PXD036656

PXD036656 is an original dataset announced via ProteomeXchange.

Title	Escherichia coli killing by Shigella sonnei is mediated by colicins found in epidemiologically successful sublineages
Description	Shigella sonnei as an enteric pathogen, can benefit from outcompeting gut commensals such as Escherichia coli and there can be several mechanisms that assist in interbacterial competition. It is, therefore, important to understand these mechanisms as they provide insights into the interactions of these pathogens in the complex environment they exist. We used our novel Bulk Phenotyping of Epidemiological Replicates (BPER) pipeline combined with bacterial Genome Wide Association Studies (GWAS) on a previously described real-world collection of S. sonnei isolates (n=165) to demonstrate the vital role that colicins could have played in shaping the observed epidemiology of S. sonnei. We then used targeted mass spectrometry on representative S. sonnei isolates to detect colicin sequences in cell free supernatants, which further validated our BPER results to suggest the vital role of colicins. Here, we also introduce BPER as an epidemiologically relevant way of phenotypic testing in the laboratory where the phenotypic results can be interpreted with much more relevance to the effects of those phenotypes in natural settings.
HostingRepository	PRIDE
AnnounceDate	2023-11-14
AnnouncementXML	Submission_2023-11-14_09:08:41.006.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD036656
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Lauriane Kuhn
SpeciesList	scientific name: Shigella sonnei; NCBI TaxID: 624;
ModificationList	acetylated residue; monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2022-09-12 06:21:04	ID requested
1	2023-10-24 12:10:06	announced
⏵ 2	2023-11-14 09:08:42	announced	2023-11-14: Updated project metadata.

10.6019/PXD036656;

De Silva PM, Bennett RJ, Kuhn L, Ngondo P, Debande L, Njamkepo E, Ho B, Weill FX, Marteyn BS, Jenkins C, Baker KS, Escherichia coli killing by epidemiologically successful sublineages of Shigella sonnei is mediated by colicins. EBioMedicine, 97():104822(2023) [pubmed]

submitter keyword: Colicins, BPER,Shigella

Kate Baker
contact affiliation	Department of Clinical Infection, Microbiology, and Immunology; Institute for Infection, Veterinary, and Ecological Sciences (IVES), University of Liverpool, L69 7ZB, Liverpool, United Kingdom.
contact email	kbaker@liverpool.ac.uk
lab head
Lauriane Kuhn
contact affiliation	CNRS, IBMC, FRC1589
contact email	l.kuhn@ibmc-cnrs.unistra.fr
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/2023/10/PXD036656

PRIDE project URI

• PRIDE
  1. PXD036656
     1. Label: PRIDE project
     2. Name: Escherichia coli killing by Shigella sonnei is mediated by colicins found in epidemiologically successful sublineages