Table 4 List of various genes found in isolate and reference genomes.

From: Emergence of multidrug resistant, ctx negative seventh pandemic Vibrio cholerae O1 El Tor sequence type (ST) 69 in coastal water of Kerala, India

Isolate name/accession No

Source

Species specific gene

Serogroup specific gene

Biotype specific genes

7th pandemic gene

Virulence genes

Pathogenicity islands

Antibiotic resistance genes

NC_012667.1

/NC_012668.1 Vibrio cholerae MJ-1236 complete sequence

Clinical

ompW

rfb-O1

tcpAet3, ctxB-1, rstRcc

VC2346

als,mshA, toxR, ompT, rtxA, VgrG, ompU, ctxA,

ace, zot,

makA, VasX, hlyA

VSP2_VC0498, VSP2_VC0493, VPI2_VC1809, VPI2_VC1776, VSP1_VC0180, VPI2_VC1783, VSP2_VC0514, VPI1_VC0819, VSP2_VC0512, VPI2_VC1790, VPI2_VC1758, VPI1_VC0840, VSP2_VC0516, VSP1_VC0178, VPI2_VC1765, VSP2_VC0502, VPI2_VC1760, VSP2_VC0490, VPI1_VC0827, VSP1_VC0175, VPI1_VC0847, VSP1_VC0183, VSP1_VC0185, VSP2_VC0504, VSP1_VC0185, VPI2_VC1790, VSP1_VC0183, VSP1_VC0180, VSP1_VC0175, VSP1_VC0178

catB9

VC1786ICE9_floR,

dfrA1,

sul2,

parC,

gyrA,

strB,

parE,

strA

VC6

This study

ompW

rfb-O1

tcpAet3

VC2346

mshA, ompT, rtxA, als,

makA, VasX, ompU, hlyA, VgrG, toxR

VSP1-VC0180, VSP2-VC0516, VSP2-VC0514, VSP2-VC0512, VPI2-VC1760, VSP1-VC0185, VSP2-VC0502, VPI2-VC1790,

VPI-VC0827, VPI1-VC0847, VSP1-VC0178, VPI2-VC1776, VSP1-VC0183, VSP2-VC0498, VPI2-VC1765, VPI1-VC0819, VSP2-VC0504, VPI2-VC1758, VPI2-VC1809, VPI1-VC0840, VSP2-VC0493, VSP1-VC0175,

VSP2- VC0490, VPI2-VC1783

VC1786ICE9-floR,

strB,

strA,

parE,

dfrA1,

gyrA,

parC,

sul2,

catB9

NZ-AP018677.1

V. cholerae strain V060002

chromosome, complete genome

Clinical

ompW

rfb-O1

ctxB-1, rstRcc, tcpAet3

VC2346

mpU, VgrG, VasX, ctxA,

zot, makA, mshA, toxR, ompT, hlyA,

rtxA, als,

ace

VSP1-VC0185, VSP2-VC0514, VSP1-VC0180, VSP2-VC0490, VSP2-VC0498, VSP2-VC0493, VPI2-VC1790, VSP2-VC0502, VPI1-VC0840, VSP2-VC0504, VSP2-VC0512, VSP1-VC0178, VPI2-VC1765, VSP1-VC0175, VPI2-VC1776, VPI2-VC1783, VSP1-VC0183,

VPI2-VC1809, VPI1-VC0819, VPI1-VC0847, VPI2-VC1760, VPI2-VC1758, VSP2-VC0516, VPI1-VC0827

gyrA,

catB9,

parC,

parE

AE003852.1/

AE003853.1 .V. cholerae O1 biovar El Tor strain N16961, complete sequence

Clinical

ompW

rfb-O1

rstRet, tcpAet3, ctxB-3

VC2346

ctxA, mshA,

als, VgrG, toxR, ompT, ompU, rtxA, zot, ace, makA, VasX,

hlyA

VSP2-VC0516, VPI2-VC1758, VSP1-VC0185, VPI2-VC1809, VSP2-VC0502, VSP1-VC0183, VPI2-VC1776, VSP2-VC0514, VSP2-VC0498, VPI2-VC1783, VSP1-VC0180, VSP2-VC0493, VPI1-VC0847, VPI1-VC0819, VPI1-VC0840, VPI1-VC0827, VSP2-VC0512,

VPI2-VC1760, VSP2-VC0504, VSP1-VC0175, VSP1-VC0178, VPI2-VC1765, VSP2_VC0490, VPI2-VC1790,

VPI2_VC1790

parE,

gyrA,

parC

catB9

NC-012578.1/NC-

012,580.1 V. cholerae M66-2 complete sequence

 

ompW

rfb-O1

tcpA-et3

none

als,

ompU, VgrG, ompT, toxR, mshA, rtxA,

hlyA, VasX, makA

VPI2-VC1760, VPI2-VC1790, VPI2-VC1758, VPI2-VC1776, VPI1-VC0819, VPI2-VC1783, VPI2-VC1765, VPI1-VC0847, VPI2-VC1809,

VPI-VC0840,

VPI1-VC0827, VPI2-VC1790

parC,

parE,

gyrA

CP012998.1 /

CP012997.1 V. cholerae

strain

2012Env-9 complete

sequence

Environmental

ompW

rfb-O1

none

none

ompU,

rtxA,

als,

mshA,

toxR,

ompT,

hlyA

VPI1-VC0819,

VPI1-VC0847,

VPI2-VC1758,

VPI2-VC1790,

VPI2-VC1760,

VPI2_VC1790

gyrA,

parC,

parE,

catB9

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