Table 1.
MLST profiles and background information for the 120 F. psychrophilum isolates from 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 x2, 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 |
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).
b Allele types (AT) for the seven loci ordered trpB, gyrB, dnaK, fumC, murG, tuf and atpA.
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 -).
d Geographical origin of the isolate in Japan. (MR) indicates an isolate from the model river in the Shiga prefecture.
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.