TABLE 2.
List of V. parahaemolyticus genomes from NCBI used for further testing of the newly created cgMLST
| Isolate | CFSAN no.a | Yr | Country | Sourceb | ST | Serotypec | Accession no. | Reference or source |
|---|---|---|---|---|---|---|---|---|
| From our lab | ||||||||
| MDVP1d | CFSAN007429 | 2012 | USA | C | 631 | unk | JNSM02000000 | This study |
| MDVP8d | CFSAN007430 | 2012 | USA | C | 631 | unk | JNSN02000000 | This study |
| MDVP9d | CFSAN007431 | 2012 | USA | C | 631 | unk | JNSO02000000 | This study |
| MDVP31d | CFSAN007432 | 2013 | USA | C | 631 | unk | JNSP02000000 | This study |
| MDVP35d | CFSAN007433 | 2013 | USA | C | 631 | unk | JNSQ02000000 | This study |
| MDVP41d | CFSAN007434 | 2013 | USA | C | 631 | unk | JNSR02000000 | This study |
| MDVP44d | CFSAN007435 | 2013 | USA | C | 631 | unk | JNSS02000000 | This study |
| MDVP45d | CFSAN007436 | 2013 | USA | C | 631 | unk | JNST02000000 | This study |
| MDVP2d | CFSAN007437 | 2012 | USA | C | 651 | unk | JNSU02000000 | This study |
| MDVP3d | CFSAN007438 | 2012 | USA | C | 652 | unk | JNSV02000000 | This study |
| MDVP4d | CFSAN007439 | 2012 | USA | C | 653 | unk | JNSW02000000 | This study |
| MDVP34d | CFSAN007440 | 2013 | USA | C | 653 | unk | JNSX02000000 | This study |
| MDVP5d | CFSAN007441 | 2012 | USA | C | 113 | unk | JNSY02000000 | This study |
| MDVP7d | CFSAN007442 | 2012 | USA | C | 34 | unk | JNSZ02000000 | This study |
| MDVP11d | CFSAN007443 | 2012 | USA | C | 1116 | unk | JNTA02000000 | This study |
| MDVP6d | CFSAN007444 | 2012 | USA | C | 677 | unk | JNTB02000000 | This study |
| MDVP10d | CFSAN007445 | 2012 | USA | C | 43 | unk | JNTC02000000 | This study |
| MDVP13d | CFSAN007446 | 2012 | USA | C | 678 | unk | JNTD02000000 | This study |
| MDVP14d | CFSAN007447 | 2012 | USA | C | 162 | unk | JNTE02000000 | This study |
| MDVP15d | CFSAN007448 | 2012 | USA | C | 679 | unk | JNTF02000000 | This study |
| MDVP39d | CFSAN007455 | 2013 | USA | E | 896 | unk | JNTL02000000 | This study |
| 090-96-70d | CFSAN001595 | 1996 | Peru | C | 189a | O4:K8 | JFFP02000000 | This study |
| VP16MDd | CFSAN007449 | 2012 | USA | C | 3 | unk | JNTG02000000 | This study |
| VP17MDd | CFSAN007450 | 2012 | USA | C | 3 | unk | JNTH02000000 | This study |
| VP18MDd | CFSAN007451 | 2012 | USA | C | 3 | unk | JNTI02000000 | This study |
| MDVP19d | CFSAN007452 | 2010 | USA | C | 8 | unk | JNTJ02000000 | 15 |
| MDVP20d | CFSAN007453 | 2010 | USA | C | 8 | unk | JNTK02000000 | 15 |
| MDVP22d | CFSAN007454 | 2010 | USA | E | 676 | unk | JNUO02000000 | 15 |
| MDVP25d | CFSAN007456 | 2010 | USA | E | 810 | unk | JNUK02000000 | 15 |
| MDVP26d | CFSAN007457 | 2010 | USA | E | 811 | unk | JNUL02000000 | 15 |
| MDVP27d | CFSAN007458 | 2010 | USA | E | 34 | unk | JNUM02000000 | 15 |
| MDVP28d | CFSAN007459 | 2010 | USA | E | 768 | unk | JNUN02000000 | 15 |
| MDVP21d | CFSAN012491 | 2010 | USA | E | 8 | unk | JNUG02000000 | 15 |
| MDVP23d | CFSAN012492 | 2010 | USA | E | 8 | unk | JNUH02000000 | 15 |
| MDVP24d | CFSAN012493 | 2010 | USA | E | 8 | unk | JNUI02000000 | 15 |
| MDVP29d | CFSAN012494 | 2010 | USA | E | 8 | unk | JNUJ02000000 | 15 |
| 281-09d | CFSAN025052 | 2009 | Peru | C | 120 | O3:K59 | LKQB00000000 | 16 |
| 283-09d | CFSAN025053 | 2009 | Peru | C | 120 | O3:K59 | LKQA00000000 | 16 |
| C220-09d | CFSAN025054 | 2009 | Peru | C | 120 | O3:KUT | LKQC00000000 | 16 |
| C224-09d | CFSAN025055 | 2009 | Peru | C | 120 | O3:K59 | LKQD00000000 | 16 |
| C226-09d | CFSAN025056 | 2009 | Peru | C | 120 | O3:K59 | LKQE00000000 | 16 |
| C244-09d | CFSAN025057 | 2009 | Peru | C | 120 | O3:K59 | LKQF00000000 | 16 |
| C235d | CFSAN025058 | 2009 | Peru | C | 120 | O3:K59 | LKQG00000000 | 16 |
| PIURA 17d | CFSAN025059 | 2009 | Peru | C | 120 | O3:K59 | LKQH00000000 | 16 |
| C237d | CFSAN025060 | 2009 | Peru | C | 120 | O3:K59 | LKQI00000000 | 16 |
| 239-09d | CFSAN025061 | 2009 | Peru | C | 120 | O3:K59 | LKQJ00000000 | 16 |
| 241-09d | CFSAN025062 | 2009 | Peru | C | 120 | O3:K59 | LKQK00000000 | 16 |
| 245-09d | CFSAN025063 | 2009 | Peru | C | 120 | O3:K59 | LKQL00000000 | 16 |
| CO1409d | CFSAN025064 | 2009 | Peru | C | 120 | O3:K59 | LKQM00000000 | 16 |
| CO1609d | CFSAN025065 | 2009 | Peru | C | 120 | O3:K59 | LKQN00000000 | 16 |
| 285-09d | CFSAN025066 | 2009 | Peru | C | 120 | O3:K59 | LKQO00000000 | 16 |
| 287-09d | CFSAN025067 | 2009 | Peru | C | 120 | O3:K59 | LKQP00000000 | 16 |
| 379-09d | CFSAN025068 | 2009 | Peru | C | 120 | O3:K59 | LKQQ00000000 | 16 |
| P306d | CFSAN029653 | 2009 | Peru | E | 120 | O3:K59 | LKQR00000000 | 16 |
| Guillen 151 Perud | CFSAN029654 | 2009 | Peru | E | 120 | O3:K59 | LKQS00000000 | 16 |
| P310d | CFSAN029656 | 2009 | Peru | E | 120 | O3:K59 | LKQT00000000 | 16 |
| From other labs | ||||||||
| 10-4287d | NA | 2003 | Canada | C | 50 | O6:K18 | JYJU00000000 | Unpublished datai |
| BB22OPg | NA | 1995 | Bangladesh | E | 88 | O4:K8 | NC_019955.1, NC_019971.1 | 51 |
| CDC_K4557e | NA | 2006 | USA | C | 799 | O1:K53 | NC_021822.1, NC_021848.1 | 52 |
| FDA_R31e | NA | 2007 | USA | E | 23 | O1:Kunk | NC_021847.1, NC_021821.1 | 52 |
| RIMD 2210633h | NA | 2003 | Japan | C | 3 | O3:K6 | NC_004605.1, NC_004603.1 | 35 |
| FORC_008d,e,g | NA | 2004 | South Korea | E | 984 | unk | NZ_CP009982.1, NZ_CP009983.1 | Unpublished dataj |
| UCM-V493d,e | NA | 2002 | Spain | E | 471 | O2:K28 | CP007004, CP007005 | 53 |
| CHN25g | NA | 2011 | China | E | 395 | unk | NZ_CP010884.1, NZ_CP010883.1 | Unpublished datak |
| FORC_004e | NA | 2014 | South Korea | E | 1628 | unk | NZ_CP009848.1, NZ_CP009847.1 | Unpublished datak |
| FORC_006d,e | NA | 2014 | South Korea | E | 1630 | unk | NZ_CP009765.1, NZ_CP009766.1 | Unpublished datak |
| FORC_014e | NA | 2015 | South Korea | E | 1629 | unk | NZ_CP011407.1, NZ_CP011406.1 | Unpublished datak |
| KVp10d | NA | 2007 | Sweden | E | 1579 | unk | MBTR01 | Unpublished datal |
| R10B2_71d | NA | 1997 | USA | E | 1556 | unk | MCFR01 | Unpublished datam |
| 04-2192d | NA | 2004 | Canada | C | 629 | unk | LQCB01 | Unpublished datan |
| 04-2550d | NA | 2004 | Canada | C | 630 | unk | LRAH01 | Unpublished datan |
| 05-3133d | NA | 2005 | Canada | C | 43 | unk | LRAI01 | Unpublished datan |
| 05-4792d | NA | 2005 | Canada | C | 199 | unk | LPUZ01 | Unpublished datan |
| 07-2964d | NA | 2007 | Canada | C | 8 | unk | LRSV01 | Unpublished datan |
| 09-1772d | NA | 2009 | Canada | C | 417 | unk | LRSX01 | Unpublished datan |
| 09-3219d | NA | 2009 | Canada | C | 36 | unk | LRSW01 | Unpublished datan |
| 09-4436d | NA | 2009 | Canada | C | 631 | unk | LRAJ01 | Unpublished datan |
| 09-4661d | NA | 2009 | Canada | C | 417 | unk | LNTR01 | Unpublished datan |
| 09-4662d | NA | 2009 | Canada | C | 417 | unk | LRTH01 | Unpublished datan |
| 09-4665d | NA | 2009 | Canada | C | 417 | unk | LRFL01 | Unpublished datan |
| 09-4666d | NA | 2009 | Canada | C | 417 | unk | LQCC01 | Unpublished datan |
| A0EZ383d | NA | 2000 | Canada | C | 638 | unk | LRSY01 | Unpublished datan |
| A0EZ608d | NA | 2000 | Canada | C | 36 | unk | LRFM01 | Unpublished datan |
| A0EZ664d | NA | 2000 | Canada | C | 50 | unk | LRFN01 | Unpublished datan |
| A0EZ713d | NA | 2000 | Canada | C | 50 | unk | LRFO01 | Unpublished datan |
| A1EZ679d | NA | 2001 | Canada | C | 36 | unk | LRSZ01 | Unpublished datan |
| A1EZ919d | NA | 2001 | Canada | C | 36 | unk | LNTX01 | Unpublished datan |
| A1EZ952d | NA | 2001 | Canada | C | 43 | unk | LRTI01 | Unpublished datan |
| A2EZ523d | NA | 2002 | Canada | C | 36 | unk | LRTA01 | Unpublished datan |
| A2EZ614d | NA | 2002 | Canada | C | 43 | unk | LRFP01 | Unpublished datan |
| A2EZ715d | NA | 2002 | Canada | C | 36 | unk | LRFQ01 | Unpublished datan |
| A2EZ743d | NA | 2002 | Canada | C | 324 | unk | LRFR01 | Unpublished datan |
| A3EZ136d | NA | 2003 | Canada | C | 3 | unk | LRFS01 | Unpublished datan |
| A3EZ634d | NA | 2003 | Canada | C | 50 | unk | LRTB01 | Unpublished datan |
| A3EZ710d | NA | 2003 | Canada | C | 43 | unk | LRTC01 | Unpublished datan |
| A3EZ711d | NA | 2003 | Canada | C | 43 | unk | LRTD01 | Unpublished datan |
| A3EZ770d | NA | 2003 | Canada | C | 50 | unk | LRTE01 | Unpublished datan |
| A3EZ799d | NA | 2003 | Canada | C | 43 | unk | LRTF01 | Unpublished datan |
| A3EZ936d | NA | 2003 | Canada | C | 1060 | unk | LRTG01 | Unpublished datan |
| A4EZ700d | NA | 2004 | Canada | C | 43 | unk | LOBT01 | Unpublished datan |
| A4EZ703d | NA | 2004 | Canada | C | 141 | unk | LODO01 | Unpublished datan |
| A4EZ724d | NA | 2004 | Canada | C | 43 | unk | LOHO01 | Unpublished datan |
| A4EZ927d | NA | 2004 | Canada | C | 3 | unk | LOHN01 | Unpublished datan |
| A4EZ964d | NA | 2004 | Canada | C | 636 | unk | LQGX01 | Unpublished datan |
| A5Z1022d | NA | 2005 | Canada | C | 15 | unk | LRFT01 | Unpublished datan |
| A5Z273d | NA | 2005 | Canada | C | ? | unk | LQCD01 | Unpublished datan |
| A5Z652d | NA | 2005 | Canada | C | 36 | unk | LQCE01 | Unpublished datan |
| A5Z853d | NA | 2005 | Canada | C | 3 | unk | LQCF01 | Unpublished datan |
| A5Z860d | NA | 2005 | Canada | C | 43 | unk | LQCS01 | Unpublished datan |
| A5Z878d | NA | 2005 | Canada | C | 36 | unk | LQCT01 | Unpublished datan |
| A5Z905d | NA | 2005 | Canada | C | 36 | unk | LQCU01 | Unpublished datan |
| A5Z924d | NA | 2005 | Canada | C | 36 | unk | LQCV01 | Unpublished datan |
| C140d | NA | 2008 | Canada | C | 332 | unk | LQCW01 | Unpublished datan |
| C142d | NA | 2008 | Canada | C | 417 | unk | LPVA01 | Unpublished datan |
| C143d | NA | 2008 | Canada | C | 36 | unk | LPVB01 | Unpublished datan |
| C144d | NA | 2008 | Canada | C | 36 | unk | LPVC01 | Unpublished datan |
| C145d | NA | 2008 | Canada | C | 417 | unk | LPVK01 | Unpublished datan |
| C146d | NA | 2008 | Canada | C | 1060 | unk | LPVL01 | Unpublished datan |
| C147d | NA | 2008 | Canada | C | 36 | unk | LPVM01 | Unpublished datan |
| C148d | NA | 2008 | Canada | C | 43 | unk | LPVN01 | Unpublished datan |
| C150d | NA | 2008 | Canada | C | 417 | unk | LPVU01 | Unpublished datan |
| F1419d | NA | 2006 | Canada | C | 43 | unk | LRSU01 | Unpublished datan |
| F30368d | NA | 2006 | Canada | C | 8 | unk | LRFV01 | Unpublished datan |
| F4395d | NA | 2006 | Canada | C | 36 | unk | LRFU01 | Unpublished datan |
| F63267d | NA | 2006 | Canada | C | 3 | unk | LRFW01 | Unpublished datan |
| H11523d | NA | 2006 | Canada | C | 36 | unk | LRFY01 | Unpublished datan |
| H18983d | NA | 2006 | Canada | C | 36 | unk | LRST01 | Unpublished datan |
| H64024d | NA | 2006 | Canada | C | 36 | unk | LRFZ01 | Unpublished datan |
| M59787d | NA | 2006 | Canada | C | 36 | unk | LRJZ01 | Unpublished datan |
| T8994d | NA | 2006 | Canada | C | 36 | unk | LRGA01 | Unpublished datan |
| W501d | NA | 2006 | Canada | C | 635 | unk | LRFX01 | Unpublished datan |
| HS-06-05d | NA | 2014 | Canada | E | 614 | unk | LIRS01 | Unpublished datan |
| ISF-29-3d | NA | 2011 | Canada | E | 1518 | unk | LFYM01 | Unpublished datan |
| ISF-54-12d | NA | 2011 | Canada | E | 1631 | unk | LIRR01 | Unpublished datan |
| S357-21d | NA | 2010 | Canada | E | 102 | unk | LFYN01 | Unpublished datan |
| S372-5d | NA | 2011 | Canada | E | 324 | unk | LIRQ01 | Unpublished datan |
| ISF-94-1d | NA | 2011 | Canada | E | 1632 | unk | LIRT01 | Unpublished datan |
| RM-14-5d | NA | 2014 | Canada | E | 1663 | unk | LFXK01 | Unpublished datan |
| Gxw_7004f | NA | 2007 | China | C | 3 | unk | LPZS01 | Unpublished datao |
| Gxw_9143f | NA | 2009 | China | C | 265 | unk | LPZT01 | Unpublished datap |
| K23d | NA | 2013 | India | E | 1052 | unk | LQGU01 | 54 |
a
NA, not applicable.
b
C, clinical; E, environmental.
c
unk–unknown.
d
MiSeq sequencing platform.
e
PacBio sequencing platform.
f
HiSeq sequencing platform.
g
454 sequencing platform.
h
Sanger sequencing platform.
i
J. Ronholm, N. Petronella, R. Kenwell, and S. Banerjee.
j
J.-H. Lee, D.-H. Lee, S. Kim, H.-J. Ku, H. Y. Chung, H. Kim, S. Ryu, and S.-H. Choi.
k
C. Zhu, B. Sun, T. Liu, H. Zheng, and L. Chen.
l
J. W. Turner, R. N. Paranjpye, B. Collin, L. J. Pinnell, and J. Tallman.
m
K. C. Liu.
n
J. Ronholm, N. Petronella, and S. Banerjee.
o
Y. Huang, H. Wang, Y. Pang, Z. Tang, Y. Zhou, and G. Sun.
p
Y. Huang, H. Wang, Y. Pang, Z. Tang, Y. Zhou, C. Qu, L. Lan, C. Wei, and C. Wang.