The contig sizes sum up to 2,829,971 bp. The total contigs size of 2.83 Mbp provides a lower bound of the chromosome size of CF-Marseille. The 131 contigs are available in the EMBL Nucleotide Sequence Database, accession number DS:71627. We compared the CF-Marseille strain to other S. aureus strains on the basis of their protein contents. A CoDing Sequence (CDS) prediction was performed http://www.selleckchem.com/products/VX-770.html with the Glimmer software 1, which revealed the presence of 2736 hypothetical proteins in the 131 contigs. As compared to the other S. aureus proteins available in the UniProtKB/Swiss-Prot database 2 (considered strains were N315, MW2, USA300, Mu50, NCTC 8325, COL and MRSA252), 2675 out of 2736 predicted proteins showed a match of at least 90% of aminoacid identity.
The strains USA300/Mu50 shows the closest protein content with 2522 matches, corresponding to more that 95% of the detected CF-Marseille proteome. The 61 proteins that did not match mostly consist of phagic proteins and very short CDS that are likely to be false positive (Open reading frame that do not correspond to CDS). Analysis of the accessory genome of CF-Marseille revealed the presence of a new phage of 44 Kb closely related to the recently sequenced phage phiETA3 found in S. aureus strain JH1-JH9 [31]. Similarity search at the protein level showed that parts of this element are found in numerous other phages including phiETA3, phiROSA, phiNM4 or phage 96, whereas the function of an important number of putative ORFs remain hypothetical.
Most of the genes differentially expressed between strains found in CF patient and isolates never found in CF patient (see Additional file 2), involved phage elements or resistance determinants, which is consistent with the CGH results. The only gene showing higher expression in the non-CF isolates compared to CF isolates was spxA, a transcription regulator involved in the biosysnthesis of thioredoxin reductase, an enzyme found down-regulated during treatment with hypochlorite [32] or in the presence of berberine chloride [33] and whose deletion yields to the accumulation of biofilm onto surface. Comparison between strains currently isolated in Marseille and CF-Marseille yields a limited number of differentially regulated genes. All these genes belong to phage elements and resistance determinants. Among these were ermC (a gene conferring resistance to erythromycin) and ORFs of the phage (Additional file 2).
Most of the targets showing differential expression corresponded to GSK-3 up-regulated genes in one of the phages identified in strain CF-Marseille and potentially in other strains of our collection. Antibiotic resistance gene s in the genome of strain CF-Marseille In the genome of CF-Marseille, resistance to beta-lactams and ofloxacin are chromosomally-encoded (Table (Table1).1).