Table 1 Primers and probes used in the nucleic acid amplification test
Organism | Target | Sequence | Reference | |
|---|---|---|---|---|
Streptococcus pneumoniae | lytA | Primer Forward | ACGCAATCTAGCAGATGAAGCA | Silva-Costa C, Gomes-Silva J, Pinho MD, Friães A, Ramirez M, Melo-Cristino J. Continued Vaccine Breakthrough Cases of Serotype 3 Complicated Pneumonia in Vaccinated Children, Portugal (2016–2019). Microbiol Spectr. 2022; e0107722. [1] |
Primer Reverse | TCGTGCGTTTTAATTCCAGCT | |||
Probe | TGCCGAAAACGCTTGATACAGGGAG | |||
wzg | Primer Forward | GCTGTTTTAGCAGATAGTGAGATCGA | Silva-Costa C, Gomes-Silva J, Pinho MD, Friães A, Ramirez M, Melo-Cristino J. Continued Vaccine Breakthrough Cases of Serotype 3 Complicated Pneumonia in Vaccinated Children, Portugal (2016–2019). Microbiol Spectr. 2022; e0107722. [1] | |
Primer Reverse | TCCCAGTCGGTGCTGTCA | |||
Probe | AATGTTACGCAACTGACGAG | |||
Streptococcus pyogenes | spy | Primer Forward | GCACTCGCTACTATTTCTTACCTCAA | Pernica JM, Moldovan I, Chan F, Slinger R. Real-Time Polymerase Chain Reaction for Microbiological Diagnosis of Parapneumonic Effusions in Canadian Children. Canadian Journal of Infectious Diseases and Medical Microbiology. 2014; 25: 151–154 |
Primer Reverse | GTCACAATGTCTTGGAAACCAGTAAT | |||
Probe | CCGCAACTCATCAAGGATT TCTGTTACCA | |||
Staphylococcus aureus | nuc | Primer Forward | AAATTACATAAAGAACCTGCGACA | Edin A, Granholm S, Koskiniemi S, Allard A, Sjöstedt A, Johansson A. Development and laboratory evaluation of a real-time PCR assay for detecting viruses and bacteria of relevance for community-acquired pneumonia. J Mol Diagn. 2015;17: 315–324 |
Primer Reverse | GAATGTCATTGGTTGACCTTTGTA | |||
Probe | AATTTAACCGTATCACCATCAATCGCTTT | |||
Haemophilus influenzae | siaT | Primer Forward | AATGCGTGATGCTGGTTATGAC | Price EP, Harris TM, Spargo J, Nosworthy E, Beissbarth J, Chang AB, et al. Simultaneous identification of Haemophilus influenzae and Haemophilus haemolyticus using real-time PCR. Future Microbiology. 2017; 12: 585–593 |
Primer Reverse | AAGAGTTTTGCGATAGATTCATTGG | |||
Probe | AGAAGCAGCAGTAATT | |||
Mycoplasma pneumoniae | P1 | Primer Forward | GGAATCCCAATGCACAAGAACA | Edin A, Granholm S, Koskiniemi S, Allard A, Sjöstedt A, Johansson A. Development and laboratory evaluation of a real-time PCR assay for detecting viruses and bacteria of relevance for community-acquired pneumonia. J Mol Diagn. 2015; 17: 315–324 |
Primer Reverse | GCTTTGGTCAACACATCAACCTT | |||
Probe | AACTCTTACGCAATCTAGCAGATGAA | |||
Mycobacterium tuberculosis | IS6110 | Primer Forward | GTCGAACGGCTGATGACCAAACT | Choi Y, Jeon B-Y, Shim TS, Jin H, Cho S–N, Lee H. Development of a highly sensitive one-tube nested real-time PCR for detecting Mycobacterium tuberculosis. Diagnostic Microbiology and Infectious Disease. 2014; 80: 299–303 |
Primer Reverse | TCCGAAGCGGCGCTGGACGA | |||
Probe | ACCACGATCGCTGATCCGGCCACA | |||
Streptococcus agalactiae | cfb | Primer Forward | GGGAACAGATTATGAAAAACCG | Diaz MH, Waller JL, Napoliello RA, Islam MS, Wolff BJ, Burken DJ, et al. Optimization of Multiple Pathogen Detection Using the TaqMan Array Card: Application for a Population-Based Study of Neonatal Infection. PLOS ONE. 2013; 8: e66183 |
Primer Reverse | AAGGCTTCTACACGACTACCAA | |||
Probe | AGACTTCATTGCGTGCCAACCCTGAGAC | |||
Human (positive control) | RNAseP | Primer Forward | CCAAGTGTGAGGGCTGAAAAG | Centers for Disease Control and Prevention (CDC). PCR for Detection and Characterization of Bacterial Meningitis Pathogens: Neisseria meningitidis, Haemophilus influenzae, and Streptococcus pneumoniae. Available: http://www.cdc.gov/meningitis/lab-manual/chpt10-pcr.pdf |
Primer Reverse | TGTTGTGGCTGATGAACTATAAAAGG | |||
Probe | CCCCAGTCTCTGTCAGCACTCCCTTC | |||