# Patent

## Title
Method for identification, isolation and production of antigens to a specific pathogen

## Abstract

Described is a method for identification, isolation and production of hyperimmune serum-reactive antigens from a specific pathogen, a tumor, an allergen or a tissue or host prone to autoimmunity, said antigens being suited for use in a vaccine for a given type of animal or for humans, which is characterized by the following steps: —providing an antibody preparation from a plasma pool of said given type of animal or from a human plasma pool or individual sera with antibodies against said specific pathogen, tumor, allergen or tissue or host prone to auto-immunity, —providing at least one expression library of said specific pathogen, tumor, allergen or tissue or host prone to auto-immunity, —screening said at least one expression library with said antibody preparation, —identifying antigens which bind in said screening to antibodies in said antibody preparation, —screening the identified antigens with individual antibody preparations from individual sera from individuals with antibodies against said specific pathogen, tumor, allergen or tissue or host prone to auto-immunity, —identifying the hyperimmune serum-reactive antigen portion of said identified antigens and which hyperimmune serum-reactive antigens bind to a relevant portion of said individual antibody preparations from said individual sera and —optionally isolating said hyperimmune serum-reactive antigens and producing said hyperimmune serum-reactive antigens by chemical or recombinant methods.

## Background
This application is a continuation of U.S. application Ser. No. 10/470,048 filed Feb. 6, 2004, which is a U.S. National Phase Application under 35 U.S.C. §371 of PCT Application No. PCT/EP2002/00546 filed Jan. 21, 2002 which claims priority to Austrian Application No. A 130/2001 filed Jan. 21, 2001, the entire contents of each of which are incorporated herein by reference.


The invention relates to a method for identification, isolation and production of antigens to a specific pathogen as well as new antigens suitable for use in a vaccine for a given type of animal or for humans.
Vaccines can save more lives (and resources) than any other medical intervention. Owing to world-wide vaccination programmes the incidence of many fatal diseases has been decreased drastically. Although this notion is valid for a whole panel of diseases, e.g. diphtheria, pertussis, measles and tetanus, there are no effective vaccines for numerous infectious disease including most viral infections, such as HIV, HCV, CMV and many others. There are also no effective vaccines for other diseases, infectious or noninfectious, claiming the lifes of millions of patients per year including malaria or cancer. In addition, the rapid emergence of antibiotic-resistant bacteria and microorganisms calls for alternative treatments with vaccines being a logical choice. Finally, the great need for vaccines is also illustrated by the fact that infectious diseases, rather than cardiovascular disorders or cancer or injuries remain the largest cause of death and disability in the world.
Several established vaccines consist of live attenuated organisms where the risk of reversion to the virulent wild-type strain exists. In particular in immunocompromised hosts this can be a live threatening scenario. Alternatively, vaccines are administered as a combination of pathogen-derived antigens together with compounds that induce or enhance immune responses against these antigens (these compounds are commonly termed adjuvant), since these subunit vaccines on their own are generally not effective.
Whilst there is no doubt that the above vaccines are valuable medical treatments, there is the disadvantage that, due to their complexity, severe side effects can be evoked, e.g. to antigens that are contained in the vaccine that display cross-reactivity with molecules expressed by cells of vaccinated individuals. In addition, existing requirements from regulatory authorities, e.g. the World Health Organization (WHO), the Food and Drug Administration (FDA), and their European counterparts, for exact specification of vaccine composition and mechanisms of induction of immunity, are difficult to meet.
Some widely used vaccines are whole cell-vaccines (attenuated bacteria or viruses (e.g. Bacille Calmette-Guerin (BCG) (tuberculosis), Measles, Mumps, Rubella, Oral Polio Vaccine (Sabin), killed bacteria or viruses (e.g. Pertussis, Inactivated polio vaccine (Salk)), subunit-vaccines (e.g. Toxoid (Diphtheria, Tetanus)), Capsular polysaccharide (H. influenzae type B), Yeast recombinant subunit (Hepatitis B surface protein).
A vaccine can contain a whole variety of different antigens. Examples of antigens are whole-killed organisms such as inactivated viruses or bacteria, fungi, protozoa or even cancer cells. Antigens may also consist of subfractions of these organisms/tissues, of proteins, or, in their most simple form, of peptides. Antigens can also be recognized by the immune system in form of glycosylated proteins or peptides and may also be or contain polysaccharides or lipids. Short peptides can be used since for example cytotoxic T-cells (CTL) recognize antigens in form of short usually 8-11 amino acids long peptides in conjunction with major histocompatibility complex (MHC). B-cells can recognize linear epitopes as short as 4-5 amino acids, as well as three dimensional structures (conformational epitopes). In order to obtain sustained, antigen-specific immune responses, adjuvants need to trigger immune cascades that involve all cells of the immune system necessary. Primarily, adjuvants are acting, but are not restricted in their mode of action, on so-called antigen presenting cells (APCs). These cells usually first encounter the antigen(s) followed by presentation of processed or unmodified antigen to immune effector cells. Intermediate cell types may also be involved. Only effector cells with the appropriate specificity are activated in a productive immune response. The adjuvant may also locally retain antigens and co-injected other factors. In addition the adjuvant may act as a chemoattractant for other immune cells or may act locally and/or systemically as a stimulating agent for the immune system.
Antigen presenting cells belong to the innate immune system, which has evolved as a first line host defense that limits infection early after exposure to microorganisms. Cells of the innate immune system recognize patterns or relatively non-specific structures expressed on their targets rather than more sophisticated, specific structures which are recognized by the adaptive immune system. Examples of cells of the innate immune system are macrophages and dendritic cells but also granulocytes (e.g. neutrophils), natural killer cells and others. By contrast, cells of the adaptive immune system recognize specific, antigenic structures, including peptides, in the case of T-cells and peptides as well as three-dimensional structures in the case of B-cells. The adaptive immune system is much more specific and sophisticated than the innate immune system and improves upon repeated exposure to a given pathogen/antigen. Phylogenetically, the innate immune system is much older and can be found already in very primitive organisms. Nevertheless, the innate immune system is critical during the initial phase of antigenic exposure since, in addition to containing pathogens, cells of the innate immune system, i.e. APCs, prime cells of the adaptive immune system and thus trigger specific immune responses leading to clearance of the intruders. In sum, cells of the innate immune system and in particular APCs play a critical role during the induction phase of immune responses by a) containing infections by means of a primitive pattern recognition system and b) priming cells of the adaptive immune system leading to specific immune responses and memory resulting in clearance of intruding pathogens or of other targets. These mechanisms may also be important to clear or contain tumor cells.
The antigens used for such vaccines have often been selected by chance or by easiness of availability. There is a demand to identify efficient antigens for a given pathogen or—preferably—an almost complete set of all antigens of a given pathogen which are practically (clinically) relevant. Such antigens may be preferred antigen candidates in a vaccine.
It is therefore an object of the present invention to comply with these demands and to provide a method with which such antigens may be provided and with which a practically complete set of antigens of e.g. a given pathogen may be identified with a given serum as antibody source. Such a method should also be suitable for rapidly changing pathogens which evolve a fast resistance against common drugs or vaccines. The method should also be applicable to identify and isolate tumor antigens, allergens, auto-immune antigens.
Therefore, the present invention provides a method for identification, isolation and production of hyperimmune serum-reactive antigens from a specific pathogen, a tumor, an allergen or a tissue or host prone to auto-immunity, especially from a specific pathogen, said antigens being suited for use in a vaccine for a given type of animal or for humans, said method being characterized by the following steps:

    
    
        providing an antibody preparation from a plasma pool of said given type of animal or from a human plasma pool or individual sera with antibodies against said specific pathogen, a tumor, an allergen or a tissue or host prone to auto-immunity,
        providing at least one expression library of said specific pathogen, a tumor, an allergen or a tissue or host prone to auto-immunity,
        screening said at least one expression library with said antibody preparation,
        identifying antigens which bind in said screening to antibodies in said antibody preparation,
        screening the identified antigens with individual antibody preparations from individual sera from individuals with antibodies against said specific pathogen, tumor, allergen or tissue or host prone to auto-immunity,
        identifying the hyperimmune serum-reactive antigen portion of said identified antigens which hyperimmune serum-reactive antigens bind to a relevant portion of said individual antibody preparations from said individual sera and
        optionally isolating said hyperimmune serum-reactive antigens and producing said hyperimmune serum-reactive antigens by chemical or recombinant methods.
    
    


This method is also suitable in general for identifying a practically complete set of hyperimmune serum-reactive antigens of a specific pathogen with given sera as antibody sources, if at least three different expression libraries are screened in a pathogen/antigen identification programme using the method according to the present invention. The present invention therefore also relates to a method for identification, isolation and production of a practically complete set of hyperimmune serum-reactive antigens of a specific pathogen, said antigens being suited for use in a vaccine for a given type of animal or for humans, which is characterized by the following steps:

    
    
        providing an antibody preparation from a plasma pool of said given type of animal or from a human plasma pool or individual sera with antibodies against said specific pathogen,
        providing at least three different expression libraries of said specific pathogen,
        screening said at least three different expression libraries with said antibody preparation,
        identifying antigens which bind in at least one of said at least three screenings to antibodies in said antibody preparation,
        screening the identified antigens with individual antibody preparations from individual sera from individuals with antibodies against said specific pathogen,
        identifying the hyperimmune serum-reactive antigen portion of said identified antigens which hyperimmune serum-reactive antigens bind to a relevant portion of said individual antibody preparations from said individual sera,
        repeating said screening and identification steps at least once,
        comparing the identified hyperimmune serum-reactive antigens identified in the repeated screening and identification steps with the identified hyperimmune serum-reactive antigens identified in the initial screening and identification steps,
        further repeating said screening and identification steps, if at least 5% of the hyperimmune serum-reactive antigens have been identified in the repeated screening and identification steps only, until less than 5% of the hyperimmune serum-reactive antigens are identified in a further repeating step only to obtain a complete set of hyperimmune serum-reactive antigens of a specific pathogen and
        optionally isolating said hyperimmune serum-reactive antigens and producing said hyperimmune serum-reactive antigens by chemical or recombinant methods.
    
    


The method according to the present invention mainly consists of three essential parts, namely 1. identifying hyperimmune serum sources containing specific antibodies against a given pathogen, 2. screening of suitable expression libraries with a suitable antibody preparation wherein candidate antigens (or antigenic fragments of such antigens) are selected, and—3. in a second screening round, wherein the hyperimmune serum-reactive antigens are identified by their ability to bind to a relevant portion of individual antibody preparations from individual sera in order to show that these antigens are practically relevant and not only hyperimmune serum-reactive, but also widely immunogenic (i.e. that a lot of individual sera react with a given antigen). With the present method it is possible to provide a set of antigens of a given pathogen which is practically complete with respect to the chosen pathogen and the chosen serum. Therefore, a bias with respect to “wrong” antigen candidates or an incomplete set of antigens of a given pathogen is excluded by the present method.
Completeness of the antigen set of a given pathogen within the meaning of the present invention is, of course, dependent on the completeness of the expression libraries used in the present method and on the quality and size of serum collections (number of individual plasmas/sera) tested, both with respect to representability of the library and usefulness of the expression system. Therefore, preferred embodiments of the present method are characterized in that at least one of said expression libraries is selected from a ribosomal display library, a bacterial surface library and a proteome.
A serum collection used in the present invention should be tested against a panel of known antigenic compounds of a given pathogen, such as polysaccharide, lipid and proteinaceous components of the cell wall, cell membranes and cytoplasma, as well as secreted products. Preferably, three distinct serum collections are used: 1. With very stable antibody repertoire: normal adults, clinically healthy people, who overcome previous encounters or currently carriers of e.g. a given pathogen without acute disease and symptoms, 2. With antibodies induced actually by the presence of the pathogenic organism: patients with acute disease with different manifestations (e.g. S. aureus sepsis or wound infection, etc.), 3. With no specific antibodies at all (as negative controls): 5-8 months old babies who lost the maternally transmitted immunoglobulins 5-6 months after birth. Sera have to react with multiple pathogen-specific antigens in order to consider hyperimmune for a given pathogen (bacteria, fungus, worm or otherwise), and for that relevant in the screening method according to the present invention.
In the antigen identification programme for identifying a complete set of antigens according to the present invention, it is preferred that said at least three different expression libraries are at least a ribosomal display library, a bacterial surface library and a proteome. It has been observed that although all expression libraries may be complete, using only one or two expression libraries in an antigen identification programme will not lead to a complete set of antigens due to preferential expression properties of each of the different expression libraries. While it is therefore possible to obtain hyperimmune serum-reactive antigens by using only one or two different expression libraries, this might in many cases not finally result in the identification of a complete set of hyperimmune serum-reactive antigens. Of course, the term “complete” according to the present invention does not indicate a theoretical maximum but is indeed a practical completeness, i.e. that at least 95% of the practically relevant antigens or antigenic determinants have been identified of a given pathogen. The practical relevance is thereby defined by the occurrence of antibodies against given antigens in the patient population.
According to the present invention also serum pools or plasma fractions or other pooled antibody containing body fluids are “plasma pools”.
An expression library as used in the present invention should at least allow expression of all potential antigens, e.g. all surface proteins of a given pathogen. With the expression libraries according to the present invention, at least one set of potential antigens of a given pathogen is provided, this set being preferably the complete theoretical complement of (poly-)peptides encoded by the pathogen's genome (i.e. genomic libraries as described in Example 2) and expressed either in a recombinant host (see Example 3) or in vitro (see Example 4). This set of potential antigens can also be a protein preparation, in the case of extracellular pathogens preferably a protein preparation containing surface proteins of said pathogen obtained from said pathogen grown under defined physiological conditions (see Example 5). While the genomic approach has the potential to contain the complete set of antigens, the latter one has the advantage to contain the proteins in their naturally state i.e. including for instance post-translational modifications or processed forms of these proteins, not obvious from the DNA sequence. These or any other sets of potential antigens from a pathogen, a tumor, an allergen or a tissue or host prone to auto-immunity are hereafter referred to as “expression library”. Expression libraries of very different kinds may be applied in the course of the present invention. Suitable examples are given in e.g. Ausubel et al., 1994. Especially preferred are expression libraries representing a display of the genetic set of a pathogen in recombinant form such as in vitro translation techniques, e.g. ribosomal display, or prokaryotic expression systems, e.g. bacterial surface expression libraries or which resemble specific physiological expression states of a given pathogen in a given physiological state, such as a proteome.
Ribosome display is an established method in recombinant DNA technology, which is applicable for each specific pathogen for the sake of the present invention (Schaffitzel et al, 1999). Bacterial surface display libraries will be represented by a recombinant library of a bacterial host displaying a (total) set of expressed peptide sequences of a given pathogen on e.g. a selected outer membrane protein at the bacterial host membrane (Georgiou et al., 1997). Apart from displaying peptide or protein sequences in an outer membrane protein, other bacterial display techniques, such as bacteriophage display technologies and expression via exported proteins are also preferred as bacterial surface expression library (Forrer et al., 1999; Rodi and Makowski, 1993; Georgiou et al., 1997).
The antigen preparation for the first round of screening in the method according to the present invention may be derived from any source containing antibodies to a given pathogen. Preferably, if a plasma pool is used as a source for the antibody preparation, a human plasma pool is selected which comprises donors which had experienced or are experiencing an infection with the given pathogen. Although such a selection of plasma or plasma pools is in principle standard technology in for example the production of hyperimmunoglobulin preparations, it was surprising that such technologies have these effects as especially shown for the preferred embodiments of the present invention.
Preferably the expression libraries are genomic expression libraries of a given pathogen, or alternatively m-RNA, libraries. It is preferred that these genomic or m-RNA libraries are complete genomic or m-RNA expression libraries which means that they contain at least once all possible proteins, peptides or peptide fragments of the given pathogen are expressable. Preferably the genomic expression libraries exhibit a redundancy of at least 2×, more preferred at least 5×, especially at least 10×.
Preferably, the method according to the present invention comprises screening at least a ribosomal display library, a bacterial surface display library and a proteome with the antibody preparation and identifying antigens which bind in at least two, preferably which bind to all, of said screenings to antibodies in said antibody preparation. Such antigens may then be regarded extremely suited as hyperimmunogenic antigens regardless of their way of expression. Preferably the at least two screenings should at least contain the proteome, since the proteome always represents the antigens as naturally expressed proteins including post-translational modifications, processing, etc. which are not obvious from the DNA sequence.
The method according to the present invention may be applied to any given pathogen. Therefore, preferred pathogens are selected from the group of bacterial, viral, fungal and protozoan pathogens. The method according to the present invention is also applicable to cancer, i.e. for the identification of tumor-associated antigens, and for the identification of allergens or antigens involved in auto-immune diseases. Of course, especially the recombinant methods are rather simple for pathogens having a small genome or a comparatively small number of expressed proteins (such as bacterial or viral pathogens) and are more complicated for complex (eukaryotic) organisms having large genomes. However, also such large genomic libraries of higher organism pathogens may well be analyzed with the method according to the present invention, at least in a faster and more reliable way than with known methods for identifying suitable antigens.
Preferred pathogens to be analyzed or which antigens are to be extracted, respectively, include human immunodeficiency virus (HIV), hepatitis A virus (HAV), hepatitis B virus (HBV), hepatitis C virus (HCV), Rous sarcoma virus (RSV), Epstein-Barr virus (EBV), influenza virus (IV), rotavirus (RV), Staphylococcus aureus (S. aureus), Staphylococcus epidermidis (S. epidermidis), Chlamydia pneumoniae (C. pneumoniae), Chlamydia trachomatis (C. trachomatis), Mycobacterium tuberculosis (M. tuberculosis), Mycobacterium leprae (M. leprae), Streptococcus pneumoniae (S. pneumoniae), Streptococcus pyogenes (S. pyogenes), Streptococcus agalactiae (S. agalactiae), Enterococcus faecalis (E. faecalis), Bacillus anthracis (B. anthracis), Vibrio cholerae (V. cholerae), Borrelia burgdorferi (B. burgdorferi), Plasmodium sp., fungal diseases such as Pneumocystis carinii, Aspergillus sp., Cryptococcus sp., Candida albicans or parasitic infections such as ascariasis (Ascaris lumbricoides) and taeniasis (Taenia saginata). The method according to the present invention is most applicable for bacteria, worms or candida.
As a model organism for the present application Staphylococcus aureus has been chosen to demonstrate the applicability and efficacy of the method according to the present invention. Especially with respect to the examples it is clear that the invention is easily transferable to all potential pathogens, especially the ones listed above.
It was surprising that the method according to the present invention allows an efficient and fast biological screening of a given pathogen, especially in view of the fact that only a small fraction of a patient's antibody repertoire is directed to a given pathogen, even in a state where this pathogen is effectively defeated. It has been discovered within the course of the present invention, especially during performance of the S. aureus example that only 1-2% of the antibody repertoire of a patient having high titers against S. aureus are indeed antibodies directed against S. aureus. Moreover, over 70% of this specific 1% portion is directed against non-protein antigens, such as teichoic acid, so that only a total of 0.1% or less of the antibodies are directed to proteinaceous antigens.
One of the advantages of using recombinant expression libraries, especially ribosome display libraries and bacterial surface display libraries, is that the identified hyperimmune serum-reactive antigens may be instantly produced by expression of the coding sequences of the screened and selected clones expressing the hyperimmune serum-reactive antigens without further recombinant DNA technology or cloning steps necessary.
The hyperimmune serum-reactive antigens obtainable by the method according to the present invention may therefore be immediately finished to a pharmaceutical preparation, preferably by addition of a pharmaceutically acceptable carrier and/or excipient, immediately after its production (in the course of the second selection step), e.g. by expression from the expression library platform.
Preferably, the pharmaceutical preparation containing the hyperimmune serum-reactive antigen is a vaccine for preventing or treating an infection with the specific pathogen for which the antigens have been selected.
The pharmaceutical preparation may contain any suitable auxiliary substances, such as buffer substances, stabilisers or further active ingredients, especially ingredients known in connection of vaccine production.
A preferable carrier/or excipient for the hyperimmune serum-reactive antigens according to the present invention is a immunostimulatory compound for further stimulating the immune response to the given hyperimmune serum-reactive antigen. Preferably the immunostimulatory compound in the pharmaceutical preparation according to the present invention is selected from the group of polycationic substances, especially polycationic peptides, immunostimulatory deoxynucleotides, alumn, Freund's complete adjuvans, Freund's incomplete adjuvans, neuroactive compounds, especially human growth hormone, or combinations thereof.
The polycationic compound(s) to be used according to the present invention may be any polycationic compound which shows the characteristic effects according to the WO 97/30721. Preferred polycationic compounds are selected from basic polypeptides, organic polycations, basic polyamino acids or mixtures thereof. These polyamino acids should have a chain length of at least 4 amino acid residues (see: Tuftsin as described in Goldman et al. (1983)). Especially preferred are substances like polylysine, polyarginine and polypeptides containing more than 20%, especially more than 50% of basic amino acids in a range of more than 8, especially more than 20, amino acid residues or mixtures thereof. Other preferred polycations and their pharmaceutical compositions are described in WO 97/30721 (e.g. polyethyleneimine) and WO 99/38528. Preferably these polypeptides contain between 20 and 500 amino acid residues, especially between 30 and 200 residues.
These polycationic compounds may be produced chemically or recombinantly or may be derived from natural sources.
Cationic (poly)peptides may also be anti-microbial with properties as reviewed in Ganz et al, 1999; Hancock, 1999. These (poly)peptides may be of prokaryotic or animal or plant origin or may be produced chemically or recombinantly (Andreu et al., 1998; Ganz et al., 1999; Simmaco et al., 1998). Peptides may also belong to the class of defensins (Ganz, 1999; Ganz et al., 1999). Sequences of such peptides can be, for example, be found in the Antimicrobial sequences Database on the world wide web at: bbcm.univ.trieste.it/.about.tossi/pag2.html
Such host defense peptides or defensives are also a preferred form of the polycationic polymer according to the present invention. Generally, a compound allowing as an end product activation (or down-regulation) of the adaptive immune system, preferably mediated by APCs (including dendritic cells) is used as polycationic polymer.
Especially preferred for use as polycationic substance in the present invention are cathelicidin derived antimicrobial peptides or derivatives thereof (International patent application PCT/EP01/09529, incorporated herein by reference), especially antimicrobial peptides derived from mammal cathelicidin, preferably from human, bovine or mouse.
Polycationic compounds derived from natural sources include HIV-REV or HIV-TAT (derived cationic peptides, antennapedia peptides, chitosan or other derivatives of chitin) or other peptides derived from these peptides or proteins by biochemical or recombinant production. Other preferred polycationic compounds are cathelin or related or derived substances from cathelin. For example, mouse cathelin is a peptide which has the amino acid sequence NH2—RLAGLLRKGGEKIGEKLKKIGQKIKNFFQKLVPQPE-COOH (SEQ ID NO:599). Related or derived cathelin substances contain the whole or parts of the cathelin sequence with at least 15-20 amino acid residues. Derivations may include the substitution or modification of the natural amino acids by amino acids which are not among the 20 standard amino acids. Moreover, further cationic residues may be introduced into such cathelin molecules. These catheline molecules are preferred to be combined with the antigen. These cathelin molecules surprisingly have turned out to be also effective as an adjuvant for an antigen without the addition of further adjuvants. It is therefore possible to use such cathelin molecules as efficient adjuvants in vaccine formulations with or without further immunactivating substances.
Another preferred polycationic substance to be used according to the present invention is a synthetic peptide containing at least 2 KLK-motifs separated by a linker of 3 to 7 hydrophobic amino acids (International patent application PCT/EP01/12041, incorporated herein by reference).
Immunostimulatory deoxynucleotides are e.g. neutral or artificial CpG containing DNA, short stretches of DNA derived from non-vertebrates or in form of short oligonucleotides (ODNs) containing non-methylated cytosine-guanine di-nucleotides (CpG) in a certain base context (e.g. Krieg et al., 1995) but also inosine containing ODNs (I-ODNs) as described in WO 01/93905.
Neuroactive compounds, e.g. combined with polycationic substances are described in WO 01/24822.
According to a preferred embodiment the individual antibody preparation for the second round of screening are derived from patients with have suffered from an acute infection with the given pathogen, especially from patients who show an antibody titer to the given pathogen above a certain minimum level, for example an antibody titer being higher than 80 percentile, preferably higher than 90 percentile, especially higher than 95 percentile of the human (patient or carrier) sera tested. Using such high titer individual antibody preparations in the second screening round allows a very selective identification of the hyperimmune serum-reactive antigens to the given pathogen.
It is important that the second screening with the individual antibody preparations (which may also be the selected serum) allows a selective identification of the hyperimmune serum-reactive antigens from all the promising candidates from the first round. Therefore, preferably at least 10 individual antibody preparations (i.e. antibody preparations (e.g. sera) from at least 10 different individuals having suffered from an infection to the chosen pathogen) should be used in identifying these antigens in the second screening round. Of course, it is possible to use also less than 10 individual preparations, however, selectivity of the step may not be optimal with a low number of individual antibody preparations. On the other hand, if a given hyperimmune serum-reactive antigen (or an antigenic fragment thereof) is recognized in at least 10 individual antibody preparations, preferably at least 30, especially at least 50 individual antibody preparations, identification of hyperimmune serum-reactive antigen is also selective enough for a proper identification. Hyperimmune serum-reactivity may of course be tested with as many individual preparations as possible (e.g. with more than 100 or even with more than 1000).
Therefore, the relevant portion of the hyperimmune serum-reactive antibody preparation according to the method of the present invention should preferably be at least 10, more preferred at least 30, especially at least 50 individual antibody preparations. Alternatively (or in combination) hyperimmune serum-reactive antigen may preferably be also identified with at least 20%, preferably at least 30%, especially at least 40% of all individual antibody preparations used in the second screening round.
According to a preferred embodiment of the present invention, the sera from which the individual antibody preparations for the second round of screening are prepared (or which are used as antibody preparations), are selected by their titer against the specific pathogen (e.g. against a preparation of this pathogen, such as a lysate, cell wall components and recombinant proteins). Preferably, some are selected with a total IgA titer above 4000 U, especially above 6000 U, and/or an IgG titer above 10 000 U, especially above 12 000 U (U=units, calculated from the OD405nm reading at a given dilution) when whole organism (total lysate or whole cells) is used as antigen in ELISA. Individual proteins with Ig titers of above 800-1000 U are specifically preferred for selecting the hyperimmune serum-reactive antigens according to the present invention only for total titer. The statement for individual proteins can be derived from FIG. 9.
According to the demonstration example which is also a preferred embodiment of the present invention the given pathogen is a Staphylococcus pathogen, especially Staphylococcus aureus and Staphylococcus epidermidis. Staphylococci are opportunistic pathogens which can cause illnesses which range from minor infections to life threatening diseases. Of the large number of Staphylococci at least 3 are commonly associated with human disease: S. aureus, S. epidermidis and rarely S. saprophyticus (Crossley and Archer, 1997). S. aureus has been used within the course of the present invention as an illustrative example of the way the present invention functions. Besides that, it is also an important organism with respect to its severe pathogenic impacts on humans. Staphylococcal infections are imposing an increasing threat in hospitals worldwide. The appearance and disease causing capacity of Staphylococci are related to the wide-spread use of antibiotics which induced and continue to induce multi-drug resistance. For that reason medical treatment against Staphylococcal infections cannot rely only on antibiotics anymore. Therefore, a tactic change in the treatment of these diseases is desperately needed which aims to prevent infections. Inducing high affinity antibodies of the opsonic and neutralizing type by vaccination helps the innate immune system to eliminate bacteria and toxins. This makes the method according to the present invention an optimal tool for the identification of staphylococcal antigenic proteins.
Every human being is colonized with S. epidermidis. The normal habitats of S. epidermidis are the skin and the mucous membrane. The major habitats of the most pathogenic species, S. aureus, are the anterior nares and perineum. Some individuals become permanent S. aureus carriers, often with the same strain. The carrier stage is clinically relevant because carriers undergoing surgery have more infections than noncarriers. Generally, the established flora of the nose prevents acquisition of new strains. However, colonization with other strains may occur when antibiotic treatment is given that leads to elimination of the susceptible carrier strain. Because this situation occurs in the hospitals, patients may become colonized with resistant nosocomial Staphylococci. These bacteria have an innate adaptability which is complemented by the widespread and sometimes inappropriate use of antimicrobial agents. Therefore hospitals provide a fertile environment for drug resistance to develop (close contact among sick patients, extensive use of antimicrobials, nosocomial infections). Both S. aureus and S. epidermidis have become resistant to many commonly used antibiotics, most importantly to methicillin (MRSA) and vancomycin (VISA). Drug resistance is an increasingly important public health concern, and soon many infections caused by staphylococci may be untreatable by antibiotics. In addition to its adverse effect on public health, antimicrobial resistance contributes to higher health care costs, since treating resistant infections often requires the use of more toxic and more expensive drugs, and can result in longer hospital stays for infected patients.
Moreover, even with the help of effective antibiotics, the most serious staphylococcal infections have 30-50% mortality.
Staphylococci become potentially pathogenic as soon as the natural balance between microorganisms and the immune system gets disturbed, when natural barriers (skin, mucous membrane) are breached. The coagulase-positive S. aureus is the most pathogenic staphylococcal species, feared by surgeons for a long time. Most frequently it causes surgical wound infections, and induces the formation of abscesses. This local infection might become systemic, causing bacteraemia and sepsis. Especially after viral infections and in elderly, it can cause severe pneumonia. S. aureus is also a frequent cause of infections related to medical devices, such as intravascular and percutan catheters (endocarditis, sepsis, peritonitis), prosthetic devices (septic arthritis, osteomyelitis). S. epidermidis causes diseases mostly related to the presence of foreign body and the use of devices, such as catheter related infections, cerebrospinal fluid shunt infections, peritonitis in dialysed patients (mainly CAPD), endocarditis in individuals with prosthetic valves. This is exemplified in immunocompromised individuals such as oncology patients and pre-mature neonates in whom coagulase-negative staphylococcal infections frequently occur in association with the use of intravascular device. The increase in incidence is related to the increased used of these devices and increasing number of immunocompromised patients.
Much less is known about S. saprophyticus, another coagulase-negative staphylococci, which causes acute urinary tract infection in previously healthy people. With a few exceptions these are women aged 16-25 years.
The pathogenesis of staphylococci is multifactorial. In order to initiate infection the pathogen has to gain access to the cells and tissues of the host, that is adhere. S. aureus expresses-surface proteins that promote attachment to the host proteins such as laminin, fibronectin, elastin, vitronectin, fibrinogen and many other molecules that form part of the extracellular matrix (extracellular matrix binding proteins, ECMBP). S. epidermidis is equipped with cell surface molecules which promote adherence to foreign material and through that mechanism establish infection in the host. The other powerful weapons staphylococci use are the secreted products, such as enterotoxins, exotoxins, and tissue damaging enzymes. The toxins kill or misguide immune cells which are important in the host defense. The several different types of toxins are responsible for most of the symptoms during infections.
Host defense against S. aureus relies mainly on innate immunological mechanisms. The skin and mucous membranes are formidable barriers against invasion by Staphylococci. However, once the skin or the mucous membranes are breached (wounds, percutan, catheters, etc), the first line of nonadaptive cellular defense begins its co-ordinate action through complement and phagocytes, especially the polymorphonuclear leukocytes (PMNs). These cells can be regarded as the cornerstones in eliminating invading bacteria. As Staphylococci are primarily extracellular pathogens; the major anti-staphylococcal adaptive response comes from the humoral arm of the immune system, and is mediated through three major mechanisms: promotion of opsonization, toxin neutralisation, and inhibition of adherence. It is believed that opsonization is especially important, because of its requirement for an effective phagocytosis. For efficient opsonization the microbial surface has to be coated with antibodies and complement factors for recognition by PMNs through receptors to the Fc fragment of the IgG molecule or to activated C3b. After opsonization, staphylococci are phagocytosed and killed. Moreover, S. aureus can attach to endothelial cells, and be internalised by a phagocytosis-like process. Antibodies bound to specific antigens on the cell surface of bacteria serve as ligands for the attachment to PMNs and promote phagocytosis. The very same antibodies bound to the adhesins and other cell surface proteins are expected to neutralize adhesion and prevent colonization.
There is little clinical evidence that cell mediated immunity has a significant contribution in the defense against Staphylococci, yet one has to admit that the question is not adequately addressed. It is known, however, that Staphylococcus aureus utilizes an extensive array of molecular countermeasures to manipulate the defensive microenvironment of the infected host by secreting polypeptides referred to as superantigens, which 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. Moreover, one cannot expect a long lasting antibody (memory) response without the involvement of T-cells. It is also known that the majority of the anti-staphylococcal antibodies are against T-cell independent antigens (capsular polysaccharides, lipoteichoic acid, peptidoglycan) without a memory function. The T-cell dependent proteinaceous antigens can elicit long-term protective antibody responses. These staphylococcal proteins and peptides have not yet been determined.
For all these above mentioned reasons, a tactic change on the war field against staphylococcal infections is badly needed. One way of combating infections is preventing them by active immunisation. Vaccine development against S. aureus has been initiated by several research groups and national institutions worldwide, but there is no effective vaccine approved so far. It has been shown that an antibody-deficiency state contributes to staphylococcal persistence, suggesting that anti-staphylococcal antibodies are important in host defense. Antibodies—added as passive immunisation or induced by active vaccination—directed towards surface components could both prevent bacterial adherence, neutralize toxins and promote phagocytosis. A vaccine based on fibronectin binding protein induces protective immunity against mastitis in cattle and suggest that this approach is likely to work in humans (refs). Taking all this together it is suggestive that an effective vaccine should be composed of proteins or polypeptides, which are expressed by all strains and are able to induce high affinity, abundant antibodies against cell surface components of S. aureus. The antibodies should be IgG1 and/or IgG3 for opsonization, and any IgG subtype and IgA for neutralisation of adherence and toxin action. A chemically defined vaccine must be definitely superior compared to a whole cell vaccine (attenuated or killed), since components of S. aureus which paralyze TH cells (superantigens) or inhibit opsonization (protein A) can be eliminated, and the individual proteins inducing protective antibodies can be selected. Identification of the relevant antigens help to generate effective passive immunisation (humanised monoclonal antibody therapy), which can replace human immunoglobulin administration with all its dangerous side-effects. Neonatal staphylococcal infections, severe septicemia and other life-threatening acute conditions are the primary target of passive immunisation. An effective vaccine offers great potential for patients facing elective surgery in general, and those receiving endovascular devices, in particular. Moreover, patients suffering from chronic diseases which decrease immune responses or undergoing continuous ambulatory peritoneal dialysis are likely to benefit from such a vaccine.
For the illustrative example concerning Staphylococcus aureus three different approaches have been employed in parallel. All three of these methods are based on the interaction of Staphylococcus proteins or peptides with the antibodies present in human sera with the method according to the present invention. This interaction relies on the recognition of epitopes within the proteins which can be short peptides (linear epitopes) or polypeptide domains (structural epitopes). The antigenic proteins are identified by the different methods using pools of pre-selected sera and—in the second screening round—by individual selected sera.
Following the high throughput screening, the selected antigenic proteins are expressed as recombinant proteins or in vitro translated products (in case it can not be expressed in prokaryotic expression systems), and tested in a series of ELISA and Western blotting assays for the assessment of immunogeneicity with a large human serum collection (>100 uninfected, >50 patients sera). The preferred antigens are located on the cell surface or secreted, that is accessible extracellularly. Antibodies against the cell wall proteins (such as the Extracellular matrix binding proteins) are expected to serve double purposes: to inhibit adhesion and promote phagocytosis. The antibodies against the secreted proteins are beneficial in toxin neutralisation. It is also known that bacteria communicate with each other through secreted proteins. Neutralizing antibodies against these proteins will interrupt growth promoting cross-talk between or within staphylococcal species. Bioinformatics (signal sequences, cell wall localisation signals, transmembrane domains) proved to be very useful in assessing cell surface localisation or secretion. The experimental approach includes the isolation of antibodies with the corresponding epitopes and proteins from human serum, and use them as reagents in the following assays: cell surface staining of staphylococci grown under different conditions (FACS, microscopy), determination of neutralizing capacity (toxin, adherence), and promotion of opsonization and phagocytosis (in vitro phagocytosis assay).
The recognition of linear epitopes by antibodies can be based on sequences as short as 4-5 aa. Of course it does not necessarily mean that these short peptides are capable of inducing the given antibody. in vivo. For that reason the defined epitopes, polypeptides and proteins may further be tested in animals (mainly in mice) for their capacity to induce antibodies against the selected proteins in vivo. The antigens with the proven capability to induce antibodies will be tested in animal models for the ability to prevent infections.
The antibodies produced against Staphylococci by the human immune system and present in human sera are indicative of the in vivo expression of the antigenic proteins and their immunogenicity.
Accordingly, novel hyperimmune serum-reactive antigens from Staphylococcus aureus or Staphylococcus epidermidis have been made available by the method according to the present invention.
According to another aspect of the present invention the invention relates to a hyperimmune serum-reactive antigen selected from the group consisting of the sequences listed in any one of Tables 2a, 2b, 2c, 2d, 3, 4 and 5, especially selected from the group consisting of Seq. ID No. 56, 57, 59, 60, 67, 70, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 85, 87, 88, 89, 90, 92, 95, 96, 97, 99, 100, 101, 102, 103, 104, 106, 108, 110, 112, 114, 116, 118, 120, 122, 126, 128, 132, 134, 138, 140, 142, 151, 152, 154, 155 and hyperimmune fragments thereof. Accordingly, the present invention also relates to a hyperimmune serum-reactive antigen obtainable by the method according to the present invention and being selected from the group consisting of the sequences listed in any one of Tables 2a, 2b, 2c, 2d, 3, 4 and 5, especially selected from the group consisting of Seq. ID No. 56, 57, 59, 60, 67, 70, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 85, 87, 88, 89, 90, 92, 95, 96, 97, 99, 100, 101, 102, 103, 104, 106, 108, 110, 112, 114, 116, 118, 120, 122, 126, 128, 132, 134, 138, 140, 142, 151, 152, 154, 155 and hyperimmune fragments thereof.
Antigens from Staphylococcus aureus and Staphylococcus epidermidis have been extracted by the method according to the present invention which may be used in the manufacture of a pharmaceutical preparation, especially for the manufacture of a vaccine against Staphylococcus aureus and Staphylococcus epidermidis infections. Examples of such hyperimmune serum-reactive antigens of Staphylococcus aureus and Staphylococcus epidermidis to be used in a pharmaceutical preparation are selected from the group consisting of the sequences listed in any one of Tables 2a, 2b, 2c, 2d, 3, 4 and 5, especially selected from the group consisting of Seq. ID No. 55, 56, 57, 58, 59, 60, 62, 66, 67, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 87, 88, 89, 90, 92, 94, 95, 96, 97, 99, 100, 101, 102, 103, 104, 106, 108, 110, 112, 114, 116, 118, 120, 122, 126, 128, 130, 132, 134, 138, 140, 142, 151, 152, 154, 155, 158 and hyperimmune fragments thereof for the manufacture of a pharmaceutical preparation, especially for the manufacture of a vaccine against Staphylococcus aureus and Staphylococcus epidermidis infections.
A hyperimmune fragment is defined as a fragment of the identified antigen which is for itself antigenic or may be made antigenic when provided as a hapten. Therefore, also antigen or antigenic fragments showing one or (for longer fragments) only a few amino acid exchanges are enabled with the present invention, provided that the antigenic capacities of such fragments with amino acid exchanges are not severely deteriorated on the exchange(s). i.e. suited for eliciting an appropriate immune response in a individual vaccinated with this antigen and identified by individual antibody preparations from individual sera.
Preferred examples of such hyperimmune fragments of a hyperimmune serum-reactive antigen are selected from the group consisting of peptides comprising the amino acid sequences of column “predicted immunogenic aa”, “Location of identified immunogenic region” and “Serum reactivity with relevant region” of Tables 2a, 2b, 2c and 2d and the amino acid sequences of column “Putative antigenic surface areas” of Table 4 and 5, especially peptides comprising amino acid No. aa 12-29, 34-40, 63-71, 101-110, 114-122, 130-138, 140-195, 197-209, 215-229, 239-253, 255-274 and 39-94 of Seq. ID No. 55,
aa 5-39, 111-117, 125-132, 134-141, 167-191, 196-202, 214-232, 236-241, 244-249, 292-297, 319-328, 336-341, 365-380, 385-391, 407-416, 420-429, 435-441, 452-461, 477-488, 491-498, 518-532, 545-556, 569-576, 581-587, 595-602, 604-609, 617-640, 643-651, 702-715, 723-731, 786-793, 805-811, 826-839, 874-889, 37-49, 63-77 and 274-334, of Seq. ID No. 56,

aa 28-55, 82-100, 105-111, 125-131, 137-143, 1-49, of Seq. ID No. 57,

aa 33-43, 45-51, 57-63, 65-72, 80-96, 99-110, 123-129, 161-171, 173-179, 185-191, 193-200, 208-224, 227-246, 252-258, 294-308, 321-329, 344-352, 691-707, 358-411 and 588-606, of Seq. ID No. 58,

aa 16-38, 71-77, 87-94, 105-112, 124-144, 158-164, 169-177, 180-186, 194-204, 221-228, 236-245, 250-267, 336-343, 363-378, 385-394, 406-412, 423-440, 443-449, 401-494, of Seq. ID No. 59,

aa 18-23, 42-55, 69-77, 85-98, 129-136, 182-188, 214-220, 229-235, 242-248, 251-258, 281-292, 309-316, 333-343, 348-354, 361-367, 393-407, 441-447, 481-488, 493-505, 510-515, 517-527, 530-535, 540-549, 564-583, 593-599, 608-621, 636-645, 656-670, 674-687, 697-708, 726-734, 755-760, 765-772, 785-792, 798-815, 819-824, 826-838, 846-852, 889-904, 907-913, 932-939, 956-964, 982-1000, 1008-1015, 1017-1024, 1028-1034, 1059-1065, 1078-1084, 1122-1129, 1134-1143, 1180-1186, 1188-1194, 1205-1215, 1224-1230, 1276-1283, 1333-1339, 1377-1382, 1415-1421, 1448-1459, 1467-1472, 1537-1545, 1556-1566, 1647-1654, 1666-1675, 1683-1689, 1722-1737, 1740-1754, 1756-1762, 1764-1773, 1775-1783, 1800-1809, 1811-1819, 1839-1851, 1859-1866, 1876-1882, 1930-1939, 1947-1954, 1978-1985, 1999-2007, 2015-2029, 2080-2086, 2094-2100, 2112-2118, 2196-2205, 2232-2243, 198-258, 646-727 and 2104-2206, of Seq. ID No. 60,

aa 10-29, 46-56, 63-74, 83-105, 107-114, 138-145, 170-184, 186-193, 216-221, 242-248, 277-289, 303-311, 346-360, 379-389, 422-428, 446-453, 459-469, 479-489, 496-501, 83-156, of Seq. ID No. 62,

aa 14-22, 32-40, 52-58, 61-77, 81-93, 111-117, 124-138, 151-190, 193-214, 224-244, 253-277, 287-295, 307-324, 326-332, 348-355, 357-362, 384-394, 397-434, 437-460, 489-496, 503-510, 516-522, 528-539, 541-547, 552-558, 563-573, 589-595, 602-624, 626-632, 651-667, 673-689, 694-706, 712-739, 756-790, 403-462, of Seq. ID No. 66,

aa 49-56, 62-68, 83-89, 92-98, 109-115, 124-131, 142-159, 161-167, 169-175, 177-188, 196-224, 230-243, 246-252, 34-46, of Seq. ID No. 67,

aa 11-20, 26-47, 69-75, 84-92, 102-109, 119-136, 139-147, 160-170, 178-185, 190-196, 208-215, 225-233, 245-250, 265-272, 277-284, 300-306, 346-357, 373-379, 384-390, 429-435, 471-481, 502-507, 536-561, 663-688, 791-816, 905-910, 919-933, 977-985, 1001-1010, 1052-1057, 1070-1077, 1082-1087, 1094-1112, 493-587, 633-715 and 704-760, of Seq. ID No. 70,

aa. 6-20, 53-63, 83-90, 135-146, 195-208, 244-259, 263-314, 319-327, 337-349, 353-362, 365-374, 380-390, 397-405, 407-415, 208-287 and 286-314, of Seq. ID No. 71,

aa 10-26, 31-43, 46-58, 61-66, 69-79, 85-92, 100-115, 120-126, 128-135, 149-155, 167-173, 178-187, 189-196, 202-222, 225-231, 233-240, 245-251, 257-263, 271-292, 314-322, 325-334, 339-345, 59-74, of Seq. ID No. 72,

aa 4-9, 15-26, 65-76, 108-115, 119-128, 144-153, 38-52 and 66-114, of Seq. ID No. 73,

aa 5-22, 42-50, 74-81, 139-145, 167-178, 220-230, 246-253, 255-264, 137-237 and 250-267, of Seq. ID No. 74,

aa 10-26, 31-44, 60-66, 99-104, 146-153, 163-169, 197-205, 216-223, 226-238, 241-258, 271-280, 295-315, 346-351, 371-385, 396-407, 440-446, 452-457, 460-466, 492-510, 537-543, 546-551, 565-582, 590-595, 635-650, 672-678, 686-701, 705-712, 714-721, 725-731, 762-768, 800-805, 672-727, of Seq. ID No. 75,

aa 5-32, 35-48, 55-76, of Seq. ID No. 76,

aa 7-35, 54-59, 247-261, 263-272, 302-320, 330-339, 368-374, 382-411, 126-143 and 168-186, of Seq. ID No. 77,

aa 5-24, 88-94, 102-113, 132-143, 163-173, 216-224, 254-269, 273-278, 305-313, 321-327, 334-341, 31-61 and 58-74, of Seq. ID No. 78,

aa 16-24, 32-39, 43-49, 64-71, 93-99, 126-141, 144-156, 210-218, 226-233, 265-273, 276-284, 158-220, of Seq. ID No. 79,

aa 49-72, 76-83, 95-105, 135-146, 148-164, 183-205, 57-128, of Seq. ID No. 80,

aa 6-15, 22-32, 58-73, 82-88, 97-109, 120-131, 134-140, 151-163, 179-185, 219-230, 242-255, 271-277, 288-293, 305-319, 345-356, 368-381, 397-406, 408-420, 427-437, 448-454, 473-482, 498-505, 529-535, 550-563, 573-580, 582-590, 600-605, 618-627, 677-685, 718-725, 729-735, 744-759, 773-784, 789-794, 820-837, 902-908, 916-921, 929-935, 949-955, 1001-1008, 1026-1032, 1074-1083, 1088-1094, 1108-1117, 1137-1142, 1159-1177, 1183-1194, 1214-1220, 1236-1252, 1261-1269, 1289-1294, 1311-1329, 1336-1341, 1406-1413, 1419-1432, 1437-1457, 1464-1503, 1519-1525, 1531-1537, 1539-1557, 1560-1567, 1611-1618, 1620-1629, 1697-1704, 1712-1719, 1726-1736, 1781-1786, 1797-1817, 1848-1854, 1879-1890, 1919-1925, 1946-1953, 1974-1979, 5 to 134, of Seq. ID No. 81,

aa 6-33, 40-46, 51-59, 61-77, 84-104, 112-118, 124-187, 194-248, 252-296, 308-325, 327-361, 367-393, 396-437, 452-479, 484-520, 535-545, 558-574, 582-614, 627-633, 656-663, 671-678, 698-704, 713-722, 725-742, 744-755, 770-784, 786-800, 816-822, 827-837, 483-511, of Seq. ID No. 82,

aa 4-19, 57-70, 79-88, 126-132, 144-159, 161-167, 180-198, 200-212, 233-240, 248-255, 276-286, 298-304, 309-323, 332-346, 357-366, 374-391, 394-406, 450-456, 466-473, 479-487, 498-505, 507-519, 521-530, 532-540, 555-565, 571-581, 600-611, 619-625, 634-642, 650-656, 658-665, 676-682, 690-699, 724-733, 740-771, 774-784, 791-797, 808-815, 821-828, 832-838, 876-881, 893-906, 922-929, 938-943, 948-953, 969-976, 1002-1008, 1015-1035, 1056-1069, 1105-1116, 1124-1135, 1144-1151, 1173-1181, 1186-1191, 1206-1215, 1225-1230, 1235-1242, 6-66, 65-124 and 590-604, of Seq. ID No. 83,

aa 5-32, 66-72, 87-98, 104-112, 116-124, 128-137, 162-168, 174-183, 248-254, 261-266, 289-303, 312-331, 174-249, of Seq. ID No. 84,

aa 4-21, 28-40, 45-52, 59-71, 92-107, 123-137, 159-174, 190-202, 220-229, 232-241, 282-296, 302-308, 312-331, 21-118, of Seq. ID No. 85,

aa 9-28, 43-48, 56-75, 109-126, 128-141, 143-162, 164-195, 197-216, 234-242, 244-251, 168-181, of Seq. ID No. 87,

aa 4-10, 20-42, 50-86, 88-98, 102-171, 176-182, 189-221, 223-244, 246-268, 276-284, 296-329, 112-188, of Seq. ID No. 88,

aa 4-9, 13-24, 26-34, 37-43, 45-51, 59-73, 90-96, 99-113, 160-173, 178-184, 218-228, 233-238, 255-262, 45-105, 103-166 and 66-153, of Seq. ID No. 89,

aa 13-27, 42-63, 107-191, 198-215, 218-225, 233-250, 474-367, of Seq. ID No. 90;

aa 26-53, 95-123, 164-176, 189-199, 8-48, of Seq. ID No. 92,

aa 7-13, 15-23, 26-33, 68-81, 84-90, 106-117, 129-137, 140-159, 165-172, 177-230, 234-240, 258-278, 295-319, 22-56, 23-99, 97-115, 233-250 and 245-265, of Seq. ID No. 94,

aa 13-36, 40-49, 111-118, 134-140, 159-164, 173-183, 208-220, 232-241, 245-254, 262-271, 280-286, 295-301, 303-310, 319-324, 332-339, 1-85, 54-121 and 103-185, of Seq. ID No. 95,

aa 39-44, 46-80, 92-98, 105-113, 118-123, 133-165, 176-208, 226-238, 240-255, 279-285, 298-330, 338-345, 350-357, 365-372, 397-402, 409-415, 465-473, 488-515, 517-535, 542-550, 554-590, 593-601, 603-620, 627-653, 660-665, 674-687, 698-718, 726-739, 386-402, of Seq. ID No. 96,

aa 5-32, 34-49, 1-43, of Seq. ID No. 97,

aa 10-27, 37-56, 64-99, 106-119, 121-136, 139-145, 148-178, 190-216, 225-249, 251-276, 292-297, 312-321, 332-399, 403-458, 183-200, of Seq. ID No. 99,

aa 5-12, 15-20, 43-49, 94-106, 110-116, 119-128, 153-163, 175-180, 185-191, 198-209, 244-252, 254-264, 266-273, 280-288, 290-297, 63-126, of Seq. ID No. 100,

aa 5-44, 47-55, 62-68, 70-78, 93-100, 128-151, 166-171, 176-308, 1-59, of Seq. ID No. 101,

aa 18-28, 36-49, 56-62, 67-84, 86-95, 102-153, 180-195, 198-218, 254-280, 284-296, 301-325, 327-348, 353-390, 397-402, 407-414, 431-455, 328-394, of Seq. ID No. 102,

aa 7-37, 56-71, 74-150, 155-162, 183-203, 211-222, 224-234, 242-272, 77-128, of Seq. ID No. 103,

aa 34-58, 63-69, 74-86, 92-101, 130-138, 142-150, 158-191, 199-207, 210-221, 234-249, 252-271, 5-48, of Seq. ID No. 104,

aa 12-36, 43-50, 58-65, 73-78, 80-87, 108-139, 147-153, 159-172, 190-203, 211-216, 224-232, 234-246, 256-261, 273-279, 286-293, 299-306, 340-346, 354-366, 167-181, of Seq. ID No. 106,

aa 61-75, 82-87, 97-104, 113-123, 128-133, 203-216, 224-229, 236-246, 251-258, 271-286, 288-294, 301-310, 316-329, 337-346, 348-371, 394-406, 418-435, 440-452 of Seq. ID No. 112,

aa 30-37, 44-55, 83-91, 101-118, 121-128, 136-149, 175-183, 185-193, 206-212, 222-229, 235-242 of Seq. ID No. 114,

aa 28-38, 76-91, 102-109, 118-141, 146-153, 155-161, 165-179, 186-202, 215-221, 234-249, 262-269, 276-282, 289-302, 306-314, 321-326, 338-345, 360-369, 385-391 of Seq. ID No. 116,

aa 9-33, 56-62, 75-84, 99-105, 122-127, 163-180, 186-192, 206-228, 233-240, 254-262, 275-283, 289-296, 322-330, 348-355, 416-424, 426-438, 441-452, 484-491, 522-528, 541-549, 563-569, 578-584, 624-641, 527-544, of Seq. ID No. 142,

aa 37-42, 57-62, 121-135, 139-145, 183-190, 204-212, 220-227, 242-248, 278-288, 295-30, 304-309, 335-341, 396-404, 412-433, 443-449, 497-503, 505-513, 539-545, 552-558, 601-617, 629-649, 702-711, 736-745, 793-804, 814-829, 843-858, 864-885, 889-895, 905-913, 919-929, 937-943, 957-965, 970-986, 990-1030, 1038-1049, 1063-1072, 1080-1091, 1093-1116, 1126-1136, 1145-1157, 1163-1171, 1177-1183, 1189-1196, 1211-1218, 1225-1235, 1242-1256, 1261-1269, 624-684, of Seq. ID No. 151,

aa 8-23, 31-38, 42-49, 61-77, 83-90, 99-108, 110-119, 140-147, 149-155, 159-171, 180-185, 189-209, 228-234, 245-262, 264-275, 280-302, 304-330, 343-360, 391-409, 432-437, 454-463, 467-474, 478-485, 515-528, 532-539, 553-567, 569-581, 586-592, 605-612, 627-635, 639-656, 671-682, 700-714, 731-747, 754-770, 775-791, 797-834, 838-848, 872-891, 927-933, 935-942, 948-968, 976-986, 1000-1007, 1029-1037, 630-700, of Seq. ID No. 152,

aa 17-25, 27-55, 84-90, 95-101, 115-121, 55-101, of Seq. ID No. 154,

aa 13-28, 40-46, 69-75, 86-92, 114-120, 126-137, 155-172, 182-193, 199-206, 213-221, 232-238, 243-253, 270-276, 284-290, 22-100, of Seq. ID No. 155 and

aa 7-19, 46-57, 85-91, 110-117, 125-133, 140-149, 156-163, 198-204, 236-251, 269-275, 283-290, 318-323, 347-363, 9-42 and 158-174, of Seq. ID No. 158,

aa 7-14, 21-30, 34-50, 52-63, 65-72, 77-84, 109-124, 129-152, 158-163, 175-190, 193-216, 219-234 of Seq. ID. No. 168,

aa 5-24, 38-44, 100-106, 118-130, 144-154, 204-210, 218-223, 228-243, 257-264, 266-286, 292-299 of Seq. ID. No. 174,

aa 29-44, 74-83, 105-113, 119-125, 130-148, 155-175, 182-190, 198-211, 238-245 of Seq. ID. No. 176, and fragments comprising at least 6, preferably more than 8, especially more than 10 aa of said sequences. All these fragments individually and each independently form a preferred selected aspect of the present invention.

Especially suited helper epitopes may also be derived from these antigens. Especially preferred helper epitopes are peptides comprising fragments selected from the peptides mentioned in column “Putative antigenic surface areas” in Tables 4 and 5 and from the group of aa 6-40, 583-598, 620-646 and 871-896 of Seq. ID. No. 56, aa 24-53 of Seq. ID. No. 70, aa 240-260 of Seq. ID. No. 74, aa 1660-1682 and 1746-1790 of Seq. ID. No. 81, aa 1-29, 680-709, and 878-902 of Seq. ID. No. 83, aa 96-136 of Seq. ID. No. 89, aa 1-29, 226-269 and 275-326 of Seq. ID. No. 94, aa 23-47 and 107-156 of Seq. ID. No. 114 and aa 24-53 of Seq. ID. No. 142 and fragments thereof being T-cell epitopes.
According to another aspect, the present invention relates to a vaccine comprising such a hyperimmune serum-reactive antigen or a fragment thereof as identified above for Staphylococcus aureus and Staphylococcus epidermidis. Such a vaccine may comprise one or more antigens against S. aureus or S. epidermidis. Optionally, such S. aureus or S. epidermidis antigens may also be combined with antigens against other pathogens in a combination vaccine. Preferably this vaccine further comprises an immunostimulatory substance, preferably selected from the group comprising polycationic polymers, especially polycationic peptides, immunostimulatory deoxynucleotides (ODNs), neuroactive compounds, especially human growth hormone, alumn, Freund's complete or incomplete adjuvans or combinations thereof. Such a vaccine may also comprise the antigen displayed on a surface display protein platform on the surface of a genetically engineered microorganism such as E. coli. 
According to another aspect, the present invention relates to specific preparations comprising antibodies raised against at least one of the Staphylococcus aureus and Staphylococcus epidermidis antigens or Staphylococcus aureus and Staphylococcus epidermidis antigen fragments as defined above. These antibodies are preferably monoclonal antibodies.
Methods for producing such antibody preparations, polyclonal or monoclonal, are well available to the man skilled in the art and properly described in the prior art. A preferred method for producing such monoclonal antibody preparation is characterized by the following steps

    
    
        initiating an immune response in a non human animal by administering a Staphylococcus antigen or a fragment thereof, as defined above, to said animal,
        removing the spleen or spleen cells from said animal,
        producing hybridoma cells of said spleen or spleen cells,
        selecting and cloning hybridoma cells specific for said antigen and
        producing the antibody preparation by cultivation of said cloned hybridoma cells and optionally further purification steps.

Preferably, removing of the spleen or spleen cells is connected with killing said animal.

    
    


Monoclonal antibodies and fragments thereof can be chimerized or humanized (Graziano et al. 1995) to enable repeated administration. Alternatively human monoclonal antibodies and fragments thereof can be obtained from phage-display libraries (McGuinnes et al., 1996) or from transgenic animals (Bruggemann et al., 1996).
A preferred method for producing polyclonal antibody preparations to said Staphylococcus aureus or Staphylococcus epidermidis antigens identified with the present invention is characterized by the following steps

    
    
        initiating an immune response in a non human animal by administering a Staphylococcus antigen or a fragment thereof, as defined above, to said animal,
        removing an antibody containing body fluid from said animal,
        and
        producing the antibody preparation by subjecting said antibody containing body fluid to further purification steps.
    
    


These monoclonal or polyclonal antibody preparations may be used for the manufacture of a medicament for treating or preventing diseases due to staphylococcal infection. Moreover, they may be used for the diagnostic and imaging purposes.



The method is further described in the following examples and in the figures, but should not be restricted thereto.
FIG. 1 shows the pre-selection of sera based on anti-staphylococcal antibody titers measured by ELISA.
FIG. 2 shows the size distribution of DNA fragments in the LSA50/6 library in pMAL4.1.
FIG. 3 shows the MACS selection with biotinylated human serum. The LSA50/6 library in pMAL9.1 was screened with 10 μg biotinylated, human serum in the first (A) and with 1 μg in the second selection round (B). P. serum, patient serum; B. serum, infant serum. Number of cells selected after the 2nd and 3rd elution are shown for each selection round.
FIG. 4 shows the serum reactivity with specific clones isolated by bacterial surface display as analyzed by Western blot analysis with patient serum at a dilution of 1:5000.
FIG. 5 shows peptide ELISA with serum from patients and healthy individuals with an epitope identified by ribosome display.
FIG. 6 shows representative 2D Immunoblot of S. aureus surface proteins detected with human sera. 800 μg protein from S. aureus/COL grown on BHI were resolved by IEF (pI 4-7) and SDS-PAGE (9-16%), and subsequently transferred to PVDF membrane. After blocking, the membrane was incubated with sera IC35 (1:20,000). Binding of serum IgG was visualized by an anti-human IgG/HRPO conjugate and ECL development.
FIG. 7 demonstrates a representative 2D gel showing S. aureus surface proteins stained by Coomassie Blue. 1 mg protein from S. aureus/COL were resolved by IEF (pI 4-7) and SDS-PAGE (9-16%). Spots selected for sequencing after serological proteome analysis are marked.
FIGS. 8A and 8B show the structure of LPXTG (SEQ ID NO:641) cell wall proteins (SEQ ID NOS:604 through 638 639).
FIG. 9 shows the IgG response in uninfected (N, C) and infected (P) patients to LPXTGV (SEQ ID NO:640), a novel antigen and probable surface adhesin of S. aureus, discovered by both the inventive bacterial
FIG. 10 shows the surface staining of S. aureus with purified anti-LPXTGV (SEQ ID NO:640) IgGs.
FIG. 11 shows a 2D gel where S. aureus surface proteins are stained by Coomassie Blue (left). 1 mg protein from S. aureus/agr grown to early log phase was resolved by IEF (pI 6-11) and SDS-PAGE (9-16%). Spots selected for sequencing after serological proteome analysis are marked. Corresponding 2D-immunoblot (right). 800 μg protein from the same preparation was resolved in parallel by 2DE, and subsequently transferred to PVDF membrane. After blocking, the membrane was incubated with the P-pool (1:10,000). Binding of serum IgG was visualized by an anti-human IgG/HRPO conjugate and ECL development.



EXAMPLES
Discovery of Novel Staphyloccocus aureus Antigens
Example 1
Preparation of Antibodies from Human Serum
The antibodies produced against staphylococci by the human immune system and present in human sera are indicative of the in vivo expression of the antigenic proteins and their immunogenicity. These molecules are essential for the identification of individual antigens in the approach as the present invention which is based on the interaction of the specific anti-staphylococcal antibodies and the corresponding S. aureus peptides or proteins. To gain access to relevant antibody repertoires, human sera were collected from I. patients with acute S. aureus infections, such as bacteriaemia, sepsis, infections of intravascular and percutan catheters and devices, wound infections, and superficial and deep soft tissue infection. S. aureus was shown to be the causative agent by medical microbiological tests. II. A collection of serum samples from uninfected adults was also included in the present analysis, since staphylococcal infections are common, and antibodies are present as a consequence of natural immunization from previous encounters with Staphylococci from skin and soft tissue infections (furunculus, wound infection, periodontitits etc.).
The sera were characterized for S. aureus antibodies by a series of ELISA assays. Several styaphylococcal antigens have been used to prove that the titer measured was not a result of the sum of cross-reactive antibodies. For that purpose not only whole cell S. aureus (protein A deficient) extracts (grown under different conditions) or whole bacteria were used in the ELISA assays, but also individual cell wall components, such as lipoteichoic acid and peptidoglycan isolated from S. aureus. More importantly, a recombinant protein collection was established representing known staphylococcal cell surface proteins for the better characterization of the present human sera collections.
Recently it was reported that not only IgG, but also IgA serum antibodies can be recognized by the FcRIII receptors of PMNs and promote opsonization (Phillips-Quagliata et al., 2000; Shibuya et al., 2000). The primary role of IgA antibodies is neutralization, mainly at the mucosal surface. The level of serum IgA reflects the quality, quantity and specificity of the dimeric secretory IgA. For that reason the serum collection was not only analyzed for anti-staphylococcal IgG, but also for IgA levels. In the ELISA assays highly specific secondary reagents were used to detect antibodies from the high affinity types, such as IgG and IgA, and avoided IgM. Production of IgM antibodies occurs during the primary adaptive humoral response, and results in low affinity antibodies, while IgG and IgA antibodies had already undergone affinity maturation, and are more valuable in fighting or preventing disease
Experimental Procedures
Enzyme linked immune assay (ELISA). ELISA plates were coated with 2-10 μg/ml of the different antigens in coating buffer (sodium carbonate pH 9.2). Serial dilutions of sera (100-100.000) were made in TBS-BSA. Highly specific (cross-adsorbed) HRP (Horse Radish Peroxidase)-labeled anti-human IgG or anti-human IgA secondary antibodies (Southern Biotech) were used according to the manufacturers' recommendations ( ̃2.000×). Antigen-antibody complexes were quantified by measuring the conversion of the substrate (ABTS) to colored product based on OD405nm readings in an automated ELISA reader (Wallace Victor 1420). The titers were compared at given dilution where the dilution response was linear (Table 1). The  ̃100 sera were ranked based on the reactivity against multiple staphylococcal components, and the highest ones (above 90 percentile) were selected for further analysis in antigen identification. Importantly, the anti-staphylococcal antibodies from sera of clinically healthy individuals proved to be very stable, giving the same high ELISA titers against all the staphylococcal antigens measured after 3, 6 and 9 months (data not shown). In contrast, anti-S. aureus antibodies in patients decrease, then disappear after a couple of weeks following the infection (Coloque-Navarro et al, 1998). However, antibodies from patients are very important, since these are direct proof of the in vivo expression of the bacterial antigens tested in or ELISAs or identified as immunogenic during the screens according to the present invention.
This comprehensive approach followed during antibody characterization is unique, and led to unambiguous identification of anti-staphylococcal hyperimmune sera.
Purification of antibodies for genomic screening. Five sera from both the patient and the noninfected group were selected based on the overall anti-staphylococcal titers. Antibodies against E. coli proteins were removed by either incubating the heat inactivated sera with whole cell E. coli (DH5a, transformed with pHIE11, grown under the same condition as used for bacterial display) or with E. coli lysate affinity chromatography for ribosome display. Highly enriched preparations of IgG from the pooled, depleted sera were generated by protein G affinity chromatography, according to the manufacturer's instructions (UltraLink Immobilized Protein G, Pierce). IgA antibodies were purified also by affinity chromatography using biotin-labeled anti-human IgA (Southern Biotech) immobilized on Streptavidin-agarose (GIBCO BRL). The efficiency of depletion and purification was checked by SDS-PAGE, Western blotting, ELISA, and protein concentration measurements. For proteomics, the depletion the IgG and IgA preparation was not necessary, since the secondary reagent ensured the specificity.
Example 2
Generation of Highly Random, Frame-Selected, Small-Fragment, Genomic DNA Libraries of Staphylococcus aureus 
Experimental Procedures
Preparation of staphylococcal genomic DNA. This method was developed as a modification of two previously published protocols (Sohail, 1998, Betley et al., 1984) and originally specifically adapted for the methicillin resistant Staphylococcus aureus strain COL to obtain genomic DNA in high quality and large scale. 500 ml BHI (Brain Heart Infusion) medium supplemented with 5 μg/ml Tetracycline was inoculated with bacteria from a frozen stab and grown with aeration and shaking for 18 h at 37°. The culture was then harvested in two aliquots of 250 ml each, centrifuged with 1600×g for 15 min and the supernatant was removed. Bacterial pellets were carefully re-suspended in 26 ml of 0.1 mM Tris-HCl, pH 7.6 and centrifuged again with 1600×g for 15 min. Pellets were re-suspended in 20 ml of 1 mM Tris-HCl, pH 7.6, 0.1 mM EDTA and transferred into sterile 50 ml polypropylene tubes. 1 ml of 10 mg/ml heat treated RNase A and 200 U of RNase T1 were added to each tube and the solution mixed carefully. 250 μl of Lysostaphin (10 mg/ml stock, freshly prepared in ddH2O) was then added to the tubes, mixed thoroughly and incubated at 40° C. for 10 min in a shaking water bath under continuous agitation. After the addition of 1 ml 10% SDS, 40 μl of Proteinase K (25 mg/ml stock) and 100 μl of Pronase (10 mg/ml), tubes were again inverted several times and incubated at 40° C. for 5 min in a shaking water bath. 3.75 ml of 5 M NaCl and 2.5 ml of cetyl trimethyl-ammonium bromide solution (CTAB) (10% w/v, 4% w/v NaCl) were then added and tubes were further incubated at 65° C. in a shaking water bath for 10 min. Samples were cooled to room temperature and extracted with PhOH/CHCl3/IAA (25:24:1) and with CHCl3/IAA (24:1). Aqueous phases were carefully collected and transferred to new sterile 50-ml tubes. To each tube 1.5 ml of StratacleanTM Resin was added, mixed gently but thoroughly and incubated for one minute at room temperature. Samples were centrifuged and the upper layers containing the DNA were collected into clean 50 ml-tubes. DNA was precipitated at room temperature by adding 0.6× volume of Isopropanol, spooled from the solution with a sterile Pasteur pipette and transferred into tubes containing 80% ice cold ethanol. DNA was recovered by centrifuging the precipitates with 10-12.000×g, then dried on air and dissolved in ddH2O.
Preparation of small genomic DNA fragments. Genomic DNA fragments were mechanically sheared into fragments ranging in size between 150 and 300 bp using a cup-horn sonicator (Bandelin Sonoplus UV 2200 sonicator equipped with a BB5 cup horn, 10 sec. pulses at 100% power output) or into fragments of size between 50 and 70 bp by mild DNase I treatment (Novagen). It was observed that sonication yielded a much tighter fragment size distribution when breaking the DNA into fragments of the 150-300 bp size range. However, despite extensive exposure of the DNA to ultrasonic wave-induced hydromechanical shearing force, subsequent decrease in fragment size could not be efficiently and reproducibly achieved. Therefore, fragments of 50 to 70 bp in size were obtained by mild DNase I treatment using Novagen's shotgun cleavage kit. A 1:20 dilution of DNase I provided with the kit was pre-pared and the digestion was performed in the presence of MnCl2 in a 60 μl volume at 20° C. for 5 min to ensure double-stranded cleavage by the enzyme. Reactions were stopped with 2 μl of 0.5 M EDTA and the fragmentation efficiency was evaluated on a 2% TAE-agarose gel. This treatment resulted in total fragmentation of genomic DNA into near 50-70 bp fragments. Fragments were then blunt-ended twice using T4 DNA Polymerase in the presence of 100 μM each of dNTPs to ensure efficient flushing of the ends. Fragments were used immediately in ligation reactions or frozen at −20° C. for subsequent use.
Description of the vectors. The vector pMAL4.1 was constructed on a pEH1 backbone (Hashemzadeh-Bonehi et al., 1998) with the Kanamycin resistance gene. In addition it harbors a b-lactamase (bla) gene cloned into the multiple cloning site. The bla gene is pre-ceded by the leader peptide sequence of ompA to ensure efficient secretion across the cytoplasmic membrane. A Sma I restriction site serves for library insertion. The Sma I site is flanked by an upstream FseI site and a downstream NotI site which were used for recovery of the selected fragments. The three restriction sites are inserted after the ompA leader sequence in such a way that the bla gene is transcribed in the −1 reading frame resulting in a stop codon 15 bp after the NotI site. A +1 bp insertion restores the bla ORF so that b-lactamase protein is produced with a consequent gain of Ampicillin resistance.
The vector pMAL4.31 was constructed on a pASK-IBA backbone (Skerra, 1994) with the b-lactamase gene exchanged with the Kanamycin resistance gene. In addition it harbors a b-lactamase (bla) gene cloned into the multiple cloning site. The sequence encoding mature b-lactamase is preceded by the leader peptide sequence of ompA to allow efficient secretion across the cytoplasmic membrane. Furthermore a sequence encoding the first 12 amino acids (spacer sequence) of mature b-lactamase follows the ompA leader peptide sequence to avoid fusion of sequences immediately after the leader peptidase cleavage site, since e.g. clusters of positive charged amino acids in this region would decrease or abolish translocation across the cytoplasmic membrane (Kajava et al., 2000). A SmaI restriction site serves for library insertion. The SmaI site is flanked by an upstream FseI site and a down-stream NotI site which were used for recovery of the selected fragment. The three restriction sites are inserted after the sequence encoding the 12 amino acid spacer sequence in such a way that the bla gene is transcribed in the −1 reading frame resulting in a stop codon 15 bp after the NotI site. A +1 bp insertion restores the bla ORF so that b-lactamase protein is produced with a consequent gain of Ampicillin resistance.
The vector pMAL9.1 was constructed by cloning the lamB gene into the multiple cloning site of pEH1. Subsequently, a sequence was inserted in lamB after amino acid 154, containing the restriction sites FseI, SmaI and NotI. The reading frame for this insertion was chosen in a way that transfer of frame-selected DNA fragments excised by digestion with FseI and NotI from plasmids pMAL4.1 or pMAL4.31 to plasmid pMAL9.1 will yield a continuous reading frame of lamB and the respective insert.
The vector pHIE11 was constructed by cloning the fhuA gene into the multiple cloning site of pEH1. Thereafter, a sequence was inserted in fhuA after amino acid 405, containing the restriction site FseI, XbaI and NotI. The reading frame for this insertion was chosen in a way that transfer of frame-selected DNA fragments excised by digestion with FseI and NotI from plasmids pMAL4.1 or pMAL4.31 to plasmid pHIE11 will yield a continuous reading frame of fhuA and the respective insert.
Cloning and evaluation of the library for frame selection. Genomic S. aureus DNA fragments were ligated into the SmaI site of either the vector pMAL4.1 or pMAL4.31. Recombinant DNA was electroporated into DH10B electrocompetent E. coli cells (GIBCO BRL) and transformants plated on LB-agar supplemented with Kanamycin (50 μg/ml) and Ampicillin (50 μg/ml). Plates were incubated over night at 37° C. and colonies collected for large scale DNA extraction. A representative plate was stored and saved for collecting colonies for colony PCR analysis and large-scale sequencing. A simple colony PCR assay was used to initially determine the rough fragment size distribution as well as insertion efficiency. From sequencing data the precise fragment size was evaluated, junction intactness at the insertion site as well as the frame selection accuracy (3n+1 rule).
Cloning and evaluation of the library for bacterial surface display. Genomic DNA fragments were excised from the pMAL4.1 or pMAL4.31 vector, containing the S. aureus library with the restriction enzymes FseI and NotI. The entire population of fragments was then transferred into plasmids pMAL9.1 (LamB) or pHIE11 (FhuA) which have been digested with FseI and NotI. Using these two restriction enzymes, which recognise an 8 bp GC rich sequence, the reading frame that was selected in the pMAL4.1 or pMAL4.31 vector is maintained in each of the platform vectors. The plasmid library was then transformed into E. coli DH5a cells by electroporation. Cells were plated onto large LB-agar plates supplemented with 50 μg/ml Kanamycin and grown over night at 37° C. at a density yielding clearly visible single colonies. Cells were then scraped off the surface of these plates, washed with fresh LB medium and stored in aliquots for library screening at −80° C.
Results
Libraries for frame selection. Two libraries (LSA50/6 and LSA250/1) were generated in the pMAL4.1 vector with sizes of approximately 50 and 250 bp, respectively. For both libraries a total number of clones after frame selection of 1-2×106 was received using approximately 1 μg of pMAL4.1 plasmid DNA and 50 ng of fragmented genomic S. aureus DNA. To assess the randomness of the LSA50/6 library, 672 randomly chosen clones were sequenced. The bioinformatic analysis showed that of these clones none was present more than once. Furthermore, it was shown that 90% of the clones fell in the size range of 19 to 70 bp with an average size of 25 bp (FIG. 2). All 672 sequences followed the 3n+1 rule, showing that all clones were properly frame selected.
Bacterial surface display libraries. The display of peptides on the surface of E. coli required the transfer of the inserts from the LSA50/6 library from the frame selection vector pMAL4.1 to the display plasmids pMAL9.1 (LamB) or pHIE11 (FhuA). Genomic DNA fragments were excised by FseI and NotI restriction and ligation of 5 ng inserts with 0.1 μg plasmid DNA resulted in 2-5×106 clones. The clones were scraped off the LB plates and frozen without further amplification.
Example 3
Identification of Highly Immunogenic Peptide Sequences from S. aureus Using Bacterial Surface Displayed Genomic Libraries and Human Serum
Experimental Procedures
MACS screening. Approximately 2.5×108 cells from a given library were grown in 5 ml LB-medium supplemented with 50 μg/ml Kanamycin for 2 h at 37° C. Expression was induced by the addition of 1 mm IPTG for 30 min. Cells were washed twice with fresh LB medium and approximately 2×107 cells re-suspended in 100 μl LB medium and transferred to an Eppendorf tube.
10 μg of biotinylated, human serum was added to the cells and the suspension incubated over night at 4° C. with gentle shaking. 900 μl of LB medium was added, the suspension mixed and subsequently centrifuged for 10 min at 6000 rpm at 4° C. Cells were washed once with 1 ml LB and then re-suspended in 100 μl LB medium. 10 μl of MACS microbeads coupled to streptavidin (Miltenyi Biotech, Germany) were added and the incubation continued for 20 min at 4° C. Thereafter 900 μl of LB medium was added and the MACS microbead cell suspension was loaded onto the equilibrated MS column (Miltenyi Biotech, Germany) which was fixed to the magnet. (The MS columns were equilibrated by washing once with 1 ml 70% EtOH and twice with 2 ml LB medium.)
The column was then washed three times with 3 ml LB medium. The elution was performed by removing the magnet and washing with 2 ml LB medium. After washing the column with 3 ml LB medium, the 2 ml eluate was loaded a second time on the same column and the washing and elution process repeated. The loading, washing and elution process was performed a third time, resulting in a final eluate of 2 ml.
A second round of screening was performed as follows. The cells from the final eluate were collected by centrifugation and re-suspended in 1 ml LB medium supplemented with 50 μg/ml Kanamycin. The culture was incubated at 37° C. for 90 min and then induced with 1 mM IPTG for 30 min. Cells were subsequently collected, washed once with 1 ml LB medium and suspended in 10 μl LB medium. Since the volume was reduced, 1 μg of human, biotinylated serum was added and the suspension incubated over night at 4° C. with gentle shaking. All further steps were exactly the same as in the first selection round. Cells selected after two rounds of selection were plated onto LB-agar plates supplemented with 50 μg/ml Kanamycin and grown over night at 37° C.
Evaluation of selected clones by sequencing and Western blot analysis. Selected clones were grown over night at 37° C. in 3 ml LB medium supplemented with 50 μg/ml Kanamycin to prepare plasmid DNA using standard procedures. Sequencing was performed at MWG (Germany) or in a collaboration with TIGR (U.S.A.).
For Western blot analysis approximately 10 to 20 μg of total cellular protein was separated by 10% SDS-PAGE and blotted onto HybondC membrane (Amersham Pharmacia Biotech, England). The LamB or FhuA fusion proteins were detected using human serum as the primary antibody at a dilution of 1:5000 and anti human IgG antibodies coupled to HRP at a dilution of 1:5000 as secondary antibodies. Detection was performed using the ECL detection kit (Amersham Pharmacia Biotech, England). Alternatively, rabbit anti FhuA or mouse anti LamB antibodies were used as primary antibodies in combination with the respective secondary antibodies coupled to HRP for the detection of the fusion proteins.
Results
Screening of bacterial surface display libraries by magnetic activated cell sorting (MACS) using biotinylated human serum. The libraries LSA50/6 in pMAL9.1 and LSA250/1 in pHIE11 were screened with a pool of biotinylated, human patient sera (see Example 1) Preparation of antibodies from human serum). The selection procedure was performed as described under Experimental procedures. As a control, pooled human sera from infants that have most likely not been infected with S. aureus was used. Under the described conditions between 10 and 50 fold more cells with the patient compared to the infant serum were routinely selected (FIG. 3). To evaluate the performance of the screen, approximately 100 selected clones were picked randomly and subjected to Western blot analysis with the same pooled patient serum. This analysis revealed that 30 to 50% of the selected clones showed reactivity with antibodies present in patient serum whereas the control strain expressing LamB or FhuA without a S. aureus specific insert did not react with the same serum. Colony PCR analysis showed that all selected clones contained an insert in the expected size range.
Subsequent sequencing of a larger number of randomly picked clones (500 to 800 per screen) led to the identification of the gene and the corresponding peptide or protein sequence that was specifically recognized by the human patient serum used for screening. The frequency with which a specific clone is selected reflects at least in part the abundance and/or affinity of the specific antibodies in the serum used for selection and recognizing the epitope presented by this clone. In that regard it is striking that some clones (ORF2264, ORF1951, ORF0222, lipase and IsaA) were picked up to 90 times, indicating their highly immunogenic property. All clones that are presented in Table 2 have been verified by Western blot analysis using whole cellular extracts from single clones to show the indicated reactivity with the pool of human serum used in the screen.
It is further worth noticing that most of the genes identified by the bacterial surface display screen encode proteins that are either attached to the surface of S. aureus and/or are secreted. This is in accordance with the expected role of surface attached or secreted proteins in virulence of S. aureus. 
Assessment of reactivity of highly immunogenic peptide sequences with different human sera. 10 to 30 different human patient sera were subsequently used to evaluate the presence of antibodies against the selected immunogenic peptide sequences that have been discovered in the screen according to the present invention. To eliminate possible cross-reactivity with proteins expressed by E. coli, all sera were pre-adsorbed with a total cellular lysate of E. coli DHa cells expressing FhuA protein.
This analysis is summarized in Table 2 and as an example shown in FIG. 4 and is indicative of the validity of the present screen. It further shows that already short selected epitopes can give rise to the production of antibodies in a large number of patients (ORF1618, ORF1632, IsaA, Empbp, Protein A). Those peptide sequences that are not recognized by a larger set of patient sera may still be part of an highly immunogenic protein, but the recombinant protein itself may be tested for that purpose for each single case.
Example 4
Identification of Highly Immunogenic Peptide Sequences from Genomic Fragments from S. aureus Using Ribosome Display and Human Serum
Experimental Procedures
Ribosome display screening: 2.4 ng of the genomic library from S. aureus LSA 250/1 in pMAL4.1 (described above) was PCR amplified with oligos ICC277 and ICC202 in order to be used for ribosome display. Oligos ICC277 (CGAATAATACGACTCACTATAGGGAGACCACAACGGTTTCCCACTAGTAATAATTT TGTTTAACTTTAAGAAGGAGATATATCCATGCAGACCTTGGCCGGCCTCCC—SEQ ID NO:600) and ICC202 (GGCCCACCCGTGAAGGTGAGCCGGCGTAAGATGCTTTTCTGTGACTGG—SEQ ID NO:601) hybridize 5′ and 3′ of the Fse I-Not I insertion site of plasmid pMAL4.1, respectively. ICC277 introduces a T7 phage RNA polymerase promoter, a palindromic sequence resulting in a stem-loop structure on the RNA level, a ribosome binding site (RBS) and the translation start of gene 10 of the T7 phage including the ATG start codon. Oligo ICC202 hybridizes at nucleotide position 668 of the β-lactamase open reading frame and also introduces a stem-loop structure at the 3′ end of the resulting RNA. PCR was performed with the High fidelity PCR kit (Roche Diagnostic) for 25 cycles at 50° C. hybridization temperature and otherwise standard conditions.
The resulting PCR library was used in 5 consecutive rounds of selection and amplification by ribosome display similar as described previously (Hanes et al., 1997) but with modifications as described below.
One round of ribosome display contained the following steps: In vitro transcription of 2 μg PCR product with the RiboMax kit (Promega) resulted in ca. 50 μg RNA. In vitro translation was performed for 9 minutes at 37° C. in 22 μl volume with 4.4 μl Premix Z (250 mM TRIS-acetate pH 7.5, 1.75 mM of each amino acid, 10 mM ATP, 2.5 mM GTP, 5 mM cAMP, 150 mM acetylphosphate, 2.5 mg/ml E. coli tRNA, 0.1 mg/ml folinic acid. 7.5% PEG 8000, 200 mM potassium glutamate, 13.8 mM Mg(Ac)2, 8 μl S30 extract (x mg/ml) and about 2 μg in vitro transcribed RNA from the pool. S30 extract was prepared as described (Chen et al., 1983). Next, the sample was transferred to an ice-cold tube containing 35.2 μl 10% milk-WBT (TRIS-acetate pH 7.5, 150 mM NaCl, 50 mM Mg(Ac)2, 0.1% Tween-20, 10% milk powder) and 52.8 μl WBTH (as before plus 2.5 mg/ml heparin). Subsequently, immuno precipitation was performed by addition of 10 μg purified IgGs, incubation for 90 minutes on ice, followed by addition of 30 μl MAGmol Protein G beads (Miltenyi Biotec, 90 minutes on ice). The sample was applied to a pre-equilibrated μ column (Miltenyi Biotec) and washed 5 times with ice-cold WBT buffer. Next 20 ηl EB20 elution buffer (50 mM TRIS-acetate, 150 mM NaCl, 20 mM EDTA, 50 μg/ml S. cerevisiae RNA) was applied to the column, incubated for 5 minutes at 4° C. Elution was completed by adding 2×50 μl EB20. The mRNA from the elution sample was purified with the High pure RNA isolation kit (Roche Diagnostics). Subsequent reverse transcription was performed with Superscript II reverse transcriptase kit (Roche Diagnostics) according to the instruction of the manufacturer with 60 pmol oligo ICC202 for 1 hour at 50° C. in 50 μl volume. 5 μl of this mix was used for the following PCR reaction with primers ICC202 and ICC277 as described above.
Three rounds of ribosome display were performed and the resulting selected PCR pool subsequently cloned into plasmid pHIE11 (described above) by cleavage with restriction endonucleases NotI and FseI.
Evaluation of selected clones by sequencing and peptide-ELISA analysis: Selected clones were grown over night at 37° C. in 3 ml LB medium supplemented with 50 μg/ml Kanamycin to prepare plasmid DNA using standard procedures. Sequencing was performed at MWG (Germany) or at the Institute of Genomic Research (TIGR; Rockville, Md., U.S.A.). Peptides corresponding to the inserts were synthesized and coated in 10 mM NaHCO3 pH 9.3 at a concentration of 10 μg/ml (50 μl) onto 96-well microtiter plates (Nunc). After blocking with 1% BSA in PBS at 37° C., 1:200 and 1:1000 dilutions of the indicated sera were diluted in 1% BSA/PBS and applied to the wells. After washing with PBS/0.1% Tween-20, biotin-labeled anti-human IgG secondary antibodies (SBA) were added and these were detected by subsequent adding horseradish-peroxidase-coupled streptavidin according to standard procedures.
Results
The 250-bp genomic library (L5A250/1) as described above was used for screening. Purified IgGs from uninfected adults but with high titer against S. aureus as described above were used for selection of antigenic peptides.
Three rounds of ribosome display selection and amplification were performed according to Experimental procedures; finished by cloning and sequencing the resulting PCR pool.
Sequence analyses of a large number of randomly picked clones (700) led to the identification of the gene and the corresponding peptide or protein sequence that was specifically recognized by the high titer serum used for screening. The frequency with which a specific clone was selected reflects at least in part the abundance and/or affinity of the specific antibodies in the serum used for selection and recognizing the epitope presented by this clone. Remarkably, some clones (ORFs) were picked up to 50 times, indicating their highly immunogenic property. Table 2 shows the ORF name, the Seq. ID No. and the number of times it was identified by the inventive screen.
For a number of immuno-selected ORFs peptides corresponding to, the identified immunogenic region were synthesized and tested in peptide-ELISA for their reactivity towards the sera pool they were identified with and also a number of additional sera from patients who suffered from an infection by S. aureus. The two examples in the graphs in FIG. 5 show the values of peptides from aureolysin and Pls. They are not only hyperimmune reactive against the high titer sera pool but also towards a number of individual patient's sera. All synthesized peptides corresponding to selected immunogenic regions showed reactivity towards the high titer sera pool and Table 2 summarizes the number of times the peptides were reactive towards individual patients sera, similar as described above.
In addition, it is striking that for those ORFs that were also identified by bacterial surface display described above), very often the actual immunogenic region within the ORF was identical or overlapping with the one identified by ribosome display. This comparison can be seen in Table 2.
Example 5
Identification of Highly Immunogenic Antigens from S. aureus Using Serological Proteome Analysis
Experimental Procedures
Surface protein preparations from S. aureus containing highly immunogenic antigens. S. aureus-strains COL (Shafer and Iandolo, 1979) and agr− (Recsei et al., 1986) were stored as glycerol stocks at −80° C. or on BHI (DIFCO) plates at 4° C. Single clones were used for inoculation of overnight cultures in either BHI (“standard conditions”) or RPMI 1640 (GibcoBRL), last one depleted from iron (“stress conditions”) by treating o/n with iminodiacetic acid (Sigma). Fresh medium was inoculated 1:100 the next day and bacteria were grown to O.D.600 between 0.3 and 0.7. Bacteria were harvested by centrifugation and washed with ice-cold PBS. Surface proteins were prepared by lysostaphin treatment under isotonic conditions (Lim et al. 1998). Briefly  ̃3×109 bacteria (according to O.D.600=1 are about 5×107-bacteria) were re-suspended in 1 ml digestion buffer containing 35% raffinose (Aldrich Chemical Company), protease inhibitors (Roche) and 5 units lysostaphin (Sigma). After incubation at 37° C. for 30 min, protoplasts were carefully sedimented by low-speed centrifugation. This treatment releases surface proteins covalently linked to the pentaglycine bridge of the peptidoglycan cell wall to the supernatant (in Crossley, 1997). Cell surface proteins were either precipitated with methanol/chlorophorm (Wessel, 1984) or concentrated in centrifugal filter-tubes (Millipore). Protein samples were frozen and stored at −80° C. or dissolved in sample buffer and used for isoelectric focusing (IEF) immediately (Pasquali et al. 1997).
Serological proteome analysis of surface protein preparations from S. aureus. Samples were obtained from a) S. aureus/agr grown under “stress conditions”, b) S. aureus/COL grown under “standard conditions” and c) S. aureus/COL “stress conditions”. Loading onto 17 cm-strips containing immobilized pH gradients (pH 4-7, BioRad) was done using the “in-gel-reswelling procedure” (Pasquali et al., 1997). The gels for blotting were loaded with 100-800 μg protein, the preparative gels with 400-1,000 μg protein. Isoelectric focusing and SDS-PAGE (9-16% gradient gels) were performed as described (Pasquali et al., 1997). For Western blotting, proteins were transferred onto PVDF-membranes (BioRad) by semi-dry blotting. Transfer-efficiency was checked by amido-black staining. After blocking (PBS/0.1% Tween 20/10% dry milk, 4° C. for 16 h), blots were incubated for two hours with serum (1:2,500-1:100,000 in blocking solution, see Table 3). After washing, specific binding of serum IgG was visualized with a goat-anti-human-IgG/peroxidase conjugate (1:25,000, Southern Biotech) as secondary antibody and development with a chemiluminescence substrate (ECLTM, Amersham). A representative result is shown in FIG. 6. Membranes were stripped by treatment with 2% β-ME/Laemmli buffer for 30 min at 50-65° C., immediately re-probed with a different serum, and developed as described above. This procedure was repeated up to five times. Signals showing up with patient and/or healthy donor control sera but not with the infant pool, were matched to the Coomassie (BioRad) stained preparative gels (example shown in FIG. 7). The results of these serological proteome analyses of surface protein preparations from S. aureus are summarized in Table 3.
Sequencing of protein spots by peptide-fingerprint MALDI-TOF-MS and tandem MS/MS. Gel pieces were washed alternately three times with 10 μl digestion buffer (10 mM NH4HCO3/CAN, 1:1). Afterwards the gel pieces were shrunken with 10 μl ACN and reswollen with 2 μl protease solution (0.05 μg/μl trypsin, Promega, Madison, USA). Digestion was performed for 10-12 h at 37° C. For MALDI-TOF-MS peptides were extracted from the gel pieces with 10 μl digestion buffer. The supernatant was concentrated with ZipTipTM (Millipore, Bedford, USA), the peptides were eluted onto the MALDI target with 0.5 μl extraction buffer (0.1% TFA/CAN, 1:1) and 0.5 μl matrix solution (HCCA in ACN/0.1% TFA, 1:1) was added. MALDI-TOF-MS was done using a REFLEX III (Bruker Daltonik, Bremen, Germany) equipped with a SCOUT384 ion source. The acceleration voltage was set to 25 kV, and the reflection voltage to 28.7 kV. The mass range was set from 700 Da to 4000 Da. Data acquisition was done on a SUN Ultra using XACQ software, version 4.0. Post-analysis data processing was done using XMASS software, version 4.02 (Bruker Daltonik, Bremen, Germany). The results are summarized in tables 3 and 4.
Example 6
Characterisation of Highly Immunogenic Proteins from S. aureus 
The antigens identified by the different screening methods with the IgG and IgA preparations form pre-selected sera are further characterized, by the following ways: 1. The proteins are purified, most preferably as recombinant proteins expressed in E. coli or in a Gram+ expression system or in an in vitro translation system, and evaluated for antigenicity by a series of human sera. The proteins are modified based on bioinformatic analysis: N-terminal sequences representing the signal peptide are removed, C-terminal regions downstream of the cell wall anchor are also removed, and extra amino acids as tags are introduced for the ease of purification (such as Strep-tagII, His-tag, etc.) A large number of sera is then used in ELISA assays to assess the fraction of human sera containing specific antibodies against the given protein (see FIG. 9 as an example). One of the selected antigens is an 895 aa long protein, what was called LPXTGV (SEQ ID NO:640) (see Tables 2 and 4), since it contains the Gram+ cell wall anchor sequence LPXTG (SEQ ID NO:641). This signature has been shown to serve as cleavage site for sortase, a trans-peptidase which covalently links LPXTG (SEQ ID NO:641) motif containing proteins to the peptidoglycan cell wall. LPXTGV (SEQ ID NO:640) is also equipped with a typical signal peptide (FIG. 8). ELISA data using this protein as a Strep-tagged recombinant protein demonstrate that this protein is highly immunogenic (high titers relative to other recombinant proteins) in a high percentage of sera (FIG. 9). Importantly, patients with acute S. aureus infection produce significantly more of these anti-LPXTGV (SEQ ID NO:640) antibodies, than healthy normals, suggesting that the protein is expressed during in vivo infection. The overall ELISA titers of the individual antigenic proteins are compared, and the ones inducing the highest antibody levels (highly immunogenic) in most individuals (protein is expressed by most strains in vivo) are favored. Since the antigen specificity and quality (class, subtype, functional, nonfunctional) of the antibodies against S. aureus produced in individual patients can vary depending on the site of infection, accompanying chronic diseases (e.g. diabetes) and chronic conditions (e.g. intravascular device), and the individual's immune response, special attention was paid to the differences detected among the different patient groups, since medical records belonging to each sera were available. In addition, each patient serum is accompanied by the pathogenic strain isolated from the patient at the time of serum sampling.
Specific antibodies are purified for functional characterization. The purity and the integrity of the recombinant proteins are checked (e.g. detecting the N-terminal Strep-tag in Western blot analysis in comparison to silver staining in SDS-PAGE). The antigens are immobilized through the tags to create an affinity matrix, and used for the purification of specific antibodies from highly reactive sera. Using as an example strep-tagged LPXTGV (SEQ ID NO:640) as the capture antigen, 20 μgof antibody from 125 mg of IgG were purified. Based on the ELISA data a pure preparation was received, not having e.g. anti-LTA and anti-peptidoglycan (both dominant with unfractionated IgG) activity. The antibodies are then used to test cell surface localization by FACS and fluorescent microscopy (FIG. 10).
3. Gene Occurrence in Clinical Isolates
An ideal vaccine antigen would be an antigen that is present in all, or the vast majority of, strains of the target organism to which the vaccine is directed. In order to establish whether the genes encoding the identified Staphylococcus aureus antigens occur ubiquitously in S. aureus strains, PCR was performed on a series of independent S. aureus isolates with primers specific for the gene of interest. S. aureus isolates were obtained from patients with various S. aureus infections. In addition several nasal isolates from healthy carriers and several lab strains were also collected and analyzed. The strains were typed according to restriction fragment length polymorphism (RFLP) of the spa and coa genes (Goh et al. 1992, Frénay et al., 1994, vanden Bergh et al. 1999). From these results 30 different strains were identified—24 patient isolates, 3 nasal isolates and 3 lab strains. To establish the gene distribution of selected antigens, the genomic DNA of these 30 strains was subjected to PCR with gene specific primers that flank the selected epitope (ORF1361: Seq. ID No. 187 and 188; ORF2268: Seq. ID No. 193 and 194; ORF1951: Seq. ID No. 195 and 196; ORF1632: Seq. ID No. 181 and 182; ORF0766: Seq. ID No. 183 and 184; ORF0576: Seq. ID No. 185 and 186; ORF0222: Seq. ID No. 189 and 190; ORF0360: Seq. ID No. 191 and 192). The PCR products were analyzed by gel electrophoresis to identify a product of the correct predicted size. ORFs 1361, 2268, 1951, 1632, 0766 and 0222 are present in 100% of strains tested and ORF0576 in 97%. However ORF0360 occurred in only 71% of the strains. Thus ORFs 1361, 2268, 1951, 1632, 0766, 0576 and 0222 each have the required ubiquitous presence among S. aureus isolates.
These antigens (or antigenic fragments thereof, especially the fragments identified) are especially preferred for use in a vaccination project against S. aureus. 
4. Identification of Highly Promiscuous HLA-class II Helper Epitopes Within the ORFs of Selected Antigens
The ORFs corresponding to the antigens identified on the basis of recognition by antibodies in human sera, most likely also contain linear T-cell epitopes. Especially the surprising finding in the course of the invention that even healthy uninfected, non-colonized individuals show extremely high antibody titers (>100,000 for some antigens, see Example 5) which are stable for >1 year (see Example 1), suggests the existence of T-cell dependent memory most probably mediated by CD4+ helper-T-cells. The molecular definition of the corresponding HLA class II helper-epitopes is useful for the design of synthetic anti-staphylococcal vaccines, which can induce immunological memory. In this scenario the helper-epitopes derived from the staphylococcal antigens provide “cognate help” to the B-cell response against these antigens or fragments thereof. Moreover it is possible to use these helper-epitopes to induce memory to T-independent antigens like for instance carbohydrates (conjugate vaccines). On the other hand, intracellular occurring staphylococci can be eliminated by CD8+ cytotoxic T-cells, which recognize HLA class I restricted epitopes.
T-cell epitopes can be predicted by various public domain algorithms: http://bimas.dcrt.nih.gov/molbio/hla_bind/ (Parker et al. 1994), http://134.2.96.221/scripts/MHCServer.dll/home.htm (Rammensee at al. 1999), http://mypage.ihost.com/usinet.hamme76/ (Sturniolo et al. 1999). The latter prediction algorithm offers the possibility to identify promiscuous helper-epitopes, i.e. peptides that bind to several HLA class II molecules. In order to identify highly promiscuous helper-epitopes within staphylococcal antigens the ORFs corresponding to Seq ID 64 (IsaA), Seq ID 114 (POV2), Seq ID 89 (ORF0222), Seq ID 70 (LPXTGIV), Seq ID 56 (LPXTGV), Seq ID 142 (LPXTGVI), Seq ID 81 (ORF3200), Seq ID 74 (ORF1951), Seq ID 94 (Empbp), Seq ID 83 (autolysin) and Seq ID 58 (ORF2498) were analyzed using the TEPITOPE package http://mypage.ihost.com/usinet.hamme76/ (Sturniolo et al. 1999). The analysis was done for 25 prevalent DR-alleles and peptides were selected if they were predicted to be a) strong binders (1% threshold) for at least 10/25 alleles or b) intermediate (3% threshold) binders for at least 17/25 alleles.
The following peptides containing one or several promiscuous helper-epitopes were selected (and are claimed):
















Seq ID 56:
pos. 6-40, 583-598, 620-646, 871-896



Seq ID 58:
no peptide fulfills selection criteria



Seq ID 64:
no peptide fulfills selection criteria



Seq ID 70:
pos. 24-53



Seq ID 74:
pos. 240-260



Seq ID 81:
pos. 1660-1682, 1746-1790



Seq ID 83:
pos. 1-29, 680-709, 878-902



Seq ID 89:
pos. 96-136



Seq ID 94:
pos. 1-29, 226-269, 275-326



Seq ID 114:
pos. 23-47, 107-156



Seq ID 142:
pos. 24-53










The corresponding peptides or fragments thereof (for instance overlapping 15-mers) can be synthesized and tested for their ability to bind to various HLA molecules in vitro. Their immunogenicity can be tested by assessing the peptide (antigen)-driven proliferation (BrdU or 3H-thymidine incorporation) or the secretion of cytokines (ELIspot, intracellular cytokine staining) of T-cells in vitro (Mayer et al. 1996, Schmittel et al. 2000, Sester et al. 2000). In this regard it will be interesting to determine quantitative and qualitative differences in the T-cell response to the staphylococcal antigens or the selected promiscuous peptides or fragments thereof in populations of patients with different staphylococcal infections, or colonization versus healthy individuals neither recently infected nor colonized. Moreover, a correlation between the antibody titers and the quantity and quality of the T-cell response observed in these populations is expected. Alternatively, immunogenicity of the predicted peptides can be tested in HLA-transgenic mice (Sonderstrup et al. 1999).
Similar approaches can be taken for the identification of HLA class I restricted epitopes within staphylococcal antigens.
Synthetic Peptides Representing One or More Promiscuous T Helper Epitopes from S. aureus 
Partially overlapping peptides spanning the indicated regions of Seq ID 56 (LPXTGV), Seq ID 70 (LPXTGIV), Seq ID 74 (ORF1hom1), Seq ID 81 (EM_BP), Seq ID 83 (Autolysin), Seq ID 89 (ORF1hom2), Seq ID 94 (EMPBP), Seq ID 114 (POV2) and Seq ID 142 (LPXTGVI) were synthesized. Sequences of the individual peptides are given in Table 5. All peptides were synthesized using Fmoc chemistry, HPLC purified and analyzed by mass spectrometry. Lyophilized peptides were dissolved in DMSO and stored at −20° C. at a concentration of 5-10 mM.
Binding of Synthetic Peptides Representing Promiscuous T Helper Epitopes to HLA Molecules In Vitro
Binding of peptides to HLA molecules on the surface of antigen-presenting cells is a prerequisite for activation of T cells. Binding was assessed in vitro by two independent biochemical assays using recombinant soluble versions of HLA class II molecules. One assay measures the concentration dependent competitive replacement of a labeled reference peptide by the test peptides. The second assay is based on the formation of SDS-stable complexes upon binding of high- and intermediate affinity ligands. A summary of the results obtained by the two assays is given in Table 5.
Soluble HLA molecules (DRA1*0101/DRB1*0101 and DRA1*0101/DRB1*0401) were expressed in SC-2 cells and purified as described in Aichinger et al., 1997. For the competition assay (Hammer et al. 1995) HLA molecules were applied between 50 and 200 ng/well. For DRB1*0101 biotinilated indicator peptide HA (PKYVKQNTLKLAT—SEQ ID NO:602, Valli et al. 1993) was used at 0.008 μM. For DRB1*0401 biotinilated indicator peptide UD4 (YPKFVKQNTLKAA—SEQ ID NO:603, Valli et al. 1993) was used between 0.03 and 0.06 μM. Molecules, indicator and test peptides were incubated overnight at 37° C., pH 7. HLA:peptide complexes obtained after incubation with serial dilutions of test and reference peptides (the known high-affinity binders HA and UD4 were used as positive control) were captured in ELISA plates coated with antibody L243, which is known to recognize a conformational epitope formed only by correctly associated heterodimers. Incorporated biotin was measured by standard colorimetric detection using a streptavidin-alkaline phosphatase conjugate (Dako) with NBT/BCIP tablets (Sigma) as substrate and automated OD reading on a Victor reader (Wallac).
T Cell Response Against Promiscuous T Helper Epitopes Assessed by IFNg ELIspot Assay
Upon antigenic stimulation T cells start to proliferate and to secrete cytokines such as interferon gamma (IFNg). Human T cells specifically recognizing epitopes within S. aureus antigens were detected by IFNg-ELIspot (Schmittel et al. 2000). PBMCs from healthy individuals with a strong anti-S. aureus IgG response were isolated from 50-100 ml of venous blood by ficoll density gradient centrifugation and used after freezing and thawing. Cells were seeded at 200,000/well in 96-well plates. Peptides were added as mixtures corresponding to individual antigens, in both cases at 10 μg/ml each. Concanavalin A (Amersham) and PPD (tuberculin purified protein derivate, Statens Serum Institute) served as assay positive controls, assay medium without any peptide as negative control. After overnight incubation in Multi Screen 96-well filtration plates (Millipore) coated with the anti-human IFNg monoclonal antibody B140 (Bender Med Systems) the ELIspot was developed using the biotinylated anti-human IFNg monoclonal antibody B308-BT2 (Bender Med Systems), Streptavidin-alkaline phosphatase (DAKO) and BCIP/NBT alkaline phosphatase substrate (SIGMA). Spots were counted using an automatic plate reader (Bioreader 2000, BIO-SYS). Spots counted in wells with cells stimulated with assay medium only (negative control, generally below 10 spots/100.000 cells) were regarded as background and subtracted from spot numbers counted in wells with peptides.







TABLE 5







Promiscuous T helper epitopes contained in S. aureus antigens









Amino acid sequences within S. aureus antigens

IFNg


containing highly promiscuous T helper epitopes
binding1)
ELIspot2)










Seq ID 56 (LPXTGV): pos. 6-40










p6-28
>PKLRSFYSIRKSTLGVASVIVST//
+



p24-40
                  >VIVSTLFLISQHQAQA//
−
44; 80; 8;





95; 112


 







Seq ID 56 (LPXTGV): pos. 620-646










p620-646
>FPYIPDKAVYNAIVKVVVANIGYEGQ//
+



 







Seq ID 56 (LPXTGV): pos. 871-896










p871-896
>QSWWGLYALLGMLALFIPKFRKESK//
−



 







Seq ID 70 (LPXTGIV): pos. 24-53










p24-53
>YSIRKFTVGTASILIGSLMYLGTQQEAEA//
nd
34; 14; 0;





57; 16


 







Seq ID 74 (ORF1hom1): pos. 240-260










p240-260
>MNYGYGPGVVTSRTISASQA//
+
47; 50; 0;





85; 92


 







Seq ID 81 (EM_BP): pos. 1660-1682










p1660-1682
>NEIVLETIRDINNAHTLQQVEA//
nd
2; 14; 5;





77; 26


 







Seq ID 81 (EM_BP): pos. 1746-1790










p1746-1773
>LHMRHFSNNFGNVIKNAIGVVGISGLLA//
nd



p1753-1779
       >NNFGNVIKNAIGVVGISGLLASFWFFI//
nd


p1777-1789
                              >FFIAKRRRKEDEE/
nd


 







Seq ID 83 (Autolysin) pos. 1-29










p1-29:
>MAKKFNYKLPSMVALTLVGSAVTAHQVQA//
nd
6; 35; 7;





60; 49


 







Seq ID 83 (Autolysin) pos. 878-902










p878-902:
>NGLSMVPWGTKNQVILTGNNIAQG/
nd



 







Seq ID 89 (ORF1hom2): pos. 96-136










p96-121
>GESLNIIASRYQVSVDQLMAANNLRG//
−
0; 35; 0;


p117-136
                     >NNLRGYLIMPNQTLQIPNG//
−
29; 104


 







Seq ID 94 (EMPBP): pos. 1-29










p4-29:
>KLLVLTMSTLFATQIMNSNHAKASV//
+



 







Seq ID 94 (EMPBP): pos. 226-269










p226-251
>IKINHFCVVPQINSFKVIPPYGHNS//
−
26; 28; 16;


p254-270
>MHVPSFQNNTTATHQN//
+
43; 97


 







Seq ID 94 (EMPBP): pos. 275-326










p275-299
>YDYKYFYSYKVVKGVKKYFSFSQS//
+



p284-305
        >YKVVKGVKKYFSFSQSNGYKIG//
+


p306-326
>PSLNIKNVNYQYAVPSYSPT//
+


 







Seq ID 114 (POV2): pos. 23-47










p23-47
>AGGIFYNQTNQQLLVLCDGMGGHK//
−
49; 20; 4;





77; 25


 







Seq ID 114 (POV2): pos. 107-156










p107-124
>ALVFEKSVVIANVGDSRA/
−



p126-146
>RAYVINSRQIEQITSDHSFVN//
nd


p142-158
                 >SFVNHLVLTGQITPEE//
nd


 







Seq ID 142 (LPXTGVI): pos. 1-42










p6-30
>KEFKSFYSIRKSSLGVASVAISTL//
++
0; 41; 20;


p18-42
           >SSLGVASVAISTLLLLMSNGEAQA//
nd
88; 109


 







Seq ID 142 (LPXTGVI): pos. 209-244










p209-233
>IKLVSYDTVKDYAYIRFSVSNGTKA//
+



p218-244
         >KDYAYIRFSVSNGTKAVKIVSSTHFNN//
+


 







Seq ID 142 (LPXTGVI): pos. 395-428










p395-418
>FMVEGQRVRTISTYAINNTRCTIF//
−



p416-428
                     >TIFRYVEGSLYE//
−


 







Seq ID 142 (LPXTGVI): pos. 623-647










p623-647
>MTLPLMALLALSSIVAFVLPRKRKN//
−





1)binding to soluble DRA1*0101/DRB1*0401 molecules was determined using a competition assay (+, ++: binding, −: no competition up to 200 μM test peptide; nd: not done)


2)results from 5 healthy individuals with strong anti-S. aureus IgG response. Data are represented as spots/200.000 cells (background values are subtracted






5. Antigens may be Injected into Mice—and the Antibodies Against these Proteins can be Measured.

6. Protective Capacity of the Antibodies Induced by the Antigens Through Vaccination can be Assessed in Animal Models.

Both 5. and 6. are methods well available to the skilled man in the art.
Example 7
Applications
A) An effective vaccine offers great potential for patients facing elective surgery in general, and those receiving endovascular devices, in particular. Patients suffering from chronic diseases with decreased immune responses or undergoing continuous ambulatory peritoneal dialysis are likely to benefit from a vaccine with S. aureus by immunogenic serum-reactive antigens according to the present invention. Identification of the relevant antigens will help to generate effective passive immunization (humanized monoclonal antibody therapy), which can replace human immunoglobulin administration with all its dangerous side-effects. Therefore an effective vaccine offers great potential for patients facing elective surgery in general, and those receiving endovascular devices, in particular.
S. aureus can cause many different diseases.

    1. Sepsis, bacteriaemia
    2. Haemodialysed patients—bacteriemia, sepsis
    3. Peritoneal dialyses patients—peritonitis
    4. Patients with endovascular devices (heart surgery, etc)—endocarditis, bacteriemia, sepsis
    5. Orthopedic patients with prosthetic devices septic arthritis
    6. Preventive vaccination of general population


B) Passive and active vaccination, both with special attention to T-cells with the latter one: It is an aim to induce a strong T helper response during vaccination to achieve efficient humoral response and also immunological memory. Up till now, there is no direct evidence that T-cells play an important role in clearing S. aureus infections, however, it was not adequately addressed, so far. An effective humoral response against proteinaceous antigens must involve T help, and is essential for developing memory. Naïve CD4+ cells can differentiated into Th1 or Th2 cells. Since, innate immunological responses (cytokines) will influence this decision, the involvement of T-cells might be different during an acute, serious infection relative to immunization of healthy individuals with subunit vaccines, not containing components which impair the immune response during the natural course of the infection. The consequences of inducing Th1 or Th2 responses are profound. Th1 cells lead to cell-mediated immunity, whereas Th2 cells provide humoral immunity.
C) Preventive and Therapeutic Vaccines
Preventive: active vaccination/passive immunization of people in high risk groups, before infection
Therapeutic: passive vaccination of the already sick.
Active Vaccination to Remove Nasal Carriage
Specific Example for an Application
Elimination of MRSA Carriage and Prevention of Colonization of the Medical Staff
Carriage rates of S. aureus in the nares of people outside of the hospitals varies from 10 to 40%. Hospital patients and personnel have higher carriage rates. The rates are especially high in patients undergoing hemodialysis and in diabetics, drug addicts and patients with a variety of dermatologic conditions. Patients at highest risk for MRSA infection are those in large tertiary-care hospitals, particularly the elderly and immunocompromised, those in intensive care units, burn patients, those with surgical wounds, and patients with intravenous catheters.
The ELISA data strongly suggest that there is a pronounced IgA response to S. aureus, which is not obvious or known from the literature. Since the predominant mucosal immune response is the production of IgA with neutralizing activity, it is clear that the staphylococcal epitopes and antigens identified with the highly pure IgA preparations lead to an efficient mucosal vaccine.

    
    
        Clear indication: Everybody's threat in the departments where they perform operation (esp. orthopedics, traumatology, gen. surgery)
        Well-defined population for vaccination (doctors and nurses)
        Health care workers identified as intranasal carriers of an epidemic strain of S. aureus are currently treated with mupirocin and rifampicin until they eliminate the bacteria. Sometimes it is not effective, and takes time.
        Available animal model: There are mice models for intranasal carriage.
    
    









TABLE 1





ELISA titers of sera from non-infected individuals against multiple staphylococcal proteins.
























Sera ID#
BHI lysate
LTA
PG
ClfA
D1 + D3
FnBPA
sdrE
sdrC
EBP





 1


 2
2 . . .
2 . . .

8 . . .
4 . . .






 3
7 . . .


3 . . .


1 . . .
1 . . .



 4
1******
1******
1 . . .
6 . . .
2 . . .
2 . . .
3 . . .
6 . . .
2 . . .


 5


 6







4 . . .



 7

6 . . .




7 . . .

7 . . .


 8






8 . . .

8 . . .


 9
4, 5, 6 . . .
4 . . .
5 . . .

5 . . .

6 . . .
3 . . .
1 . . .


10











11




6 . . .






12











13






5 . . .
2 . . .



14


15
3 . . .
5 . . .
2, 3 . . .


5 . . .





16











17


18


6, 7 . . .
1 . . .




3 . . .


19











20


21



2 . . .







22


23
4, 5, 6 . . .


5 . . .
3 . . .
6 . . .
2 . . .
7 . . .
4 . . .


24






4 . . .

6 . . .


25


5 . . .


26
8 . . .










27







8 . . .



28


29











30


31




1 . . .
1 . . .





32


4 . . .


33


8 . . .
4 . . .

4 . . .

5 . . .


34




7, 8 . . .






35
4, 5, 6 . . .
8 . . .
2, 3 . . .





5 . . .


36

3 . . .


37



7 . . .
7, 8 . . .






38



8 . . .







39


40

7 . . .
6, 7 . . .


3 . . .




















Sera ID#
enolase
LP309
LP342
coagul
Fib
SrtA
ClfB
Map-w







 1



 2


6 . . .

3 . . .



 3

3 . . .
2 . . .
2 . . .
2 . . .
3 . . .
7 . . .
4 . . .



 4
6, 7 . . .
8 . . .
3 . . .


4 . . .
1 . . .
3 . . .



 5



 6

5 . . .



 7
5 . . .



4 . . .


7 . . .



 8




5 . . .
7 . . .
8, 9 . . .



 9
3, 4 . . .



1 . . .

5, 6 . . .



10






5, 6 . . .



11





6 . . .



12



4, 5 . . .



13




8 . . .



14



15

6 . . .
7 . . .


8 . . .

8, 9 . . .



16







6 . . .



17



18






4 . . .



19







1 . . .



20



21







2 . . .



22



23
6, 7 . . .
7 . . .

6, 7 . . .

2 . . .
2 . . .



24







8, 9 . . .



25



26




7 . . .



27

4 . . .
4, 5 . . .
4, 5 . . .

5 . . .



28



29
1 . . .



30



31



1 . . .



32



33



34
2 . . .
2 . . .
1 . . .
6, 7 . . .
6 . . .
1 . . .



35

1******




3 . . .
4 . . .



36



37



3 . . .



38
3, 4 . . .



39



40


4, 5 . . .



8, 9 . . .







Anti-staphylococcal antibody levels were measured individually by standard ELISA with total lysate prepared from S. aureus grown in BHI medium (BHI), lipoteichoic acid (LTA), peptidoglycan (PG), 13 recombinant proteins, representing cell surface and secreted proteins, such as clumping factor A and B (ClfA, ClfB), Fibronectin-binding protein (FnBPA), SD-repeat proteins (sdrC, sdrE), MHC Class II analogous protein (map-w), Elastin-binding protein (EBP), enolase (reported to be cell surface located and immunogenic), iron transport lipoproteins (LP309, LP342), sortase (srtA), coagulase (coa), extracellular fibrinogen-binding protein (fib). Two short synthetic peptides representing 2 of the five immunodominant D repeat domains from FnBPA was also included (D1 + D3) as antigens. The individual sera were ranked based on the IgG titer, and obtained a score from 1-9. Score 1 labels the highest titer serum and score 8 or 9 labels the sera which were 8th or 9th among all the sera tested for the given antigen. It resulted in the analyses of the top 20 percentile of sera (8-9/40). The five “best sera” meaning the most hyper reactive in terms of anti-staphylococcal antibodies were selected based on the number of scores 1-8.



******means that the antibody reactivity against the particular antigen was exceptionally high (>2x ELISA units relative to the 2nd most reactive serum).













TABLE 2a





Immunogenic proteins identified by bacterial surface


and ribosome display: s. aureus


















S. aureus
Old




antigenic
ORF
Putative function



protein
number
(by homology)
predicted immunogenic aa**





SaA0003
ORF2963P
repC
5-20, 37-44, 52-59, 87-94, 116-132


SaA0003
ORF2967P
repC
7-19, 46-57, 85-91, 110-117, 125-133,





140-149, 156-163, 198-204,





236-251, 269-275, 283-290, 318-323,





347-363


0093
ORF1879
SdrC
23-51, 75-80, 90-99, 101-107, 151-157,





173-180, 186-205, 215-226,





239-263, 269-274, 284-304, 317-323,





329-336, 340-347, 360-366,





372-379, 391-397, 399-406, 413-425,





430-436, 444-455, 499-505,





520-529, 553-568, 586-592, 600-617,





631-639, 664-678, 695-701,





891-903, 906-912, 926-940


0095
ORF1881
SdrE
25-45, 72-77, 147-155, 198-211,





217-223, 232-238, 246-261, 266-278,





281-294, 299-304, 332-340,





353-360, 367-380, 384-396, 404-409,





418-429, 434-440, 448-460,





465-476, 493-509, 517-523, 531-540,





543-555, 561-566, 576-582,





584-591, 603-617, 633-643, 647-652,





668-674, 677-683, 696-704,





716-728, 744-752, 755-761, 789-796,





809-815, 826-840, 854-862,





887-903, 918-924, 1110-1116,





1125-1131, 1145-1159


0123
ORF1909
unknown
9-28, 43-48, 56-75, 109-126, 128-141,





143-162, 164-195, 197-216,





234-242, 244-251


0160
ORF1941
unknown
4-10, 20-42, 50-86, 88-98, 102-171,





176-182, 189-221, 223-244, 246-268,





276-284, 296-329


0222
ORF1988
homology with
4-9, 13-24, 26-34, 37-43, 45-51,




ORF1
59-73, 90-96, 99-113, 160-173,





178-184, 218-228, 233-238, 255-262


0308
ORF2077
Complement, unknown
13-27, 42-63, 107-191, 198-215,





218-225, 233-250


0317
ORF2088
preprotein translocase
16-29, 64-77, 87-93, 95-101, 127-143,




seca subunit
150-161, 204-221, 225-230,





236-249, 263-269, 281-309, 311-325,





337-343, 411-418, 421-432,





435-448, 461-467, 474-480, 483-489,





508-516, 542-550, 580-589,





602-611, 630-636, 658-672, 688-705,





717-723, 738-746, 775-786,





800-805, 812-821, 828-834


0337
ORF2110
Hypothetical protein
26-53, 95-123, 164-176, 189-199


0358
ORF2132
Clumping factor A
8-35, 41-48, 59-66, 87-93, 139-144,





156-163, 198-209, 215-229, 236-244,





246-273, 276-283, 285-326,





328-342, 349-355, 362-370, 372-384,





396-402, 405-415, 423-428,





432-452, 458-465, 471-477, 484-494,





502-515, 540-547, 554-559,





869-875, 893-898, 907-924


0360
ORF2135
extracellular
7-13, 15-23, 26-33, 68-81, 84-90,



Empbp
matrix and plasma
106-117, 129-137, 140-159, 165-172,




binding protein
177-230, 234-240, 258-278,





295-319


0453
ORF2227
coma operon
17-25, 27-55, 84-90, 95-101, 115-121




protein 2



0569
ORF1640
V8 protease
5-32, 66-72, 87-98, 104-112, 116-124,





128-137, 162-168, 174-183,





248-254, 261-266, 289-303, 312-331


0576
ORF1633
autolysin, adhesion
4-19, 57-70, 79-88, 126-132, 144-159,



Autolysin

161-167, 180-198, 200-212,





233-240, 248-255, 276-286, 298-304,





309-323, 332-346, 357-366,





374-391, 394-406, 450-456, 466-473,





479-487, 498-505, 507-519,





521-530, 532-540, 555-565, 571-581,





600-611, 619-625, 634-642,





650-656, 658-665, 676-682, 690-699,





724-733, 740-771, 774-784,





791-797, 808-815, 821-828, 832-838,





876-881, 893-906, 922-929,





938-943, 948-953, 969-976, 1002-1008,





1015-1035, 1056-1069, 1105-1116,





1124-1135, 1144-1151, 1173-1181,





1186-1191, 1206-1215, 1225-1230,





1235-1242


0657
ORF unknown
LPXTGVI protein
9-33, 56-62, 75-84, 99-105, 122-127,





163-180, 186-192, 206-228,





233-240, 254-262, 275-283, 289-296,





322-330, 348-355, 416-424,





426-438, 441-452, 484-491, 541-549,





563-569, 578-584, 624-641


0749
ORF1462
Carbamoyl-phosphate
8-23, 31-38, 42-49, 61-77, 83-90,




synthase
99-108, 110-119, 140-147, 149-155,





159-171, 180-185, 189-209, 228-234,





245-262, 264-275, 280-302,





304-330, 343-360, 391-409, 432-437,





454-463, 467-474, 478-485,





515-528, 532-539, 553-567, 569-581,





586-592, 605-612, 627-635,





639-656, 671-682, 700-714, 731-747,





754-770, 775-791, 797-834,





838-848, 872-891, 927-933, 935-942,





948-968, 976-986, 1000-1007,





1029-1037


944
ORF1414
Yfix
6-33, 40-46, 51-59, 61-77, 84-104,





112-118, 124-187, 194-248, 252-296,





308-325, 327-361, 367-393,





396-437, 452-479, 484-520, 535-545,





558-574, 582-614, 627-633,





656-663, 671-678, 698-704, 713-722,





725-742, 744-755, 770-784,





786-800, 816-822, 827-837


1050
ORF1307
unknown
49-72, 76-83, 95-105, 135-146,





148-164, 183-205


1209
ORF3006
hemN homolog
12-36, 43-50, 58-65, 73-78, 80-87,





108-139, 147-153, 159-172, 190-203,





211-216, 224-232, 234-246,





256-261, 273-279, 286-293, 299-306,





340-346, 354-366


1344
ORF0212
NifS protein
8-16, 22-35, 49-58, 70-77, 101-121,




homolog
123-132, 147-161, 163-192, 203-209,





216-234, 238-249, 268-274,





280-293, 298-318, 328-333, 339-345,





355-361, 372-381


1356
ORF0197
Hypothetical protease
28-55, 82-100, 105-111, 125-131,





137-143


1361
ORF0190
LPXTGV protein
5-39, 111-117, 125-132, 134-141,





167-191, 196-202, 214-232, 236-241,





244-249, 292-297, 319-328,





336-341, 365-380, 385-391, 407-416,





420-429, 435-441, 452-461,





477-488, 491-498, 518-532, 545-556,





569-576, 581-587, 595-602,





604-609, 617-640, 643-651, 702-715,





723-731, 786-793, 805-811,





826-839, 874-889


1371
ORF0175
YtpT, conserved
37-42, 57-62, 121-135, 139-145,




hypothetical protein
183-190, 204-212, 220-227, 242-248,





278-288, 295-30, 304-309,





335-341, 396-404, 412-433, 443-449,





497-503, 505-513, 539-545,





552-558, 601-617, 629-649, 702-711,





736-745, 793-804, 814-829,





843-858, 864-885, 889-895, 905-913,





919-929, 937-943, 957-965,





970-986, 990-1030, 1038-1049,





1063-1072, 1080-1091, 1093-1116,





1126-1136, 1145-1157, 1163-1171,





1177-1183, 1189-1196, 1211-1218,





1225-1235, 1242-1256, 1261-1269


1491
ORF0053
Cmp binding factor
12-29, 34-40, 63-71, 101-110, 114-122,




1 homolog
130-138, 140-195, 197-209,





215-229, 239-253, 255-274


1616
ORF1180
leukocidin F homolog
16-24, 32-39, 43-49, 64-71, 93-99,





126-141, 144-156, 210-218, 226-233,





265-273, 276-284


1618
ORF1178
LukM homolog
5-24, 88-94, 102-113, 132-143,





163-173, 216-224, 254-269, 273-278,





305-313, 321-327, 334-341


1632
ORF1163
SdrH homolog
7-35, 54-59, 247-261, 263-272,





302-320, 330-339, 368-374, 382-411


1763
ORF1024
unknown
5-32, 35-48, 55-76


1845
ORF0942
Hyaluronate lyase
10-26, 31-44, 60-66, 99-104, 146-153,





163-169, 197-205, 216-223,





226-238, 241-258, 271-280, 295-315,





346-351, 371-385, 396-407,





440-446, 452-457, 460-466, 492-510,





537-543, 546-551, 565-582,





590-595, 635-650, 672-678, 686-701,





705-712, 714-721, 725-731,





762-768, 800-805


1951
ORF0831
homology with
5-22, 42-50, 74-81, 139-145, 167-178,




ORF1
220-230, 246-253, 255-264


1955
ORF0826
homology with
4-9, 15-26, 65-76, 108-115, 119-128,




ORF1
144-153


2031
ORF0749
unknown
10-26, 31-43, 46-58, 61-66, 69-79,





85-92, 100-115, 120-126, 128-135,





149-155, 167-173, 178-187, 189-196,





202-222, 225-231, 233-240,





245-251, 257-263, 271-292, 314-322,





325-334, 339-345


2086
ORF0691
IgG binding
6-20, 53-63, 83-90, 135-146, 195-208,



Sbi
protein
244-259, 263-314, 319-327,





337-349, 353-362, 365-374, 380-390,





397-405, 407-415


2180
ORF0594
LPXTGIV protein
11-20, 26-47, 69-75, 84-92, 102-109,





119-136, 139-147, 160-170,





178-185, 190-196, 208-215, 225-233,





245-250, 265-272, 277-284,





300-306, 346-357, 373-379, 384-390,





429-435, 471-481, 502-507,





536-561, 663-688, 791-816, 905-910,





919-933, 977-985, 1001-1010,





1052-1057, 1070-1077, 1082-1087,





1094-1112


2184
ORF0590
FnbpB
5-12, 18-37, 104-124, 139-145,





154-166, 175-181, 185-190, 193-199,





203-209, 235-244, 268-274,





278-292, 299-307, 309-320, 356-364,





375-384, 390-404, 430-440,





450-461, 488-495, 505-511, 527-535,





551-556, 567-573, 587-593,





599-609, 624-631, 651-656, 665-671,





714-726, 754-766, 799-804,





818-825, 827-833, 841-847, 855-861,





876-893, 895-903, 927-940


2186
ORF0588
Fnbp
8-29, 96-105, 114-121, 123-129,





141-147, 151-165, 171-183, 198-206,





222-232, 253-265, 267-277,





294-300, 302-312, 332-338, 362-368,





377-383, 396-402, 410-416,





451-459, 473-489, 497-503, 537-543,





549-559, 581-600, 623-629,





643-649, 655-666, 680-687, 694-700,





707-712, 721-727, 770-782,





810-822, 874-881, 883-889, 897-903,





911-917, 925-931, 933-939,





946-963, 965-973, 997-1010


2224
ORF0551
unknown
49-56, 62-68, 83-89, 92-98, 109-115,





124-131, 142-159, 161-167,





169-175, 177-188, 196-224, 230-243,





246-252


2254
ORF0519
Conserved hypothetical
14-22, 32-40, 52-58, 61-77, 81-93,




protein
111-117, 124-138, 151-190, 193-214,





224-244, 253-277, 287-295,





307-324, 326-332, 348-355, 357-362,





384-394, 397-434, 437-460,





489-496, 503-510, 516-522, 528-539,





541-547, 552-558, 563-573,





589-595, 602-624, 626-632, 651-667,





673-689, 694-706, 712-739,





756-790


2264
ORF0509
ORF1; homology
5-31, 47-55, 99-104, 133-139, 156-172,




with putative secreted
214-224, 240-247




antigen





precursor from S. epidermidis



2268
ORF0503
IsaA, possibly adhesion/
7-19, 26-45, 60-68, 94-100, 111-119,




aggregation
126-137, 143-148, 169-181,





217-228


2344
ORF0426
Clumping factor B
4-10, 17-45, 120-127, 135-141,





168-180, 187-208, 216-224, 244-254,





256-264, 290-312, 322-330,





356-366, 374-384, 391-414, 421-428,





430-437, 442-449, 455-461,





464-479, 483-492, 501-512, 548-555,





862-868, 871-876, 891-904


2351
ORF0418
aureolysin
10-29, 46-56, 63-74, 83-105, 107-114,





138-145, 170-184, 186-193,





216-221, 242-248, 277-289, 303-311,





346-360, 379-389, 422-428,





446-453, 459-469, 479-489, 496-501


2359
ORF0409
ISSP, immunogenic
4-29, 92-99, 119-130, 228-236,




secreted
264-269, 271-280, 311-317, 321-331,




protein precursor,
341-353, 357-363, 366-372,




putative
377-384, 390-396, 409-415, 440-448,





458-470, 504-520, 544-563,





568-581, 584-592, 594-603, 610-616


2378
ORF0398
SrpA
18-23, 42-55, 69-77, 85-98, 129-136,





182-188, 214-220, 229-235,





242-248, 251-258, 281-292, 309-316,





333-343, 348-354, 361-367,





393-407, 441-447, 481-488, 493-505,





510-515, 517-527, 530-535,





540-549, 564-583, 593-599, 608-621,





636-645, 656-670, 674-687,





697-708, 726-734, 755-760, 765-772,





785-792, 798-815, 819-824,





826-838, 846-852, 889-904, 907-913,





932-939, 956-964, 982-1000,





1008-1015, 1017-1024, 1028-1034,





1059-1065, 1078-1084, 1122-1129,





1134-1143, 1180-1186, 1188-1194,





1205-1215, 1224-1230, 1276-1283,





1333-1339, 1377-1382, 1415-1421,





1448-1459, 1467-1472, 1537-1545,





1556-1566, 1647-1654, 1666-1675,





1683-1689, 1722-1737, 1740-1754,





1756-1762, 1764-1773, 1775-1783,





1800-1809, 1811-1819, 1839-1851,





1859-1866, 1876-1882, 1930-1939,





1947-1954, 1978-1985, 1999-2007,





2015-2029, 2080-2086, 2094-2100,





2112-2118, 2196-2205, 2232-2243


2466
ORF0302
YycH protein
16-38, 71-77, 87-94, 105-112, 124-144,





158-164, 169-177, 180-186,





194-204, 221-228, 236-245, 250-267,





336-343, 363-378, 385-394,





406-412, 423-440, 443-449


2470
ORF0299
Conserved hypothetical
4-9, 17-41, 50-56, 63-69, 82-87,




protein
108-115, 145-151, 207-214, 244-249,





284-290, 308-316, 323-338,





348-358, 361-378, 410-419, 445-451,





512-522, 527-533, 540-546,





553-558, 561-575, 601-608, 632-644,





656-667, 701-713, 727-733,





766-780


2498
ORF0267
Conserved hypothetical
33-43, 45-51, 57-63, 65-72, 80-96,




protein
99-110, 123-129, 161-171, 173-179,





185-191, 193-200, 208-224, 227-246,





252-258, 294-308, 321-329,





344-352, 691-707


2548
ORF2711
IgG binding
4-16, 24-57, 65-73, 85-91, 95-102,




protein A
125-132, 146-152, 156-163, 184-190,





204-210, 214-221, 242-252,





262-268, 272-279, 300-311, 320-337,





433-440, 472-480, 505-523


2577
ORF2683
Hypothetical protein
4-21, 49-56, 65-74, 95-112, 202-208,





214-235


2642
ORF2614
unknown
34-58, 63-69, 74-86, 92-101, 130-138,





142-150, 158-191, 199-207,





210-221, 234-249, 252-271


2664
ORF2593
Conserved hypothetical
7-37, 56-71, 74-150, 155-162, 183-203,




protein
211-222, 224-234, 242-272


2670
ORF2588
Hexose transporter
18-28, 36-49, 56-62, 67-84, 86-95,





102-153, 180-195, 198-218, 254-280,





284-296, 301-325, 327-348,





353-390, 397-402, 407-414, 431-455


2680
ORF2577
Coagulase
4-18, 25-31, 35-40, 53-69, 89-102,





147-154, 159-165, 185-202, 215-223,





284-289, 315-322, 350-363,





384-392, 447-453, 473-479, 517-523,





544-550, 572-577, 598-604,





617-623


2740
ORF2515
Hypothetical protein
5-44, 47-55, 62-68, 70-78, 93-100,





128-151, 166-171, 176-308


2746
ORF2507
homology with
5-12, 15-20, 43-49, 94-106, 110-116,




ORF1
119-128, 153-163, 175-180,





185-191, 198-209, 244-252, 254-264,





266-273, 280-288, 290-297


2797
ORF2470
unknown
10-27, 37-56, 64-99, 106-119, 121-136,





139-145, 148-178, 190-216,





225-249, 251-276, 292-297, 312-321,





332-399, 403-458


2798
ORF2469
Lipase (geh)
12-35, 93-99, 166-179, 217-227,





239-248, 269-276, 288-294, 296-320,





322-327, 334-339, 344-356,





362-371, 375-384, 404-411, 433-438,





443-448, 455-464, 480-486,





497-503, 516-525, 535-541, 561-570,





579-585, 603-622, 633-641


2815
ORF2451
Conserved hypothetical
5-32, 34-49




protein


2914
ORF2351
metC
39-44, 46-80, 92-98, 105-113, 118-123,





133-165, 176-208, 226-238,





240-255, 279-285, 298-330, 338-345,





350-357, 365-372, 397-402,





409-415, 465-473, 488-515, 517-535,





542-550, 554-590, 593-601,





603-620, 627-653, 660-665, 674-687,





698-718, 726-739


2960
ORF2298
putative Exotoxin
13-36, 40-49, 111-118, 134-140,





159-164, 173-183, 208-220, 232-241,





245-254, 262-271, 280-286,





295-301, 303-310, 319-324, 332-339


2963
ORF2295
putative Exotoxin
13-28, 40-46, 69-75, 86-92, 114-120,





126-137, 155-172, 182-193,





199-206, 213-221, 232-238, 243-253,





270-276, 284-290


3002
ORF1704
homology with
4-21, 28-40, 45-52, 59-71, 92-107,




ORF1
123-137, 159-174, 190-202, 220-229,





232-241, 282-296, 302-308,





312-331


3200
ORF1331
putative extracellular
6-15, 22-32, 58-73, 82-88, 97-109,




matrix binding
120-131, 134-140, 151-163, 179-185,




protein
219-230, 242-255, 271-277,





288-293, 305-319, 345-356, 368-381,





397-406, 408-420, 427-437,





448-454, 473-482, 498-505, 529-535,





550-563, 573-580, 582-590,





600-605, 618-627, 677-685, 718-725,





729-735, 744-759, 773-784,





789-794, 820-837, 902-908, 916-921,





929-935, 949-955, 1001-1008,





1026-1032, 1074-1083, 1088-1094,





1108-1117, 1137-1142, 1159-1177,





1183-1194, 1214-1220, 1236-1252,





1261-1269, 1289-1294, 1311-1329,





1336-1341, 1406-1413, 1419-1432,





1437-1457, 1464-1503, 1519-1525,





1531-1537, 1539-1557, 1560-1567,





1611-1618, 1620-1629, 1697-1704,





1712-1719, 1726-1736, 1781-1786,





1797-1817, 1848-1854, 1879-1890,





1919-1925, 1946-1953, 1974-1979

















No. of selected
Location of





S. aureus
clones per
identified
Serum reactivity



antigenic
ORF and
immunogenic
with relevant region
Seq ID no:



protein
screen
region
(positive/total)
(DNA + Prot)







SaA0003
C: 3
aa 112-189
C: GSBYM94(112-189):
171, 172






26/30



SaA0003
C: 18
aa 9-42
C: GSBYI53(9-42):
150, 158





aa 158-174
1/1



0093
A: 1, D: 5,
aa 98-182
A: GSBXL70(98-182):
34, 86




C: 1, F: 6,
aa 684-764
9/30




G: 2
aa 836-870
D: n.d.






C: GSBYH73(815-870):






3/16



0095
C: 12, E: 2
aa 147-192
C: GSBYH31(147-192):
145, 153






2/14






E: GSBZA27(144-162):






23/41



0123
B: 3, E: 7,
aa 168-181
B: GSBXF80(168-181):
35, 87




G: 1

5/27






E: GSBZC17(168-181):






25/41



0160
A: 1
aa 112-188
A: GSBXO07(112-188):
36, 88






5/30



0222
A: 52,
aa 45-105
A: GSBXM63(65-95):
37, 89




C: 18*,
aa 103-166
1/1




H: 19
aa 66-153
A: GSBXM82(103-166):






14/29






A: GSBXK44-






bmd3(65-153):






47/51



0308
A: 6, B: 2,
complement
A: GSBXK03(bp473-367):
38, 90




C: 47,
bp 474-367
28/69




E: 35

B: GSBXD29(bp465-431):






10/27



0317
A: 1
aa 1-19
A: GSBXP37(1-19):
39, 91






6/29



0337
D: 12
aa 8-48
D: n.d.
40, 92



0358
C: 1, D: 2,
aa 706-809
D: n.d.
41, 93




E: 1



0360
A: 46,
aa 22-56
A: GSBXK24(23-55):
42, 94




B: 21,
aa 23-99
1/1




C: 11, E: 2,
aa 97-115
B: GSBXB43(39-54):




F: 18, G: 7,
aa 233-250
58/71




H: 12
aa 245-265
A: GSBXK02-






bmd1(22-99): 59/59






B: GSBXD82-






bdb19(97-115): 1/1






F: SALAL03(233-250):






15/41



0453
C: 3
aa 55-101
C: GSBYG07(55-101):
146, 154






1/1



0569
A: 1, F: 1
aa 174-249
A: GSBXS51(174-249):
32, 84






11/30



0576
A: 21,
aa 6-66
A: GSBXN93(6-66):
31, 83




B: 46,
aa 65-124
5/16




C: 55, E: 5,
aa 579-592
C: GSBYH05(45-144):




F: 85,
aa 590-604
7/8




H: 19

A: GSBXK66-






bmd18(65-124):






16/30






B: GSBXB89(108-123):






1/1






B: GSBXB02(590-603):






39/71






F: SALAM15(579-592):






25/41



0657
A: 2, B: 27,
aa 527-544
B: GSBXE07-
1, 142




F: 15

bdb1(527-542):






11/71






F: SALAX70(526-544):






11/41



0749
C: 2
aa 630-700
C: GSBYK17(630-700):
144, 152






5/9



944
D: 4
aa 483-511
D: n.d.
30, 82



1050
A: 1, H: 45
aa 57-128
A: GSBXM26(57-128):
28, 80






7/30



1209
B: 7, F: 8
aa 167-181
B: GSBXB76(167-179):
54, 106






25/71






F: SALBC54(169-183):






18/41



1344
A: 11
aa 34-94
A: GSBXK59-
5, 141






bmd21(34-94): 6/29



1356
D: 12
aa 1-49
D: n.d.
4, 57



1361
A: 1, B: 23,
aa 37-49
B: GSBXF81(37-49):
3, 56




E: 3, F: 31
aa 63-77
1/1





aa 274-334
B: GSBXD45-






bdb4(62-77): 12/70






A: GSBXL77(274-334):






5/30






F: SALAP81(62-77):






10/41



1371
C: 3, E: 2,
aa 624-684
C: GSBYG95(624-684):
143, 151




G: 1
aa 891-905
7/22






E: GSBZB45(891-905):






10/41



1491
A: 7, C: 2,
aa 39-94
A: GSBXM13(39-94):
2, 55




E: 7, F: 4

10/29






F: SALAY30(39-53):






4/41



1616
A: 10
aa 158-220
A: GSBXK06(158-220):
27, 79






8/29



1618
A: 13, B: 3
aa 31-61
A: GSBXK60(31-61):
26, 78




C: 36, E: 4,
aa 58-74
20/29




F: 12, G: 2,

B: GSBXB48(58-74):




H: 10

49/71






F: SALAY41(58-74):






30/41



1632
B: 6, E: 11,
aa 105-119
B: GSBXG53(168-186):
25, 77




F: 34
aa 126-143
39/71





aa 168-186
F: SALAP07(105-119):






11/41



1763
C: 3
complement
C: GSBYI30(98aa): 1/1
24, 75





bp 237-170



1845
D: 5, F: 2
aa208-224
D: n.d.
23, 75





aa 672-727



1951
A: 223,
aa 137-237
B: GSBXC07(180-190):
22, 74




B: 56,
aa 250-267
1/1




C: 167,

A: GSBXK29(177-195):




E: 43,

15/29




F: 100,

B: GSBXD43(250-267):




G: 13,

10/71




H: 102

F: SALAM13(178-191):






20/41



1955
A: 1, B: 3,
aa 38-52
A: GSBXR10(66-114):
21, 73




E: 1, F: 8
aa 66-114
5/30






F: SALAM67(37-52):






16/41



2031
B: 2, F: 2
aa 59-74
B: GSBXC01(59-71):
20, 72






11/26



2086
A: 1, B: 8,
aa 208-287
A: GSBXS55(208-287):
19, 71




E: 24, F: 9,
aa 261-276
38/46




G: 137
aa 286-314
B: GSBXB34(299-314)::






11/71






F: SALAX32(261-276):






21/41



2180
A: 3, C: 3,
aa 493-587
A: GSBXS61(493-555):
18, 70




E: 6, F: 2,
aa 633-715
1/1




H: 6
aa 704-760#
A: GSBXL64(496-585):





aa 760-832
1/1





(aa 832-887)#
A: GSBXS92(760-841):






1/1






A: bmd4(704-760):






16/30#






(A: bmd4(830-885):






16/30)#






F: SALBC43(519-533):






4/41



2184
A: 2, C: 4,
aa 701-777
A: GSBXM62(702-777):
17, 69




G: 9
aa 783-822
28/28






A: GSBXR22(783-855):






1/1



2186
A: 4, C: 4,
aa 710-787
C: GSBYN05(710-787):
16, 68




D: 5, E: 2
as 855-975
19/25





aa 916-983
D: n.d.






A: GSBXP01(916-983):






17/30



2224
B: 2
aa 34-46
B: GSBXD89(34-46):
15, 67






1/1



2254
D: 3
aa 403-462
D.n.d.
14, 66



2264
A: 131,
aa 7-87
A: GSBXP22(145-196):
13, 65




B: 51,
aa 133-242
1/1




C: 13,

A: GSBXK05-




E: 43,

bmd16(178-218):




F: 78, G: 2,

6/29




H: 17

B: GSBXE24-






bdb20(167-178): 1/1






F: SALAQ91(173-184):






15/41



2268
A: 7, B: 65,
aa 67-116
A: GSBXK88(67-116):
12, 64




C: 3, E: 2,
aa 98-184
1/1




F: 53
aa 182-225
A: GSBXN19(98-184):






22/29






A: GSBXN32(182-225):






34/71






B: GSBXB71(196-209):






16/29






F: SALAL22(196-210):






16/41



2344
D: 9, E: 1,
aa 706-762
D: n.d.
11, 63




F: 3, H: 4
aa 810-852



2351
A: 1, C: 6
aa 83-156
A: GSBXO46(83-156):
10, 62






14/29



2359
B: 4, F: 11
aa 168-184
B: GSBXD01(168-184):
9, 61





aa 206-220
1/1





aa 297-309
B: GSBXD62(205-220):






1/1






B: GSBXC17(297-309):






6/27






F: SALAL04(205-220):






9/41



2378
C: 1, D: 7,
aa 198-258
C: GSBYI73(646-727):
8, 60




F: 4, H: 11
aa 646-727
2/9





aa 846-857
F: SALAO33(846-857):





aa 2104-2206
10/41






D: n.d.



2466
D: 14
aa 401-494
D: n.d.
7, 59



2470
C: 3
aa 414-455
C: GSBYH60(414-455):
169, 170






28/31



2498
D: 12
aa 358-411
D: 17/21
6, 58





aa 588-606



2548
A: 55,
aa 1-48
A: GSBXK68(1-73):
53, 105




B: 54,
aa 47-143
21/30




C: 35,
aa 219-285
A: GSBXK41(47-135):




F: 59,
aa 345-424
1/1




G: 56,

A: GSBXN38(219-285):




H: 38

19/30






A: GSBXL11(322-375):






10/30






B: GSBXB22(406-418):






37/71






F: SALAM17(406-418):






29/41



2577
C: 6
aa 99-171
C: GSBYL56(99-171):
149, 157






1/1



2642
C: 1, E: 1
aa 5-48
C: bhe3(5-48):
52, 104






25/30##



2664
D: 35
aa 77-128
D: n.d.
51, 103



2670
D: 16
aa 328-394
D: n.d.
50, 102



2680
C: 26, G: 4,
aa 438-516
C: GSBYHI6(438-516):
148, 156




H: 8
aa 505-570
3/5





aa 569-619
C: GSBYG24(505-570):






1/7






C: GSBYL82(569-619):






2/7



2740
D: 4
aa 1-59
D: n.d.
49, 101



2746
A: 1, H: 13
aa 63-126
A: GSBXO40(66-123):
48, 100






8/29



2797
B: 3, E: 2,
aa 183-200
B: GSBXE85(183-200):
47, 99




F: 13, H: 3
aa 349-363
11/27






F: SALAQ47(183-200):






8/41



2798
A: 41,
aa 48-136
C: GSBYG01(48-136):
46, 98




B: 42, C: 3,
aa 128-172
2/6




F: 35, G: 1,
aa 201-258
A: GSBXM31-




H: 11

bmd12(128-188):






11/30






B: GSBXE16(165-177):






10/30






A: GSBXN20(201-258):






8/30






F: SALAW05(165-177):






13/41



2815
D: 21
aa 1-43
D: n.d.
45, 97



2914
A: 1, C: 14,
aa 386-402
A: GSBXM18(386-402):
44, 96




F: 2

17/29



2960
C: 101,
aa 1-85
C: GSBYG32(1-85)::
43, 95




E: 2, H: 58
aa 54-121
6/7





aa 103-195
C: GSBYG61-






bhe2(54-121): 26/30






C: GSBYN80(103-195):






13/17



2963
C: 3, E: 3,
aa 22-100
C: GSBYJ58(22-100):
147, 155




G: 1

9/15



3002
A: 2, C: 1,
aa 21-118
A: GSBXL06(21-118):
33, 85




H: 4

50/52



3200
A: 11,
aa 5-134
A: GSBXL07(5-134):
29, 81




B: 11,

6/28




C: 36







Bacterial surface display: A, LSA250/1 library in fhuA with patient sera 1 (655); B, LSA50/6 library in lamB with patient sera 1 (484); C, LSA250/1 library in fhuA with IC sera 1 (571); E, LSA50/6 library in lamB with IC sera 2 (454); F, LSA50/6 library in lamB with patient sera P1 (1105); G, LSA50/6 library in lamb with IC sera 1 (471)); H, LSA250/1 library in fhuA with patient sera 1 (IgA, 708). Ribosome display: D, LSA250/1 library with IC sera (1686).



*identified 18 times of 33 screened; was therefore eliminated from screen C.



**prediction of antigenic sequences longer than 5 amino acids was performed with the programme ANTIGENIC (Kolaskar and Tongaonkar, 1990);



#identical sequence present twice in ORF;



##clone not in database (not sequence by TIGR).













TABLE 2b







Additional immunogenic proteins identified by bacterial


surface and ribosome display: S. aureus
















No. of








selected
Location of





clones
identified

Seq ID


S. aureus


per ORF
immuno-

no:


antigenic
Putative function

and
genic
Serum reactivity with relevant
(DNA +


protein
(by homology)
predicted immunogenic aa**
screen
region
region (positive/total)
Prot)





ARF0280
Putative protein
7-14
F: 6
aa 25-43
SALAM59(25-43): 1/1
401, 402


CRF0145
Putative protein
18-28, 31-37, 40-47, 51-83, 86-126
F: 5
aa 81-90
SALAZ40(81-90): 2/12
403, 404


CRF0250
Putative protein
4-24, 26-46, 49-86
G: 8
aa 60-76
SALAJ87(60-76): n.d.
365, 378


CRF0308
Putative protein
40-46
A: 6, B: 2,
aa 5-38
A: GSBXK03(7-36): 28/69
391, 392





C: 47,

B: GSBXD29(10-20): 10/27





E: 35


CRF0337
Unknown
4-17
D: 3
aa 1-20
D: n.d.
469; 486


CRF0497
Putative protein
4-28, 31-53, 58-64
B: 13, F: 5
aa 18-34
GSBXF31(19-34): 1/7
366, 379


CRF0538
Unknown
4-20
D: 7
aa 1-11
D: n.d.
470; 487


CRF0750
Putative protein
4-11, 18-24, 35-40
G: 44
aa 25-39
SALAG92(26-39): n.d.
367, 380


CRF1145
Unknown
4-57
D: 28
aa 16-32
D: n.d.
464; 481


CRF1247
Putative protein
4-25, 27-56
F: 6
aa 36-46
SALAR23(36-46): n.d.
368, 381


CRF1256
Putative protein
19-25, 38-47, 55-74, 77-87
G: 5
aa 54-67
SALAG65(54-67): n.d.
369, 382


CRF1356
Unknown
8-15; 18-24; 27-38
D: 5
aa 5-33
D: n.d.
471; 488


CRF1763
Putative protein
4-9, 23-41, 43-58, 71-85
C: 3
aa 1-22
C: GSBYI30(1-22): 1/1
407, 408


CRF1783
Unknown
8-161
D: 5
aa 76-127
D: n.d.
465; 482


CRF1845
Unknown
4-28; 30-36
D: 272
aa 1-17
D: n.d.
472; 489


CRF1861
Unknown
6-11; 13-34; 36-50
D: 8
aa 4-27
D: n.d.
466; 483


CRF1928
Putative protein
4-9, 17-30
F: 9
aa 13-22
SALAR41(13-22): n.d.
370, 383


CRF2004
Putative protein
18-38
F: 13
aa 16-32
SALAM75(16-32): n.d.
371, 384


CRF2155
Putative protein
4-15, 30-58
F: 9
aa 54-66
SALAQ54(54-66): 1/12
372, 385


CRF2180
Putative protein
4-61, 65-72, 79-95, 97-106
E: 13
aa 86-99
GSBZE08(86-99): n.d.
373, 386


CRF2207
Unknown
4-13
D: 3
aa 17-39
D: n.d.
473; 490


CRF2305
Putative protein
4-9, 22-33, 44-60
C: 5
aa 80-116
GSBYL75(80-116): n.d.
374, 387


CRF2341
Putative protein
4-23, 30-44, 49-70
F: 8
aa 46-55
SALAW31(46-55): n.d.
375, 388


CRF2349
Putative protein
4-32, 39-46, 62-69, 77-83
B: 10, F: 4
aa 46-67
GSBXC92(52-67): 2/11
376, 389


CRF2356
Unknown
4-18
D: 3
aa 3-18
D: n.d.
475; 492


CRF2452
Unknown
4-31
D: 9
aa 7-21
D: n.d.
476; 493


CRF2498
Putative protein
4-29, 31-41
G: 8
aa 2-15
SALAF30(3-15): n.d.
377, 390


CRF2553
Unknown
4-35; 37-42
D: 4
aa 1-20
D: n.d.
474; 491


CRF2578
Unknown
5-25; 30-39
D: 11
aa 9-30
D: n.d.
467; 484


CRF2664
Unknown
11-21
D: 17
aa 1-14
D: n.d.
477; 494


CRF2729
Putative protein
10-41, 50-57
F: 3
aa 40-56
SALAQ25(40-56): 1/1
405, 406


CRF2863/1
Unknown
4-43
D: 78
aa 17-40
D: n.d.
478; 495


CRF2863/2
Unknown
4-46
D: 78
aa 44-49
D: n.d.
479; 496


CRFA002
Unknown
17-39; 52-59
D: 3
aa 38-55
D: n.d.
463; 480


CRFNI
Unknown
5-20; 37-44; 52-59; 87-94; 116-132
D: 4
aa 94-116
D: n.d.
468; 485


ORF0188
UDP-N-acetyl-
11-18, 43-56, 58-97, 100-118, 120-148,
B: 4, F: 29
aa 197-210
SALAM14(198-209): n.d.
397, 398



D-mannosamine
152-171, 195-203, 207-214,



transferase, putative
220-227, 233-244


ORF0254
Multidrug efflux
4-33, 35-56, 66-99, 109-124, 136-144,
D: 3
aa 155-175
D: n.d.
297, 325



transporter
151-180, 188-198, 201-236,




238-244, 250-260, 266-290, 294-306,




342-377


ORF0307
Conserved
4-23, 25-67, 76-107, 109-148
D: 3
aa 9-44
D: n.d.
298, 326



hypothetical protein


ORF0452
Conserved
4-35, 41-47, 55-75, 77-89, 98-113,
D: 5
aa 105-122
D: n.d.
299, 327



hypothetical protein
116-140, 144-179, 194-215, 232-254,




260-273, 280-288, 290-302,




315-323, 330-369, 372-385, 413-432


ORF0456
Na+/H+Antiporter
4-81
D: 66
aa 1-21
D: n.d.
300, 328


ORF0556
Iron(III)dicitrate
5-23, 50-74, 92-99, 107-122, 126-142,
D: 10
aa 1-18
D: n.d.
301, 329



binding protein
152-159, 172-179, 188-196,




211-218, 271-282


ORF0629
Hypothetical
9-44, 63-69, 75-82, 86-106, 108-146,
D: 313
aa 13-37
D: n.d.
302, 330



Protein
153-161, 166-178, 185-192,




233-239, 258-266, 302-307


ORF0637
GTP-binding
10-19, 22-32, 95-105, 112-119, 121-133,
F: 3
aa 107-119
F: SALAX70(107-119): 10/41
393, 395



protein TypA
140-154, 162-174, 186-200,




207-224, 238-247, 254-266, 274-280,




288-294, 296-305, 343-351,




358-364, 366-373, 382-393, 403-413,




415-422, 440-447, 499-507,




565-575, 578-588


ORF0713
Conserved
22-51, 53-71, 80-85, 93-99, 105-112,
D: 3
aa 487-513
D: n.d.
303, 331



hypothetical
123-146, 151-157, 165-222,



transmembrane
226-236, 247-270, 290-296, 301-324,



protein, putative
330-348, 362-382, 384-391,




396-461, 463-482, 490-515


ORF0788
Cell division protein
104-111, 158-171, 186-197, 204-209,
D: 4
aa 152-178
D: n.d.
304, 332




230-247, 253-259, 269-277,




290-314, 330-340, 347-367, 378-388


ORF0797
Conserved
11-40, 56-75, 83-102, 112-117, 129-147,
D: 12
aa 196-218
D: n.d.
305, 333



hypothetical
154-168, 174-191, 196-270,



protein
280-344, 354-377, 380-429, 431-450,




458-483, 502-520, 525-532,




595-602, 662-669, 675-686, 696-702,




704-711, 720-735, 739-748,




750-756, 770-779, 793-800, 813-822,




834-862


ORF0836
Cell Division Protein
34-91, 100-119, 126-143, 147-185,
D: 5
aa 26-56
D: n.d.
306, 334




187-197, 319-335, 349-355, 363-395,




397-412, 414-422, 424-440,




458-465, 467-475, 480-505, 507-529,




531-542, 548-553, 577-589,




614-632, 640-649, 685-704, 730-741,




744-751, 780-786


ORF1318
Amino acid permease
11-21, 25-32, 34-54, 81-88, 93-99,
D: 8
aa127-152
D: n.d.
307, 335




105-117, 122-145, 148-174, 187-193,




203-218, 226-260, 265-298,




306-318, 325-381, 393-399, 402-421,




426-448


ORF1321
Pyruvat kinase
4-11, 50-67, 89-95, 103-109, 112-135,
E: 6
aa 420-432
E: GSBZE16(420-432): 5/41
197, 216




139-147, 158-170, 185-204,




213-219, 229-242, 248-277, 294-300,




316-323, 330-335, 339-379,




390-402, 408-422, 431-439, 446-457,




469-474, 484-500, 506-513,




517-530, 538-546, 548-561


ORF1388
LPXTG cell wall
11-31, 86-91, 103-111, 175-182,
D: 3
aa 508-523
D: n.d.
308, 336



anchor motif
205-212, 218-226, 242-247, 260-269,




279-288, 304-313, 329-334,




355-360, 378-387, 390-399, 407-435,




468-486, 510-516, 535-547,




574-581, 604-615, 635-646, 653-659,




689-696, 730-737, 802-812,




879-891, 893-906, 922-931, 954-964,




997-1009, 1031-1042, 1089-1096,




1107-1120, 1123-1130, 1149-1162,




1176-1184, 1192-1207, 1209-1215,




1253-1259, 1265-1275, 1282-1295,




1304-1310, 1345-1361, 1382-1388,




1394-1400, 1412-1430, 1457-1462,




1489-1507, 1509-1515, 1535-1540,




1571-1591, 1619-1626, 1635-1641,




1647-1655, 1695-1701, 1726-1748,




1750-1757, 1767-1783, 1802-1807,




1809-1822, 1844-1875, 1883-1889,




1922-1929, 1931-1936, 1951-1967,




1978-1989, 1999-2008, 2023-2042,




2056-2083, 2101-2136, 2161-2177


ORF1402
3,4-dihydroxy-2-
18-23, 32-37, 54-63, 65-74, 83-92,
E: 3
aa 121-137
E: GSBZB68(121-137): 7/41
198, 217



butanone-4-
107-114, 123-139, 144-155, 157-164,



phosphate synthase
191-198, 232-240, 247-272,




284-290, 295-301, 303-309, 311-321,




328-341, 367-376


ORF1473
hemolysin II
4-36, 39-47, 57-65, 75-82, 108-114,
F: 1
aa 245-256
F: SALAP76(245-256): 6/41
199, 218



(LukD-Leuktoxin)
119-126, 135-143, 189-195, 234-244,




250-257, 266-272, 311-316


ORF1523
Iron uptake regulator
13-27, 29-44, 46-66, 68-81, 97-116,
D: 3
aa 120-135
D: n.d.
309, 337




138-145


ORF1707
inner membrane
4-23, 57-77, 89-103, 119-125, 132-172,
F: 1
aa 104-118
F: SALBC82(104-118): 7/41
200, 219



protein, 60 kDa
179-197, 210-254, 256-265,




281-287


ORF1754
amiB
5-10, 16-24, 62-69, 77-96, 100-115,
D: 3
aa 293-312
D: n.d.
310, 338




117-126, 137-156, 165-183, 202-211,




215-225, 229-241, 250-260,




267-273, 290-300, 302-308, 320-333,




336-342, 348-356, 375-382,




384-389


ORF1783
Mrp protein
5-29, 46-52, 70-76, 81-87, 155-170,
F: 2
aa 850-860
F: SALAQ36(850-860): 8/41
201, 220



(fmtB)
192-197, 206-213, 215-220, 225-231,




249-258, 273-279, 281-287,




300-306, 313-319, 323-332, 335-341,




344-351, 360-382, 407-431,




443-448, 459-468, 475-496, 513-520,




522-537, 543-550, 556-565,




567-573, 580-585, 593-615, 619-631,




633-642, 670-686, 688-698,




759-766, 768-782, 799-808, 842-848,




868-877, 879-917, 945-950,




979-988, 996-1002, 1025-1036,




1065-1084, 1101-1107, 1113-1119,




1125-1142, 1163-1169, 1183-1189,




1213-1219, 1289-1301, 1307-1315,




1331-1342, 1369-1378, 1385-1391,




1410-1419, 1421-1427, 1433-1447,




1468-1475, 1487-1494, 1518-1529,




1564-1570, 1592-1609, 1675-1681,




1686-1693, 1714-1725, 1740-1747,




1767-1774, 1793-1807, 1824-1841,




1920-1937, 1953-1958, 1972-1978,




1980-1986, 1997-2011, 2048-2066,




2161-2166, 2219-2224, 2252-2257,




2292-2298, 2375-2380, 2394-2399,




2435-2440, 2449-2468


ORF1848
Map-ND2C
4-27, 42-66, 70-76, 102-107, 113-118,
E: 5
aa 75-90
E: GSBZB15(75-90): 6/41
202, 221



protein
133-138


ORF1891
ribosomal protein
31-39, 48-54, 61-67, 75-83, 90-98,
F: 4
aa 239-257
F: SALAV36(239-257): 19/41
203, 222



L2 (rplB)
103-119, 123-145, 160-167, 169-176,




182-193, 195-206, 267-273


ORF2011
Putative drug
5-27, 79-85, 105-110, 138-165, 183-202,
D: 5
aa 205-224
D: n.d.
311, 339



transporter
204-225, 233-259, 272-292,




298-320, 327-336, 338-345, 363-376,




383-398, 400-422, 425-470,




489-495, 506-518, 536-544, 549-554,




562-568, 584-598, 603-623


ORF2027
lactase permease,
10-33, 38-71, 73-103, 113-125, 132-147,
E: 2
aa 422-436
E: GSBZF58(422-436): 6/41
204, 223



putative
154-163, 170-216, 222-248,




250-269, 271-278, 287-335, 337-355,




360-374, 384-408, 425-442,




453-465, 468-476, 478-501, 508-529


ORF2087
Hemolysin II
8-27, 52-59, 73-80, 90-99, 104-110,
D: 3
aa 126-147
D: n.d.
312, 340



(putative)
117-124, 131-140, 189-209, 217-232,




265-279, 287-293, 299-306


ORF2090
preLukS
8-26, 75-82, 118-126, 136-142, 163-177,
F: 2
aa 270-284
F: SALAQ77(270-284): 23/41
205, 224




182-189, 205-215, 221-236,




239-248, 268-274


ORF2092
Hemolysin II
5-22, 30-47, 58-65, 75-81, 87-92,
F: 3
aa 238-253
F: SALAQ67(237-252): 10/41
206, 225



(preLUK-F)
99-105, 107-113, 119-126, 189-195,




217-223, 234-244, 250-257, 266-272


ORF2107
Multidrug
10-28, 30-43, 50-75, 80-113, 116-125,
D: 9
aa 54-104
D: n.d.
313, 341



resistance protein
136-167, 170-191, 197-245,



(putative)
253-329, 345-367, 375-396


ORF2192
Transcriptional
20-31, 46-52, 55-69, 74-79, 89-97,
D: 3
aa 15-35
D: n.d.
314,



regulator GntR
108-113, 120-128, 141-171, 188-214



342



family, putative


ORF2305
Amino acid permease
25-79, 91-103, 105-127, 132-149,
D: 53
aa 363-393
D: n.d.
315, 343




158-175, 185-221, 231-249, 267-293,




307-329, 336-343, 346-359,




362-405, 415-442, 446-468


ORF2324
Citrate dransporter
10-77, 85-96, 99-109, 111-138, 144-155,
D: 7
aa 37-83
D: n.d.
316, 344




167-176, 178-205, 225-238,




241-247, 258-280, 282-294, 304-309,




313-327, 333-383, 386-402,




405-422, 429-453


ORF2422
Anion transporter
7-26, 28-34, 36-53, 55-73, 75-81,
D: 16
aa 275-295
D: n.d.
317, 345



family protein
87-100, 108-117, 121-138, 150-160,




175-181, 184-195, 202-215, 221-247,




265-271, 274-314, 324-337,




341-412, 414-423, 425-440, 447-462,




464-469


ORF2553
SirA
5-22, 54-78, 97-103, 113-123, 130-148,
D: 3
aa 1-22
D: n.d.
318, 346




166-171, 173-180, 192-201,




254-261, 266-272, 310-322


ORF2555
ornithine cyclode-
20-35, 37-50, 96-102, 109-120, 123-137,
E: 2
aa 32-48
E: GSBZB37(32-48): 11/41
207, 226



aminase
141-150, 165-182, 206-224,




237-256, 267-273, 277-291, 300-305,




313-324


ORF2558
Multidrug resistance
11-63, 79-129, 136-191, 209-231,
D: 8
aa 84-100
D: n.d.
319, 347



efflux proten,
237-250, 254-276, 282-306, 311-345,



putative
352-373, 376-397


ORF2610
Cap5M
4-30, 34-40, 79-85, 89-98, 104-118,
D: 13
aa 114-141
D: n.d.
320, 348




124-139, 148-160, 167-178


ORF2613
Cap5P (UDP-N-
4-9, 17-24, 32-38, 44-54, 68-82,
B: 3, F: 11
aa 321-341
F: SALAU27(325-337): 9/41
208, 227



acetylglucosamine
89-95, 101-120, 124-131, 136-142,



2-epimerase)
145-157, 174-181, 184-191, 196-204,




215-224, 228-236, 243-250,




259-266, 274-281, 293-301, 314-319,




325-331, 355-367, 373-378


ORF2628
Hypothetical protein
9-15, 28-36, 44-62, 69-88, 98-104,
F: 6
aa 694-708
F: SALBD82(1288-1303):
209, 228




111-136, 139-149, 177-186, 195-217,

aa 790-800
9/41




224-236, 241-257, 260-278,

aa




283-290, 292-373, 395-408, 411-443,

1288-1305




465-472, 475-496, 503-520,




552-559, 569-589, 593-599, 607-613,




615-636, 648-654, 659-687,




689-696, 721-733, 738-759, 783-789,




795-801, 811-823, 827-836,




839-851, 867-875, 877-883, 890-898,




900-908, 912-931, 937-951,




961-992, 994-1002, 1005-1011,




1016-1060, 1062-1074, 1088-1096,




1101-1123, 1137-1153, 1169-1192,




1210-1220, 1228-1239, 1242-1251,




1268-1275, 1299-1311, 1322-1330,




1338-1361, 1378-1384, 1393-1412,




1419-1425, 1439-1459, 1469-1482,




1489-1495, 1502-1519, 1527-1544,




1548-1555, 1600-1607, 1609-1617,




1624-1657, 1667-1691, 1705-1723,




1727-1742, 1749-1770, 1773-1787,




1804-1813, 1829-1837, 1846-1852,




1854-1864, 1869-1879, 1881-1896,




1900-1909, 1922-1927, 1929-1935,




1942-1962, 1972-2005, 2009-2029,




2031-2038, 2055-2076, 2101-2114,




2117-2124, 2147-2178, 2188-2202,




2209-2217, 2224-2230, 2255-2266,




2271-2280, 2282-2302, 2307-2316,




2319-2324, 2379-2387


ORF2644
PTS system, sucrose-
8-15, 24-30, 49-68, 80-93, 102-107,
F: 4
aa 106-159
F: SALAW60(106-125): 3/41
210, 229



specific
126-147, 149-168, 170-180, 185-193,



IIBC component
241-305, 307-339, 346-355,




358-372, 382-390, 392-415, 418-425,




427-433, 435-444, 450-472


ORF2654
Oligopeptide ABC
5-61, 72-84, 87-99, 104-109, 124-145,
D: 5
aa 182-209
D: n.d.
321, 349



transporter, putative
158-170, 180-188, 190-216,




223-264, 270-275, 296-336, 355-372


ORF2662
maltose ABC
4-21, 71-79, 99-105, 110-121, 143-161,
F: 1
aa 306-323
F: SALBC05(306-323): 2/41
211, 230



transporter, putative
199-205, 219-235, 244-258,




265-270, 285-291, 300-308, 310-318,




322-328, 346-351, 355-361,




409-416


ORF2710
sorbitol
4-12, 19-40, 61-111, 117-138, 140-153,
B: 2, F: 4
aa 244-257
F: SALAX93(249-256): 6/41
212, 231



dehydrogenase
161-180, 182-207, 226-235,




237-249, 253-264, 267-274, 277-292,




311-323


ORF2742
Hypothetical protein
4-41, 49-56, 61-67, 75-82, 88-104,
D: 188,
aa 303-323
D: n.d.
322, 350




114-125, 129-145, 151-165, 171-178,
H: 4




187-221, 224-230, 238-250,




252-275, 277-304, 306-385


ORF2780
brnQ
4-29, 41-63, 74-95, 97-103, 107-189,
D: 3
aa 26-40
D: n.d.
323, 351




193-209, 220-248, 260-270,




273-299, 301-326, 328-355, 366-397,




399-428


ORF2806
Phage related protein
10-17, 23-29, 31-37, 54-59, 74-81,
F: 3
aa 104-116
F: SALBC34: 1/1
213, 232




102-115, 127-137, 145-152, 158-165,




178-186, 188-196, 203-210,




221-227, 232-237


ORF2900
Conserved
4-27, 34-43, 62-73, 81-90, 103-116,
D: 24
aa 360-376
D: n.d.
324, 352



hypothetical protein
125-136, 180-205, 213-218, 227-235,




238-243, 251-259, 261-269,




275-280, 284-294, 297-308, 312-342,




355-380, 394-408, 433-458,




470-510, 514-536, 542-567


ORF2931
conserved
4-19, 43-54, 56-62, 84-90, 96-102,
E: 6
aa 22-37
E: GSBZA13(22-37): 7/41
214, 233



hypothetical
127-135, 157-164, 181-187



protein


ORF2958
Exotoxin 2
7-19, 26-39, 44-53, 58-69, 82-88,
F: 1
aa 154-168
F: SALBB59(154-168): 4/41
215, 234




91-107, 129-141, 149-155, 165-178,




188-194


ORF2970
Surface protein,
9-23, 38-43, 55-60, 69-78, 93-101,
H: 5
aa 1-70
H: GSBYU66: n.d.
399, 400



putative
103-112, 132-148, 187-193, 201-208,




216-229, 300-312, 327-352,




364-369, 374-383, 390-396, 402-410,




419-426, 463-475, 482-491





Bacterial surface display: A, LSA250/1 library in fhuA with patient sera 1 (655); B, LSA50/6 library in lamB with patient sera 1 (484); C, LSA250/1 library in fhuA with IC sera 1 (571); E, LSA50/6 library in lamB with IC sera 2 (454); F, LSA50/6 library in lamB with patient sera P1 (1105); G, LSA50/6 library in lamb with IC sera 1 (471); H, LSA250/1 library in fhuA with patient sera 1 (IgA, 708). Ribosome display: D, LSA250/1 library with IC sera (1686).


**prediction of antigenic sequences longer than 5 amino acids was performed with the programme ANTIGENIC (Kolaskar and Tongaonkar, 1990). ORF, open reading frame; CRF, reading frame on complementary strand; ARF, alternative reading frame.













TABLE 2c







Immunogenic proteins identified by bacterial surface


and ribosome display: S. epidermidis.
















No. of








selected
Location of


S.


clones
identified

Seq ID


epidermidis


per ORF
immuno-

no:


antigenic
Putative function

and
genic
Serum reactivity with relevant
(DNA +


protein
(by homology)
predicted immunogenic aa**
screen
region
region (positive/total)
Prot)





ARF0172
cation-transporting
4-34, 37-43
D: 6
aa3-32
D: nd
497,



ATPase, E1-E2




548



family


ARF0183
condensing enzyme,
4-22, 24-49
D: 4
aa1-52
D: nd
498,



putative,




549



FabH-related


ARF2455
NADH
4-29
D: 3
aa1-22
D: nd
499,



dehydrogenase,




550



putative


CRF0001
Unknown
4-14, 16-26
D: 3
aa5-21
D: nd
500,








551


CRF0002
Unknown
4-13, 15-23, 36-62
D: 5
aa21-70
D: nd
501,








552


CRF0003
Unknown
4-12, 14-28
D: 3
aa 4-31
D: nd
502,








553


CRF0004
Unknown
5-15, 35-71, 86-94
D: 4
aa31-72
D: nd
503,








554


CRF0005
Unknown
8-26, 28-34
D: 3
aa: 9-33
D: nd
504,








555


CRF0006
Unknown
4-11, 15-28
D: 3
aa10-22
D: nd
505,








556


CRF0007
Unknown
4-19, 30-36
D: 3
aa 7-44
D: nd
506,








557


CRF0008
Unknown
10-48
D: 4
aa: 9-44
D: nd
507,








558


CRF0009
Unknown
41883
D: 3
aa5-14
D: nd
508,








559


CRF0192
Putative protein
4-23, 25-68
C: 4
aa 15-34
C: GSBBM10(15-34): n.d.
445,








446


CRF0275
Putative protein
4-40, 49-65
B: 5
aa 35-68
B: SELAK28(35-68): n.d.
447,








448


CRF0622
Putative protein
4-12, 17-57, 62-70, 75-84, 86-100
C: 4
aa 75-99
C: GSBBR74(76-99): n.d.
449,








450


CRF0879
Putative protein
4-14, 38-44
A: 3, B: 10
aa 9-40
B: SELAC39(10-40): n.d.
451,








452


CRF1004
Putative protein
4-40
A: 3, B: 5
aa 29-65
B: SELAI63(35-63): n.d.
453,








454


CRF2248
Putative protein
4-10, 19-40, 53-64, 74-91
C: 30
aa 74-111
C: GSBBN64(16-35): n.d.
455,








456


CRF2307
Putative protein
4-19, 35-41, 80-89
A: 19
aa 41-87
A: SEFAL47(41-87): n.d.
457,








458


CRF2309
Putative protein
15-21
B: 6
aa 4-16
B: SELAL02(4-16): n.d.
459,








460


CRF2409
Putative protein
6-25
B: 6
aa 2-24
B: SELAB48(5-24): n.d.
461,








462


ORF0005
hypothetical protein
13-27, 33-67, 73-99, 114-129, 132-158,
D: 3
aa105-128
D: nd
509,




167-190, 193-234, 237-267,



560




269-299, 316-330, 339-351, 359-382,




384-423


ORF0008
Streptococcal
9-14, 16-24, 26-32, 41-50, 71-79,
B: 2
aa 895-926
B: SELAF79(895-926): 7/12
239,



hemagglutinin
90-96, 177-184, 232-237, 271-278,



268




293-301, 322-330, 332-339, 349-354,




375-386, 390-396, 403-409,




453-459, 466-472, 478-486, 504-509,




518-525, 530-541, 546-552,




573-586, 595-600, 603-622, 643-660,




668-673, 675-681, 691-697,




699-711, 713-726, 732-749, 753-759,




798-807, 814-826, 831-841,




846-852, 871-878, 897-904, 921-930,




997-1003, 1026-1031, 1033-1039,




1050-1057, 1069-1075, 1097-1103,




1105-1111, 1134-1139, 1141-1147,




1168-1175, 1177-1183, 1205-1211,




1213-1219, 1231-1237, 1241-1247,




1267-1273, 1304-1309, 1311-1317,




1329-1335, 1339-1345, 1347-1353,




1382-1389, 1401-1407, 1411-1417,




1447-1453, 1455-1461, 1483-1489,




1491-1497, 1527-1533, 1545-1551,




1556-1561, 1581-1587, 1591-1597,




1627-1638, 1661-1667, 1684-1689,




1691-1697, 1708-1715, 1719-1725,




1765-1771, 1813-1820, 1823-1830,




1835-1856


ORF0038
extracellular
6-25, 29-35, 39-45, 64-71, 82-88,
C: 6
aa 136-165
C: GSBBN08(136-165): 1/1
353,



elastase precursor
96-102, 107-113, 119-131, 170-176,



359




186-192, 196-202, 215-220, 243-248,




302-312, 345-360, 362-371,




378-384, 458-470, 478-489, 495-504


ORF0099
hypothetical
6-18, 31-37, 42-49, 51-67, 73-85,
D: 5
aa218-265
D: nd
510,



protein
87-93, 102-109, 119-126, 150-157,



561




170-179, 185-191, 204-214, 217-223,




237-248, 269-275, 278-316,




320-340, 359-365


ORF0101
hypothetical
4-10, 15-27, 67-94, 123-129, 167-173,
D: 18
aa26-109
D: nd
511,



protein
179-184, 187-198, 217-222,



562




229-235, 238-246


ORF0121
C4-dicarboxylate
4-20, 24-62, 73-86, 89-106, 110-122,
D: 5
aa323-379
D: nd
512,



transporter, anaerobic,
131-164, 169-193, 204-213,



563



putative
219-236, 252-259, 263-281, 296-306,




318-324, 328-352, 356-397,




410-429


ORF0143
amino acid permease
25-79, 91-103, 105-127, 132-150,
D: 35
aa247-339
D: nd
513,




157-174, 184-206, 208-219, 231-249,



564




267-294, 310-329, 336-343,




346-405, 417-468


ORF0162
Immunodominant
4-27, 35-45, 52-68, 83-89, 113-119,
A: 11,
aa 90-227
B: SELAA19(100-118): 1/1
240,



Antigen A
133-150, 158-166, 171-176, 198-204,
B: 11;

B: SELAE24(170-190): 11/12
269




219-230
C: 153


ORF0201
capa protein,
10-17, 27-53, 81-86, 98-105, 126-135,
D: 9
aa11-53
D: nd
514,



putative
170-176, 182-188, 203-217,



565




223-232, 246-252, 254-269, 274-280,




308-314


ORF0207
Ribokinase (rbsK)
5-11, 15-23, 47-55, 82-90, 98-103,
B: 10
aa 20-45
B: SELAQ30 (20-45): 12/12
241,




108-114, 126-132, 134-156, 161-186,



270




191-197, 210-224, 228-235,




239-248, 258-264, 275-290


ORF0288
LrgB
7-28, 34-56, 68-119, 127-146, 149-180,
D: 4
aa112-149
D: nd
515,




182-189, 193-200, 211-230



566


ORF0304
Herpesvirus
8-16, 30-36, 83-106, 116-122, 135-143,
D: 8
aa69-117
D: nd
516,



saimiri ORF73
152-165, 177-188, 216-225



567



homolog, putative


ORF0340
nitrate transporter
7-21, 24-93, 101-124, 126-139,
D: 5
aa238-309
D: nd
517,




141-156, 163-179, 187-199, 202-242,



595




244-261, 267-308, 313-322,




340-353, 355-376


ORF0346
hypothetical protein
8-27, 65-73, 87-93, 95-105
D: 8
aa 1-29
D: nd
518,








568


ORF0355
conserved
5-30, 37-43, 57-66, 85-94, 103-111,
C: 5
aa 63-86
C: GSBBL39(63-86): 1/1
354,



hypothetical
118-125



360



protein


ORF0356
conserved
4-14, 21-53, 60-146, 161-173, 175-182,
D: 5
aa51-91
D: nd
519,



hypothetical protein
190-198, 200-211



569


ORF0406
hypothetical protein
12-32, 35-63, 68-102, 106-137,
D: 19
aa1-48,
D: nd
520,




139-145, 154-168, 173-185, 203-222,

aa69-102

570




230-259, 357-364, 366-374


ORF0425
amino acid permease
40-58, 75-86, 93-110, 117-144,
D: 3
aa401-440
D: nd
521,




150-173, 199-219, 229-260, 264-300,



571




317-323, 329-356, 360-374,




377-390, 392-398, 408-424, 427-452


ORF0442
SceB precursor
7-22, 42-48, 55-66, 83-90, 109-118,
C: 38
aa 60-102
C: GSBBM60(65-84): 1/1
355,




136-141



361


ORF0448
SsaA precursor
6-25, 39-47, 120-125, 127-135,
C: 170
aa 15-208
C: GSBBN58(81-105): 1/1
356,




140-148, 157-168, 200-208, 210-220,


C: GSBBL13(167-184): 1/1
362




236-243, 245-254


C: GSBBL25(22-45): 1/1


ORF0503
Ribosomal protein
31-39, 48-54, 61-67, 75-83, 90-98,
A: 1, B: 3
aa 212-273
B: SELAA47(238-259): 12/12
242,



L2
103-115, 123-145, 160-167, 169-176,



271




182-193, 195-206, 267-273


ORF0551
Conserved
5-25, 29-36, 45-53, 62-67, 73-82,
A: 16, B: 9
aa 162-213
B: SELAL12(164-197): 8/12
243,



hypothetical protein
84-91, 99-105, 121-142, 161-177,



272




187-193, 203-224, 242-251, 266-271,




278-285


ORF0556
hypothetical protein
4-24, 30-41, 43-68, 82-90, 107-114,
D: 3
aa 1-26
D: nd
522,




123-143, 155-168



596


ORF0623
Fumble, putative
10-17, 32-38, 55-72, 77-84, 88-96,
A: 10,
aa 95-150
B: SELAB86(95-128): 3/12
244,




126-134, 152-160, 176-185, 190-203,
B: 12; C: 1


273




208-214, 217-225, 233-252,




257-262


ORF0740
Hypothetical protein
18-24, 47-61, 69-83, 90-96, 125-132,
B: 3
aa
B: SELAB23(1097-1114): 7/12
245,




140-163, 171-188, 222-249,

1093-1114

274




281-296, 305-315, 322-330, 335-351,




354-368, 390-397, 411-422,




424-431, 451-469, 479-485, 501-507,




517-524, 539-550, 560-568,




588-599, 619-627, 662-673, 678-689,




735-742, 744-749, 780-786,




797-814, 821-827, 839-847, 857-863,




866-876, 902-911, 919-924,




967-982, 1005-1015, 1020-1026,




1062-1070, 1078-1090, 1125-1131,




1145-1150, 1164-1182, 1208-1213,




1215-1234, 1239-1251, 1256-1270,




1298-1303, 1316-1325, 1339-1349,




1362-1369, 1373-1384, 1418-1427,




1440-1448, 1468-1475, 1523-1532,




1536-1542, 1566-1573, 1575-1593,




1603-1619, 1626-1636, 1657-1667,




1679-1687, 1692-1703, 1711-1718,




1740-1746, 1749-1757, 1760-1769,




1815-1849, 1884-1890, 1905-1914,




1919-1925, 1937-1947, 1955-1963,




1970-1978, 2003-2032, 2075-2089,




2117-2124, 2133-2140, 2146-2151,




2161-2167, 2173-2179, 2184-2196,




2204-2220, 2244-2254, 2259-2264,




2285-2296, 2300-2318, 2328-2334,




2347-2354, 2381-2388, 2396-2408,




2419-2446, 2481-2486, 2493-2500,




2506-2516, 2533-2540, 2555-2567,




2576-2592, 2599-2606, 2615-2639,




2647-2655


ORF0757
hypothetical
13-20, 22-28, 33-40, 60-76, 79-86,
C: 6
aa 260-284
C: GSBBN01(260-284): 1/1
357,



protein
90-102, 112-122, 129-147, 157-170,



363




178-185, 188-193, 200-205, 218-228,




234-240, 243-250, 265-273,




285-291, 310-316, 330-348, 361-380,




399-405, 427-446, 453-464


ORF0912
DNA mismatch
9-16, 28-39, 47-56, 69-76, 104-121,
A: 25
aa 242-304
SEFAT31(242-290): n.d.
441,



repair protein
124-130, 137-144, 185-195, 199-214,



442




238-243, 293-307, 317-337,




351-370, 385-390, 411-428, 472-488,




498-516, 518-525, 528-535,




538-545, 553-559, 563-568, 579-588,




592-607, 615-622, 632-638,




641-648, 658-674, 676-705, 709-720,




727-739, 742-750, 753-760,




768-773, 783-788, 811-819, 827-838


ORF0923
GTP-binding
4-10, 18-27, 42-55, 64-72, 77-92,
B: 13
aa 144-163
B: SELAD55(151-163): 8/12
246,



protein
114-126, 132-157, 186-196, 206-217,



275




236-243, 257-280, 287-300,




306-312, 321-328, 338-351, 360-367,




371-382, 385-399


ORF0979
Conserved
4-28, 44-51, 53-84, 88-107, 113-192
A: 9, B: 18
aa 12-51
B: SELAH01(26-49): 5/12
247,



hypothetical protein




276


ORF0982
sodium/alanine
13-21, 24-50, 73-84, 91-118, 126-133,
D: 3
aa277-305
D: nd
523,



symporter(alsT)
142-149, 156-175, 189-249,



572




251-273, 294-332, 339-347, 358-381,




393-413, 425-448, 458-463


ORF1230
Signal peptidase I
6-33, 44-59, 61-69, 74-82, 92-98,
D: 14
aa 1-53
D: nd
524,




133-146, 163-175



573


ORF1232
Exonuclease
4-12, 16-32, 36-48, 50-65, 97-127,
B: 6
aa 188-219
B: SELAA13(188-216): n.d.
443,



RexA
136-142, 144-165, 176-190, 196-202,



444




211-222, 231-238, 245-251,




268-274, 280-286, 305-316, 334-356,




368-376, 395-402, 410-417,




426-440, 443-449, 474-486, 499-508,




510-525, 540-549, 568-576,




608-617, 624-639, 646-661, 672-678,




688-703, 706-717, 727-734,




743-755, 767-773, 783-797, 806-814,




830-839, 853-859, 863-871,




877-895, 899-918, 935-948, 976-990,




998-1007, 1020-1030, 1050-1062,




1070-1077, 1111-1125, 1137-1149,




1153-1160, 1195-1211


ORF1284
permease PerM,
10-60, 72-96, 103-109, 127-133,
D: 27
aa55-106
D: nd
525,



putative
146-177, 182-189, 196-271, 277-289,



574




301-319, 323-344, 347-354


ORF1319
2-oxoglutarate
9-31, 36-45, 59-67, 71-81, 86-94,
B: 5; C: 1
aa 400-413
B: SELAF54(404-413): 11/12
248,



decarboxylase
96-107, 111-122, 127-140, 153-168,



277



(menD)
180-211, 218-224, 226-251, 256-270,




272-289, 299-305, 310-323,




334-341, 345-353, 358-364, 369-379,




384-390, 396-410, 417-423,




429-442, 454-464, 470-477, 497-505,




540-554


ORF1326
autolysin AtlE
6-25, 40-46, 75-81, 150-155, 200-205,
B: 7; C: 5
aa
B: SELAD20(1282-1298): 10/12
249,



(lytD)
237-243, 288-295, 297-306,

1282-1298

278




308-320, 341-347, 356-363, 384-391,




417-429, 440-452, 465-473,




481-514, 540-546, 554-560, 565-577,




585-590, 602-609, 611-617,




625-634, 636-643, 661-668, 676-684,




718-724, 734-742, 747-754,




766-773, 775-781, 785-798, 800-807,




825-832, 840-857, 859-879,




886-892, 917-923, 950-956, 972-978,




987-1002, 1028-1035, 1049-1065,




1071-1099, 1111-1124, 1150-1172,




1185-1190, 1196-1207, 1234-1241,




1261-1271, 1276-1281, 1311-1320,




1325-1332


ORF1333
quinol oxidase
4-27, 33-55, 66-88
D: 4
aa 3-93
D: nd
526,



polypeptide iv (ec




575



1.9.3.—) (quinol



oxidase aa3-600,



subunit qoxd)


ORF1356
hypothetical protein
9-36, 44-67, 74-97, 99-149, 161-181,
D: 32
aa54-95
D: nd
527,




189-198, 211-224, 245-253,



597




267-273, 285-290, 303-324, 342-394,




396-427


ORF1373
dihydrolipoamide
33-39, 42-78, 103-109, 126-136,
A: 3, B: 1
aa 124-188
A: SEFAP57(124-188): 2/12
250,



acetyltransferase
184-191, 225-232, 258-279, 287-294,



279




306-315, 329-334, 362-379,




381-404, 425-430


ORF1381
hypothetical protein
21-45, 62-67, 74-106, 108-142,
D: 5
aa7-44
D: nd
528,




154-160, 230-236, 245-251, 298-305



576


ORF1420
Muts2 protein,
8-32, 34-41, 46-55, 70-76, 81-89,
B: 7
aa 581-608
B: SELAM40(581-604): 9/12
251,



putative
97-115, 140-148, 153-159, 165-171,



280




175-188, 207-239, 256-276, 280-289,




297-319, 321-335, 341-347,




352-360, 364-371, 384-411, 420-440,




449-460, 495-502, 505-516,




560-566, 573-588, 598-605, 607-614,




616-624, 674-694, 702-717


ORF1443
cell division
61-66, 111-117, 148-155, 173-182,
D: 4
aa175-229
D: nd
529,



protein (divIB)
194-224, 263-293, 297-303, 313-321,



577




334-343, 345-356, 375-381,




384-395, 408-429, 448-454


ORF1500
Cell division protein
100-107, 154-167, 182-193, 200-206,
A: 2, B: 3
aa 77-182
B: SELAP37(139-162): 9/12
252,



FtsY
223-231, 233-243, 249-257,



281




265-273, 298-310, 326-336, 343-362,




370-384


ORF1665
amino acid ABC
4-25, 44-55, 66-76, 82-90, 93-99,
D: 5
aa 1-52
D: nd
530,



transporter,
104-109, 176-209, 227-242, 276-283,



578



permease protein
287-328, 331-345, 347-376,




400-407, 409-416, 418-438, 441-474


ORF1707
putative host cell
12-31, 40-69, 129-137, 140-151,
D: 4
aa 20-76
D: nd
531,



surface-exposed
163-171, 195-202, 213-218



598



lipoprotein


ORF1786
D-3-
4-10, 16-32, 45-55, 66-78, 87-95,
D: 5
aa400-442
D: nd
532,



phosphoglycerate
103-115, 118-124, 135-150, 154-161,



579



dehydrogenase,
166-174, 182-193, 197-207,



putative
225-231, 252-261, 266-304, 310-315,




339-347, 351-359, 387-402,




411-423, 429-436, 439-450, 454-464,




498-505, 508-515


ORF1849
yhjN protein
8-51, 53-69, 73-79, 85-132, 139-146,
D: 5
aa254-301
D: nd
533,




148-167, 179-205, 212-224,



580




231-257, 264-293, 298-304, 309-317,




322-351


ORF1877
protein-export
6-19, 26-39, 41-51, 59-67, 72-85,
D: 7
aa367-409
D: nd
534,



membrane protein
91-98, 104-111, 120-126, 147-153,



581



SecD (secD-1)
158-164, 171-178, 199-209, 211-218,




233-249, 251-257, 269-329,




362-368, 370-385, 392-420, 424-432,




454-489, 506-523, 534-539,




550-556, 563-573, 576-596, 603-642,




644-651, 655-666, 685-704,




706-733, 747-753


ORF1912
unknown conserved
23-35, 37-70, 75-84, 90-112, 129-135,
D: 4
aa131-187
D: nd
535,



protein
137-151, 155-180, 183-209,



582



(conserved)
211-217, 219-225, 230-248, 250-269,




274-284, 289-320, 325-353,




357-371, 374-380, 384-399, 401-411,


ORF2015
Trehalose-6-
8-17, 30-54, 82-89, 94-103, 157-166,
A: 3, B: 8
aa 465-498
B: SELAH62(465-498): 5/12
253,



phosphate
178-183, 196-204, 212-219,



282



hydrolase
222-227, 282-289, 297-307, 345-364,




380-393, 399-405, 434-439,




443-449, 453-475, 486-492, 498-507,




512-535, 538-548


ORF2018
Glucose-6-
4-16, 21-27, 39-51, 60-69, 76-83,
B: 17
aa 250-287
B: SELAI19(250-279): 3/12
254,



phosphate 1-DH
97-118, 126-132, 159-167, 171-177,



283




192-204, 226-240, 247-259, 281-286,




294-305, 314-320, 330-338,




353-361, 367-372, 382-392, 401-413,




427-434, 441-447, 457-463


ORF2040
LysM domain
51-56, 98-108, 128-135, 138-144,
D: 23
aa259-331
D: nd
536,



protein protein
152-158, 177-192, 217-222, 232-251,



583




283-305, 406-431, 433-439


ORF2098
PilB related
13-18, 36-43, 45-50, 73-79, 95-100,
A: 60
aa 1-57
A: SEFAQ50(15-57): 5/12
255,



protein
111-126, 133-139



284


ORF2139
sodium:sulfate
7-12, 22-97, 105-112, 121-128,
D: 41
aa42-118
D: nd
537,



symporter family
130-146, 152-164, 169-189, 192-203,



584



protein, putative
211-230, 238-246, 260-281,




304-309, 313-325, 327-357, 367-386,




398-444, 447-476, 491-512


ORF2172
SceB precursor
4-23, 28-34, 38-43, 45-51, 63-71,
A: 438,
aa 6-215
B: SELAH53(188-209): 3/12
256,



(lytE)
85-96, 98-112, 118-126, 167-174,
B: 40, D: 4


285




179-185, 219-228, 234-239, 256-263


ORF2200
zinc ABC
4-31, 33-40, 48-64, 66-82, 92-114,
D: 19
aa162-225
D: nd
538,



transporter,
118-133, 137-159, 173-246, 248-266



585



permease protein,



putative


ORF2248
membrane protein,
4-11, 17-34, 72-78, 127-137, 178-227,
D: 17
aa1-59,
D: nd
539,



MmpL family,
229-255, 262-334, 352-380,

aa159-225,

586



putative
397-405, 413-419, 447-454, 462-467,

aa634-674




478-490, 503-509, 517-558,




560-568, 571-576, 582-609, 623-629,




631-654, 659-710, 741-746,




762-767, 771-777, 788-793, 856-867


ORF2260
Unknown conserved
5-10, 18-29, 31-37, 66-178, 196-204,
B: 4
aa 123-142
B: SELAG77(123-142): 12/12
257,



protein in
206-213



286



others


ORF2282
conserved hypothetical
16-22, 41-50, 52-64, 66-74, 89-95,
A: 4
aa 51-97
A: SEFAR88(51-97): 3/12
258,



protein
107-114, 123-130, 135-159, 167-181,



287




193-199, 223-231, 249-264,




279-289


ORF2376
DivIC homolog,
27-56, 102-107, 111-116
D: 7
aa15-58
D: nd
540,



putative




587


ORF2439
membrane-bound
4-9, 11-26, 36-56, 59-73, 83-100,
A: 459,
aa 10-217
B: SELAC31(75-129): 12/12
259,



lytic murein
116-130, 148-163, 179-193, 264-270,
B: 2, D: 53


288



transglycosidase
277-287, 311-321



D, putative


ORF2493
conserved
4-29, 37-77, 80-119
D: 6
aa69-113
D: nd
541,



hypothetical protein




588


ORF2535
ATP-binding
5-28, 71-81, 101-107, 128-135,
D: 8
aa1-65
D: nd
542,



cassette
146-52, 178-188, 209-214, 224-233,



589



transporter-like
279-294, 300-306, 318-325, 342-347,



protein, putative
351-357


ORF2627
cation-
8-31, 34-80, 125-132, 143-153,
D: 3
aa61-105
D: nd
543,



transporting
159-165, 176-189, 193-198, 200-206,



590



ATPase, E1-E2
215-242, 244-262, 264-273,



family, putative
281-289, 292-304, 318-325, 327-338,




347-371, 404-416, 422-429,




432-450, 480-488, 503-508, 517-525,




539-544, 551-562, 574-587,




600-631, 645-670


ORF2635
Hypothetical
4-10, 17-24, 26-42, 61-71, 90-96,
A: 2, B: 2
aa 139-169
B: SELAB63(138-163): 7/12
260,



protein
102-111, 117-125, 158-164, 173-182,



289




193-201, 241-255, 268-283,




289-298, 305-319, 340-353, 360-376,




384-390, 394-406


ORF2669
Hypothetical
4-21, 35-42, 85-90, 99-105, 120-125,
A: 14, B: 8
aa 22-81
B: SELAE27(22-51): 5/12
261,



protein
148-155, 175-185, 190-196,



290




205-210, 217-225


ORF2671
Hypothetical protein
4-23, 43-49, 73-84, 93-98, 107-113,
A: 44,
aa 23-68
B: SELAD21(36-61): 5/12
262,




156-163, 179-190, 197-204, 208-218,
B: 14


291




225-231, 248-255


ORF2673
Hypothetical
4-20, 65-71, 99-105, 148-155, 171-182,
A: 16, B: 3
aa 23-68
B: SELAE25(23-54): 2/12
263,



protein
190-196, 204-210, 221-228,



292




240-246


ORF2694
Hypothetical
4-26, 93-98, 121-132, 156-163,
A: 19,
aa 25-82
B: SELAB26(27-60): 5/12
264,



protein
179-192, 198-204, 212-220, 225-238
B: 30


293


ORF2695
Hypothetical
4-26, 43-50, 93-98, 107-113, 156-163,
A: 7
aa 22-78
A: SEFAH77(22-66): 6/12
265,



protein
179-190, 198-204, 212-218,



294




225-231, 247-254


ORF2719
two-component
5-52, 60-71, 75-84, 91-109, 127-135,
B: 4
aa 123-132
B: SELAA62(123-132): 6/12
266,



sensor histidine
141-156, 163-177, 185-193,



295



kinase, putative
201-214, 222-243, 256-262, 270-279,




287-293, 298-303, 321-328,




334-384, 390-404, 411-418, 427-435,




438-448, 453-479, 481-498,




503-509


ORF2728
Accumulation-
4-13, 36-44, 76-86, 122-141, 164-172,
A: 265,
aa 803-1001
B: SELAA10(850-878): 11/12
267,



associated protein
204-214, 235-242, 250-269,
B: 448;


296




291-299, 331-337, 362-369, 377-396,
C: 4, D: 9




419-427, 459-469, 505-524,




547-555, 587-597, 618-625, 633-652,




675-683, 715-727, 740-753,




761-780, 803-811, 842-853, 962-968,




1006-1020


ORF2740
lipase precursor
4-21, 190-200, 218-228, 233-241,
C: 3
aa 110-177
C: GSBBL80(110-177): 1/1
358,




243-261, 276-297, 303-312, 316-325,



364




346-352, 381-387, 436-442,




457-462, 495-505, 518-532, 543-557,




574-593


ORF2764
oligopeptide ABC
14-36, 62-131, 137-147, 149-162,
D: 4
aa 6-41
D: nd
544,



transporter, permease
164-174, 181-207, 212-222, 248-268,



591



protein,
279-285



putative


ORF2767
unknown conserved
7-20, 22-35, 40-50, 52-61, 63-92,
D: 4
aa276-316
D: nd
545,



protein in
94-101, 103-126, 129-155, 161-178,



592



others
192-198, 200-208, 210-229, 232-241,




246-273, 279-332, 338-359,




369-383


ORF2809
sodium:sulfate
4-29, 37-53, 56-82, 87-100, 108-117,
D: 9
aa266-317,
D: nd
546,



symporter family
121-138, 150-160, 175-180,

aa357-401

593



protein
189-195, 202-214, 220-247, 269-315,




324-337, 341-355, 361-412,




414-423, 425-440, 447-467


ORF2851
putative
7-13, 20-32, 37-90, 93-103, 107-126,
D: 11
aa137-185
D: nd
547,



transmembrane efflux
129-155, 159-173, 178-189,



594



protein
195-221, 234-247, 249-255, 268-303,




308-379





Bacterial surface display: A, LSE150 library in fhuA with patient sera 2 (957); B, LSE70 library in lamB with patient sera 2 (1420); C, LSE70 library in lamB with patient sera 1 (551). Ribosome display: D, LSE150 in pMAL4.31 with P2 (1235).


**prediction of antigenic sequences longer than 5 amino acids was performed with the programme ANTIGENIC (Kolaskar and Tongaonkar, 1990). ORF, open reading frame; ARF, alternative reading frame; CRF, reading frame on complementary strand. ORF, open reading frame; CRF, reading frame on complementary strand.













TABLE 2d







Immunogenic proteins identified by bacterial surface


and ribosome display: S. aureus (new annotation)


















No. of









selected
Location of

Seq


S. aureus
Old
Putative

clones per
Identified

ID no:


antigenic
ORF
function (by

ORF and
immunogenic
Serum reactivity with relevant
(DNA +


protein
number
homology)
predicted immunogenic aa**
screen
region
region (positive/total)
Prot)





SaA0003
ORF2967 &
repC
7-19, 46-57, 85-91, 110-117,
B: 3,
aa 9-42
C: GSBYI53(9-42): 1/1
394,



ORF2963

125-133, 140-149, 156-163, 198-204,
C: 14;
aa 156-241
C: GSBYG39(156-241): 1/1
396





236-251, 269-275, 283-290, 318-323,
F: 29
aa 300-314
C: GSBYM94(343-420): 26/30





347-363

aa 343-420


ORF0123
ORF1909 -
unknown
4-10, 25-30, 38-57, 91-108, 110-123,
B: 3, E: 7,
aa 145-163
B: GSBXF80(150-163): 5/27
409,



18 aa at

125-144, 146-177, 179-198,
G: 1

E: GSBZC17(150-163): 25/41
410



N-

216-224, 226-233



terminus


ORF0160
ORF1941 -
unknown
4-26, 34-70, 72-82, 86-155, 160-166,
A: 1
aa 96-172
A: GSBXO07(96-172): 5/30
411,



16 aa at

173-205, 207-228, 230-252,



412



N-

260-268, 280-313



terminus


ORF0657
ORF un-
LPXTGVI
9-33, 56-62, 75-84, 99-105, 122-127,
A: 2,
aa 526-544
B: GSBXE07-bdb1(527-542):
413,



known
protein
163-180, 186-192, 206-228,
B: 27,

11/71
414





233-240, 254-262, 275-283, 289-296,
F: 15

F: SALAX70(526-544): 11/41





322-330, 348-355, 416-424,





426-438, 441-452, 484-491, 541-549





563-569, 578-584, 624-641


ORF1050
ORF1307 -
unknown
45-68, 72-79, 91-101, 131-142,
A: 1,
aa 53-124
A: GSBXM26(53-124): 7/30
415,



4 aa at

144-160, 179-201
H: 45


416



N-terminus


ORF1344
ORF0212 -
NifS protein
13-26, 40-49, 61-68, 92-112,
A: 11
aa 24-84
A: GSBXK59-bmd21(24-84):
417,



10 aa at
homolog
114-123, 138-152, 154-183, 194-200,


6/29
418



N-

207-225, 229-240, 259-265, 271-284,



terminus

289-309, 319-324, 330-336,





346-352, 363-372


ORF1632
ORF1163 -
SdrH
4-31, 50-55, 243-257, 259-268,
B: 6,
aa 101-115
B: GSDXG53(164-182): 39/71
419,



4 aa at
homolog
298-316, 326-335, 364-370, 378-407
E: 11,
aa 115-139
F: SALAP07(101-115): 11/41
420



N-


F: 34
aa 158-186



terminus


ORF2180
ORF0594 -
LPXTGIV
9-17, 24-45, 67-73, 82-90, 100-107,
A: 3, C: 3,
aa 491-587
A: GSBXS61(491-555): 1/1
421,



2 aa at
protein
117-134, 137-145, 158-168, 176-183
E: 6, F: 2,
aa 633-715
A: GSBXL64(494-585): 1/1
422



N-

188-194, 206-213, 223-231,
H: 6
aa 702-757#
A: GSBXS92(758-841): 1/1



terminus

243-248, 263-270, 275-282, 298-304,

aa 758-830
A: bmd4(702-757): 16/30#





344-355, 371-377, 382-388,

(aa 830-885)#
(A: bmd4(830-885): 16/30)#





427-433, 469-479, 500-505, 534-559,


F: SALBC43(519-533): 4/41





597-607, 662-687, 790-815,





918-943, 1032-1037, 1046-1060,





1104-1112, 1128-1137, 1179-1184,





1197-1204, 1209-1214, 1221-1239


ORF2184
ORF0590 -
FnbpB
10-29, 96-116, 131-137, 146-158,
A: 2, C: 4,
aa 694-769
A: GSBXM62(694-769): 28/28
423,



8 aa at

167-173, 177-182, 185-191, 195-201,
G: 9
aa 774-847
A: GSBXR22(774-847): 1/1
424



N-terminus

227-236, 260-266, 270-284,





291-299, 301-312, 348-356, 367-376





382-396, 422-432, 442-453,





480-487, 497-503, 519-527, 543-548,





559-565, 579-585, 591-601,





616-623, 643-648, 657-663, 706-718





746-758, 791-796, 810-817,





819-825, 833-839, 847-853, 868-885,





887-895, 919-932


ORF2470
ORF0299 -
Conserved
4-27, 36-42, 49-55, 68-73, 94-101,
C: 3
aa 400-441
C: GSBYH60(400-441): 28/31
425,



14 aa at
hypothetical
131-137, 193-200, 230-235, 270-276,



426



N-
protein
294-302, 309-324, 334-344,



terminus

347-364, 396-405, 431-437, 498-508,





513-519, 526-532, 539-544,





547-561, 587-594, 618-630, 642-653,





687-699, 713-719, 752-766


ORF2498
ORF0267
Conserved
8-19, 21-44, 63-76, 86-92, 281-286,
D: 12,
aa 358-411
D: 17/21
427,



ORF app.
hypothetical
303-322, 327-338, 344-354, 364-373,
F: 6
aa 588-606
F: SALAT38(895-909): 8/41
428



580 aa
protein
379-394, 405-412, 453-460,

aa 895-909



longer at

501-506, 512-518, 526-542, 560-570,



N terminus;

577-583, 585-604, 622-630,



plus

645-673, 677-691, 702-715, 727-741,



other

748-753, 770-785, 789-796,



changes

851-858, 863-869, 876-881, 898-913,





917-924, 979-986, 991-997,





1004-1009, 1026-1041, 1045-1052,





1107-1114, 1119-1125, 1132-1137,





1154-1169, 1173-1192, 1198-1204,





1240-1254, 1267-1274, 1290-1298,





1612-1627


ORF2548
ORF2711 -
IgG binding
4-37, 44-53, 65-71, 75-82, 105-112,
A: 55,
aa 1-123
A: GSBXK68(1-73): 21/30
429,



12 aa at
protein A
126-132, 136-143, 164-170, 184-190,
B: 54,
aa 207-273
A: GSBXK41(35-123): 1/1
430



N-

194-201, 222-232, 242-248,
C: 35,
aa 310-410
A: GSBXN38(207-273): 19/30



terminus

252-259, 280-291, 300-317, 413-420,
F: 59,

A: GSBXL11(310-363): 10/30





452-460, 485-503
G: 56,

B: GSBXB22(394-406): 37/71






H: 38

F: SALAM17(394-406): 29/41


ORF2746
ORF2507 -
homology
4-9, 12-17, 40-46, 91-103, 106-113,
A: 1,
aa 63-126
A: GSBXO40(66-123): 8/29
431,



3 aa at
with
116-125, 150-160, 172-177, 182-188,
H: 13


432



N-
ORF1
195-206, 241-261, 263-270,



terminus

277-285, 287-294


ORF2797
ORF2470 -
unknown
13-32, 40-75, 82-95, 97-112,
B: 3, E: 2,
aa 159-176
B: GSBXE85(159-176): 11/27
433,



24 aa at

115-121, 124-154, 166-192, 201-225,
F: 13,
aa 325-339
F: SAIAQ47(159-176): 8/41
434



N-terminus

227-252, 268-273, 288-297, 308-375,
H: 3





379-434


ORF2960
ORF2298 -
putative
8-31, 35-44, 106-113, 129-135,
C: 101,
aa 1-80
C: GSBYG32(1-80):: 6/7
435,



5 aa at
Exotoxin
154-159, 168-178, 203-215, 227-236,
E: 2,
aa 48-121
C: GSBYG61-bhe2(48-116):
436



N-

240-249, 257-266, 275-281,
H: 58
aa 98-190
26/30



terminus

290-296, 298-305, 314-319, 327-334


C: GSBYN80(98-190): 13/17


ORF2963
ORF2295 -
putative
8-23, 35-41, 64-70, 81-87, 109-115,
C: 3, E: 3,
aa 17-95
C: GSBYJ58(17-95): 9/15
437,



5 aa at
Exotoxin
121-132, 150-167, 177-188, 194-201,
G: 1


438



N-

208-216, 227-233, 238-248,



terminus

265-271, 279-285


ORF3200
ORF1331
putative
8-32, 45-52, 92-103, 154-159,
A: 11,
aa 8543-8601
A: GSBXL07(8543-8601): 6/28
439,



+8506
extracellular
162-168, 207-214, 232-248, 274-280,
B: 11,
aa 8461-8475

440



aa
matrix
297-303, 343-349, 362-375, 425-442,
C: 36,



at N-
binding
477-487, 493-498, 505-512,
H: 32



terminus
protein
522-533, 543-550, 558-564, 568-574,





580-600, 618-630, 647-652,





658-672, 692-705, 711-727, 765-771,





788-798, 812-836, 847-858,





870-898, 903-910, 1005-1015,





1018-1025, 1028-1036, 1058-1069,





1075-1080, 1095-1109, 1111-1117,





1119-1133, 1166-1172, 1183-1194,





1200-1205, 1215-1222, 1248-1254,





1274-1280, 1307-1317, 1334-1340,





1381-1391, 1414-1420, 1429-1439,





1445-1467, 1478-1495, 1499-1505,





1519-1528, 1538-1550, 1557-1562,





1572-1583, 1593-1599, 1654-1662,





1668-1692, 1701-1707, 1718-1724,





1738-1746, 1757-1783, 1786-1793,





1806-1812, 1815-1829, 1838-1848,





1853-1860, 1875-1881, 1887-1893,





1899-1908, 1933-1940, 1952-1961,





1964-1970, 1977-1983, 1990-1996,





2011-2018, 2025-2038, 2086-2101,





2103-2117, 2177-2191, 2195-2213,





2220-2225, 4′′2237-2249, 2273-2279,





2298-2305, 2319-2327, 2349-2354,





2375-2381, 2391-2398, 2426-2433,





2436-2444, 2449-2454, 2463-2469,





2493-2499, 2574-2589, 2593-2599,





2605-2611, 2615-2624, 2670-2684,





2687-2698, 2720-2727, 2734-2754,





2762-2774, 2846-2866, 2903-2923,





2950-2956, 2985-2998, 3011-3031,





3057-3064, 2′′3102-3117,





3137-3143, 3186-3195, 3211-3219,





3255-3270, 3290-3300, 3327-3334,





3337-3343, 3390-3396, 3412-3419,





3439-3446, 3465-3470, 3492-3500,





3504-3510, 3565-3573, 3642-3650,





3691-3698, 3766-3775, 3777-3788,





3822-3828, 3837-3847, 3859-3864,





3868-3879, 3895-3902, 3943-3951,





3963-3971, 3991-3997, 4018-4030,





4054-4060, 4074-4099, 4123-4129,





4147-4153, 4195-4201, 4250-4255,





4262-4267, 4270-4277, 4303-4310,





4321-4330, 4343-4352, 4396-4408,





4446-4451, 4471-4481, 4503-4509,





4516-4534, 4596-4604, 4638-4658,





4698-4710, 4719-4732, 4776-4783,





4825-4833, 4851-4862, 4882-4888,





4894-4909, 4937-4942, 5047-5054,





5094-5100, 5102-5112, 5120-5125,





5146-5153, 5155-5164, 5203-5214,





5226-5236, 5278-5284, 5315-5321,





5328-5342, 5348-5359, 5410-5420,





5454-5466, 5481-5489, 5522-5538,





5597-5602, 5607-5614, 0′′5623-5629,





5650-5665, 5707-5719, 5734-5742,





5772-5778, 5785-5790, 5833-5845,





5857-5863, 5899-5904, 5908-5921,





5959-5971, 5981-5989, 6010-6017,





6034-6043, 6058-6064, 6112-6120,





6154-6169, 6210-6217, 6231-6240,





6261-6268, 6288-6294, 6318-6324,





6340-6349, 6358-6369, 6402-6407,





6433-6438, 6483-6493, 6513-6519,





6527-6546, 6561-6574, 6599-6608,





6610-6616, 6662-6673, 6696-6705,





6729-6743, 6769-6775, 6792-6801,





6819-6828, 6840-6846, 6860-6870,





6915-6928, 6966-6972, 7021-7028,





7032-7047, 7096-7101, 7109-7117,





7138-7149, 7157-7162, 7201-7206,





7238-7253, 7283-7294, 7296-7302,





7344-7365, 7367-7376, 7389-7404,





7413-7433, 7475-7482, 7493-7500,





7535-7549, 7596-7608, 7646-7651,





7661-7678, 7722-7731, 7741-7754,





7764-7769, 7776-7782, 7791-7806,





7825-7837, 7862-7875, 7891-7897,





7922-7931, 7974-7981, 7999-8005,





8039-8045, 8049-8065, 8070-8075,





8099-8112, 8119-8125, 8151-8158,





8169-8181, 8226-8232, 8258-8264,





8291-8299, 8301-8310, 8325-8335,





8375-8389, 8394-8400, 8405-8412,





8421-8436, 8478-8485, 8512-8521,





8528-8538, 8564-8579, 8587-8594,





8603-8615, 8626-8637, 8640-8646,





8657-8672, 8684-8691, 8725-8736,





8748-8761, 8777-8783, 8794-8799,





8810-8825, 8851-8862, 8874-8887,





8903-8912, 8914-8926, 8933-8943,





8954-8960, 8979-8988, 9004-9011,





9035-9041, 9056-9069, 9077-9086,





9088-9096, 9106-9111, 9124-9133,





9183-9191, 9224-9231, 9235-9241,





9250-9265, 9279-9290, 9295-9300,





9326-9343, 9408-9414, 9422-9427,





9435-9441, 9455-9461, 9507-9517





9532-9538, 9580-9589, 9594-9600,





9614-9623, 9643-9648, 9665-9683,





9688-9700, 9720-9726, 9742-9758,





9767-9775, 9795-9800, 9817-9835,





9842-9847, 9912-9919, 9925-9938,





9943-9963, 9970-10009,





10025-10031, 10037-10043,





10045-10063, 10066-10073,





10117-10124, 10126-10136,





10203-10210, 10218-10225,





10232-10242, 10287-10292,





10303-10323, 10352-10360,





10385-10396, 10425-10431,





10452-10459, 10480-10485





Bacterial surface display: A, LSA250/1 library in fhuA with patient sera 1 (655); B, LSA50/6 library in lamB with patient sera 1 (484); C, LSA250/1 library in fhuA with IC sera 1 (571); E, LSA50/6 library in lamB with IC sera 2 (454); F, LSA50/6 library in lamB with patient sera P1 (1105); G, LSA50/6 library in lamb with IC sera 1 (471). Ribosome display: D, LSA250/1 library with IC sera (1686).


**prediction of antigenic sequences longer than 5 amino acids was performed with the programme ANTIGENIC (Kolaskar and Tongaonkar, 1990);


#identical sequence present twice in ORF.













TABLE 3





Serological proteome analysis of S. aureus surface


proteins using human sera







a) S. aureus/agr “stress conditions”
















IC35,
Infant pool C2, 5, 6, 10, 12
N22 1:10.000


Spot ID/sera
IC40 1:20,000
N26, C4 1:50,000 each
1:10,000
IC40 1:50,000





PCK2
+
+
−
+


PCK4
+
+++
−
+++


PCK5
−
(+)
−
+


PCK6
+
+
−
+














IC35,
P-pool (P6, 18, 25, 28, 29)
Infant pool C2, 5, 6, 10, 12


Spot ID/sera
40 1:50,000 N22 1:10,000
1:50,000 each
1:10,000





PAC1
++
++
−


PAC2
++
+++
−


PAC3
−
+
−


PAC5
−
++
−















P-pool

IC pool/
IC pool/



(P6, 18, 25, 28, 29)

IgG (N26, IC34, 35)
IgA (N26, IC34, 35)


Spot ID/sera
1:50,000 each
Infant 14 1:10,000
1:30,000 each
1:30,000 each





PAC11
++
−
++
++


PAC12
++
−
++
++


PAC13
−
−
−
++


PAC14
−
−
+
+


PAC15
−
−
+++
+++


PAC16
+
−
+
+


PAC17
+
−
+
+


PAC18
++
−
−
−


PAC19
−
−
++
++


PAC20
++
−
−
−


POV31
+++
−
−
−


POV32
+
−
−
−


POV33
+
−
−
−


POV34
+
−
−
−


POV35
+
−
−
−


POV36
+
−
−
−


POV37
++
−
−
−


POV38
++
−
−
−


POV39
+++
−
−
−


POV40
+++
−
−
−










b) S. aureus/COL “standard conditions”















IC pool









(N26, IC34, 35)
IC35
P18
P25
P1
P29
Infant 18


Spot ID/sera
1:30,000 each
1:20,000
1:10,000
1:10,000
1:5,000
1:2,500
1:10,000





POV2
+++
+++
+++
+++
+++
−
−


POV3.1
+++
+++
+++
+++
+++
−
−


POV3.2
+++
+++
+++
+++
+++
−
−


POV4
+
+++
−
−
−
−
−


POV7
−
−
+++
−
−
−
−


POV10
−
++
(+)
(+)
−
(+)
−


POV12
−
−
−
−
−
+++
−


POV13
++
+++
+++
+++
++
++
−


POV14
++
+++
+++
++
++
++
−


POV15
+
+
−
+
(+)
−
−










c) S. aureus/COL “stress conditions”













P-pool







(P6, 18, 25, 28, 29)
IC34 + IC35

P29



Spot ID/sera
1:50,000 each
1:20,000 each
P18 1:10,000
1:10,000
Infant 14 1:10,000





POV16
−
+++
−
−
−


POV17
−
+++
(+)
−
−


POV18
+
−
++
−
−


POV19
(+)
−
+++
−
−


POV21
−
−
+
−
−


POV23
−
+
−
−
−


POV24
−
+
−
−
−


POV25
+
−
−
−
−
















TABLE 4





S. aureus antigens identified by MALDI-TOF-MS sequencing


(ORFs in bold were also identified by bacterial surface display)


Prediction of antigenic regions in selected antigens identified


by serological proteome analysis using human sera




















S. aureus protein

Seq ID no:
Putative


spot ID
(ORF no./abbrev.)
Putative function (by homology)
(DNA, Prot)
localization





PCK2
ORF0599
Glycinamide-ribosyl synthase
107, 108
cytoplasmic


PCK5
ORF0484 yitU
conserved hypoth. protein (yitU)
109, 110
cytoplasmic


PCK6
ORF2309
membrane-associated malate-quinone
111, 112
peripheral



mqo
oxidase

membrane


POV2
ORF0766 aux1
protein phosphatase contributing to methicilin
113, 114
trans-membrane




resistance


POV4, 17
ORF0078 EF-
C-terminal part of 44 kDa protein similar
115, 116
cytoplasmic/


PAC14, 19
Tu
to elongation factor Tu

secreted


POV51)
ORF0782
3-ketoacyl-acyl carrier protein reductase
117, 118
cytoplasmic




(fabG)


POV7
ORF0317 SecA
protein transport across the membrane
39, 91
cytoplasmic




SecA


POV10
ORF1252 yrzC
hypothetical BACSU 11.9 kd protein
119, 120
cytoplasmic




(upf0074 (rff2) family)


POV12
ORF0621 pdhB
dihydrolipoamide acetyltransferase
121, 122
cytoplasmic




(pdhB)


POV14
ORF0072 rpoB
DNA-directed RNA polymerase β
125, 126
cytoplasmic


POV15
ORF0077 EF-G
85 kD vitronectin binding protein
127, 128
cytoplasmic


POV18
not found
general stress protein YLY1
129, 130
cytoplasmic



YLY1


POV301)
ORF0069 RL7
ribosomal protein L7
131, 132
cytoplasmic


POV21
ORF0103
probable hexulose-6-phosphate synthase
133, 134
cytoplasmic



yckG
(yckG)


,POV24
ORF0419
conserved hypothetical protein (yurX)
137, 138
cytoplasmic



yurX


POV25
ORF2441
glucose inhibited division protein a (gidA)
139, 140
cytoplasmic



gidA


PAC1
ORF1490
protein export protein prsa precursor
173, 174
periplasmic



prsA
(prsA)


PAC2
ORF1931
periplasmic molybdate binding protein
175, 176
surface



ModA
(ModA)


PAC3
ORF2053
heavy metal dependent transcriptional
177, 178
cytoplasmic




activator, putative regulator of multidrug




resistance efflux pump pmrA


PAC5
ORF2233
pyruvate oxidase (ydaP)
179, 180
cytoplasmic



ydaP


PAC11
ORF1361
LPXTGV, extracellularmatrix-bdg.
 3, 56
surface


PAC12
ORF1244
alanyl-tRNA synthetase
159, 160
cytoplasmic



alaS


PAC13
ORF0835
RNA processing enzyme/ATP-bdg.
161, 162
cytoplasmic



ymfA


PAC15
ORF1124
lipoamid acyltransferase component of
163, 164
cytoplasmic



bfmBB
branched-chain alpha-keto acid dehydrogenase




complex


PAC16
ORF0340
glyceraldehydes-3-phosphate
165, 166
cytoplasmic



GAPDH
dehydrogenase


PAC17
not found
5′-methylthioadenosine nucleosidase/

cytoplasmic



ContigB3
S-adenosylhomo-cysteine nucleosidase


PAC20
ORF2711
75% Identity to ORF2715
167, 168
unknown




similar to hypothetical proteins


POV31
ORF0659
29 kDa surface protein
236, 238
surface


POV32
ORF0659
29 kDa surface protein
236, 238
surface


POV33
ORF0659
29 kDa surface protein
236, 238
surface


POV34
ORF0659
29 kDa surface protein
236, 238
surface


POV35
ORF0659
29 kDa surface protein
236, 238
surface


POV36
ORF00661
LPXTG-motif cell wall anchor domain
235, 237
surface




protein


POV37
ORF0659
29 kDa surface protein
236, 238
surface


POV38
ORF0659
29 kDa surface protein
236, 238
surface


POV39
ORF0657
LPXTG-anchored surface protein
 1, 142
surface


POV40
not identified
















S. aureus ORF

Putative antigenic surface areas


Seq ID no: (Protein)
spot ID
no./abbrev.
Putative localization
(Antigenic package)





112
PCK6
ORF2309
peripheral
61-75, 82-87, 97-104, 113-123, 128-133,




mqo
membrane
203-216, 224-229, 236-246, 251-258, 271-286,






288-294, 301-310, 316-329, 337-346,






348-371, 394-406, 418-435, 440-452


114
POV2
ORF766 aux1
trans-membrane
30-37, 44-55, 83-91, 101-118, 121-128,






136-149, 175-183, 185-193, 206-212, 222-229,






235-242


116
POV4
ORF078 EF-Tu
cytoplasmic/secreted
28-38, 76-91, 102-109, 118-141, 146-153,






155-161, 165-179, 186-202, 215-221, 234-249,






262-269, 276-282, 289-302, 306-314,






321-326, 338-345, 360-369, 385-391


176
PAC2
ORF1931
periplasmic
29-44, 74-83, 105-113, 119-125, 130-148,




ModA

155-175, 182-190, 198-211, 238-245


174
PAC1
ORF1490
periplasmic
5-24, 38-44, 100-106, 118-130, 144-154,




prsA

204-210, 218-223, 228-243, 257-264, 266-286,






292-299


168
PAC20
ORF2711
unknown
7-14, 21-30, 34-50, 52-63, 65-72, 77-84,






109-124, 129-152, 158-163, 175-190, 193-216,






219-234
















S. aureus protein

Seq ID no:


spot ID
GI no. or TIGR no.
(ORF no./abbrev.)
Putative function (by homology)
(DNA, Prot)





PCK2
TIGR1280
ORF0599
Glycinamide-ribosyl synthase
107, 108


PCK4
7672993
ORF2268 IsaA
possibly adhesion/aggregation
12, 64


PCK5
TIGR6209
ORF0484 yitU
conserved hypoth. protein (yitU)
109, 110


PCK6
TIGR6182
ORF2309
membrane-associated malate-quinone
111, 112





oxidase


POV2
6434044
ORF0766 aux1
protein phosphatase contributing to methicilin
113, 114





resistance


POV3.1
7672993
ORF2268 IsaA
possibly adhesion/aggregation
12, 64


POV3.2
7672993
ORF2268 IsaA
possibly adhesion/aggregation
12, 64


POV4
TIGR8079
ORF0078 EF-
C-terminal part of 44 kDa protein similar
115, 116




Tu
to elongation factor Tu


POV51)
TIGR8091
ORF0782
3-ketoacyl-acyl carrier protein reductase
117, 118





(fabG)


POV7
2500720
ORF0317 SecA
protein transport across the membrane
39, 91





SecA


POV10
TIGR8097
ORF1252 yrzC
hypothetical BACSU 11.9 kd protein
119, 120





(upf0074 (rff2) family)


POV12
2499415
ORF0621 pdhB
dihydrolipoamide acetyltransferase (pdhB)
121, 122


POV13
7470965
ORF0094 SdrD
fibrinogen-bdg. (LPXTG) protein homolog
123, 124





(SdrD)


POV14
1350849
ORF0072 rpoB
DNA-directed RNA polymerase β
125, 126


POV15
6920067
ORF0077 EF-G
85 kD vitronectin binding protein
127, 128


POV17
TIGR8079
ORF0078
C-terminal part of 44 kDa protein similar
115, 116





to elongation factor Tu


POV18
3025223
not found
general stress protein YLY1
129, 130


POV301)
350771
ORF0069 RL7
ribosomal protein L7
131, 132


POV21

ORF0103
probable hexulose-6-phosphate synthase
133, 134





(yckG)


POV23

ORF0182
S. epidermis)
135, 136





1)identified from a total lysate from S. aureus 8325-4 spa-grown under standard conditions. Seroreactivity with 1/1 patient and 2/4 normal sera but not with infant serum (C5).






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## Claims

1. An isolated antigen comprising the sequence of SEQ ID NO. 142 or an antigenic fragment of SEQ ID NO. 142, wherein the antigenic fragment of SEQ ID NO: 142 comprises the sequence of one or more of amino acids 9-33, 56-62, 75-84, 99-105, 122-127, 163-180, 186-192, 206-228, 233-240, 254-262, 275-283, 289-296, 322-330, 348-355, 416-424, 426-438, 441-452, 484-491, 522-528, 526-544, 527-544, 541-549, 563-569, 578-584, 624-641, 1-42, 6-30, 18-42, 24-53, 209-244, 209-233, 218-244, 395-428, 395-418, 416-428, or 623-647 of SEQ ID NO. 142.

2. The isolated antigen of claim 1 consisting of the sequence of SEQ ID NO. 142.

3. The isolated antigen of claim 1, wherein said antigen consists of an antigenic fragment of SEQ ID NO. 142.

4. The isolated antigen of claim 1, wherein the antigenic fragment of SEQ ID NO. 142 comprises at least 6 amino acids of SEQ ID NO. 142.

5. The isolated antigen of claim 1, wherein the antigenic fragment of SEQ ID NO. 142 comprises at least 8 amino acids of SEQ ID NO. 142.

6. The isolated antigen of claim 1, wherein the antigenic fragment of SEQ ID NO. 142 comprises at least 12 amino acids of SEQ ID NO. 142.

7. The isolated antigen of claim 1, wherein the antigenic fragment of SEQ ID NO. 142 is selected from the group consisting of amino acids 9-33, 56-62, 75-84, 99-105, 122-127, 163-180, 186-192, 206-228, 233-240, 254-262, 275-283, 289-296, 322-330, 348-355, 416-424, 426-438, 441-452, 484-491, 522-528, 526-544, 527-544, 541-549, 563-569, 578-584, and 624-641 of SEQ ID NO. 142.

8. The isolated antigen of claim 1, wherein the antigenic fragment of SEQ ID NO. 142 is selected from the group consisting of amino acids 527-544 of SEQ ID NO. 142 and amino acids 484-491 of SEQ ID NO. 142.

9. The isolated antigen of claim 1, wherein the antigen comprises amino acids 527-544 of SEQ ID NO. 142 or amino acids 484-491 of SEQ ID NO. 142.

10. The isolated antigen of claim 9, wherein the antigen comprises SEQ ID NO. 142.

11. The isolated antigen of claim 1, wherein the antigenic fragment of SEQ ID NO. 142 is selected from the group consisting of amino acids 1-42, 6-30, 18-42, 24-53, 209-244, 209-233, 218-244, 395-428, 395-418, 416-428, 623-647 of SEQ ID NO. 142.

12. A method of producing an antibody comprising:
initiating an immune response in a non-human animal by administering an antigen of claim 1 to said animal;
removing the spleen or spleen cells from said animal;
producing hybridoma cells of said spleen or spleen cells;
selecting and cloning hybridoma cells specific for the antigen; and
producing the antibody by cultivation of said cloned hybridoma cells.

13. A method of producing an antibody preparation comprising:
initiating an immune response in a non-human animal by administering an antigen of claim 1 to said animal;
removing an antibody containing body fluid from said animal; and
producing the antibody preparation by subjecting said antibody containing body fluid to purification steps.