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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.