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Table 1 MLST profiles and background information for the 120 F. psychrophilum isolates from Japan

From: Population structure of the fish pathogen Flavobacterium psychrophilum at whole-country and model river levels in Japan

Isolatea

ATsb

STc

Prefectured

Hoste

Tissue

Year

FPC 837*

5, 4, 4, 4, 2, 4, 4

ST5

Tokushima

P. altivelis (ayu)

Kidney

1987

FPC 840*

5, 4, 4, 4, 2, 4, 4

ST5

Tokushima

Kidney

1987

PH9351

19,24,19, 5, 8, 1, 8

ST45

Hiroshima

Ovary

1993

CS-1

19,24,19, 5, 8, 1, 8

ST45

Gifu

Kidney

1995

96-4

5,24, 4, 4, 2, 4, 4

ST52

Gifu

Kidney

1996

PH-0003

19,24,19, 5, 8, 1, 8

ST45

Hiroshima

Kidney

2000

SG011227

5,24, 2, 6, 8, 1, 8

ST56

Shiga

Kidney

2001

PH-0209

19,24,19, 6, 8, 1, 8

ST48

Hiroshima

Kidney

2002

AK-0527

19,19,19, 2,13,29,28

ST53

Kyoto

Lower jaw

2005

AK-0536

19,19,19, 2,13,29,28

ST53

Kyoto

Lower jaw

2005

AK-0531

19,19,19, 2,13,29,28

ST53

Kyoto

Kidney

2005

AK-05137

19,19,19, 2,13,29,28

ST53

Kyoto

Skin lesion

2005

KU050822-1

5,24, 4, 4, 2, 4, 4

ST52

Shiga (MR)

Skin lesion

2005

KU050822-3 ~ 4

5,24, 4, 4, 2, 4, 4

ST52(2)

Shiga (MR)

Skin lesion

2005

KU051024-5

5,24, 4, 4, 2, 4, 4

ST52

Shiga (MR)

Gill

2005

KU051024-6

5,24, 4, 4, 2, 4, 4

ST52

Shiga (MR)

Coelomic fluid

2005

KU051024-7

5,24, 4, 4, 2, 4, 4

ST52

Shiga (MR)

Coelomic fluid

2005

KU051024-8 ~ 11

5,24, 2, 6,10, 1, 8

ST65(4)

Shiga (MR)

Egg

2005

KU051024-12 ~ 13

5,24, 4, 4, 2, 4, 4

ST52(2)

Shiga (MR)

Egg

2005

KU051024-14 ~ 17

5,24, 4, 4, 2, 4, 4

ST52(4)

Shiga (MR)

Egg

2005

KU060427-1

5,24, 4, 4, 2, 4, 4

ST52

Shiga (MR)

Gill

2006

KU060626-1 ~ 3

19,24,19, 6, 8, 1, 8

ST48(1)

Shiga (MR)

Kidney

2006

 

5,24, 4, 4, 2, 4, 4

ST52(2)

-

-

-

KU060626-4 ~ 6

5,24, 2, 6, 8, 1,27

ST49(3)

Shiga (MR)

Kidney

2006

KU060626-7 ~ 9

5,24, 4, 4, 2, 4, 4

ST52(3)

Shiga (MR)

Kidney

2006

KU060626-10 ~ 12

5,24, 4, 4, 2, 4, 4

ST52(3)

Shiga (MR)

Kidney

2006

KU060626-13 ~ 15

5,24, 4, 4, 2, 4, 4

ST52(3)

Shiga (MR)

Kidney

2006

KU060626-16 ~ 18

5,24, 4, 4, 2, 4, 4

ST52(3)

Shiga (MR)

Kidney

2006

KU060626-19 ~ 21

19,24,19, 6, 8, 1, 8

ST48(2)

Shiga (MR)

Kidney

2006

 

5,24, 2, 5, 8, 1,35

ST67(1)

-

-

-

KU060626-22 ~ 24

5,24, 4, 4, 2, 4, 4

ST52(3)

Shiga (MR)

Kidney

2006

KU060626-25 ~ 27

5,24, 4, 4, 2, 4, 4

ST52(3)

Shiga (MR)

Kidney

2006

KU060626-28 ~ 36

19,24,19, 6, 8, 1, 8

ST48(1)

Shiga (MR)

Kidney

2006

 

5,24, 4, 4, 2, 4, 4

ST52(7)

-

-

-

KU060626-37 ~ 39

19,24,19, 6, 8, 1, 8

ST48(3)

Shiga (MR)

Kidney

2006

KU060626-40 ~ 42

5,24, 4, 4, 2, 4, 4

ST52(3)

Shiga (MR)

Kidney

2006

KU060626-43 ~ 46

19,24,19, 6, 8, 1, 8

ST48(1)

Shiga (MR)

Kidney

2006

 

5,24, 4, 4, 2, 4, 4

ST52(3)

-

-

-

KU060626-57

5,24, 4, 4, 2, 4, 4

ST52

Shiga (MR)

Skin lesion

2006

KU060626-59

19,24,19, 6, 8, 1, 8

ST48

Shiga (MR)

Skin lesion

2006

KU060920-5 ~ 6

5,24, 4, 4, 2, 4, 4

ST52(2)

Shiga (MR)

Gill

2006

KU060920-7 ~ 8

5,24, 4, 4, 2, 4, 4

ST52(2)

Shiga (MR)

Gill

2006

KU060920-19

5,24, 4, 4, 2, 4, 4

ST52

Shiga (MR)

Milt

2006

OH-0224

2,30,20, 2,22,22,23

ST54

Hiroshima

O. masou subsp. (resp. yamame, amago x 2, and biwamasu)

Gill

2003

96-1

17,26,18, 9,19,24,24

ST43

Gifu

Kidney

1996

OH-0519

2,30,20, 2,23,22,23

ST55

Hiroshima

Kidney

2005

SG030207

15,24,10, 3, 2,12,11

ST40

Shiga

Kidney

2003

FPC 813*

2, 8, 2, 2, 2,10, 2

ST17

Tokyo

O. mykiss (rainbow trout)

Kidney

1992

FPC 814*

2, 8, 2, 2, 2,10, 2

ST17

Tokyo

Kidney

1992

CS-3

14,23, 4,10, 6,22, 2

ST39

Gifu

Kidney

1995

SG950607

2, 8, 2, 2, 2, 2, 2

ST10

Shiga

Kidney

1995

SG010808

2,29,15,12,17,27,26

ST47

Shiga

Kidney

2001

OH-0203

2, 8, 2, 2, 2, 2, 2

ST10

Hiroshima

Kidney

2002

0312

7,28, 4, 5,21,28,21

ST50

Yamanashi

Kidney

2003

y-2

2, 8, 2, 2, 2, 2, 2

ST10

Iwate

Kidney

2005

y-3

4,25, 4, 5,18,23,23

ST42

Iwate

Kidney

2005

FPC 830*

4, 7, 6, 5, 6, 8, 4

ST13

Miyagi

O. kisutch (coho salmon)

Kidney

1990

FPC 831*

11,18, 7, 5,14,18,17

ST30

Iwate

Peduncle

1990

FPM960724

11,18, 7, 5,14,18,17

ST30

Miyagi

not available

1996

FPM960726

4, 7, 6, 5, 6, 5, 4

ST9

Miyagi

Kidney

1996

x-2

11,18, 7, 5,14,18,17

ST30

Iwate

Kidney

2005

SG020617

16, 4,17, 5,10,12,22

ST41

Shiga

S. leuc. (iwana)

Kidney

2002

SG980216

18,27,10, 7,20,25,25

ST44

Shiga

H. nipponensis (wakasagi)

Egg

1998

SG010619

5,24, 4, 4, 2, 4, 4

ST52

Shiga

Kidney

2001

SG040302

20,31,19, 2,23,30,28

ST57

Shiga

Kidney

2004

GM2127

4,28, 8,11, 1,26, 4

ST46

Gunma

T. hakonensis (ugui)

Skin lesion

1999

CH-9401

5,24, 8, 6, 8, 1, 8

ST51

Hiroshima

C. carpio (koi)

Skin lesion

1994

KU061226-2 ~ 3

24,21,15, 1, 8,34,33

ST63(2)

Shiga (MR)

Cyprinid fish

Gill

2006

CH-0411

5,24, 8, 6, 8, 1, 8

ST51

Hiroshima

C. carassius (funa)

Kidney

2004

KU061226-1

25,35,10, 2,16, 1, 4

ST64

Shiga (MR)

P. jouyi (takahaya)

Gill

2006

PH-9348

21,32,10, 7,24,31,29

ST58

Hiroshima

Z. platypus (oikawa)

Kidney

1993

ZH-0001

5,24, 8, 6, 8, 1, 8

ST51

Hiroshima

Kidney

2000

KU051024-4

5,24, 4, 4, 2, 4, 4

ST52

Shiga (MR)

T. bre. (numachichibu)

Gill

2005

KU051128-1

1,15,16, 5,19,35,34

ST66

Shiga (MR)

Gymnogobius sp.

Gill

2005

KU051128-4

23,29,11,13,13, 5,1

ST60

Shiga (MR)

L. rei. (sunayatsume)

Gill

2005

KU051128-8

23,29,11,13,13, 5,1

ST60

Shiga (MR)

River water

not applicable

2005

KU051128-10

22,31, 4,10,19,32,3

ST59

Shiga (MR)

not applicable

2005

KU060920-2

5,24, 4, 4, 2, 4, 4

ST52

Shiga (MR)

not applicable

2006

KU060920-4

5,24, 4, 4, 2, 4, 4

ST52

Shiga

not applicable

2006

KU061128-1

5, 34, 8, 1, 26, 26, 32

ST62

Shiga (MR)

not applicable

2006

KU051128-6

8, 33, 8, 1, 25, 33, 31

ST61

Shiga (MR)

Case of caddisfly

not applicable

2005

  1. a Isolate identifier. Isolates are ordered by host fish species and then by sampling year; * indicates isolates already included in Nicolas et al. [17]. When several isolates have been collected from the same individual fish their identifiers are reported in a condensed format (i.e. KU060626-40 ~ 42 stands for KU060626-40, KU060626-41 and KU060626-42).
  2. b Allele types (AT) for the seven loci ordered trpB, gyrB, dnaK, fumC, murG, tuf and atpA.
  3. c Sequence type (ST). When several isolates were collected from the same individual fish the number in parentheses indicates the frequency of each ST. If different ST were found in the same fish, each ST is reported on a separate line but information on prefecture, tissue and year are not repeated (replaced by -).
  4. d Geographical origin of the isolate in Japan. (MR) indicates an isolate from the model river in the Shiga prefecture.
  5. e The host fish species or environmental sample source. The common name used in Japan is given in parentheses. Genus and sometimes species names have been abbreviated in this column. Full species names: Plecoglossus altivelis, Oncorhynchus masou, Oncorhynchus mykiss, Oncorhynchus kisutch, Salvelinus leucomaenis, Hypomesus nipponensis, Trybolodon hakonensis, Cyprinus carpio, Carassius carassius, Phoxinus jouyi, Zacco platypus, Tridentiger brevispinis, and Lethenteron reissneri.
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Veterinary Research

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