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Table 4 Alleles of tcdB, corresponding probes, GenBank entries and typing data

From: DNA-Microarray-based Genotyping of Clostridium difficile

tcdB allele Reference sequence Other GenBank entries Hybridization pattern Associated slpA alleles Associated ribotypes Associated clades Associated sequence types Associated hybridization profiles
tcdB 630 AM180355.1 ABHD02000008.1, ABKJ02000013.1, ABKL02000008.1, ADEJ01000447.1, ADNX01000011.1, ADVM01000023.1, AGAC01000012.1, AM180355.1, FN665653.1, FN668944.1, HM062501.1, HM062503.1, HM062505.1, HM062506.1, HM062507.1, HM062508.1, X53138.1, X92982 probe1119+ probe1122+ probe1129 slpA 23m63, slpA 79685, slpA DJNS0578, slpA JND08037, slpA JND08162, slpA JND09041, slpA MRY060211, slpA R12885, slpA R13540, slpA R13711, slpA 630, slpA 6407, slpA 6503 trunc., slpA BI9, slpA J9952 trunc., slpA Kohn, slpA R12884 trunc., slpA R12884, slpA R13541, slpA-negatives RT-001, RT-002, RT-005, RT-009, RT-011, RT-012, RT-013, RT-014, RT-015, RT-023, RT-029, RT-031, RT-045, RT-046, RT-049, RT-054, RT-056, RT-057, RT-064, RT-070, RT-071, RT-072, RT-078, RT-081, RT-087, RT-094, RT-103, RT-137, RT-150, RT-159, RT-163 I, III, V ST-03, ST-04, ST-08, ST-09, ST-11, ST-17, ST-35, ST-42, ST-45, ST-46, ST-54, ST-55, ST-58 HP-01, HP-02, HP-03, HP-04, HP-05, HP-06, HP-07, HP-08, HP-09, HP-10, HP-12, HP-13, HP-14, HP-16, HP-17, HP-18, HP-19, HP-20, HP-22, HP-23, HP-24, HP-25, HP-30, HP-33, HP-34, HP-37, HP-38, HP-39
tcdB R20291 FN545816.1 AAML04000007.1, ABFD02000006.1, ABHE02000016.1, ABHF02000018.1, ABHG02000011.1, ABKK02000013.1, FN538970.1, FN545816.1, FN665654.1, FN668941.1, HM062498.1, HM062509.1, HM062510.1 probe1119+ probe1121+ (probe1126) + probe1130 slpA R20291 RT-027 II ST-01 HP-31, HP-32
tcdB CF5 FN665652.1 AF217292.1, AGAA01000013.1, AGAB01000024.1, FN668375.1, HM062499.1, Z23277.1 probe1118+ probe1122+ probe1127+ probe1129 slpA CF5, slpA 79685 RT-017 IV ST-37, ST-86 HP-35, HP-36
tcdB 51680 HM062504.1 - probe1118+ probe1121+ probe1126+ probe1127+ probe1130 - - - - -
tcdB 8864 AJ011301.1 HM062500.1 probe1118+ probe1121+ probe1124+ probe1127+ probe1130 - - - - -
tcdB R9385/R10870 HM062497.1 HM062502.1 - probe1118+ probe1121+ (probe1126) + probe1130 - - - - -
tcdB SE844 HM062511.1 - probe1119+ probe1121+ probe1129 - - - - -
tcdB negative - - none slpA 1446, slpA 23m63, slpA R13711, slpA 6407, slpA 6503,slpA Kohn, slpA R13700 RT-009, RT-010, RT-011, RT-012, RT-015, RT-031, RT-039, RT-049, RT-056, RT-057, RT-070, RT-071, RT-094 I, ”VI” ST-03, ST-54, ST-55, ST-58, ST-127dlv HP-11, HP-15, HP-21, HP-26, HP-27, HP-29, HP-40
  1. Note, ADDE01000319.1, ADDE01000337.1, ADEH01001038.1, ADEH01001419.1, ADEH01001594.1, AJ002558.1, AJ294944.1, AY238986.1, AY238987.1, DQ683724.1, X60984.1 were excluded from analysis because these were partial sequences only that did not cover all probe binding sites