Specification
This invention relates tolmmunogenic Compositions of Staphylococcus Epidermidis
Polypeptide Antigens
FIELD OF THE INVENTION
The present invention relates to immunogenic compositions, comprising
polypeptides isolated from Staphylococcus epidermidis. The invention also relates to
polynucleotides encoding Staphylococcus epidermidis polypeptides and their use in
immunogenic compositions. In addition, the invention relates to methods of inducing an
immune response in mammals against Staphylococcus epidermidis and Staphylococcus
aureus using immunogenic compositions of the Staphylococcus epidermidis
polypeptides and polynucleotides. The invention also relates to methods for detecting
Staphylococcus epidermidis in a biological sample.
BACKGROUND OF THE INVENTION
Staphylococcus epidermidis is a major component of the normal human
microbial flora on the skin and mucous membranes and was once considered only a
contaminant when cultured from an infected patient. See Heilmann, C. and G. Peters,
Biology and pathogenicity of Staphylococcus epidermidis, in Gram-positive pathogens,
V.A. Fischetti, Editor. 2000, American Society for Microbiology: Washington, D.C. p.
442-449; von Eiff, C., et a/., Lancet Infect Dis, 2(11): p. 677-85 (2002). It is now widely
accepted to be an opportunistic pathogen of great importance and a leading cause of
nosocomial bloodstream infections. See Am J Infect Control, 27: p. 520-32 (1999);
Diekema, D.J., et a/., Int J Antimicrob Agents, 20(6): p. 412-8 (2002); Edmond, M.B., et
at., Clin Infect Dis, 29(2): p. 239-44 (1999). These infections are primarily associated
with the presence of an indwelling foreign polymer body such as a venous catheter,
prosthetic joint or prosthetic heart valve. See Heilmann, C. and G. Peters, Biology and
pathogenicity of Staphylococcus epidermidis, in Gram-positive pathogens, V.A.
Fischetti, Editor. 2000, American Society for Microbiology: Washington, D.C. p. 442-449;
von Eiff, C., et a/., Lancet Infect Dis, 2(11): p. 677-85 (2002). Infection is thought to
result from introduction of Staphylcoccus epidermidis from the patient's skin upon
insertion of the prosthetic device. Colonization and subsequent biofilm formation can
lead to bacteremia with the potential for hematogenous spread to other sites in the
body. These infections are often difficult to treat, arising from the reduced killing of
bacteria within a biofilm by antibiotics and also an increase in antibiotic resistance
among clinical isolates. See Diekema, D.J., et a/., Int J Antimicrob Agents, 20(6): p.
412-8 (2002); Edmond, M.B., et a/., Clin Infect Dis, 29(2): p. 239-44 (1999); Lewis, K.,
Antimicrob Agents Chemother, 45(4): p. 999-1007 (2001); Raad, I. et a/., Clin Infect Dis,
26(5): p. 1182-7 (1998). Staphylcoccus epidermidis with reduced susceptibility to
vancomycin have been reported. See Sanyal, D. and D. Greenwood, J Med Microbiol,.
39(3): p. 204-10 (1993); Sanyal, D., et a/., Lancet, 337(8732): p. 54 (1991). Difficulty
treating these infections necessitates the use of immunization as a means to prevent
infection.
Biofilm formation is a major virulence determinant for Staphylcoccus epidermidis
infections. Consequently, research on Staphylcoccus epidermidis surface proteins has
focused on those proteins involved in biofilm formation. These proteins have been
subdivided into groups based on their involvement in the two major steps of biofilm
formation: 1) primary attachment, staphylococcal surface protein-1 (SSP-1), autolysin
(AtlE), Fbe (SdrG) and GehD and 2) bacterial cell accumulation, Bap homologous
protein (Bhp), accumulation associated protein (AAP) and autolysin (AtlE). See von Eiff,
C., et a/., Lancet Infect Dis, 2002. 2(11): p. 677-85; Vuong, C., et a/., J Infect Dis,
188(5): p. 706-18 (2003); Veenstra, G.J., et a/., J Bacteriol., 178(2): p. 537-41 (1996);
Rupp, M.E., et a/., J Infect Dis, 183(7): p. 1038-42 (2001); Hussain, M., et a/., Infect
Immun, 65(2): p. 519-24 (1997); Nilsson, M., et a/., Infect Immun, 66(6): p. 2666-73
(1998); Davis, S.L., et a/., J Biol Chem, 276(30): p. 27799-805 (2001); and Bowden,
M.G., et a/., J Biol Chem, 277(45): p. 43017-43023 (2002). Comparatively less effort
has been exerted towards the identification of surface proteins expressed upon
exposure to the environmental cues within the host or those involved in host-parasite
interactions.
Staphylcoccus epidermidis must undergo a transition from commensal to
pathogen and adapt to its microenvironment within the host. For a commensal to
transition to a pathogen it must gain access to host tissue, sense changes in its
environment, alter gene expression so that it is able to evade host defenses, attach and
adhere to host factors, grow and divide in the presence of different nutrients and host
defenses. Proteins on the bacterial surface make initial contact with the new
environment within the host. The many functions of these proteins include sensing the
environment, scavenging and transporting nutrients, defending against the host immune
system and binding host proteins. Surface exposed proteins can also serve as points of
contact or recognition by the host immune system and can be targets for a humoral
immune response against the bacterium. Josefsson, E., et a/., J Infect Dis, 184(12): p.
1572-80 (2001); Swiatlo, E., et a/., Infect Immun, 71(12): p. 7149-53 (2003); Grifantini,
R., et a/., Nat Biotechnol, 20(9): p. 914-21 (2002). Thus, there is an immediate need for
identifying promising candidates among Staphylococcus epidermidis proteins for use in
immunogenic compositions that induce immune responses to disease causing
serotypes of Staphylococcus epidermidis.
SUMMARY OF THE INVENTION
The present invention provides an immunogenic composition comprising a
polypeptide having an amino acid sequence chosen from one or more of SEQ ID NO: 1
through SEQ ID NO: 32, a biological equivalent thereof, or a fragment thereof. In a
particular embodiment, the polypeptide is immunoreactive with antibodies in the serum
of rabbits infected with Staphylococcus epidermidis. In another embodiment, the
polypeptide binds to one or more rabbit serum proteins.
In certain embodiments, the immunogenic composition further comprises a
pharmaceutically acceptable carrier. In other embodiments, the immunogenic
compositions of the invention also comprise one or more adjuvants. In still another
embodiment, the immunogenic composition further comprises a Staphylococcus
epidermidis polysaccharide antigen. In still another embodiment, the immunogenic
composition further comprises a Staphylococcus aureus polysaccharide or polypeptide
antigen.
The present invention provides immunogenic compositions, comprising a
polypeptide isolated from Staphylococcus epidermidis.
The present invention provides an immunogenic composition comprising a
Staphylococcus epidermidis polypeptide wherein the polypeptide further comprises
heterologous amino acids. In a particular embodiment, the polypeptide is a fusion
polypeptide. In another embodiment, the polypeptide is a recombinant polypeptide. In
still another embodiment, the invention provides an immunogenic composition
comprising a Staphylococcus epidermidis polypeptide wherein the polypeptide
comprises a neutralizing epitope of Staphylococcus epidermidis. In a certain
embodiment, the polypeptide is a lipoprotein.
The present invention further provides immunogenic compositions, comprising a
Staphylococcus epidermidis polypeptide, wherein the polypeptide is encoded by a
polynucleotide comprising a nucleotide sequence having at least about 95% identity to a
nucleotide sequence chosen from one of SEQ ID NO: 33 through SEQ ID NO: 64 or a
degenerate variant thereof, or a fragment thereof. In a particular embodiment, the
Staphylococcus epidermidis polynucleotide sequence is selected from the group
consisting of SEQ ID NO: 40, SEQ ID NO: 42, SEQ ID NO: 43, SEQ ID NO: 44, SEQ ID
NO: 46, SEQ ID NO: 50, SEQ ID NO: 51, SEQ ID NO: 52, SEQ ID NO: 55, SEQ ID NO:
58, SEQ ID NO: 59, and SEQ ID NO: 62, or a degenerate variant thereof, or a fragment
thereof.
The present invention provides an immunogenic composition, wherein the
polynucleotide is derived from Staphylococcus epidermidis. In a particular embodiment,
the polynucleotide further comprises heterologous nucleotides.. In another
embodiment, the polynucleotide is in an expression vector. In still another embodiment,
the expression vector is plasmid DNA. In a certain embodiment, the polynucleotide is a
recombinant polynucleotide. In another embodiment, the polynucleotide is operatively
linked to one or more gene expression regulatory elements. In still another
embodiment, the polynucleotide directs the expression of a neutralizing epitope of
Staphylococcus epidermidis.
The invention also provides an immunogenic composition comprising a
Staphylococcus epidermidis polypeptide encoded by a polynucleotide, wherein the
immunogenic composition further comprises a transfection facilitating agent. In a
particular embodiment, said transfection facilitating agent is bupivicaine.
The present invention also provides a method of inducing an immune response
against Staphylococcus epidermidis comprising administering to a mammal an
immunogenic amount of a composition comprising: a polypeptide having an amino acid
sequence chosen from one or more of SEQ ID NO: 1 through SEQ ID NO: 32 or a
biological equivalent thereof, or a fragment thereof, and a pharmaceutically acceptable
carrier.
In addition, the present invention provides a method of inducing an immune
response against Staphylococcus epidermidis comprising administering to a mammal an
immunogenic amount of a composition comprising: a polynucleotide having a nucleotide
sequence chosen from one or more of SEQ ID NO: 33 through SEQ ID NO: 64, a
degenerate variant thereof, or a fragment thereof and a pharmaceutically acceptable
carrier.
In one embodiment, the invention provides an immunogenic composition
comprising a polynucleotide having a nucleotide sequence chosen from one of SEQ ID
NO: 33 through SEQ ID NO: 64, a degenerate variant thereof, or a fragment thereof and
is comprised in an expression vector. In another embodiment, the polynucleotide is
derived from Staphylococcus epidermidis. In still another embodiment the
polynucleotide comprises heterologous nucleotides.
In a certain embodiment, the invention provides a method for the detection
and/or identification of Staphylococcus epidermidis in a biological sample comprising:
(a) contacting the sample with an oligonucleotide probe of a polynucleotide comprising
the nucleotide sequence chosen from one of SEQ ID NO:33 through SEQ ID NO: 64, or
a degenerate variant thereof, or a fragment thereof, under conditions permitting
hybridization; and (b) detecting the presence of hybridization complexes in the sample,
wherein hybridization complexes indicate the presence of Staphylococcus epidermidis in
the sample.
In other embodiments, the invention provides a method for the detection and/or
identification of antibodies to Staphylococcus epidermidis in a biological sample
comprising: (a) contacting the sample with a polypeptide comprising an amino acid
sequence chosen from one of SEQ ID NO: 1 through SEQ ID NO: 32 or a biological
equivalent thereof, or a fragment thereof, under conditions permitting immune complex
formation; and detecting the presence of immune complexes in the sample, wherein
immune complexes indicate the presence of Streptococcus pneumoniae in the sample.
In a particular embodiment, the immunogenic composition comprises a
Staphylococcus epidermidis polypeptide sequence selected from the group consisting of
SEQ ID NO: 8, SEQ ID NO: 10, SEQ ID NO: 11, SEQ ID NO: 12, SEQ ID NO: 14, SEQ
ID NO: 18, SEQ ID NO: 19, SEQ ID NO: 20, SEQ ID NO: 23, SEQ ID NO: 26, SEQ ID
NO: 27, SEQ ID NO: 30, a biological equivalent thereof, or a fragment thereof. In
another embodiment, the immunogenic composition comprises a Staphylococcus
epidermidis polynucleotide sequence selected from the group consisting of SEQ ID NO:
40, SEQ ID NO: 42, SEQ ID NO: 43, SEQ ID NO: 44, SEQ ID NO: 46, SEQ ID NO: 50,
SEQ ID NO: 51, SEQ ID NO: 52, SEQ ID NO: 55, SEQ ID NO: 58, SEQ ID NO: 59, SEQ
ID NO: 62, or a degenerate variant thereof, or a fragment thereof.
In yet another embodiment, the invention provides a method of inducing an
immune response against Staphylococcus aureus comprising administering to a
mammal an immunogenic amount of a composition comprising: a Staphylococcus
epidermidis polypeptide sequence selected from the group consisting of SEQ ID NO: 8,
SEQ ID NO: 10, SEQ ID NO: 11, SEQ ID NO: 12, SEQ ID NO: 14, SEQ ID NO: 18, SEQ
ID NO: 19, SEQ ID NO: 20, SEQ ID NO: 23, SEQ ID NO: 26, SEQ ID NO: 27, SEQ ID
NO: 30, a biological equivalent thereof, or a fragment thereof.
In a particular embodiment, the invention provides a method of inducing an
immune response against Staphylococcus aureus comprising administering to a
mammal an immunogenic amount of a composition comprising: a Staphylococcus
epidermidis polynucleotide sequence selected from the group consisting of SEQ ID NO:
40, SEQ ID NO: 42, SEQ ID NO: 43, SEQ ID NO: 44, SEQ ID NO: 46, SEQ ID NO: 50,
SEQ ID NO: 51, SEQ ID NO: 52, SEQ ID NO: 55, SEQ ID NO: 58, SEQ ID NO: 59, SEQ
ID NO: 62, or a degenerate variant thereof, or a fragment thereof.
BRIEF DESCRIPTION OF THE DRAWINGS
Figure 1 depicts protein expression profiles of cell wall fractions from S.
epidermidis 0-47 grown in TSB (1A and 1C) or 70% rabbit serum (1B and 1D), which
were compared by 2D gel electrophoresis. Proteins were separated on pH 4-7 IPG
strips in the first dimension followed by SDS-PAGE in the second dimension, transferred
to nitrocellulose and detected by fluorescent stain (1A and 1C). Immunoreactive
proteins were visualized with immune sera (1B and 1D) from rabbits infected with S.
epidermidis 0-47. Molecular weight markers are labeled to the left.
Figure 2 depicts fluorescent stained blot (2A) and immunoblot (2B) of a cell
surface fraction from S. epidermidis 0-47 grown in 70% rabbit serum separated on pH 4-
7 IPG strips in the first dimension and SDS-PAGE in the second dimension. The
proteins in the spots were identified by mass spec analysis.
Figure 3 depicts proteins, which were eluted from the surface of S. epidermidis
0-47 grown in TSB or 70% rabbit serum with increasing concentrations of NaCI or 4.0M
urea. Asteriks indicate enriched proteins eluted from the surface of S. Epi grown in the
presence of serum. Bacteria were washed 3X with TBS then sequentially with 0.5M and
1.0 M NaCI and 4.0 M urea. Protein concentrations were determined for each of the
samples and 0.75 ug was run on a 4-20% gradient gel. No protein was detected by
protein assay in the samples eluted from the surface of TSB-grown bacteria (lanes 2-5),
so 25 ul was loaded onto the gel. Lane 1, rabbit serum; Lanes 2 and 6 - 0.15M NaCI
eluate; Lanes 3 and 7 - 0.5M NaCI, Lanes 4 and 8 -1.0 M NaCI; Lane 5 and 9 - 4.0 M
urea.
Figure 4 depicts a 2D transfer of cell surface proteins from S. epidermidis, which
was fluorescently stained for protein (4A) and probed with biotinylated serum proteins
(4B) eluted from S. epidermidis grown in 70% rabbit serum. The spots were visualized
with a streptavidin-alkaline phosphatase conjugate. The proteins in the spots were
identified by mass spectroscopy.
DETAILED DESCRIPTION OF THE INVENTION
Upon exposure to the bloodstream of the host, invading bacteria encounter
environmental cues specific to the new environment. These cues are detected by the
bacteria and signal adaptive changes in protein expression that may be detectable in
cell wall purified proteins. Often, proteins and carbohydrates at the bacterial cell wall
are candidates for inclusion in immunogenic compositions for treating or preventing
bacterial infections. Whether an upregulated protein interacts with the host or plays a
role in nutrient acquisition, it is important to the bacteria and therefore plays a role in
survival of the bacteria and pathogenesis. Growth of bacteria in body fluids (ie. serum,
peritoneal dialysate fluid, and urine) has been used as a model system to mimic some of
the signals bacteria encounter within the host. See Wiltshire, M.D. and S.J. Foster,
Infect Immun, 69(8): p. 5198-202 (2001); Shepard, B.D. and M.S. Gilmore, Infect
Immun, 70(8): p. 4344-52 (2002); Smith, D.G., et al., Infect Immun, 59(2): p. 617-24
(1991); McDermid, K.P., et al., Infect Immun, 61(5): p. 1743-9 (1993). One or more of
these culture conditions was found to alter gene expression in Enterococcus faecalis, S.
aureus and Staphylcoccus epidermidis and those proteins identified as being increased
in expression in the altered culture conditions were found to belong to different classes
of proteins having a variety of functions. See Wiltshire, M.D. and S.J. Foster, Infect
Immun, 69(8): p. 5198-202 (2001); Shepard, B.D. and M.S. Gilmore, Infect Immun,
70(8): p. 4344-52 (2002).
The most common predisposing factor for a Staphylcoccus epidermidis infection
is the implantation of a prosthetic device. An implanted prosthetic device becomes
coated with plasma and matrix proteins including fibrinogen, vitronectin, von Willebrand
factor and fibronectin. See von Eiff, C., et al.,. Eur J Clin Microbiol Infect Dis, 18(12): p.
843-6 (1999). These proteins often act as ligands for Staphylococcal epidermidis
surface proteins, thus allowing the bacteria to bind and colonize the prosthetic device.
Staphylcoccus epidermidis is known to express proteins that bind to fibrinogen,
vitronectin and fibronectin. See Nilsson, M., et al., A fibrinogen-binding protein of
Staphylococcus epidermidis. Infect Immun, 66(6), p. 2666-73 (1998); Davis, S.L., et al.,
J Biol Chem, 276(30), p. 27799-805 (2001); Williams, R.J., et al., Infect Immun,. 70(12),
p. 6805-10 (2002); Heilmann, C., et al., Mol Microbiol, 24(5), p. 1013-24 (1997). It is
reasonable to expect that Staphylcoccus epidermidis will bind additional serum proteins
in making the transition from commensal to pathogen.
The invention described hereinafter addresses the need for Staphylococcus
epidermidis immunogenic compositions that effectively prevent or treat most or all of the
disease caused by serotypes of Staphylococcus epidermidis. The invention further
addresses the need for methods of diagnosing Staphylococcus epidermidis infection.
The present invention has identified Staphylococcus epidermidis open reading frames,
hereinafter ORFs, which encode antigenic polypeptides. More particularly, the
Staphylococcus epidermidis ORFs encode polypeptides that serve as potential
antigenic polypeptides in immunogenic compositions. In certain embodiments, the
invention comprises Staphylococcus epidermidis polynucleotide ORFs encoding surface
localized, exposed, secreted or membrane associated polypeptide antigens.
In other embodiments, the invention comprises vectors comprising ORF
sequences and host cells or animals transformed, transfected or infected with these
vectors. The invention also comprises transcriptional gene products of Staphylococcus
epidermidis ORFs, such as, for example, mRNA, antisense RNA, antisense
oligonucleotides and ribozyme molecules, which can be used to inhibit or control growth
of the microorganism. The invention relates also to methods of detecting these nucleic
acids or polypeptides and kits for diagnosing Staphylococcus epidermidis infection. The
invention also relates to immunogenic compositions for the prevention and/or treatment
of bacterial infection, in particular infection caused by or exacerbated by Staphylococcus
epidermidis. In particular embodiments, the immunogenic compositions are used for the
treatment or prevention of systemic diseases, which are induced or exacerbated by
Staphylococcus epidermidis. In other embodiments, the immunogenic compositions are
used for the treatment or prevention of non-systemic diseases, which are induced or
exacerbated by Staphylococcus epidermidis.
A. Staphylococcus epidermidis ORF Polynucleotides and Polypeptides
Isolated and purified Staphylococcus epidermidis ORF polynucleotides are
identified which are used in the production of Staphylococcus epidermidis polypeptides
for inclusion in immunogenic compoitions. More specifically, in certain embodiments,
the ORFs encode Staphylococcus epidermidis surface localized, exposed, membrane
associated or secreted polypeptides, particularly antigenic polypeptides. Thus, in one
aspect, the present invention identifies isolated and purified polynucleotides (ORFs) that
encode Staphylococcus epidermidis surface localized, exposed, membrane associated
or secreted polypeptides for inclusion in immunogenic compositions. In particular
embodiments, a polynucleotide of the present invention is a DMA molecule, wherein the
DMA may be genomic DMA, chromosomal DMA, plasmid DMA or cDNA. In another
embodiment, a polynucleotide is a recombinant polynucleotide, which encodes a
Staphylococcus epidermidis polypeptide comprising an amino acid sequence that has at
least 95% identity to an amino acid sequence of one of SEQ ID NO: 1 through SEQ ID
NO: 32 or a fragment thereof. In another embodiment, an isolated and purified ORF
polynucleotide comprises a nucleotide sequence that has at least 95% identity to one of
the ORF nucleotide sequences of SEQ ID NO: 33 through SEQ ID NO: 64, a
degenerate variant thereof, or a complement thereof. In one embodiment, an ORF
polynucleotide of one of SEQ ID NO: 33 through SEQ ID NO: 64 is comprised in a
plasmid vector and expressed in a prokaryotic host cell.
As used hereinafter, the term "polynucleotide" means a sequence of nucleotides
connected by phosphodiester linkages. Polynucleotides are presented hereinafter in
the direction from the 5' to the 3' direction. A polynucleotide of the present invention can
comprise from about 10 to about several hundred thousand base pairs. In one
embodiment, a polynucleotide comprises from about 10 to about 3,000 base pairs.
Example lengths of particular polynucleotide are set forth hereinafter.
A polynucleotide as described herein can be a deoxyribonucleic acid (DNA)
molecule, a ribonucleic acid (RNA) molecule, or analogs of the DNA or RNA generated
using nucleotide analogs. The nucleic acid molecule can be single-stranded or doublestranded,
but preferably is double-stranded DNA. Where a polynucleotide is a DNA
molecule, that molecule can be a gene, a cDNA molecule or a genomic DNA molecule.
Nucleotide bases are indicated hereinafter by a single letter code: adenine (A), guanine
(G), thymine (T), cytosine (C), inosine (I) and uracil (U).
"Isolated" means altered "by the hand of man" from the natural state. If a
composition or substance occurs in nature, in order for it to be considered "Isolated" it
must have been changed or removed from its original environment, or both. For
example, a polynucleotide or a polypeptide naturally present in a living animal is not
"isolated," but the same polynucleotide or polypeptide separated from the coexisting
materials of its natural state is "isolated," as the term is employed hereinafter.
As used herein, an "isolated" polynucleotide is free of sequences which naturally
flank the nucleic acid (i.e., sequences located at the 5' and 3' ends of the nucleic acid) in
the genomic DNA of the organism from which the nucleic acid is derived. For example,
in various embodiments, the isolated Staphylococcus epidermidis nucleic acid molecule
can contain less than about 5 kb, 4 kb, 3 kb, 2 kb, 1 kb, 0. 5 kb or 0. 1 kb of nucleotide
sequences which naturally flank the nucleic acid molecule in genomic DNA of the cell
from which the nucleic acid is derived. However, the Staphylococcus epidermidis
nucleic acid molecule can be fused to other protein encoding or regulatory sequences
and still be considered isolated.
ORF polynucleotides and thus the polypeptides described herein may be
obtained using standard cloning and screening techniques from a cDNA library derived
from mRNA. Polynucleotides of the invention can also be obtained from natural sources
such as genomic DMA libraries (e.g., a Staphylococcus epidermidis library) or can be
synthesized using well known and commercially available techniques.
Also encompassed herein are nucleic acid molecules that differ from the
nucleotide sequences shown in SEQ ID NO:33 through SEQ ID NO:64 (and fragments
thereof) due to degeneracy of the genetic code and thus encode the same
Staphylococcus epidermidis polypeptide as that encoded by the nucleotide sequence
shown in SEQ ID NO:33 through SEQ ID NO:64.
Orthologues and allelic variants of the Staphylococcus epidermidis
polynucleotides can readily be identified using methods well known in the art. Allelic
variants and Orthologues of the polynucleotides will comprise a nucleotide sequence
that is typically at least about 70-75%, more typically at least about 80-85%, and most
typically at least about 90-95% or more homologous to the nucleotide sequence shown
in SEQ ID NO:33 through SEQ ID NO:64, or a fragment of these nucleotide sequences.
Such nucleic acid molecules can readily be identified as being able to hybridize under
stringent conditions, to the nucleotide sequence shown in SEQ ID NO:33 through SEQ
ID NO:64, or a fragment of these nucleotide sequences.
Moreover, the polynucleotides can comprise only a fragment of the coding region
of a Staphylococcus epidermidis polynucleotide or gene, such as a fragment of one of
SEQ ID NO:33 through SEQ ID NO:64. In certain embodiments, such fragments
encode immunogenic fragments.
When these Staphylococcus epidermidis ORF polynucleotides of the invention
are used for the recombinant production of Staphylococcus epidermidis polypeptides for
inclusion in immunogenic compositions, the polynucleotide may include the coding
sequence for the mature polypeptide, by itself, or the coding sequence for the mature
polypeptide in reading frame with other coding sequences, such as those encoding a
leader or secretory sequence, a pre-, or pro- or prepro- protein sequence, or other
fusion peptide portions. For example, a marker sequence which facilitates purification of
the fused polypeptide can be linked to the coding sequence (see Gentz et a/., Proc,
Natl. Acad. Sci. USA, 86:821-824, 1989, incorporated by reference hereinafter in its
entirety). Thus, contemplated herein is the preparation of polynucleotides encoding
fusion polypeptides permitting His-tag purification of expression products. The
polynucleotide may also contain non-coding 5' and 3' sequences, such as transcribed,
non-translated sequences, splicing and polyadenylation signals.
Thus, a polynucleotide encoding a polypeptide for inclusion in immunogenic
compositions of the present invention, including homologs and orthologs from species
other than Staphylococcus epidermidis, such as Staphylococcus aureus may be
obtained by a process which comprises the steps of screening an appropriate library
under stringent hybridization conditions with a labeled probe having the sequence of
one of SEQ ID NO:33 through SEQ ID NO:64, a fragment thereof; and isolating fulllength
cDNA and genomic clones containing the polynucleotide sequence. Such
hybridization techniques are well known to the skilled artisan. The skilled artisan will
appreciate that, in many cases, an isolated cDNA sequence will be incomplete, in that
the region coding for the polypeptide is cut short at the 5' end of the cDNA. This is a
consequence of reverse transcriptase, an enzyme with inherently low "processivity" (a
measure of the ability of the enzyme to remain attached to the template during the
polymerization reaction), failing to complete a DMA copy of the mRNA template during
first strand cDNA synthesis.
Thus, in certain embodiments, the polynucleotide sequence information provided
herein allows for the preparation of relatively short DMA (or RNA) oligonucleotide
sequences having the ability to specifically hybridize to gene sequences of the selected
polynucleotides disclosed hereinafter. The term "oligonucleotide" as used hereinafter is
defined as a molecule comprised of two or more deoxyribonucleotides or
ribonucleotides, usually more than three (3), and typically more than ten (10) and up to
one hundred (100) or more (although preferably between twenty and thirty). The exact
size will depend on many factors, which in turn depends on the ultimate function or use
of the oligonucleotide. Thus, in particular embodiments, nucleic acid probes of an
appropriate length are prepared based on a consideration of a selected nucleotide
sequence, e.g., a sequence such as that shown in SEQ ID NO:33 through SEQ ID
NO:64. The ability of such nucleic acid probes to specifically hybridize to a
polynucleotide encoding a Staphylococcus epidermidis polypeptide lends them
particular utility in a variety of embodiments. Most importantly, the probes can be used
in a variety of assays for detecting the presence of complementary sequences in a given
sample.
In certain embodiments, it is advantageous to use oligonucleotide primers.
These primers may be generated in any manner, including chemical synthesis, DMA
replication, reverse transcription, or a combination thereof. The sequence of such
primers is designed using a polynucleotide described herein for use in detecting,
amplifying or mutating a defined segment of an ORF polynucleotide that encodes a
Staphylococcus epidermidis polypeptide from prokaryotic cells using polymerase chain
reaction (PCR) technology.
In certain embodiments, it is advantageous to employ a polynucleotide described
herein in combination with an appropriate label for detecting hybrid formation. A wide
variety of appropriate labels are known in the art, including radioactive, enzymatic or
other ligands, such as avidin/biotin, which are capable of giving a detectable signal.
Polynucleotides which are identical or sufficiently identical to a nucleotide
sequence contained in one of SEQ ID NO:33 through SEQ ID NO:64, or a fragment
thereof, may be used as hybridization probes for cDNA and genomnic DMA or as
primers for a nucleic acid amplification (PCR) reaction, to isolate full-length cDNAs and
genomic clones encoding polypeptides described herein and to isolate cDNA and
genomic clones of other genes (including genes encoding homologs and orthologs from
species other than Staphylococcus epidermidis) that have a high sequence similarity to
the polynucleotide sequences set forth in of SEQ ID NO:33 through SEQ ID NO:64, or a
fragment thereof. Typically these nucleotide sequences are from at least about 70%
identical to at least about 95% identical to that of the reference polynucleotide
sequence. The probes or primers will generally comprise at least 15 nucleotides,
preferably, at least 30 nucleotides and may have at least 50 nucleotides. Particularly
preferred probes will have between 30 and 50 nucleotides.
There are several methods available and well known to those skilled in the art to
obtain full-length cDNAs, or extend short cDNAs, for example those based on the
method of Rapid Amplification of cDNA ends (RACE). See Frohman et a/., Proc. Natl.
Acad. Sci. USA 85, 8998-9002, 1988. Recent modifications of the technique,
exemplified by the Marathon™ technology (Clontech Laboratories Inc.) for example,
have significantly simplified the search for longer cDNAs. In the Marathon™ technology,
cDNAs have been prepared from mRNA extracted from a chosen tissue and an
"adaptor" sequence ligated onto each end. Nucleic acid amplification (PCR) is then
carried out to amplify the "missing" 5' end of the cDNA using a combination of gene
specific and adaptor specific oligonucleotide primers. The PCR reaction is then
repeated using "nested" primers, that is, primers designed to anneal within the amplified
product (typically an adaptor specific primer that anneals further 3' in the adaptor
sequence and a gene specific primer that anneals further 5' in the known gene
sequence). The products of this reaction can then be analyzed by DMA sequencing and
a full-length cDNA constructed either by joining the product directly to the existing cDNA
to give a complete sequence, or carrying out a separate full-length PCR using the new
sequence information for the design of the 5' primer.
To provide certain of the advantages in accordance with the present invention, a
preferred nucleic acid sequence employed for hybridization studies or assays includes
probe molecules that are complementary to at least a 10 to about 70 nucleotides long
stretch of a polynucleotide that encodes a Staphylococcus epidermidis polypeptide,
such as that shown in one of SEQ ID NO:33 through SEQ ID NO:64. A size of at least
10 nucleotides in length helps to ensure that the fragment will be of sufficient length to
form a duplex molecule that is both stable and selective. Molecules having
complementary sequences over stretches greater than 10 bases in length are generally
preferred, though, in order to increase stability and selectivity of the hybrid, and thereby
improve the quality and degree of specific hybrid molecules obtained. One will generally
prefer to design nucleic acid molecules having gene-complementary stretches of 25 to
40 nucleotides, 55 to 70 nucleotides, or even longer where desired. Such fragments
can be readily prepared by, for example, directly synthesizing the fragment by chemical
means, by application of nucleic acid reproduction technology, such as the PCR
technology of (U.S. Patent 4,683,202, incorporated hereinafter by reference) or by
excising selected DNA fragments from recombinant plasmids containing appropriate
inserts and suitable restriction enzyme sites.
In another embodiment, it is contemplated that an isolated and purified
polynucleotide comprises a nucleotide sequence that is identical or complementary to a
segment of at least 10 contiguous bases of one of SEQ ID NO:33 through SEQ ID
NO:64, wherein the polynucleotide hybridizes to a polynucleotide that encodes a
Staphylococcus epidermidis polypeptide. Preferably, the isolated and purified
polynucleotide comprises a base sequence that is identical or complementary to a
segment of at least 25 to about 70 contiguous bases of one of SEQ ID NO:33 through
SEQ ID NO:64. For example, the polynucleotide can comprise a segment of bases
identical or complementary to 40 or 55 contiguous bases of the disclosed nucleotide
sequences.
Accordingly, a polynucleotide probe molecule can be used for its ability to
selectively form duplex molecules with complementary stretches of the gene.
Depending on the application envisioned, one will desire to employ varying conditions of
hybridization to achieve varying degree of selectivity of the probe toward the target
sequence (see Table 1 below). For applications requiring a high degree of selectivity,
one will typically desire to employ relatively stringent conditions to form the hybrids. For
some applications, for example, where one desires to prepare mutants employing a
mutant primer strand hybridized to an underlying template or where one seeks to isolate
a Staphylococcus epidermidis homologous polypeptide coding sequence from other
cells, functional equivalents, or the like, less stringent hybridization conditions are
typically needed to allow formation of the heteroduplex (see Table 1). Cross-hybridizing
species can thereby be readily identified as positively hybridizing signals with respect to
control hybridizations. Thus, hybridization conditions are readily manipulated, and thus
will generally be a method of choice depending on the desired results.
For some applications, for example, where one desires to prepare mutants
employing a mutant primer strand hybridized to an underlying template or where one
seeks to isolate a homologous polypeptide coding sequence from other cells, functional
equivalents, or the like, less stringent hybridization conditions are typically needed to
allow formation of the heteroduplex. Cross-hybridizing species are thereby readily
identified as positively hybridizing signals with respect to control hybridizations. In any
case, it is generally appreciated that conditions can be rendered more stringent by the
addition of increasing amounts of formamide, which serves to destabilize the hybrid
duplex in the same manner as increased temperature. Thus, hybridization conditions
are readily manipulated, and thus will generally be a method of choice depending on the
desired results.
Also described herein are polynucleotides capable of hybridizing under reduced
stringency conditions, more preferably stringent conditions, and most preferably highly
stringent conditions, to polynucleotides described hereinafter. Examples of stringency
conditions are shown in Table 1 below: highly stringent conditions are those that are at
least as stringent as, for example, conditions A-F; stringent conditions are at least as
stringent as, for example, conditions G-L; and reduced stringency conditions are at least
as stringent as, for example, conditions M-R.
(Table Removed)
(bp): The hybrid length is that anticipated for the hybridized region(s) of the hybridizing
polynucleotides. When hybridizing a polynucleotide to a target polynucleotide of unknown
sequence, the hybrid length is assumed to be that of the hybridizing polynucleotide. When
polynucleotides of known sequence are hybridized, the hybrid length can be determined by
aligning the sequences of the polynucleotides and identifying the region or regions of optimal
sequence complementarity.
Buffer: SSPE (IxSSPE is 0.15M NaCI, 10mM NaH2PO4, and 1.25mM EDTA, pH 7.4)
can be substituted for SSC (1xSSC is 0.15M NaCI and 15mM sodium citrate) in the hybridization
and wash buffers; washes are performed for 15 minutes after hybridization is complete.
TB through TR: The hybridization temperature for hybrids anticipated to be less than 50
base pairs in length should be 5-10°C less than the melting temperature (Tm) of the hybrid, where
Tm is determined according to the following equations. For hybrids less than 18 base pairs in
length, Tm(°C) = 2(# of A + T bases) + 4(# of G + C bases). For hybrids between 18 and 49 base
pairs in length, Tm(°C) = 81.5 + 16.6(log10[Na+]) + 0.41 (%G+C) - (600/N), where N is the number
of bases in the hybrid, and [Na+] is the concentration of sodium ions in the hybridization buffer
([Na+]for1xSSC = 0.165M).
Additional examples of stringency conditions for polynucleotide hybridization are
provided in Sambrook et a/., 1989, Molecular Cloning: A Laboratory Manual, Cold
Spring Harbor Laboratory Press, Cold Spring Harbor, NY, chapters 9 and 11, and
Ausubel et a/., 1995, Current Protocols in Molecular Biology, eds., John Wiley & Sons,
Inc., sections 2.10 and 6.3-6.4, incorporated hereinafter by reference.
B. Staphylococcus epidermidis Polypeptides
In particular embodiments, the present invention provides isolated and purified
Staphylococcus epidermidis polypeptides for use in immunogenic compositions.
Preferably, a Staphylococcus epidermidis polypeptide used in an immunogenic
composition of the invention is a recombinant polypeptide. In certain embodiments, a
Staphylococcus epidermidis polypeptide comprises the amino acid sequence that has at
least 95% identity to the amino acid sequence of one of SEQ ID NO: 1 through SEQ ID
NO: 32, a biological equivalent thereof, or a fragment thereof.
A Staphylococcus epidermidis polypeptide used in an immunogenic composition
of the present invention encompasses a polypeptide that comprises: 1) the amino acid
sequence shown in one of SEQ ID NO: 1 through SEQ ID NO: 32; 2) functional and
non-functional naturally occurring variants or biological equivalents of Staphylococcus
epidermidis polypeptides of SEQ ID NO: 1 through SEQ ID NO: 32; 3) recombinantly
produced variants or biological equivalents of Staphylococcus epidermidis polypeptides
of SEQ ID NO: 1 through SEQ ID NO: 32; and 4) polypeptides isolated from organisms
other than Staphylococcus epidermidis (orthologues of Staphylococcus epidermidis
polypeptides).
A biological equivalent or variant of such a Staphylococcus epidermidis
polypeptide encompasses 1) a polypeptide isolated from Staphylococcus epidermidis;
and 2) a polypeptide that contains substantially homology to a Staphylococcus
epidermic/is polypeptide.
Biological equivalents or variants of Staphylococcus epidermidis include both
functional and non-functional Staphylococcus epidermidis polypeptides. Functional
biological equivalents or variants are naturally occurring amino acid sequence variants
of a Staphylococcus epidermidis polypeptide that maintains the ability to elicit an
immunological or antigenic response in a subject. Functional variants will typically
contain only conservative substitutions of one or more amino acids of one of SEQ ID
NO: 1 through SEQ ID NO: 32, or substitution, deletion or insertion of non-critical
residues in non-critical regions of the polypeptide (e.g., not in regions containing
antigenic determinants or protective epitopes).
The present invention further provides non-Step/?y/ococcus epidermidis
orthologues of Staphylococcus epidermidis polypeptides. Orthologues of
Staphylococcus epidermidis polypeptides are polypeptides that are isolated from non-
Staphylococcus epidermidis organisms and possess antigenic capabilities of the
Staphylococcus epidermidis polypeptide. Orthologues of a Staphylococcus epidermidis
polypeptide can readily be identified as comprising an amino acid sequence that is
substantially homologous to one of SEQ ID NO: 1 through SEQ ID NO: 32.
Modifications and changes can be made in the structure of a polypeptide of the
present invention and still obtain a molecule having Staphylococcus epidermidis
antigenicity. For example, certain amino acids can be substituted for other amino acids
in a sequence without appreciable loss of antigenicity. Because it is the interactive
capacity and nature of a polypeptide that defines that polypeptide's biological functional
activity, certain amino acid sequence substitutions can be made in a polypeptide
sequence (or, of course, its underlying DNA coding sequence) and nevertheless obtain
a polypeptide with like properties.
In making such changes, the hydropathic index of amino acids can be
considered. The importance of the hydropathic amino acid index in conferring
interactive biologic function on a polypeptide is generally understood in the art (Kyte and
Doolittle, J Mol Biol, 157: p. 105-132, 1982). It is known that certain amino acids can be
substituted for other amino acids having a similar hydropathic index or score and still
result in a polypeptide with similar biological activity. Each amino acid has been
assigned a hydropathic index on the basis of its hydrophobicity and charge
characteristics. Those indices are: isoleucine (+4.5); valine (+4.2); leucine (+3.8);
phenylalanine (+2.8); cysteine/cystine (+2.5); methionine (+1.9); alanine (+1.8); glycine
(-0.4); threonine (-0.7); serine (-0.8); tryptophan (-0.9); tyrosine (-1.3); proline (-1.6);
histidine (-3.2); glutamate (-3.5); glutamine (-3.5); aspartate (-3.5); asparagine (-3.5);
lysine (-3.9); and arginine (-4.5).
It is believed that the relative hydropathic character of the amino acid residue
determines the secondary and tertiary structure of the resultant polypeptide, which in
turn defines the interaction of the polypeptide with other molecules, such as enzymes,
substrates, receptors, antibodies, antigens, and the like. It is known in the art that an
amino acid can be substituted by another amino acid having a similar hydropathic index
and still obtain a functionally equivalent polypeptide. In such changes, the substitution of
amino acids whose hydropathic indices are within +1-2 is preferred, those that are within
+/-1 are particularly preferred, and those within +/-0.5 are even more particularly
preferred.
Substitution of like amino acids can also be made on the basis of hydrophilicity,
particularly where the biological functional equivalent polypeptide or peptide thereby
created is intended for use in immunological embodiments. U.S. Patent 4,554,101,
incorporated hereinafter by reference, states that the greatest local average
hydrophilicity of a polypeptide, as governed by the hydrophilicity of its adjacent amino
acids, correlates with its immunogenicity and antigenicity, i.e. with a biological property
of the polypeptide.
As detailed in U.S. Patent 4,554,101, the following hydrophilicity values have
been assigned to amino acid residues: arginine (+30); lysine (+3.0); aspartate (+3.0
±1); glutamate (+3.0 ±1); serine (+0.3); asparagine (+0.2); glutamine (+0.2); glycine (0);
proline (-0.5 ±1); threonine (-0.4); alanine (-0.5); histidine (-0.5); cysteine (-1.0);
methionine (-1.3); valine (-1.5); leucine (-1.8); isoleucine (-1.8); tyrosine (-2.3);
phenylalanine (-2.5); tryptophan (-3.4). It is understood that an amino acid can be
substituted for another having a similar hydrophilicity value and still obtain a biologically
equivalent, and in particular, an immunologically equivalent polypeptide. In such
changes, the substitution of amino acids whose hydrophilicity values are within ±2 is
preferred, those that are within ±1 are particularly preferred, and those within ±0.5 are
even more particularly preferred.
As outlined above, amino acid substitutions are generally therefore based on the
relative similarity of the amino acid side-chain substituents, for example, their
hydrophobicity, hydrophilicity, charge, size, and the like. Exemplary substitutions which
take various of the foregoing characteristics into consideration are well known to those
of skill in the art and include: arginine and lysine; glutamate and aspartate; serine and
threonine; glutamine and asparagine; and valine, leucine and isoleucine (See Table 2,
below). The present invention thus contemplates immunogenic compositions
comprising functional or biological equivalents of a Staphylococcus epidermidis
polypeptide as set forth above.
(Table Removed)
Biological or functional equivalents of a polypeptide can also be prepared using
site-specific mutagenesis. Site-specific mutagenesis is a technique useful in the
preparation of second generation polypeptides, or biologically functional equivalent
polypeptides or peptides, derived from the sequences thereof, through specific
mutagenesis of the encoding DMA. As noted above, such changes can be desirable
where amino acid substitutions are desirable. The technique further provides a ready
ability to prepare and test sequence variants, for example, incorporating one or more of
the foregoing considerations, by introducing one or more nucleotide sequence changes
into the DMA. Site-specific mutagenesis allows the production of mutants through the
use of specific oligonucleotide sequences which encode the DNA sequence of the
desired mutation, as well as a sufficient number of adjacent nucleotides, to provide a
primer sequence of sufficient size and sequence complexity to form a stable duplex on
both sides of the deletion junction being traversed. Typically, a primer of about 17 to 25
nucleotides in length is preferred, with about 5 to 10 residues on both sides of the
junction of the sequence being altered.
In general, the technique of site-specific mutagenesis is well known in the art.
As will be appreciated, the technique typically employs a phage vector which can exist
in both a single stranded and double stranded form. Typically, site-directed
mutagenesis in accordance herewith is performed by first obtaining a single-stranded
vector which includes within its sequence a DMA sequence which encodes all or a
portion of the Staphylococcus epidermidis polypeptide sequence selected. An
oligonucleotide primer bearing the desired mutated sequence is prepared (e.g.,
synthetically). This primer is then annealed to the singled-stranded vector, and
extended by the use of enzymes such as E. coli polymerase I Klenow fragment, in order
to complete the synthesis of the mutation-bearing strand. Thus, a heteroduplex is
formed wherein one strand encodes the original non-mutated sequence and the second
strand bears the desired mutation. This heteroduplex vector is then used to transform
appropriate cells such as E. coli cells and clones are selected which include
recombinant vectors bearing the mutation. Commercially available kits come with all the
reagents necessary, except the oligonucleotide primers.
A Staphylococcus epidermidis polypeptide or polypeptide antigen used in an
immunogenic composition of the present invention is understood to be any
Staphylococcus epidermidis polypeptide comprising substantial sequence similarity,
structural similarity and/or functional similarity to a Staphylococcus epidermidis
polypeptide comprising the amino acid sequence of one of SEQ ID NO: 1 through SEQ
ID NO: 32. In addition, such a Staphylococcus epidermidis polypeptide or polypeptide
antigen is not limited to a particular source. Thus, the invention provides for the general
detection and isolation of the polypeptides from a variety of sources.
It is contemplated in the present invention, that a Staphylococcus epidermidis
polypeptide may advantageously be cleaved into fragments for use in further structural
or functional analysis, or in the generation of reagents such as Staphylococcus
ep/cterm/d/s-related polypeptides and Staphylococcus ep/cterm/of/s-specific antibodies.
This can be accomplished by treating purified or unpurified Staphylococcus epidermidis
polypeptides with a peptidase such as endoproteinase glu-C (Boehringer, Indianapolis,
IN). Treatment with CNBr is another method by which peptide fragments may be
produced from natural Staphylococcus epidermidis polypeptides. Recombinant
techniques also can be used to produce specific fragments of a Staphylococcus
epidermidis polypeptide.
Fragments of the Staphylococcus epidermidis polypeptides are also included in
the immunogenic compositions of the invention. A fragment is a polypeptide having an
amino acid sequence that is entirely the same as part, but not all, of the amino acid
sequence. The fragment can comprise, for example, at least 7 or more (e.g., 8, 10, 12,
14, 16, 18, 20, or more) contiguous amino acids of an amino acid sequence of one of
SEQ ID NO: 1 through SEQ ID NO: 32. Fragments may be "freestanding" or comprised
within a larger polypeptide of which they form a part or region, most preferably as a
single, continuous region. In one embodiment, the fragments include at least one
epitope of the mature polypeptide sequence.
"Fusion protein" refers to a protein or polypeptide encoded by two, often
unrelated, fused genes or fragments thereof. For example, fusion proteins or
polypeptides comprising various portions of constant region of immunoglobulin
molecules together with another human protein or part thereof have been described. In
many cases, employing an immunoglobulin Fc region as a part of a fusion protein or
polypeptide is advantageous for use in therapy and diagnosis resulting in, for example,
improved pharmacokinetic properties (see e.g., International Application EP-A 0232
2621). On the other hand, for some uses it is desirable to be able to delete the Fc part
after the fusion protein or polypeptide has been expressed, detected and purified.
It is contemplated that Staphylococcus epidermidis polypeptides may be isolated
from Staphylococcus epidermidis or prepared recombinantly as described herein.
C. STAPHYLOCOCCUS EPIDERMIDIS POLYNUCLEOTIDE AND POLYPEPTIDE VARIANTS
"Variant" as the term is used hereinafter, is a polynucleotide or polypeptide that
differs from a reference polynucleotide or polypeptide respectively, but retains essential
properties. A typical variant of a polynucleotide differs in nucleotide sequence from
another, reference polynucleotide. Changes in the nucleotide sequence of the variant
may or may not alter the amino acid sequence of a polypeptide encoded by the
reference polynucleotide. Nucleotide changes may result in amino acid substitutions,
additions, deletions, fusions and truncations in the polypeptide encoded by the
reference sequence, as discussed below. A typical variant of a polypeptide differs in
amino acid sequence from another, reference polypeptide. Generally, differences are
limited so that the sequences of the reference polypeptide and the variant are closely
similar overall and, in many regions, identical. A variant and reference polypeptide may
differ in amino acid sequence by one or more substitutions, additions, deletions in any
combination. A substituted or inserted amino acid residue may or may not be one
encoded by the genetic code. A variant of a polynucleotide or polypeptide may be a
naturally occurring such as an allelic variant, or it may be a variant that is not known to
occur naturally. Non-naturally occurring variants of polynucleotides and polypeptides
may be made by mutagenesis techniques or by direct synthesis.
"Identity," as known in the art, is a relationship between two or more polypeptide
sequences or two or more polynucleotide sequences, as determined by comparing the
sequences. In the art, "identity" also means the degree of sequence relatedness
between polypeptide or polynucleotide sequences, as the case may be, as determined
by the match between strings of such sequences. "Identity" and "similarity" can be
readily calculated by known methods, including but not limited to those described in
(Computational Molecular Biology, Lesk, A. M., ed., Oxford University Press, New York,
1988; Biocomputing: Informatics and Genome Projects, Smith, D. W., ed., Academic
Press, New York, 1993; Computer Analysis of Sequence Data, Part I, Griffin, A. M., and
Griffin, H. G., eds., Humana Press, New Jersey, 1994; Sequence Analysis in Molecular
Biology, von Heinje, G., Academic Press, 1987; and Sequence Analysis Primer,
Gribskov, M. and Devereux, J., eds., M Stockton Press, New York, 1991; and Carillo,
H., and Lipman, D., SIAM J. Applied Math., 48: 1073 (1988). Methods to determine
identity are designed to give the largest match between the sequences tested. Methods
to determine identity and similarity are codified in publicly available computer programs.
Computer program methods to determine identity and similarity between two sequences
include, but are not limited to, the GCG program package (Devereux et a/., Nucleic
Acids Research 12(1):387, 1984), BLASTP, BLASTN, TBLASTN and FASTA (Altschul
et a/., J. Molec. Biol. 215:403-410, 1990). The BLASTX program is publicly available
from NCBI and other sources (BLAST Manual, Altschul, S., et a/., NCBI NLM NIH
Bethesda, Md. 20894; Altschul et a/., J. Molec. Biol. 215:403-410, 1990.). The well
known Smith-Waterman algorithm may also be used to determine identity.
By way of example, a polynucleotide sequence described herein may be
identical to the reference sequence of one of SEQ ID NO: 33 through SEQ ID NO: 64,
that is be 100% identical, or it may include up to a certain integer number of nucleotide
alterations as compared to the reference sequence. Such alterations are selected from
the group consisting of at least one nucleotide deletion, substitution, including transition
and transversion, or insertion, and wherein said alterations may occur at the 5' or 3'
terminal positions of the reference nucleotide sequence or anywhere between those
terminal positions, interspersed either individually among the nucleotides in the
reference sequence or in one or more contiguous groups within the reference
sequence. The number of nucleotide alterations is determined by multiplying the total
number of nucleotides in one of SEQ ID NO: 33 through SEQ ID NO: 64 by the
numerical percent of the respective percent identity (divided by 100) and subtracting
that product from said total number of nucleotides in one of SEQ ID NO: 33 through
SEQ ID NO: 64.
For example, an isolated Staphylococcus epidermidis polynucleotide comprising
a polynucleotide sequence that has at least 70% identity to the nucleic acid sequence of
one of SEQ ID NO: 33 through SEQ ID NO: 64; a degenerate variant thereof or a
fragment thereof, wherein the polynucleotide sequence may include up to nn nucleic
acid alterations over the entire polynucleotide region of the nucleic acid sequence of
one of SEQ ID NO: 33 through SEQ ID NO: 64, wherein nn is the maximum number of
alterations and is calculated by the formula:
nn
50% bacterial killing, as determined by comparison to assay controls. Specimens that
demonstrate less than 50% killing at the lowest serum dilution tested (1:8), are reported
as having an OPA titer of 4. The highest dilution tested is 1:2560. Samples with >50%
killing at the highest dilution are repeated, beginning with a higher initial dilution. The
method described above is a modification of Gray's method (Gray, Conjugate Vaccines
Supplement, p. 694-697, 1990).
A test serum control, which contains test serum plus bacterial cells and heat
inactivated complement, is included for each individual serum. This control is used to
assess whether the presence of antibiotics or other serum components are capable of
killing the bacterial strain directly (i.e. in the absence of complement or PMN's). A
human serum with known opsonic titer is used as a positive human serum control. The
opsonic antibody titer for each unknown serum is calculated as the reciprocal of the
initial dilution of serum giving 50% cfu reduction compared to the control without serum.
A whole cell ELISA assay is also used to assess in vitro immunogenicity and
surface exposure of the polypeptide antigen, wherein the bacterial strain of interest
(Staphylococcus epidermidis) is coated onto a plate, such as a 96 well plate, and test
sera from an immunized animal is reacted with the bacterial cells. If any antibody,
specific for the test polypeptide antigen, is reactive with a surface exposed epitope of
the polypeptide antigen, it can be detected by standard methods known to one skilled in
the art.
Any polypeptide demonstrating the desired in vitro activity.is then tested in an in
vivo animal challenge model. In certain embodiments, immunogenic compositions are
used in the immunization of an animal (e.g., a mouse) by methods and routes of
immunization known to those of skill in the art (e.g., intranasal, parenteral, oral, rectal,
vaginal, transdermal, intraperitoneal, intravenous, subcutaneous, etc.). Following
immunization of the animal with a particular Staphylococcus epidermidis immunogenic
composition, the animal is challenged with Staphylococcus epidermidis and assayed for
resistance to Staphylococcus epidermidis infection.
The Staphylococcus epidermidis polynucleotides and polypeptides are
incorporated into immunogenic compositions suitable for administration to a subject,
e.g., a human. Such compositions typically comprise the nucleic acid molecule or
protein, together with a pharmaceutically acceptable carrier. As used hereinafter the
language "pharmaceutically acceptable carrier" is intended to include any and all
solvents, dispersion media, coatings, antibacterial and antifungal agents, isotonic and
absorption delaying agents, and the like, compatible with pharmaceutical administration.
The use of such media and agents for pharmaceutically active substances is well known
in the art. Except insofar as any conventional media or agent is incompatible with the
active compound, such media can be used in the compositions of the invention.
Supplementary active compounds can also be incorporated into the compositions.
An immunogenic composition of the invention is formulated to be compatible with
its intended route of administration. Examples of routes of administration include
parenteral (e.g., intravenous, intradermal, subcutaneous, intraperitoneal), transmucosal
(e.g., oral, rectal, intranasal, vaginal, respiratory) and transdermal (topical). Solutions or
suspensions used for parenteral, intradermal, or subcutaneous application can include
the following components: a sterile diluent such as water for injection, saline solution,
fixed oils, polyethylene glycols, glycerine, propylene glycol or other synthetic solvents;
antibacterial agents such as benzyl alcohol or methyl parabens; antioxidants such as
ascorbic acid or sodium bisulfite; chelating agents such as ethylenediaminetetraacetic
acid; buffers such as acetates, citrates or phosphates and agents for the adjustment of
tonicity such as sodium chloride or dextrose. pH can be adjusted with acids or bases,
such as hydrochloric acid or sodium hydroxide. The parenteral preparation can be
enclosed in ampoules, disposable syringes or multiple dose vials made of glass or
plastic.
Pharmaceutical compositions suitable for injectable use include sterile aqueous
solutions (where water soluble) or dispersions and sterile powders for the
extemporaneous preparation of sterile injectable solutions or dispersion. For
intravenous administration, suitable carriers include physiological saline, bacteriostatic
water, Cremophor EL™ (BASF, Parsippany, NJ) or phosphate buffered saline (PBS). In
all cases, the composition must be sterile and should be fluid to the extent that easy
syringability exists. It must be stable under the conditions of manufacture and storage
and must be preserved against the contaminating action of microorganisms such as
bacteria and fungi. The carrier can be a solvent or dispersion medium containing, for
example, water, ethanol, polyol (for example, glycerol, propylene glycol, and liquid
polyetheylene glycol, and the like), and suitable mixtures thereof. The proper fluidity
can be maintained, for example, by the use of a coating such as lecithin, by the
maintenance of the required particle size in the case of dispersion and by the use of
surfactants. Prevention of the action of microorganisms can be achieved by various
antibacterial and antifungal agents, for example, parabens, chlorobutanol, phenol,
ascorbic acid, and the like. In many cases, isotonic agents are included, for example,
sugars, polyalcohols such as manitol, sorbitol, sodium chloride in the composition.
Prolonged absorption of the injectable compositions can be brought about by including
in the composition an agent which delays absorption, for example, aluminum
monostearate and gelatin.
Sterile injectable solutions can be prepared by incorporating the active
compound (e.g., a Staphylococcus epidermidis polypeptide or ar\l\-Staphylococcus
epidermidis antibody) in the required amount in an appropriate solvent with one or a
combination of ingredients enumerated above, as required, followed by filtered
sterilization. Generally, dispersions are prepared by incorporating the active compound
into a sterile vehicle that contains a basic dispersion medium and the required other
ingredients from those enumerated above. In the case of sterile powders for the
preparation of sterile injectable solutions, the preferred methods of preparation are
vacuum drying and freeze-drying which yields a powder of the active ingredient plus any
additional desired ingredient from a previously sterile-filtered solution thereof.
Oral compositions generally include an inert diluent or an edible carrier. They
can be enclosed in gelatin capsules or compressed into tablets. For the purpose of oral
therapeutic administration, the active compound can be incorporated with excipients
and used in the form of tablets, troches, or capsules. Oral compositions can also be
prepared using a fluid carrier for use as a mouthwash, wherein the compound in the
fluid carrier is applied orally and swished and expectorated or swallowed.
Pharmaceutically compatible binding agents, and/or adjuvant materials can be included
as part of the composition. The tablets, pills, capsules, troches and the like can contain
any of the following ingredients, or compounds of a similar nature: a binder such as
microcrystalline cellulose, gum tragacanth or gelatin; an excipient such as starch or
lactose, a disintegrating agent such as alginic acid, Primogel, or corn starch; a lubricant
such as magnesium stearate or Sterotes; a glidant such as colloidal silicon dioxide; a
sweetening agent such as sucrose or saccharin; or a flavoring agent such as
peppermint, methyl salicylate, or orange flavoring.
For administration by inhalation, the compounds are delivered in the form of an
aerosol spray from pressured container or dispenser which contains a suitable
propellant, e.g., a gas such as carbon dioxide, or a nebulizer. Systemic administration
can also be by transmucosal or transdermal means. For transmucosal or transdermal
administration, penetrants appropriate to the barrier to be permeated are used in the
formulation. Such penetrants are generally known in the art, and include, for example,
for transmucosal administration, detergents, bile salts, and fusidic acid derivatives.
Transmucosal administration can be accomplished through the use of nasal sprays or
suppositories. For transdermal administration, the active compounds are formulated
into ointments, salves, gels, or creams as generally known in the art.
The compounds can also be prepared in the form of suppositories (e.g., with
conventional suppository bases such as cocoa butter and other glycerides) or retention
enemas for rectal delivery.
In one embodiment, the active compounds are prepared with carriers that will
protect the compound against rapid elimination from the body, such as a controlled
release formulation, including implants and microencapsulated delivery systems.
Biodegradable, biocompatible polymers can be used, such as ethylene vinyl
acetate, polyanhydrides, polyglycolic acid, collagen, polyorthoesters, and polylactic acid.
Methods for preparation of such formulations will be apparent to those skilled in the art.
The materials can also be obtained commercially from Alza Corporation and Nova
Pharmaceuticals, Inc. Liposomal suspensions (including liposomes targeted to infected
cells with monoclonal antibodies to viral antigens) can also be used as pharmaceutically
acceptable carriers. These can be prepared according to methods known to those
skilled in the art, for example, as described in U.S. Patent 4,522,811, which is
incorporated hereinafter by reference.
It is especially advantageous to formulate oral or parenteral compositions in
dosage unit form for ease of administration and uniformity of dosage. Dosage unit form
as used hereinafter refers to physically discrete units suited as unitary dosages for the
subject to be treated; each unit containing a predetermined quantity of active compound
calculated to produce the desired therapeutic effect in association with the required
pharmaceutical carrier. The specification for the dosage unit forms of the invention are
dictated by and directly dependent on the unique characteristics of the active compound
and the particular therapeutic effect to be achieved, and the limitations inherent in the
art of compounding such an active compound for the treatment of individuals.
Combination immunogenic compositions are provided by including two or more
of the polypeptides of the invention, as well as by combining one or more of the
polypeptides of the invention with one or more known r\on-Staphylococcus epidermidis
polypeptides such as Staphylococcus aureus polypeptides.
The following twelve Staphylococcus epidermidis polypeptide sequences SEQ
ID NO: 8, SEQ ID NO: 10, SEQ ID NO: 11, SEQ ID NO: 12, SEQ ID NO: 14, SEQ ID
NO: 18, SEQ ID NO: 19, SEQ ID NO: 20, SEQ ID NO: 23, SEQ ID NO: 26, SEQ ID NO:
27, and SEQ ID NO: 30 have polypeptide sequences with at least 90% identity to the
homologs from Staphylococcus aureus. Therefore, these twelve polypeptides may also
be used in immunogenic compositions against Staphylococcus aureus. In addition, the
following twelve Staphylococcus epidermidis polynucleotide sequences encoding the
the polypeptides with at least 90% identity to the Staphylococcus aureus homologs may
also be used in immunogenic compositions: SEQ ID NO: 40, SEQ ID NO: 42, SEQ ID
NO: 43, SEQ ID NO: 44, SEQ ID NO: 46, SEQ ID NO: 50, SEQ ID NO: 51, SEQ ID NO:
52, SEQ ID NO: 55, SEQ ID NO: 58, SEQ ID NO: 59, and SEQ ID NO: 62, or a
degenerate variant thereof, or a fragment thereof.
In other embodiments, combination immunogenic compositions are provided by
combining one or more of the polypeptides of the invention with one or more known S.
epidermidis polysaccharides or polysaccharide-protein conjugates. See, for example,
the Staphylococcus epidermidis and Staphylococcus aureus capsular polysaccharide
adhesin, PNSG, poly-N-succinyl beta-1-6 N-acetyl glucosamine (also known as PI A,
PS/A, PNAG). See Mckenney, D., et al., Infect. Immun. 66:4711 (1998) and
Mckenney, D., et al., Science 284:1523 (1998), the disclosures of which are hereby
incorporated by reference in their entirety.
In other embodiments, combination immunogenic compositions are provided by
combining one or more polypeptides of the invention with one or more known S. aureus
polysaccharides or S. aureus polysaccharide-protein conjugates. For example, of the
12 known capsular serotypes of S. aureus, serotype 5 (CP5) and serotype 8 (CP8)
account for approximately 85-90% of all clinical isolates Q. Most methicillin-resistant S.
aureus isolates express CP5 ]. Antibodies to CP5 and CP8 induce type-specific
opsonophagocytic killing by human polymorphonuclear neutrophils in vitro and confer
protection in animals [Karakawa, W. W., Sutton, A., et al., Infect Immun 56(5):1090-
1095 (1988); Fattom, A. I., Sarwar, J., et al., Infection & Immunity 64(5): 1659-1665
(1996)]. Several laboratories have synthesized immunogenic conjugates consisting of
CP5 and CP8 covalently linked to protein. These conjugates are highly immunogenic in
mice and humans and induce antibodies that opsonize microencapsulated S. aureus for
phagocytosis [Fattom, A., Schneerson, R, et al., Infect Immun 61 (3): 1023-1032 (1993);
Gilbert, F. B., Poutrel, B., et al., Vaccine 12(4):369-374 (1994); Reynaud-Rondier, L,
Voiland, A., et al., FEMS Microbiol Immunol 3(4):193-199 (1991)]. Monovalent
immunogenic compositions containing CP5 conjugated to Pseudomonas aeruginosa
recombinant exotoxin A are immunogenic and well tolerated in healthy adults and in
patients with end-stage renal disease [Welch, P. G., Fattom, A., Moore, J. Jr., et al., J.
Am. Soc. Nephrol. 7:247-253 [Abstract] (1996)]. In a double-blind trial involving patients
with end-stage renal disease who were receiving hemodialysis, a bivalent conjugate
vaccine composed of CP5 and CP8 covalently bound to Pseudomonas aeruginosa
recombinant exotoxin A conferred partial immunity against S. aureus bacteremia for
approximately 40 weeks, after which protection decreased as antibody levels decreased
[Shinefield, H., Black, S., et al., N Engl J Med 346(7):491-496 (2002)]. The outcome of
this trial indicates a need for an improved immunogenic composition that could
contribute to broader and more complete protection.
As described above, in certain embodiments, combination immunogenic
compositions are provided by combining one or more polypeptides of the invention with
one or more known S. aureus polysaccharide-protein conjugates. The "protein
component" of the carbohydrate-protein conjugates is known as a carrier protein. The
term "carrier proteins", as a group are preferably proteins that are non-toxic and nonreactogenic
and obtainable in sufficient amount and purity. Carrier proteins should be
amenable to standard conjugation procedures. In a particular embodiment of the
present invention, CRM197 is used as the carrier protein. CRMi97 (Wyeth, Sanford, NC)
is a non-toxic variant (i.e., toxoid) of diphtheria toxin isolated from cultures of
Corynebacterium diphtheria strain C7 (P197) grown in casamino acids and yeast
extract-based medium. CRM197 is purified through ultra-filtration, ammonium sulfate
precipitation, and ion-exchange chromatography. Other diphtheria toxoids are also
suitable for use as carrier proteins. The immunogenic composition may further
comprise an adjuvant, such as an aluminum-based adjuvant, such as aluminum
phosphate, aluminum sulfate and aluminum hydroxide.
Other suitable carrier proteins include inactivated bacterial toxins such as
tetanus toxoid, pertussis toxoid, cholera toxoid (e.g., as described in International Patent
Application WO2004/083251 [38]), E. coli LT, E. coli ST, and exotoxin A from
Pseudomonas aeruginosa. Bacterial outer membrane proteins such as outer
membrane complex c (OMPC), porins, transferrin binding proteins, pneumolysis,
pneumococcal surface protein A (PspA), pneumococcal adhesin protein (PsaA), or
Haemophilus influenzae protein D, can also be used. Other proteins, such as
ovalbumin, keyhole limpet hemocyanin (KLH), bovine serum albumin (BSA) or purified
protein derivative of tuberculin (PPD) can also be used as carrier proteins.
Immunogenic compositions comprising polynucleotides are delivered to the
recipient by a variety of vectors and expression systems. Such systems include, among
others, chromosomal, episomal and virus-derived systems, e.g., vectors derived from
bacterial plasmids, attenuated bacteria such as Salmonella (U.S. Patent 4,837,151),
from bacteriophage, from transposons, from yeast episomes, from insertion elements,
from yeast chromosomal elements, from viruses such as vaccinia and other poxviruses,
adenovirus, baculoviruses, papova viruses, such as SV40, fowl pox viruses,
pseudorabies viruses and retroviruses, alphaviruses such as Venezuelan equine
encephalitis virus (U.S. Patent 5,643,576), sindbis virus and semiliki forest virus,
nonsegmented negative-stranded RNA viruses such as vesicular stomatitis virus (U.S.
Patent 6,168,943), and vectors derived from combinations thereof, such as those
derived from plasmid and bacteriophage genetic elements, such as cosmids and
phagemids. The expression systems should include control regions that regulate as
well as engender expression, such as promoters and other regulatory elements (such as
a polyadenylation signal). Generally, any system or vector suitable to maintain,
propagate or express polynucleotides to produce a polypeptide in a host may be used.
The appropriate nucleotide sequence may be inserted into an expression system by any
of a variety of well-known and routine techniques, such as, for example, those set forth
in Sambrook et a/., "Molecular Cloning: A Laboratory Manual" 2nd, ed, Cold Spring
Harbor Laboratory, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY,
1989.
A pharmaceutically acceptable vehicle is understood to designate a compound
or a combination of compounds entering into a pharmaceutical or immunogenic
composition which does not cause side effects and which makes it possible, for
example, to facilitate the administration of the active compound, to increase its life
and/or its efficacy in the body, to increase its solubility in solution or alternatively to
enhance its preservation. These pharmaceutically acceptable vehicles are well known
and will be adapted by persons skilled in the art according to the nature and the mode of
administration of the active compound chosen.
As defined hereinafter, an "adjuvant" is a substance that serves to enhance the
immunogenicity of an "antigen" or the immunogenic compositions comprising one or
more polypeptide antigens having an amino acid sequence chosen from one of SEQ ID
NO: 1 through SEQ ID NO: 32. Thus, adjuvants are often given to boost or modulate
the immune response and are well known to the skilled artisan. Examples of adjuvants
contemplated in the present invention include, but are not limited to, aluminum salts
(alum) such as aluminum phosphate and aluminum hydroxide, Mycobacterium
tuberculosis, bacterial lipopolysaccharides, aminoalkyl glucosamine phosphate
compounds (AGP), or derivatives or analogs thereof, which are available from Corixa
(Hamilton, MT), and which are described in United States Patent Number 6,113,918;
one such AGP is 2-[(R)-3-Tetradecanoyloxytetradecanoylamino]ethyl 2-Deoxy-4-Ophosphono-
3-O-[(R)-3-tetradecanoyoxytetradecanoyl]-2-[(R)-3-
tetradecanoyoxytetradecanoylamino]-b-D-glucopyranoside, which is also known as 529
(formerly known as RC529), which is formulated as an aqueous form or as a stable
emulsion, MPL™ (3-O-deacylated monophosphoryl lipid A) (Corixa) described in U.S.
Patent Number 4,912,094, synthetic polynucleotides such as oligonucleotides
containing a CpG motif (U.S. Patent Number 6,207,646), polypeptides, saponins such
as Quil A or STIMULON™ QS-21 (Antigenics, Framingham, Massachusetts), described
in U.S. Patent Number 5,057,540, a pertussis toxin (PT), or an E. coli heat-labile toxin
(LT), particularly LT-K63, LT-R72, CT-S109, PT-K9/G129; see, e.g., International Patent
Publication Nos. WO 93/13302 and WO 92/19265, cholera toxin (either in a wild-type or
mutant form, e.g., wherein the glutamic acid at amino acid position 29 is replaced by
another amino acid, preferably a histidine, in accordance with published International
Patent Application number WO 00/18434). Similar cholera toxin mutants are described
in published International Patent Application number WO 02/098368 (wherein the
isoleucine at amino acid position 16 is replaced by another amino acid, either alone or in
combination with the replacement of the serine at amino acid position 68 by another
amino acid; and/or wherein the valine at amino acid position 72 is replaced by another
amino acid). Other cholera toxin mutants are described in published International
Patent Application number WO 02/098369 (wherein the arginine at amino acid position
25 is replaced by another amino acid; and/or an amino acid is inserted at amino acid
position 49; and/or two amino acids are inserted at amino acid positions 35 and 36).
Various cytokines and lymphokines are suitable for use as adjuvants. One such
adjuvant is granulocyte-macrophage colony stimulating factor (GM-CSF), which has a
nucleotide sequence as described in U.S. Patent Number 5,078,996. A plasmid
containing GM-CSF cDNA has been transformed into E. coli and has been deposited
with the American Type Culture Collection (ATCC), 1081 University Boulevard,
Manassas, VA 20110-2209, under Accession Number 39900. The cytokine Interleukin-
12 (IL-12) is another adjuvant which is described in U.S. Patent Number 5,723,127.
Other cytokines or lymphokines have been shown to have immune modulating activity,
including, but not limited to, the interleukins 1-alpha, 1-beta, 2, 4, 5,6, 7, 8, 10, 13, 14,
15, 16, 17 and 18, the interferons-alpha, beta and gamma, granulocyte colony
stimulating factor, and the tumor necrosis factors alpha and beta, and are suitable for
use as adjuvants.
A composition of the present invention is typically administered parenterally in
unit dosage formulations containing standard, well-known nontoxic physiologically
acceptable carriers, adjuvants, and vehicles as desired.
Injectable preparations, for example sterile injectable aqueous or oleaginous
suspensions, are formulated according to the known art using suitable dispersing or
wetting agents and suspending agents. The sterile injectable preparation can also be a
sterile injectable solution or suspension in a nontoxic parenterally acceptable diluent or
solvent, for example, as a solution in 1,3-butanediol.
Among the acceptable vehicles and solvents that may be employed are water,
Ringer's solution, and isotonic sodium chloride solution. In addition, sterile, fixed oils
are conventionally employed as a solvent or suspending medium. For this purpose any
bland fixed oil can be employed including synthetic mono- or di-glycerides. In addition,
fatty acids such as oleic acid find use in the preparation of injectables.
Preferred carriers include neutral saline solutions buffered with phosphate,
lactate, Tris, and the like. Of course, when administering viral vectors, one purifies the
vector sufficiently to render it essentially free of undesirable contaminants, such as
defective interfering adenovirus particles or endotoxins and other pyrogens such that it
does not cause any untoward reactions in the individual receiving the vector construct.
A preferred means of purifying the vector involves the use of buoyant density gradients,
such as cesium chloride gradient centrifugation.
A carrier can also be a liposome. Means for using liposomes as delivery
vehicles are well known in the art (see, e.g. Gabizon et a/., 1990; Ferruti et a/., 1986;
and Ranade, 1989).
The immunogenic compositions of this invention also comprise a polynucleotide
sequence of this invention operatively associated with a regulatory sequence that
controls gene expression. The polynucleotide sequence of interest is engineered into
an expression vector, such as a plasmid, under the control of regulatory elements which
will promote expression of the DMA, that is, promoter and/or enhancer elements. In a
preferred embodiment, the human cytomegalovirus immediate-early promoter/enhancer
is used (U.S. Patent 5,168,062). The promoter may be cell-specific and permit
substantial transcription of the polynucleotide only in predetermined cells.
The polynucleotides of the invention are introduced directly into the host either
as "naked" DMA (U.S. Patent 5,580,859) or formulated in compositions with facilitating
agents, such as bupivicaine and other local anesthetics (U.S. Patent 5,593,972) and
cationic polyamines (U.S. Patent 6,127,170), which are hereby incorporated by
reference in their entirety.
In this polynucleotide immunization procedure, the polypeptides of the invention
are expressed on a transient basis in vivo; no genetic material is inserted or integrated
into the chromosomes of the host. This procedure is to be distinguished from gene
therapy, where the goal is to insert or integrate the genetic material of interest into the
chromosome. An assay is used to confirm that the polynucleotides administered by
immunization do not give rise to a transformed phenotype in the host (U.S. Patent
6,168,918).
H. Uses and Methods of the Invention
The Staphylococcus epidermidis polynucleotides, polypeptides and polypeptide
homologues described herein are used in methods of immunization. The isolated
polynucleotides are used to express Staphylococcus epidermidis polypeptides (e.g., via
a recombinant expression vector in a host cell or in polynucleotide immunization
applications).
As described in detail in the Examples herein, Staphylococcus epidermidis was
grown in the presence of serum to stimulate the expression of proteins and
carbohydrates at the bacterial cell wall that may be significant to systemic bacterial
infection. As a result, thirty two polypeptides and the corresponding polynucleotides
were identified as expressed by Staphylococcus epidermidis when grown in 70% serum.
In addition, twenty-four of these proteins were found to be reactive with immune sera
from rabbits infected with Staphylococcus epidermidis.
The genes corresponding to the proteins expressed when Staphylococcus
epidermidis was grown in serum were cloned and used to express the proteins
recombinantly. The recombinant proteins were used to immunize mice and twenty five
of twenty six proteins induced antibodies that reacted with whole cell lysates of
Staphylococcus epidermidis. In addition, eighteen of these sera also reacted with whole
cell lysates of Staphylococcus aureus. Finally, when immunized mice were challenged
with Staphylococcus epidermidis it was found that eleven of the proteins had induced
antibodies that reduced the amount of detectable bacteria found in the spleen after
challenge.
The invention further provides immunogenic compositions comprising one or
more polypeptides just described, which have an amino acid sequence chosen from one
SEQ ID NO: 1 through SEQ ID NO: 32, a biological equivalent thereof or a fragment
thereof. The immunogenic composition may further comprise a pharmaceutically
acceptable carrier. In certain embodiments, the immunogenic composition will comprise
one or more adjuvants.
In another embodiment, the invention provides immunogenic compositions
comprising a polynucleotide having a nucleotide sequence chosen from one of SEQ ID
NO: 33 through SEQ ID NO: 64, wherein the polynucleotide is comprised in a
recombinant expression vector. Preferably the vector is plasmid DNA. The
polynucleotide may further comprise heterologous nucleotides, e.g., the polynucleotide
is operatively linked to one or more gene expression regulatory elements, and further
comprise one or more adjuvants. In a preferred embodiment, the immunogenic
polynucleotide composition directs the expression of one or more neutralizing epitopes
of Staphylococcus epidermidis.
Provided also are methods for immunizing a host against Staphylococcus
epidermidis infection. In a preferred embodiment, the host is human. Thus, a host or
subject is administered an immunizing amount of an immunogenic composition
comprising a polypeptide having an amino acid sequence chosen from one of SEQ ID
NO: 1 through SEQ ID NO: 32, a biological equivalent thereof or a fragment thereof and
a pharmaceutically acceptable carrier. An immunizing amount of an immunogenic
composition is determined by performing a dose response study in which subjects are
immunized with gradually increasing amounts of the immunogenic composition and the
immune response analyzed to determine the optimal dosage. Starting points for the
study are inferred from immunization data in animal models. The dosage amount can
vary depending upon specific conditions of the individual. The amount is determined in
routine trials by means known to those skilled in the art.
An immunologically effective amount of the immunogenic composition in an
appropriate number of doses is administered to the subject to elicit an immune
response. Immunologically effective amount, as used herein, means the administration
of that amount to a mammalian host (preferably human), either in a single dose or as
part of a series of doses, sufficient to at least cause the immune system of the individual
treated to generate a response that reduces the clinical impact of the bacterial infection.
Ideally, the treated individual will not exhibit the more serious clinical manifestations of
the Staphloccocal epidermidis or Staphlocccal aureus infection. The dosage amount
can vary depending upon specific conditions of the individual, such as age and weight.
This amount can be determined in routine trials by means known to those skilled in the
art.
All patents and publications cited herein are hereby incorporated by reference.
EXAMPLES
The following examples were carried out using standard techniques, which are
well known and routine to those of skill in the art, except where otherwise described in
detail. All chemicals were obtained from Sigma (Sigma Chemical Co., St. Louis, MO)
unless stated otherwise. The following examples are presented for illustrative purpose,
and should not be construed in any way limiting the scope of this invention.
Example 1
Bacterial Growth in 70% Serum
The following examples were performed using the clinical isolate Staphylcoccus
epidermidis 0-47. The unannotated genomic sequence was available for this isolate
from Incyte Corporation of Palo Alto, CA. See Heilmann, C., et a/., Infect Immun, 64(1):
p. 277-82 (1996). To stimulate the expression of proteins, which may be clinically
relevant to pathogenicity, cultures of bacteria were grown overnight in either 100%
tryptic soy broth (TSB) or 70: 30 rabbit serum:TSB with shaking (200 rpm) at 37°C. The
rabbit serum was obtained from Life Technologies, Rockville, MD. Bacteria were diluted
from an overnight culture to an OD600 ~ 0.1 and grown for 4h until mid log phase. At mid
log phase, the cells were harvested by centrifugation and further processed as
described in the following examples.
Example 2
Preparation Of Cell Wall Fractions For 2-D Gel Electrophoresis
The cell walls of Staphylcoccus epidermidis 0-47 grown as described in Example
1 were isolated and then prepared for two-dimensional gel electrophoresis. Bacterial
pellets were resuspended to an OD6oo ~ 20 and washed twice with rocking for 15
minutes at 4°C using Tris buffered saline (TBS, 20 mM Tris, pH 8.0, 150 mM NaCI).
Serum proteins bound to the surface of the bacteria were removed by washing for 15
minutes at 4°C with 20 mM Tris, pH 8.0 containing 1M NaCI. Bacteria grown in TSB
were treated in the same manner as the bacteria grown in serum. The bacteria were
again pelleted by centrifugation. To create protoplasts, the bacteria were then
resuspended to OD60o ~ 40 in TBS containing 30% sucrose, 100 ^ig/ml lysostaphin, 10
|ig /ml DNase, 1 jig /ml Pefablock (Boehringer Mannheim, Indianapolis, IN), 10 jag /ml
lysozyme and 100 units/ml mutanolysin and incubated at 37°C for 1 hour. The resulting
protoplasts were pelleted by centrifugation at 5000 rpm for 10 minutes and the
supernatant containing the cell wall material was decanted. The decanted supernatants
containing the cell wall fractions were supplemented with Complete Mini protease
inhibitor tablets (Roche Diagnostics, Indianapolis, IN) and dialyzed overnight against
water at 4°C using a 10,000 kD MWCO dialysis membrane (Pierce Biotechnology, Inc.,
Rockford, IL). After dialysis, the cell wall fractions were frozen at -20°C.
Following isolation, the cell wall fraction samples were prepared for 2-D gel
electrophoresis as follows: the frozen cell wall extracts were thawed and precipitated
with 70% acetone on ice for 4 hours. The protein precipitate was pelleted, dried in a
SpeedVac (Thermo Savant, Holbrook, NY) and solubilized with ReadyPrep (BioRad)
SEQUENTIAL EXTRACTION REAGENT 3, which contains 5 M urea, 2 M thiourea, 2%
(w/v) CHAPS, 2% (w/v) SB 3-10, 40 mM Tris and 0.2% Bio-Lyte 3/10.
The prepared cell wall fraction samples were loaded onto 11 cm immobilized pH
gradient (IPG) strips, pH 4-7 (BioRad) by allowing each sample to re-hydrate a gel strip
during an overnight incubation at room temperature. The sample size was 250 |ig in a
total volume of 200 |j.l. During the overnight incubation, the strips were covered with
mineral oil (BioRad) to prevent evaporation. Following completion of rehydration of the
strips, excess mineral oil was removed onto blotting paper that was saturated with water
and the hydrated strips were then loaded into a pHaser Iso-electric focusing (IEF)
apparatus (Genomic Solutions Inc., Ann Arbor, Ml). The strips were prefocused with a
current limit of 50 mA/strip with the voltage gradually increasing from 250 V to 5,000 V.
Voltage was then held constant at 5,000 V for a total 50 kVh (~16h). Second dimension
SDS-PAGE was carried out using 12.5% Criterion precast gels (BioRad). For mass
spectrometric analysis, gels were stained with Sypro Ruby protein gel stain (BioRad)
according to the manufacturer's instructions.
Two-dimensional (2D) gel profiles of cell wall associated proteins from
Staphylococcus epidermidis grown in TSB or 70% rabbit serum were compared. See
Figure 1. Growth in 70% rabbit serum resulted in a change in the protein expression
profile of cell wall associated proteins from Staphylcoccus epidermidis that was easily
detectable in fluorescent stained transfers of 2D gels (Figures 1A and 1B).
Eight proteins were detected by fluorescent stain to be differentially regulated
between Staphylcoccus epidermidis grown in TSB or in the presence of rabbit serum.
See Table 3 and Figure 1. Most notable was an increase in the fluorescent staining of
three protein streaks between 25 kDa and 37 kDa in the cells grown in 70% serum
(Figure 1B, spots e, g and h).
(Table Removed)
List of spots detected on 2D blots by reactivity with immune sera or binding to
serum components.
"Some spots contained more that one protein.
°Method by which the spot was detected following transfer to nitrocellulose,
reactive immune sera from infected rabbits, I, or binding serum components, S.
dNGID = no gene in database
Example 3
Binding of Immune Serum and Biotinylated Serum Proteins to Cell Wall Proteins
After completion of the first and second dimensions of electrophoresis, the
protein content of the gels was transferred onto nitrocellulose for binding assays.
Specifically, the protein content of the gels was electro-blotted to nitrocellulose
membranes (BioRad) using a semi-dry blotting apparatus (Owl Separations Systems,
Portsmouth, NH) at 12V for 1 hour. The protein containing nitrocellulose membranes
(blots) were then stained with Sypro Ruby protein blot stain (BioRad) following the
manufacturer's instructions and visualized in a FluorS Imager (BioRad). Each blot was
incubated in blocking buffer (PBS with 0.05% Tween 20 and 5% dry milk) for 10 minutes
at room temperature then incubated overnight with either a 1:2000 dilution of immune
sera (Western blot) or 40 ug/ml biotinylated serum proteins (see below). Following
overnight incubation, blots were washed 3x with wash buffer (PBS with 0.5% Tween 20)
and incubated with either goat anti-rabbit IgG alkaline phosphatase conjugate
(Biosource International, Camarillo, CA) or streptavidin alkaline phosphatase conjugate
(Biosource) for 2 hours at room temperature in blocking buffer. Blots were again
washed three times with wash buffer and visualized with BCIP/NBT membrane
phosphatase substrate system (KPL, Inc., Gaithersburg, MD). Pictures were taken in
the FluorS. All analysis of 2D gels was performed using Melanie 3.0 software.
Protein concentration was assayed using the BioRad protein assay kit (BioRad).
Changes in the protein expression profile of cell wall associated proteins was
more pronounced by considering the Western blots of the nitrocellulose membranes
containing the proteins transferred from the 2D gels. In the Western blots, the
nitrocellulose membranes were incubated with pooled immune sera from rabbits
repeatedly infected with Staphylcoccus epidermidis 0-47. See Figures 1C and 1D.
These upregulated proteins are also strongly immunoreactive, suggesting they were
expressed during infection of the rabbits. Five other immunoreactive streaks or spots
from the serum-grown cells were expressed at either lower or undetectable levels in
TSB grown cells. See Figure 1, spots a, b, c, d and f.
Example 4
nalysis of Serum Proteins that Interact With Staphylcoccus epidermidis Cell
Wall Associated Proteins
Elution of serum proteins from Staphylcoccus epidermidis
Staphylcoccus epidermidis 0-47 was grown in 70% rabbit serum at 37°C to
OD60o~0.8 and the cells were pelleted. The cells were resuspended at OD600 - 20 and
washed three times with TBS while rocking at 4°C. The bound serum proteins were
eluted sequentially with 20 mM Tris, pH 8.0 containing either 0.5 M NaCI, 1.0 M NaCI or
4.0 M urea for 1 hour with rocking at 4°C. The bacteria were then removed by
centrifugation and the supernatant collected. The supernatants contained the serum
proteins eluted from the surface of the bacteria. Proteins eluted under the different
conditions were analyzed by SDS-PAGE using 4-20% gradient Tris-glycine gels
(Cambrex Biosciences Rockland, Inc., Rockland, ME)
Biotinylation of serum proteins
The eluted serum proteins were dialyzed overnight against PBS at 4°C. IgG's
were depleted by overnight incubation with protein G sepharose (Amersham-Pharmacia,
Piscataway, NJ) at 4°C. Assuming an average protein mass of 50 kDa in the eluted
fraction, the proteins were labeled with a 15-molar excess of EZ-Link® NHS-biotin
(Pierce Biotechnology) for 1.5 hour at 4°C. The reaction was quenched with excess
glycine and dialyzed (10,0000 MWCO, Pierce) overnight against PBS.
Identification Of Serum Proteins Bound To The Surface Of Staphylcoccus
epidermidis
Serum proteins eluted from the bacteria under these conditions were compared
by SDS-PAGE to normal rabbit serum and to the bacterial proteins eluted from the
surface of Staphylcoccus epidermidis grown in TSB. See Figure 3. Buffers containing
0.5 NaCI, 1M NaCI and 4M urea each eluted bound serum proteins from the bacterial
cells. These eluted serum proteins represent a pool of proteins eluted from the bacterial
surface that is enriched for serum proteins. Some bacterial proteins are likely present in
this pool, however no bacterial proteins detectable by protein assay were eluted from
bacteria grown in TSB. Although some faint protein bands were detected by silver stain
to be eluted from TSB grown bacteria, they did not correspond to the more intensely
stained proteins eluted from the surface of the bacteria grown in serum. Elution with 1M
NaCI was the least denaturing condition that eluted the most proteins and was used to
elute proteins for the following examples.
In order to identify cell wall associated proteins involved in binding serum
components, biotin labeled serum proteins were used to probe 2D transfers by
incubating a solution of the labeled proteins with the nitrocellulose bound cell wall
proteins transferred from a 2D gel. To isolate serum proteins that bind to Staphylcoccus
epidermidis, bacteria grown in 70% rabbit serum were washed with 1 M NaCI. The
eluted serum proteins were collected and dialyzed into PBS. Next, the naturally
occurring immune IgG that may be present in the eluted serum proteins was depleted by
incubation with protein G sepharose. Removal of IgG reduces the likelihood of
identifying a protein that is reactive with host antibodies. The eluted serum proteins
were then biotin labeled as described above and used to probe a 2D blot of
Staphylcoccus epidermidis cell surface proteins. See Fig 4A and 4B. Thirty-four spots
and regions were visualized by this method and are likely involved in the interaction of
Staphylcoccus epidermidis with host serum proteins. Of the 34 spots consistently found
to interact with serum components all but 4 were found to react with the immune sera
from infected rabbits. See Fig 2 and Table 3.
Staphylcoccus epidermidis grown in serum had serum proteins bound to
bacterial surface proteins that were eluted with 0.5M and 1M NaCI. Under the same
conditions few staphylococcal proteins were eluted from bacteria grown in TSB however
it is possible that a staphylococcal protein expressed only in the serum is eluted by the
high salt treatment.
Example 5
Mass Spectroscopy Identification of Serum Upregulated Proteins
Bacteria grown in 70% serum were used in subsequent proteomic experiments
and analyses, working under the assumption that the changes detected during growth in
serum may more accurately reflect alterations in gene expression made by the bacteria
in response to environmental cues seen within a host. In the following mass
spectroscopy studies, proteins isolated from spots on 2D gel electrophoresis
separations were first subjected to time-of-flight mass spectroscopy. If a positive,
unambiguous identification was obtained then no further mass spectrometric analysis
was performed. See Table 4. In the cases where some ambiguity remained after timeof-
flight mass spectroscopy, such as when multiple proteins resolved to the same spot
on the 2D gel, then electrospray mass spectroscopy was performed to resolve the
ambiguity. See Table 4.
(Table Removed)
Sample Preparation
Prior to performing mass spectrometry, the target protein spots were subjected
to in-gel tryptic digestion. Protein spots were removed from the gel and cut into ~1mm
pieces. The gel pieces were washed three times with 0.2 ml of 50% (v/v) acetonitrile
(Burdick & Jackson, Muskegon, Ml) in 10mM ammonium bicarbonate (J.T. Baker,
Phillipsburg, NJ) for 15 minutes with occasional vortexing. The gel pieces were
dehydrated with acetonitrile for 5 minutes, lyophylized, and stored frozen at -20°C.
Proteins in the gel were then digested with 50 ul of 12 ng/ml sequencing grade modified
trypsin (Promega Corporation, Madison, Wl) overnight at 37 °C. The trypsin solution
was then removed and the gel again dehydrated in 50 ul acetonitrile. The peptidecontaining
acetonitrile was then removed and the gel pieces washed in 50 pi 5% formic
acid (Riedel-de Hae'n, Seelze, Germany) for 15 minutes at room temperature in a bath
sonicator (Branson Cleaning Equipment Co., Shelton, CT). The peptide-containing
supernatant was removed and combined with the initial acetonitrile wash. The gel was
again washed in acetonitrile and the supernatant combined with two previous extraction
steps and dried in a SpeedVac (Thermo Savant) to -10 ul, then diluted to 100ul with
0.1% (v/v) aqueous formic acid. The sample was then loaded onto a Zip-TipCis P10
column (Waters Corporation, Milford, MA) and eluted in 50ul of 50% acetonitrile/ 0.1%
formic acid. Samples were transferred to a 96 X 2 well Teflon coated stainless steel
plate (PerSeptive Biosystems, Framingham, MA) for mass fingerprinting analysis on the
MALDI-ToF instrument (PerSeptive Biosystems) glass nanospray tips (New Objective
Inc., Woburn, MA) to be sprayed in the orifice of the ion trap mass spectrometer.
Peptide Mass Fingerprinting Using ToF Mass Spectrometry
Each sample was applied to the Teflon coated stainless steel 96 X 2 well plate
with the a-cyano-4-hydroxycinnamic acid thin-layer application. The samples were
allowed to dry at room temperature. Mass spectral data were acquired on a Voyager
DE-STR MALDI-ToF mass spectrometer (PerSeptive Biosystems) equipped with
delayed extraction technology, and a reflector. The mass spectrometer was equipped
with a nitrogen laser at 337 nm and a laser rate of 3 Hz. Accelerating voltage was set at
20 kV, mode of operation (reflector), extraction mode (delayed), polarity (positive), grid
voltage (65%), mirror voltage ratio (1.12), extraction delay time (200 nsec), mass range
(800-3500 Da), and laser shots per spectrum (200).
Static Nanospray Ion Trap-Mass Spectrometry
Mass spectral data were acquired on a ThermoFinnigan LCQ DECA quadrupole
ion trap mass spectrometer (ThermoFinnigan, San Jose, CA) equipped with a nanoelectrospray
interface. The nano-electrospray interface consisted of a silica spray
needle, ~27 mm length by 120/69 urn OD/ID, 2 urn orifice diameter (New Objective
Inc.). The glass tip was mounted in a x,y,z axis holder (ThermoFinnigan) held on a base
positioned at the front of the mass spectrometer detector. Electrical current was applied
to the standard coating of the glass tip to supply an electrical connection for the
electrospray interface through a metal connection on the static nanospray probe
(ThermoFinnigan). The nanospray delivered a flow of 20 -80 nl/min.
Two to five microliters of the tryptic digest was analyzed using a nanospray glass
tip spraying directly into the orifice of the mass spectrometer. Peptide analyses were
conducted on the LCQ-DECA ion trap mass spectrometer (Thermofinnigan) operating at
a variable spray voltage of -1 kV, and using a heated capillary temperature of 200° C.
Data sets were acquired in automated MS/MS mode using the data acquisition software
provided with the instrument. The acquisition method included 1 MS scan (400-1800
m/z) followed by MS/MS scans of the top three most abundant ions in the MS scan.
The dynamic exclusion function was employed to increase the number of peptide ions
that were analyzed (settings: 3 amu = exclusion width, 0.5 minutes = exclusion
duration). The current experiment was analyzed in groups of samples and in a manual
fashion.
Automated analysis of mass fingerprinting data was performed using MSFIT
(Protein Prospector) and MASCOT (Matrix Science) software database search engines
using Incyte's PathoSeq(c) Staphylcoccus epidermidis 0-47 database. The resultant
spectra were processed with baseline correction, noise removal, and peak de-isotoping
before utilizing the search engines. The database search parameters were set at the
following levels: MW (1000 - 150 kDa), pi (3 - 10), Digest (trypsin), max. number of
missed cleavages (2), missed cleavages pfactor (0.4), static modification (cysteine
modified by acrylamide), N terminus (hydrogen), C terminus (free acid), variable mods
(oxidation of methionine, N-terminus acetylation, phosphorylation of serine, threonine,
and tyrosine), Mass (monoisotopic), min. number of peptides required to match (4) with
a mass tolerance of 300 ppm, and the application of iterative calibration (Intelcast) with
a mass tolerance of 15 ppm. Protein identifications were determined by MOWSE score
and a 95% confidence score by MS-FIT and MASCOT respectively.
Automated analysis of MS/MS data was performed using SEQUEST
incorporated into the Finnigan Bioworks data analysis package (ThermoFinnigan). See
Eng, J.K., et a/., J Amer Soc Mass Spec, 5(11): p. 976-89 (1994). The following
variable modifications were allowed in the software: cysteine acrylamide modification
and oxidation of methionine. The search parameters were set at the following
designations: mass range (400 - 3500 Da), lower intensity MS signal (1e +5), peptide
tolerance (2.0 Da), min. number of fragment ions (15), min. number of scans in a group
(1), and maximum number of missed cleavages (2). All protein identifications were
manually verified for accuracy.
Identification Of Proteins By Mass Spectrometry
Spots consistently detected on both fluorescent and immunostained transfers
from Staphylcoccus epidermidis grown in 70% serum, were located and labeled for
identification by mass spectrometry. See Figures 2A and 2B. A total of 40
immunoreactive spots were cut and subjected to mass spectrometric analysis for
identification. See Table 4. The complete protein sequences are shown in the
sequence listing (SEQ ID NOS:1-32). The protein-containing gel spots were cut out of a
gel and identified by mass fingerprint analysis using MALDI-TOF followed by searching
Incyte's PathSeq(c) Staphylcoccus epidermidis 0-47 database for the corresponding
coding region. See Table 4. Spots with multiple protein hits or questionable signal were
further analyzed using static nanospray. A total of 32 proteins was identified, with some
spots containing more than one protein. See Tables 3 and 4. Twenty-four of the
proteins identified were immunoreactive, 26 bound to serum components and 20 of the
proteins were both immunoreactive and serum binding. This large overlap was
expected, as most proteins on the surface of Staphylcoccus epidermidis involved in
binding to serum factors would likely elicit an immune response.
Six proteins were consistently present in immunostained blots, but no
corresponding spots were visibly present on the fluorescent stained transfers. See
Figure 2B, white circles and arrow. Although these proteins are likely expressed during
an infection and elicit an immune response they are not expressed at levels that allow
for their detection by fluorescent protein staining under the conditions used in these
experiments.
Example 6
Prediction of Protein Function
The predicted function of the proteins was determined by comparison with
complete genome homologs from ATCC12228. See Zhang, Y.Q., et a/., Mol Microbiol,
49(6), p. 1577-93 (2003). The predicted functions shown in Table 5, are attributed to
the respective ORFs by prior publications involving the specific protein or by homology
to previously characterized proteins occurring in other organisms.
(Table Removed)
The predicted function of the proteins was determined by comparison with complete genome
homologs from ATCC12228.
bMethod by which the spot was detected following transfer to nitrocellulose, reactive immune
sera from infected rabbits, I, or binding serum components, S.
As discussed above, the expression profile of cell wall associated proteins from
Staphylococcus epidermidis 0-47 grown in 70% rabbit serum was analyzed by 2D gel
electrophoresis. The overall expression profile in serum was determined to be
significantly different from that occurring following growth in TSB. Numerous proteins
that were upregulated during growth in serum were identified by mass spectroscopy and
their functions predicted by sequence comparison. See Table 5. Three proteins
predicted to be involved in nutrient acquisition, 305, 1450, and 1703 were all
significantly increased. See Tables 4 and 5. All three proteins form streaks across the
gel. See Figure 4. Without being bound by theory, this may be the consequence of
multiple charge isomers or related to their predicted lipoprotein composition.
Additionally, all three proteins are highly reactive with immune sera from rabbits infected
with Staphylcoccus epidermidis 0-47 suggesting that these proteins are also expressed
in the host during an infection. See Figure 2 and Table 5. In total, 24 of these proteins
were identified as reactive with immune sera from infected rabbits. Not only are these
proteins expressed during growth in serum, but they also elicited an immune response
in an infected animal. See Example 8. Taken together, these data suggest that these
antigens are all expressed during an infection. Expression of the transcripts from these
ORFs within the bloodstream of an infected mouse was confirmed by RT-PCR for all of
the identified proteins (data not shown).
Example 7
Cloning And Expression Of Recombinant Proteins
Genes were cloned using primers designed based on the proteins identified by
mass spectrometry of the expressed proteins and the Staphylcoccus epidermidis 0-47
database. Individual genes were amplified by polymerase chain reaction (PCR) using
Pfu Turbo DNA polymerase (Stratagene, La Jolla, CA) and adenine overhangs were
added with Taq DNA polymerase (Roche Diagnostics). The reaction products were
cloned into pCRT7/NT-TOPO or pBAD/TOPOThio (Invitrogen, Carlsbad, CA) following
the manufacturer's instructions and transformed into E. co//Top10 (Invitrogen). Positive
clones were detected by colony PCR using ReddyMix PCR mastermix (ABgene,
Rochester, NY) and sequenced to ensure that no spurious mutations had arisen.
Plasmids from pCRT7 clones were purified and transformed into E. coli BL21 (DE3)
(Invitrogen) for expression using the T7 polymerase. Proteins were expressed by
growth of the positive clones in HySoy broth (1% HySoy, Quest Intl, Stockbridge, GA
0.5% yeast extract, 100 mM NaCI, 50 mM Na2HP04-7H2O, 40 mM NaH2PO4-H2O)
supplemented with 100 ug/ml ampicillin at 37 °C with shaking (200 rpm) until OD60o
1.0. Protein expression was induced with either 1 mM IPTG (pCRT7) or 0.2 %
arabinose (pBAD) and the cultures were grown an additional 3 hours. The cells were
then harvested by centrifugation and expression was assessed by SDS-PAGE of whole
cell lysates.
Purification Of Recombinant Proteins
Cell pellets were resuspended in 100 ml TBS (20 mM Tris, pH 8.0, 150 mM
NaCI) and lysed by one passage through a French pressure cell (SLM-Aminco,
Rochester, NY). Samples were then separated into a soluble fraction or insoluble pellet
by centrifugation at 10,000 x g for 10 minutes. The location of recombinant protein was
assessed by SDS-PAGE. If a recombinant protein was in the soluble fraction, then the
protein was loaded onto iminodiacetic acid agarose resin charged with Ni2+. See Table
6. Next, the column was washed with 30 mM imidazole in TBS. Bound proteins were
eluted with 300 mM imidazole in TBS. If an additional purification step was required, the
proteins were dialyzed into 20 mM Tris, pH 8.0, containing 50 mM NaCI, 1 mM EDTA
and loaded onto a column packed with POROS-Q resin (Applied Biosystems, Foster
City, CA). Bound proteins were eluted with a 50 mM to 500 mM NaCI gradient in 20 mM
Tris, pH 8.0, 1 mM EDTA. Fractions containing the protein of interest were determined
by SDS-PAGE and frozen at -20 °C.
If a recombinant protein was found in the insoluble fraction, then the insoluble
fraction was treated with 100 ml 1% Triton X-100 in TBS for 4 hours at 4°C. See Table
6. The insoluble proteins were pelleted by centrifugation and the supernatant discarded.
The insoluble pellet was then extracted withlOO ml of 8 M urea in TBS for at least 8
hours at room temperature. Insoluble debris was pelleted and the protein was purified as
above except all buffers contained 2M urea. Following purification Triton X-100 was
added to a final concentration of 0.1%. The proteins were then dialyzed into TBS
containing 0.1% Triton and stored at -20°C.
All liquid chromatography was performed using an AKTA explorer (Amersham-
Pharmacia Biotech, Piscataway, NJ). All SDS-PAGE was performed using 4-20%
gradient Tris-glycine gels (Cambrex).
(Table Removed)
X indicates the protein was found in that fraction. NT indicates not tested.
Example 8
Immunogenic Compositions Using Recombinant Staphylcoccus epidermidis
Proteins
Four week-old female Balb/C mice (Charles River Laboratories, Wilmington, MA)
were immunized at 0, 3 and 6 weeks with 10 ug recombinant protein formulated with 20
|jg STIMULON™ QS-21 by subcutaneous injection. The mice were bled on week 0
prior to the first immunization and on week 8. Two days following the final bleed, the
mice were challenged by intraperitoneal injection of 5 x 108 cfu Staphylcoccus
epidermidis 0-47 grown overnight on Columbia salt agar (1x Columbia agar, 0.1%
glucose, 1% yeast extract, 0.5% NaCI). Twenty-four hours following challenge, the mice
were sacrificed and the bacteria were enumerated in the spleen and blood.
Active immunization of mice with recombinant proteins
Twenty-seven orfs encoding either serum-binding or immunoreactive proteins
were cloned from Staphylococcus epidermidis 0-47 and the recombinant proteins were
expressed in E. coli with a hexahistidine tag (The His-tag was used as a matter of
convenience; an immunogenic composition of this invention would contain proteins
expressed without a His-tag). See Table 7. These proteins were purified using a Ni2+
chelate column followed by ion exchange chromatography. The three remaining cloned
orfs (2006, 2975 and 2907) were cloned but not expressed at levels sufficient for
purification. Balb/C mice were immunized at 0, 3 and 6 weeks with individual
recombinant proteins. The animals were bled at 0 and 8 weeks and challenged (i.p.) on
week 8 with Staphylcoccus epidermidis 0-47. Twenty-four hours following challenge,
the animals were euthanized and the number of bacteria present in the blood and
spleen enumerated. This initial screen of immunogenic composition candidates was
performed on groups of 5 animals to enable for the screening of numerous proteins.
The resulting data are not statistically significant but they did provide valuable
information as to the immunogenic composition potential of a large number of
candidates. Eight of twenty-seven recombinant proteins reduced the number of bacteria
recovered from the spleen and/or blood by one log or more. See Table 7 (NT = not
tested).
(Table Removed)
NT indicates not tested.
The sera obtained from the immunized mice were evaluated for antibody
reactivity to the bacterial proteins. See Table 8. Twenty-three of twenty-four immune
sera tested reacted with the native proteins, as determined by western blots of whole
cell lysates of Staphylcoccus epidermidis grown to mid-log phase in rabbit serum. See
Table 8 (NT = not tested).
(Table Removed)
NT indicates not tested.
As shown in Table 8, many of the animals immunized with Staphylcoccus
epidermidis antigens also developed antibody responses to Staphylcoccus aureus.
Therefore, immunogenic compositions against Staphylcoccus epidermidis antigens
could be effective in the treatment or prevention of Staphylcoccus aureus as well as
Staphylcoccus epidermidis. See Table 8.
A subset of the recombinant proteins used in immunogenic compositions above
were used to immunize larger groups of mice. Groups of 10 female (4 week-old) Balb/C
mice were immunized by subcutaneous injection with saline or 10 ug of antigen with 20
ug STIMULON™ QS-21 as adjuvant. Two weeks following the last immunization, the
mice were challenged with ~5 x 108cfu S. epidermidis 0-47 by intraperitoneal injection.
Twenty-four hours after challenge, bacteria were enumerated in the blood and spleen.
See Table 9. Reduction in log CPU was determined as compared to a control of
STIMULON™ QS-21 in saline. Data were analyzed by student's-T test with resulting pvalues
of *0.05 or "0.01.
(Table Removed)
The Staphylcoccus epidermidis proteins shown in Table 9 showed the greatest
effectiveness when used in immunogenic compositions that reduced the severity of a
bacterial infection following a subsequent challenge.
Example 9
Protection from Staphylcoccus aureus Challenge Following Immunization With
Staphylcoccus epidermidis Proteins
As suggested by the antibody binding data in Example 8, (Table 8),
immunogenic compositions against Staphylcoccus epidermidis antigens could be
effective in the treatment or prevention of Staphylcoccus aureus. Therefore, a
challenge was performed using Staphylcoccus aureus following immunization with
immunogenic compositions of Staphylcoccus epidermidis antigens.
Four week-old female CD-1 mice (Charles River Laboratories, Wilmington, MA)
were immunized at 0, 3 and 6 weeks with 10 ug recombinant protein in 20 ug
STIMULON™ QS-21 by subcutaneous injection. The mice were bled on week 0 prior to
the first immunization and on week 8. Two days following the final bleed the mice were
challenged by intraperitoneal injection of 3 x 108 cfu S. aureus Reynolds grown
overnight on Columbia salt agar (1x Columbia agar, 0.1% glucose, 1% yeast extract,
0.5% NaCI). Twenty-four hours following challenge, the mice were sacrificed and the
bacteria were enumerated in the kidney.
(Table Removed)
As shown in Table 10, certain Staphylcoccus epidermidis antigens were effective
in inducing antibodies that recognized and bound to Staphylcoccus aureus. In addition,
the induced antibodies had the beneficial effect of reducing the level of bacteria
enumerated after a Staphylcoccus aureus challenge.
The percent identity of the amino acid sequence of the Staphylcoccus
epidermidis polypeptide antigens of SEQ ID NOS:1 through SEQ ID NO:32 was
compared to the amino acid sequence of their homologs from Staphylcoccus aureus.
The results are shown in Table 11.
(Table Removed)
WE CLAIM:
1. An immunogenic composition comprising a polypeptide having an amino acid
sequence chosen from one or more of SEQ ID NO: 1 through SEQ ID NO: 32, a
biological equivalent thereof, or a fragment thereof.
2. The immunogenic composition of claim 1, wherein the polypeptide is
immunoreactive with antibodies in the serum of rabbits infected with
Staphylococcus epidermidis.
3. The immunogenic composition of claim 1 or 2, wherein the polypeptide binds to
one or more rabbit serum proteins.
4. The immunogenic composition according to any one or more of claims 1 to 3,
further comprising a pharmaceutically acceptable carrier.
5. The immunogenic composition according to any one or more of claims 1 to 4,
further comprising one or more adjuvants.
6. The immunogenic composition according to any one or more of claims 1 to 5,
wherein the polypeptide is derived from Staphylococcus epidermidis.
7. The immunogenic composition according to any one or more of claims 1 to 6,
wherein the polypeptide further comprises heterologous amino acids.
8. The immunogenic composition according to any one or more of claims 1 to 7,
wherein the polypeptide is a fusion polypeptide.
9. The immunogenic composition according to any one or more of claims 1 to 8,
wherein the polypeptide is a recombinant polypeptide.
10. The immunogenic composition according to any one or more of claims 1 to 9,
wherein the polypeptide is isolated from Staphylococcus epidermidis.
11. The immunogenic composition according to any one or more of claims 1 to 10,
wherein the polypeptide comprises a neutralizing epitope of Staphylococcus
epidermidis.
12. The immunogenic composition according to any one or more of claims 1 to 11,
wherein the polypeptide is a lipoprotein.
13. The immunogenic composition according to any one or more of claims 1 to 12,
said composition further comprising a Staphylococcus epidermidis
polysaccharide antigen.
14. The immunogenic composition according to any one or more of claims 1 to 13,
said composition further comprising a Staphylococcus aureus polysaccharide or
polypeptide antigen.
15. The immunogenic composition according to any one or more of claims 1 to 14,
wherein the polypeptide comprises a Staphylococcus epidermidis polypeptide
sequence selected from the group consisting of SEQ ID NO: 8, SEQ ID NO: 10,
SEQ ID NO: 11, SEQ ID NO: 12, SEQ ID NO: 14, SEQ ID NO: 18, SEQ ID NO:
19, SEQ ID NO: 20, SEQ ID NO: 23, SEQ ID NO: 26, SEQ ID NO: 27, and SEQ
ID NO: 30, a biological equivalent thereof, or a fragment thereof.
16. The immunogenic composition according to any one or more of claims 1 to 15,
wherein the polypeptide is encoded by a polynucleotide comprising a nucleotide
sequence having at least about 95% identity to a nucleotide sequence chosen
from one of SEQ ID NO: 33 through SEQ ID NO: 64 or a degenerate variant
thereof, or a fragment thereof.
17. The immunogenic composition according to any one or more of claims 1 to 16,
wherein the polynucleotide is derived from Staphylococcus epidermidis.
18. The immunogenic composition according to any one or more of claims 1 to 17,
wherein the the Staphylococcus epidermidis polynucleotide sequence is selected
from the group consisting of SEQ ID NO: 40, SEQ ID NO: 42, SEQ ID NO: 43,
SEQ ID NO: 44, SEQ ID NO: 46, SEQ ID NO: 50, SEQ ID NO: 51, SEQ ID NO:
52, SEQ ID NO: 55, SEQ ID NO: 58, SEQ ID NO: 59, and SEQ ID NO: 62, or a
degenerate variant thereof, or a fragment thereof.
19. The immunogenic composition according to any one or more of claims 1 to 18,
wherein the polynucleotide further comprises heterologous nucleotides.
20. An immunogenic composition comprising a polynucleotide having a nucleotide
sequence chosen from one of SEQ ID NO: 33 through SEQ ID NO: 64, a
degenerate variant thereof, or a fragment thereof and is comprised in an
expression vector.
21. The immunogenic composition of claim 20, wherein the the Staphylococcus
epidermidis polynucleotide sequence is selected from the group consisting of
SEQ ID NO: 40, SEQ ID NO: 42, SEQ ID NO: 43, SEQ ID NO: 44, SEQ ID NO:
46, SEQ ID NO: 50, SEQ ID NO: 51, SEQ ID NO: 52, SEQ ID NO: 55, SEQ ID
NO: 58, SEQ ID NO: 59, and SEQ ID NO: 62, or a degenerate variant thereof, or
a fragment thereof.
22. The immunogenic composition of claim 20 or 21, wherein the vector is plasmid
DNA.
23. The immunogenic composition according to any one or more of claims 20 to 22,
wherein the polynucleotide is a recombinant polynucleotide.
24. The immunogenic composition according to any one or more of claims 20 to 23,
wherein the polynucleotide is derived from Staphylococcus epidermidis.
25. The immunogenic composition of claim 24, wherein the polynucleotide
comprises heterologous nucleotides.
26. The immunogenic composition according to any one or more of claim 20 to 23,
wherein the polynucleotide is operatively linked to one or more gene expression
regulatory elements.
27. The immunogenic composition of claim 24, wherein the polynucleotide directs
the expression of a neutralizing epitope of Staphylococcus epidermidis.
28. The immunogenic composition according to any one or more of claims 20 to 23,
further comprising a transfection facilitating agent.
29. The immunogenic composition of claim 28, wherein said transfection facilitating
agent is bupivicaine.
30. A method of inducing an immune response against Staphylococcus epidermidis
comprising administering to a mammal an immunogenic amount of a
composition comprising: a polypeptide having an amino acid sequence chosen
from one or more of SEQ ID NO: 1 through SEQ ID NO: 32 or a biological
equivalent thereof, or a fragment thereof, and a pharmaceutically acceptable
carrier.
31. The method of claim 30, wherein the polypeptide further comprises heterologous
amino acids.
32. The method of claim 31, wherein the polypeptide is a fusion polypeptide.
33. The method of claim 30, further comprising an adjuvant.
34. The method of claim 30 or 31, wherein the polypeptide is a recombinant
polypeptide.
35. A method of inducing an immune response against Staphylococcus epidermidis
comprising administering to a mammal an immunogenic amount of a
composition comprising: a polynucleotide having a nucleotide sequence chosen
from one or more of SEQ ID NO: 33 through SEQ ID NO: 64, a degenerate
variant thereof, or a fragment thereof and a pharmaceutically acceptable carrier.
36. The method of claim 35, further comprising a vector.
37. The method of claim 35, wherein the vector is plasmid DNA.
38. The method of claim 35, wherein the polynucleotide is a recombinant
polynucleotide.
39. The method of claim 35, wherein the polynucleotide further comprises
heterologous nucleotides.
40. The method of claim 35, wherein the polynucleotide is operatively linked to one
or more gene expression regulatory elements.
41. The method of claim 35, further comprising an adjuvant.
42. The method of claim 35, wherein said composition further comprises a
transfection facilitating agent.
43. The method of claim 42, wherein said transfection facilitating agent is
bupivicaine.
44. A method of inducing an immune response against Staphylococcus aureus
comprising administering to a mammal an immunogenic amount of a
composition comprising: a Staphylococcus epidermidis polypeptide sequence
selected from the group consisting of SEQ ID NO: 8, SEQ ID NO: 10, SEQ ID
NO: 11, SEQ ID NO: 12, SEQ ID NO: 14, SEQ ID NO: 18,. SEQ ID NO: 19, SEQ
ID NO: 20, SEQ ID NO: 23, SEQ ID NO: 26, SEQ ID NO: 27, and SEQ ID NO:
30, a biological equivalent thereof, or a fragment thereof.
45. A method of inducing an immune response against Staphylococcus aureus
comprising administering to a mammal an immunogenic amount of a
composition comprising: a Staphylococcus epidermidis polynucleotide sequence
selected from the group consisting of SEQ ID NO: 40, SEQ ID NO: 42, SEQ ID
NO: 43, SEQ ID NO: 44, SEQ ID NO: 46, SEQ ID NO: 50, SEQ ID NO: 51, SEQ
ID NO: 52, SEQ ID NO: 55, SEQ ID NO: 58, SEQ ID NO: 59, and SEQ ID NO:
62, or a degenerate variant thereof, or a fragment thereof.
46. A method for the detection and/or identification of Staphylococcus epidermidis in
a biological sample comprising:
(a) contacting the sample with an oligonucleotide probe of a polynucleotide
comprising the nucleotide sequence chosen from one of SEQ ID NO:33
through SEQ ID NO: 64, or a degenerate variant thereof, or a fragment
thereof, under conditions permitting hybridization; and
(b) detecting the presence of hybridization complexes in the sample, wherein
hybridization complexes indicate the presence of Staphylococcus
epidermidis in the sample.
47. A method for the detection and/or identification of antibodies to Staphylococcus
epidermidis in a biological sample comprising:
(a) contacting the sample with a polypeptide comprising an amino acid
sequence chosen from one of SEQ ID NO: 1 through SEQ ID NO: 32 or a
biological equivalent thereof, or a fragment thereof, under conditions
permitting immune complex formation; and
(b) detecting the presence of immune complexes in the sample, wherein
immune complexes indicate the presence of Staphylococcus epidermidis
in the sample.
48. A composition according to any one or more of claims 1 to 29 for use in a
method of inducing an immune response against Staphylococcus epidermidis.
49. The invention substantially such as herein described