Table 4

Primers and probes for detection and sequencing in this study
Targets Assay Name Primers and probes
Mycoplasmas
tuf genea) real-time PCR Mollicutes 414F 5'-TCCAGGWCAYGCTGACTA-3'
Mollicutes 541R 5'-ATTTTWGGAACKCCWACTTG-3'
Probe 451Fa) 5'-G
    G
TGCTG
    C
ACA
    A
ATGG
    A
TGG-3'
tuf gene Sequencing 1st Myco-tuf-F1 5'-HATHGGCCAYRTTGAYCAYGGKAAAA-3'
Myco-tuf-F2 5'-ATGATYACHGGDGCWGCHCAAATGGA-3'
Sequencing 2nd Myco-tuf-R1 5'-CCRCCTTCRCGRATDGAGAAYTT-3'
Myco-tuf-R2 5'-TKTRTGACGDCCACCTTCYTC-3'
16s-23s rRNA intergenic spacer region nested PCR 1st MCGpF11 5'-ACACCATGGGAGYTGGTAAT-3'
R23-1R 5'-CTCCTAGTGCCAAGSCATYC-3'
nested PCR 2nd R16-2 5'-GTGSGGMTGGATCACCTCCT-3'
MCGpR21 5'-GCATCCACCAWAWACYCTT-3'
Orientia tsutsugamushi
47kDa common antigen coding gene real-time PCR Ots-47k-F 5'-AATTCGTCGTGGTATGTTAAATG-3'
Ots-47k-R 5'-AGCAATTCCACATTGTGCTG-3'
Ots-47k-P b) 5'-TGCTTAATGAATTAACTCCAGAATT-3'

a) Locked nucleic acid (LNA) bases (underlined) and was synthesized with the fluorescent reporter 6-carboxyfluorescein (FAM) covalently coupled to the 5’ end and a dark quencher to the 3’ end.

b) TaqMan probe was synthesized with the fluorescent reporter 6-carboxyfluorescein (FAM) covalently coupled to the 5’ end and a dark quencher to the 3’ end.

Ogawa et al.

Ogawa et al. BMC Microbiology 2013 13:32   doi:10.1186/1471-2180-13-32

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