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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