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Table 1 Oligonucleotide sequences

From: Development of a DNA microarray assay for rapid detection of fifteen bacterial pathogens in pneumonia

AssayOrganismGene targetPrimer (5’-3’)Probe (5’-3’)Product (bp)
Multiplex asymmetric PCR 1Acinetobacter baumanniiCitrate synthase(gltA)F:CTCTGCTGGTATCTCTGCTCTTGTTGCTGAGTTCATGGAAAAAGTTAAACG-TTTTTTTTTTTT-amino222
R:Biotin-TGCTTCAAGAACTTCGTCAC
Staphylococcus aureusThermostable nuclease (nuc)F:AGCGATTGATGGTGATACCAAAGAACTGATAAATATGGACGTGGC-TTTTTTTTTTTT-amino276
R: Biotin-AAGCCTTGACGAACTAAAG
Enterococcus faecalisD-alanine--D-alanine ligase (ddl)F:GAACGACCACAAAATAAAGTTACATGGGCCAAATGGTGAAGATGGAACA-TTTTTTTTTTTT-amino275
R: Biotin-GCCAACAGTTTGTAAAAGAT
Mycoplasma pneumoniaeAdhesin protein (P1)F:TGGTCCTACACCGACTTACATGAGGTGAATGGGTTGTTGAATCCG-TTTTTTTTTTTT-amino107
R: Biotin-TTCCCAAAATAGGTTTCCAC
Multiplex asymmetric PCR 2Enterobacter cloacaeMolecular chaperone (dnaJ)F:GTCACCAAAGAGATCCGTAGCAGGCGATCTGTACGTTCAGG-TTTTTTTTTTTT-amino524
R: Biotin-CGCATGCGGAACAGCTT
Burkholderia cepaciaRecombinase A-like (recA)F:ATATCCAGGTCGTCTCCATGGTGCGCTCGGGCTCGATCGACA-TTTTTTTTTTTT-amino453
R: Biotin-AGTTCGTGCGCTTGATCGT
Klebsiella pneumoniaeMalate dehydrogenase (mdh)F:GCGTGGCGGTAGATCTAAGTCATAAAAGCCGGCGTGTACGATAA-TTTTTTTTTTTT-amino364
R: Biotin-TTCAGCTCCGCCACAAAGGTA
Escherichia coliBacterial alkaline phosphatase (phoA)F:CCAACGATTCTGGAAATGGCGCCAAATCCGCAACGTAATGACAGTGTACCAACCC-TTTTTTTTTTTT-amino527
R: Biotin-CAATGGCTTTGTCGGTCAT
Pseudomonas aeruginosaExotoxin A (toxA)F:TCATCCACGAACTGAACGTTGTGCCTGCTCGACCCGCTGGACGGGGTCTACAACTACCTCGCCCAG-TTTTTTTTTTTT-amino325
R: Biotin-ATCTTGCCTTCCCAGGTAT
Stenotrophomonas maltophiliaChitinase A (chitA)F:TCAAGCAGCTCAAGGCCAATACCACCCGTACCTGGAC-TTTTTTTTTTTT-amino435
R: Biotin-TGGAAGTCGTAGGTCATC
Multiplex asymmetric PCR 3Haemophilus infuenzaeAdhesin protein (P6)F:TCTAACAACGATGCTGCAGGGAACGTGGTACACCAGAATACAACATCGC-TTTTTTTTTTTT-amino296
R: Biotin-CCAGCATCAACACCTTTACC
Legionella pneumophilaMacrophage infectivity potentiator (mip)F: CTACAGACAAGGATAAGTATAGCATTGGTGCCGATTTGGGGAAGAA-TTTTTTTTTTTT-amino108
R: Biotin-CTTGCATGCCTTTAGCCA
Enterococcus faeciumD-alanine--D-alanine ligase (ddl)F:GCTAAAGCCACGCCTTCTATCCTTTTTCCGTCATCAGTATAAAGTATAG-TTTTTTTTTTTT-amino264
R: Biotin-GGTGACGGATGGAAATGTT
Chlamydia pneumoniaeMajor outer membrane protein (ompA)F:GATCCGCTGCTGCAAACTATACTACTGCCGTAGATAGACCTAACCCGGCCTA-TTTTTTTTTTTT-amino85
R:Biotin-GTGAACCACTCTGCATCGTGTAA
Streptococcus pneumoniaeN-acetylmuramoyl-L-alanine amidase (lytA)F: CCATCTGGCTCTACTGTGAACAAAGTAGTACCAAGTGCCATTGATTTTC-TTTTTTTTTTTT-amino433
R: Biotin-GAGAACGGCTTGACGATT
Bacteria (universal primers)16S rDNAF:AGAGTTTGATCMTGGCTCAG(M=A/C) 575
R: Biotin-CGTATTACCGCGGCTGCTG
Acinetobacter spp.16S rDNA CCTAGAGATAGTGGACGTTAC-TTTTTTTTTTTT-amino 
Staphylococcus spp.16S rDNA ACATATGTGTAAGTAACTGTGCACATCTTGACGGTA-TTTTTTTTTTTT-amino 
Enterococcus faecalis16S rDNA AGTGCTTGCACTCAATTGGAAAGAGGAGTGG-TTTTTTTTTTTT-amino 
Mycoplasma spp.16S rDNA GACCTGCAAGGGTTCGT-TTTTTTTTTTTT-amino 
Burkholderia spp.16S rDNA TTGGCTCTAATACAGTCGG-TTTTTTTTTTTT-amino 
Klebsiella spp./Escherichia spp./Enterobacter spp.16S rDNA GGTTAATAACCTCATCGATTGACGTTACCCTGC-TTTTTTTTTTTT-amino 
Pseudomonas spp.16S rDNA TTGCTGTTTTGACGTTAC-TTTTTTTTTTTT-amino 
Stenotrophomonas spp.16S rDNA CCAGCTGGTTAATACCCGGTTGGGA-TTTTTTTTTTTT-amino 
Haemophilus spp.16S rDNA GAGGAAGGTTGATGTGTTA-TTTTTTTTTTTT-amino 
Legionella spp.16S rDNA AGGGTTGATAGGTTAAGAGCTGATTAA-TTTTTTTTTTTT-amino 
Enterococcus faecium16S rDNA CAAGGATGAGAGTAACTGTTCATCCC-TTTTTTTTTTTT-amino 
Chlamydia spp.16S rDNA CCGAATGTAGTGTAATTAGGC-TTTTTTTTTTTT-amino 
Streptococcus spp.16S rDNA TGTGAGAGTGGAAAGTTCACACTG-TTTTTTTTTTTT-amino 
Positive controlBacteria16S rDNA ACTCCTACGGGAGGCAGCAG-TTTTTTTTTTTT-amino 
Negetive control 1HumanEpidermal growth factor receptor (EGFR) TCAGAGCCTGTGTTTCTACCAA-TTTTTTTTTTTT-amino 
Negetive control 2VirusNeuraminidase (NA) CATCAATAGGGTCCGATA-TTTTTTTTTTTT-amino 
Negetive control 3FungusInternal transcribed spacer2 (ITS2) CGAACGCAAATCAATCTTTTTCCAGGT-TTTTTTTTTTTT-amino 
Quality controla 20T Biotin-TTTTTTTTTTTTTTTTTTTT-amino 
  1. F Forward, R Reverse
  2. aRepeat sequence of 20T with an amino-labeled 3’-end, Biotin-labeled 5’-end was used as microarray quality control