PXD054264

PXD054264 is an original dataset announced via ProteomeXchange.

Title	Rapid detection and capture of clinical Escherichia coli strains mediated by OmpA-targeting nanobodies
Description	Escherichia coli is a major cause of blood stream and urinary tract infections. Owing to the spread of antimicrobial resistance, it is often treated with an inadequate antibiotic. With the aim to accelerate the diagnostics of this key pathogen, we used the flycode technology to generate nanobodies against the conserved and highly abundant outer membrane protein OmpA. Two nanobodies each recognizing a different isoform of OmpA were shown by flow cytometry to recognize > 91% of 85,680 E. coli OmpA sequences deposited in a large bacterial genome database. Crystal structures of these nanobodies in complex with the respective OmpA isoform revealed interactions with all four surface accessible loops of OmpA. Steric hindrance caused by dense O-antigen layers initially impeded reliable capture of clinical E. coli strains. By generating nanobody constructs with long linkers and by thinning the O-antigen layer through alterations to growth medium and buffers, we achieved to capture <50 CFU/mL. Our work provides a framework to generate nanobodies for the specific and sensitive detection and capture of clinically relevant pathogenic bacteria.
HostingRepository	PRIDE
AnnounceDate	2025-06-11
AnnouncementXML	Submission_2025-06-11_10:12:51.943.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Michèle Sorgenfrei
SpeciesList	scientific name: Escherichia coli; NCBI TaxID: 562;
ModificationList	No PTMs are included in the dataset
Instrument	Q Exactive HF; Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2024-07-26 01:25:41	ID requested
⏵ 1	2025-06-11 10:12:52	announced

10.1038/S42003-025-08345-9;

Egloff P, Zimmermann I, Arnold FM, Hutter CAJ, Morger D, Opitz L, Poveda L, Keserue HA, Panse C, Roschitzki B, Seeger MA, Engineered peptide barcodes for in-depth analyses of binding protein libraries. Nat Methods, 16(5):421-428(2019) [pubmed]

10.1038/s41592-019-0389-8;

submitter keyword: LC-MS/MS, NestLink, E. coli

Markus Andreas Seeger
contact affiliation	Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
contact email	m.seeger@imm.uzh.ch
lab head
Michèle Sorgenfrei
contact affiliation	Institute of Medical Microbiology, University of Zurich
contact email	msorgenfrei@imm.uzh.ch
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/2025/06/PXD054264

PRIDE project URI

• PRIDE
  1. PXD054264
     1. Label: PRIDE project
     2. Name: Rapid detection and capture of clinical Escherichia coli strains mediated by OmpA-targeting nanobodies