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. 2006 May;44(5):1887–1891. doi: 10.1128/JCM.44.5.1887-1891.2006

TABLE 1.

Oligonucleotide primers and probes for multiplex PCR-based reverse line blot assay used in this study

Primera Target Specificityb Tm (°C)c GenBank accession no. Sequence (5′ to 3′)d
SpIaSbe Pneumolysin S. pneumoniae 61.43 M17717 384ATT TCT GTA ACA GCT ACC AAC GA406
SpSp Pneumolysin S. pneumoniae 65.49 M17717 531AGC GAT AGC TTT CTC CAA GTG G552
SpAp Pneumolysin S. pneumoniae 75.10 M17717 556ACC CCA GCA ATT CAA GTG TTC GCG579
SpIbAbe Pneumolysin S. pneumoniae 61.69 M17717 730GAA TTC CCT GTC TTT TCA AAG TC708
1Sb wzy Serotype 1 59.03 Z83335 10307GGG ACT TTA ATT TTA TGC AGT G10328
1Ap wzy Serotype 1 59.22 Z83335 10402AAA TTT CAC AAT TAT CAT TGC C10381
1Sp wzy Serotype 1 62.00 Z83335 10529CTG GCT TTG GCA ACT TTG10546
1Ab wzy Serotype 1 60.67 Z83335 10576CAC AAT GGC TTT AGA AGG TAG AG10554
2Sb wzy Serotype 2 59.86 AF026471 9730CGG CAT TGT ATT CTT TAT ATC G9751
2Ap wzy Serotype 2 60.40 AF026471 9849CCA ATA AAT CTT GTG TGA ATA TAA CTG9823
2Sp wzy Serotype 2 60.76 AF026471 9989GCA ACA TTT CAA TCT TAT GGT G10010
2Ab wzy Serotype 2 63.05 AF026471 10049CGT TTG TAT CCA TTT AAC TGC ATC10026
3Sb wze Serotype 3 59.32 Z47210 5807TTG ATA TTC CCC TTG ACA ATA G5828
3Sp wze Serotype 3 59.62 Z47210 5910TTT ACT ACA GTC CTC TTT CTC TGC5887
3Ap wze Serotype 3 58.63 Z47210 6056GCC TCA TCC TTA ATT GGA G6038
3Ab wze Serotype 3 61.69 Z47210 6102GGA GGC TTC AAG ATT CAA CTC6082
4Sb wzy Serotype 4 61.09 AF316639 9619CCG TCT ATA TTT ATA TGG GTT TGC9642
4Ap wzy Serotype 4 60.08 AF316639 9774TTG AAA CCC CAT ATA CTC ATT G9753
4Sp wzy Serotype 4 60.49 AF316639 9848GGA TTT TGT TTT GTT ATT CTG TAG G9872
4Ab wzy Serotype 4 59.48 AF316639 9934CCT GAT AAT TTT GTA CTT CTG AAT G9910
5Sb wzy Serotype 5 61.23 AY336008 6052GTT TTC CCA ATA GTA GTT TGC G6073
5Ap wzy Serotype 5 61.86 AY336008 6118TGC GAT AAA ATA GAT AAG GCA ATC6095
5Sp wzy Serotype 5 62.20 AY336008 6275TGC TTT GTT AGA TAT AGT TAC GGG AG6300
5Ab wzy Serotype 5 62.04 AY336008 6349CCC ACA GCC AAA TAG AGT TG6330
6B6ASb wzy Serogroup 6 (6A, 6B) 58.77 AF316640 9263TCA ACC TGC AGT AAT TTT AAC A9284
6B6AAp wzy Serogroup 6 (6A, 6B) 60.95 AF316640 9322TTA ACT AGA GCA CTT GCA ATC G9301
6B6Asp wzy Serogroup 6 (6A, 6B) 59.01 AF316640 9461GAA AGA AAT AAA TCC TTC AAA GAT AAT9487
6B6AAb wzy Serogroup 6 (6A, 6B) 60.19 AF316640 9555CTA CTT TCT GAA TTT CAC GGA TAT AAA G9528
7F7ASb wzy Serotypes 7F, 7A 61.48 CR931643 14476GCA AGT GTT TCA ATG GGA GTA14496
7F7AAp wzy Serotypes 7F, 7A 58.71 CR931643 14537AAA TTC CAC AAT ATT GGT AAT ACT G14513
7F7Asp wzy Serotypes 7F, 7A 58.58 CR931643 14776TTT TTG TAT GAT TTA AAT ATT GCG14799
7F7AAb wzy Serotypes 7F, 7A 61.51 CR931643 14820ACG GAG GGA CCA TAC AAT AAG14800
8Sb wzy Serotype 8 60.50 AF316641 10827GAT GTT AGT TTC TTC GAT TCC AG10849
8Ap wzy Serotype 8 59.15 AF316641 10870GAG GAA ACC CAC AAA GTC AAA AAA C10849
8Sp wzy Serotype 8 59.38 AF316641 11012AAA ATT ATG TTT ACT TTA CGA GTT GG11037
8Ab wzy Serotype 8 61.32 AF316641 11066TCA TAA TGA ATC GTA CCA ATC AAC11043
9N9LSb wzy Serotypes 9N, 9L 62.46 CR931647 9818TCA ATG GCG ACT TTA TTT GC9837
9N9LAp wzy Serotypes 9N, 9L 58.53 CR931647 9893GAA CTT TGG GAA TAT AAT CAA AAG9870
9N9LSp wzy Serotypes 9N, 9L 62.15 CR931647 10139GTC GGT TTC GAT TCT TTG C10157
9N9LAb wzy Serotypes 9N, 9L 60.41 CR931647 10179AGT CTA TTA TCT CCT GTA GGG TGC10156
9V9ASb wzy Serotypes 9V, 9A 58.70 AF402095 8546AAC TAT ATT TAC CCT ACT CTC CAC AG8571
9V9AAp wzy Serotypes 9V, 9A 58.76 AF402095 8639AAT CAG CGT TAC CTT ATA CTG TG8617
9V9ASp wzy Serotypes 9V, 9A 59.62 AF402095 8797GCC TCT TTT TAA CCT TTA TCT TGT8820
9V9AAb wzy Serotypes 9V, 9A 61.56 AF402095 8860ACC GGA AAA AGC AAT TGA G8842
10A10BSb wzy Serotypes 10A, 10B 61.86 CR931649 7172TGA GCT ATT TAA GGA CCT GGG7192
10A10BAp wzy Serotypes 10A, 10B 62.30 CR931649 7206GTT TAG AAA CCT TGC CCA GG7187
10A10BSp wzy Serotypes 10A, 10B 62.25 CR931649 7353ACC ATA TGG TAT TTG TTG CCT G7374
10A10BAb wzy Serotypes 10A, 10B 61.76 CR931649 7450GCA AGC GTC ACT TTC TTG A7432
11A11DSb wzy Serotypes 11A 11D 59.48 CR931653 11368GAA ATA TCG CCA TTC ATC AG11387
11A11DAp wzy Serotypes 11A, 11D 59.34 CR931653 11407TGT AAG ATG AAA AAA GCA TGC11387
11A11DSp wzy Serotypes 11A, 11D 59.42 CR931653 11676GGA TTT CTC GTA TCA GCA TAT TAC11699
11A11DAb wzy Serotypes 11A, 11D 62.68 CR931653 11744CAA CAG CAA CTG TGC CAC T11726
124446Sb wzy Serotypes 12F, 12A, 12B, 44, 46 59.41 CR931660 8914TGA ATA TGG ACG GTG GAG8931
124446Ap wzy Serotypes 12F, 12A, 12B, 44, 46 58.48 CR931660 8951GAA GAA GTT CAA CAA TCG CT8932
124446Sp wzy Serotypes 12F, 12A, 12B, 44, 46 59.37 CR931660 9104GCA TGA TAT GGG AAG TTT TG9123
124446Ab wzy Serotypes 12F, 12A, 12B, 44, 46 59.69 CR931660 9155AGC AAA GAA AGC CGA AAG9138
14Sb wzy Serotype 14 60.41 X85787 7376CCT ACT TCC AAA ACA GTT TAT GC7398
14Ap wzy Serotype 14 59.77 X85787 7494CCA TAC AAA AAG ACG GTG TAT C7473
14Sp wzy Serotype 14 59.30 X85787 7587GCA TTT AAT TGG CTA ATA GCA G7608
14Ab wzy Serotype 14 59.69 X85787 7652GTC AAT ATT GAT TGG CAT TTT C7631
15B15CSb wzy Serotypes 15B, 15C 62.63 CR931664 7797TAA TAA GCG GAT GAT TGT AGC G7818
15B15CAp wzy Serotypes 15B, 15C 58.19 CR931664 7837GAG GTA TAG TTG GAT AAA ACG C7816
15B15CSp wzy Serotypes 15B, 15C 62.54 CR931664 7976GAG CAG GAA TCA GAA CAC AAT C7997
15B15CAb wzy Serotypes 15B, 15C 60.91 CR931664 8148TAT ACT GAT TAA CTT TCC AGA TGG G8124
17FSb wzy Serotype 17F 59.84 CR931670 13988AGA GGG ATT GTT GAA GGT ATT C14009
17FAp wzy Serotype 17F 60.89 CR931670 14035GGA AGT GAA CGT CAA ATC TTT T14014
17FSp wzy Serotype 17F 61.75 CR931670 14250CAA TGC TAT GTC GCA AAT ATT G14271
17FAb wzy Serotype 17F 61.34 CR931670 14295AGT AGT CTC GCA TTT CTA TCA TCC14272
18Sb wzy Serogroup 18 (18F, 18A, 18B, 18C) 60.45 AF316642 12208AAT TGT TCT TTT CCT GTA CTC AGT C12232
18Ap wzy Serogroup 18 (18F, 18A, 18B, 18C) 58.72 AF316642 12260ATT CAA C/TTG GGT TCA TTA CG12241
18Sp wzy Serogroup 18 (18F, 18A, 18B, 18C) 58.74 AF316642 12425GGA GGA CTT AGT CAA TTT ATC TTG12448
18Ab wzy Serogroup 18 (18F, 18A, 18B, 18C) 62.13 AF316642 12478CGA ACC ATT GAA ACT ATC ATC TG12456
19ASb wzy Serotype 19A 61.40 AF094575 9260TGT ATT TGC CCT TAT TAA TGT GC9282
19AAp wzy Serotype 19A 61.12 AF094575 9336TGC CAC TAA TAA TCA AAA GAT AAG C9312
19ASp wzy Serotype 19A 60.81 AF094575 9422CCA ATT CTG GAA AAT AGC TCT TAC9445
19AAb wzy Serotype 19A 60.63 AF094575 9506AAG TGC AAG ATT ATG AAT CTC TCT C9482
19FSb wzy Serotype 19F 59.55 U09239 7693TCA GTA TTT GCA CTG GTT AAT TC7715
19FAp wzy Serotype 19F 61.85 U09239 7800TGC CAT TAA AGG AAT CGA AA7781
19FSp wzy Serotype 19F 60.35 U09239 7858CAA TTT TGG AAA ATT GCT CTA AC7880
19FAb wzy Serotype 19F 59.39 U09239 7941AAG AAC AAG GTT GTA TAT TTC CTT C7917
20Sb wzy Serotype 20 61.18 CR931679 7711CTT TAT CAG GAA TAC GCC AAT C7732
20Ap wzy Serotype 20 60.16 CR931679 7759GCA TAA AAA ACA ATC GCT GTA G7738
20Sp wzy Serotype 20 62.31 CR931679 7933CTG GGT CTG AAT TTG TAT CTC G7954
20Ab wzy Serotype 20 59.11 CR931679 8010CTG TAT AAT AAC GAG AAC CAA CG7988
22F22ASb wzy Serotypes 22F, 22A 61.86 CR931682 13190AGG ATG CAG TAG ATA CCA GTG G13211
22F22AAp wzy Serotypes 22F, 22A 59.68 CR931682 13263TAA TAC CAT GGC ACT AGG AAT AAC13240
22F22ASp wzy Serotypes 22F, 22A 58.30 CR931682 13503ATG GCT ATC AAC TTT ATC TAG GAC13526
22F22AAb wzy Serotypes 22F, 22A 60.25 CR931682 13543TAT AAA CGG AGG TTG TTG TCC13523
23FSb wzy Serotype 23F 60.39 AF057294 8583TGA TAG TGA ACT TGG GAT TGT C8604
23FAp wzy Serotype 23F 61.24 AF057294 8694CTA TTT GCA AAC ACG TTG AGA G8673
23FSp wzy Serotype 23F 58.36 AF057294 8735GGG ATT AAT TTA CAA AAT CTT CC8757
23FAb wzy Serotype 23F 58.19 AF057294 8827CTT TAT CGG TAA GGT GGA TAA G8806
33F33A37Sb wzy Serotypes 33F, 33A, 37 61.77 AJ006986 11362TCA ACT AGT CAA GGA TTT GAT GG11384
33F33A37Ap wzy Serotypes 33F, 33A, 37 60.62 AJ006986 11421TGA TAC CAC AAG TAA CAG AGT CG11399
33F33A37Sp wzy Serotypes 33F, 33A, 37 59.52 AJ006986 11589GAT GAT TTT GCA GAT GTA CTA TGA11612
33F33A37Ab wzy Serotypes 33F, 33A, 37 59.67 AJ006986 11639CGT ATC AGA TTT GCG ATT TC11620
a

S, sense; A, antisense; b, biotin-labeled primer (primers were biotin labeled at the 5′ end); p, probe (probes were 5′ end C6 amine labeled).

b

Based on published sequence data for the whole cps gene cluster, it was not possible to design primers/probes that could distinguish some individual serotypes from one or four closely related ones (shown in boldface), usually (but not always) belonging to the same serogroup.

c

Tm values were provided by the primer synthesizer (Sigma-Aldrich).

d

Numbers represent the base positions at which primer/probe sequences start and finish (starting at “1” of the corresponding GenBank sequence).

e

Two primers published previously (8) were used as species-specific probes.