PXD043567

PXD043567 is an original dataset announced via ProteomeXchange.

Title	In-host evolution of Yersinia enterocolitica during a chronic human infection
Description	Following a pacemaker implantation, a 75-years-old patient suffered from five successive bacteremia episodes between in 1999 and 2013, during which five bacterial strains were isolated. Phenotypic and whole-genome sequencing analysis of four isolates identified the strains as Yersinia enterocolitica bioserotype 4/O:3. Phylogenetic reconstruction showed that the patient was chronically infected by the same strain, which evolved within the host during 14 years. Single-nucleotide polymorphhism (SNP) analysis indicates that the last two isolates which displayed severe growth defects in vitro and acquired resistance to quinolones, evolved in parallel and formed two independent lineages within the host. Pan-genome analysis and genome comparison showed that their common evolution was characterized by 41 small insertion/deletion events and loss of three large DNA fragments. These mutations, which may account for the observed growth defect and also for the appearance of vegetations on the pacemaker, support antibiotics tolerance. Quinolone resistance was acquired through a so far undescribed deletion in the gyrA gene. 140 genes containing mutations vertically acquired from a common ancestor were also identified in the two lineages. A phylogenetic analysis by maximum likelihood identified two genes presenting a positive selection signal, suggesting that these mutations provided a survival advantage to bacteria during chronic infection. This is the first report allowing identification of genetic changes associated to within-host adaptation of a pathogenic Yersinia species.
HostingRepository	PRIDE
AnnounceDate	2025-05-26
AnnouncementXML	Submission_2025-05-26_00:52:19.967.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Thibaut Douché
SpeciesList	scientific name: Yersinia enterocolitica; NCBI TaxID: 630; scientific name: Bacteria; NCBI TaxID: NCBITaxon:2;
ModificationList	acetylated residue; monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Q Exactive HF

Revision	Datetime	Status	ChangeLog Entry
0	2023-07-05 16:00:01	ID requested
⏵ 1	2025-05-26 00:52:20	announced

Dataset with its publication pending

submitter keyword: Yersinia enterocolitica, genetic changes, DIA-MS, SPEED, Q Exactive HF

Javier Pizzaro-Cerda
contact affiliation	Institut Pasteur, Universite Paris Cite, CNRS UMR6047, Yersinia Research Unit, Paris,France
contact email	javier.pizarro-cerda@pasteur.fr
lab head
Thibaut Douché
contact affiliation	Institut Pasteur
contact email	thibaut.douche@pasteur.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/2025/05/PXD043567

PRIDE project URI

• PRIDE
  1. PXD043567
     1. Label: PRIDE project
     2. Name: In-host evolution of Yersinia enterocolitica during a chronic human infection