Comparative Genomics:
Vibrio spp.
ICGEB Workshop Group 4
Albert Auguste, Reia Guppy, Amalia Hosein, Andrés
López, Maria Jose Muňoz, Silvia Vasquez, Jerome
Foster
Study organism

Vibrio spp. of anaerobic
bacteria (curved rods)

> 70 species, across 4
families

symbiotic, communalistic,
pathogenic

at least 12 are important
human pathogens
(Vibrionaceae)
Study organism

Pathogenic species are major causative agents of
several clinical illnesses in humans (gastroenteritis ,
wound infections w/ septicaemia)

Transmission usually by consumption of raw/uncooked
shellfish, or exposure to contaminated or warm sea
water

E.g. V. cholerae, V. parahaemolyticus, V. vulnificus
Study organism

Invasive infections such as that of V. cholerae may
rapidly progress to death

Patients w/ liver malfunction are at high morbidity &
mortality risk (e.g. V. vulnificus)

CDC, 2008: 131 per 100,00 lab-confirmed infections of
Vibrio spp. in the U.S.
Study organism

Other Vibrio spp. are marine pathogens e.g.

V. Harveyi - pathogen of fish and invertebrates, including
sharks, sea bass, seahorses, lobster, and shrimp

V. splendidus inflicts disease and death in many marine
species including fish, oysters, mussels, and scallops

Non-pathogenic include V. fischeri, V. logei
Vibrio genome organization
Project Objectives

Compare nonpathogenic vs. pathogenic Vibrio
spp.
similarities?
 unique traits?
 genome organization?

Methodology


Pairwise comparison between Vibrio spp. using
ACT (Artemis Comparison Tool; Carver et al., 2005)
V. fischeri as a “reference” species for all
comparisons

basal in taxonomy & phylogeny* of Vibrio spp to other
available complete genomes (based on 16s rRNA;
Thompson et al., 2009)

non-pathogenic in both humans & marine life
Methodology

Dataset of eight (8) complete & published Vibrio
genomes each with 2 chromosomes ( I and II)

WebACT used to generate sequence & blast
comparisons (blastn only*)

ACT used on local server for actual comparative
analyses
Methodology

Total of 14 ACT runs (7 x 2 chromosomes), V. fischeri
(MJ11) vs.

V. cholerae (M66_2)

V. cholerae (MJ_1236)

V. harveyi (ATCC_BAA_1116)

V. parahaemolyticus (RIMD 2210633)

V. vulnificus (YJ016)

V. Sp. Ex25

V. splendidus (LGP32)
RESULTS
ACTs for Chromosome I
V. sp Ex25
V. vulnificus
V. harveyi
V. cholerae MJ66
V. cholerae MJ1236
V. splendidus
V. parahaemolyticus
ACTs for Chromosome II
V. sp Ex25
V. vulnificus
V. harveyi
V. cholerae MJ 1236
V. cholerae MJ66
V. parahaemolyticus
V.splendidus
Selected genes for comparison

TCP – encodes pili protein (pathogenicity island)

toxR – virulence regulation

rtxA – modulation of toxicity

ompU – membrane protein assoc. with virulence


Pili– genes associated with pili formation
(responsible for attachment to epithelium)
PutA – part of PutAB operon (osmotic tolerance)
Genes
Strain
TCP
Pili
ompU
rtxA
toxR
PutA
Vibrio fischeri
1
5
1
-
-
-
V. Cholerae (MJ1236)
1
8
1
-
1
-
V. harveyi**
-
-
-
-
-
-
V. parahaemolyticus
-
6
1
1
1
-
V. vulnificus
-
8
1
-
1
-
V. sp Ex25
-
8
1
1*
1
-
V. splendidus
-
9
1
-
-
-
V. cholerae (MJ66)
2
8
1
5
1
-
TABLE 1. Select genes for pathogenesis and virulence (chromosome 1)
Genes
Strain
TCP
Pili
ompU
rtxA
toxR
PutA
Vibrio fischeri
1
5
1
-
-
-
V. Cholerae (MJ1236)
1
8
1
-
1
-
V. harveyi**
-
-
-
-
-
-
V. parahaemolyticus
-
6
1
1
1
-
V. vulnificus
-
8
1
-
1
-
V. sp Ex25
-
8
1
1*
1
-
V. splendidus
-
9
1
-
-
-
V. cholerae (MJ66)
2
8
1
5
1
-
TABLE 1. Select genes for pathogenesis and virulence (chromosome 1)
Genes
Strain
TCP
Pili
ompU
rtxA
toxR
PutA
Vibrio fischeri
1
5
1
-
-
-
V. Cholerae (MJ1236)
1
8
1
-
1
-
V. harveyi**
-
-
-
-
-
-
V. parahaemolyticus
-
6
1
1
1
-
V. vulnificus
-
8
1
-
1
-
V. sp Ex25
-
8
1
1*
1
-
V. splendidus
-
9
1
-
-
-
V. cholerae (MJ66)
2
8
1
5
1
-
TABLE 1. Select genes for pathogenesis and virulence (chromosome 1)
Genes
Strain
TCP
Pili
ompU
rtxA
toxR
PutA
Vibrio fischeri
2
-
-
-
-
1
V. Cholerae (MJ1236)
-
-
-
-
-
-
V. harveyi**
-
-
-
-
-
-
V. parahaemolyticus
-
3
1
-
2
-
V. vulnificus
-
1`
-
-
-
-
V. Sp Ex25
-
2
1
-
-
1
V. splendidus
-
-
-
-
-
-
V. cholerae (MJ66)
-
-
-
-
-
1
TABLE 2. Select genes for pathogenesis and virulence (chromosome 2)
Genes
Strain
TCP
Pili
ompU
rtxA
toxR
PutA
Vibrio fischeri
2
-
-
-
-
1
V. Cholerae (MJ1236)
-
-
-
-
-
-
V. harveyi**
-
-
-
-
-
-
V. parahaemolyticus
-
3
1
-
2
-
V. vulnificus
-
1`
-
-
-
-
V. Sp Ex25
-
2
1
-
-
1
V. splendidus
-
-
-
-
-
-
V. cholerae (MJ66)
-
-
-
-
-
1
TABLE 2. Select genes for pathogenesis and virulence (chromosome 2)
CDSs (at 100% Identity) showing reassortment (V. Fischeri vs V. Cholerae M66)
Chrom. 2: Bifunctional protein PutA, absent in V. sp Ex25 (possibly
reassorted & pseudogeneized?)
Limitations

Only pairwise comparisons possible


time constraints
Inexperience with software e.g.
CDS key queries - “PutA” vs “puta”
 Tblastx run error (WebACT) – only Blastn used

CONCLUSIONS





Seems to be numerous reassortments among Vibrio spp.
in comparison to V. fischeri
Genomes very similar but “messy” (reassortments,
duplicated stretches of sequence)
Common gene products across all species, e.g. pilusassociated genes
Toxin genes maintained across pathogenic species
Group needs more practice in analyzing this kind of data
(steep learning curve)!!
ACKNOWLEDGEMENTS
All the module instructors (esp. Dr. Pain!)
 Organizers @ UWI, UNU-BIOLAC & ICGEB
