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