Comparative Proteomics of Commensal and Pathogenic Strains of Escherichia coli

Background: Most of the proteomic studies in Escherichia coli have focussed on pathogenic strains, while very few studies have studied the commensal strains. It is important to study the commensal strains because under the selective pressure of their habitat, commensal strains might serve as reservoirs of virulent and pathogenic strains. Objective: In this study, we have performed a comparative proteomic analysis of commensal and pathogenic strains of E. coli isolated from a major river flowing through northern India. Methods: Proteins were resolved by two dimensional gel electrophoresis and the differentially expressed proteins were identified using matrix-assisted laser desorption ionization-time of flight mass-spectrometry (MALDI-TOF MS). Results: Many proteins of the commensal strain showed an increased expression compared to the pathogenic strain, of which seventeen proteins were identified by MALDI-TOF MS. Functional classification of these proteins revealed that they belonged to different functional pathways like energy metabolism, nucleotide and nucleoside conversions, translation, biosynthesis of amino acids and motility and energytaxis/chemotaxis. Conclusion: As per the best of our knowledge, this is the first report on comparative proteomic analysis of E. coli commensal and pathogenic strains of aquatic origin. Our results suggest that the increased production of these proteins might play an important role in adaptation of E. coli to a commensal/pathogenic lifestyle. However, further experiments are required to understand the precise role of these proteins in regulating the pathogenicity/commensalism of E. coli.

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Comparative proteomic analysis on human L-02 liver cells treated with varying concentrations of trichloroethylene

Toxicology and Industrial Health ◽

10.1177/0748233707078223 ◽

2007 ◽

Vol 23 (2) ◽

pp. 91-101 ◽

Cited By ~ 14

Author(s):

Jianjun Liu ◽

Haiyan Huang ◽

Xiumei Xing ◽

Renrong Xi ◽

Zhixiong Zhuang ◽

...

Keyword(s):

Proteomic Analysis ◽

Underlying Mechanism ◽

Liver Cells ◽

Control Group ◽

Two Dimensional Gel Electrophoresis ◽

Comparative Proteomic Analysis ◽

Maldi Tof ◽

Flight Mass Spectrometry ◽

Peptide Mass ◽

Tof Ms

To determine the differential proteomic expressions in human L-02 liver cells induced by varying concentrations of trichloroethylene (TCE), comparative proteomic analysis was performed on human L-02 liver cells which were treated with varying concentrations of TCE. According to the result of MTT test, we designed four different groups, in which the cells were treated with 0 μM (control group), 3, 10 or 40 μM TCE for 24 h, respectively. Comparative analysis of approximately 800 spots resolved by two-dimensional gel electrophoresis (2DE) in the soluble proteomes of L-02 cells from the four different groups resulted in 10 differential proteins. To identify the differential spots, matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF-MS) was carried out; if the results from the tool were insufficient, tandem MS (MALDI-TOF-TOF-MS) was then performed. The raw data of peptide mass fingerprints (PMFs) and MS/MS spectra were searched against the IPI human data base for exact matches. Then western blot was employed to verify the result of proteomic analysis, the following result confirmed that the results of proteomic analysis were reliable. These results might provide an insight into the underlying mechanism of TCE intoxication and find biological markers for diagnosis and therapy of TCE-induced diseases.

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Investigation of High-Risk ST131 Clone in Extended Spectrum β-Lactamase–Producing Escherichia coli Isolates in Children

Journal of Pediatric Infectious Diseases ◽

10.1055/s-0041-1730995 ◽

2021 ◽

Author(s):

Mehmet E. Bulut ◽

Gülen Hürkal ◽

Nazan Dalgıç

Keyword(s):

Escherichia Coli ◽

High Risk ◽

Pediatric Patients ◽

Pediatric Population ◽

Maldi Tof Ms ◽

E Coli ◽

Maldi Tof ◽

Extended Spectrum ◽

St131 Clone ◽

Tof Ms

Abstract Objective Antimicrobial resistance poses a serious threat to children's health. In recent years, high-risk Escherichia coli ST131 has become an important target for global surveillance studies. The E.coli ST131 clone is associated with extended spectrum β-lactamase (ESBL) production, as well as multidrug resistance and treatment failure. Studies on this clone in the pediatric age group are limited. We aim to investigate the rate of high-risk E. coli ST131 clone in ESBL-positive E. coli isolates obtained from pediatric patients. Methods A total of 292 ESBL-positive E. coli isolates from clinical samples of pediatric patients was included in the study. MALDI-TOF MS system was used for bacterial identification. Susceptibility tests were performed using BD Phoenix automated system. ST131 detection was done by MALDI-TOF-MS. Fisher's exact test was used to compare the groups (significance <0.05). Results A total of 292 isolates was analyzed. The high-risk ST131 clone was detected in 117 (40%) of the 292 ESBL-positive isolates. ST131 rates were found to be significantly higher in children under the age of 5 years compared with children over the age of 5 years (49.3 vs. 31.1%, p = 0.0019). Ciprofloxacin resistance was higher in ST131 isolates (45.6 vs. 31.7%; p < 0.05). Conclusion The rate of the ST131 clone was found to be high in the pediatric population. The significantly high rate of resistance to ciprofloxacin, which is not commonly used in the pediatric population, in ST131 isolates reveals the importance of the spread of high-risk clones for the development of resistance.

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Detection of Carbapenemase-Producing Enterobacteriaceae in the Baltic Countries and St. Petersburg Area

BioMed Research International ◽

10.1155/2014/548960 ◽

2014 ◽

Vol 2014 ◽

pp. 1-7 ◽

Cited By ~ 8

Author(s):

Anastasia Pavelkovich ◽

Arta Balode ◽

Petra Edquist ◽

Svetlana Egorova ◽

Marina Ivanova ◽

...

Keyword(s):

Escherichia Coli ◽

Cost Effective ◽

Maldi Tof Ms ◽

E Coli ◽

Maldi Tof ◽

Baltic Countries ◽

Exact Data ◽

Cost Effective Method ◽

The Baltic ◽

Tof Ms

The spread of carbapenemase-producing Enterobacteriaceae is a global problem; however, no exact data on the epidemiology of carbapenemase in the Baltic countries and St. Petersburg area is available. We aimed to evaluate the epidemiology of carbapenemase-producingEscherichia coliandKlebsiella pneumoniaein the Baltic States and St. Petersburg, Russia, and to compare the different methods for carbapenemase detection. From January to May 2012, allK. pneumoniae n=1983andE. coli n=7774clinical isolates from 20 institutions in Estonia, Latvia, Lithuania, and St. Petersburg, Russia were screened for carbapenem susceptibility. The IMP, VIM, GIM, NDM, KPC, and OXA-48 genes were detected using real-time PCR and the ability to hydrolyze ertapenem was determined using MALDI-TOF MS. Seventy-seven strains were found to be carbapenem nonsusceptible. From these, 15K. pneumoniaestrains hydrolyzed ertapenem and carried theblaNDMgene. All of these strains carried integron 1 and most carried integron 3 as well as genes of the CTX-M-1 group. No carbapenemase-producingE. coliorK. pneumoniaestrains were found in Estonia, Latvia, or Lithuania; however, NDM-positiveK. pneumoniaewas present in the hospital in St. Petersburg, Russia. A MALDI-TOF MS-based assay is a suitable and cost-effective method for the initial confirmation of carbapenemase production.

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Mass Spectrometry Proteotyping-Based Detection and Identification of Staphylococcus aureus, Escherichia coli, and Candida albicans in Blood

Frontiers in Cellular and Infection Microbiology ◽

10.3389/fcimb.2021.634215 ◽

2021 ◽

Vol 11 ◽

Author(s):

Nahid Kondori ◽

Amra Kurtovic ◽

Beatriz Piñeiro-Iglesias ◽

Francisco Salvà-Serra ◽

Daniel Jaén-Luchoro ◽

...

Keyword(s):

Escherichia Coli ◽

Staphylococcus Aureus ◽

Candida Albicans ◽

Blood Cultures ◽

Blood Samples ◽

Maldi Tof Ms ◽

E Coli ◽

Maldi Tof ◽

Detection And Identification ◽

Tof Ms

Bloodstream infections (BSIs), the presence of microorganisms in blood, are potentially serious conditions that can quickly develop into sepsis and life-threatening situations. When assessing proper treatment, rapid diagnosis is the key; besides clinical judgement performed by attending physicians, supporting microbiological tests typically are performed, often requiring microbial isolation and culturing steps, which increases the time required for confirming positive cases of BSI. The additional waiting time forces physicians to prescribe broad-spectrum antibiotics and empirically based treatments, before determining the precise cause of the disease. Thus, alternative and more rapid cultivation-independent methods are needed to improve clinical diagnostics, supporting prompt and accurate treatment and reducing the development of antibiotic resistance. In this study, a culture-independent workflow for pathogen detection and identification in blood samples was developed, using peptide biomarkers and applying bottom-up proteomics analyses, i.e., so-called “proteotyping”. To demonstrate the feasibility of detection of blood infectious pathogens, using proteotyping, Escherichia coli and Staphylococcus aureus were included in the study, as the most prominent bacterial causes of bacteremia and sepsis, as well as Candida albicans, one of the most prominent causes of fungemia. Model systems including spiked negative blood samples, as well as positive blood cultures, without further culturing steps, were investigated. Furthermore, an experiment designed to determine the incubation time needed for correct identification of the infectious pathogens in blood cultures was performed. The results for the spiked negative blood samples showed that proteotyping was 100- to 1,000-fold more sensitive, in comparison with the MALDI-TOF MS-based approach. Furthermore, in the analyses of ten positive blood cultures each of E. coli and S. aureus, both the MALDI-TOF MS-based and proteotyping approaches were successful in the identification of E. coli, although only proteotyping could identify S. aureus correctly in all samples. Compared with the MALDI-TOF MS-based approaches, shotgun proteotyping demonstrated higher sensitivity and accuracy, and required significantly shorter incubation time before detection and identification of the correct pathogen could be accomplished.

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Proteomic analysis of proteins differentially expressed in conidia and mycelium of the entomopathogenic fungus Aschersonia placenta

Canadian Journal of Microbiology ◽

10.1139/w2012-111 ◽

2012 ◽

Vol 58 (12) ◽

pp. 1327-1334 ◽

Cited By ~ 4

Author(s):

Junzhi Qiu ◽

Yubin Su ◽

Ivan Gelbǐc ◽

Yunfeng Qiu ◽

Xiaocong Xie ◽

...

Keyword(s):

Proteomic Analysis ◽

Entomopathogenic Fungus ◽

Developmental Stages ◽

Differentially Expressed ◽

Uridine Diphosphate ◽

Maldi Tof Ms ◽

Maldi Tof ◽

Flight Mass Spectrometry ◽

Oxidation Reduction ◽

Tof Ms

The infection of insects by the entomopathogenic fungus Aschersonia placenta depends on conidia. To identify proteins differentially expressed in A. placenta conidia vs mycelia, we performed a comparative proteomic analysis of A. placenta using 2-dimensional gel electrophoresis (2-DE) and matrix-assisted laser desorption ionization/time-of-flight mass spectrometry (MALDI-TOF-MS). We detected 1022 2-DE protein spots in conidia and 1049 in mycelia and analyzed 48 (13 from conidia and 35 from mycelia) using MALDI-TOF-MS. Finally, we identified 28 proteins (7 from conidia and 21 from mycelia). The identified proteins exclusive to conidia included major proteins participating in oxidation–reduction processes and vegetative insecticidal protein 1 (Vip1), a protein that is likely involved in pathogenicity. The identified proteins exclusive to mycelia were those involved in biosynthesis and metabolism, including uridine diphosphate galactopyranose mutase, which might play key roles in hyphal morphogenesis. This report provides the first proteomic analysis of different developmental stages of an Aschersonia species. Although only a small number of proteins were identified, the data represent a useful foundation for future studies concerning the molecular basis of entomopathogenicity in the species A. placenta and in the genus Aschersonia.

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Detection of Colistin Resistance in Escherichia coli by Use of the MALDI Biotyper Sirius Mass Spectrometry System

Journal of Clinical Microbiology ◽

10.1128/jcm.01427-19 ◽

2019 ◽

Vol 57 (12) ◽

Cited By ~ 3

Author(s):

R. Christopher D. Furniss ◽

Laurent Dortet ◽

William Bolland ◽

Oliver Drews ◽

Katrin Sparbier ◽

...

Keyword(s):

Mass Spectrometry ◽

Escherichia Coli ◽

Cost Effective ◽

Colistin Resistance ◽

Content Type ◽

Maldi Tof Ms ◽

E Coli ◽

Maldi Tof ◽

Maldi Biotyper ◽

Tof Ms

ABSTRACT Polymyxin antibiotics are a last-line treatment for multidrug-resistant Gram-negative bacteria. However, the emergence of colistin resistance, including the spread of mobile mcr genes, necessitates the development of improved diagnostics for the detection of colistin-resistant organisms in hospital settings. The recently developed MALDIxin test enables detection of colistin resistance by matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS) in less than 15 min but is not optimized for the mass spectrometers commonly found in clinical microbiology laboratories. In this study, we adapted the MALDIxin test for the MALDI Biotyper Sirius MALDI-TOF MS system (Bruker Daltonics). We optimized the sample preparation protocol by using a set of 6 mobile colistin resistance (MCR) protein-expressing Escherichia coli clones and validated the assay with a collection of 40 E. coli clinical isolates, including 19 confirmed MCR protein producers, 12 colistin-resistant isolates that tested negative for commonly encountered mcr genes (i.e., likely chromosomally resistant isolates), and 9 polymyxin-susceptible isolates. We calculated polymyxin resistance ratio (PRR) values from the acquired spectra; PRR values of 0, indicating polymyxin susceptibility, were obtained for all colistin-susceptible E. coli isolates, whereas positive PRR values, indicating resistance to polymyxins, were obtained for all resistant strains, independent of the genetic basis of resistance. Thus, we report a preliminary feasibility study showing that an optimized version of the MALDIxin test adapted for the routine MALDI Biotyper Sirius system provides an unbiased, fast, reliable, cost-effective, and high-throughput way of detecting colistin resistance in clinical E. coli isolates.

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Comparative proteomic analysis of salt-responsive proteins in canola roots by 2-DE and MALDI-TOF MS

Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics ◽

10.1016/j.bbapap.2018.12.009 ◽

2019 ◽

Vol 1867 (3) ◽

pp. 227-236 ◽

Cited By ~ 4

Author(s):

Maryam Kholghi ◽

Mahmoud Toorchi ◽

Ali Bandehagh ◽

Anna Ostendorp ◽

Steffen Ostendorp ◽

...

Keyword(s):

Proteomic Analysis ◽

Maldi Tof Ms ◽

Comparative Proteomic Analysis ◽

Maldi Tof ◽

Tof Ms

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Rapid susceptibility testing of multi-drug resistant Escherichia coli and Klebsiella by glucose metabolization monitoring

Clinical Chemistry and Laboratory Medicine (CCLM) ◽

10.1515/cclm-2018-1178 ◽

2019 ◽

Vol 57 (8) ◽

pp. 1271-1279 ◽

Cited By ~ 2

Author(s):

Maximilian Kittel ◽

Peter Findeisen ◽

Beniam Ghebremedhin ◽

Thomas Miethke ◽

Alexander Grundt ◽

...

Keyword(s):

Escherichia Coli ◽

Antibiotic Therapy ◽

Susceptibility Testing ◽

Gram Negative Bacteria ◽

Drug Resistant ◽

Gram Negative ◽

Maldi Tof Ms ◽

E Coli ◽

Maldi Tof ◽

Tof Ms

Abstract Background The increasing number of multi-drug resistant (MDR) bacteria provides enormous challenges for choosing an appropriate antibiotic therapy in the early phase of sepsis. While bacterial identification has been greatly accelerated by the introduction of matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS), the antibiotic susceptibility testing (AST) remains time-consuming. Here, we present a rapid susceptibility testing method for testing Gram-negative bacteria, exemplarily validated for Escherichia coli and Klebsiella spp. Methods Gram-negative isolates (E. coli and Klebsiella spp.) were either taken as single colonies from agar plates (n=136) or directly extracted and identified from positive blood cultures (n=42) using MALDI-TOF MS. Bacteria were incubated in glucose-supplemented Luria broths (LBs) each containing one antibiotic (ceftazidime, piperacillin, imipenem and ciprofloxacin), routinely used to classify Gram-negative bacteria in Germany. To determine susceptibility the dynamics of glucose utilization in bacterial suspensions were quantitatively measured in the presence or absence of antibiotics designated liquid-AST (L-AST). Results The L-AST can be run on clinical-chemistry analyzers and integrated into laboratory routines. It yields critical resistance information within 90–150 min downstream of a MS-based identification. The results showed a high concordance with routine susceptibility testing, with less than 1% very major errors (VME) and 3.51% major errors (ME) for 178 assessed isolates. Analysis of turnaround time (TAT) for 42 clinical samples indicated that L-AST results could be obtained 34 h earlier than the routine results. Conclusions As exemplified for E. coli and Klebsiella spp., L-AST provides substantial acceleration of susceptibility testing following MALDI-TOF MS identification. The assay is a simple and low-cost method that can be integrated into clinical laboratory to allow for 24/7 AST. This approach could improve antibiotic therapy.

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Rapid identification of mcr-1-positive Escherichia coli from patient urine using a novel lipid-based MALDI-TOF-MS assay

Access Microbiology ◽

10.1099/acmi.0.000309 ◽

2021 ◽

Vol 3 (12) ◽

Author(s):

Richard D. Smith ◽

Jerilyn R. Izac ◽

Michael Ha ◽

Hyojik Yang ◽

J. Kristie Johnson ◽

...

Keyword(s):

Escherichia Coli ◽

Ex Vivo ◽

Multidrug Resistant ◽

Rapid Identification ◽

Ionization Time ◽

Content Type ◽

Maldi Tof Ms ◽

Maldi Tof ◽

Flight Mass Spectrometry ◽

Tof Ms

Mobilized colistin resistance (mcr) genes confer resistance to colistin, a last-resort antibiotic for multidrug-resistant Gram-negative infections. In this case report, we describe a novel lipid-based matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) diagnostic used to rapidly identify an mcr-1-positive Escherichia coli directly from a patient with a urinary tract infection without the need for ex vivo growth.

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