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PF8 Tel + (33) 1 45 68 83 24 |
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- Genes The Mycobacterium abscessus MLST scheme uses internal fragments of the following seven housekeeping genes:
- Primers for PCR amplification
argH : ARGHF GACGAGGGCGACAGCTTC
argH : ARGHSR1 GTGCGCGAGCAGATGATG
cya : ACF : GTGAAGCGGGCCAAGAAG
cya : ACSR1 : AACTGGGAGGCCAGGAGC
glpK : GLPKSF1 : AATCTCACCGGCGGTGTC
glpK : GLPKSR2 : GGACAGACCCACGATGGC
gnd : GNDF : GTGACGTCGGAGTGGTTGG
gnd : GNDSR1 : CTTCGCCTCAGGTCAGCTC
murC : MURCSF1 : CGGACGAAAGCGACGGCT
rmurC : MURCSR2 : CCAAAACCCTGCTGAGCC
pta : PTASF1 : GATCGGGCGTCATGCCCT
pta : PTASR2 : ACGAGGCACTGCTCTCCC
purH : PURHSF1 : CGGAGGCTTCACCCTGGA
purH : PURHSR2 : CAGGCCACCGCTGATCTG
- Sequencing primers
The same primers as for PCR are used.
- PCR conditions Conditions for housekeeping genes amplification were 5 minutes at 94°C followed by 30 cycles of 94°C for 1 minute, 58°C for 1 minute and 72°C for 1 minute with a final extension step at 72°C for 10 minutes. - Allele templates (M. abscessus CIP104536T alleles) argH (480 bp)
GTGAGCACCAACGAAGGCTCGCTGTGGGGCGGCCGGTTCGCCGGCGGCCCAGCCCCGGCGCTGGCGGCATTGAGCAAATCCACTC
ATTTCGATTGGGCGCTGGCGCCTTACGACATTCAGGCGTCGGTTGCTCATGCCCGAGTGCTCCGCAAGGCGGGCCTGCTCACCGA TGAACAACTCGGTGCCCTGGTCGAGGGCTTAGAGCAGCTGGGTCGGGATGTCGCGTCGGGCGTGTTCGTCCCAGCCGATACCGAC GAGGACGTACACGGTGCCCTCGAACGCGGGTTGATCGAACGGGTGGGCCCTGACATCGGCGGCCGTCTCCGTGCCGGCCGATCCC GAAACGATCAGGTGGCCACACTGTTTCGGATGTGGCTGCGCGACGCGGCCGGACGCATCTCCGAGGGCGTGCTCGACGTCGTGCA GGCATTGGCGGATCAGGCCGGGGCACATCCGGATGCGATCATGCCGGGCAAGACT cya (510 bp)
CTGGTGGGGTCCACCCAGTTGGCGTCCACTCGGGGGCCTGCGGTGGTCGTACGGGTGCTCAACGAGTTCTTCCGGGTCATCGTCG
ACACCGTCAACAAGCACGGCGGCTTCGTGAACAAGTTCCAGGGTGACGCGGCGCTGGCGATTTTTGGTGCCCCGATCGACCACCC GGACGGCGCCGCAGCGGCACTTGCGGCCGCTCGTGAGCTGTCGGGCGAGCTGACCAATGTGTTGGGCTCCAATGACTTCGGCATA GGAGTCTCCGCCGGACGGGCGATCGCCGGGCATATCGGCGCACAGGCCCGATTCGAGTACACCGTGATCGGCGACCCGGTGAACG AAGCGGCCCGACTCACCGAGCTGGCTAAGAACGAGCCGGGCAACGTGCTCGCGTCGGCCTCCGCAGTCATGGAGGCGCGCGACGA GGAGGCACTGCGCTGGGATGTCGGCGAGACCGTCGAACTGCGCGGCCGCACGGTCTCAACGCAGGTTGCGCGCCCGCGTCACGGC glpK (534 bp)
GTGACAAATGCCAGTCGCACCATGTTGATGAACCTGGAGACCCTGGACTGGGATGACGAGCTGTTGTCGTTCTTTTCCATTCCGC
GCCAGATGCTTCCGCCGATCAAGGCGTCGTCGCCGGTGGAGCCGTTCGGCTTCACGACGCAGCTGGGTCCGCTGGGCGGAGAGGT TCCCATCGCCGGCGATCTGGGTGATCAGCAGGCCGCGATGGTGGGGCAGGTGTGCCTGAACCCCGGCGAGGCCAAGAACACCTAC GGCACCGGAAACTTCTTGCTACTCAACACCGGTGAGGAACTGGTCCATTCGAGCAATGGGCTGTTGACCACCGTCTGTTATCAAT TCGGCGACAACAAGCCGGTGTATGCGCTGGAGGGATCGATCGCGGTGACGGGCTCCGCGGTGCAGTGGCTGCGCGACCAGCTGGG CATCATCAGCGGTGCCTCGCAAAGCGAGGACCTGGCGCGCCAGGTCGAGGACAACGGCGGCGTCTATTTCGTGCCGGCCTTTTCC GGGCTGTTCGCGCCGTACTGGCGA gnd (480 bp)
CAGTTCGTTGAAGATGTGCGCCAAGCGCTGTACGCCTCCAAGATCGTGGCCTACGCCCAGGGGTTCAACCAGATCGCGGCGGGC
AGCGCCGAGTACGGCTGGAACGTCAGCCCTGGCGATCTGGCCACCATTTGGCGTGGCGGCTGCATCATCCGCGCGCAGTTCCTCA ATCGGGTCAAAGAAGCATTCGCCGATCGGCCGGACCTGGCCACGCTGATCGCGGCACCGTACTTCCGCGACGCCGTCGAGAAGGG CATCGACAGCTGGCGGCGCGTGGTGGTCACCGCCACCCAGCTGGGTATTCCGGTACCAGGCTTCGCCTCGTCGCTGTCTTACTAC GACGGTCTGCGTACCGATCGCCTGCCCGCCGCACTGACCCAGGCGCAACGCGACTTCTTCGGTGCCCACACCTATGAGCGCATCG ACGCCCCCGGCAAGTTCCACACGCTCTGGAGCGGCGACCGCAACGAAGTAGAGGCG murC (537 bp)
CCGAACCTGATCATCGTGACCAATATCGAGGCGGATCACCTGGATCACTTCGGCAGCGTGGAGGCTTACTCCGCGGTGTTCGA
CGAATTCGCCGAAACCCTGGGTTCCGAAGGGGTGTTGGTGGTGTGTCTGGATGACCCGGGTGCCGCGGCGCTGGCCCGCCGGGCA CATGAGCGCGGTATCCGGGTGCGCGGCTACGGCAGCGCCGACCAGGCCGAGGCGGGCGATGTCCCGGTGGCGGGGCAACTGCGGG ATTGGCAGTTCAAGGACACCGGGGCCACCGCGCAGATCCAGCTGGCGGGGGAGAGCGCGCCGCGGACCATGCGGTTGTCGGTACC GGGCCGGCATATGGCCCTGAACGCACTGGCCGCCGTGGTGACGGCCGCCGAGATCGGGGCGGCCGTCGACGATGTCCTGGACGGA TTGGCCGGATTCGAGGGTGTGCGCCGCCGATTCGAACTGGTCGGGTCGGTGGAGTCGGTGCGGGTTTTCGATGACTATGCGCACC ATCCCACCGAGGTGCGTACGGTGCTGCAG pta (486 bp)
GACGTACTACTCGCCGTGGCAAGTGCGCATGTGGCAGAAGGCTTTCCGTCGCTATCGGCCATCATCTTGAATGGTGGGCTCAAG
CTGCACCCGCGCATCGCAGATCTGGTGGACGGTATCGGGCTGCGGTTGCCGATCATCGAGACGGACTCCGGCACCTTCGAGACCG CGAGCGCGGCCGCGCATGCGCGTGGCCGGGTGACGGTGGCTTCTGCGCGCAAGATCGATACCGCGCTCGCGCTGATGGACAGGTA CGTGGATGGCGCGGATCTCGTTGCGCAGCTCGCTATCCCGATACCGTCGGTTACCACGCCGCAGATGTTCGAGTACCAGCTGCTG GACCGGGCACGCGACAACCGCAAGCGCATCGTGTTGCCCGAGGGCGACGACGACAGGATTCTCAAGGCCGCCGGCCGGCTATTGC AGCGTCAGGTCGCCGACCTGACGATCCTGGGCGAAGAGGCCGAAATCCGCTCCCGTGCCGCC purH (549 bp)
AAGGTTTTGGCTGCCAAGGCGTTCCGGCACACCGCAGAATACGATGTGGCGGTCGCGGGGTGGCTCTCCGGTGTGGCAGAGCCC GGGGACGCCGAGCTGCCCTCATGGATCGGCGGCACGTGGAACCGTTCGGCGGTGCTGCGCTATGGAGAGAACCCGCACCAGCAGG CGGCCCTGTATATCGGTGCCGCCGGGCAGGGCCTTGCTCAGGCCGAGCAGCTGCACGGAAAAGAGATGTCGTACAACAACTACAC CGACGCCGACGCCGCGTGGCGTGCCGCATGGGATCAGGACAAGGCATGCGCGGCGATCATCAAGCACGCCAACCCATGTGGTATC GCGGTGTCGGACATCTCGATTGCCGATGCGCACCTCAAGGCGCACGAATGCGATCCATTGAGTGCGTTCGGCGGCGTGATCGCCG TCAACCGTGAGGTGAGTGTGGAGATGGCCGAGCGGGTGGCCGACATCTTCACCGAGGTGATCGTGGCCCCGGGGTACGCCGATGG CGCCGTCGAGGTGCTGAGCCGCAAGAAGAACGTGCGGCTG |
