tools - engage benchmarking for amr gene detection · tools - engage benchmarking for amr gene...
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Tools - ENGAGE benchmarking for AMR gene detection
Pimlapas Leekitcharoenphon (Shinny)Research Group of Genomic Epidemiology, DTU-Food
WHO Collaborating Centre for Antimicrobial Resistance in Foodborne Pathogens and Genomics
European Union Reference Laboratory for Antimicrobial Resistance (EURL-AMR)
The Use of Whole Genome Sequencing (WGS) in Monitoring of Antimicrobial Resistance EURL-AR Training course 2017
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http://www.engage-europe.eu/resources/protocols-and-training
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Global phylogeny of DT104
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1.E1
1.E2
1.E3
1.E4
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2.97 x 10-7 SNP/site/year
4619 variable sites
~ 1.47 SNP/year
1946 (1931 - 1959)
109
60 (n = 297)
103
MDR DT104
Leekitcharoenphon P. et al, Appl Environ Microbiol. 2016
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Time1960 1970 1980 1990 2000 2010
1.E1
1.E2
1.E3
1.E4
Eff
ectiv
e po
pula
tion
size
Time1960 1970 1980 1990 2000 2010
Demographic history of global DT104
Leekitcharoenphon P. et al, Appl Environ Microbiol. 2016
14
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6191
Ken
ya 20
05 R
1
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2015EL-1157 Kenya unkn 1
HC-77A1 Haiti 2010 R1
DT
U20
15 4
87 P
RJ1
014
Vib
rio C
hole
rae
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22 R
1
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hina 2001 1
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ista
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10 1
7685
Ken
ya 2
009
R1
VC-18 Nepal 2
010 R1
1627 Mozam
bique 2005 R1
DTU
2015
499
PR
J101
4 V
ibrio
Cho
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SM
657
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DT
U20
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91 P
RJ1
014
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rio C
hole
rae
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R 2
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1
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F18K
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3 Pakistan 201 0 1
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VC-17 Nepal 2010 R1
DTU2016-1979-PRJunkn-Vibrio-cholerae-VC-3 S3 L001 R1 001.trim.fq.sorted
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-6 N
epal
201
0 R
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DTU2013 1366 PRJ941 Vibrio cholerae P36 V cholerae El Tor Ogawa R1.trim.fq.sorted
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3304-CDC China 1979 1
DTU
2015
498
PR
J101
4 V
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656
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3564-CDC China 1982 1
A131 India 1989 1
VC-21113 N
epal 2003 R
1
2011EL-2314H Haiti 2011 R1
L-3226 Russia 2010
3546-06 India 2006 R1
V109 India 1990 1
4642 India 2006 R1
DTU
2015
509
PR
J101
4 V
ibrio
Cho
lera
e V
SM
721
R1
HC-81A1 Haiti 2010
2011EL-1841 Haiti 2011 R1
A241
Viet
nam
198
9 1
HC-28A1 Haiti 2010 R1
S8K
CH
18 Pakistan 2010 1
6310-CDC Indonesia 1961 1
A245
Vietna
m 1
989
1
HC-67A1 Haiti 2010 R1
2012V-1060 USA FL 2012 R1
DTU2013 1370 PRJ941 Vibrio cholerae P48 V cholerae Ei Tor Ogawa R1.trim.fq.sorted
HC-19A1 Haiti 2010 R1
DTU
2013
135
7 PR
J941
Vib
rio c
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25 Pakistan 2010 1
HC-57A2 Haiti 2010 R1
DTU
2015
475
PR
J101
4 Vi
brio
Cho
lera
e C
MC
027
R1
A316 Argentina 1993 1
4536 India 2007 R1
S17
HH
3 P
akis
tan
2010
1
4784
Tanz
ania
2009
R1
DTU
2013
135
9 PR
J941
Vib
rio c
hole
rae
P44
V ch
oler
ae E
l Tor
Inab
a R
1.tri
m.fq
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ted
DTU2013 929 PRJ923 Vibrio cholera 278 8A R1
C6706 Peru 1991
HC-80A1 Haiti 2010 R1
6193 Kenya
2005 R1
2009V-1096 USA SxxIndiaxxE
2009
M66-2 Indonesia 1937
DTU
2015
496
PR
J101
4 V
ibrio
Cho
lera
e B
RH
121
A R
1
V5 India 1989 1
DTU
2013 1347 PR
J941 Vibrio cholerae V
cholerae El Tor O
gawa 22127 R
1.trim.fq.sorted
VC-21 Nepal 2010 R1
A185 Colombia 1992 1
936-CD
C C
hina 1998 1
DTU
2015
503
PR
J101
4 V
ibrio
Cho
lera
e V
SM
661
R1
2010EL-2026 Haiti 2010 R1
2011EL-1818 Haiti 2011 R1
2894-CDC China 1961 1
3024-CDC China 1973 1
DTU
2014
105
5 PR
J941
Vib
rio c
hole
rae
4053
0243
03 R
1.tri
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ted
GP152 India 1979 1
VC-12 N
epal 2010 R1
F4D
48 P
akis
tan
2010
1
4070-CD
C C
hina 1994 1
DTU
2015
471
PR
J101
4 Vi
brio
Cho
lera
e C
MC
023
R1
DT
U2015 515 P
RJ1014 V
ibrio Cholerae G
MH
032 R1
A6 Indonesia 1957 1
4039-CD
C C
hina 1993 1
2011EL-2315 Haiti 2011 R1
DTU
2015
477
PR
J101
4 Vi
brio
Cho
lera
e C
MC
029
R1
2010EL-1787 Haiti 2010 R1
1346 Mozam
bique 2005 R1
DTU2013 938 PRJ923 Vibrio cholera 355 1A R1
VC
-19
Nep
al 2
010
R1
A32 Peru 1991 1
SF20015 Bangladesh 1969 2011EL-2323 Haiti 2011 R1
V212-1 India 1991 1
KS72
0 Ba
ngla
desh
201
1 R
1
F5D
38 P
akis
tan
2010
1
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956-CD
C C
hina 2001 1
2710
-CDC C
hina
1986
1
A200 Argentina 1992 1
NH
CC
-010
F B
angl
ades
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10 R
1
2012EL-2176 Haiti 2012
2010EL-1795 Haiti 2010 R1
4322 India 2004 R1
MJ1485 Bangladesh 1994 1
VC-21106 N
epal 2003 R
1
H1 Haiti 2010
DTU
2013 1348 PR
J941 Vibrio cholerae V
cholerae El Tor O
gawa 22128 R
1.trim.fq.sorted
642345-CDC China 1964 1
VC-7 Nepal 2010 R1
DT
U20
15 5
13 P
RJ1
014
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rio C
hole
rae
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19 R
1
2011V-1021 Dominican Republic 2011
DTU
2015
465
PR
J101
4 Vi
brio
Cho
lera
e C
MC
017
R1
DTU2013 939 PRJ923 Vibrio cholera 322 3E R1
F7D
30 P
akis
tan
2010
1
RND19187 Russia 2010
2011
EL-
1938
Indi
a 20
09 R
1
S12
P76
Pak
ista
n 20
10 1
HC-48B2 Haiti 2010 R1
S21H
H15 P
akistan 2010 1
2574-CDC China 1980 1
DTU2013 1361 PRJ941 Vibrio cholerae P1 V cholerae El tor Ogawa R1.trim.fq.sorted
F16K
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Pak
ista
n 20
10 1
4585 India 2007 R1
6215
Ken
ya 20
05 R
1
2012EL-1410 Haiti 2012 R1
F17K
TH4
Pak
ista
n 20
10 1
S19
HH
5 P
akis
tan
2010
1
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59 P
akis
tan
2010
1
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CH
15 Pakistan 2010 1
S10P
57 Pakistan 2010 1
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2010EL-1961 Haiti 2010
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hina 2002 1
DT
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15 4
89 P
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014
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rio C
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14656 India 2006 R
1
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01 B
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2010EL-1791 Haiti 2010 R1
DTU2013 920 PRJ923 Vibrio cholera 089 10A R1
6194
Ken
ya 20
07 R
1
A27 Peru 1991 1
2580-CDC China 1989 1
DTU2014 1053 PRJ941 Vibrio cholerae 4053022989 R1.trim.fq.sorted
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outh Africa 2009 R
1
A201 Argentina 1992 1
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dia 19
73 1
DTU
2013 1342 PR
J941 Vibrio cholerae V
cholerae El Tor Inaba 22116 R
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199
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hina 1995 1
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133
4 PRJ9
41 V
ibrio
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rae
349
264
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.sorte
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epal 2010 R1
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DTU
2015
-837
-PR
J101
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DTU
2015
472
PR
J101
4 Vi
brio
Cho
lera
e C
MC
024
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2011EL-1089 Haiti 2010
GP143 B
ahrai
n 197
8 1
200106-CD
C C
hina 2001 1
DTU2013 1363 PRJ941 Vibrio cholerae P17 V cholerae El Tor Ogawa R1.trim.fq.sorted
S5KCH10 Pakistan 2010 1
2757
-CDC C
hina
198
7 1
DTU
2015
497
PR
J101
4 V
ibrio
Cho
lera
e B
RH
121
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1
HC-32A1 Haiti 2010 R1
DTU
2015 484 PR
J1014 Vibrio C
holerae EV
R 004 R
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2015
500
PR
J101
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2010EL-1786 Haiti 2010 R1
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angl
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1
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ya 2
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A177 Colombia 1992 1
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U20
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90 P
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014
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rio C
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rae
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R 2
85 R
1
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VC-8 Nepal 2010 R1
DTU
2013
135
6 PR
J941
Vib
rio c
hole
rae
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V ch
oler
ae E
l Tor
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1.tri
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HC-33A2 Haiti 2010 R1
2010EL-1788 Haiti 2010 R16312-CDC Indonesia 1961 1
2015EL-1160 Kenya unkn 1
S6KCH7 Pakistan 2010 1
DTU2
013
1353
PRJ
941
Vibr
io c
hole
rae
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oler
ae E
l Tor
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ted
3500-05 India 2005 R1
A482
Djib
outi
2007
R1
DTU2013 925 PRJ923 Vibrio cholera 196 6A R1
DTU
2013 1344 PR
J941 Vibrio cholerae V
cholerae El Tor Inaba 22118 R
1.trim.fq.sorted
A346 2 Bangladesh 1994 1
2011
EL-
1939
Indi
a 20
09 R
1
SC2000-C
DC
China 2000 1
2010EL-1801 Haiti 2010 R1
HC-38A1 Haiti 2010 R1
1575
-CDC
Chi
na 1
990
1
VC-10 N
epal 2010 R1
DTU
2015
469
PR
J101
4 Vi
brio
Cho
lera
e C
MC
021
R1
MB
N17 India 2004 R
1 F12D
1 P
akis
tan
2010
1
DTU
2015
468
PR
J101
4 Vi
brio
Cho
lera
e C
MC
020
R1
A487Sxx1xxE Bangladesh 2007 R1
CP1042 Thailand 2010 R1
GP145 India 1979 1
3582-05 Pakistan 2005 R
12010EL-2010H Haiti 2010
SC1998 242-1-C
DC
China 1998 1
DTU
2015
473
PR
J101
4 Vi
brio
Cho
lera
e C
MC
025
R1
DTU2
013
1352
PRJ
941
Vibr
io c
hole
rae
P34
V ch
oler
ae E
l Tor
Inab
a R
1.tri
m.fq
.sor
ted
4111 Vietnam
2002 R1
6210
Ken
ya 20
07 R
1
2015EL-1162 Kenya unkn 1
DTU2013
1335
PRJ9
41 V
ibrio
chole
rae 5
10 77
R1.t
rim.fq
.sorte
d
VC-26 Nepal 2010 R1
2848
-CDC
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na 1
988
1
2010EL-1749 Cameroon SxxAfrica W
xxE 2010
S25
R22
Pak
ista
n 20
10 1
F11D
4 P
akis
tan
2010
1
S20H
H14 P
akistan 2010 1
2914-CDC China 1966 1
2015EL-1159 Kenya unkn 1
DT
U2015 481 P
RJ1014 V
ibrio Cholerae E
VR
001 R1
HC-7A1 Haiti 2010
S13P
83 Pakistan 2010 1
DTU
2015
508
PR
J101
4 V
ibrio
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lera
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SM
720
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A SxxN
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S2KCH17 Pakistan 2010 1
DTU
2015
480
PR
J101
4 Vi
brio
Cho
lera
e C
MC
032
R1
DTU
2013
135
8 PR
J941
Vib
rio c
hole
rae
P43
V ch
oler
ae E
l Tor
Inab
a R
1.tri
m.fq
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ted
DTU2013 924 PRJ923 Vibrio cholera 151 4A R1
4605 India 2007 R1
VC-11 N
epal 2010 R1
DTU
2015
470
PR
J101
4 Vi
brio
Cho
lera
e C
MC
022
R1
2009V-1131 USA SxxIndiaxxE 2009
2957-CDC China 1964 1
G7555 Bangladesh 1969
DTU2013 926 PRJ923 Vibrio cholera 238 5A R1
HC-71A1 Haiti 2010 R1
2009
V-1
116
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A S
xxP
akis
tanx
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009
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C C
hina 1994 1
S18
HH
4 P
akis
tan
2010
1
2010EL-1798 Haiti 2010
4675
Ban
glad
esh
2001
R1
DTU
2015
505
PR
J101
4 V
ibrio
Cho
lera
e V
SM
717
R1
A19 B
angla
desh
1971
1
HC-65A1 Haiti 2010 R1
A130 India 1989 1
DTU
2015
502
PR
J101
4 V
ibrio
Cho
lera
e V
SM
660
R1
DTU2013 927 PRJ923 Vibrio cholera 278 1A R1
6311-CDC Indonesia 1961 1
HC-64A1 Haiti 2010 R1
DTU
2015
507
PR
J101
4 V
ibrio
Cho
lera
e V
SM
719
R1
2011EL-2321 Haiti 2011 R1
2783-CDC China 1964 1
HC-40A1 Haiti 2010 R1
132-CDC China 1978 1
4110 Vietnam
1995 1
DTU
2015
474
PR
J101
4 Vi
brio
Cho
lera
e C
MC
026
R1
A31 Peru 1991 1
MG
1160
25 B
angl
ades
h 19
91 1
DTU
2015
-846
-PR
J101
4-Vi
brio
-cho
lera
e-13
ARSC
MC
-028
-738
S7
L001
R1
001.
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q.so
rted
3270-CDC C
hina 1977 1
DTU
2013
135
1 PR
J941
Vib
rio c
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rae
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V c
hole
rae
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or In
aba
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A231 Mexico 1991 1
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epal 2010 R1
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DTU20
13 1
339
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Vibr
io ch
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CP
1038 Zimbabw
e 2009 R1
1551-CDC China 1979 1
4623 India 2007 R1
2011EL-2319 Haiti 2011 R1
4552 India 2007 R1
S7KCH20 Pakistan 2010 1
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2015
492
PR
J101
4 V
ibrio
Cho
lera
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RH
117
R1 4113 V
ietnam 2003 R
1
DTU
2015
501
PR
J101
4 V
ibrio
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SM
659
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U2015 511 P
RJ1014 V
ibrio Cholerae C
MC
090 R1
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2014
105
6 PR
J941
Vib
rio c
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rae
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0237
24 R
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Djib
outi
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R1
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C C
hina 2000 1
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Indi
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hina 1993 1
2012V-1001 USA 2011 R1
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hina 1998 1
2011EL-1941 India 2010 R1
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U2015 482 P
RJ1014 V
ibrio Cholerae E
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akistan 2010 1
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1
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U2015 512 P
RJ1014 V
ibrio Cholerae C
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2011EL-2320 Haiti 2011 R1
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U2015 483 P
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U2015 516 P
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hina 1997 1
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2015
506
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J101
4 V
ibrio
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718
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2013 1346 PR
J941 Vibrio cholerae V
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gawa 22126 R
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135
4 PR
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Vib
rio c
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l Tor
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4121 Vietnam
2004 R1
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epal 2010 R1
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1338
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41 V
ibrio
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1 R1.t
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2015
467
PR
J101
4 Vi
brio
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019
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2015
495
PR
J101
4 V
ibrio
Cho
lera
e B
RH
120
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HC-42A1 Haiti 2010 R1
2015EL-1158 Kenya unkn 1
A346 1 Bangladesh 1994 1
9-CD
C C
hina 2001 1
HC-46A1 Haiti 2010 R1
4672 Bangladesh 2000 R1
3075-CDC China 1974 1
S26
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Pak
ista
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10 1
A10
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lade
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DTU2013 1360 PRJ941 Vibrio cholerae P46 V cholerae El Tor Inaba R1.trim.fq.sorted
DTU2013 918 PRJ923 Vibrio cholera 066 13A R1
DTU2013
1337
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ibrio
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rae 8
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rae
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A29 Peru 1991 1
1583
-CDC
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2013 1345 PR
J941 Vibrio cholerae V
cholerae El Tor O
gawa 22125 R
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2865-CDC China 1961 1
DTU2013 1362 PRJ941 Vibrio cholerae P8 V cholerae El Tor Ogawa R1.trim.fq.sorted
MJ1236 Bangladesh 1994
SF20011 Bangladesh 1969
VC-22 Nepal 2010 R1
1362 Mozam
bique 2005 R1
DTU2013 917 PRJ923 Vibrio cholera 063 9A R1
2011
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hani
stan
200
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1
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angl
ades
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1
X190-CDC Peru 1991 1
S24R
G6 P
akistan 2010 1
2010EL-1799 Haiti 2010 R1
SF20012 Bangladesh 1969
HC-49A2 Haiti 2010 R1
4646 India 2007 R1
HC-70A1 Haiti 2010 R1
2011EL-2317 Haiti 2011 R1
DTU2013 932 PRJ923 Vibrio cholera 315 4A R1
DTU2013 921 PRJ923 Vibrio cholera 094 13A R1
2015EL-1156 Kenya unkn 1
DT
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88 P
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014
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rio C
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rae
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R 1
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1
2010EL-2010N Haiti 2010
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glad
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2010
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bia 20
04 R
1
GP160 India 1980 1
P27457 Bangladesh 1976
4538 India 2007 R1
S9KCH9 Pakistan 2010 1
7684
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009
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2308-CDC China 1978 1
6201
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ya 20
07 R
1
DT
U2015 510 P
RJ1014 V
ibrio Cholerae C
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DTU2013 930 PRJ923 Vibrio cholera 281 8A R1
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RND6878 Russia 2012
DT
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io c
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DTU2013 1365 PRJ941 Vibrio cholerae P33 V cholerae El Tor Ogawa R1.trim.fq.sorted
3497-CDC China 1980 1
A397 Bangladesh 1987 1
3014-CDC China 1969 1
VC-5 Nepal 2010 R1
DTU
2015
479
PR
J101
4 V
ibrio
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lera
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MC
031
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2744-CDC China 1962 1
HC-20A2 Haiti 2010
2011EL-2318 Haiti 2011 R1
HC-47A1 Haiti 2010 R1
2981-CDC China 1965 1
DTU
2013
136
4 PR
J941
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rio c
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oler
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l Tor
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.fq.s
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2015
504
PR
J101
4 V
ibrio
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SM
716
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A232 Mexico 1991 1
DTU2013 1368 PRJ941 Vibrio cholerae P45 V cholerae El Tor Ogawa R1.trim.fq.sorted
A488S
xx2xxE B
angladesh 2006 R1
HC-43A1 Haiti 2010
DT
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85 P
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rio C
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1
A18 India 1977 1
C6706-CDC Peru 1991 1
A186 Argentina 1992 1
2752-CDC China 1981 1
RND19191 Russia 2001
DTU2013 935 PRJ923 Vibrio cholera 342 3A R1
HC-06A1 Haiti 2010 R1
4210-CD
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hina 1999 1
G4222 South Africa 2001
2011EL-2316 Haiti 2011 R1
DTU
2015
493
PR
J101
4 V
ibrio
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lera
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RH
118
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Country
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S23HH18 Pakistan 2010 1
6191
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1
DTU2013 916 PRJ923 Vibrio cholera 041 A R1
3626-CDC China 1983 1
2015EL-1157 Kenya unkn 1
HC-77A1 Haiti 2010 R1
DT
U20
15 4
87 P
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014
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rio C
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1
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hina 2001 1
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ista
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10 1
7685
Ken
ya 2
009
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010 R1
1627 Mozam
bique 2005 R1
DTU
2015
499
PR
J101
4 V
ibrio
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lera
e V
SM
657
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DT
U20
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91 P
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014
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rio C
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rae
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R 2
87 R
1
3289-CDC China 1978 1
F18K
TH
3 Pakistan 201 0 1
DTU2013 913 PRJ923 Vibrio cholera 004 18A R1
VC-17 Nepal 2010 R1
DTU2016-1979-PRJunkn-Vibrio-cholerae-VC-3 S3 L001 R1 001.trim.fq.sorted
A481
Djib
outi
2007
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VC
-6 N
epal
201
0 R
1
DTU2013 936 PRJ923 Vibrio cholera 342 10A R1
1909-CD
C C
hina 1998 1
DTU2013 1366 PRJ941 Vibrio cholerae P36 V cholerae El Tor Ogawa R1.trim.fq.sorted
2015EL-1161 Kenya unkn 1
AHV1003-CDC China 2010 1
3304-CDC China 1979 1
DTU
2015
498
PR
J101
4 V
ibrio
Cho
lera
e V
SM
656
R1
SF20014 Bangladesh 1969
3564-CDC China 1982 1
A131 India 1989 1
VC-21113 N
epal 2003 R
1
2011EL-2314H Haiti 2011 R1
L-3226 Russia 2010
3546-06 India 2006 R1
V109 India 1990 1
4642 India 2006 R1
DTU
2015
509
PR
J101
4 V
ibrio
Cho
lera
e V
SM
721
R1
HC-81A1 Haiti 2010
2011EL-1841 Haiti 2011 R1
A241
Viet
nam
198
9 1
HC-28A1 Haiti 2010 R1
S8K
CH
18 Pakistan 2010 1
6310-CDC Indonesia 1961 1
A245
Vietna
m 1
989
1
HC-67A1 Haiti 2010 R1
2012V-1060 USA FL 2012 R1
DTU2013 1370 PRJ941 Vibrio cholerae P48 V cholerae Ei Tor Ogawa R1.trim.fq.sorted
HC-19A1 Haiti 2010 R1
DTU
2013
135
7 PR
J941
Vib
rio c
hole
rae
P42
V ch
oler
ae E
l Tor
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a R
1.tri
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ted
F8D
25 Pakistan 2010 1
HC-57A2 Haiti 2010 R1
DTU
2015
475
PR
J101
4 Vi
brio
Cho
lera
e C
MC
027
R1
A316 Argentina 1993 1
4536 India 2007 R1
S17
HH
3 P
akis
tan
2010
1
4784
Tanz
ania
2009
R1
DTU
2013
135
9 PR
J941
Vib
rio c
hole
rae
P44
V ch
oler
ae E
l Tor
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a R
1.tri
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.sor
ted
DTU2013 929 PRJ923 Vibrio cholera 278 8A R1
C6706 Peru 1991
HC-80A1 Haiti 2010 R1
6193 Kenya
2005 R1
2009V-1096 USA SxxIndiaxxE
2009
M66-2 Indonesia 1937
DTU
2015
496
PR
J101
4 V
ibrio
Cho
lera
e B
RH
121
A R
1
V5 India 1989 1
DTU
2013 1347 PR
J941 Vibrio cholerae V
cholerae El Tor O
gawa 22127 R
1.trim.fq.sorted
VC-21 Nepal 2010 R1
A185 Colombia 1992 1
936-CD
C C
hina 1998 1
DTU
2015
503
PR
J101
4 V
ibrio
Cho
lera
e V
SM
661
R1
2010EL-2026 Haiti 2010 R1
2011EL-1818 Haiti 2011 R1
2894-CDC China 1961 1
3024-CDC China 1973 1
DTU
2014
105
5 PR
J941
Vib
rio c
hole
rae
4053
0243
03 R
1.tri
m.fq
.sor
ted
GP152 India 1979 1
VC-12 N
epal 2010 R1
F4D
48 P
akis
tan
2010
1
4070-CD
C C
hina 1994 1
DTU
2015
471
PR
J101
4 Vi
brio
Cho
lera
e C
MC
023
R1
DT
U2015 515 P
RJ1014 V
ibrio Cholerae G
MH
032 R1
A6 Indonesia 1957 1
4039-CD
C C
hina 1993 1
2011EL-2315 Haiti 2011 R1
DTU
2015
477
PR
J101
4 Vi
brio
Cho
lera
e C
MC
029
R1
2010EL-1787 Haiti 2010 R1
1346 Mozam
bique 2005 R1
DTU2013 938 PRJ923 Vibrio cholera 355 1A R1
VC
-19
Nep
al 2
010
R1
A32 Peru 1991 1
SF20015 Bangladesh 1969 2011EL-2323 Haiti 2011 R1
V212-1 India 1991 1
KS72
0 Ba
ngla
desh
201
1 R
1
F5D
38 P
akis
tan
2010
1
3633-CDC China 1984 1
956-CD
C C
hina 2001 1
2710
-CDC C
hina
1986
1
A200 Argentina 1992 1
NH
CC
-010
F B
angl
ades
h 20
10 R
1
2012EL-2176 Haiti 2012
2010EL-1795 Haiti 2010 R1
4322 India 2004 R1
MJ1485 Bangladesh 1994 1
VC-21106 N
epal 2003 R
1
H1 Haiti 2010
DTU
2013 1348 PR
J941 Vibrio cholerae V
cholerae El Tor O
gawa 22128 R
1.trim.fq.sorted
642345-CDC China 1964 1
VC-7 Nepal 2010 R1
DT
U20
15 5
13 P
RJ1
014
Vib
rio C
hole
rae
GM
H 0
19 R
1
2011V-1021 Dominican Republic 2011
DTU
2015
465
PR
J101
4 Vi
brio
Cho
lera
e C
MC
017
R1
DTU2013 939 PRJ923 Vibrio cholera 322 3E R1
F7D
30 P
akis
tan
2010
1
RND19187 Russia 2010
2011
EL-
1938
Indi
a 20
09 R
1
S12
P76
Pak
ista
n 20
10 1
HC-48B2 Haiti 2010 R1
S21H
H15 P
akistan 2010 1
2574-CDC China 1980 1
DTU2013 1361 PRJ941 Vibrio cholerae P1 V cholerae El tor Ogawa R1.trim.fq.sorted
F16K
TH6
Pak
ista
n 20
10 1
4585 India 2007 R1
6215
Ken
ya 20
05 R
1
2012EL-1410 Haiti 2012 R1
F17K
TH4
Pak
ista
n 20
10 1
S19
HH
5 P
akis
tan
2010
1
VC51 India 1992 1
F2D
59 P
akis
tan
2010
1
S1K
CH
15 Pakistan 2010 1
S10P
57 Pakistan 2010 1
DTU2016-1930-PRJunkn-Vibrio-cholerae-VC-2 S2 L001 R1 001.trim.fq.sorted
VC-20 Nepal 2010 R1
7686
Ken
ya 2
009
R1
VC-2 Nepal 2010 R1
VC-14 Nepal 2010 R1
2010EL-1796 Haiti 2010 R1
GP140 Malaysi
a 1978 1
2010EL-1961 Haiti 2010
SF20013 Bangladesh 1969
HC-48A1 Haiti 2010 R1
4551 India 2007 R1
V011506-C
DC
China 2001 1
147-CD
C C
hina 2002 1
DT
U20
15 4
89 P
RJ1
014
Vib
rio C
hole
rae
EV
R 2
84 R
1
4656 India 2006 R1
A180 Colombia 1992 1
A488S
xx1xxE B
angladesh 2006 R1
HC-61A1 Haiti 2010 R1
2833-CDC China 1979 1
CIR
S 1
01 B
angl
ades
h 20
02
HC-39A1 Haiti 2010 R1
DTU2013 914 PRJ923 Vibrio cholera 011 17A R1
2010EL-1791 Haiti 2010 R1
DTU2013 920 PRJ923 Vibrio cholera 089 10A R1
6194
Ken
ya 20
07 R
1
A27 Peru 1991 1
2580-CDC China 1989 1
DTU2014 1053 PRJ941 Vibrio cholerae 4053022989 R1.trim.fq.sorted
2011EL-1137 S
outh Africa 2009 R
1
A201 Argentina 1992 1
GP60 In
dia 19
73 1
DTU
2013 1342 PR
J941 Vibrio cholerae V
cholerae El Tor Inaba 22116 R
1.trim.fq.sorted
T21-
CDC Tha
iland
199
0 1
2657-CD
C C
hina 1995 1
2011EL-2322 Haiti 2011 R1
S16H
H1 P
akistan 2010 1
DTU2014 1057 PRJ941 Vibrio cholerae 4053024306 R1.trim.fq.sorted
MB
RN
14 India 2004 R1
HC-23A1 Haiti 2010 R1
VC-15 Nepal 2
010 R1
2011EL-1300 Haiti 2011 R1
DTU2013
133
4 PRJ9
41 V
ibrio
chole
rae
349
264
R1.tri
m.fq
.sorte
d
4663 Bangladesh 2001 R1
VC-3 N
epal 2010 R1
2881-CDC China 1961 1
DTU
2015
-837
-PR
J101
4-Vi
brio
-cho
lera
e-13
ARSC
MC
-018
-706
S2
L001
R1
001.
fast
q.so
rted
DTU
2015
472
PR
J101
4 Vi
brio
Cho
lera
e C
MC
024
R1
2011EL-1089 Haiti 2010
GP143 B
ahrain 197
8 1
200106-CD
C C
hina 2001 1
DTU2013 1363 PRJ941 Vibrio cholerae P17 V cholerae El Tor Ogawa R1.trim.fq.sorted
S5KCH10 Pakistan 2010 1
2757
-CDC C
hina
198
7 1
DTU
2015
497
PR
J101
4 V
ibrio
Cho
lera
e B
RH
121
B R
1
HC-32A1 Haiti 2010 R1
DTU
2015 484 PR
J1014 Vibrio C
holerae EV
R 004 R
12530-C
DC
China 1996 1
4488 India 2006 R1
2921-CDC China 1962 1
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Pak
ista
n 20
10 1
DTU
2015
500
PR
J101
4 V
ibrio
Cho
lera
e V
SM
658
R1
2009V-1085 USA SxxSri L
ankaxxESxxI
ndiaxxE 2009
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2010EL-1786 Haiti 2010 R1
PC
S-0
23 B
angl
ades
h 20
10 R
1
7687
Ken
ya 2
009
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A177 Colombia 1992 1
63244-CDC China 1963 1
DT
U20
15 4
90 P
RJ1
014
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rio C
hole
rae
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R 2
85 R
1
HCUF01 Haiti 2010 R1
S4KCH16 Pakistan 2010 1
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DTU
2013
135
6 PR
J941
Vib
rio c
hole
rae
P39
V ch
oler
ae E
l Tor
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a R
1.tri
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.sor
ted
HC-33A2 Haiti 2010 R1
2010EL-1788 Haiti 2010 R1
6312-CDC Indonesia 1961 12015EL-1160 Kenya unkn 1
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DTU2
013
1353
PRJ
941
Vibr
io c
hole
rae
P35
V ch
oler
ae E
l Tor
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a R
1.tri
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.sor
ted
3500-05 India 2005 R1
A482
Djib
outi
2007
R1
DTU2013 925 PRJ923 Vibrio cholera 196 6A R1
DTU
2013 1344 PR
J941 Vibrio cholerae V
cholerae El Tor Inaba 22118 R
1.trim.fq.sorted
A346 2 Bangladesh 1994 1
2011
EL-
1939
Indi
a 20
09 R
1
SC2000-C
DC
China 2000 1
2010EL-1801 Haiti 2010 R1
HC-38A1 Haiti 2010 R1
1575
-CDC
Chi
na 1
990
1
VC-10 N
epal 2010 R1
DTU
2015
469
PR
J101
4 Vi
brio
Cho
lera
e C
MC
021
R1
MB
N17 India 2004 R
1 F12D
1 P
akis
tan
2010
1
DTU
2015
468
PR
J101
4 Vi
brio
Cho
lera
e C
MC
020
R1
A487Sxx1xxE Bangladesh 2007 R1
CP1042 Thailand 2010 R1
GP145 India 1979 1
3582-05 Pakistan 2005 R
12010EL-2010H Haiti 2010
SC1998 242-1-C
DC
China 1998 1
DTU
2015
473
PR
J101
4 Vi
brio
Cho
lera
e C
MC
025
R1
DTU2
013
1352
PRJ
941
Vibr
io c
hole
rae
P34
V ch
oler
ae E
l Tor
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a R
1.tri
m.fq
.sor
ted
4111 Vietnam
2002 R1
6210
Ken
ya 20
07 R
1
2015EL-1162 Kenya unkn 1
DTU2013
1335
PRJ9
41 V
ibrio
chole
rae 5
10 77
R1.t
rim.fq
.sorte
d
VC-26 Nepal 2010 R1
2848
-CDC
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na 1
988
1
2010EL-1749 Cameroon SxxAfrica W
xxE 2010
S25
R22
Pak
ista
n 20
10 1
F11D
4 P
akis
tan
2010
1
S20H
H14 P
akistan 2010 1
2914-CDC China 1966 1
2015EL-1159 Kenya unkn 1
DT
U2015 481 P
RJ1014 V
ibrio Cholerae E
VR
001 R1
HC-7A1 Haiti 2010
S13P
83 Pakistan 2010 1
DTU
2015
508
PR
J101
4 V
ibrio
Cho
lera
e V
SM
720
R1
3554-08 US
A SxxN
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09V-
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009
2873-CDC China 1961 1
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2015
480
PR
J101
4 Vi
brio
Cho
lera
e C
MC
032
R1
DTU
2013
135
8 PR
J941
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rio c
hole
rae
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oler
ae E
l Tor
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DTU2013 924 PRJ923 Vibrio cholera 151 4A R1
4605 India 2007 R1
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epal 2010 R1
DTU
2015
470
PR
J101
4 Vi
brio
Cho
lera
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022
R1
2009V-1131 USA SxxIndiaxxE 2009
2957-CDC China 1964 1
G7555 Bangladesh 1969
DTU2013 926 PRJ923 Vibrio cholera 238 5A R1
HC-71A1 Haiti 2010 R1
2009
V-1
116
US
A S
xxP
akis
tanx
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009
129-CD
C C
hina 1994 1
S18
HH
4 P
akis
tan
2010
1
2010EL-1798 Haiti 2010
4675
Ban
glad
esh
2001
R1
DTU
2015
505
PR
J101
4 V
ibrio
Cho
lera
e V
SM
717
R1
A19 B
angla
desh
1971
1
HC-65A1 Haiti 2010 R1
A130 India 1989 1
DTU
2015
502
PR
J101
4 V
ibrio
Cho
lera
e V
SM
660
R1
DTU2013 927 PRJ923 Vibrio cholera 278 1A R1
6311-CDC Indonesia 1961 1
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DTU
2015
507
PR
J101
4 V
ibrio
Cho
lera
e V
SM
719
R1
2011EL-2321 Haiti 2011 R1
2783-CDC China 1964 1
HC-40A1 Haiti 2010 R1
132-CDC China 1978 1
4110 Vietnam
1995 1
DTU
2015
474
PR
J101
4 Vi
brio
Cho
lera
e C
MC
026
R1
A31 Peru 1991 1
MG
1160
25 B
angl
ades
h 19
91 1
DTU
2015
-846
-PR
J101
4-Vi
brio
-cho
lera
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ARSC
MC
-028
-738
S7
L001
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001.
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rted
3270-CDC C
hina 1977 1
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2013
135
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J941
Vib
rio c
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rae
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V c
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rae
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or In
aba
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.fq.s
orte
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A231 Mexico 1991 1
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epal 2010 R1
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863-CDC Mauritania 1986 1
DTU20
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339
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io ch
olera
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trim
.fq.so
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HC-22A1 Haiti 2010 R1
4593 India 2007 R1
CP
1038 Zimbabw
e 2009 R1
1551-CDC China 1979 1
4623 India 2007 R1
2011EL-2319 Haiti 2011 R1
4552 India 2007 R1
S7KCH20 Pakistan 2010 1
DTU
2015
492
PR
J101
4 V
ibrio
Cho
lera
e B
RH
117
R1 4113 V
ietnam 2003 R
1
DTU
2015
501
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J101
4 V
ibrio
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lera
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659
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DT
U2015 511 P
RJ1014 V
ibrio Cholerae C
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090 R1
DTU
2014
105
6 PR
J941
Vib
rio c
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4053
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2012V-1001 USA 2011 R1
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2011EL-1941 India 2010 R1
DT
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DTU2013 933 PRJ923 Vibrio cholera 330 2A R1
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2013 1341 PR
J941 Vibrio cholerae V
cholerae El Tor Inaba 22115 R
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epal 2010 R1
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2010EL-1792 Haiti 2010
PR
L64 India 1992 1
HC-68A1 Haiti 2010 R1
DTU
2013 1346 PR
J941 Vibrio cholerae V
cholerae El Tor O
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DTU2013
1338
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41 V
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DTU2013 923 PRJ923 Vibrio cholera 150 7A R1
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TU2013 1345 P
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4646 India 2007 R1
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2011EL-2317 Haiti 2011 R1
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2015EL-1156 Kenya unkn 1
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angladesh 2006 R1
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R 1
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2752-CDC China 1981 1
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DTU2013 935 PRJ923 Vibrio cholera 342 3A R1
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2011EL-2316 Haiti 2011 R1
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ibrio
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R1
Country
Philipines
China
Thailand
Pakistan
Bangladesh
India
Nepal
Vietnam
Indonesia
Afghanistan
Bahrain
Malaysia
Haiti
USA
Mexico
Dominican_Republic
Kenya
Djibouti
Mozambique
South_Africa
Zambia
Mauritania
Tanzania
Zimbabwe
Peru
Argentina
Colombia
Bolivia
Chile
Russia
Cameroon
Continent
Asia
North_America
Africa
South_America
Russia
Biotype
El_Tor
El_Tor_variant
Tree scale: 0.01
Philipines
Haiti
Cameroon
17
Benchmarking of de novo assembly tools: AMR gene detection
18
• Take a well characterised set of 383 food pathogen isolates (164 Salmonella and 219 E.coli isolates).
• The set have been assessed for AMR using current gold standard phenotypic tests
• Determine the AMR profile using several of the currently available software for deriving resistance profile from the whole genome sequence data
Objective
19
• The genome sequences from the two ENGAGE partner labs were shared in a common data store
• The genome sequences were used to determined genotypic AMR profiles using the following tools:
• ResFinder
• KmerResistance
• SRST2
• PHE genefinder
Methods
20
21
22
23
24
• The results of the benchmarking showed that predicting antimicrobial resistance using WGS is a feasible and realistic alternative to phenotypic susceptibility testing
• The miscorrelation cases, where the tools predicted a different antimicrobial profile than the expected, were 10 - 14% in Salmonella dataset
• These miscorrelations are suspected to be mistakes in the phenotypic susceptibility test especially the isolates were all tools have identical miscorrelations
Conclusions
25
http://www.engage-europe.eu/resources/benchmarking
DTU Food, Technical University of Denmark Add Presentation Title in Footer via ”Insert”; ”Header & Footer”
Thank you for your attention
Pimlapas Leekitcharoenphon (Shinny), PhD
Research Group Genomic Epidemiology
WHO Collaborating Centre for Antimicrobial Resistance in Food borne Pathogens
and Genomics
European Union Reference Laboratory for Antimicrobial Resistance
National Food Institute, Technical University of Denmark
26