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