TABLE 2.

Primers used for amplification, sequencing, and cloning

Primer name by gene and procedure	Sequence (5′–3′)	Usea
Amplification and sequencing
cagPAI
pai_1F	TCT AGC CAG ATC ACA AGC GAA C	A
pai_1R	CCT CTA AGG CAT GCT ACT GAA GAA	A
pai_2F	TCG CTA AAT TGC TGC TCA AAA	A
pai_2R	CAC TAC TTC ATG CCT TTG GAA GAT AA	A
pai_3F	CAA ACA TTC TTC ATA GTT GCC ACC	A
pai_3R	TCT CCC TAA CTT CTT CCT CTT TGG	A
pai_4F	ATC AAT GAA GTG GCA AGA GAA AAA G	A
pai_4R	CAG GTT CAG ACA TCT TGC TTG G	A
pai_5F	AGA GTA ACA CTC GGT TCA AAG CTG	A
pai_5R	TGA TAT ACT CAA GCG ATT GAT TTC AA	A
cagA
cagA_up	GCT TTA CTT TAT GGT GAG CCA TAA C	A
cagA_down	AGC AAG GGG TGG TTT TTG CG	A
HP0547:548L23	CAC GCC CAT GAA CTT TTG ATC CG	S
HP0547:438U21	TAT GGA AAA TAT CAT ACA ACC	S
HP0547:930U25	GAG TCA TAA TGG CAT AGA ACC TGA A	S
HP0547:1232U28	ATA ATG CTA AAT TAG ACA ACT TGA GCG A	S
HP0547:1704U21	AGG ATT GTC CCT ACA AGA AGC	S
HP0547:2177U19	CCC TTA AAG GCT CGG TGA A	S
HP0547:2554U21	ACC CTA GTC GGT AAT GGG TTA	S
HP0547:3160U24	GCT AGT TTG TCA GCG AAA CTA GAC	S
oipA
oipA_up	AAA TGT TGG TTA AGC GGT G	A, S
HP0639:592U20	TTG CAT GCT TAT GGT TAT GG	A, S
hopQ1B
HP0726:823U28	GGC TCT AGC AAT GTG TGG CAG CAA CAA A	A, S
HP0724:849U23	CGC TAA TGA AAT CGC TCA TTC AA	A, S
HP1177:371U22	GAG GTT ATA CCA AAA GTC CAG G	S
HP1177:1749L24	GGT CTA GCG AGA TTG GTT CTC AAG	S
hopQ type II
hopQ_up	CTT AAA AGC TTG ATT GAG CG	A, S
HP1176:24L20	TAA AAA GGA GTT TGC CAT GG	A, S
HP1177:1479L18	TTG ATG TAG GCG TGG TTG	S
cagA CN real-time PCR
RTcagAF	CCC TTA AAG GCT CGG TGA A	A
RTcagAR	TTT TCA AGG TCG CTT TTT GC	A
RTureAF	AAA AGC CGT TAG CGT GAA AGT	A
RTureAR	CCC GCT CGC AAT GTC TAA G	A
cagY PCR-RFLP
cagY:5157L24	CCG TTC ATG TTC CAT ACA TCT TTG	A
cagX:1515U22	CTA TGG TGA ATT GGA GCG TGT G	A
Construction of knockout strains
cag8::CAT_rpsL
HP0528:62U24_XhoI	AAC CTC GAG CTA GCG TAA TAG AAG CAG CAG CAC	A, L
HP0528:546L26_SacI	AAC GAG CTC GTG GGT TAC TCA TAG CGT TAG TGA GA	A, L
HP0528:653U19_HincII	AAC GTC GAC AGG ACA TGC AAG AGC AGG C	A, R
HP0528:1545L21_NotI	AAC GCG GCC GCT TAT CTC TGA CAA GAG GGA GC	A, R
rpsL_F_SacI	AAC GAG CTC GAT GCT TTA TAA CTA TGG ATT AAA CAC	A, C
C2-CatR_HincII	AAC GTC GAC TTA TCA GTG CGA CAA ACT GGG AT	A, C
cag24,25::CAT_rpsL
HP0526up_NotI	AAC GCG GCC GCT GAT CTT GCC TTG GGT TAG TAA CA	A, L
HP0546:20L28_SacI	AAC GAG CTC ACT ACA ACT TTC TTG TAG CTG TCA GTG A	A, L
HP0545:70U23_HincII	AAC GTC GAC GTT TTC AGT TCG TAT GGG TCA GC	A, R
HP0544:523L25_XhoI	AGT CTC GAG GAG AAT AGT TGT TAG TAA GGA TCA C	A, R
rpsL_F_SacI	AAC GAG CTC GAT GCT TTA TAA CTA TGG ATT AAA CAC	A, C
C2-CatR_HincII	AAC GTC GAC TTA TCA GTG CGA CAA ACT GGG AT	A, C
cagA::CAT_rpsL
cagA_LF_XhoI	AAC CTC GAG CGT TTT TGA AGT GTC GCC TAG GTA TG	A, L
cagA_LR_EcoRI	AAC GAA TTC GGA GCG TTT TGA AGC GGA TAA TAT C	A, L
cagA_RF_BamHI	AAC GGA TCC TTA CGC CTT TGG AGA TAT GAT GTG TG	A, R
HP0549:634U26_NotI	AAC GCG GCC GCG ATG CTA TTG TGG AAT ATT TGC AGC A	A, R
rpsL_F_EcoRI	AAC GAA TTC GAT GCT TTA TAA CTA TGG ATT AAA CAC	A, C
C2-CatR_BamHI	AAC GGA TCC TTA TCA GTG CGA CAA ACT GGG AT	A, C

^aA, amplification; S, sequencing; L, left arm; R, right arm; C, CAT_rpsL.