whole genome sequence of staphylococcus saprophyticus reveals the pathogenesis of uncomplicated...

28
Whole Genome Sequence of Staphylococcus saprophyticus reveals the pathogenesis of uncomplicated urinary tract infection Comparative Microbial Genomics: A Bioinformatics Approach 5th October 2005 Ana Rita Domingues Boumediene Soufi Francisco Roque Gianni Panagiotou

Upload: ann-anderson

Post on 04-Jan-2016

221 views

Category:

Documents


4 download

TRANSCRIPT

Page 1: Whole Genome Sequence of Staphylococcus saprophyticus reveals the pathogenesis of uncomplicated urinary tract infection Comparative Microbial Genomics:

Whole Genome Sequence of

Staphylococcus saprophyticus reveals the pathogenesis of

uncomplicated urinary tract infectionComparative Microbial Genomics:

A Bioinformatics Approach

5th October 2005

Ana Rita Domingues

Boumediene Soufi

Francisco Roque

Gianni Panagiotou

Page 2: Whole Genome Sequence of Staphylococcus saprophyticus reveals the pathogenesis of uncomplicated urinary tract infection Comparative Microbial Genomics:

• PNAS is one of the world's most-cited multidisciplinary scientific serials.

• Since its establishment in 1914, it continues to publish cutting-edge research reports, commentaries, reviews, perspectives, colloquium papers, and actions of the Academy.

• Coverage in PNAS spans the biological, physical, and social sciences.

The PNAS impact factor is 10.5 for

2004

www.pnas.org

Page 3: Whole Genome Sequence of Staphylococcus saprophyticus reveals the pathogenesis of uncomplicated urinary tract infection Comparative Microbial Genomics:

Abstract

PNAS vol 102, no37, September 13, 2005

Page 4: Whole Genome Sequence of Staphylococcus saprophyticus reveals the pathogenesis of uncomplicated urinary tract infection Comparative Microbial Genomics:

Outline

Brief introduction

Genome features

Comparative genomics

Results and discussion Summary

Staphylococcus saprophyticus characteristics and importance

Genome Atlas

Comparing with S.aureus and S.epidermis

Page 5: Whole Genome Sequence of Staphylococcus saprophyticus reveals the pathogenesis of uncomplicated urinary tract infection Comparative Microbial Genomics:

Staphylococcus saprophyticus

Synonyms Micrococcus; coagulase

negative staphylococci

Classification Facultative anaerobic, Gram+ bacteria, cocci, irregular clusters

Page 6: Whole Genome Sequence of Staphylococcus saprophyticus reveals the pathogenesis of uncomplicated urinary tract infection Comparative Microbial Genomics:

Staphylococcus saprophyticus

Diseases: Hematuria, Burning on urination, Pyuria

Diagnostic Factors: Novobiocin resistant, catalase positive, growth on blood agar

• Notable uropathogen without the involvment of indwelling catheters

• Causes uncomplicated Urinary Tract Infection (UTI)

Page 7: Whole Genome Sequence of Staphylococcus saprophyticus reveals the pathogenesis of uncomplicated urinary tract infection Comparative Microbial Genomics:

Genome features

Genome Atlas Database

www.cbs.dtu.dk/services/GenomeAtlas/

Page 8: Whole Genome Sequence of Staphylococcus saprophyticus reveals the pathogenesis of uncomplicated urinary tract infection Comparative Microbial Genomics:

Genome features

Staphylococcus saprophyticus type strain ATCC 15305

Main circular chromosome

2,516,575 bp

2,446 pred. ORF’s

66.8% AT content

Plasmid SSP1 38,454 bp

45 pred. ORF’s

69.3% AT content

Plasmid SSP2

28,870 bp

23 pred ORF’s

68.7% AT content

Page 9: Whole Genome Sequence of Staphylococcus saprophyticus reveals the pathogenesis of uncomplicated urinary tract infection Comparative Microbial Genomics:
Page 10: Whole Genome Sequence of Staphylococcus saprophyticus reveals the pathogenesis of uncomplicated urinary tract infection Comparative Microbial Genomics:
Page 11: Whole Genome Sequence of Staphylococcus saprophyticus reveals the pathogenesis of uncomplicated urinary tract infection Comparative Microbial Genomics:
Page 12: Whole Genome Sequence of Staphylococcus saprophyticus reveals the pathogenesis of uncomplicated urinary tract infection Comparative Microbial Genomics:

Comparative Genomic analyses

• Staphylococcus aureus N315

• Staphylococcus epidermidis ATCC 12228

Whole genome was available

Both are recognized as major human pathogens as well

www.zum.de

Page 13: Whole Genome Sequence of Staphylococcus saprophyticus reveals the pathogenesis of uncomplicated urinary tract infection Comparative Microbial Genomics:
Page 14: Whole Genome Sequence of Staphylococcus saprophyticus reveals the pathogenesis of uncomplicated urinary tract infection Comparative Microbial Genomics:

Uncovering the pathogenesis of Staphylococcus saprophyticus

Comparison with other

uropathogenic bacteria

Specific Adhesin

Urease Activity

Comparative Genomic Analyses

S. epidermidis

S. aureus

Page 15: Whole Genome Sequence of Staphylococcus saprophyticus reveals the pathogenesis of uncomplicated urinary tract infection Comparative Microbial Genomics:

Inset on S. aureus virulence factors and toxins

S.aureus has several mechanisms whereby it can protect itself from the host immune system, and cause damage to the host tissues. 

Pathogenic Staphylococcus epidermidis

In contrast to S.aureus very little are known for the mechanisms of

pathogenesis. 

Page 16: Whole Genome Sequence of Staphylococcus saprophyticus reveals the pathogenesis of uncomplicated urinary tract infection Comparative Microbial Genomics:

Materials&

Methods

Genome Sequencing and Assembly

Shotgun Strategy: A way of determining the sequence which

requires little brainpower but lots of late nights. The practise of

randomly clipping a DNA fragment into various smaller pieces, cloning everything and then studying the

resulting individual clones to figure out what happened

Comparative Genomics

The genome sequences were obtained through the National

Center for Biotechnology Information (

www.ncbi.nlm.nih.gov). Homologous genes were identified by homoly searches in amino acid sequence by using the BLASTP

filtering expectation value of e<10 E-10

Page 17: Whole Genome Sequence of Staphylococcus saprophyticus reveals the pathogenesis of uncomplicated urinary tract infection Comparative Microbial Genomics:

Schematic circular diagrams of the S. Saprophyticus ATCC 15305 chromosome (Kuroda et al. 2005)

Page 18: Whole Genome Sequence of Staphylococcus saprophyticus reveals the pathogenesis of uncomplicated urinary tract infection Comparative Microbial Genomics:

S. saprophyticus ATCC 15305 genome characteristics - results

• 2,446 ORFs

• Two IS431 elements

• 9 putative transposases

• 2 staphylococcal cassette chromosomes (SCC15305RM and SCC15305cap)

• Genomic island (vSs15305)

• 2 plasmids (pSSP1 - 38.4kb and pSSP2 - 22.9kb)

Page 19: Whole Genome Sequence of Staphylococcus saprophyticus reveals the pathogenesis of uncomplicated urinary tract infection Comparative Microbial Genomics:

Comparison of general features of the whole genome sequenced for the three strains of Staphylococci (Kuroda et al. 2005)

Page 20: Whole Genome Sequence of Staphylococcus saprophyticus reveals the pathogenesis of uncomplicated urinary tract infection Comparative Microbial Genomics:

Table 2. Comparison of general features of the whole genome sequenced staphylococci

Page 21: Whole Genome Sequence of Staphylococcus saprophyticus reveals the pathogenesis of uncomplicated urinary tract infection Comparative Microbial Genomics:

Mobile genomic islands of S. saprophyticus ATCC 15305 (Kuroda et al. 2005)

Page 22: Whole Genome Sequence of Staphylococcus saprophyticus reveals the pathogenesis of uncomplicated urinary tract infection Comparative Microbial Genomics:

Orthologous vs Paralogous

Homologous sequences are orthologous if they were separated by a speciation event: if a gene exists in a species, and that species diverges into two species, then the copies of this gene in the resulting species are orthologous;

Homologous sequences are paralogous if they were separated by a gene duplication event: if a gene in an organism is duplicated, then the two copies are paralogous;

www.wikipedia.org

Page 23: Whole Genome Sequence of Staphylococcus saprophyticus reveals the pathogenesis of uncomplicated urinary tract infection Comparative Microbial Genomics:

Orthologous classification of predicted ORFs compared with those of S. aureus N315 and S. epidermidis ATCC 12228 (Kuroda et al. 2005)

Page 24: Whole Genome Sequence of Staphylococcus saprophyticus reveals the pathogenesis of uncomplicated urinary tract infection Comparative Microbial Genomics:

Paralog expansion of transport systems related to urine environment (Kuroda et al. 2005)

Page 25: Whole Genome Sequence of Staphylococcus saprophyticus reveals the pathogenesis of uncomplicated urinary tract infection Comparative Microbial Genomics:

Adherence to eukaryotic cell by UafA (SSP0135) (Kuroda et al. 2005)

Hemagglutination:

Positive – well 3, 4 and 5

Negative – well 1, 2 and 6

Page 26: Whole Genome Sequence of Staphylococcus saprophyticus reveals the pathogenesis of uncomplicated urinary tract infection Comparative Microbial Genomics:

None of the virulence factors found in S. aureus

Summary of the results

S. saprophyticus ATCC 15305

Contains elaborate paralog expansion of transport systems

Presence of a cell wall-anchored protein for adherence to the urinary tract

Has high urease activity

Page 27: Whole Genome Sequence of Staphylococcus saprophyticus reveals the pathogenesis of uncomplicated urinary tract infection Comparative Microbial Genomics:

S. Saprophyticus ATCC 15305

Causes uncomplicated urinary tract infection disease

Discussion

Contains additional sets of osmoprotectant transport systemsHigh urease production

Adhesion to the urinary tract is critical for pathogenicity

More metabolic enzymes are an advantage

NRAMP involved in the transport of divalent metals

pSSP1 and pSSP2 contribute to osmotic balancing

Page 28: Whole Genome Sequence of Staphylococcus saprophyticus reveals the pathogenesis of uncomplicated urinary tract infection Comparative Microbial Genomics:

Thanks for your attention!!

ANY QUESTIONS?