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. 2019 Apr 24;9:6494. doi: 10.1038/s41598-019-42846-y

Table 4.

Oligonucleotide primers and probea sequences for quantitative molecular Fluidigm detection of respiratory pathogen.

TargetName Primer/Probename Forward primer Reverse primer Probe Reference
Streptococcus pneumoniae lytA TCTTACGCAATCTAGCAGATGAAGC GTTGTTTGGTTGGTTATTCGTGC TTTGCCGAAAACGCTTGATACAGGG McAvinet al.31
Haemophilus influenzae IGA CAAAATTGCCAAGATTAAATGCTT TGCTCGCCATACTGCACA A CCTGCGGTTAAACC This study
Haemophilus influenzaetype A HiA GCAACCATCTTACAACTTAGCGAATAC GGTCTGCGGTGTCCTGTGTT AAGTGAAGCATGTCGCCATTCGTCCA Maaroufi et al.32
Haemophilus influenzaetype B HiB TGTTCGCCATAACTTCATCTTAGC CTTACGCTTCTATCTCGGTGATTAATAA CACAAAACTTCTCATTCTTCGAGCCTA Maaroufi et al.32
Haemophilus influenzaetype C HiC TCTGTGTAGATGATGGTTCAGTAG TTAGGATATTTACGCTGCCATT TGCAGCTAAGATTATT Maaroufi et al.32
Haemophilus influenzaetype D HiD TATTGATGACCGATACAACCTGTTTAAA CCAGAAATTATTTCTCCGTTATGTTGA AATGGTTGTAAAACTCTTCT Maaroufi et al.32
Haemophilus influenzaetype E HiE GTTGAAAACAAACCGCACTTT ATCTTTAATTACCAGATCCCTTTCAT AACGAATGTAGTGGTAGTTAGA Maaroufi et al.32
Haemophilus influenzaetype F HiF GGATAATCAAATACCACATTGGCTTA GTAGATTAGCCTCAATAACATGTGAATTAA TCATCGTGAGATCATTGATCACGAT Maaroufi et al.32
BexA BexA CTGAATTRGGYGATTATCTTTATGA ACAATCAAAYTCAACHGAAAGHGA AGGGATGAAAGCYCGRCTTGCAT Maaroufi et al.32
Staphylococcus aureus SA GCTCAGCAAATGCATCACAAA CACTATATACTGTTGGATCTTCAGAACCA AGATAACGGCGTAAATA This Study
Moraxella catarrhalis MCAT CCGCTTTTACAACCACTGCTT TGTATCGCCTGCCAAGACAA CAGCTGTTAGCCAGCC This Study
Streptococcus pyogenes SPY GCACTCGCTACTATTTCTTACCTCAA GTCACAATGTCTTGGAAACCAGTAAT CCGCAACTCATCAAGGATTTCTGTTACCA CDC 2008
Neisseria meningitidis SodC GCACACTTAGGTGATTTACCTGCAT CCACCCGTGTGGATCATAATAGA CATGATGGCACAGCAACAAATCCTGTTT Thomas et al.33
Neisseria lactamica LacZ TTGCCCGAGAACCATTGTATC GCGGTTCTTATCACGTTCTATATTTG TATTGGAGCGGACTAAA ThisStudy
Bordetella pertusis and Bordetella holmesii IS481 CAAGGCCGAACGCTTCAT GAGTTCTGGTAGGTGTGAGCGTAA CAGTCGGCCTTGCGTGAGTGGG Tattiet al.34
Bordetella holmesii hIS1001 GGCGACAGCGAGACAGAATC GCCGCCTTGGCTCACTT CGTGCAGATAGGCTTTTAGCTTGAGCGC Tattiet al.34
Bordetella parapertusis pIS1001 TCGAACGCGTGGAATGG GGCCGTTGGCTTCAAATAGA AGACCCAGGGCGCACGCTGTC Tattiet al.34
Bordetella pertusis, Bordetella parapertusis and Bordetella bronchiseptica PtxS CGCCAGCTCGTACTTC GATACGGCCGGCATT AATACGTCGACACTTATGGCGA Tattiet al.34
Streptococcus pneumoniae serotype 1 1 CGTGCGGTAATTGAAGCTATGA TGTGGCCCCAGCAACTCT TGCTTGCCCTTGTATAGGGT Azzariet al.35
Streptococcus pneumoniae serotype 3 3 GGTCAGCAGAAAGTATGCATTGG TCGTTTATCCAGGGTCTGATGA TATTGGATGTGGTTTATCGTGAAGA Azzariet al.35
Streptococcus pneumoniae serotype 4 4 TGGGATGACATTTCTACGCACTA CCGTCGCTGATGCTTTATCA TCCTATTGGATGGTTAGTTGGTGA Azzariet al.35
Streptococcus pneumoniae serotype 5 5 TTACGGGAGTATCTTATGTCTTTAATGG CAGCATTCCAGTAGCCTAAAACTAGA TTGTCTCAGCAACTCTATTTGGCTGTGGG Azzariet al.35
Streptococcus pneumoniae serogroup 6A/B/C/D 6A/B/C/D AAGTTTGCACTAGAGTATGGGAAGGT ACATTATGTCCRTGTCTTCGATACAAG TGTTCTGCCCTGAGCAACTGG Azzariet al.35
Streptococcus pneumoniae serogroup 6C/D 6C/D TTGGGATGATTGGTCGTATTAG CTCTTCAATTAGTTCTTCAGTTCG CCACGCAATTCGCCATC Azzariet al.35
Streptococcus pneumoniae serogroup 7A/F 7A/F GATGGCATGTGGCAAACCA TTTGCCCTCCTTAATCATTTCAC TTGGCTATCGGCATGGTGGT Azzariet al.35
Streptococcus pneumoniae serotype 7C 7C CGTCAGGAATAGGTGCAATCTCT TGAAATTCCAAGCGAAGCAA TTC ATCTATTGGTTCTTATGGTGTT ThisStudy
Streptococcus pneumoniae serotype 8 8 CCACTCATCAGTTTCCCATATGTTT TCAATAATTGAAGAAGCGAACGTT TGATGGCAGATGGGTTGGGACGAG Azzariet al.35
Streptococcus pneumoniae serogroup 9A/L/N/V 9A/L/N/V TGGAATGGGCAAAGGGTAGTA TCGGTTCCCCAAGATTTTCTC TTAATCATGCTAACGGCTCATCGA Azzariet al.35
Streptococcus pneumoniae serotype 10A 10A CCTCTCCTATCAACTATTACTCATTATACTACCT AATAACCATAAGTCCCTAGATCATTCAAAG TCATTACAACTCCCTATGTGACACGGGTCTTTT Azzariet al.35
Streptococcus pneumoniae serogroup 11A/B/C/D/F 11A/B/C/D/F ACCGCATTTCTTATCGCACTATATT TCTCCTTACCATCAAACATGTTAATCA TGAATCAGTCTGACCGTTT ThisStudy
Streptococcus pneumoniae serogroup 12ABF/44/46 12A/12B/12F/44/46 GATTATTCGCTTGCCTCTTCATG ATAGCCGAAATAAGCTTTCCAGAA ATTTGTAAGCGGACGTGCGATT Azzariet al.35
Streptococcus pneumoniae serotype 13 13 TCGGATTTAGTAGTAACCCCATTGA TTCTTGATTGAGGATGCATTTCC AGTAGTAAGAGATCATATTCAAG ThisStudy
Streptococcus pneumoniae serotype 14 14 CGACTGAAATGTCACTAGGAGAAGAT AATACAGTCCATCAATTACTGCAATACTC TGTCATTCGTTTGCCAATACTTGATGGTCTC Azzariet al.35
Streptococcus pneumoniae serogroup 15A/B/C/F 15A/B/C/F TTGAATCAGGTAGATTGATTTCTGCTA CTCTAGGAATCAAATACTGAGTCCTAATGA CTCCGGCTTTTGTCTTCTCTGT Azzariet al.35
Streptococcus pneumoniae serogroup 16F 16F GCAACTGGTATTTTTGATATTGGAGAA CAAAGGAATGCCATGCCATA AAAATGCTAACTTCGTTGGAGG ThisStudy
Streptococcus pneumoniae serotype 17F 17F GTAAAGATTTCATGTCCTATAAGGGAGAA AGGCGTCCCTGTTTATGAGAAG TTGTACATGGTCTGGATTT ThisStudy
Streptococcus pneumoniae serogroup 18A/B/C 18A/B/C CCTGTTGTTATTCACGCCTTACG TTGCACTTCTCGAATAGCCTTACTC AACCGTTGGCCCTTGTGGTGGA Azzariet al.35
Streptococcus pneumoniae serotype 19A 19A TTCGACGACGTATCAGCTTCA TCATTGAGAGCCTTAACCTCTTCA ACCCAAAACGGTTGACGCATTATACT Azzariet al.35
Streptococcus pneumoniae serogroup 19B/F 19B/F GGTCATGCGAGATACGACAGAA TCCTCATCAGTCCCAACCAATT ACCTGAAGGAGTAGCTGCTGGAACGTTG Azzariet al.35
Streptococcus pneumoniae serotype 20 20 AAAGATACTGGCTGAGGAGCTATCTATT AGTCAAAAGTACTCAACCATTCTGATATATTC AGGATAAGGTCTACTTTGTGGGAGTTC Azzariet al.35
Streptococcus pneumoniae serotype 21 21 CCATTTGAAGGACCAGTTGTTG AAAAAGCCACTATCAGGAATACCAA AATGGCATTGCTTCGTAAA ThisStudy
Streptococcus pneumoniae serotype 22A/F 22A/F TCTATTAAATAACCCATTGGAATTGAAACG TCGCAATTGAAGACCACATAAACTG TCCGTAAT”T”CGCTTATGGGCACATTCTCCA Azzariet al.35
Streptococcus pneumoniae serogroup 23A/B/F 23A/B/F GGTGGACTTTCCGATGCAA CACTGTCAACAAAAATGAGGTAATCTC AAATGTCGGTATAGATAAAG ThisStudy
Streptococcus pneumoniae serotype 23F 23F TGCTATTTGCGATCCTGTTCAT AGAGCCTCCGTTGTTTCGTAAA TTTCTCCGGCATCAAACGTTAAG Azzariet al.35
Streptococcus pneumoniae serogroup 25A/25F/38 25A/25F/38 GTCTTACGTAGAACCTCTCTGGATGA TGGTCCTACAAGCGACATGTG TTGCCACAGATTTGGAATATTTTGGTCGG ThisStudy
Streptococcus pneumoniae serogroup 34/37/17A 34/37/17A GGATACTATGTACGAACAGATGGACTTG CTCACTAACTCGCCCGAATAAAC CCGACTATACTCCATTTGA ThisStudy
Streptococcus pneumoniae serotype 35B 35B GCATGGAGGTGGAGCATACA TGTAAAGACTGCACAACTCGATATAAAA CAATTTAAACAATATTAGTAAAGCGCAGGTCAAGCAAA Azzariet al.35

Probea: Minor Grove Binding (MGB) FAM labelled TaqMan probes.