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

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

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Abstract

PNAS vol 102, no37, September 13, 2005

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

Staphylococcus saprophyticus

Synonyms Micrococcus; coagulase

negative staphylococci

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

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)

Genome features

Genome Atlas Database

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

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

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

Uncovering the pathogenesis of Staphylococcus saprophyticus

Comparison with other

uropathogenic bacteria

Specific Adhesin

Urease Activity

Comparative Genomic Analyses

S. epidermidis

S. aureus

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. 

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

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

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)

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

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

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

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;

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

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

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

Hemagglutination:

Positive – well 3, 4 and 5

Negative – well 1, 2 and 6

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

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

Thanks for your attention!!

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