Department of Biochemistry and Molecular Genetics, MCLM 552, 1530 3rd Ave S, University of Alabama at Birmingham, Birmingham, AL 35294-0005, USA
Correspondence
David G. Pritchard
davidp1{at}uab.edu
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ABSTRACT |
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The GenBank accession number for the nucleotide sequence of the GBS phage lysin and flanking regions reported in this paper is AY149214.
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INTRODUCTION |
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GBS, like most other bacterial pathogens, often harbour bacteriophages. Bacteriophages of GBS were first isolated from bovine strains of the bacteria in 1969 (Russell et al., 1969). Phages were subsequently reported to be ubiquitous in human GBS strains and they formed the basis for various phage-typing systems for GBS (Haug et al., 1981
; Stringer, 1980
). Double-stranded DNA bacteriophages usually utilize a two-component lytic system that includes both a holin and a lysin (Grundling et al., 2001
). A phage holin released intracellularly first disrupts the bacterial cell membrane, exposing the peptidoglycan to the degradative action of the lysin, which leads to cell lysis and the release of progeny phage. The lysin alone, however, is often sufficient to lyse the bacteria when they are exposed to preparations of the enzyme externally (Loeffler et al., 2001
).
The use of bacteriophage lysins to selectively destroy their bacterial targets has been the subject of three recent reports. In one case, nasopharyngeal colonization of mice by group A streptococci was eliminated by treatment with a purified lysin isolated from a group C streptococcal phage lysate (Nelson et al., 2001). This C1 phage lysin specifically killed groups A, C and E streptococci but not 14 other commensal streptococci. It also did not affect GBS or streptococci belonging to groups D, F, G, L and N. In another report, nasopharyngeal colonization of mice by pneumococci was eliminated by treatment with a recombinant pneumococcal phage lysin (Loeffler et al., 2001
). This enzyme was highly specific for Streptococcus pneumoniae. In a third report, the PlyG lysin isolated from the
phage of Bacillus anthracis was shown to specifically kill the bacteria both in vitro and in vivo (Schuch et al., 2002
). There are also many examples of micro-organisms secreting lysins to prevent the growth of other bacteria. For example, lysostaphin, a bacteriocin produced by Staphylococcus simulans, has long been known to specifically cleave the pentaglycine cross-bridges in the peptidoglycan of other susceptible staphylococci (Schindler & Schuhardt, 1964
). The enzyme was reported to dramatically reduce aortic valve vegetation bacterial counts in a rabbit model of Staphylococcus aureus endocarditis (Patron et al., 1999
). However, there have been no reports describing the lysins of GBS phages. In this paper we describe the bifunctional lysin of a GBS bacteriophage with a view to its use in the prevention of GBS infections.
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METHODS |
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Escherichia coli strains INVF' and BL21(DE3) were routinely grown with shaking in LuriaBertani (LB) broth at 37 °C or at 30 °C in Terrific broth (TB) (per litre: 4·8 g Bacto tryptone, 9·6 g Bacto yeast extract, 2·35 g glycerol, adjusted after autoclaving to pH 7 with KH2PO4) for protein expression. Recombinant clones were grown in media supplemented with 50 µg ampicillin ml1.
Induction and isolation of GBS bacteriophages.
GBS strains from our collections were screened for lysogenic bacteriophages by exposing cultures of the bacteria to mitomycin C. Bacteria were grown until they reached an OD550 of 0·4 in a cuvette with a 1 cm path length using a Spectronic 1201 spectrophotometer. Mitomycin C was added to a final concentration of 1 µg ml1, and the OD550 was monitored for the next 3 h. Cultures that showed a drop in OD550 were centrifuged and the supernatants were filtered through 0·45 µm disk filters. An aliquot of the filtrate (3 µl) was added to a top agarose consisting of 3 ml low-melting-point agarose (0·7 % w/v) in the modified ToddHewitt broth described by Stringer (1980), at 37 °C, along with 80 µl of a test GBS propagation strain (OD550 0·6). This mixture was poured onto a base layer (20 ml) of modified ToddHewitt broth containing 0·7 % (w/v) agar. On some plates clear plaques were visible after overnight incubation at 37 °C. Phage were propagated by picking a single plaque and inoculating a tube of modified ToddHewitt broth containing the propagation strain (GBS strain 3331) grown to an OD550 of 0·3. Phage lysates were prepared by adding phage, at a multiplicity of about 10 : 1, to early exponential phase cultures of strain 3331 (OD550 0·3). The cells lysed after about 1 h at 37 °C.
Identification of hyaluronate-lyase-positive GBS strains.
GBS strains were tested for hyaluronate lyase production on hyaluronic acidbovine serum albumin (BSA) agar plates essentially as described by Smith & Willet (1968). After overnight growth at 37 °C on trypticase soy agar plates containing 0·4 mg ml1 hyaluronan and 10 mg BSA ml1, the plates were developed by flooding them with 2 M acetic acid to precipitate a hyaluronanBSA complex in the gel. Positive colonies were surrounded by clear zones on a turbid background.
Cloning the GBS phage lysin gene.
Phage particles were purified by precipitation with PEG 8000 followed by CsCl density-gradient ultracentrifugation, and phage chromosomal DNA was isolated using standard procedures (Ausubel et al., 1998). A plasmid library of phage DNA was constructed by digesting the DNA with HindIII and ligating the fragments into HindIII-cut and alkaline-phosphatase-treated pUC 19. Inserts in randomly selected clones of the HindIII library were sequenced and a putative phage lysin gene was identified in one clone (plasmid 35) by its homology to the lysin gene in Streptococcus equi. Based on the sequence obtained from plasmid 35, primers were designed to sequence the rest of the lysin gene, using phage DNA as template (Sanger et al., 1977
). The nucleotide sequence of the GBS phage lysin and flanking regions appears in GenBank under accession no. AY149214.
The complete lysin gene was isolated from the phage genomic DNA by PCR amplification, using a forward primer containing an NdeI site (5' GCA CTA CAT ATG GCA ACT TAT CAA GAA TAT AAA AG 3') and a reverse primer containing an XhoI site (5' GTG GTG CTC GAG CAT ATC TGT TGC GTT AAC TAA GTA GC 3'). The PCR product was cloned into the pGEM T-vector (Promega) and transformed into INVF'. Purified plasmid DNA was then cleaved with restriction endonucleases NdeI and XhoI and the insert cloned into the expression vector pET21a (Novagen) and transformed into INV
F'. Additional amino acids were added to the carboxyl-terminal end of the protein by sequences included in the pET21a plasmid, including a 6x histidine tag to aid with affinity purification. The sequence of the resulting plasmid was confirmed by DNA sequencing. The plasmid was then transformed into E. coli strain BL21(DE3) for enzyme expression.
Expression and purification of the cloned GBS phage lysin.
A starter culture of E. coli BL21(DE3) containing the recombinant plasmid was grown overnight in TB medium containing 50 µg ampicillin ml1 at 37 °C with shaking at 250 r.p.m. This culture was diluted with 20 vols fresh medium (3 l) and grown at 37 °C until it reached mid-exponential phase (OD550 0·5). Lysin expression was induced by adding IPTG to give a final concentration of 1 mM. After growing for an additional 4·5 h at 30 °C, the cells were harvested by centrifugation and washed three times with extraction buffer (50 mM NaH2PO4, 300 mM NaCl, 10 mM imidazole, pH 8·0). The pellet was resuspended in 100 ml extraction buffer and sonicated in an ice bath for a total of 5 min at 60 % of maximum power using a model 300 Fisher Sonic Dismembrator. Sonication was carried out for 30 s periods, allowing sufficient time between each period to prevent overheating the sample. Cell debris was removed by centrifugation and the resulting supernatant passed over a 10 ml NiNTA affinity column (Qiagen), according to the manufacturer's instructions. The column was washed with 50 ml 50 mM NaH2PO4, 300 mM NaCl, 20 mM imidazole, pH 8·0, and the His-tagged lysin was eluted with 50 ml 50 mM NaH2PO4, 300 mM NaCl, 250 mM imidazole, pH 8·0. The eluate was concentrated by ultrafiltration using a Centriprep-30 ultrafiltration device (Amicon) and the buffer exchanged three times with 50 mM ammonium acetate, 1 mM DTT, pH 6·2, to remove phosphate ions, and then once with lysin buffer A (50 mM ammonium acetate, 10 mM CaCl2, 1 mM DTT, pH 6·2). The final product gave a single band with a molecular mass of 51 kDa upon SDS-PAGE.
Turbidity reduction assay for GBS phage lysin.
GBS lysin activity was assessed by following the reduction in turbidity of a suspension of strain 3331 GBS cells after enzyme addition. Buffered GBS cell suspensions do not exhibit detectable autolysis and may be stored in the refrigerator for many weeks. In order to optimize assay conditions, the effect of calcium ion concentration on lysin activity was determined at 30 °C in 50 mM ammonium acetate, 1 mM DTT, pH 6·2, containing different concentrations of CaCl2. The pH optimum of the phage lysin was then determined in the presence of 10 mM CaCl2, 1 mM DTT. A unit of activity was defined as the amount of enzyme that reduces the optical density of 1 ml of a suspension of strain 3331 GBS cells (adjusted to an initial OD550 of 0·8) by 0·001 min1 at 30 °C. The susceptibility of other species of bacteria to lysis by GBS phage lysin was also assessed by monitoring turbidity reduction. In all cases the cells were grown to an OD550 of 0·4, harvested by centrifugation, washed three times in lysin buffer A, and resuspended in the same buffer to give an OD550 of 0·8. Lysin (10 µl) was added to 0·4 ml of the cell suspension at 30 °C and the rate of decrease in turbidity during the first 2 min was determined.
Preparation of cell walls.
A crude cell wall preparation made from GBS strain 3331 cells was also a suitable substrate for the phage lysin. It was made by passing a suspension of GBS cells, grown to an OD550 of 0·4, through a French press operated at approximately 15 000 p.s.i. (1·0x108 Pa). Unbroken cells were removed by low-speed centrifugation (5000 g) for 5 min, and the cell walls were recovered from the supernatant by centrifugation at 20 000 g for 45 min. The cell walls were washed three times in lysin buffer A. For studies of the glycosidase and endopeptidase activities of the GBS phage lysin, the cell walls were washed an additional three times with water. The final stock cell wall preparation, adjusted to an OD550 of 1·0, was stored at 4 °C.
Cell walls were acetylated by a modified standard procedure (Riordan & Vallee, 1967). Stock GBS cell walls in water (2·0 ml) were diluted with an equal volume of saturated aqueous sodium acetate at 4 °C and acetylated by adding 5x40 µl aliquots of acetic anhydride over a period of 1 h with constant stirring. The acetylated cell walls were washed three times with water, then diluted with water to give a suspension with an OD550 of 1·0 at 550 nm and stored at 4 °C. A test for free amino groups using TNBS (Mokrasch, 1967
) gave a negative reaction for acetylated cell walls (i.e. the cell walls remained white), whereas the nonacetylated cell walls were strongly positive (i.e. they became yellowbrown in colour).
Measurement of endopeptidase activity.
Incubation mixtures (50 µl) in lysin buffer B (50 mM sodium acetate, 10 mM calcium chloride 1 mM DTT, pH 5·6) contained lysin (3·5 µg) and cell walls to give an OD550 of 0·90. Incubations were at 30 °C for 18 h and were stopped by heating at 100 °C for 5 min. Undigested cell walls were pelleted by centrifugation at 5000 g for 15 min and the supernatant passed through a 5000 MW filter unit (Ultrafree, Millipore). Aliquots (20 µl) of the filtrate were assayed for free amino groups using the TNBS method (Mokrasch, 1967) and serine as the standard.
The soluble products released from GBS cell walls by digestion with phage lysin were also analysed by N-terminal amino acid sequencing. In this case, incubation mixtures were clarified by centrifugation, the supernatants passed through Ultrafree-MC 5000 MW cutoff filters, and 20 µl aliquots applied to protein support disks for N-terminal sequencing. Insoluble cell wall residues from the same incubation mixtures were recovered by centrifugation, washed once with lysin buffer B, twice with water, and an equivalent aliquot applied to a protein support disk. Cell wall controls, not digested with the lysin, were treated similarly. All samples were subjected to three or four cycles of Edman degradation and the released PTH-amino acid(s) were identified following separation by RP-HPLC. Analyses were performed using a Beckman peptide microsequencer (model PI 2090E).
Measurement of glycosidase activity of GBS phage lysin.
Lysin digests of cell walls were assayed for cleavage of the peptidoglycan polysaccharide backbone using a modified ParkJohnson method (Spiro, 1966). Briefly, digests were clarified by centrifugation, when necessary, and aliquots (0·2 ml) were heated with 0·05 % (w/v) aqueous potassium ferricyanide (0·2 ml) and 0·53 % (w/v) sodium carbonate/0·065 % (w/v) potassium cyanide in water (0·2 ml) at 100 °C for 15 min. Under these alkaline conditions, reducing groups liberated by the cleavage of glycosidic bonds in the peptidoglycan glycan chain will stoichiometrically reduce ferricyanide to ferrocyanide. Upon cooling, 1·0 ml of a ferric ion reagent [0·15 % (w/v) ferric ammonium sulfate/0·1 % (w/v) SDS in 0·025 M sulfuric acid] was added, which forms a stable prussian blue colour. After 15 min at room temperature, the A690 was measured. Data were converted to glucose equivalents using a standard curve.
Site-directed mutagenesis.
Plasmid DNA was prepared using a Qiagen Midiprep Kit. Specific mutations in the lysin gene were made using a QuickChange Site-Directed Mutagenesis Kit (Stratagene Cloning Systems). The following mutagenesis forward primers were used: C26S, 5' GGC TAC GCA GAT TAC AGT AAG TAT CTA GGA ATG C 3'; C34S, 5' GGC TAC GCA GAT TAC AGT AAG TAT CTA GGA CTG C3'; C44S, 5' GCC ATA CGC AAA CAG TAC AAA TAC AGG ATA CGC 3'; C171S, 5' GCA GAT TTA ACA ACG ACT AGT CAG CAG GCG GGC 3'; H91A, 5' GAC GGT GTA ACG CCT TAC AGT GCT GTA GCA ATT TTT GAC AGC G 3'; D158A, 5' AAT AAA GGT GAT TAC TTT ATC GCT GTA TCG GCT TAT CAA CAA GC 3'; E185A, 5' CGA TTA TCA AGG TAT CCG CGT CAA TTG CTT GGC TGT CTG ACA G 3'. The reverse primers were the exact complements. The PCR reaction mixtures contained 80 ng plasmid DNA template, 12 pmol each of the forward and reverse primers containing the desired mutation, nucleoside triphosphates, reaction buffer and Pfu Turbo DNA polymerase (Stratagene Cloning Systems). After overlaying with mineral oil, each sample was placed in a thermal cycler and denatured for 1 min at 95 °C and then subjected to 25 cycles of 95 °C for 30 s, 55 °C for 1 min and 68 °C for 14 min. The reaction mixtures were then cooled and digested with 1 µl DpnI restriction enzyme to digest the parental DNA template. A 10 µl aliquot of the DpnI-treated DNA was used to transform E. coli INVF' competent cells (Invitrogen). Transformed cells were plated on LB agar containing 50 µg ampicillin ml1, and after overnight growth, colonies were picked and minipreps were prepared from the clones. The plasmid inserts were sequenced to confirm that the desired nucleotide sequence change had been introduced.
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RESULTS |
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The sequence of the gene and flanking regions revealed both an upstream (nucleotides 6699) and a downstream (nucleotides 15121539) stem-and-loop structure that could serve as transcription terminators. A putative ribosome-binding site is present starting 13 nucleotides prior to the predicted ATG start codon for the lysin gene. There is also an in-frame TAA stop codon immediately prior to the ATG start, suggesting that the predicted lysin gene is not part of some larger multi-domain protein. The calculated molecular mass of the 443 amino acid enzyme is 49 677 Da.
Lytic specificity of bacteriophage B30
We knew from previous studies that both the carrier strain of bacteriophage B30 (GBS 3330) and our propagation strain (GBS 3331) did not secrete hyaluronan lyase. Inability of GBS strains to secrete hyaluronan lyase arises because the hylB gene is interrupted by the insertion sequence IS1548 and is characteristic of a minor subtype of serotype III GBS strains, restrictiondigestion pattern type III-2 (Takahashi et al., 2002). We therefore screened a collection of 33 GBS strains for their susceptibility to lysis by bacteriophage B30. Neither the serotype Ia (6), serotype Ib (4) and serotype II (3) GBS strains nor the eight hyaluronan-lyase-positive serotype III strains were lysed by the phage. Twelve hyaluronan lyase-negative serotype III strains were tested: nine were lysed and three were not. The three strains that were not lysed all contained a lysin gene that could be amplified by PCR, suggesting that they already contained a prophage. Attempted PCR amplification of the lysin gene in the other 30 GBS strains did not yield an amplicon, except for a single hyaluronan-lyase-negative serotype III strain.
Expression of the GBS bacteriophage B30 lysin gene
Based on the sequence data, the gene was amplified by PCR from phage chromosomal DNA, digested with restriction endonucleases, and cloned into the expression vector pET21a, as described in Methods. The entire sequence of the cloned gene was confirmed in both strands by DNA sequencing. The cloned phage lysin gene was then expressed in E. coli and the product was purified on a Ni-NTA nickel affinity column. The purified enzyme, which gave a single band upon SDS-PAGE with a molecular mass of 51 kDa, rapidly reduced the turbidity of a suspension of GBS strain 3331 cells.
Properties of the phage lysin
The effect of calcium ion concentration on lysin activity was determined while optimizing the assay conditions. As shown in Fig. 1, optimal activity was obtained with a calcium ion concentration of approximately 10 mM. The pH optimum of the enzyme was then determined in the presence of 10 mM calcium chloride. Optimal lysis occurred at pH 5·56·0 and, as expected, bacterial cell killing correlated with cell lysis (data not shown).
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Identification of amino acid residues important for enzymic activity
The CHAP domain is present in a large number of enzymes that cleave peptidoglycan (Bateman & Rawlings, 2003). In the GBS phage lysin, the conserved cysteine of the CHAP domain corresponds to C26 and the conserved histidine is H91. Site-directed mutagenesis was used to convert C26 and the three other cysteine residues in the protein (C34, C44 and C171) to serine residues. Histidine 91 was replaced with an alanine. The effects of these substitutions on the two different enzymic activities of the lysin are shown in Table 2
. It can be seen that replacing C26 with a serine residue or H91 with an alanine residue completely eliminated endopeptidase activity, while having little effect on glycosidase activity. Endopeptidase activity was reduced to a lesser extent in the C34 and C44 mutants.
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DISCUSSION |
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GBS bacteriophages have been used in a variety of phage typing systems since they are highly specific for different strains of the species (Haug et al., 1981; Stringer, 1980
). In this work, we found that bacteriophage B30 lysed only a minor subgroup of serotype III GBS strains, those that do not secrete hyaluronate lyase. Such strains are classified as restriction-digestion pattern type III-2 strains (Takahashi et al., 2002
).
The rate at which GBS cells are lysed by the GBS phage enzyme was found to be dependent upon the growth stage of the cells when they are harvested, with early-exponential phase cells lysed most rapidly. The reason for this dependence is not clear, but it may be due to modifications of the cell wall that take place in stationary phase culture that make the bacteria more resistant to lysis. Modifications that may be important include increased cross-linking of the peptidoglycan layer, deacetylation of the amino sugars, and an increase in the amount of cell wall-associated proteins and polysaccharides. Heating GBS cells or cell wall preparations in boiling water made them poorer substrates for the lysin. Again, the explanation is not clear, but denatured cell wall-associated proteins may be impeding access of the lysin to the peptidoglycan.
GBS peptidoglycan consists of a glycan backbone of alternating -1,4-linked N-acetylglucosamine and
-1,4-linked N-acetylmuramic acid residues linked to a stem peptide composed of L-ala-D-igln-L-lys-D-ala-D-Ala (Schleifer & Kandler, 1972
). As shown in Fig. 4
, the stem peptides are cross-linked by an (L-ala)2 or L-ala-L-ser interpeptide bridge between the
-amino group of the L-lys of one stem peptide cross-bridge and the carboxylate of a D-Ala of another stem peptide (Karakawa & Krause, 1966
; Reinscheid et al., 2002
). This linkage is characteristic of an A3
type of peptidoglycan in the classification system described by Schleifer & Kandler (1972)
.
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In the GBS phage lysin, C26 and H91 are the highly conserved residues of the CHAP domain (Bateman & Rawlings, 2003). Site-directed mutagenesis of these residues confirmed that they were essential for the endopeptidase activity of the lysin (Table 2
). The CHAP domain is also present in a lysin of staphylococcal phage
11, where it was shown to be responsible for D-alanyl-glycine endopeptidase activity (Navarre et al., 1999
). A separate central domain (amidase-2) conferring N-acetylmuramyl-L-alanyl amidase activity was also present in this bifunctional staphylococcal phage lysin. The ability of the staphylocococcal phage
11 lysin to release N-terminal alanine residues, in addition to the glycine residues of the pentapeptide bridge, was due to N-acetylmuramyl-L-alanyl amidase activity in the enzyme (Navarre et al., 1999
). Using N-terminal amino acid sequencing, we also found that lysis was accompanied by an increase in N-terminal alanine residues. However, unlike the staphylococcal phage lysin, the GBS phage lysin lacks an N-acetylmuramyl-L-alanyl amidase domain. The N-terminal alanine residues released must be generated by another mechanism. The presence of the CHAP domain in the GBS phage enzyme suggests that the explanation for the increase in N-terminal alanine residues is that they result from endopeptidase activity cleaving between D-ala of the stem peptides and L-Ala of the interpeptide bridges (see Fig. 4
). The endopeptidase of phage
11 lysin cleaves between the D-Ala of the stem peptide and a glycine residue of the (Gly)5 bridge in the staphylocococcal peptidoglycan, but such pentaglycine bridges are not present in GBS peptidoglycan. Instead (L-ala)2 or L-ala-L-Ser interpeptide bridges are present. An endopeptidase cleaving at the N-terminus of a D-ala in gbs peptidoglycan would expose n-terminal L-Ala residues. Presumably the low yield after alanine in cycle 2 (see Table 1
) is due to the inability of the Edman degradation to cleave the lysine of the stem peptide that is linked through its
-amino group. A lysin possessing such a D-alanyl-L-alanine endopeptidase activity has not been described previously.
Several other -haemolytic streptococci that are lysed by the GBS phage lysin, including those of groups A, C, E and G streptococci, also possess (L-Ala)2 interpeptide bridges (Schleifer & Kandler, 1972
). Conversely, Strep. mutans and related organisms, which are not lysed by the enzyme, have been reported to possess L-thr-L-Ala cross-bridges (Schleifer & Kandler, 1972
). The GBS phage lysin, which normally cleaves a D-alanyl-L-alanine linkage in
-haemolytic streptococci, may be unable to cleave the D-alanyl-L-threonine linkage in Strep. mutans
The C1 phage lysin, previously shown to specifically kill streptococci of groups A, C and E, but not streptococci of groups B and G (Nelson et al., 2001), was recently sequenced (Nelson et al., 2003
). It showed no significant homology to the GBS phage lysin described in the present report. Although the C1 phage lysin possesses amidase activity (Fischetti et al., 1971
; Nelson et al., 2003
), it does not possess any known conserved sequence domains.
Our results suggest that the GBS phage lysin, like the staphylocococcal phage 11 lysin, is a bifunctional enzyme possessing two different types of lytic activity. The recent demonstration of a synergistic effect of combining two different types of phage lysins suggests that the presence of two different peptidoglycan-cleaving activities in one enzyme may significantly enhance its ability to lyse bacterial cells (Jado et al., 2003
; Loeffler & Fischetti, 2003
). Studies designed to exploit the unique bacteriolytic properties of the GBS phage lysin for the prevention of neonatal GBS infections can now be carried out.
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ACKNOWLEDGEMENTS |
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Received 27 January 2004;
revised 11 March 2004;
accepted 12 March 2004.
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