Functional Genomic Analysis of Two Staphylococcus aureus Phages Isolated from the Dairy Environment

The genomes of the two lytic mutant Staphylococcus aureus bacteriophages, vB_SauS-phiIPLA35 (phiIPLA35) and vB_SauS-phiIPLA88 (phiIPLA88), isolated from milk have been analyzed. Their genomes are 45,344 bp and 42,526 bp long, respectively, and contain 62 and 61 open reading frames (ORFS). Enzymatic analyses and sequencing revealed that the phiIPLA35 DNA molecule has 3′-protruding cohesive ends (cos) 10 bp long, whereas phiIPLA88 DNA is 4.5% terminally redundant and most likely is packaged by a headful mechanism. N-terminal amino acid sequencing, mass spectrometry, bioinformatic analyses, and functional analyses enabled the assignment of putative functions to 58 gene products, including DNA packaging proteins, morphogenetic proteins, lysis components, and proteins necessary for DNA recombination, modification, and replication. Point mutations in their lysogeny control-associated genes explain their strictly lytic behavior. Muralytic activity associated with other structural components has been detected in virions of both phages. Comparative analysis of phiIPLA35 and phiIPLA88 genome structures shows that they resemble those of φ12 and φ11, respectively, both representatives of large genomic groupings within the S. aureus-infecting phages.Staphylococcus aureus is an important etiologic agent of food-borne diseases due to its ability to produce heat-resistant staphylococcal enterotoxins (SEs) when it grows in foods. In fact some S. aureus strains may produce up to 20 serologically distinct SEs, which could be responsible for food poisoning (30). SEs have been divided initially into serological types SEA through SEE, and recently the existence of new types of SEs has also been reported (5).S. aureus strains harboring enterotoxin genes have been isolated from a variety of foods (38) including dairy products (9, 46, 56). Mastitis caused by this pathogen and poor hygienic processing conditions are the most important sources of dairy product contamination. Growth of enterotoxigenic S. aureus in both raw milk and dairy products poses a potential health hazard to consumers. In this context, new biocontrol strategies to prevent growth of S. aureus, suitable to be applied in the food industry, are being explored.Currently, there is a renewed interest in exploiting the antimicrobial potential of bacterial viruses for bacterial-control applications in agriculture, aquaculture, and the food industry (11, 18, 23, 49). In fact, the use of phages for the treatment of infectious diseases (or phage therapy) has a long successful history in the countries of Eastern Europe (or former Soviet Union) (50). Specifically, S. aureus bacteriophages have been assayed in the treatment of venous leg ulcers and eye infections (22, 42).Prior to any phage application, genome analysis is a prerequisite to examine the safety of the phages, specifically, traits which might enhance the virulence of the infected bacterium. In addition, genome analysis might uncover novel antibacterial targets or agents (33) with promising biotechnological applications (6). For example, various lytic phage proteins (endolysins) have shown great potential in veterinary and human medicine for the treatment and prophylaxis of infections (12) and have been applied as biocontrol agents in dairy products (36). Several technologies employing phages and endolysins for pathogen detection and decontamination have also been patented (7).To date, genomes of over 47 S. aureus phages are available in public databases. The number of known, strictly lytic phages is limited to the close-knit Myoviridae genus of the SPO1-like viruses, containing phages K, Twort, and G1. Apart from this group, a large number of genomes from unclassified Siphoviridae in lysogenic S. aureus strains are available (26, 37). Some temperate bacteriophages may play an important role in the pathogenicity of S. aureus by carrying virulence factors, mediating lateral gene transfer, and even facilitating the adaptation of the pathogen during infection (1, 21, 52).In previous work, we have characterized phiIPLA35 and phiIPLA88 S. aureus phages (17). These two lytic phages, previously named φ35 and φ88, were selected as mutants of the temperate phages φA72 and φH5, respectively, isolated from raw bovine milk. They belong to the Siphoviridae family of double-stranded DNA bacterial viruses in the order Caudovirales. Remarkably, these phages infect S. aureus of bovine and dairy origin while clinical isolates appear to be resistant. Both phiIPLA35 and phiIPLA88 are very well adapted to the dairy environment and effectively inhibit S. aureus growth in milk and curd-manufacturing processes (17, 20).In this study, we have sequenced and annotated the genomes of both bacteriophages, elucidated their physical genome structures, and identified peptidoglycan hydrolytic activities. Comparative genome analysis also allowed us to put phiIPLA35 and phiIPLA88 into a phylogenetic context.     

Genomic and proteomic characterization of Staphylococcus aureus mastitis isolates of bovine origin

Staphylococcus aureus colonizes and infects humans as well as animals. In the present study, 17 S. aureus strains isolated from cows suffering from mastitis were characterized. The well-established multilocus sequence typing (MLST) technique and a diagnostic microarray covering 185 S. aureus virulence and resistance genes were used for genetic and epidemiological analyses. Virulence gene expression studies were performed by analyzing the extracellular protein pattern of each isolate on 2-D gels. By this way, a pronounced heterogeneity of the extracellular proteome between the bovine isolates has been observed which was attributed to genome plasticity and variation of gene expression. Merely 12 proteins were expressed in at least 80% of the isolates, i.e. Atl, Aur, GlpQ, Hla, LtaS, Nuc, PdhB, SAB0846, SAB2176, SAB0566, SspA, and SspB forming the core exoproteome. Fifteen extracellular proteins were highly variably expressed and only present in less than 20% of the isolates. This includes the serine proteases SplB, C, and F, and the superantigens SEC-bov, SEL and TSST-1. Compared to human isolates we identified at least six proteins with significantly different expression frequencies. While SAB0846 was expressed more frequently in bovine isolates, LytM, EbpS, Spa, Geh, and LukL1 were seen less frequently in these isolates.     

Genetic Analysis of Lysine Auxotrophs of Staphylococcus aureus

The genetics of lysine biosynthesis in Staphylococcus aureus was examined by a transductional analysis of lysine auxotrophs. These mutants had previously been grouped according to their biochemical characteristics. The mutant sites appeared to be closely linked. Complementation was observed between different groups but not between mutant strains belonging to the same group. A strain was detected which seemed to have a mutant control region. Evidence is presented to support the hypothesis that the lysine biosynthetic region functions as an operon.     

Vancomycin-resistant Staphylococcus aureus

The evolution and molecular mechanisms of vancomycin resistance in Staphylococcus aureus were reviewed. Case reports and research studies on biochemestry, electron microscopy and molecular biology of Staphylococcus aureus were selected from Medline database and summarized in the following review. After almost 40 years of successful treatment of S. aureus with vancomycin, several cases of clinical failures have been reported (since 1997). S. aureus strains have appeared with intermediate susceptibility (MIC 8-16 microg/ml), as well as strains with heterogeneous resistance (global MIC < or =4 microg/ml), but with subpopulations of intermediate susceptibility. In these cases, resistance is mediated by cell wall thickening with reduced cross linking. This traps the antibiotic before it reaches its major target, the murein monomers in the cell membrane. In 2002, a total vancomycin resistant strain (MIC > or =32 microg/ml) was reported with vanA genes from Enterococcus spp. These genes induce the change of D-Ala-D-Ala terminus for D-Ala-D-lactate in the cell wall precursors, leading to loss of affinity for glycopeptides. Vancomycin resistance in S. aureus has appeared; it is mediated by cell wall modifications that trap the antibiotic before it reaches its action site. In strains with total resistance, Enterococcus spp. genes have been acquired that lead to modification of the glycopeptide target.     

Staphylococcus aureus surface protein SasG contributes to intercellular autoaggregation of Staphylococcus aureus

Staphylococcus aureus surface protein G (SasG) is one of cell surface proteins with cell-wall sorting motif. The sasG mutant showed significantly reduced cell aggregation and biofilm formation. SasG is comprised of variable A domain and multiple tandem repeats of B domain, native-PAGE and in vitro formaldehyde cross-linking experiments revealed that the recombinant protein of the A domain showed homo-oligomerization as an octamer, but B domain did not. This study shows that SasG-A domain contributes to intercellular autoaggregation by homo-oligomerization, and that may facilitate the adherence to host-tissues in the infection of S. aureus.     

Genomic diversity in Staphylococcus xylosus

Staphylococcus xylosus is a commensal of the skin of humans and animals and a ubiquitous bacterium naturally present in food. It is one of the major starter cultures used for meat fermentation, but a few strains could potentially be hazardous and are related to animal opportunistic infections. To better understand the genetic diversity of S. xylosus intraspecies, suppressive and subtractive hybridization (SSH) was carried out with the S. xylosus C2a strain, a commensal of human skin, used as the driver for three tester strains, S04002 used as a starter culture, S04009 isolated from cow mastitis, and 00-1747, responsible for mouse dermatitis. SSH revealed 122 tester-specific fragments corresponding to 149 open reading frames (ORFs). A large proportion of these ORFs resembled genes involved in specific metabolisms. Analysis of the distribution of the tester-specific fragments in 20 S. xylosus strains of various origins showed that the S. xylosus species could be divided into two clusters with one composed only of potentially hazardous strains. The genetic content diversity of this species is colocalized in a region near the origin of replication of the chromosome. This region of speciation previously observed in the Staphylococcus genus corresponded in S. xylosus species to a strain-specific region potentially implicated in ecological fitness.     

Genomic Diversity in Staphylococcus xylosus

Staphylococcus xylosus is a commensal of the skin of humans and animals and a ubiquitous bacterium naturally present in food. It is one of the major starter cultures used for meat fermentation, but a few strains could potentially be hazardous and are related to animal opportunistic infections. To better understand the genetic diversity of S. xylosus intraspecies, suppressive and subtractive hybridization (SSH) was carried out with the S. xylosus C2a strain, a commensal of human skin, used as the driver for three tester strains, S04002 used as a starter culture, S04009 isolated from cow mastitis, and 00-1747, responsible for mouse dermatitis. SSH revealed 122 tester-specific fragments corresponding to 149 open reading frames (ORFs). A large proportion of these ORFs resembled genes involved in specific metabolisms. Analysis of the distribution of the tester-specific fragments in 20 S. xylosus strains of various origins showed that the S. xylosus species could be divided into two clusters with one composed only of potentially hazardous strains. The genetic content diversity of this species is colocalized in a region near the origin of replication of the chromosome. This region of speciation previously observed in the Staphylococcus genus corresponded in S. xylosus species to a strain-specific region potentially implicated in ecological fitness.     

Staphylococcus aureus: Staphylokinase

Staphylokinase is a 136 aa long bacteriophage encoded protein expressed by lysogenic strains of Staphylococcus aureus. Present understanding of the role of staphylokinase during bacterial infection is based on its interaction with the host proteins, alpha-defensins and plasminogen. alpha-Defensins are bactericidal peptides originating from human neutrophils. Binding of staphylokinase to alpha-defensins abolishes their bactericidal properties, which makes staphylokinase a vital tool for staphylococcal resistance to host innate immunity. Complex binding between staphylokinase and plasminogen results in the formation of active plasmin, a broad-spectrum proteolytic enzyme facilitating bacterial penetration into the surrounding tissues. We have recently shown high levels of staphylokinase expression in clinical isolates of skin and mucosal origin and relative low levels in isolates invading internal organs. These findings are supported by sepsis studies using isogenic S. aureus strains demonstrating increased bacterial load in the absence of staphylokinase production. Our observations indicate that staphylokinase favours symbiosis of staphylococci with the host that makes it an important colonization factor.     

Analysis of Staphylococcus aureus cytoplasmic membrane proteins by isoelectric focusing

Cytoplasmic membranes were isolated from late-exponential phase Staphylococcus aureus 6539 P and the membrane proteins examined under non-denaturing conditions by thin-layer isoelectric focusing (TLIEF) in a pH 3.5-9.5 gradient. Isolated membrane preparations retained protein integrity as judged by the demonstration of membrane bound adenosine triphosphatase (ATPase) activity in addition to four other solubilized membrane enzyme markers. Membranes were effectively solubilized with 2.5% Triton X-100 (final concentration). Examination of Triton X-100 solubilized membrane preparations established the presence of 22 membrane proteins with isoelectric points between 3.7 and 6.0. The focused proteins displayed the following enzymatic activities and isoelectric points by zymogram methods: ATPase (EC 3.6.1.3), 4.20; malate dehydrogenase (EC 1.1.1.37), 3.90; lactate dehydrogenase (EC 1.1.1.27), 3.85; two membrane proteins exhibited multiple bands upon enzymatic staining NADH dehydrogenase (EC 1.6.99.3), 4.25, 4.35; succinate dehydrogenase (EC 1.3.99.1), 4.85, 5.10, 5.35.     

Whole Genome Analysis of Epidemiologically Closely Related Staphylococcus aureus Isolates

The change of the bacteria from colonizers to pathogens is accompanied by a drastic change in expression profiles. These changes may be due to environmental signals or to mutational changes. We therefore compared the whole genome sequences of four sets of S. aureus isolates. Three sets were from the same patients. The isolates of each pair (S1800/S1805, S2396/S2395, S2398/S2397, an isolate from colonization and an isolate from infection, respectively) were obtained within <30 days of each other and the isolate from infection caused skin infections. The isolates were then compared for differences in gene content and SNPs. In addition, a set of isolates from a colonized pig and a farmer from the same farm at the same time (S0462 and S0460) were analyzed. The isolates pair S1800/S1805 showed a difference in a prophage, but these are easily lost or acquired. However, S1805 contained an integrative conjugative element not present in S1800. In addition, 92 SNPs were present in a variety of genes and the isolates S1800 and S1805 were not considered a pair. Between S2395/S2396 two SNPs were present: one was in an intergenic region and one was a synonymous mutation in a putative membrane protein. Between S2397/S2398 only one synonymous mutation in a putative lipoprotein was found. The two farm isolates were very similar and showed 12 SNPs in genes that belong to a number of different functional categories. However, we cannot pinpoint any gene that explains the change from carrier status to infection. The data indicate that differences between the isolate from infection and the colonizing isolate for S2395/S2396 and S2397/S2398 exist as well as between isolates from different hosts, but S1800/S1805 are not clonal.     

Nonenteric Toxins of Staphylococcus aureus

[This corrects the article on p. 337 in vol. 43.].     

Immune proteomics of Staphylococcus aureus

Immune proteomics is an increasingly powerful tool for the investigation of the adaptive immune response to natural encounters between micro-organisms and their hosts. The versatile species Staphylococcus aureus serves to illustrate how these techniques can be employed to appreciate the complexity and diversity of the host-pathogen interactions in unprecedented detail and completeness. Such knowledge is important for the development of effective vaccines as well as informative diagnostic and novel therapeutic tools. From high-resolution immune proteome studies, general rules underlying the human adaptive immune response to S. aureus colonization and infection are beginning to emerge against a background of extreme diversity: S. aureus carriers develop immune memory for their colonizing strain, but even non-carriers are frequently exposed to S. aureus, resulting in specific antibodies. During bacterial invasion, immune-competent individuals rapidly mount an antibody response to a large panel of S. aureus antigens. However, every patient starts from a personal baseline antibody profile reflecting his or her history of encounters with S. aureus.     

Alpha-toxin of Staphylococcus aureus.

Alpha-toxin, the major cytotoxic agent elaborated by Staphylococcus aureus, was the first bacterial exotoxin to be identified as a pore former. The protein is secreted as a single-chain, water-soluble molecule of Mr 33,000. At low concentrations (less than 100 nM), the toxin binds to as yet unidentified, high-affinity acceptor sites that have been detected on a variety of cells including rabbit erythrocytes, human platelets, monocytes and endothelial cells. At high concentrations, the toxin additionally binds via nonspecific absorption to lipid bilayers; it can thus damage both cells lacking significant numbers of the acceptor and protein-free artificial lipid bilayers. Membrane damage occurs in both cases after membrane-bound toxin molecules collide via lateral diffusion to form ring-structured hexamers. The latter insert spontaneously into the lipid bilayer to form discrete transmembrane pores of effective diameter 1 to 2 nm. A hypothetical model is advanced in which the pore is lined by amphiphilic beta-sheets, one surface of which interacts with lipids whereas the other repels apolar membrane constitutents to force open an aqueous passage. The detrimental effects of alpha-toxin are due not only to the death of susceptible targets, but also to the presence of secondary cellular reactions that can be triggered via Ca2+ influx through the pores. Well-studied phenomena include the stimulation of arachidonic acid metabolism, triggering of granule exocytosis, and contractile dysfunction. Such processes cause profound long-range disturbances such as development of pulmonary edema and promotion of blood coagulation.(ABSTRACT TRUNCATED AT 250 WORDS)     

The Hemolysins of Staphylococcus aureus

[This corrects the article on p. 321 in vol. 39.].     

Evolving superantigens of Staphylococcus aureus

Staphylococcus aureus bacteria utilize an extensive array of molecular countermeasures to manipulate the defensive microenvironment of the infected host and colonize potentially any tissue. The secreted polypeptides referred to as superantigens are unique among these countermeasures, because they target the multireceptor communication between T cells and antigen-presenting cells that is fundamental to initiating pathogen-specific immune clearance. Superantigens play a critical role in toxic-shock syndrome and food poisoning, yet their function in routine infections is not well understood. While an association of superantigens with cases of human autoimmune disease seems tantalizing, convincing data are not yet available. Blocking antigen-specific T-cell recognition is the primary evolutionary driving force behind superantigen selection, whereas superantigen-specific pathologies are by-products that are apparent only under select conditions.