PXD023033

PXD023033 is an original dataset announced via ProteomeXchange.

Title	Mass Spectrometry Proteotyping-Based Detection and Identification of Staphylococcus aureus, Escherichia coli and Candida albicans in Blood
Description	Bloodstream infections (BSIs), the presence of microorganisms in blood, are potentially serious conditions that can quickly develop into sepsis and life-threatening situations. When assessing proper treatment, rapid diagnosis is the key; besides clinical judgement performed by attending physicians, supporting microbiological tests typically are performed, often requiring microbial isolation and culturing steps, which increases the time required for confirming positive cases of BSI. The additional waiting time forces physicians to prescribe broad-spectrum antibiotics and empiric treatment, before determining the precise cause of the disease. Thus, alternative and more rapid cultivation-independent methods are needed to improve clinical diagnostics, supporting prompt and accurate treatment and reducing the development of antibiotic resistance. In this study, a culture-independent workflow for pathogen detection and identification in blood samples was developed, using peptide biomarkers and applying bottom-up proteomics analyses, i.e., so-called ”proteotyping”. To demonstrate the feasibility of detection of blood infectious pathogens using proteotyping, Escherichia coli and Staphylococcus aureus were included in the study, as the most prominent bacterial causes of bacteremia and sepsis, as well as Candida albicans, one of the most prominent causes of fungemia. Model systems including spiked negative blood samples, as well as positive blood cultures, without further culturing steps, were investigated. Furthermore, an experiment designed to study the incubation time needed for correct identification of the infectious pathogens in blood cultures was performed. Compared to the MALDI-TOF MS-based approaches, shotgun proteotyping demonstrated higher sensitivity and accuracy, and required shorter incubation time before detection and identification of the correct pathogen could be accomplished.
HostingRepository	PRIDE
AnnounceDate	2021-07-20
AnnouncementXML	Submission_2021-10-24_22:19:29.625.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Gelio Alves
SpeciesList	scientific name: Escherichia coli; NCBI TaxID: 562; scientific name: Candida albicans (Yeast); NCBI TaxID: 5476; scientific name: Staphylococcus aureus; NCBI TaxID: 1280;
ModificationList	No PTMs are included in the dataset
Instrument	Q Exactive HF

Revision	Datetime	Status	ChangeLog Entry
0	2020-12-09 23:55:33	ID requested
1	2021-07-19 21:41:26	announced
⏵ 2	2021-10-24 22:19:30	announced	2021-10-25: Updated publication reference for PubMed record(s): 34381737.

Kondori N, Kurtovic A, Pi, ñ, eiro-Iglesias B, Salv, à, -Serra F, Ja, é, n-Luchoro D, Andersson B, Alves G, Ogurtsov A, Thorsell A, Fuchs J, Tunovic T, Kamenska N, Karlsson A, Yu YK, Moore ERB, Karlsson R, in Blood. Front Cell Infect Microbiol, 11():634215(2021) [pubmed]

submitter keyword: Proteotyping, Bloodstream infections, Pathogen Identification, LC-MS/MS

Roger Karlsson
contact affiliation	Department of Clinical Microbiology, Sahlgrenska University Hospital, Gothenburg, Sweden
contact email	roger.karlsson@vgregion.se
lab head
Gelio Alves
contact affiliation	CBB
contact email	alves@ncbi.nlm.nih.gov
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2021/07/PXD023033

PRIDE project URI

• PRIDE
  1. PXD023033
     1. Label: PRIDE project
     2. Name: Mass Spectrometry Proteotyping-Based Detection and Identification of Staphylococcus aureus, Escherichia coli and Candida albicans in Blood