Summary of Study ST003024

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.

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 IDST003024
Study TitleIdentifying and mathematically modeling the time-course of extracellular metabolic markers associated with resistance to ceftolozane/tazobactam in Pseudomonas aeruginosa - Part 1
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
DepartmentMonash Institute of Pharmaceutical Sciences
LaboratoryCornelia Landersdorfer
Last NameLandersdorfer
First NameCornelia
Address399 Royal Pd
Emaildovile.anderson@monash.edu
Phone0448671141
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:SU003138
Subject Type:Bacteria
Subject Species:Pseudomonas aeruginosa
Taxonomy ID:287
Genotype Strain:CW41
Age Or Age Range:NA
Weight Or Weight Range:NA
Height Or Height Range:NA
Gender:Not applicable
Cell Strain Details:hypermutable clinical isolate

Factors:

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

mb_sample_id local_sample_id treatment
SA327725BR_Cefto3g_000_2BR_Cefto3g_0h
SA327726BR_Cefto3g_000_3BR_Cefto3g_0h
SA327727BR_Cefto3g_000_1BR_Cefto3g_0h
SA327728BR_Cefto3g_215_2BR_Cefto3g_215h
SA327729BR_Cefto3g_215_1BR_Cefto3g_215h
SA327730BR_Cefto3g_047_3BR_Cefto3g_47h
SA327731BR_Cefto3g_047_2BR_Cefto3g_47h
SA327732BR_Cefto3g_047_1BR_Cefto3g_47h
SA327733BR_Cefto6g_000_3BR_Cefto6g_0h
SA327734BR_Cefto6g_000_2BR_Cefto6g_0h
SA327735BR_Cefto6g_000_1BR_Cefto6g_0h
SA327736BR_Cefto6g_215_2BR_Cefto6g_215h
SA327737BR_Cefto6g_215_1BR_Cefto6g_215h
SA327738BR_Cefto6g_047_3BR_Cefto6g_47h
SA327739BR_Cefto6g_047_1BR_Cefto6g_47h
SA327740BR_Cefto6g_047_2BR_Cefto6g_47h
SA327741BR_Control_000_3BR_Control_0h
SA327742BR_Control_000_2BR_Control_0h
SA327743BR_Control_000_1BR_Control_0h
SA327744BR_Control_215_1BR_Control_215h
SA327745BR_Control_215_2BR_Control_215h
SA327746BR_Control_047_1BR_Control_47h
SA327747BR_Control_047_3BR_Control_47h
SA327748BR_Control_047_2BR_Control_47h
SA327749Blank_1Extraction blank
SA327750Blank_4Extraction blank
SA327751Blank_5Extraction blank
SA327752Blank_3Extraction blank
SA327753Blank_2Extraction blank
SA327754Blank_10Extraction blank
SA327755Blank_12Extraction blank
SA327756Blank_6Extraction blank
SA327757Blank_11Extraction blank
SA327758Blank_7Extraction blank
SA327759Blank_9Extraction blank
SA327760Blank_8Extraction blank
SA327761M_Cefto3g_000_3M_Cefto3g_0h
SA327762M_Cefto3g_000_1M_Cefto3g_0h
SA327763M_Cefto3g_000_2M_Cefto3g_0h
SA327764M_Cefto3g_143_1M_Cefto3g_143h
SA327765M_Cefto3g_143_2M_Cefto3g_143h
SA327766M_Cefto3g_143_3M_Cefto3g_143h
SA327767M_Cefto3g_167_1M_Cefto3g_167h
SA327768M_Cefto3g_167_2M_Cefto3g_167h
SA327769M_Cefto3g_167_3M_Cefto3g_167h
SA327770M_Cefto3g_191_2M_Cefto3g_191h
SA327771M_Cefto3g_191_3M_Cefto3g_191h
SA327772M_Cefto3g_215_3M_Cefto3g_215h
SA327773M_Cefto3g_215_1M_Cefto3g_215h
SA327774M_Cefto3g_215_2M_Cefto3g_215h
SA327775M_Cefto3g_023_2M_Cefto3g_23h
SA327776M_Cefto3g_023_3M_Cefto3g_23h
SA327777M_Cefto3g_023_1M_Cefto3g_23h
SA327778M_Cefto3g_047_1M_Cefto3g_47h
SA327779M_Cefto3g_047_2M_Cefto3g_47h
SA327780M_Cefto3g_047_3M_Cefto3g_47h
SA327781M_Cefto3g_071_3M_Cefto3g_71h
SA327782M_Cefto3g_071_1M_Cefto3g_71h
SA327783M_Cefto3g_071_2M_Cefto3g_71h
SA327784M_Cefto3g_007_1M_Cefto3g_7h
SA327785M_Cefto3g_007_2M_Cefto3g_7h
SA327786M_Cefto3g_007_3M_Cefto3g_7h
SA327787M_Cefto3g_095_3M_Cefto3g_95h
SA327788M_Cefto3g_095_1M_Cefto3g_95h
SA327789M_Cefto3g_095_2M_Cefto3g_95h
SA327790M_Cefto6g_143_3M_Cefto6g_143h
SA327791M_Cefto6g_143_1M_Cefto6g_143h
SA327792M_Cefto6g_143_2M_Cefto6g_143h
SA327793M_Cefto6g_167_1M_Cefto6g_167h
SA327794M_Cefto6g_167_2M_Cefto6g_167h
SA327795M_Cefto6g_167_3M_Cefto6g_167h
SA327796M_Cefto6g_191_3M_Cefto6g_191h
SA327797M_Cefto6g_191_2M_Cefto6g_191h
SA327798M_Cefto6g_215_2M_Cefto6g_215h
SA327799M_Cefto6g_215_3M_Cefto6g_215h
SA327800M_Cefto6g_215_1M_Cefto6g_215h
SA327801M_Cefto6g_023_1M_Cefto6g_23h
SA327802M_Cefto6g_023_2M_Cefto6g_23h
SA327803M_Cefto6g_023_3M_Cefto6g_23h
SA327804M_Cefto6g_047_1M_Cefto6g_47h
SA327805M_Cefto6g_047_2M_Cefto6g_47h
SA327806M_Cefto6g_047_3M_Cefto6g_47h
SA327807M_Cefto6g_071_1M_Cefto6g_71h
SA327808M_Cefto6g_071_2M_Cefto6g_71h
SA327809M_Cefto6g_071_3M_Cefto6g_71h
SA327810M_Cefto6g_007_1M_Cefto6g_7h
SA327811M_Cefto6g_007_2M_Cefto6g_7h
SA327812M_Cefto6g_007_3M_Cefto6g_7h
SA327813M_Cefto6g_095_3M_Cefto6g_95h
SA327814M_Cefto6g_095_1M_Cefto6g_95h
SA327815M_Cefto6g_095_2M_Cefto6g_95h
SA327819M_Control_000_2M_Control_0h
SA327820M_Control_000_3M_Control_0h
SA327821M_Control_000_1M_Control_0h
SA327822M_Control_143_2M_Control_143h
SA327823M_Control_143_3M_Control_143h
SA327824M_Control_143_1M_Control_143h
SA327825M_Control_167_1M_Control_167h
SA327826M_Control_167_2M_Control_167h
SA327827M_Control_167_3M_Control_167h
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Collection:

Collection ID:CO003131
Collection Summary:For metabolomic footprint analysis, the supernatant from centrifuged bacterial samples was collected. These bacterial samples were obtained from the hollow-fiber cartridges for all untreated control and treated arms for each of the five biological replicates at 7, 23, 47, 71, 143, and 167 h. Additional bacterial samples were collected from the cartridges at 0 and 215 h for replicates 3 to 5. Matrix blank samples (of CAMHB not containing any bacteria) were collected from the diluent media bottles every 48 h for all untreated control and treated arms.
Sample Type:Bacterial cells
Storage Conditions:-80℃

Treatment:

Treatment ID:TR003147
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:continuous infusion
Treatment Compound:Ceftolozane-tazobactam
Treatment Dose:3 g and 6 g
Treatment Dosevolume:10.6 and 21.3 mg/L

Sample Preparation:

Sampleprep ID:SP003144
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.
Processing Storage Conditions:-80℃
Extract Storage:-80℃

Combined analysis:

Analysis ID AN004958 AN004959
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:CH003742
Chromatography Summary:ZIC-pHILIC chromatography at ph9, biological replicates 3-5
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 Pressure:60 bar at starting conditions. 180 bar at %A
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
Injection Temperature:4 C
Sample Injection:10 uL
Solvent A:20 mM ammonium carbonate
Solvent B:acetonitrile
Analytical Time:32 min
Capillary Voltage:4 kV
Washing Buffer:syringe wash 50% IPA
Sample Loop Size:25 uL
Sample Syringe Size:25 uL
Randomization Order:yes
Chromatography Type:HILIC

MS:

MS ID:MS004698
Analysis ID:AN004958
Instrument Name:Thermo Q Exactive Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:Full scan LCMS data acquired using polarity switching. raw data processed using IDEOM workflow ( 10.1007/978-1-0716-0239-3_21).
Ion Mode:POSITIVE
Capillary Temperature:300 C
Capillary Voltage:4 kV
Collision Energy:NA
Collision Gas:NA
Dry Gas Flow:50
Dry Gas Temp:120
Ion Source Temperature:120 C
Ionization:ESI
Mass Accuracy:3 ppm
Precursor Type:[M+H]+
Source Temperature:300
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:MS004699
Analysis ID:AN004959
Instrument Name:Thermo Q Exactive Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:Full scan LCMS data acquired using polarity switching. raw data processed using IDEOM workflow ( 10.1007/978-1-0716-0239-3_21).
Ion Mode:NEGATIVE
Capillary Temperature:300 C
Capillary Voltage:3.5 kV
Collision Energy:NA
Collision Gas:NA
Dry Gas Flow:50
Dry Gas Temp:120
Ion Source Temperature:120 C
Ionization:ESI
Mass Accuracy:3 ppm
Precursor Type:[M-H]-
Source Temperature:300
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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