Summary of Study ST002449

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 PR001064. The data can be accessed directly via it's Project DOI: 10.21228/M85H6W 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.

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Study IDST002449
Study TitleIdentify putative volatile biomarkers of Valley fever using a murine lung infection model (Human studies)
Study TypeUntargeted metabolomics
Study SummaryCoccidioides immitis and Coccidioides posadasii are soil-dwelling fungi of arid regions in North and South America that are responsible for Valley fever (coccidioidomycosis). Forty percent of patients with Valley fever exhibit symptoms ranging from mild, self-limiting respiratory infections, to severe, life-threatening pneumonia that requires treatment. Misdiagnosis as bacterial pneumonia commonly occurs in symptomatic Valley fever cases, resulting in inappropriate treatment with antibiotics, increased medical costs, and delay in diagnosis. In this study, we explored the feasibility of developing breath-based diagnostics for Valley fever using lung specimens from persons with community-acquired pneumonia (CAP). To investigate potential volatile biomarkers of Valley fever that arise from host-pathogen interactions, we collected bronchoalveolar lavage fluid (BALF) and sputum from patients treated at Mayo Clinic in Scottsdale, Arizona for untargeted volatile metabolomics via solid phase microextraction (SPME) and two-dimensional gas chromatography coupled to time-of-flight mass spectrometry (GC×GC-TOFMS). We identified 244 total volatile organic compounds (VOCs). Using Random Forest, we identified a subset of these VOCs that were also able to separate Coccidioides positive samples from bacteria positive samples. The data presented here show that Coccidioides and/or the host produce volatile metabolites that may yield biomarkers for a Valley fever breath test that can detect Coccidioidal infection.
Institute
Arizona State University
DepartmentSchool of Life Sciences
LaboratoryBean Laboratory
Last NameBean
First NameHeather
AddressPO Box 874501
EmailHeather.D.Bean@asu.edu
Phone4807273395
Submit Date2022-12-17
Raw Data AvailableYes
Raw Data File Type(s)smp
Analysis Type DetailGC-MS
Release Date2024-01-31
Release Version1
Heather Bean Heather Bean
https://dx.doi.org/10.21228/M85H6W
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Project:

Project ID:PR001064
Project DOI:doi: 10.21228/M85H6W
Project Title:Volatile Biomarkers for a Valley Fever Breath Test
Project Type:GCxGC-TOFMS metabolomics
Project Summary:Coccidioidomycosis, or valley fever, is prevalent in AZ, with more than 12,000 new human infections diagnosed every year. In highly endemic areas, e.g., Phoenix and Tucson, up to 30% of community-acquired pneumonia may be caused by Valley fever, and cases are on the rise. The current diagnostics for Valley fever are severely lacking due to invasiveness (biopsy) and poor sensitivity (serology), strongly contributing to an unacceptable 23-day median time-to-diagnosis. There is a critical need for sensitive and non-invasive diagnostics for identifying Valley fever lung infections. Our long-term goal is to substantially shorten the time-to-diagnosis for Valley fever through the development of sensitive and specific breath-based diagnostics for coccidioidomycosis lung infections. The overall objective of this application is to identify and validate putative volatile biomarkers of Coccidioides infections via metabolomics analyses of in vitro cultures, mouse model lung infections, and lung specimens from humans with Valley fever. At the completion of the proposed study, we expect to have identified and validated a panel of 10-15 volatile biomarkers for the sensitive and specific detection of valley fever in lung specimens.
Institute:Arizona State University
Department:School of Life Sciences
Laboratory:Bean Laboratory
Last Name:Bean
First Name:Heather
Address:PO Box 874501, Tempe, AZ, 85287, USA
Email:Heather.D.Bean@asu.edu
Phone:480-727-3395
Funding Source:Arizona Biomedical Research Centre New Investigator Award to HDB

Subject:

Subject ID:SU002538
Subject Type:Mammal
Subject Species:Homo sapiens
Taxonomy ID:9606
Gender:Male and female

Factors:

Subject type: Mammal; Subject species: Homo sapiens (Factor headings shown in green)

mb_sample_id local_sample_id Subject treatment
SA244821Standard_mix_3Alkane Standard and Grob Mix Standard Mix
SA244822Standard_mix_2Alkane Standard and Grob Mix Standard Mix
SA244823Standard_1Alkane Standard and Grob Mix Standard Mix
SA244824Standard mix_1Alkane Standard and Grob Mix Standard Mix
SA244825Standard_mix_1Alkane Standard and Grob Mix Standard Mix
SA244826Blank_2Empty run NA
SA244827Blank_7Empty run NA
SA244828Blank_1Empty run NA
SA244829Blank_3Empty run NA
SA244830Blank_4Empty run NA
SA244831Blank_8Empty run NA
SA244832Blank_6Empty run NA
SA244833Blank_5Empty run NA
SA244834MNBAL-165B_1Human BALF Bacterial
SA244835MNBAL-165C_1Human BALF Bacterial
SA244836MNBAL-165A_1Human BALF Bacterial
SA244837MNBAL-192A_1Human BALF Bacterial
SA244838MNBAL-198B_1Human BALF Bacterial
SA244839MNBAL-161C_1Human BALF Bacterial
SA244840MNBAL-198A_1Human BALF Bacterial
SA244841MNBAL-192C_1Human BALF Bacterial
SA244842MNBAL-192B_1Human BALF Bacterial
SA244843MNBAL-153B_2xprep_1Human BALF Bacterial
SA244844MNBAL-198C_1Human BALF Bacterial
SA244845MNBAL-153A_1Human BALF Bacterial
SA244846MNBAL-152C_1Human BALF Bacterial
SA244847MNBAL-153C_1Human BALF Bacterial
SA244848MNBAL-154A_1Human BALF Bacterial
SA244849MNBAL-161A_1Human BALF Bacterial
SA244850MNBAL-154C_1Human BALF Bacterial
SA244851MNBAL-154B_1Human BALF Bacterial
SA244852MNBAL-161B_1Human BALF Bacterial
SA244853MNBAL-5B_1Human BALF Bacterial
SA244854MNBAL-82A_1Human BALF Bacterial
SA244855MNBAL-77C_1Human BALF Bacterial
SA244856MNBAL-77B_1Human BALF Bacterial
SA244857MNBAL-82B_1Human BALF Bacterial
SA244858MNBAL-82C_1Human BALF Bacterial
SA244859MNBAL-97C_1Human BALF Bacterial
SA244860MNBAL-97B_1Human BALF Bacterial
SA244861MNBAL-97A_1Human BALF Bacterial
SA244862MNBAL-77A_1Human BALF Bacterial
SA244863MNBAL-76C_1Human BALF Bacterial
SA244864MNBAL-33B_1Human BALF Bacterial
SA244865MNBAL-33A_1Human BALF Bacterial
SA244866MNBAL-212B_1Human BALF Bacterial
SA244867MNBAL-33C_1Human BALF Bacterial
SA244868MNBAL-5A_1Human BALF Bacterial
SA244869MNBAL-76B_1Human BALF Bacterial
SA244870MNBAL-76A_1Human BALF Bacterial
SA244871MNBAL-152B_1Human BALF Bacterial
SA244872MNBAL-212A_1Human BALF Bacterial
SA244873MNBAL-212C_1Human BALF Bacterial
SA244874MNBAL-115B_1Human BALF Bacterial
SA244875MNBAL-108C_1Human BALF Bacterial
SA244876MNBAL-108B_1Human BALF Bacterial
SA244877MNBAL-111A_1Human BALF Bacterial
SA244878MNBAL-111B_1Human BALF Bacterial
SA244879MNBAL-115C_1Human BALF Bacterial
SA244880MNBAL-152A_1Human BALF Bacterial
SA244881MNBAL-111C_1Human BALF Bacterial
SA244882MNBAL-108A_1Human BALF Bacterial
SA244883MNBAL-115A_1Human BALF Bacterial
SA244884MNBAL-136B_1Human BALF Bacterial
SA244885MNBAL-136C_1Human BALF Bacterial
SA244886MNBAL-102C_1Human BALF Bacterial
SA244887MNBAL-136A_1Human BALF Bacterial
SA244888MNBAL-102B_1Human BALF Bacterial
SA244889MNBAL-102A_1Human BALF Bacterial
SA244890MNBAL-71C_1Human BALF Cocci
SA244891MNBAL-71B_1Human BALF Cocci
SA244892MNBAL-72B_1Human BALF Cocci
SA244893MNBAL-73A_1Human BALF Cocci
SA244894MNBAL-39C_1Human BALF Cocci
SA244895MNBAL-72A_1Human BALF Cocci
SA244896MNBAL-119C_1Human BALF Cocci
SA244897MNBAL-61A_1Human BALF Cocci
SA244898MNBAL-73B_1Human BALF Cocci
SA244899MNBAL-119B_1Human BALF Cocci
SA244900MNBAL-61B_1Human BALF Cocci
SA244901MNBAL-119A_1Human BALF Cocci
SA244902MNBAL-71A_1Human BALF Cocci
SA244903MNBAL-75A_1Human BALF Cocci
SA244904MNBAL-109B_1Human BALF Cocci
SA244905MNBAL-109C_1Human BALF Cocci
SA244906MNBAL-109A_1Human BALF Cocci
SA244907MNBAL-14A_1Human BALF Cocci
SA244908MNBAL-14C_1Human BALF Cocci
SA244909MNBAL-14B_1Human BALF Cocci
SA244910MNBAL-75C_1Human BALF Cocci
SA244911MNBAL-75B_1Human BALF Cocci
SA244912MNBAL-74B_1Human BALF Cocci
SA244913MNBAL-74A_1Human BALF Cocci
SA244914MNBAL-39B_1Human BALF Cocci
SA244915MNBAL-39A_1Human BALF Cocci
SA244916MNBAL-74C_1Human BALF Cocci
SA244917MNBAL-73C_1Human BALF Cocci
SA244918MNBAL-17A_1Human BALF Fungal
SA244919MNBAL-17B_1Human BALF Fungal
SA244920MNBAL-17C_1Human BALF Fungal
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Collection:

Collection ID:CO002531
Collection Summary:Human lung specimens were collected and stored in -80'C at Mayo Clinic in Scottsdale, Arizona until they were transferred to Arizona State University for VOCs analysis
Sample Type:Bronchoalveolar lavage

Treatment:

Treatment ID:TR002550
Treatment Summary:55 bronchoalveolar lavage fluid (BALF), four bronchial wash, and five sputum samples were provided by Tom Gris at Mayo Clinic, Scottsdale, Arizona. Patient samples were categorized by infecting microbial organisms; Coccidioides, fungal, bacterial, viral, multiple, and, non-infectious using hospital codes and doctors notes. A sample was considered Coccidioides positive if it had a positive serology test or was confirmed by culture. Fungal samples were either Coccidioides positive or had a positive fungal culture or fungal smear. Bacterial samples were identified by gram stain, bacterial culture, or PCR. Samples were considered viral positive by PCR. If a sample was considered positive for more than one type of infectious organism (ex, bacterial positive and viral positive) it was labeled multiple. Samples that did not fit into an infectious category, as described, they were labeled non-infectious.

Sample Preparation:

Sampleprep ID:SP002544
Sampleprep Summary:The BALF samples were allowed to thaw at 4°C overnight, and then split into technical triplicates of 200 μL that were transferred and sealed into sterilized 2 mL GC headspace vials with Supelco® PTFE/silicone septum magnetic screw caps (Sigma-Aldrich®, St. Louis, MO). All samples were stored in GC headspace vials for up to 14 d at -20°C until analyzed. Samples were randomized for analysis. Volatile metabolites sampling was performed by solid phase microextraction (SPME) using a Gerstel® MPS Robotic Pro MultiPurpose autosampler directed by Maestro® software (Gerstel®, Inc., Linthicum, MD). Volatile metabolite analysis was performed by two-dimensional gas chromatography−time-of-flight mass spectrometry (GC×GC–TOFMS) using a LECO® Pegasus® 4D and Agilent® 7890B GC (LECO® Corp., St. Joseph, MI). An external alkane standards mixture (C8 – C20; Sigma-Aldrich®) was sampled multiple times for calculating retention indices (RI). The injection, chromatographic, and mass spectrometric methods for analyzing the alkane standards were the same as for the samples.
Extraction Method:Solid-phase microextraction (SPME)

Combined analysis:

Analysis ID AN003997
Analysis type MS
Chromatography type GC
Chromatography system Agilent 7890B
Column Column 1: Rxi-624Sil MS, (60m × 0.25mm × 1.4um); Column 2: Stabilwax, (1m × 0.25mm × 0.5um)
MS Type EI
MS instrument type GC x GC-TOF
MS instrument name Leco Pegasus 4D GCxGC TOF
Ion Mode POSITIVE
Units Peak areas

Chromatography:

Chromatography ID:CH002951
Methods Filename:VF_human_GCxGC_methods.docx
Instrument Name:Agilent 7890B
Column Name:Column 1: Rxi-624Sil MS, (60m × 0.25mm × 1.4um); Column 2: Stabilwax, (1m × 0.25mm × 0.5um)
Column Temperature:230
Flow Gradient:NA
Flow Rate:2 mL∙min-1 (constant)
Solvent A:NA
Solvent B:NA
Chromatography Type:GC

MS:

MS ID:MS003745
Analysis ID:AN003997
Instrument Name:Leco Pegasus 4D GCxGC TOF
Instrument Type:GC x GC-TOF
MS Type:EI
MS Comments:See attached protocol
Ion Mode:POSITIVE
Analysis Protocol File:VF_human_MS_methods.docx
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