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Table 1 Detected hybridization pattern types and their association with ribo- and sequence types as well as toxin gene alleles and resistance markers

From: DNA-Microarray-based Genotyping of Clostridium difficile

Hybridi-sation profile Fully sequenced reference strains Additional genome sequences, that were analyzed in silico only Tested isolates Clade Associated sequence types slpA allele Associated ribotypes tcdA tcdB cdtA/B bcrA lmrB vatA cat erm (B) tet (M) vncS/vexP1
HP-01 BI-9 (FN668944) QCD-63q42* (ABHD) 71 I ST-03 slpA BI9 RT-001, RT-015, RT-072 tcdA R20291 tcdB 630 cdtA 630+ cdtB 630 bcrA 630 lmrB 630 vatA 630 - (var) - pos
HP-02 - ATCC43255* (ABKJ) 5 I ST45, ST-46* slpA BI9 RT-001, RT-013, RT-087 tcdA R20291 tcdB 630 cdtA 630+ cdtB 630 bcrA 630 lmrB 630 vatA 630 - - - -
HP-03 - - 4 I ST-58 slpA 6407 RT-011, RT-049, RT-056 tcdA R20291 tcdB 630 cdtA 630+ cdtB 630 bcrA 630 lmrB 630 vatA 630 - (var) (var) -
HP-04 - - 5 I ST-04 slpA 630 RT-137, RT-150 tcdA R20291 tcdB 630 (cdtA 630+ cdtB 630 ) bcrA 630 lmrB 630 vatA 630     -
HP-05 - - 2 I N/A slpA DJNS0578 RT-163 tcdA R20291 tcdB 630 cdtA 630+ cdtB 630 bcrA 630 lmrB 630 vatA 630 - - - -
HP-06 - - 1 I N/A slpA negative Unidentified pattern tcdA R20291 tcdB 630 cdtA 630+ cdtB 630 bcrA 630 lmrB 630 vatA 630 - - - -
HP-07 - - 1 I N/A slpA R12884 trunc. RT-054 tcdA R20291 tcdB 630 cdtA 630+ cdtB 630 bcrA 630 lmrB 630 vatA 630 - - - -
HP-08 - - 10 I ST-55 slpA R13711 RT-057, RT-070, RT-094 tcdA R20291 tcdB 630 cdtA 630+ cdtB 630 bcrA 630 lmrB 630 vatA 630 -    -
HP-09 - - 17 I ST-08 slpA R13541 RT-002, RT-159 tcdA R20291 tcdB 630 cdtA 630+ cdtB 630 bcrA 630 lmrB 630 vatA 630 - - (var) -
HP-10 -   7 I N/A slpA 23m63 N/A tcdA R20291 tcdB 630 cdtA 630+ cdtB 630 bcrA 630 lmrB 630 vatA 630 - - - -
HP-11   CD37*, (AHJJ) 2 I ST-03 slpA 23m63 RT-009 - - - bcrA 630 lmrB 630 vatA 630    (var) -
HP-12 - - 2 I N/A slpA JND08162 RT-103 tcdA R20291 tcdB 630 cdtA 630+ cdtB 630 bcrA 630 lmrB 630 vatA 630 - - - -
HP-13 - 70-100-2010*, (AGAC) 24 I ST42* slpA R12885 RT-014, RT-049 tcdA R20291 tcdB 630 cdtA 630+ cdtB 630 bcrA 630 lmrB 630 v atA 630 - - - -
HP-14 - - 1 I N/A slpA Kohn RT-015 tcdA R20291 tcdB 630 cdtA 630+ cdtB 630 bcrA 630 lmrB 630 vatA 630 - - - -
HP-15 - - 1 I N/A slpA Kohn N/A - - - bcr A 630 lmrB 630 vatA 630 - - - -
HP-16 - - 2 I N/A slpA 79685 RT-029 tcdA R20291 tcdB 630 cdtA 630+ cdtB 630 bcrA 630 lmrB 630 vatA 630 - - - -
HP-17 - - 2 I N/A slpA JND09041 RT-064 tcdA R20291 tcdB 630 cdtA 630+ cdtB 630 bcrA 630 lmrB 630 vatA 630 - - (var) -
HP-18 - - 7 I ST-17 slpA MRY060211 RT-005 tcdA R20291 tcdB 630 cdtA 630+ cdtB 630 bcrA 630 lmrB 630 vatA 630 - - (var) -
HP-19 - - 4 I N/A slpA J9952 trunc. RT-013, RT-087 tcdA R20291 tcd B 630 - bcrA 630 lmrB 630 vatA 630 - - - -
HP-20 - - 9 I ST-08 slpA R12884 RT-005, RT-045, RT-054 tcdA R20291 tcdB 630 cdtA 630+ cdtB 630 bcrA 630 lmrB 630 vatA 630 - - - -
HP-21 - - 2 I N/A slpA R13711 RT-031 - - - bcrA 630 lmrB 630 vatA 630 -    -
HP-22 - - 1 I N/A slpA R13711 N/A tcdA R20291 tcdB 630 cdtA 630+ cdtB 630 bcrA 630 lmrB 630 vatA 630 - pos pos pos
HP-23 - - 1 I ST-54 slpA R13711 RT-012 tcdA R20291 tcdB 630 cdtA 630+ cdtB 630 bcrA 630 lmrB 630 vatA 630 - pos pos pos
HP-24 Strain 630 (AM180355) Strain 6534* (ADEJ) 18 I ST-54 slpA 630 RT-012 tcdA R20291 tcdB 630 c dtA 630+ cdtB 630 bcrA 630 lmrB 630 vatA 630 (var) (var) (var) pos
HP-25 - - 7 I ST-35 slpA JND08037 RT-046 tcdA R20291 tcdB 630 - b crA 630 lmrB 630 vatA 630 pos pos pos pos
HP-26 - - 2 I N/A slpA 1446 RT-039 - - - bcrA 630 lmrB 630 vatA 630 - pos pos pos
HP-27 - - 2 I N/A slpA R13700 RT-010 - - - bcrA 630 lmrB 630 vatA 630 - pos - -
HP-28 - Strain 6407* (ADEH) - I ST-58 or related (2 loci incomplete)* slpA 6407* N/A tcdA CF5* tcdB 630* -* bcrA 630* lmr B 630* vatA 630* -* -* -* -*
HP-29 - - 2 I N/A slpA 6407 RT-071 - - - bcrA 630 lmrB 630 vatA 630 - - - -
HP-30 - - 5 I ST-09 slpA negative (probe-1164 sometimes ambiguous) RT-029, RT-081, RT-094 tcdA R20291 tcdB 630 - bcrA 630 lmrB 630 vatA 630 - (var) - -
HP-31 CD196 (FN538970) BI1*, (FN668941), CIP107932*, (ABKK), QCD-76w55*, (ABHE), QCD-97b34*, (ABHF) 2 II ST-01* slpA R20291 RT-027 tcdA R20291 tcdB R20291 cdtA R20291+ cdtB R20291 bcrA 630 lmrB 630 vatA 630 - - - -
HP-32 R20291 (FN545816) Strain 2,007,855* (FN665654), QCD-32 g58*, (AAML), QCD-37x79*, (ABHG), QCD-66c26*, (ABFD) - II ST-01* slp A R20291* RT-027 tcdA R20291* tcdB R20291* cdtA R20291+ cdtB R20291 bcrA 630* lmrB 630* vatA 630* -* (var)* - pos*
HP-33 - - 2 III N/A slpA R12884 RT-023 tcdA R20291 tcdB 630 c dtA Clade III+ cdtBR20291 - lmrB 630 vatA 630 - (var) - -
HP-34 - - 1 III N/A slpA R12884 trunc. N/A tcdA R20291 tcdB 630 cdtA Clade III+ cdtB R20291 - lmrB 630 vatA 630 - - - -
HP-35 CF5, (FN665652) 002-P50-2011* (AGAA), 050-P50-2011* (AGAB), M68*, (FN668375) 1 IV ST-37*, ST-86* slpA CF5 RT-017 tcdA CF5 tcdB CF5 - bcrA CF5 lmrB 630 vatA 630 - (var) (var) pos
HP-36 - - 1 IV N/A slpA 79685 RT-017 tcdA CF5 tcdB CF5 - bcrA CF5 lmrB 630 vatA 630 - - - -
HP-37 Strain M120, (FN665653) NAP07*, (ADVM), NAP08*, (ADNX) 8 V ST11 slpA R13540 RT-078 tcdA R20291 tcdB 630 cdtA R20291+ c dtB M120 bcrA NAP07 lmrB NAP07 vatA NAP07 - (var) (var) -
HP-38 - Strain 6466 *, (ADDE) - V ST-11*, (1 mismatch) slpA R13540* N/A tcdA R20291* tcdB 630* cdtA R20291+ cdtB M120* bcrA NAP07* lmrB NAP07* vatA NAP07* -* -* pos* pos*
HP-39 - QCD-23 m63*, (ABKL) 2 V ST-11*, (1 mismatch) slpA 23m63 N/A tcdA R20291 tcdB 630 cdtA R20291+ cdtB M120 bcrA NAP07 lmrB NAP07 vatA NAP07 - - - -
HP-40 - Strain 6503*, (ADEI) - “VI” ST127 dlv* slpA 6503* N/A -* -* -* bcrA CF5* lmrB 630* vatA 630* -* -* -* -*
  1. Full hybridization profiles are provided as Additional file 2
  2. Asterisk indicates in silico analysis only