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

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)

Methodology

RESULTS

ACTs for Chromosome IV. sp Ex25 V. harveyi V. splendidusV. cholerae MJ66

V. vulnificus V. cholerae MJ1236 V. parahaemolyticus

ACTs for Chromosome IIV. sp Ex25 V. harveyi

V.splendidus

V. cholerae MJ66

V. vulnificus V. cholerae MJ 1236 V. parahaemolyticus

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)

Strain

Genes

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)

Strain

Genes

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)

Strain

Genes

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)

Strain

Genes

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)

Strain

Genes

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. pilus-

associated 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