Summary of Study ST003036

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 PR001879. The data can be accessed directly via it's Project DOI: 10.21228/M8TX45 This work is supported by NIH grant, U2C- DK119886.

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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 IDST003036
Study TitleIdentifying and mathematically modeling the time-course of extracellular metabolic markers associated with resistance to ceftolozane/tazobactam in Pseudomonas aeruginosa - Part 2
Study TypeBiomedical research
Study SummaryExtracellular bacterial metabolites have potential as markers of bacterial growth and resistance emergence, but have not been evaluated in dynamic in vitro studies. We investigated the dynamic metabolomic footprint of a multidrug-resistant hypermutable Pseudomonas aeruginosa isolate exposed to ceftolozane/tazobactam as continuous infusion (4.5g/day, 9g/day) in a hollow-fiber infection model over 7-9 days in biological replicates (n=5). Bacterial samples were collected at 0, 7, 23, 47, 71, 95, 143, 167, 191 and 215h, the supernatant quenched and extracellular metabolites extracted. Metabolites were analyzed via untargeted metabolomics, including hierarchical clustering and correlation with quantified total and resistant bacterial populations. The time-courses of five metabolites were mathematically modeled. These five (of 1921 detected) metabolites were from enriched pathways (arginine and central carbon metabolism). Absorbed L-arginine and secreted L-ornithine were highly correlated with the total bacterial population (r -0.79 and 0.82 respectively, p<0.0001). Ribose-5-phosphate, sedoheptulose-7-phosphate and trehalose-6-phosphate correlated with the resistant subpopulation (0.64, 0.64 and 0.67, respectively, p<0.0001), and were likely secreted due to resistant growth overcoming oxidative and osmotic stress induced by ceftolozane/tazobactam. Using PK/PD-based transduction models, these metabolites were successfully modeled based on the total or resistant bacterial populations. The models well described the abundance of each metabolite across the differing time-course profiles of biological replicates, based on bacterial killing and, importantly, resistant regrowth. These proof-of-concept studies suggest further exploration is warranted to determine the generalizability of these findings. The metabolites modeled in this work are not exclusive to bacterial cells. Future studies may use this approach to identify bacteria-specific metabolites correlating with resistance, which would ultimately be extremely useful for clinical translation.
Institute
Monash Institute of Pharmaceutical Sciences
DepartmentDrug Delivery, Disposition and Dynamics
LaboratoryCornelia Landersdorfer
Last NameLandersdorfer
First NameCornelia
Address399 Royal Pd
Emailcornelia.landersdorfer@monash.edu
Phone+61 3 9903 9061
Submit Date2023-12-17
Num Groups6 groups with time points
Total SubjectsNA
Num MalesNA
Num FemalesNA
PublicationsIdentifying and mathematically modeling the time-course of extracellular metabolic markers associated with resistance to ceftolozane/tazobactam in Pseudomonas aeruginosa
Raw Data AvailableYes
Raw Data File Type(s)raw(Thermo)
Analysis Type DetailLC-MS
Release Date2024-01-11
Release Version1
Cornelia Landersdorfer Cornelia Landersdorfer
https://dx.doi.org/10.21228/M8TX45
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:

Project:

Project ID:PR001879
Project DOI:doi: 10.21228/M8TX45
Project Title:Identifying and mathematically modeling the time-course of extracellular metabolic markers associated with resistance to ceftolozane/tazobactam in Pseudomonas aeruginosa
Project Type:Biomedical research
Project Summary:Extracellular bacterial metabolites have potential as markers of bacterial growth and resistance emergence, but have not been evaluated in dynamic in vitro studies. We investigated the dynamic metabolomic footprint of a multidrug-resistant hypermutable Pseudomonas aeruginosa isolate exposed to ceftolozane/tazobactam as continuous infusion (4.5g/day, 9g/day) in a hollow-fiber infection model over 7-9 days in biological replicates (n=5). Bacterial samples were collected at 0, 7, 23, 47, 71, 95, 143, 167, 191 and 215h, the supernatant quenched and extracellular metabolites extracted. Metabolites were analyzed via untargeted metabolomics, including hierarchical clustering and correlation with quantified total and resistant bacterial populations. The time-courses of five metabolites were mathematically modeled. These five (of 1921 detected) metabolites were from enriched pathways (arginine and central carbon metabolism). Absorbed L-arginine and secreted L-ornithine were highly correlated with the total bacterial population (r -0.79 and 0.82 respectively, p<0.0001). Ribose-5-phosphate, sedoheptulose-7-phosphate and trehalose-6-phosphate correlated with the resistant subpopulation (0.64, 0.64 and 0.67, respectively, p<0.0001), and were likely secreted due to resistant growth overcoming oxidative and osmotic stress induced by ceftolozane/tazobactam. Using PK/PD-based transduction models, these metabolites were successfully modeled based on the total or resistant bacterial populations. The models well described the abundance of each metabolite across the differing time-course profiles of biological replicates, based on bacterial killing and, importantly, resistant regrowth. These proof-of-concept studies suggest further exploration is warranted to determine the generalizability of these findings. The metabolites modeled in this work are not exclusive to bacterial cells. Future studies may use this approach to identify bacteria-specific metabolites correlating with resistance, which would ultimately be extremely useful for clinical translation.
Institute:Monash Institute of Pharmaceutical Sciences
Department:Monash Institute of Pharmaceutical Sciences
Laboratory:Cornelia Landersdorfer
Last Name:Landersdorfer
First Name:Cornelia
Address:399 Royal Pd
Email:dovile.anderson@monash.edu
Phone:0448671141
Publications:Identifying and mathematically modeling the time-course of extracellular metabolic markers associated with resistance to ceftolozane/tazobactam in Pseudomonas aeruginosa
Contributors:Jessica R. Tait, Dovile Anderson, Roger L. Nation, Darren J. Creek, Cornelia B. Landersdorfer

Subject:

Subject ID:SU003150
Subject Type:Bacteria
Subject Species:Pseudomonas aeruginosa
Taxonomy ID:287
Genotype Strain:CW41
Age Or Age Range:NA
Weight Or Weight Range:NA
Gender:Not applicable

Factors:

Subject type: Bacteria; Subject species: Pseudomonas aeruginosa (Factor headings shown in green)

mb_sample_id local_sample_id treatment
SA328785BR_Blank_broth_B0_B0BR_Blank_broth_B0
SA328786BR_Blank_broth_B1_EBR_Blank_broth_B1
SA328787BR_Blank_broth_B2_JBR_Blank_broth_B2
SA328788BR_Blank_broth_B2_FBR_Blank_broth_B2
SA328789BR_Blank_broth_B2_EBR_Blank_broth_B2
SA328790BR_Blank_broth_B3_iBR_Blank_broth_B3
SA328791BR_Blank_broth_B3_i_20200426061728BR_Blank_broth_B3
SA328792BR_Blank_broth_B3_JBR_Blank_broth_B3
SA328793BR_Blank_broth_B3_F_20200425222826BR_Blank_broth_B3
SA328794BR_Blank_broth_B3_FBR_Blank_broth_B3
SA328795BR_Blank_broth_B3_EBR_Blank_broth_B3
SA328796BR_Blank_broth_B4_ABR_Blank_broth_B4
SA328797BR_Blank_broth_B4_BBR_Blank_broth_B4
SA328798BR_Blank_broth_B4_iBR_Blank_broth_B4
SA328799BR_Blank_broth_B4_JBR_Blank_broth_B4
SA328800Blank_4Extraction blank
SA328801Blank_5Extraction blank
SA328802Blank_6Extraction blank
SA328803Blank_2Extraction blank
SA328804Blank_3Extraction blank
SA328805Blank_1Extraction blank
SA328806M_Cefto_3g_143h_EM_Cefto_3g_143h
SA328807M_Cefto_3g_143h_FM_Cefto_3g_143h
SA328808M_Cefto_3g_167h_EM_Cefto_3g_167h
SA328809M_Cefto_3g_167h_FM_Cefto_3g_167h
SA328810M_Cefto_3g_23h_EM_Cefto_3g_23h
SA328811M_Cefto_3g_23h_FM_Cefto_3g_23h
SA328812M_Cefto_3g_47h_FM_Cefto_3g_47h
SA328813M_Cefto_3g_47h_EM_Cefto_3g_47h
SA328814M_Cefto_3g_71h_FM_Cefto_3g_71h
SA328815M_Cefto_3g_71h_EM_Cefto_3g_71h
SA328816M_Cefto_3g_7h_EM_Cefto_3g_7h
SA328817M_Cefto_3g_7h_FM_Cefto_3g_7h
SA328818M_Cefto_3g_95h_EM_Cefto_3g_95h
SA328819M_Cefto_3g_95h_FM_Cefto_3g_95h
SA328820M_Cefto_6g_143h_iM_Cefto_6g_143h
SA328821M_Cefto_6g_143h_JM_Cefto_6g_143h
SA328822M_Cefto_6g_167h_JM_Cefto_6g_167h
SA328823M_Cefto_6g_167h_iM_Cefto_6g_167h
SA328824M_Cefto_6g_23h_iM_Cefto_6g_23h
SA328825M_Cefto_6g_23h_JM_Cefto_6g_23h
SA328826M_Cefto_6g_47h_iM_Cefto_6g_47h
SA328827M_Cefto_6g_47h_JM_Cefto_6g_47h
SA328828M_Cefto_6g_71h_iM_Cefto_6g_71h
SA328829M_Cefto_6g_71h_JM_Cefto_6g_71h
SA328830M_Cefto_6g_7h_JM_Cefto_6g_7h
SA328831M_Cefto_6g_7h_iM_Cefto_6g_7h
SA328832M_Cefto_6g_95h_iM_Cefto_6g_95h
SA328833M_Cefto_6g_95h_JM_Cefto_6g_95h
SA328834M_Control_143h_AM_Control_143h
SA328835M_Control_143h_BM_Control_143h
SA328836M_Control_167h_BM_Control_167h
SA328837M_Control_167h_AM_Control_167h
SA328838M_Control_23h_BM_Control_23h
SA328839M_Control_23h_AM_Control_23h
SA328840M_Control_47h_AM_Control_47h
SA328841M_Control_47h_BM_Control_47h
SA328842M_Control_71h_BM_Control_71h
SA328843M_Control_71h_AM_Control_71h
SA328844M_Control_7h_BM_Control_7h
SA328845M_Control_7h_AM_Control_7h
SA328846M_Control_95h_AM_Control_95h
SA328847M_Control_95h_BM_Control_95h
SA328848QC_6Pooled QC
SA328849QC_5Pooled QC
SA328850QC_1Pooled QC
SA328851QC_2Pooled QC
SA328852QC_3Pooled QC
SA328853QC_4Pooled QC
Showing results 1 to 69 of 69

Collection:

Collection ID:CO003143
Collection Summary:A hypermutable P. aeruginosa clinical isolate, CW41, was challenged with ceftolozane-tazobactam (Zerbaxa®, MSD, Australia) in the HFIM (C3008-1 cartridges; FiberCell Systems Inc., Frederick, MD, USA), in five biological replicates performed across two studies. The first study, with replicates 1 and 2, was conducted over 167 h and the second study, with replicates 3, 4 and 5, over 215 h. Briefly, the studied isolate was characterized as susceptible to ceftolozane-tazobactam (MIC 4 mg/L), and MDR (i.e. resistant to at least 1 antibiotic from each of ≥3 antibiotic classes) (17-20). The HFIM studies used cation-adjusted Mueller Hinton broth (CAMHB) and agar (CAMHA) [Becton Dickinson & Co., Sparks, MD, USA, with 25.0 mg/L Ca2+ and 12.5 mg/L Mg2+]. Ceftolozane-tazobactam was administered to simulate steady-state concentrations of ceftolozane predicted to occur in the epithelial lining fluid of the lung in patients with CF, following daily doses of 3 g/1.5 g and 6 g/3 g via continuous infusion (10.6 and 21.3 mg/L, respectively) (21-23). Total bacterial populations were quantified on antibiotic-free CAMHA, and resistant subpopulations on CAMHA containing ceftolozane-tazobactam (12 and 20 mg/L).
Sample Type:Bacterial cells

Treatment:

Treatment ID:TR003159
Treatment Summary:Ceftolozane-tazobactam was administered to simulate steady-state concentrations of ceftolozane predicted to occur in the epithelial lining fluid of the lung in patients with CF, following daily doses of 3 g/1.5 g and 6 g/3 g via continuous infusion (10.6 and 21.3 mg/L, respectively) (21-23). Total bacterial populations were quantified on antibiotic-free CAMHA, and resistant subpopulations on CAMHA containing ceftolozane-tazobactam (12 and 20 mg/L).
Treatment Compound:Ceftolozane-tazobactam
Treatment Dose:3 g and 6 g
Treatment Dosevolume:10.6 and 21.3 mg/L

Sample Preparation:

Sampleprep ID:SP003156
Sampleprep Summary:Each sample (25 µL) was added to 100 µL of pre-chilled methanol containing the internal standards (CHAPS, CAPS, TRIS and PIPES) at 1 µM. This mixture was vortexed, and subsequently centrifuged at 14800 x g and 4°C for 10 min .The final supernatant samples containing the extracted extracellular metabolites were stored at -80°C until LC-MS analysis was performed (Figure S2B).
Processing Method:IDEOM
Processing Storage Conditions:-80℃
Extract Storage:-80℃

Combined analysis:

Analysis ID AN004977 AN004978
Analysis type MS MS
Chromatography type HILIC HILIC
Chromatography system Thermo Dionex Ultimate 3000 Thermo Dionex Ultimate 3000
Column Merck SeQuant ZIC-pHILIC (150 x 4.6mm,5um) Merck SeQuant ZIC-pHILIC (150 x 4.6mm,5um)
MS Type ESI ESI
MS instrument type Orbitrap Orbitrap
MS instrument name Thermo Q Exactive Orbitrap Thermo Q Exactive Orbitrap
Ion Mode POSITIVE NEGATIVE
Units peak height peak height

Chromatography:

Chromatography ID:CH003758
Chromatography Summary:ZIC-pHILIC chromatography at pH 9 using pos neg switching
Methods Filename:Metabolomics_pHILIC_Parkville_v1.pdf
Instrument Name:Thermo Dionex Ultimate 3000
Column Name:Merck SeQuant ZIC-pHILIC (150 x 4.6mm,5um)
Column Temperature:25 C
Flow Gradient:0 min - 80%B, 15 min - 50%B, 18 min - 5%B, 21 min - 5%B, 24 min - 80%B, 32 min - 80%B
Flow Rate:0.3 ml/min
Solvent A:20 mM ammonium carbonate
Solvent B:acetonitrile
Washing Buffer:syringe wash 50% IPA
Chromatography Type:HILIC
  
Chromatography ID:CH003759
Chromatography Summary:ZIC-pHILIC chromatography at pH 9 using pos neg switching
Methods Filename:Metabolomics_pHILIC_Parkville_v1.pdf
Instrument Name:Thermo Dionex Ultimate 3000
Column Name:Merck SeQuant ZIC-pHILIC (150 x 4.6mm,5um)
Column Temperature:25 C
Flow Gradient:0 min - 80%B, 15 min - 50%B, 18 min - 5%B, 21 min - 5%B, 24 min - 80%B, 32 min - 80%B
Flow Rate:0.3 ml/min
Solvent A:20 mM ammonium carbonate
Solvent B:acetonitrile
Washing Buffer:syringe wash 50% IPA
Chromatography Type:HILIC

MS:

MS ID:MS004717
Analysis ID:AN004977
Instrument Name:Thermo Q Exactive Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:polarity switching used, resolution 35 k, full scan
Ion Mode:POSITIVE
Capillary Temperature:300 C
Capillary Voltage:3.5 kV
Collision Energy:NA
Dry Gas Flow:50
Dry Gas Temp:120
Ion Source Temperature:120 C
Mass Accuracy:3 ppm
Precursor Type:[M+H]+
Acquisition Parameters File:Metabolomics_pHILIC_Parkville_v1.pdf
Analysis Protocol File:PQMS3-MPMF-WIN-0501_LCMS_data_acquisition_for_untargeted_metabolomics_analysis.pdf
  
MS ID:MS004718
Analysis ID:AN004978
Instrument Name:Thermo Q Exactive Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:polarity switching used, resolution 35 k, full scan
Ion Mode:NEGATIVE
Capillary Temperature:300 C
Capillary Voltage:4 kV
Collision Energy:NA
Dry Gas Flow:50
Dry Gas Temp:120
Ion Source Temperature:120 C
Mass Accuracy:3 ppm
Precursor Type:[M-H]-
Acquisition Parameters File:Metabolomics_pHILIC_Parkville_v1.pdf
Analysis Protocol File:PQMS3-MPMF-WIN-0501_LCMS_data_acquisition_for_untargeted_metabolomics_analysis.pdf
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