PXD002000

PXD002000 is an original dataset announced via ProteomeXchange.

Title	Mechanisms of antibiotic resistance to enrofloxacin in uropathogenic Escherichia coli in dog
Description	Escherichia coli (E. coli) urinary tract infections (UTIs) are becoming a serious problem both for pets and humans (zoonosis) due to the close contact and to the increasing resistance to antibiotics. Great progress has been made in the discovery of novel antibiotics to counteract E. coli pathogens. However, this huge progress has been undercut by the evolution of bacteria in the way of drug resistance. Enrofloxacin is one of the most efficient antibiotics against E. coli pathogens and there is considerable evidence that documents how this microorganism is becoming more resistant to this antibiotic and is developing multidrug resistance. This study has been performed in order to unravel the mechanism of induced enrofloxacin resistance in canine E. coli isolates that represent a good tool to study this pathology. For a comprehensive investigation about antibiotic resistance mechanisms, an E. coli isolate from urinary tract infection (UTI) was induced to grow under a concentration of 10 µg/ml of enrofloxacin. Proteins represent the main contributors to the mechanisms involved in antibiotic resistance in bacteria. Their abundance profile provides reliable information about the mechanisms involved in this process. Three biological replicates of control and resistant isolate have been analyzed both through 2D DIGE and shotgun proteomics. In our case, prior to perform the proteomics analysis, the screening with MS profiling of control and resistant isolates was performed highlighting the differences among strains and successfully clustering experimental strains according to PC analysis (PCA). The results clearly demonstrate differential profiles in peptide expression among clusters and between isolate and reference strain. According to these preliminary results, the protein profile of the resistant group was compared with the one of its sensitive counterpart by a proteomic analysis based on 2D-DIGE to separate proteins combined to MALDI MS analysis and database search to identify differentially expressed proteins. This analysis showed the modulation of 19 proteins between the two conditions. At the same time, another comparative proteomics investigation was also carried out by free-label nLC-MSE. This method has allowed the qualitative and quantitative analysis of total protein extracts of the two groups for the simultaneous screening of a larger number of proteins. A total of 57 differentially expressed proteins were identified and a comprehensive study on the proteins associated with enrofloxacin resistance was carried out. We classified these modulated proteins by their molecular functions and pathways where they are principally involved. This approach allowed to highlight some pathways that can be involved in an increased antibiotic resistance. Two major mechanisms were discovered. The first one was related to the stabilization of DNA structure through the up-regulation of Dsp protein. The second one was the downregulation of outer membrane protein W in order to reduce the membrane permeability to enrofloxacin. Discovered differentilally expressed proteins are principally involved in antibiotic resistance and linked to the oxidative stress response, to DNA protection and in membrane permeability. Moreover, since enrofloxacin is an inhibitor of DNA gyrase, the overexpression of DNA starvation/stationary phase protection protein (Dsp) could be a central point to discover the mechanism of this clone to counteract the effects of enrofloxacin. In parallel, the dramatic decrease of the synthesis of the outer membrane protein W, which represents one of the main gates for enrofloxacin entrance, could explain additional mechanism of E. coli defense against this antibiotic. The proteins differentially expressed could represent putative targets for the development of new strategies to counteract drug and multidrug resistance.
HostingRepository	PRIDE
AnnounceDate	2015-06-05
AnnouncementXML	Submission_2015-10-16_02:37:50.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD002000
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Paola Roncada
SpeciesList	scientific name: Escherichia coli; NCBI TaxID: 562;
ModificationList	monohydroxylated residue; monohydroxylated residue: 15.99491; iodoacetamide derivatized residue; iodoacetamide derivatized residue: 57.02146
Instrument	ultraflex; nanoACQUITY UPLC

Revision	Datetime	Status	ChangeLog Entry
0	2015-03-31 05:27:08	ID requested
1	2015-06-05 07:40:23	announced
⏵ 2	2015-10-16 02:37:51	announced	Updated publication reference for PubMed record(s): 26066767.

Piras C, Soggiu A, Greco V, Martino PA, Del Chierico F, Putignani L, Urbani A, Nally JE, Bonizzi L, Roncada P, Mechanisms of antibiotic resistance to enrofloxacin in uropathogenic Escherichia coli in dog. J Proteomics, 127(Pt B):365-76(2015) [pubmed]

curator keyword: Biomedical

submitter keyword: Escherichia coli, antibiotic resistance, Urinary tract infections, enrofloxacin

Paola Roncada
contact affiliation	1. Istitituto Sperimentale Italiano L. Spallanzani,Milano, Italy; 2. Dipartimento di Scienze Veterinarie e Sanità Pubblica, Università degli Studi di Milano, Milano, Italy.
contact email	paola.roncada@guest.unimi.it
lab head
Paola Roncada
contact affiliation	DIVET, Università degli studi di Milano
contact email	paola.roncada@guest.unimi.it
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD002000
     1. Label: PRIDE project
     2. Name: Mechanisms of antibiotic resistance to enrofloxacin in uropathogenic Escherichia coli in dog