Materials and Methods
Bacterial isolates and culture conditions. There were 328 non-duplicate S. aureus clinical isolates comprised of 138 methicillin-resistant S. aureus (MRSA) and 190 methicillin-sensitive S. aureus (MSSA) isolates used in this study. These isolates were obtained from Shenzhen Nanshan People’s Hospital, China, from January 2010 to December 2017. All clinical isolates were simultaneously identified by the BD Phoenix™ 100 automated microbiology system (BD, USA) and mass spectrometer (IVD MALDI Biotyper®, Germany). S. aureus isolates were grown in cation-adjusted Mueller-Hinton broth (CAMHB) at 37°C with shaking for antimicrobial susceptibility and time-killing assays. For biofilm assay, S. aureus isolates were grown in TSBG (tryptic soy broth with 0.5% glucose) at 37°C. The Ca2+ (50 mg/l) was added to CAMHB media in the experiments with daptomycin.
Chemicals and natural products. Vancomycin hydrochloride (catalogue no. HY-17362), linezolid (catalogue no. HY-10394), daptomycin (catalogue no. HY-B0108), and α-mangostin (catalogue no. HY-N0328) were purchased from MedChemExpress (China). Propidium iodide (PI) (catalogue no. P4170) and bis(1,3-dibutylbarbituric acid) trimethine oxonol (DiBAC4(3)) (catalogue no. D8189) were purchased from Sigma-Aldrich (China).
Antimicrobial susceptibility test. The minimum inhibitory concentration (MICs) of α-mangostin against S. aureus isolates was determined by the broth macro dilution method in CAMHB according to the Clinical and Laboratory Standards Institute guidelines (CLSI-M100-S30) (CLSI 2020) and the previous study (Song et al. 2020). Briefly, α-mangostin or other antimicrobials were two-fold diluted with CAMHB and mixed with S. aureus suspensions (1.5 × 106 CFU/ml). After 18 h incubation at 37°C, the MICs were defined as the lowest concentrations of antibiotics in tubes with no visible growth of bacteria. All experiments were performed in triplicate.
Bacterial growth curve and time-killing assay. The effect of α-mangostin, daptomycin, vancomycin, linezolid, and their synergistic combinations on the growth of S. aureus planktonic cells was explored based on a previous study (Wang et al. 2021). S. aureus suspension (OD600 = 0.2) with α-mangostin or antimicrobials (at ½ × MIC) was inoculated into 96-well polystyrene microtiter plates (300 μl/well) and cultured for 24 h at 37°C. The optical density at 600 (OD600) was measured with a Bioscreen C system (Lab Systems Helsinki, Finland). All experiments were performed in triplicate. The time-killing assay aimed to measure the rapid bactericidal activity of α-mangostin against S. aureus (Zheng et al. 2019). Briefly, this assay was conducted in a final volume of 4 ml CAMHB with α-mangostin or antimicrobials (at 4 × MIC). The samples were incubated at 37°C for 24 h. After 1, 3, and 24 h of time-killing assay, 1 ml aliquots were sampled, and the number of CFU/ml was determined. All experiments were performed in triplicate.
The effect of α-mangostin on S. aureus established biofilms. The eradicating effect of α-mangostin on established biofilms of S. aureus was measured by crystal violet staining (Zheng et al. 2020). The overnight S. aureus cultures were diluted with fresh TSBG (200 μl/well) and inoculated into 96 polystyrene microtiter plates. After static incubation at 37°C for 24 h (mature biofilms formed), the supernatant was discarded and washed, and then fresh TSBG containing α-mangostin was added. After static incubation at 37°C for 24 h, the supernatant was discarded, and plates were washed three times with 0.9% saline. The biomass of the remaining biofilms of S. aureus still attached to the wells was determined by crystal violet staining. All experiments were performed in triplicate.
Induction of α-mangostin non-sensitive clones in vitro. The α-mangostin non-sensitive S. aureus clones were selected in vitro (Zheng et al. 2021). S. aureus SA113 (MSSA) and YUSA145 (MRSA) strains were subcultured in CAMHB with α-mangostin. The initial concentration of α-mangostin was equal to ½ × MIC, then successively increased to a high concentration of 64 × MIC. Individual bacteria clones from the last passage of each concentration were selected and cultured without α-mangostin for two passages. Then the bacterial species were identified by mass spectrometry, and the MIC of α-mangostin was determined again. Finally, the α-mangostin non-sensitive clones (MIC of α-mangostin: ≥ 12.5 μM) were stored at –20°C for further analysis.
Whole-genome sequencing. The genomic DNA of the parental S. aureus isolate YUSA145 and α-mangostin non-sensitive clone YUSA145-L12 was obtained by the DNeasy Blood and Tissue Kit (QIAGEN, Germany). The genomic DNA per sample (1 μg) was used, and sequencing libraries were generated with the NEBNext® Ultra™ DNA Library Prep Kit for Illumina® (New England Biolabs®, Inc., USA). The whole genome sequencing was performed in the Illumina® HiScan™SQ system (Illumina®, USA) based on our previous research (Zheng et al. 2021). Briefly, the coding genes, repetitive sequences, and other sequences were predicted by the following software or tools: GeneMarkS and RepeatMasker (http://www.repeatmasker.org) (Smit et al. 2013). Gene functions were analyzed by the following databases: GO (Gene Ontology) and KEGG (Kyoto Encyclopedia of Genes and Genomes). Genomic alignments and SNPs analysis between the α-mangostin non-sensitive clone YUSA145-L12 genome and the parental YUSA145 genome (subcultured in MHB containing no α-mangostin) and reference genome (USA300 FPR3757, GenBank: CP000255.1) were completed with MUMmer and LASTZ.
Proteomics analysis. To illuminate the antibacterial mechanism of α-mangostin against S. aureus, the proteomics analysis was conducted in S. aureus YUSA145 with the treatment of α-mangostin (at ½ × MIC) for 4 h. Bacterial cultures were harvested at OD600 ∼ 0.8 and transferred to a precooled 2 ml screw-cap tube. 1.5 volumes of zirconia/silica beads (Biospec, 0.1 mm) and RIPA lysis buffer (Beyotime Biotechnology, China) were added to the tube. The cells were lysed with a cell disruption device, and the protein concentrations were measured using a commercial BCA assay. The pretreatment of harvested protein samples (100 μg) before LC-MS detection was performed according to our previous study (Wen et al. 2022). Briefly, the harvested protein samples were reduced with 10 mM DTT (Sigma-Aldrich, USA), then alkylated with 50 mM iodoacetamide (IAA; Sigma-Aldrich, USA), avoiding light. The samples were desalted and washed with 0.5 M ammonium bicarbonate with Amicon® Ultra Centrifugal Filters (10 kDa cutoff; Merk Millipore, USA), and digested with trypsin (Promega, USA).
LC-MS/MS detection was conducted in the UltiMate™ 3000 RSLCnano system coupled to a Q Exactive™ Plus Hybrid Quadrupole-Orbitrap Mass Spectrometer (Thermo Scientific, USA). Peptides (250 mm) were loaded on 75 μm Acclaim™ PepMap™ C18 reverse-phase analytical column (Thermo Scientific, USA), and eluted with 0.1% acetic acid (containing ~ 53% acetonitrile). The full scan was performed in the Orbitrap (m/z 300–1500) with a resolution of 70,000. The corresponding MS2 spectra for MS detection were at the resolution of 17,500 (maximally 50 ms). The different abundance proteins were determined with the Proteome Discoverer 2.4 base with the Sequest HT, according to the Uniprot reference proteome of S. aureus (strain NCTC 8325/PS47). The minimum unused score of 1.3 (equivalent to 95% confidence) and the false discovery rate (FDR) of less than 1% were used for all reported proteins (decreasing false-positive identification results). The different abundance proteins were analyzed with the OMICSBEAN database (http://www.omicsbean.com) for GO annotation, KEGG pathway analysis, and PPI networks.
Membrane integrity assay. Both propidium iodide staining and bis(1,3-dibutylbarbituric acid) trimethine oxonol uptake assay were performed following the protocol of Fan et al. (2019). The PI staining method mainly aimed to evaluate the integrity of the S. aureus cell membrane. S. aureus suspension (OD600 = 0.2) was diluted 100-fold with PBS and pipetted into a 24-well plate. α-Mangostin was added into each well at final concentrations 1 × MIC and 4 × MIC, respectively. Sodium chloride solution and DMSO were used as the negative control group, and 1% Triton was used as the positive control group. PI solution (7.5 μg/ml) was added to each well and kept the plate at room temperature for 30 min. A microplate reader was used to detect fluorescence intensity at excitation and emission wavelengths of 535 and 615 nm, respectively. DiBAC4(3) was a fluorescent dye and sensitive to membrane potential. Briefly, S. aureus suspension (OD600 = 0.2) was added into a black, opaque, flat-bottomed 96-well plate, followed by the incubation with DiBAC4(3) (1 μM) at 37°C in the dark for 30 min. Likewise, α-mangostin has added into each well with the final concentrations of 1 × MIC and 4 × MIC, respectively. Subsequently, the fluorescence intensity was detected at 492 nm and 515 nm. The controls were chosen as described above. Results were expressed in relative fluorescence units. All experiments were performed in triplicate.
Statistical Analysis. The results were shown as mean±SD and were compared by Student’s t-test or one-way analysis of variance (ANOVA). All the data were analyzed by the IBM® SPSS® software package (version 19.0, USA), and the p < 0.05 was determined as statistically significant.