Supplementary table 1. PCR primers and reaction parameters

Primer / Sequence (5’ -> 3’) / Target gene/purpose / DNA pol / Annealing T (°C) / Extension time (s) / Expected product size (bp) / Reference
Tn6604 / taagagtgtgttgatagtgc / Tn5398ermB(1) & leader peptide (LP) / Phusion / 54 / 30 / 492 / {Farrow, 2001 #472}
Tn4210 / tcaatagacgttacctgtttac / Phusion
E5 / CTCAAAACTTTTTAACGAGTG / Tn5398 ermB(2) / Phusion / 57 / 30 / 711 / {Spigaglia, 2004 #466}
E6 / CCTCCCGTTAAATAATAGATA / Phusion
TetMd / TGGAATTGATTTATCAACGG / tet(M) / Taq / 60 / 60 / 1080 / {Marchese, 1998 #467}
TetMr / TTCCAACCATACAATCCTTG
NK9 / CCACCAGCTGCAGCCATA / tcdA / Taq / 63 / 45 / 1265 / {Kato, 1998 #468}
NK11 / TGATGCTAATAATGAATCTAAAATGGTAAC
NK104 / GTGTAGCAATGAAAGTCCAAGTTTACGC / tcdB / Taq / 72 / 30 / 203 / {Kato, 1998 #468}
NK105 / CACTTAGCTCTTTGATTGCTGCACCT
PtetM(F110) / GTGATAAGAGTATCTGTCACTGGG / Tn916tet(M)int / Phusion / 64 / 90 / 5700 / This study
IntR1 / CTGGATCCTACTAAGCAACAAGACG
tetM(F) / GTGATAAGAGTATCTGTCACTGGG / Tn5397tet(M)tndX / Phusion / 61 / 90 / 6000
tndX(R1612) / GAGAATGTATCAATGAGACACTG
SG2F / acttaagagtgtgttgatagtgc / Tn5398 DR upstream of LP / Phusion / 57-65 / Dependent on reverse primer
SG3R / gtgggaatggtgcaagt / Tn5398orf3 direct repeat / 65 / 75 / 4137
invF2 / GAAGGAGTGATTACATGAACAAAAA / Gene 11 (ermB) / Phire II / 64 / 120 / Unknown
invR2 / TAGCATCTAATTTAACTTCAATTCC
invF3 / ATATTATGGGGGATAAGACGGTTCGTGTTC / Gene 13 / Phire II / 74 / 60 / Unknown
invR3 / TTGTCATAGCCTTTGTGTTCTGTAATGCC / Gene 12
invF2.1 / TTCTCAAAACTTTTTAACGAGTGA / Gene 11 (ermB) / Phire II / 62 / 60 / Unknown
invR2.1 / CTGCACTATCAACACACTCTTAAGT
P6 / AGTCATACAGTGTCTTAGAAAAGAAC / Transcriptional regulator / Phusion / 61 / 180 / 543 (empty/regenerated site), 13kb
P5 / TCATAATCCTCCAACATACAATATG
TRR4 / TTCAATTCTAGCAAAGCCTG / Transcriptional regulator / Phusion / 62 / 90 / 6000
TPLHSout1 / ATTTCAAGGTCAGCCATGAG / Gene 7
P4 / CTACTTTTCCGGGAGTGT / Gene 17 / Phusion or Taq / 56-60
or
48-57 / 15
or
60 / 524-543
P2 / AAAATCCTTGTCCATGAGG / Gene 1 (ssr)
P1 / CGGTCAAGAACGAGGACG / Gene 1 (ssr)
P3 / ATGTGGGACGTCTTTACTATC / Gene 16 / Phusion
or
Taq / 57-65
or
44-54 / 15
or
60 / 862-880
P2 / AAAATCCTTGTCCATGAGG / Gene 1 (ssr)
P1 / CGGTCAAGAACGAGGACG / Gene 1 (ssr)
P5 / TCATAATCCTCCAACATACAATATG / Transcriptional regulator / Taq / 52 / 60 / 570
P2 / AAAATCCTTGTCCATGAGG / Gene 1 (ssr)
P4 / CTACTTTTCCGGGAGTGT / Gene 17 / Taq / 49 / 60 / 1518
P7 / CAAATGGAAAGCAAGGAATC / Transcriptional regulator
int-F / CATGTGTATGTCGCAAGCAA / ϕC2 integrase / Phusion / 67 / 15 / 1006
Int-R / GGCGTAAGAAAACGTGGAAA
CD80C3U57F / AATGATGGCTCCAATGCTTC / Putative ABC transporter / Taq / 53 / 60 / 379
CD80C3U57R / CATTTCCACCTGGTTTTTCAA
PS13 / GGAGGCAGCAGTGGGGAATA / 16S rRNA / Taq / 53 or 50 / 60 / 1062 / {Persson, 2008 #529}
PS14 / TGACGGGCGGTGTGTACAAG
gntR-F.1 / TTTAGAAGTAAATTCCTTTGTTCCTTT / gntR transcriptional regulator / Taq / 50 / 60 / 599 (uninterrupted ) / {Goh, 2007 #450}
gntR-R / TTGCACATTTAAGATGGTCAGAA
int-3 / CAACCACTATGGACACATATTC / attP / Taq / 50 / 60 / 345
patt-1 / GTAAAGATGATGAAGTGGATGAAG / attP’ / Taq / 50 / 60 / 734

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