Table 1. Vibrio cholerae and other Vibrio spp. isolates analysed in this study.
| Strain Name | Original Strain Name | Category | Serogroup | Location (year) | VPI† | T3SS§ | CTX | rtxA | NAG-ST | adk | gyrB | mdh | metE | pntA | purM | pyrC | ST | Clonal Complex (CC)# | Subpopulation¶ |
| M2565 | AQ 24151 | Clinical | O94 | Bangladesh (2001) | − | + | − | + | − | 26 | 5 | 2 | 1 | 31 | 19 | 45 | 50 | CC2 | I |
| M2549 | AO 823 | Clinical | O12 | Bangladesh (1999) | − | − | − | + | − | 12 | 23 | 2 | 49 | 30 | 1 | 40 | 9 | Singleton | I |
| M553 | 141-94 | Environmental | O70 | Germany (1994) | + | − | − | + | − | 17 | 5 | 14 | 50 | 31 | 14 | 23 | 22 | Singleton | I |
| M1121 | 208 | Clinical | O27 | Thailand (1992) | + | − | − | + | − | 19 | 9 | 12 | 23 | 9 | 1 | 5 | 26 | Singleton | I |
| M1576 | Clinical | O124 | India (1981) | − | − | − | + | + | 2 | 7 | 8 | 22 | 39 | 1 | 45 | 31 | Singleton | I | |
| M1052 | 334-72 | Clinical | O26 | Phillipines (1972) | − | − | − | + | − | 24 | 5 | 14 | 50 | 31 | 14 | 45 | 39 | Singleton | I |
| M2559 | AQ 9921 | Clinical | O2 | Bangladesh (2001) | − | + | − | + | − | 26 | 23 | 2 | 50 | 31 | 1 | 45 | 43 | Singleton | I |
| M2547 | AN 26575 | Clinical | O44 | Bangladesh (1998) | − | − | − | + | − | 26 | 3 | 1 | 50 | 14 | 18 | 45 | 44 | Singleton | I |
| M2561 | AQ 13192 | Clinical | O145 | Bangladesh (2001) | − | + | − | + | − | 26 | 5 | 1 | 8 | 14 | 14 | 45 | 45 | Singleton | I |
| M2560 | AQ 11489 | Clinical | O15 | Bangladesh (2001) | − | + | − | + | − | 26 | 5 | 14 | 50 | 31 | 14 | 2 | 46 | Singleton | I |
| M535 | #82 | Environmental | O1 | Thailand (1992) | − | + | − | + | + | 26 | 5 | 14 | 50 | 31 | 15 | 45 | 47 | Singleton | I |
| M2564 | AQ 18953 | Clinical | O24 | Bangladesh (2001) | − | − | − | + | − | 27 | 5 | 9 | 21 | 30 | 6 | 45 | 51 | Singleton | I |
| M2556 | AP 20403 | Clinical | ND | Bangladesh (2000) | − | + | − | + | − | 26 | 5 | 2 | 1 | 31 | 17 | 45 | 49 | CC2 | II |
| M536 | #35 | Environmental | O1 | Thailand (1992) | − | + | − | + | + | 1 | 15 | 19 | 15 | 24 | 5 | 14 | 3 | Singleton | II |
| M1562 | AU256 | Environmental | O110 | Japan (1992) | − | + | − | + | + | 1 | 41 | 21 | 4 | 2 | 16 | 43 | 4 | Singleton | II |
| M1095 | 27973 | Clinical | O77 | India (1976) | + | − | − | + | + | 1 | 42 | 4 | 60 | 20 | 1 | 12 | 5 | Singleton | II |
| M2563 | AQ 16457 | Clinical | O24 | Bangladesh (2001) | − | − | − | + | − | 12 | 23 | 2 | 6 | 30 | 17 | 40 | 10 | Singleton | II |
| M1105 | 984-81 | Clinical | O89 | India (1981) | − | + | − | + | + | 12 | 5 | 3 | 33 | 31 | 18 | 26 | 11 | Singleton | II |
| M555 | 905-93 | Environmental | O97 | Argentina (1993) | + | − | − | + | + | 13 | 40 | 17 | 46 | 3 | 9 | 39 | 12 | Singleton | II |
| M559 | 179-94 | Environmental | O52 | Denmark (1994) | − | − | − | − | − | 14 | 1 | 14 | 44 | 6 | 9 | 39 | 13 | Singleton | II |
| M1071 | 1154-74 | Clinical | O49 | India (1974) | − | − | − | + | − | 14 | 14 | 4 | 53 | 22 | 17 | 35 | 14 | Singleton | II |
| M1098 | 1421-77 | Clinical | O80 | India (1977) | + | + | − | + | + | 14 | 23 | 6 | 47 | 11 | 1 | 36 | 15 | Singleton | II |
| 12129 | Genome* | Environmental | O1 | Australia (1985) | + | + | − | + | − | 14 | 31 | 20 | 39 | 16 | 1 | 13 | 16 | Singleton | II |
| M1118 | 577-88 | Clinical | O105 | China (1988) | + | + | + | − | − | 14 | 38 | 14 | 43 | 8 | 21 | 11 | 17 | Singleton | II |
| M560 | 190-94 | Environmental | O39 | Denmark (1994) | − | + | − | + | − | 14 | 6 | 14 | 7 | 3 | 20 | 47 | 18 | Singleton | II |
| M548 | ATCC33653 | Environmental | O25 | Germany (1993) | + | + | − | + | + | 14 | 6 | 29 | 11 | 25 | 1 | 24 | 19 | Singleton | II |
| VL426 | Genome | Environmental | non-O1/non-O139 | UK | − | − | − | + | − | 15 | 29 | 16 | 18 | 10 | 1 | 22 | 20 | Singleton | II |
| M1049 | 169-68 | Clinical | O22 | Phillipines (1968) | − | − | − | + | − | 18 | 5 | 14 | 40 | 17 | 1 | 1 | 24 | Singleton | II |
| M1051 | 14438-62 | Clinical | O24 | Phillipines (1962) | + | − | − | + | − | 19 | 23 | 14 | 12 | 1 | 1 | 6 | 25 | Singleton | II |
| RC385 | Genome | Environmental | O135 | Chesapeake bay (1998) | − | − | − | + | + | 2 | 10 | 18 | 45 | 4 | 8 | 48 | 27 | Singleton | II |
| MZO-2 | Genome | Clinical | O14 | Bangladesh (2001) | − | − | − | + | − | 2 | 23 | 15 | 42 | 18 | 13 | 10 | 28 | Singleton | II |
| AM-19226 | Genome | Clinical | O39 | Bangladesh (2001) | + | + | − | + | − | 2 | 5 | 13 | 19 | 6 | 6 | 5 | 29 | Singleton | II |
| 1587 | Genome | Clinical | O12 | Peru (1994) | + | − | − | + | − | 2 | 6 | 29 | 2 | 25 | 1 | 3 | 30 | Singleton | II |
| M556 | 921-93 | Environmental | O74 | Argentina (1993) | − | − | − | + | − | 22 | 39 | 10 | 38 | 3 | 17 | 15 | 36 | Singleton | II |
| M1078 | 1463-76 | Clinical | O57 | India (1976) | − | − | − | + | + | 24 | 5 | 1 | 6 | 39 | 18 | 2 | 38 | Singleton | II |
| M1036 | 8394-62 | Clinical | O7 | India (1962) | − | + | − | − | + | 24 | 5 | 14 | 55 | 30 | 1 | 44 | 40 | Singleton | II |
| M1575 | 345-81 | Clinical | O123 | India (1981 | − | − | − | − | + | 24 | 5 | 14 | 55 | 7 | 1 | 45 | 41 | Singleton | II |
| M1593 | 243-93 | Clinical | O141 | India (1993) | + | + | + | + | + | 25 | 5 | 22 | 16 | 21 | 8 | 11 | 42 | Singleton | II |
| V51 | Genome | Clinical | O141 | US | + | + | + | + | − | 25 | 5 | 22 | 16 | 21 | 8 | 11 | 42 | Singleton | II |
| TM11079-80 | Genome | Environmental | O1 | Brazil (1980) | + | − | − | + | − | 26 | 5 | 14 | 54 | 28 | 14 | 45 | 48 | Singleton | II |
| M549 | 1085-93 | Environmental | O37 | Germany (1993) | − | − | − | + | − | 4 | 23 | 28 | 13 | 25 | 1 | 9 | 65 | Singleton | II |
| MZO-3 | Genome | Clinical | O37 | Bangladesh (2001) | − | − | − | + | − | 4 | 23 | 28 | 13 | 25 | 1 | 9 | 65 | Singleton | II |
| M563 | 370-94 | Environmental | O81 | Korea (1994) | − | + | − | − | + | 5 | 26 | 14 | 34 | 2 | 4 | 47 | 66 | Singleton | II |
| M2552 | AO 21097 | Clinical | O27 | Bangladesh (1999) | − | + | − | + | − | 6 | 4 | 14 | 35 | 15 | 3 | 46 | 67 | Singleton | II |
| M1618 | N1 (V523) | Environmental | non-O1/non-O139 | Australia (1977) | + | − | + | + | + | 7 | 11 | 4 | 17 | 23 | 1 | 35 | 68 | Singleton | II |
| M2129 | ATCC 25872 | Clinical | O37 | Czechoslovakia (1965) | + | − | + | + | + | 7 | 11 | 4 | 17 | 23 | 1 | 35 | 68 | Singleton | II |
| M2130 | S-21 | Clinical | O37 | Sudan (1968) | + | − | + | + | + | 7 | 11 | 4 | 17 | 23 | 1 | 35 | 68 | Singleton | II |
| V52 | Genome | Clinical | O37 | Sudan | + | − | + | + | − | 7 | 11 | 4 | 17 | 23 | 1 | 35 | 68 | Singleton | II |
| M1086 | 981-75 | Clinical | O65 | India (1975) | + | − | − | + | − | 7 | 12 | 14 | 37 | 12 | 1 | 36 | 74 | Singleton | II |
| CT5369-93 | Genome | Environmental | non-O1/non-O139 | − | − | − | + | − | 7 | 24 | 30 | 59 | 3 | 1 | 45 | 76 | Singleton | II | |
| M562 | 369-94 | Environmental | O10 | Korea (1994) | − | − | − | + | − | 8 | 30 | 27 | 36 | 3 | 9 | 39 | 78 | Singleton | II |
| TMA21 | Genome | Environmental | non-O1/non-O139 | Brazil (1993) | + | + | − | + | − | 9 | 25 | 3 | 41 | 6 | 1 | 5 | 79 | Singleton | II |
| N16961 | Genome | 7th pandemic | O1 | Bangladesh (197X) | + | − | + | + | − | 7 | 11 | 4 | 37 | 12 | 1 | 20 | 69 | CC1 | III |
| M2140 | SIMP/77 | Australian toxigenic | O1 | Australia (1977) | + | − | + | + | + | 7 | 11 | 4 | 37 | 12 | 1 | 37 | 70 | CC1 | III |
| M2141 | M4287/77 | Australian toxigenic | O1 | Australia (1977) | + | − | + | + | + | 7 | 11 | 4 | 37 | 12 | 1 | 37 | 70 | CC1 | III |
| BX330286 | Genome | Australian toxigenic | O1 | Australia (1986) | + | − | + | + | + | 7 | 11 | 4 | 37 | 12 | 1 | 37 | 70 | CC1 | III |
| M802 | M66-2/Makassar 759 (Genome) | pre-7th pandemic | O1 | Indonesia (1937) | + | − | + | + | − | 7 | 11 | 4 | 37 | 12 | 1 | 38 | 71 | CC1 | III |
| M1616 | O395 (Genome) | 6th pandemic | O1 | India (1965) | + | − | + | − | + | 7 | 11 | 4 | 9 | 12 | 1 | 38 | 73 | CC1 | III |
| M796 | 4808 | US Gulf Coast | O1 | USA (1978) | + | − | + | + | + | 7 | 2 | 4 | 37 | 12 | 1 | 38 | 75 | CC1 | III |
| M2562 | AQ 14875 | Clinical | O49 | Bangladesh (2001) | − | + | − | + | − | 1 | 1 | 4 | 48 | 29 | 1 | 41 | 1 | CC3 | III |
| M2553 | AP 2007 | Clinical | O49 | Bangladesh (2000) | − | + | − | + | − | 1 | 1 | 4 | 48 | 29 | 17 | 41 | 2 | CC3 | III |
| M2554 | AP 9172 | Clinical | O49 | Bangladesh (2000) | − | + | − | + | − | 1 | 1 | 4 | 48 | 29 | 17 | 41 | 2 | CC3 | III |
| M2555 | AP 14558 | Clinical | O49 | Bangladesh (2000) | − | + | − | + | − | 1 | 1 | 4 | 48 | 29 | 17 | 41 | 2 | CC3 | III |
| M2558 | AQ 5961 | Clinical | O49 | Bangladesh (2001) | + | + | − | + | − | 1 | 1 | 4 | 48 | 29 | 17 | 41 | 2 | CC3 | III |
| M1619 | N19 (V58) | Environmental | non-O1/non-O139 | Australia (1977) | + | − | + | + | + | 1 | 8 | 15 | 5 | 13 | 1 | 7 | 6 | Singleton | III |
| M1035 | B4202-64 | Clinical | O5 | Phillipines (1964) | − | + | − | − | + | 11 | 27 | 11 | 56 | 19 | 1 | 4 | 8 | Singleton | III |
| M1092 | 113-79 | Clinical | O73 | India (1979) | − | + | − | + | − | 11 | 27 | 11 | 56 | 19 | 1 | 4 | 8 | Singleton | III |
| 623-39 | Genome | Environmental | non-O1/non-O139 | Bangladesh (2002) | + | − | − | + | − | 20 | 41 | 5 | 3 | 18 | 2 | 4 | 32 | Singleton | III |
| M550 | 1089-93 | Environmental | O99 | Germany (1993) | − | + | − | + | − | 3 | 28 | 11 | 56 | 19 | 12 | 4 | 54 | Singleton | III |
| M561 | 366-94 | Environmental | O74 | Korea (1994) | − | − | − | + | − | 7 | 36 | 7 | 10 | 38 | 1 | 42 | 77 | Singleton | III |
| M554 | Environmental | O83 | Germany (1994) | + | − | − | + | + | 10 | 13 | 25 | 57 | 34 | 10 | 25 | 7 | Singleton | IV | |
| M1565 | AU105 | Environmental | O113 | Japan (1995) | − | + | − | + | − | 16 | 33 | 26 | 31 | 34 | 11 | 26 | 21 | Singleton | IV |
| M1563 | AU291 | Environmental | O111 | Japan (1993) | − | + | − | − | + | 17 | 5 | 25 | 32 | 36 | 11 | 29 | 23 | Singleton | IV |
| M1093 | 429-79 | Clinical | O75 | India (1979) | + | − | − | − | − | 21 | 37 | 23 | 58 | 35 | 7 | 28 | 33 | Singleton | IV |
| M557 | 928-93 | Environmental | O6 | Argentina (1993) | − | − | − | − | − | 22 | 32 | 24 | 20 | 33 | 9 | 27 | 34 | Singleton | IV |
| M558 | 929-93 | Environmental | O66 | Argentina (1993) | − | − | − | − | − | 22 | 32 | 24 | 20 | 5 | 1 | 27 | 35 | Singleton | IV |
| M1560 | AU124 | Environmental | O108 | Japan (1990) | + | − | − | − | − | 23 | 34 | 26 | 57 | 37 | 10 | 25 | 37 | Singleton | IV |
| M2548 | AN 28767 | Clinical | O37 | Bangladesh (1998) | − | − | − | − | − | 26 | 3 | 1 | N/A‡ | 14 | 18 | N/A | |||
| M2550 | AO 13987 | Clinical | O8 | Bangladesh (1999) | N/A | N/A | N/A | N/A | N/A | N/A | 1 | 11 | N/A | N/A | N/A | N/A | |||
| M2551 | AO 21097 | Clinical | O27 | Bangladesh (1999) | − | − | − | − | − | 34 | 41 | 33 | 58 | 26 | 31 | N/A | |||
| M547 | ATCC33653 | V. mimicus | 31 | 18 | 41 | 52 | 40 | 23 | 33 | 56 | |||||||||
| M1566 | 246-79 | V. mimicus | O114 | USA (1979) | 32 | 20 | 39 | 29 | 44 | 30 | 19 | 58 | |||||||
| M1567 | 523-80 | V. mimicus | O115 | USA (1980) | 32 | 21 | 38 | 26 | 46 | 25 | 34 | 59 | |||||||
| M1115 | 559-88 | V. mimicus | O101 | China (1988) | 32 | 22 | 42 | 27 | 41 | 27 | 18 | 60 | |||||||
| M1569 | 381-82 | V. mimicus | O117 | Japan (1982) | 33 | 19 | 35 | 30 | 42 | 29 | 31 | 61 | |||||||
| M1568 | 980-78 | V. mimicus | O116 | USA (1978) | 34 | 17 | 34 | 28 | 43 | 31 | 16 | 62 | |||||||
| RC341 | Genome | V. metecus | 28 | 35 | 31 | 14 | 27 | 22 | 8 | 52 | |||||||||
| M552 | O103 | Germany (1993) | 37 | 42 | 43 | 47 | 27 | 34 | 50 | 95 | |||||||||
| RC586 | Genome | V. parilis | 29 | 35 | 33 | 51 | 26 | 32 | 21 | 53 | |||||||||
| VM223 | Genome | V. mimicus | Brazil | 30 | 16 | 36 | 62 | 40 | 24 | 30 | 55 | ||||||||
| MB451 | Genome | V. mimicus | Bangladesh | 31 | 22 | 40 | 24 | 41 | 28 | 17 | 57 | ||||||||
| SX-4 | Genome | V. mimicus | China (2009) | 32 | 21 | 38 | 26 | 46 | 25 | 34 | 59 | ||||||||
| VM573 | Genome | V. mimicus | USA (1990s) | 32 | 21 | 38 | 26 | 46 | 25 | 34 | 59 | ||||||||
| VM603 | Genome | V. mimicus | Brazil (1990s) | 35 | 19 | 37 | 25 | 45 | 26 | 32 | 63 | ||||||||
| CMCP6 | Genome | V. vulnificus | 36 | 43 | 32 | 61 | 32 | 33 | 49 | 64 |
*
Genome strains 1587 (GenBank Accession No. AAUR00000000); 623-39 (Accession No. AAWG00000000); AM-19226 (Accession No. AATY00000000); BX330286 (Accession No. ACIA00000000); CMCP6 (Accession No. AE016795.3); CT5369-93 (Accession No. ADAL00000000); M66-2 (Accession No. CP001233); MB451 (Accession No. ADAF00000000); MZO-2 (Accession No. AAWF00000000); MZO-3 (Accession No. AAUU00000000); N16961 (Accession No. AE003852); M1616/O395 (Accession No. CP000626); RC341 (Accession No. ACZT00000000); RC385 (Accession No. AAKH00000000); RC586 (Accession No. ADBD00000000); SX-4 (Accession No. ADOO00000000); TM11079-80 (Accession No. ACHW00000000); TMA21 (Accession No. ACHY00000000); V51 (Accession No. AAKI00000000); V52 (Accession No. AAKJ00000000); VL426 (Accession No. ACHV00000000); VM223 (Accession No. ADAJ00000000); VM573 (Accession No. ACYV00000000); VM603 (Accession No. ACYU00000000); 12129 (Accession No. ACFQ00000000).
†
Two primer pairs were used as previously described in Tay et al. [44] to amplify divergent tcpA genes.
§
Two primer pairs were used for typing the type III secretion system (T3SS), one for vcsC2 and one for vcsV2.
‡
N/A: Data not available.
#
Clonal complex (CC) as defined by eBURST analysis.
¶
Subpopulations are derived from STRUCTURE analysis.