Summary of Study ST001244

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 PR000831. The data can be accessed directly via it's Project DOI: 10.21228/M88H5F 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.

Show all samples | Perform analysis on untargeted data
Download mwTab file (text) | Download mwTab file(JSON) | Download data files (Contains raw data)

Study ID	ST001244
Study Title	Uropathogenic versus Urocolonizing Escherichia coli
Study Summary	Urinary tract infections (UTIs) represent a major burden across the population, although key facets of their pathogenesis challenge physicians and investigators alike. Escherichia coli epitomizes these obstacles: this Gram-negative bacterial species is the most prevalent agent of UTIs worldwide and can also colonize the urogenital tract in a phenomenon known as asymptomatic bacteriuria (ASB). Unfortunately, at the level of the organism, the relationship between symptomatic UTI and ASB is poorly defined, confounding our understanding of microbial pathogenesis and strategies for clinical management. Unlike diarrheagenic pathotypes of E. coli, the definition of uropathogenic E. coli (UPEC) remains phenomenologic, without conserved phenotypes and (known) genetic determinants that rigorously distinguish UTI- and ASB-associated strains. This manuscript provides a cross-disciplinary review of the current issues – from interrelated mechanistic and diagnostic perspectives – and describes new opportunities by which clinical resources can be leveraged to overcome molecular challenges. Specifically, we present our work harnessing a large collection of patient-derived isolates to identify features that do (and do not) distinguish UTI- from ASB-associated E. coli strains. Analyses of biofilm formation, previously reported to be higher in ASB strains, revealed extensive phenotypic heterogeneity that did not correlate with symptomatology. However, metabolomic experiments revealed distinct signatures between ASB and cystitis isolates, including species in the purine pathway (previously shown to be critical for intracellular survival during acute infection). Together, these studies demonstrate how large-scale, wild-type approaches can help dissect the physiology of colonization-versus-infection, suggesting that the molecular definition of UPEC may rest at the level of global bacterial metabolism.
Institute	Vanderbilt University
Last Name	Rutledge
First Name	Alexandra
Address	7330 Stevenson Center Lane, NASHVILLE, TENNESSEE, 37235, USA
Email	a.rutledge@vanderbilt.edu
Phone	6155046923
Submit Date	2019-08-14
Raw Data Available	Yes
Raw Data File Type(s)	raw(Thermo)
Analysis Type Detail	LC-MS
Release Date	2020-03-03
Release Version	1

Select appropriate tab below to view additional metadata details:

Sample Preparation:

Sampleprep ID:	SP001320
Sampleprep Summary:	Global untargeted metabolomic analyses were performed on the supernatant-fraction of ASB and cystitis pools. Aliquots of each pool (200µL) were added to individual Eppendorf tubes containing 200µL ice cold lysis buffer (1:1:2, ACN:MeOH:Ammonium Bicarbonate (0.1M, pH 8.0)) (LC-MS grade). Labeled creatinine-D3 and lysine-D4 were added to each sample to assess the metabolite extraction (sample preparation) step. Samples were first subjected to protein precipitation by addition of 800µL of ice cold methanol (4x by volume), then incubated at -80C overnight. Following incubation, samples were centrifuged (10,000 rpm, 10 min) to pellet precipitated proteins; the metabolite-containing supernatant was transferred to a clean Eppendorf tube, dried in vacuo and stored at -80C until further LC-MS analysis. The pellet-fraction of each sample pool prepared as described above was lysed using 400µL ice cold lysis buffer (1:1:2, ACN:MeOH:Ammonium Bicarbonate (0.1M, pH 8.0) (LC-MS grade), followed by sonication in an ice bath for 10 min. Sample volume for each pool was adjusted such that all samples have the same cell number in each vial. Samples were first subjected to protein precipitation by addition of 1000µL of ice cold methanol (4x by volume), then incubated at -80C overnight. Following incubation, samplwere were centrifuged (10,000 rpm, 10 min) to pellet precipitated proteins; the metabolite-containing extract was transferred to a clean Eppendorf tube, dried in vacuo and stored at -80C until further LC-MS analysis.

Sampleprep ID:

SP001320

Sampleprep Summary:

Global untargeted metabolomic analyses were performed on the supernatant-fraction of ASB and cystitis pools. Aliquots of each pool (200µL) were added to individual Eppendorf tubes containing 200µL ice cold lysis buffer (1:1:2, ACN:MeOH:Ammonium Bicarbonate (0.1M, pH 8.0)) (LC-MS grade). Labeled creatinine-D3 and lysine-D4 were added to each sample to assess the metabolite extraction (sample preparation) step. Samples were first subjected to protein precipitation by addition of 800µL of ice cold methanol (4x by volume), then incubated at -80C overnight. Following incubation, samples were centrifuged (10,000 rpm, 10 min) to pellet precipitated proteins; the metabolite-containing supernatant was transferred to a clean Eppendorf tube, dried in vacuo and stored at -80C until further LC-MS analysis. The pellet-fraction of each sample pool prepared as described above was lysed using 400µL ice cold lysis buffer (1:1:2, ACN:MeOH:Ammonium Bicarbonate (0.1M, pH 8.0) (LC-MS grade), followed by sonication in an ice bath for 10 min. Sample volume for each pool was adjusted such that all samples have the same cell number in each vial. Samples were first subjected to protein precipitation by addition of 1000µL of ice cold methanol (4x by volume), then incubated at -80C overnight. Following incubation, samplwere were centrifuged (10,000 rpm, 10 min) to pellet precipitated proteins; the metabolite-containing extract was transferred to a clean Eppendorf tube, dried in vacuo and stored at -80C until further LC-MS analysis.