Comparative Microbial Genomics: A Bioinformatics Approach

1. 5th October 2005 Whole Genome Sequence of Staphylococcussaprophyticus reveals the pathogenesis of uncomplicated urinary tract infection Comparative Microbial Genomics: A Bioinformatics Approach Ana Rita Domingues Boumediene Soufi Francisco Roque Gianni Panagiotou

2. 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

3. PNAS vol 102, no37, September 13, 2005 Abstract

4. Outline • Brief introduction • Genome features • Comparative genomics • Results and discussion • Summary • Staphylococcussaprophyticus characteristics and importance • GenomeAtlas • Comparing with S.aureus and S.epidermis

5. Classification • Facultative anaerobic, Gram+ bacteria, cocci, irregular clusters Staphylococcus saprophyticus • Synonyms • Micrococcus; coagulase negative staphylococci

6. Staphylococcus saprophyticus • Notable uropathogen without the involvment of indwelling catheters Diseases: Hematuria, Burning on urination, Pyuria DiagnosticFactors: Novobiocin resistant, catalase positive, growth on blood agar • Causes uncomplicated Urinary Tract Infection (UTI)

7. Genome features Genome Atlas Database www.cbs.dtu.dk/services/GenomeAtlas/

8. 38,454 bp • 45 pred. ORF’s • 69.3% AT content • Plasmid SSP1 • 28,870 bp • 23 pred ORF’s • 68.7% AT content • Plasmid SSP2 Genome features Staphylococcus saprophyticus type strain ATCC 15305 • 2,516,575 bp • 2,446 pred. ORF’s • 66.8% AT content • Main circular chromosome

12. www.zum.de Comparative Genomic analyses • Staphylococcus epidermidis ATCC 12228 • Staphylococcus aureus N315 • Whole genome was available • Both are recognized as major human pathogens as well

14. Uncovering the pathogenesis of Staphylococcus saprophyticus S. aureus Specific Adhesin Comparison with other uropathogenic bacteria Comparative Genomic Analyses Urease Activity S. epidermidis

15. 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 contrastto S.aureus very little are known for the mechanisms of pathogenesis.

16. 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 Materials & Methods 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

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

18. 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) S. saprophyticus ATCC 15305 genome characteristics - results

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

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

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

22. 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

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

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

25. Hemagglutination: • Positive – well 3, 4 and 5 • Negative – well 1, 2 and 6 Adherence to eukaryotic cell by UafA (SSP0135) (Kuroda et al. 2005)

26. Summary of the results S. saprophyticus ATCC 15305 • None of the virulence factors found in S. aureus • Contains elaborate paralog expansion of transport systems • Presence of a cell wall-anchored protein for adherence to the urinary tract • Has high urease activity

27. S. Saprophyticus ATCC 15305 Discussion • Causes uncomplicated urinary tract infection disease • Contains additional sets of osmoprotectant transport systems • High 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

28. Thanks for your attention!! ANY QUESTIONS?