of the insert | MN182491.1 |
| Reference | [61] |
| PCR target | GIM-type beta-lactamase |
| Target gene | bla GIM |
| Detection limit | <102 copies/µL |
| Forward primer | 5′-TCG-ACA-CAC-CTT-GGT-CTG-AA-3′ |
| Reverse primer | 5′-AAC-TTC-CAA-CTT-TGC-CAT-GC-3′ |
| Probe and modifications | 5′-FAM-CAC-GAA-GTT-GTT-ATT-ATC-CTG-GGC-GAC-T-TAMRA-3′ |
| Positive control plasmid insert | 5′-GCC-TAT-ATT-ATC-GAC-ACA-CCT-TGG-TCT-GAA-GAA-GAC-ACG-AAG-TTG-TTA-TTA-TCC-TGG-GCG-ACT-GAC-AGG-GGA-TAC-CAG-GTT-ATG-GCT-AGC-ATC-TCA-ACT-CAT-TCT-CAT-GGA-GAT-CGC-ACT-GCT-GGT-ATC-AAG-TTG-CTA-AAT-TCA-AAG-TCA-ATT-CCT-ACA-TAC-ACA-TCA-GAG-TTA-ACT-AAA-AAG-CTT-CTT-GCC-CGT-GAA-GGA-AAG-CCG-GTT-CCT-ACC-CAC-TAC-TTT-AAA-GAC-GAC-GAA-TTC-ACA-CTG-GGA-AAT-GGG-CTT-ATA-GAG-CTC-TAC-TAT-CCA-GGT-GCT-GGG-CAT-ACA-GAG-GAT-AAT-ATT-GTT-GCT-TGG-TTA-CCC-AAA-AGC-AAA-ATA-CTA-TTT-GGT-GGC-TGC-CTC-GTG-AGG-AGT-CAT-GAG-TGG-GAA-GGC-TTA-GGT-TAC-GTA-GGC-GAC-GCC-TCA-ATT-AGC-TCT-TGG-GCT-GAC-TCA-ATT-AAA-AAT-ATT-GTA-TCG-AAA-AAA-TAT-CCC-ATT-CAA-ATG-GTC-GTT-CCG-GGG-CAT-GGC-AAA-GTT-GGA-AGT-TCA-GAT-ATA-TT-3′ |
| GenBank accession number of the insert | MK847892.1 |
| Reference | [62], probe from this study |
| PCR target | DIM-type beta-lactamase |
| Target gene | bla DIM |
| Detection limit | <102 copies/µL |
| Forward primer | 5′-GCT-TGT-CTT-CGC-TTG-CTA-ACG-3′ |
| Reverse primer | 5′-CGT-TCG-GCT-GGA-TTG-ATT-TG-3′ |
| Probe and modifications | 5′-Cy5-ACA-CAT-CAT-ACA-GTC-GTG-TGA-ATG-GGT-TTG-BHQ2-3′ |
| Positive control plasmid insert | 5′-CTT-CTA-TTC-AGC-TTG-TCT-TCG-CTT-GCT-AAC-GAC-GAG-GTA-CCT-GAG-CTA-AGA-ATC-GAG-AAA-GTA-AAA-GAG-AAC-ATC-TTT-TTG-CAC-ACA-TCA-TAC-AGT-CGT-GTG-AAT-GGG-TTT-GGT-TTG-GTC-AGT-TCA-AAC-GGC-CTT-GTT-GTC-ATA-GAT-AAG-GGT-AAT-GCT-TTC-ATT-GTT-GAT-ACA-CCT-TGG-TCA-GAC-CGA-GAT-ACA-GAA-ACG-CTC-GTA-CAT-TGG-ATT-CGT-AAA-AAT-GGT-TAT-GAG-CTA-CTG-GGG-AGT-GTT-TCT-ACT-CAT-TGG-CAT-GAG-GAT-AGA-ACC-GCA-GGA-ATT-AAA-TGG-CTT-AAT-GAC-CAA-TCA-ATT-TCT-ACG-TAT-GCC-ACG-ACT-TCA-ACC-AAC-CAT-CTC-TTG-AAA-GAA-AAT-AAA-AAA-GAG-CCA-GCG-AAA-TAC-ACC-TTG-AAA-GGA-AAT-GAG-TCC-ACA-TTG-GTT-GAC-GGC-CTT-ATC-GAA-GTA-TTT-TAT-CCA-GGA-GGT-GGT-CAT-ACA-ATA-GAC-AAC-GTA-GTG-GTG-TGG-TTG-CCA-AAG-TCG-AAA-ATC-TTA-TTT-GGC-GGC-TGT-TTT-GTG-CGT-AGC-CTT-GAT-TCC-GAG-GGG-TTA-GGC-TAC-ACT-GGT-GAA-GCC-CAT-ATT-GAT-CAA-TGG-TCC-CGA-TCA-GCT-CAG-AAT-GCT-CTG-TCT-AGG-TAC-TCA-GAA-GCC-CAG-ATA-GTA-ATT-CCT-GGC-CAT-GGG-AAA-ATC-GGG-GAT-ATA-GCG-CTG-TTA-AAA-CAC-ACC-AAA-AGT-CTG-GCT-GAG-ACA-GCC-TCT-AAC-AAA-TCA-ATC-CAG-CCG-AAC-GCT-AAC-GCG-TC-3′ |
| GenBank accession number of the insert | NG_049077.1 |
| Reference | [62], probe from this study |
| PCR target | Treponema pallidum |
| Target gene | polA |
| Detection limit | <102 copies/µL |
| Forward primer | 5′-AGG-ATC-CGG-CAT-ATG-TCC-AA-3′ |
| Reverse primer | 5′-GTG-AGC-GTC-TCA-TCA-TTC-CAA-A-3′ |
| Probe and modifications | 5′-FAM-ATG-CAC-CAG-CTT-CGA-MGB-NFQ-3′ |
| Positive control plasmid insert | 5′-TCT-GCT-GTG-CAG-GAT-CCG-GCA-TAT-GTC-CAA-GCT-GTC-ATG-CAC-CAG-CTT-CGA-CGT-CTT-TGG-AAT-GAT-GAG-ACG-CTC-ACA-CTT-GTT-ATG-3′ |
| GenBank accession number of the insert | U57757.1 |
| Reference | [63] |
| PCR target | Chlamydia trachomatis (screening) |
| Target gene | Chlamydia trachomatis cryptic plasmid sequence |
| Detection limit | <102 copies/µL |
| Forward primer | 5′-GGA-TTG-ACT-CCG-ACA-ACG-TAT-TC-3′ |
| Reverse primer | 5′-ATC-ATT-GCC-ATT-AGA-AAG-GGC-ATT-3′ |
| Probe and modifications | 5′-Cy5-TTA-CGT-GTA-GGC-GGT-TTA-GAA-AGC-GG-BHQ2-3′ |
| Positive control plasmid insert | 5′-TAC-TAA-TAC-AGG-ATT-GAC-TCC-GAC-AAC-GTA-TTC-ATT-ACG-TGT-AGG-CGG-TTT-AGA-AAG-CGG-TGT-GGT-ATG-GGT-TAA-TGC-CCT-TTC-TAA-TGG-CAA-TGA-TAT-TTT-AGG-AA-3′ |
| GenBank accession number of the insert | CP010570.1 |
| Reference | [64] |
| PCR target | Chlamydia trachomatis (differentiation) |
| Target gene | pmpH |
| Detection limit | <102 copies/µL |
| Forward primer | 5′-GGA-TAA-CTC-TGT-GGG-GTA-TTC-TCC-T-3′ |
| Reverse primer | 5′-AGA-CCC-TTT-CCG-AGC-ATC-ACT-3′ |
| Probe and modifications (pan-serovar) | 5′-FAM-CCT-GCT-CCA-ACA-GT-MGB-NFQ-3′ |
| Probe and modifications (A-K-serovars only) | 5′-ROX-GCT-TGA-AGC-AGC-AGG-AGC-TGG-TG-BHQ2-3′ |
| Positive control plasmid insert (pan-serovar) | 5′-TTG-ATT-TTC-TGG-GAT-AAC-TCC-GTG-GGG-TAT-TCT-CCT-TTA-TCT-ACT-GTG-CCA-ACC-TCA-TCA-TCA-ACT-CCG-CCT-GCT-CCA-ACA-GTT-AGT-GAT-GCT-CGG-AAA-GGG-TCT-ATT-TTT-TCT-G-3′ |
| GenBank accession number of the insert | AY184168.1 |
| Positive control plasmid insert (A-K-serovars only) | 5′-GTG-ATT-TTT-TGG-GAT-AAC-TCT-GTG-GGG-TAT-TCT-CCT-TTG-TCT-ATT-GTG-CCA-GCA-TCG-ACT-CCA-ACT-CCT-CCA-GCA-CCA-GCA-CCA-GCT-CCT-GCT-GCT-TCA-AGC-TCT-TTA-TCT-CCA-ACA-GTT-AGT-GAT-GCT-CGG-AAA-GGG-TCT-ATT-TTT-TCT-G-3′ |
| GenBank accession number of the insert | AY184158.1 |
| Reference | [64] |
| PCR target | Mycoplasma genitalium |
| Target gene | sequence of the MgPA operon |
| Detection limit | <102 copies/µL |
| Forward primer | 5′-GAG-AAA-TAC-CTT-GAT-GGT-CAG-CAA-3′ |
| Reverse primer | 5′-GTT-AAT-ATC-ATA-TAA-AGC-TCT-ACC-GTT-GTT-ATC-3′ |
| Probe and modifications | 5‘-ROX-AC*T-TT*G-CAA-*TC*A-*GAA-*GGT-BHQ2-3‘ |
| Positive control plasmid insert | 5′-CAA-TGC-TGT-TGA-GAA-ATA-CCT-TGA-TGG-TCA-GCA-AAA-CTT-TGC-AAT-CAG-AAG-GTA-TGA-TAA-CAA-CGG-TAG-AGC-TTT-ATA-TGA-TAT-TAA-CTT-AGC-AAA-AA-3′ |
| GenBank accession number of the insert | M31431.1 |
| Reference | [65,66] |
| PCR target | Neisseria gonorrhoeae (PCR 1 out of 2) |
| Target gene | multi-copy opa genes |
| Detection limit | <102 copies/µL |
| Forward primer | 5′-TTG-AAA-CAC-CGC-CCG-GAA-3′ |
| Reverse primer | 5′-TTT-CGG-CTC-CTT-ATT-CGG-TTT-AA-3′ |
| Probe and modifications | 5′-JOE-CCG-ATA-TAA-TC*C-GTC-*CTT-CAA-*CAT-CAG-BHQ1-3′ |
| Positive control plasmid insert | 5′-CCA-TAT-TGT-GTT-GAA-ACA-CCG-CCC-GGA-ACC-CGA-TAT-AAT-CCG-TCC-TTC-AAC-ATC-AGT-GAA-AAT-CTT-TTT-TTA-ACC-GGT-TAA-ACC-GAA-TAA-GGA-GCC-GAA-AAT-GAA-TCC-AG-3′ |
| GenBank accession number of the insert | X52372.1 |
| Reference | [67] |
| PCR target | Neisseria gonorrhoeae (PCR 2 out of 2) |
| Target gene | porA pseudogene |
| Detection limit | <102 copies/µL |
| Forward primer | 5′-CAG-CAT-TCA-ATT-TGT-TCC-GAG-TC-3′ |
| Reverse primer | 5′-GAA-CTG-GTT-TCA-TCT-GAT-TAC-TTT-CCA-3′ |
| Probe and modifications | 5′-Cy5-CGC-CTA-TAC-GCC-TGC-TAC-TTT-CAC-GC-BHQ2-3′ |
| Positive control plasmid insert | 5′-GTT-TCA-GCG-GCA-GCA-TTC-AAT-TTG-TTC-CGA-GTC-AAA-ACA-GCA-AGT-CCG-CCT-ATA-CGC-CTG-CTA-CTT-TCA-CGC-TGG-AAA-GTA-ATC-AGA-TGA-AAC-CAG-TTC-CGG-CTG-TTG-T-3′ |
| GenBank accession number of the insert | AJ010732.1 |
| Reference | [67] |
| PCR target | Schistosoma haematobium complex |
| Target gene | Dra1 multi-copy sequence |
| Detection limit | 5 × 102 copies/µL |
| Forward primer | 5′-GAT-CTC-ACC-TAT-CAG-ACG-AAA-C-3′ |
| Reverse primer | 5′-TCA-CAA-CGA-TAC-GAC-CAA-C-3′ |
| Probe and modifications | 5′-JOE-TGT-TGG-TGG-AAG-GCC-TGT-TTG-CAA-BHQ1-3′ |
| Positive control plasmid insert | 5‘-AAA-TTG-GAT-CTC-ACC-TAT-CAG-ACG-AAA-CAA-AGA-AAA-TTT-TAA-AAT-TGT-TGG-TGG-AAG-TGC-CTG-TTT-CGC-AAT-ATC-TCC-GGA-ATG-GTT-GGT-CGT-ATC-GTT-GTG-AAA-ATT-G-3‘ |
| GenBank accession number of the insert | DQ157698.1 |
| Reference | [68] |
| PCR target | Schistosoma mansoni complex |
| Target gene | Sm1-7 multi-copy sequence |
| Detection limit | 5 × 102 copies/µL |
| Forward primer | 5′-CCA-CGC-TCT-CGC-AAA-TAA-TCT-3′ |
| Reverse primer | 5′-CAA-CCG-TTC-TAT-GAA-AAT-CGT-TGT-3′ |
| Probe and modifications | 5′-FAM-TCC-GAA-ACC-ACT-GGA-CGG-ATT-TTT-ATG-AT-BHQ1-3′ |
| Positive control plasmid insert | 5‘-TCC-GAC-CAA-CCG-TTC-TAT-GAA-AAT-CGT-TGT-ATC-TCC-GAA-ACC-ACT-GGA-CGG-ATT-TTT-ATG-ATG-TTT-GTT-TTA-GAT-TAT-TTG-CGA-GAG-CGT-GGG-CGT-TA-3‘ |
| GenBank accession number of the insert | M61098.1 |
| Reference | [68] |
MGB = minor groove binding, * = subsequent base is locked nucleic acid (LNA).