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. 2019 Apr 16;10(2):e00446-19. doi: 10.1128/mBio.00446-19

TABLE 1.

Summary of intra- and interspecies clonal groupsa

CG Clone n Transmission C. difficile source Range Yr Comments
1 RT078 3 Intraspecies CDI International
and national		 2010–2012 3 HCFs in Rotterdam,
Netherlands,
and in Australia
(WA and NSW)
2 RT078 2 Interspecies Piglet feces and
asymptomatic
farm worker		 Local 2011 1 farm in Heino, Netherlands;
corroborates work of
Knetsch et al. (4)
3 RT126 6 Intraspecies CDI International
and national		 2007–2013 3 HCFs in Australia
(NSW, WA, and VIC) and
1 HCF in Tainan, Taiwan
4 RT126 12 Intraspecies CDI International
and national		 2006–2013 3 HCFs in Toscana
region of Italy,
1 HCF in Illinois,
and 3 HCFs in 2
Australian states
(WA and NSW)
5 RT126 2 Intraspecies CDI Local 2012 1 HCF in NSW, Australia
6 RT126 2 Intraspecies CDI Local 2006 1 HCF in NSW, Australia
7 RT126 2 Intraspecies CDI (both CA-CDI) Local 2011 2 distinct HCFs in NSW
and VIC, Australia
8b RT078 2 QCc
9 RT078 2 Intraspecies CDI (1 CA-CDI) National 2013–2016 2 distinct HCFs in
WA and NSW,
Australia
10 RT078 2 Intraspecies CDI National Unknown 1 HCF in Illinois
11 RT126 7 Interspecies CDI, calf feces and
calf carcass washing		 National 2012–2013 3 distinct farms in 2 Australian
states (VIC and QLD) and
1 HCF in NSW, Australia
12 RT127 24 Interspecies CDI (one CA-CDI),
calf feces and
calf carcass washing		 National 2011–2014 5 distinct farms in 2 Australian
states (VIC and NSW) and
5 distinct HCFs in 2
Australian states (NSW and WA)
13 RT127 4 Intraspecies CDI (1 pediatric) National 2006–2008 3 distinct HCFs in Australia
(NSW and WA)
14 RT127 3 Interspecies CDI, calf feces National 2011–2012 1 HCF in NSW, Australia,
and 1 farm in QLD, Australia
15 RT127 2 Intraspecies CDI (both CA-CDI) Local 2006 1 HCF in VIC, Australia
16 RT127 6 Intraspecies CDI Local 2010 1 HCF (ward) in Tokyo, Japan
17 RT127 2 Intraspecies CDI Local 2011–2012 1 HCF in Tainan, Taiwan
18 RT127 4 Intraspecies CDI Local 2005–2006 3 distinct HCFs in WA, Australia
19 RT126b 5 Interspecies CDI (1 pediatric,
1 CA-CDI) and
kangaroo feces		 Local 2009–2012 3 distinct HCFs and 1
veterinary hospital, all in
WA, Australia (26)
20 RT033 3 Intraspecies CDI Local 2006 1 HCF in VIC, Australia
21 RT033 2 Intraspecies CDI Local 1980–1982 1 HCF in VIC, Australia
22 RT033/288 6 Interspecies CDI (1 pediatric),
calf feces, and
calf carcass washing		 National 2012–2013 4 distinct farms in 3 Australian
states (NSW, VIC, and QLD) and
2 HCFs in WA/VIC, Australiae
23 RT033 6 Intraspeciesd Piglet feces, soil
irrigated with
effluent, and
treated liquid
effluent		 Local 2012–2015 2 farms in SA, Australia
24 RT033 6 Intraspecies CDI National 2011–2013 6 CDI epidemiologically
unrelated cases from 6 distinct
hospitals in the northern,
central, and southern regions
of France, previously described
by Eckert et al. (25)
25 RT288 2 Intraspecies Calf carcass washing Local 2013 1 farm in SA, Australia
a

CG, clonal group; RT, PCR ribotype; CDI, Clostridium difficile infection; CA-CDI, community-associated CDI; HCF, health care facility; SA, South Australia; QLD; Queensland; NSW, New South Wales; VIC, Victoria; WA, Western Australia; QC, quality control.

b

ST258.

c

M120 (accession no. NC_017174) was used as a reference chromosome for read mapping and SNV calling. For quality control purposes, the original paired-end reads for this strain (accession no. ERR027342) were obtained from the study by He et al. (41) and processed and analyzed as an additional test genome. SNV analysis correctly showed C137 and M120 to be indistinguishable (zero core genome SNV differences).

d

Transmission between piglets (feces) and environment (soil/effluent).

e

Notably, one strain is RT288, and the remainder are RT033.