TABLE 1.

Primer sequences used in this study and predicted amplicon sizes

Primer name	Sequence (5′–3′)	Predicted amplicon size (nt)a
16S For	GGT CAA GAC TGA CGC TGA GTC A	136
16S Rev	GGC GGC ACA CTT AAC ACG TTA G
flaB For	GGG TCT CAA GCG TCT TGG	139
flaB Rev	GAA CCG GTG CAG CCT GAG
ospA For	ATG AAA AAA TAT TTA TTG GGA ATA GG	829
ospA Rev	ATT CTC CTT ATT TTA AAG CG
ospC Forb	ATG AAA AAG AAT ACA TTA AGT GC	638
ospC Rev	CTT AAT TAA GGT TTT TTT GG
p66 For	GAT TTT TCT ATA TTT GGA CAC AT	755
p66 Rev	TGT AAA TCT TAT TAG TTT TTC AAG
16S IGS For	AGT GCG GCT GGA TCA CCT CC	950
ileT IGS Revb	GTC TGA TAA ACC TGA GGT CGG A
nid1 For	CCA GCC ACA GAA TAC CAT CC	153
nid1 Rev	GGA CAT ACT CTG CTG CCA TC
recA For	GTG GAT CTA TTG TAT TAG ATG AGG CT	171
recA Rev	GCC AAA GTT CTG CAA CAT TAA CAC CT
I. scap 16S For	CGG TCT GAA CTC AGA TCA AG	300
I. scap 16S Rev	GGG ACA AGA AGA CCC TAT C
MLST primers for amplification and sequencingc
clpA For	AAA GAT AGA TTT CTT CCA GAC	982
clpA Rev	GAA TTT CAT CTA TTA AAA GCT TTC
clpX For	GCT GCA GAG ATG AAT GTG CC	884
clpX Rev	GAT TGA TTT CAT ATA ACT CTT TTG
nifS For	ATG GAT TTC AAA CAA ATA AAA AG	1,049
nifS Rev	GAT ATT ATT GAA TTT CTT TTA AG
pepX For	ACA GAG ACT TAA GCT TAG CAG	811
pepX Rev	GTT CCA ATG TCA ATA GTT TC
pyrG For	GAT TGC AAG TTC TGA GAA TA	801
pyrG Rec	CAA ACA TTA CGA GCA AAT TC
recG For	CCC TTG TTG CCT TGC TTT C	805
recG Rev	GAA AGT CCA AAA CGC TCA G
rplB For	TGG GTA TTA AGA CTT ATA AGC	760
rplB Rev	GCT GTC CCC AAG GAG ACA
uvrA For	GAA ATT TTA AAG GAA ATT AAA AGT AG	911
uvrA Rev	CAA GGA ACA AAA ACA TCT GG

^aThe predicted amplicon sizes were determined using the following accession versions: B. burgdorferi B31, AE000783.1 (chromosome), AE000790.2 (lp54), and AE000792.1 (cp26); mouse, NC_000079.6 (nid1). nt, nucleotides.

^bPrimers ospC For and ileT IGS Rev were obtained from reference 36.

^cFrom borrelia.mlst.net/misc/info.asp.