Summary of Study ST003777
This data is available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench, https://www.metabolomicsworkbench.org, where it has been assigned Project ID PR002355. The data can be accessed directly via it's Project DOI: 10.21228/M8753X This work is supported by NIH grant, U2C- DK119886.
See: https://www.metabolomicsworkbench.org/about/howtocite.php
This study contains a large results data set and is not available in the mwTab file. It is only available for download via FTP as data file(s) here.
| Study ID | ST003777 |
| Study Title | Separation and Characterization of a Clinically-Derived Staphylococcus epidermidis Strain HE23: Revealing Its Antibiotic Resistome and Metabolic Potential |
| Study Summary | Neonatal incubators, while essential for infant care, are high-risk environments for nosocomial infections due to microbial colonization. Staphylococcus epidermidis, a biofilm-forming opportunistic pathogen, frequently contaminates medical devices, yet its metabolic adaptation mechanisms and virulence potential in incubator settings remain poorly understood. This study integrates genomics and metabolomics to comprehensively profile a multidrug-resistant S. epidermidis HE23 strain isolated from neonatal incubators, aiming to reveal its antibiotic resistance determinants and toxic metabolite production linked to clinical pathogenicity. A bacterial strain (HE23) was isolated from a neonatal incubator and identified as Staphylococcus epidermidis by 16S rRNA sequencing. Whole genome sequencing was performed using Illumina and Oxford Nanopore platforms, and a high-quality genome was obtained by hybrid assembly (Unicycler). And metabolomic analysis was performed by liquid mass spectrometry detection. Metabolomic profiling of Staphylococcus epidermidis HE23 revealed 47 differentially expressed metabolites (15 upregulated, 32 downregulated; VIP > 1.0, p < 0.05). Among upregulated metabolites, two clinically significant toxins were identified:Harmaline (m/z 446.2529 ), Cinobufagin (m/z 460.2686). Pathway enrichment highlighted glutathione metabolism (VIP = 2.1, p = 0.008) and branched-chain amino acid degradation (VIP = 1.8, p = 0.015), suggesting redox stress adaptation and nutrient scavenging strategies. |
| Institute | Anhui Medical University |
| Department | College of Life Sciences |
| Laboratory | College of Life Sciences, Anhui Medical University |
| Last Name | Chen |
| First Name | Qingru |
| Address | 81 Meishan Road, Hefei, Anhui 230032, China |
| chenqr95@foxmail.com | |
| Phone | 18156455228 |
| Submit Date | 2025-03-02 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | mzML, raw(Thermo) |
| Analysis Type Detail | LC-MS |
| Release Date | 2025-03-07 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR002355 |
| Project DOI: | doi: 10.21228/M8753X |
| Project Title: | Metabolomics of Staphylococcus epidermidis HE23 isolated from the hospital environment |
| Project Summary: | Metabolomic analysis of Staphylococcus epidermidis HE23 isolated from the hospital environment to investigate its metabolic profile and potential hazards |
| Institute: | Anhui Medical University |
| Last Name: | Chen |
| First Name: | Qingru |
| Address: | 81 Meishan Road, Hefei, Anhui 230032, China |
| Email: | chenqr95@foxmail.com |
| Phone: | 18156455228 |
Subject:
| Subject ID: | SU003911 |
| Subject Type: | Bacteria |
| Subject Species: | Staphylococcus epidermidis |
| Taxonomy ID: | 1282 |
| Genotype Strain: | Staphylococcus epidermidis HE23 |
Factors:
Subject type: Bacteria; Subject species: Staphylococcus epidermidis (Factor headings shown in green)
| mb_sample_id | local_sample_id | Sample source | Sample_type |
|---|---|---|---|
| SA409971 | H1 | Bacteria | Bacterial cells |
| SA409972 | H2 | Bacteria | Bacterial cells |
| SA409973 | H3 | Bacteria | Bacterial cells |
| SA409974 | C1 | Blank | control |
| SA409975 | C2 | Blank | control |
| SA409976 | C3 | Blank | control |
| SA409977 | QC01 | QC | QC(Internal Standard) |
| SA409978 | QC02 | QC | QC(Internal Standard) |
| SA409979 | QC03 | QC | QC(Internal Standard) |
| Showing results 1 to 9 of 9 |
Collection:
| Collection ID: | CO003904 |
| Collection Summary: | The Staphylococcus epidermidis HE23 strain was isolated from the inner surface of a neonatal incubator in the Neonatal Intensive Care Unit (NICU) at the First Affiliated Hospital of Anhui Medical University (Hefei, China). Post-sampling, the isolate was purified via streak-plating on LB agar. Taxonomic classification was confirmed through 16S ribosomal RNA gene sequencing (primers 27F/1492R). For experimental analyses, HE23 was cultured in standard LB broth (10 g/L tryptone, 5 g/L yeast extract, 10 g/L NaCl; pH 7.2) under aerobic conditions. Pre-inoculum was prepared by incubating at 37°C with 200 rpm orbital shaking for 16–18 hours to reach mid-log phase (OD₆₀₀ ≈ 0.8). Cells were harvested by centrifugation (4,000 ×g, 10 min, 4°C) and washed twice with sterile phosphate-buffered saline (PBS) prior to downstream assays. |
| Sample Type: | Bacterial cells |
Treatment:
| Treatment ID: | TR003920 |
| Treatment Summary: | NA |
Sample Preparation:
| Sampleprep ID: | SP003917 |
| Sampleprep Summary: | Accurately pipette 200 μL of sample into a 1.5 mL centrifuge tube; Add 400 μL of extraction solution (methanol:acetonitrile=1:1 (v:v)) containing four internal standards (e.g., L-2-chlorophenylalanine (0.02 mg/mL), etc.); vortex and mix for 30 s, and then ultrasonic extraction was carried out for 30 min at low temperature (5°C, 40 KHz); the sample was left at -20°C for 30 min; centrifuged for 15 min (13,000g, 4°C), and the supernatant was removed and The samples were allowed to stand at -20℃ for 30 minutes, centrifuged for 15 minutes (13000g, 4℃), the supernatant was pipetted and blown dry with nitrogen; 120 μL of reconstituted solution (acetonitrile:water=1:1) was added to reconstitute the sample; the samples were vortexed again for 30 seconds, and then sonicated at low temperature for 5 minutes (5℃, 40KHz); the samples were then centrifuged for 10 minutes (13000g, 4℃), and the supernatant was pipetted to the feeder vials with the cannulae for analysis. In addition, 20 μL of supernatant was pipetted separately for each sample and mixed as a quality control sample. |
Chromatography:
| Chromatography ID: | CH004706 |
| Instrument Name: | Thermo Dionex Ultimate 3000 |
| Column Name: | Waters ACQUITY UPLC HSS T3 (100 x 2.1mm,1.8um) |
| Column Temperature: | 40℃ |
| Flow Gradient: | 0–0.5 min: 40% B (isocratic) 0.5–3.5 min: 40% B → 55% B (linear) 3.5–6.0 min: 55% B → 70% B (linear) 6.0–7.0 min: 70% B → 100% B (linear) 7.0–8.0 min: 100% B (isocratic) Mobile Phase B gradient changes throughout the process. |
| Flow Rate: | 0.4 mL/min |
| Solvent A: | 95% water/5% acetonitrile; 0.1% formic acid |
| Solvent B: | 47.5% acetonitrile/47.5% isopropanol/5% water; 0.1% formic acid |
| Chromatography Type: | Reversed phase |
Analysis:
| Analysis ID: | AN006203 |
| Analysis Type: | MS |
| Chromatography ID: | CH004706 |
| Has Mz: | 1 |
| Has Rt: | 1 |
| Rt Units: | Minutes |
| Results File: | ST003777_AN006203_Results.txt |
| Units: | Peak area |
| Analysis ID: | AN006204 |
| Analysis Type: | MS |
| Chromatography ID: | CH004706 |
| Has Mz: | 1 |
| Has Rt: | 1 |
| Rt Units: | Minutes |
| Results File: | ST003777_AN006204_Results.txt |
| Units: | Peak area |
