Bacterial strains, bacteriophages, plasmids, and growth conditions
All bacterial strains used in this study are listed in two tables (additional file 1, Table S1, additional file 2, Table S2). Cell culture media were obtained from HiMedia labs (India). Phage K was obtained from the National Collection of Type Culture (NC07814-02) and propagated on S. aureus RN4220 . The methicillin-resistant S. aureus (MRSA) strain B911 was used for bactericidal activity assays, and RN4220 was used for zymograms.Plasmid pET21a (Novagen, USA) was used for cloning and the constructs were expressed under the control of a T7 promoter. Plasmid pRG5 (ATCC) carrying full-length lysostaphin was used as a template for amplifying the SH3b domain. All cultures were grown in Luria Bertani (LB) broth at 37°C, 200 rpm. Ampicillin (100 μg/ml) or isopropyl β-D-1-thiogalactopyranoside (IPTG, 1 mM) were added to the cultures as needed. All reagents used in this study were purchased from Sigma (USA) unless otherwise stated.
Cloning of orf56 and its truncated forms
Phage K DNA was prepared as previously described . All DNA manipulations were performed according to the methods of Sambrook and Russell . Briefly, the full-length orf56 gene was amplified from phage K DNA by polymerase chain reaction (PCR) using a forward primer containing a unique NdeI site: 5'-CCGGAATTCCATATGCGTAGAATAAGACCTAAG-3' and a reverse primer incorporating an XhoI site: 5'-CCGCCGCTCGAGTTATTTCTTATCGTAAATGAATTGTGC-3'. Amplification was carried out using a Smart Cycler (BioRad, USA). The 2427-bp PCR product was gel-purified (GenElute™ gel extraction kit, Sigma, USA) and then digested with NdeI and XhoI. After gel purification, the DNA sequence was ligated into the pET21a vector. Escherichia coli DH5α cells were transformed with the ligation mixture, and transformants were selected on LB plates containing 100 μg/ml ampicillin. Plasmids (clones) were isolated from the transformants, screened by NdeI/XhoI digestion, and sequenced. The plasmid containing the full-length orf56 was designated as pGMB617. Truncated forms of orf56 were generated by PCR amplification using sets of primers for specific regions and cloned into the pET21a vector. Clone integrity was verified by restriction analysis and DNA sequencing.
Construction of chimera P128
The DNA fragment encoding Lys16, excluding the stop codon, was PCR-amplified incorporating an NdeI site in the forward primer and XhoI site in the reverse primer. The fragment was cloned into the pET21a vector to generate pGDC108. The SH3b binding domain of lysostaphin was PCR-amplified from the plasmid pRG5 with XhoI restriction sites in both primers: forward primer 5'-CCGCCGCTCGAGACGCCGAATACAGGTTGGAAAACAAAC-3' and reverse primer 5'-CCGCCGCTCGAGTCACTTTATAGTTCCCCAAAGAAC-3'. The 300-bp PCR product was then cloned into pGDC108 to generate pGDC128. Transcription of the chimeric gene Lys16-SH3b in pGDC128 was driven by the T7 promoter.
Protein expression and purification
The highly inducible T7 expression system of E. coli was used for hyperexpression of the target proteins. E. coli ER2566 (NEB Inc, MA, USA) harboring the different constructs was grown in LB at 37°C until absorbance at 600 nm (A600) reached 0.8, as determined by spectrophotometry (BioRad, CA, USA). Protein expression was induced by incubation with 1 mM IPTG at 37°C for 4 h. Cells were harvested by centrifugation at 7500 × g for 10 min, resuspended in 25 mM Tris-HCl (pH 7.5), and disrupted by ultrasonication. The cell lysate soluble and insoluble fractions were separated by centrifugation at 11000 × g for 15 min, and protein expression was analyzed by 12% polyacrylamide gel electrophoresis (PAGE). A crude soluble fraction containing the protein of interest was used for zymogram analysis and the bactericidal activity assay. After ammonium sulphate precipitation, soluble P128 was purified by two-step ion-exchange chromatography.
Denaturing SDS-PAGE (Sodium Dodecyl Sulfate - Polyacrylamide Gel Electrophoresis) and zymograms were performed as previously described . Briefly, muralytic activity was detected by separating protein samples by 12% SDS-PAGE on gels containing 0.2% of autoclaved S. aureus RN4220 cells. After electrophoresis, the zymograms were washed for 30 min with distilled water at room temperature, transferred to a buffer containing 25 mM Tris-HCl (pH 7.5) and 0.1% Triton X-100, and incubated for 16 h at 37°C for in situ protein renaturation. The zymograms were rinsed with distilled water, stained with 0.1% methylene blue and 0.001% KOH for 2 h at room temperature, and then destained with distilled water. Peptidoglycan hydrolase activity was detected as a clear zone against the dark blue background of methylene blue.
Phage K particles were purified by CsCl density-gradient ultracentrifugation. Immunoelectron microscopy was performed by incubating approximately 5 × 108 phage particles with Lys16 antibodies conjugated to 10-nm gold particles (1:100) at room temperature overnight. The 1-ml samples were briefly centrifuged at 16000 × g, and the supernatant was collected and centrifuged at 16000 × g for 150 min. The resulting pellet was resuspended in 25 mM Tris-HCl (pH 7.5). A 20-μl aliquot of this sample was loaded onto Formvar-coated grids (TAAB Laboratories Equipment Ltd, UK) and dried. The grids were stained with 1% phosphotungstic acid and observed by transmission electron microscopy (Tecnai G2 Spirit).
Bactericidal activity assay
Bactericidal activity was assessed by measuring reduction in viable cells (CFU) after addition of P128 protein. The method is a modified version of the National Committee on Clinical Laboratory Standards assay used for determination of Minimum Bactericidal concentration . Briefly, the MRSA clinical isolate B911 was grown in LB broth until A600 reached 1.0, and then an aliquot was diluted in LB broth to obtain 1 × 108 cells/ml. Aliquots (100 μl) were transferred to 1.5-ml microfuge tubes, treated with 100 μl crude or purified protein, and incubated at 37°C for 60 min at 200 rpm. Unless otherwise indicated, bactericidal activity was always performed using 10 μg/ml of P128. Residual viable cells were enumerated as colony-forming units (CFUs) by serial dilution and plating on LB agar plates.
Turbidity reduction assay
Exponentially growing cells were harvested and resuspended in 25 mM Tris-HCl (pH 7.5). For gram-negative cultures, cells were pelleted, resuspended in CHCl3-saturated 50 mM Tris-HCl (pH 7.5), incubated for 45 min to expose the peptidoglycan layer, and then centrifuged at 3000 × g. The resulting pellet was resuspended in 25 mM Tris-HCl (pH 7.5), and the concentration was adjusted to about A600 of 0.8 for use as substrate for the assay. Purified P128 (50 μg/ml) was added, and A600 was determined at different time points (total assay volume 1 ml).
In vivo efficacy of P128 in a rat nasal colonization model
Animal experiments were approved by the Institutional Animal Ethics Committee and the Committee for the Purpose of Control and Supervision of Experiments on Animals (CPCSEA). Gangagen is registered with CPCSEA (registration No. 1193/c/08/CPCSEA dated 21/4/2008). Healthy female Wistar rats (6-7 weeks old) were used in all experiments.
Evaluation of commensal nasal flora
The commensal nasal flora of the rats was evaluated by nasal swabbing. Rat nares were swabbed by gentle insertion and withdrawal of a sterile Microbrush×(Microbrush® International), which was moistened with sterile 0.85% NaCl. The swab portions of the Microbrush were cut and then completely immersed in 0.85% NaCl (150 μl) in microfuge tubes. Tubes were thoroughly vortexed, and the supernatant was diluted as needed and plated on agar containing 5% sheep blood. Staphylococcus colonies were identified based on morphology, biochemical tests and also analyzed using the HiStaph™ Identification kit (HiMedia). An S. aureus-specific enzyme-linked immunosorbent assay (ELISA) was used for confirmation.
Experimental colonization of rat nares and evaluation of P128 efficacy
MRSA USA300 was grown overnight on nutrient agar containing 5% sheep blood. Colonies were harvested by flooding the plate with sterile 0.85% NaCl. Cells were pelleted by centrifugation (5800 × g, 10 min) and resuspended in sterile 0.85% NaCl (2 × 108-5 × 108 cells/μl) for nasal instillation.
Rats were grouped and anaesthetized by intraperitoneal injection of ketamine (90 mg/kg body weight) and xylazine (9 mg/kg body weight). A 10-μl aliquot of S. aureus cell suspension was instilled into the nares of all animals on day 1. After 24 h, twice daily intranasal treatments to anaesthetized rats were initiated according to treatment group: P128 formulated as a hydrogel (50 mg/dose containing 100 μg P128), placebo gel that contained phosphate buffered saline in place of the protein, or Bactroban Nasal (30 mg/dose, 2% mupirocin ointment, GlaxoSmithKline). On day 3, the rats were euthanized by anesthetic overdose. The nasal tissue (except for the skin around the nares) was removed and processed for quantitative evaluation of colonization as described previously [33, 34]. Aliquots of the supernatant (diluted as needed) were plated on nutrient agar containing 5% sheep blood and incubated overnight at 37°C. The S. aureus USA300 colonies were enumerated by tentative identification of hemolytic phenotype. Representative colonies from each USA300-positive animal were then purified on LB agar for biochemical characterization and confirmation by ELISA.
Confirmation of S. aureus by ELISA
Purified colonies were suspended in 0.05 M carbonate-bicarbonate buffer (pH 9.6) to a cell density of about 1 × 109 cells/mL. A 200-μL aliquot of this cell suspension was used to coat 96-well plates and incubated overnight at 4°C. The wells were washed with Tris buffered saline with 0.1% Tween20 (TBST) and blocked with 1% bovine serum albumin (200 μL) in TBST for 1 h at 37°C. After repeated washes with TBST, rabbit polyclonal anti-RN4220 antiserum (100 μL, 1:20000) was added, and plates were incubated for 1 h at 37°C. The wells were washed again with TBST before adding alkaline phosphatase-labeled goat anti-rabbit antibody (100 μl, 1:5000). Plates were incubated for 1 h at 37°C. After washing the wells, the substrate p-nitro phenyl phosphate (100 μL) was added, the plates were incubated for 40 min, and absorbance at 405 nm was determined.