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

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}+ cdtB_R20291

-

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*

-*

-*

-*

-*