Primers used for MLST of Arcobacter

Amplification / sequencing primers

Asp, atp, gln, glt, pgm and tkt primers used for amplification and sequencing of the aspA, atpA, glnA, gltA, pgm and tkt loci. GlyA primers used for sequencing only - for glyA amplification primers, see below.

A. butzleri

aspABF ATTTTRAGAGATTCTTTTCRCRATAAA aspABR AACATTATTCATACAAATTTCAGSATT
atpABF CWGTTGCKATTGATACAATTCTTAA atpABR CAATTTGTTTTTCAATAACTAATGGTTT
glnABF TGCAGTTAGTGCWTCTMCTTTAGATAA glnABR ATAGRTTTTTCCCATCTTTCCAA
gltABF TTGATGGAGARAATTCTGAGTTAAG gltABR GGAACATTTTTAACATCACCAATTA
glyABF TGGWTGTAAATWTGCAAATGTTCAA glyABR CATCTTTYCCTGAAAATGGTTTATT
pgmABF1 TCCRAAAAATYTRACWYTAAAAGGT pgmABR AAAGTCTRATTTTATTYTCTGTKCC
tktABF GCTGATATTGCAACAGTWTTAAGTA tktABR TAAATCCWGCTTTTTCTTTWGATTT

 

A. cryaerophilus

aspACF2 AAATATTRMGAGATGCTTTTTATGGAA aspACR2 TACAAACTTCAGGATTWGCWGTAAT
atpACF GATACAATTCTTAAYCAAAAAGGTGA atpACR AAAACTTCWACCATTCTTTGWCCAA
glnACF2 AAATGGAATGCCTTTTGATGGTT glnACR1 TTRTCWCCATAAAGWGGTTTTGGCA
gltACF TGATATWGCTGATTTRGCTGGTAAA gltACR CCAATCATTCTTARYTGATCCATAAC
glyACF TGCAAATGTTCAACCWCATAGTGGA glyACR GCATCTTTTCCWSWRAATGGTTTAT
pgmACF1 GGATTAAGAATTGTYCTTGAYTGTGC pgmACR TCAACATCTTTTYTATTTTTACCTTCA
tktACF CTCCTATGGGAMTKGCTGATATTG tktACR2 ATTAAAYCCAGCTTTTATTTTTGCTTG

 

A. skirrowii

aspASF GCTTATCCAACTGCWATTAAAMTTACA aspASR CTTCAGGATTTGCTGYAATTCC
atpACF GATACAATTCTTAAYCAAAAAGGTGA atpACR AAAACTTCWACCATTCTTTGWCCAA
glnACF2 AAATGGAATGCCTTTTGATGGTT glnACR1 TTRTCWCCATAAAGWGGTTTTGGCA
gltACF TGATATWGCTGATTTRGCTGGTAAA gltACR CCAATCATTCTTARYTGATCCATAAC
glyACF TGCAAATGTTCAACCWCATAGTGGA glyACR GCATCTTTTCCWSWRAATGGTTTAT
pgmASF1 AAAAGGKCTTAGAATTGTWCTTGATTG pgmACR TCAACATCTTTTYTATTTTTACCTTCA
tktACF CTCCTATGGGAMTKGCTGATATTG tktACR2 ATTAAAYCCAGCTTTTATTTTTGCTTG

 

A. 'skirrowii-like'

aspASF GCTTATCCAACTGCWATTAAAMTTACA aspASR CTTCAGGATTTGCTGYAATTCC
atpACF GATACAATTCTTAAYCAAAAAGGTGA atpACR AAAACTTCWACCATTCTTTGWCCAA
glnACF2 AAATGGAATGCCTTTTGATGGTT glnACR1 TTRTCWCCATAAAGWGGTTTTGGCA
gltACF TGATATWGCTGATTTRGCTGGTAAA gltACR CCAATCATTCTTARYTGATCCATAAC
glyACF TGCAAATGTTCAACCWCATAGTGGA glyACR GCATCTTTTCCWSWRAATGGTTTAT
pgmASF1 AAAAGGKCTTAGAATTGTWCTTGATTG pgmACR TCAACATCTTTTYTATTTTTACCTTCA
tktACF CTCCTATGGGAMTKGCTGATATTG tktACR2 ATTAAAYCCAGCTTTTATTTTTGCTTG

 

glyA amplification primers

Two nearly identical glyA genes exist in each strain from all characterized Arcobacter species. Therefore, to obtain a clean trace for each glyA gene, a flanking primer must be used for amplification. The glyA1 gene is linked to lysS and the glyA2 gene is linked to ada. glyA1 is the locus used in constructing the sequence profile. For example, to sequence the butzleri glyA1 gene, amplify with ABlysS and glyABR and sequence with glyABF and glyABR.

glyA1: butzleri

ABlysS AAATGGAYGARGAYTTTGTWAATGC glyABR CATCTTTYCCTGAAAATGGTTTATT

 

glyA1: cryaerophilus, skirrowii and 'skirrowii-like'

ABlysS AAATGGAYGARGAYTTTGTWAATGC glyACR GCATCTTTTCCWSWRAATGGTTTAT

 

glyA2: butzleri, 'skirrowii-like'

glyABNF ATGCAGAAGGTTATCCATATAAAAG ABada2 GTAACACCWACATACTCTTTRAATACTCT

 

glyA2: cryaerophilus, skirrowii

glyACF TGCAAATGTTCAACCWCATAGTGGA ABada3 AWAAGWGCYTTCCAWACATTTATTT or
glyACF TGCAAATGTTCAACCWCATAGTGGA ABada8 TTTTCTTTCWATKCCCCATCT