Progress Report
1. Comparative Genomic Analysis
VPAHPND strains
Only present in 3HP
No.
Functional Categories
1
Mannose Metabolism
2
IncF Conjugal transfer system
3
Capsular heptose biosynthesis
4
Programmed cell death systems
5
Prophage-encoded Rst operon
Present in VPAHPND study strains but not In 3HP
1
Phage replication
2
Phage packaging machinery
3
Phage tail fiber protein
4
5
Protein metabolism
Capsular polysaccharides biosynthesis
6
Toxin-antitoxin replicon stabilization
Table 5: Difference of functional categories between VPAHPND strains.
*Red highlighted categories are the
categories I choose to further analyse
but still haven’t complete it.
Non-VPAHPND strains
Only present in 3HP
No.
Functional Categories
1
Melibiose Utilization
2
Ribosome Biogenesis Bacterial
3
IncF Conjugal Transfer System
4
Widespread Colonization Island
5
Type VI Secretion System (VgrG-3 protein, Uncharacterized protein similar to VCA0109, Outer membrane protein
ImpK/VasF, OmpA/MotB domain)
6
Capsular Heptose Biosynthesis
7
Vibrio Core Oligosaccharides Biosynthesis
8
Programmed Cell Death and Toxin-antitoxin System
9
Cholera Toxin (zot, ace, tox S. tox R)
10
Prophage-encoded Rst operon (rstA phage related integrase, rst phage related replication protein)
11
Mannose Metabolism (GDP-mannose mannosyl hydrolase, Mannose-1-phosphate guanylyltransferase (GDP) )
Present in Non-VPAHPND strains
1
Dihydroxyacetone Kinases
2
Maltose and Maltodextrin Utilization
3
LOS core oligosaccharides
4
Phage Packaging Machinery
5
Phage Capsid proteins
6
Phage tail fiber protein
7
Capsular and Extracellular Polysaccharides
Table 6: Difference of functional categories between non-VPAHPND strains.
2. Pan Genome Analysis
AHPND vs Non-AHPND
Thai (AHPND) vs Non-AHPND
• 3HP vs SA2D2
• 3HP vs SDA1
• 3HP vs SA2D2 vs SDA1
3HP
3HP
845
4130
666
SA2D2
432
4543
249
SDA1
SA2D2
42
393
632
4088
453
34
217
SDA1
3HP
Viet (AHPND) vs Non-AHPND
• SDA4 vs SA2D2
• SDA4 vs SDA1
• SDA4 vs SA2D2 vs SDA1
SDA4
SDA4
592
4084
712
SA2D2
458
4218
578
SDA1
SA2D2
59
397
618
4023
197
96
476
SDA1
SDA4
Mal (AHPND) vs Non-AHPND
• SEB2 vs SA2D2
• SEB2 vs SDA1
• SEB2 vs SA2D2 vs SDA1
SEB2
SEB2
872
4146
650
SA2D2
538
4480
312
SDA1
SA2D2
60
479
615
4085
394
36
277
SDA1
SEB2
AHPND vs AHPND
AHPND (Thai) vs AHPND (Viet)
• 3HP vs SDA4
3HP
733
4242
434
SDA4
AHPND (Thai) vs AHPND (Mal)
• 3HP vs SEB2
3HP
• 3HP vs SEA5
• 3HP vs SAB6
• 3HP vs SEB2, SEA5, SAB6
224
4751
267
SEB2
3HP
219
4756
3HP
239
4736
282
272
SEA5
SAB6
SEB2
SEA5
6
195
11
6
14
14
3HP
11
SAB6
29
243
4707
9
11
9
9
4
AHPND (Viet) vs AHPND (Mal)
• SDA4 vs SEB2
SDA4
224
• SDA4 vs SEA5
• SDA4 vs SAB6
• SDA4 vs SEB2, SEA5, SAB6
4751
267
SEB2
SDA4
219
4756
SDA4
239
4736
282
272
SEA5
SAB6
SEB2
SEA5
3
9
2
22
40
385
12
SDA4
686
10
4257
4
7
10
1
13
SAB6
AHPND (Mal) vs AHPND (Mal)
• SEB2 vs SEA5
• SEB2 vs SAB6
• SEB2 vs SEA5, SAB6
SEB2
SEB2
55
4963
26
4992
45
SAB6
SAB6
13
12
20
4950
43
25
20
SEA5
SEB2
46
SEA5
AHPND (Thai) vs AHPND (Mal) vs AHPND (Viet)
SEB2
• 3HP vs SEB2, SEA5, SAB6 vs SDA4
11
3HP
SEA5
188
20
4201
365
SDA4
19
SAB6
3. Phylogenomic Analysis
Method:
20 draft genomes of Vibrio parahaemolyticus strains were constructed with the Reference sequence
Alignment based Phylogeny builder (REALPHY) (https://realphy.unibas.ch/fcgi/realphy).
No.
1.
Nature
Shrimp Farm
Organism
Vibrio parahaemolyticus
Strain
3HP
2.
Vibrio parahaemolyticus
SA2D2
Malaysia
3.
Vibrio parahaemolyticus
SAB6
Malaysia
4.
Vibrio parahaemolyticus
SDA1
Vietnam
5.
Vibrio parahaemolyticus
SDA4
Vietnam
6.
Vibrio parahaemolyticus
SEA5
Malaysia
7.
Vibrio parahaemolyticus
SEB2
Malaysia
Vibrio parahaemolyticus
M0605
JALL01.1
Mexico
9.
Vibrio parahaemolyticus
TUMSAT_DE1_S1
BAVF01.1
Thailand
10.
Vibrio parahaemolyticus
TUMSAT_DE2_S2
BAVG01.1
Thailand
11.
Vibrio parahaemolyticus
NCKU_TV_5HP
JPKT01.1
Thailand
12.
Vibrio parahaemolyticus
NCKU_CV_CHN
JPKU01.1
China
13.
Non-Pathogenic (Non-AHPND) Vibrio parahaemolyticus
M1-1
PDDQ01.1
Vietnam
14.
Vibrio parahaemolyticus
KC13.17.5
BBXN01.1
Vietnam
15.
Vibrio parahaemolyticus
13-028/A2
JOKT01.1
Vietnam
16.
Vibrio parahaemolyticus
TUMSAT_H01_S4
BAVI01.1
Thailand
Vibrio parahaemolyticus
RIMD 2210633
LFUR01.1
Japan
Vibrio parahaemolyticus
Peru-466
ACFM01.1
Peru
Vibrio parahaemolyticus
VP103
LBDB01.1
Malaysia
Vibrio parahaemolyticus
AF91
JMMS01.1
Florida
8.
17.
Pathogenic (AHPND)
Clinical
18.
19.
20.
Study Strains
Environmental
WGS
Origin
Thailand
VPAHPND strains
Result:
i.
Most of the Malaysia, Thailand, and Vietnam
VPAHPND strains were clustered together and
closely related.
ii. The Malaysia VPAHPND strains SAB6, SEA5,
and SEB2 were highly close related.
iii. SDA4 were more closely related to the
VPAHPND strains from China (JPKU01.1)
iv. Non- VPAHPND strains SDA1 were more
closely related to the reference 3HP
compared to the others.
v. Non- VPAHPND strains SA2D2 were distinctly
related to the VPAHPND strains
Clinical strains
Non-VPAHPND strains