With the advent of high-throughput sequencing technologies, many staphylococcal genomes have been sequenced. Comparative analysis of these strains will provide better understanding of their biology, phylogeny, virulence and taxonomy, which may contribute to better management of diseases caused by staphylococcal pathogens. We developed StaphyloBase with the goal of having a one-stop genomic resource platform for the scientific community to access, retrieve, download, browse, search, visualize and analyse the staphylococcal genomic data and annotations. We anticipate this resource platform will facilitate the analysis of staphylococcal genomic data, particularly in comparative analyses. StaphyloBase currently has a collection of 754 032 protein-coding sequences (CDSs), 19 258 rRNAs and 15 965 tRNAs from 292 genomes of different staphylococcal species. Information about these features is also included, such as putative functions, subcellular localizations and gene/protein sequences. Our web implementation supports diverse query types and the exploration of CDS- and RNA-type information in detail using an AJAX-based real-time search system. JBrowse has also been incorporated to allow rapid and seamless browsing of staphylococcal genomes. The Pairwise Genome Comparison tool is designed for comparative genomic analysis, for example, to reveal the relationships between two user-defined staphylococcal genomes. A newly designed Pathogenomics Profiling Tool (PathoProT) is also included in this platform to facilitate comparative pathogenomics analysis of staphylococcal strains. In conclusion, StaphyloBase offers access to a range of staphylococcal genomic resources as well as analysis tools for comparative analyses. Database URL: http://staphylococcus.um.edu.my/.
Surface charge residues have been recognized as one of the stability determinants in protein. In this study, we sought to compare and analyse the stability and conformational dynamics of staphylococcal lipase mutants with surface lysine mutation using computational and experimental methods. Three highly mutable and exposed lysine residues (Lys91, Lys177, Lys325) were targeted to generate six mutant lipases in silico. The model structures were simulated in water environment at 25 °C. Our simulations showed that the stability was compromised when Lys177 was substituted while mutation at position 91 and 325 improved the stability. To illustrate the putative alterations of enzyme stability in the stabilising mutants, we characterized single mutant K325G and double mutant K91A/K325G. Both mutants showed a 5 °C change in optimal temperature compared to their wild type. Single mutant K325G rendered a longer half-life at 25 °C (T1/2 = 21 h) while double mutant K91A/K325G retained only 40% of relative activity after 12 h incubation. The optimal pH for mutant K325G was shifted from 8 to 9 and similar substrate preference was observed for the wild type and two mutants. Our findings indicate that surface lysine mutation alters the enzymatic behaviour and, thus, rationalizes the functional effects of surface exposed lysine in conformational stability and activity of this lipase.
Staphylococci are Gram-positive bacteria that are ubiquitous in the environment and able to form biofilms on a range of surfaces. They have been associated with a range of human health issues such as medical device-related infection, localized skin infection, or direct infection caused by toxin production. The extracellular material produced by these bacteria resists antibiotics and host defence mechanism which complicates the treatment process. The commonly reported Staphylococcus species are Staphylococcus aureus and S. epidermidis as they inhabit human bodies. However, the emergence of other staphylococci, such as S. haemolyticus, S. lugdunensis, S. saprophyticus, S. capitis, S. saccharolyticus, S. warneri, S. cohnii, and S. hominis, is also of concern and they have been associated with biofilm formation. This review critically assesses recent cases on the biofilm formation by S. aureus, S. epidermidis, and other staphylococci reported in health-related environments. The control of biofilm formation by staphylococci using natural compounds is specifically discussed as they represent potential anti-biofilm agents which may reduce the burden of antibiotic resistance.
INTRODUCTION: Coagulase-negative staphylococci (CoNS) are a group of micro-organisms that are increasingly implicated as a cause of significant infection and the leading cause of bloodstream infection (BSI). One important predictor of true BSI is the isolation of CoNS from multiple blood cultures, presuming that the isolates represent the same species. Thus the objective of this study was to determine the significance of repeated CoNS isolated from blood cultures.
METHODOLOGY: This was a prospective laboratory study which was initiated in June 2007 and lasted until July 2008. CoNS isolates were obtained from patients who had two positive blood cultures within a 14-day interval. CoNS were identified to the species level using an API-Staph, and antibiotics susceptibility testing was performed according to Clinical and Laboratory Standards Institute specifications. Strain relatedness was confirmed using pulsed-field gel electrophoresis.
RESULTS: During the study period, 202 CoNS-positive samples were isolated from 101 patients. The most common species isolated was Staphylococcus epidermidis (59.0%), and 83.2% of the patients isolated the same species of CoNS from repeated blood cultures. Among the isolates of the same species, only 40.7% had the same antibiogram. CoNS with the same species and antibiogram had 93.3% probability of belonging to the same strain. Most (65.5%) of the patients were treated with antibiotics, primarily from the glycopeptides group.
CONCLUSION: Speciation and antibiogram of CoNS from repeated blood cultures are adequate in determining the significance of repeated CoNS isolated from blood cultures.
We report the draft genome sequence of Staphylococcus sp. strain AL1, which degrades quorum-sensing molecules (namely, N-acyl homoserine lactones). To the best of our knowledge, this is the first documentation that reports the whole genome sequence and quorum-quenching activity of Staphylococcus sp. strain AL1.