PXD015184-1

PXD015184 is an original dataset announced via ProteomeXchange.

Title	COMPARATIVE OMICS ANALYSIS OF HISTORICAL AND RECENT ISOLATES OF BORDETELLA PERTUSSIS
Description	Despite high vaccination coverage, pertussis is on the rise in many countries including Czech Republic. To better understand B. pertussis resurgence we compared the changes in genome structures between Czech vaccine and circulating strains and subsequently, we determined how these changes translated into global transcriptomic and proteomic profiles. The whole-genome sequencing revealed that both historical and recent isolates of B. pertussis display substantial variation in genome organization and cluster separately. The RNA-seq and LC-MS/MS analyses indicate that these variations translated into discretely separated transcriptomic and proteomic profiles. Compared to vaccine strains, recent isolates displayed increased expression of flagellar genes and decreased expression of polysaccharide capsule operon. Czech strains (Bp46, K10, Bp155, Bp318 and Bp6242)exhibited increased expression of T3SS and sulphate metabolism genes when compared to Tohama I. In spite of 50 years of vaccination the Czech vaccine strains (VS67, VS393 and VS401) differ from recent isolates to a lesser extent than from another vaccine strain Tohama I.
HostingRepository	PRIDE
AnnounceDate	2021-09-08
AnnouncementXML	Submission_2021-09-08_15:25:08.467.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Denisa Petrackova
SpeciesList	scientific name: Bordetella pertussis; NCBI TaxID: 520; scientific name: Bordetella pertussis Tohama I; NCBI TaxID: 257313;
ModificationList	No PTMs are included in the dataset
Instrument	Orbitrap Fusion

Revision	Datetime	Status	ChangeLog Entry
0	2019-08-27 07:51:08	ID requested
⏵ 1	2021-09-08 15:25:10	announced
2	2024-10-22 05:26:59	announced	2024-10-22: Updated project metadata.

Dienstbier A, Amman F, Petr, á, č, kov, á D, Š, tipl D, Č, apek J, Zavadilov, á J, Fabi, á, nov, á K, Dr, ž, m, í, š, ek J, Kumar D, Wildung M, Pouchnik D, Ve, č, erek B, Comparative Omics Analysis of Historic and Recent Isolates of Bordetella pertussis and Effects of Genome Rearrangements on Evolution. Emerg Infect Dis, 27(1):57-68(2021) [pubmed]

submitter keyword: Bordetella pertussis, omics analysis, IS elements, genomic rearrangement, adaptation

Branislav Večerek
contact affiliation	Academy of Sciences of the Czech Republic Institute of Microbiology, v.v.i. Prague, Czech Republic
contact email	vecerek@biomed.cas.cz
lab head
Denisa Petrackova
contact affiliation	Institute of Microbiology of the CAS, v. v. i.
contact email	petrack@biomed.cas.cz
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/2021/09/PXD015184

PRIDE project URI

• PRIDE
  1. PXD015184
     1. Label: PRIDE project
     2. Name: COMPARATIVE OMICS ANALYSIS OF HISTORICAL AND RECENT ISOLATES OF BORDETELLA PERTUSSIS