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Insights on virulence from the complete genome of Staphylococcus capitis.

Cameron DR, Jiang JH, Hassan KA, Elbourne LD, Tuck KL, Paulsen IT, Peleg AY - Front Microbiol (2015)

Bottom Line: Methylome analysis identified significant adenine methylation across the genome involving two distinct methylation motifs (1972 putative 6-methyladenine (m6A) residues identified).Putative adenine methyltransferases were also identified.Comparative analysis of AYP1020 and the closely related CoNS, S. epidermidis RP62a, revealed a host of virulence factors that likely contribute to S. capitis pathogenicity, most notably genes important for biofilm formation and a suite of phenol soluble modulins (PSMs); the expression/production of these factors were corroborated by functional assays.

View Article: PubMed Central - PubMed

Affiliation: Department of Microbiology, Monash University Melbourne, VIC, Australia.

ABSTRACT
Staphylococcus capitis is an opportunistic pathogen of the coagulase negative staphylococci (CoNS). Functional genomic studies of S. capitis have thus far been limited by a lack of available complete genome sequences. Here, we determined the closed S. capitis genome and methylome using Single Molecule Real Time (SMRT) sequencing. The strain, AYP1020, harbors a single circular chromosome of 2.44 Mb encoding 2304 predicted proteins, which is the smallest of all complete staphylococcal genomes sequenced to date. AYP1020 harbors two large mobile genetic elements; a plasmid designated pAYP1020 (59.6 Kb) and a prophage, ΦAYP1020 (48.5 Kb). Methylome analysis identified significant adenine methylation across the genome involving two distinct methylation motifs (1972 putative 6-methyladenine (m6A) residues identified). Putative adenine methyltransferases were also identified. Comparative analysis of AYP1020 and the closely related CoNS, S. epidermidis RP62a, revealed a host of virulence factors that likely contribute to S. capitis pathogenicity, most notably genes important for biofilm formation and a suite of phenol soluble modulins (PSMs); the expression/production of these factors were corroborated by functional assays. The complete S. capitis genome will aid future studies on the evolution and pathogenesis of the coagulase negative staphylococci.

No MeSH data available.


Related in: MedlinePlus

Orthologous classification of CDS of S. capitis AYP1020 compared to S. epidermidis RP62a. Orthologs were defined by bidirectional BLASTp with an e-value cut off of 10e-30 (A). Non-orthologous CDS were grouped based on COG functional categories (B).
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Figure 3: Orthologous classification of CDS of S. capitis AYP1020 compared to S. epidermidis RP62a. Orthologs were defined by bidirectional BLASTp with an e-value cut off of 10e-30 (A). Non-orthologous CDS were grouped based on COG functional categories (B).

Mentions: S. epidermidis (RP62a) was chosen for comparative analysis as it is a close relative of S. capitis and it is the most clinically important CoNS (Figure 1) (Poyart et al., 2001; Otto, 2009). Using the Artemis Comparison Tool, we found the degree of synteny between S. capitis AYP1020 and RP62a to be high, with few significant genomic rearrangements detected (Figure S2). We used BLASTp to compare all CDS sequences of AYP1020 with S. epidermidis RP62a and identified a core set of 1844 genes present in both species, which represents 80% of the S. capitis genome (Figure 3A). We identified 480 and 646 non-orthologous genes for S. capitis and S. epidermidis, respectively (Figure 3A). When the non-orthologous genes were categorized based on function, we found that S. epidermidis RP62a had an enhanced repertoire of genes related to mobile genetic elements (Figure 3B), which are largely accounted for by IS elements. The genome of AYP1020 encodes only one predicted IS element compared to the genome of S. epidermidis RP62a that has 64 predicted IS elements (18 intact), as well as five transposons (Gill et al., 2005; Takeuchi et al., 2005). Importantly, key antibiotic resistance determinants are carried on mobile elements in RP62a and these are absent from AYP1020. These include penicillinase encoded by blaZ, as well as SCCmec, which not only harbors determinants important for resistance to methicillin, but also aminoglycosides and macrolides (Table 2) (Gill et al., 2005). The absence of these genes in AYP1020 correlates with the highly antibiotic susceptible phenotype of this S. capitis isolate (Table 2). Multidrug-resistant strains, however, are emerging, with the majority of clinical strains resistant to penicillin and methicillin, and strains with reduced susceptibility to vancomycin also emerging (Ma et al., 2011; Rasigade et al., 2012). Further sequencing projects of multi-drug resistant isolates is required to determine the genetic factors facilitating antibiotic resistance in S. capitis. One such study characterized a novel SCCmec element in pulsotype NRCS-A, which harbored genes not only important for methicillin resistance, but also resistance to cadmium, arsenic, and copper (Martins Simões et al., 2013).


Insights on virulence from the complete genome of Staphylococcus capitis.

Cameron DR, Jiang JH, Hassan KA, Elbourne LD, Tuck KL, Paulsen IT, Peleg AY - Front Microbiol (2015)

Orthologous classification of CDS of S. capitis AYP1020 compared to S. epidermidis RP62a. Orthologs were defined by bidirectional BLASTp with an e-value cut off of 10e-30 (A). Non-orthologous CDS were grouped based on COG functional categories (B).
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Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4585213&req=5

Figure 3: Orthologous classification of CDS of S. capitis AYP1020 compared to S. epidermidis RP62a. Orthologs were defined by bidirectional BLASTp with an e-value cut off of 10e-30 (A). Non-orthologous CDS were grouped based on COG functional categories (B).
Mentions: S. epidermidis (RP62a) was chosen for comparative analysis as it is a close relative of S. capitis and it is the most clinically important CoNS (Figure 1) (Poyart et al., 2001; Otto, 2009). Using the Artemis Comparison Tool, we found the degree of synteny between S. capitis AYP1020 and RP62a to be high, with few significant genomic rearrangements detected (Figure S2). We used BLASTp to compare all CDS sequences of AYP1020 with S. epidermidis RP62a and identified a core set of 1844 genes present in both species, which represents 80% of the S. capitis genome (Figure 3A). We identified 480 and 646 non-orthologous genes for S. capitis and S. epidermidis, respectively (Figure 3A). When the non-orthologous genes were categorized based on function, we found that S. epidermidis RP62a had an enhanced repertoire of genes related to mobile genetic elements (Figure 3B), which are largely accounted for by IS elements. The genome of AYP1020 encodes only one predicted IS element compared to the genome of S. epidermidis RP62a that has 64 predicted IS elements (18 intact), as well as five transposons (Gill et al., 2005; Takeuchi et al., 2005). Importantly, key antibiotic resistance determinants are carried on mobile elements in RP62a and these are absent from AYP1020. These include penicillinase encoded by blaZ, as well as SCCmec, which not only harbors determinants important for resistance to methicillin, but also aminoglycosides and macrolides (Table 2) (Gill et al., 2005). The absence of these genes in AYP1020 correlates with the highly antibiotic susceptible phenotype of this S. capitis isolate (Table 2). Multidrug-resistant strains, however, are emerging, with the majority of clinical strains resistant to penicillin and methicillin, and strains with reduced susceptibility to vancomycin also emerging (Ma et al., 2011; Rasigade et al., 2012). Further sequencing projects of multi-drug resistant isolates is required to determine the genetic factors facilitating antibiotic resistance in S. capitis. One such study characterized a novel SCCmec element in pulsotype NRCS-A, which harbored genes not only important for methicillin resistance, but also resistance to cadmium, arsenic, and copper (Martins Simões et al., 2013).

Bottom Line: Methylome analysis identified significant adenine methylation across the genome involving two distinct methylation motifs (1972 putative 6-methyladenine (m6A) residues identified).Putative adenine methyltransferases were also identified.Comparative analysis of AYP1020 and the closely related CoNS, S. epidermidis RP62a, revealed a host of virulence factors that likely contribute to S. capitis pathogenicity, most notably genes important for biofilm formation and a suite of phenol soluble modulins (PSMs); the expression/production of these factors were corroborated by functional assays.

View Article: PubMed Central - PubMed

Affiliation: Department of Microbiology, Monash University Melbourne, VIC, Australia.

ABSTRACT
Staphylococcus capitis is an opportunistic pathogen of the coagulase negative staphylococci (CoNS). Functional genomic studies of S. capitis have thus far been limited by a lack of available complete genome sequences. Here, we determined the closed S. capitis genome and methylome using Single Molecule Real Time (SMRT) sequencing. The strain, AYP1020, harbors a single circular chromosome of 2.44 Mb encoding 2304 predicted proteins, which is the smallest of all complete staphylococcal genomes sequenced to date. AYP1020 harbors two large mobile genetic elements; a plasmid designated pAYP1020 (59.6 Kb) and a prophage, ΦAYP1020 (48.5 Kb). Methylome analysis identified significant adenine methylation across the genome involving two distinct methylation motifs (1972 putative 6-methyladenine (m6A) residues identified). Putative adenine methyltransferases were also identified. Comparative analysis of AYP1020 and the closely related CoNS, S. epidermidis RP62a, revealed a host of virulence factors that likely contribute to S. capitis pathogenicity, most notably genes important for biofilm formation and a suite of phenol soluble modulins (PSMs); the expression/production of these factors were corroborated by functional assays. The complete S. capitis genome will aid future studies on the evolution and pathogenesis of the coagulase negative staphylococci.

No MeSH data available.


Related in: MedlinePlus