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

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Abstract PNAS vol 102, n o 37, 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

Genome features Staphylococcus saprophyticus type strain ATCC  Main circular chromosome 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 aureus N315 Staphylococcus epidermidis ATCC Staphylococcus epidermidis ATCC Whole genome was available Both are recognized as major human pathogens as well

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 ( Homologous genes were identified by homoly searches in amino acid sequence by using the BLASTP filtering expectation value of e<10 E-10www.ncbi.nlm.nih.gov

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

S. saprophyticus ATCC genome characteristics - results 2,446 ORFs Two IS431 elements 9 putative transposases 2 staphylococcal cassette chromosomes (SCC 15305RM and SCC 15305cap ) Genomic island (vSs ) 2 plasmids (pSSP kb and pSSP kb)

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 (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;

Orthologous classification of predicted ORFs compared with those of S. aureus N315 and S. epidermidis ATCC (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 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 Causes uncomplicated urinary tract infection disease Discussion 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

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