Escherichia coli is a significant pathogen in extraintestinal infections, and ESBL-producing E. coli poses a major clinical challenge due to its antibiotic resistance. This study comprehensively analyzed E. coli isolates from urine and blood samples of patients with urinary tract and bloodstream infections at three major tertiary hospitals in South Korea. The goal was to provide insights into the distribution, antibiotic resistance, and virulence factors of these strains. Our analysis identified CTX-M and TEM as the dominant ESBL types, found in 71.7% and 61.7% of isolates, respectively, with 46.7% showing co-occurrence. Multilocus sequence typing (MLST) revealed the predominance of high-risk clones such as ST131, ST69, ST73, and ST95, with rare sequence types like ST410 and ST405 also identified. The high prevalence of virulence factors, including iutA (80.8%) and kpsMII (74.2%), further highlights the complexity of these strains. In addition, 38.3% of clinical isolates contained a combination of siderophore, adhesin, protectin, and toxin-related genes. There was no significant difference between urinary tract and bloodstream infections or regional differentiation in Korea. This study highlights the importance of controlling ESBL-producing E. coli infections, especially given the increasing incidence among patients with underlying medical conditions and older adults who are more susceptible to urinary tract infections. These findings serve as valuable indicators for pathogen analysis, especially those harboring antibiotic resistance and toxin genes. The insights gained are expected to contribute significantly to the development of infectious disease prevention and control strategies.

• Klíčová slova
• Escherichia coli, Blood infection, Extended spectrum beta-lactamases (ESBLs), Extra-intestinal pathogenic (ExPEC), Multi-locus sequence typing (MLST), Urinary tract infection (UTI), Virulence factors,
• MeSH
• antibakteriální látky farmakologie   MeSH
• bakteriemie * mikrobiologie   epidemiologie   MeSH
• beta-laktamasy * genetika   metabolismus   MeSH
• dospělí MeSH
• Escherichia coli * genetika   izolace a purifikace   patogenita   enzymologie   účinky léků   klasifikace   MeSH
• faktory virulence genetika   MeSH
• infekce močového ústrojí * mikrobiologie   epidemiologie   MeSH
• infekce vyvolané Escherichia coli * mikrobiologie   epidemiologie   MeSH
• lidé středního věku MeSH
• lidé MeSH
• mikrobiální testy citlivosti MeSH
• mladý dospělý MeSH
• multilokusová sekvenční typizace MeSH
• prevalence MeSH
• proteiny z Escherichia coli genetika   metabolismus   MeSH
• senioři nad 80 let MeSH
• senioři MeSH
• virulence MeSH
• Check Tag
• dospělí MeSH
• lidé středního věku MeSH
• lidé MeSH
• mladý dospělý MeSH
• mužské pohlaví MeSH
• senioři nad 80 let MeSH
• senioři MeSH
• ženské pohlaví MeSH
• Publikační typ
• časopisecké články MeSH
• Geografické názvy
• Korejská republika epidemiologie   MeSH
• Názvy látek
• antibakteriální látky MeSH
• beta-laktamasy * MeSH
• faktory virulence MeSH
• proteiny z Escherichia coli MeSH

The spread of multidrug-resistant Escherichia coli in healthcare facilities is a global challenge. Hospital-acquired infections produced by Escherichia coli include gastrointestinal, blood-borne, urinary tract, surgical sites, and neonatal infections. Therefore, novel approaches are needed to deal with this pathogen and its rising resistance. The concept of attenuating virulence factors is an alternative strategy that might lead to low levels of resistance and combat this pathogen. A sub-inhibitory concentration (¼ MIC) of sitagliptin and nitazoxanide was used for phenotypic assessments of Escherichia coli virulence factors such as biofilm production, swimming motility, serum resistance, and protease production. Moreover, qRT-PCR was used to determine the impact of sub-MIC of the tested drugs on the relative expression levels of papC, fimH, fliC, kpsMTII, ompT_m, and stcE genes encoding virulence factors in Escherichia coli. Also, an in vivo model was conducted as a confirmatory test. Phenotypically, our findings demonstrated that the tested strains showed a significant decrease in all the tested virulence factors. Moreover, the genotypic results showed a significant downregulation in the relative expression levels of all the tested genes. Besides, the examined drugs were found to be effective in protecting mice against Escherichia coli pathogenesis. Sitagliptin and nitazoxanide exhibited strong anti-virulence activities against Escherichia coli. In addition, it is recommended that they might function as adjuvant in the management of Escherichia coli infections with either conventional antimicrobial agents or alone as alternative treatment measures.

• Klíčová slova
• Escherichia coli, Antibiotic resistance, Nitazoxanide, Sitagliptin, Virulence inhibitors,
• MeSH
• antibakteriální látky * farmakologie   MeSH
• biofilmy účinky léků   MeSH
• dusíkaté sloučeniny MeSH
• Escherichia coli * účinky léků   patogenita   genetika   MeSH
• faktory virulence genetika   metabolismus   MeSH
• infekce vyvolané Escherichia coli * farmakoterapie   mikrobiologie   MeSH
• lidé MeSH
• mikrobiální testy citlivosti MeSH
• mnohočetná bakteriální léková rezistence MeSH
• myši MeSH
• proteiny z Escherichia coli genetika   MeSH
• sitagliptin fosfát * farmakologie   MeSH
• thiazoly * farmakologie   MeSH
• virulence účinky léků   MeSH
• zvířata MeSH
• Check Tag
• lidé MeSH
• myši MeSH
• ženské pohlaví MeSH
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• antibakteriální látky * MeSH
• dusíkaté sloučeniny MeSH
• faktory virulence MeSH
• nitazoxanide MeSH Prohlížeč
• proteiny z Escherichia coli MeSH
• sitagliptin fosfát * MeSH
• thiazoly * MeSH

Bacterial β sliding clamp (β-clamp) is an emerging drug target currently lacking small-molecule inhibitors with good in vivo activity. Thus, there is a need for fast and simple screening methods for identifying inhibitor candidates. Here we demonstrate the use of nuclear magnetic resonance spectroscopy (NMR) for evaluating compound binding to the E. coli β-clamp. To identify suitable molecular probes, a series of tetrahydrocarbazoles were synthesized, some of which contain fluorine. Key challenges in the synthesis were formation of regioisomers during the Fischer indole reaction and reducing racemization at the stereogenic center. The tetrahydrocarbazoles were assayed against the E. coli β-clamp by saturation-transfer difference (STD) NMR, waterLOGSY and T1ρ. Analysis by isothermal titration calorimetry gave KD-values of 1.7-14 μM for three fluorinated probe candidates, and NMR chemical shift perturbation experiments confirmed these molecules to directly interact with the β-clamp binding pocket. Binding of the fluorinated molecules to β-clamp was easily observed with 19F-observed T2-based binding experiments, and proof of concept for a fluorine-based binding assay for E. coli β-clamp binders is provided.

• Klíčová slova
• (19)F NMR displacement assay, E. coli, Racemization, STD NMR, Tetrahydrocarbazole, β sliding clamp,
• MeSH
• Escherichia coli * účinky léků   MeSH
• halogenace MeSH
• karbazoly * chemie   chemická syntéza   farmakologie   metabolismus   MeSH
• magnetická rezonanční spektroskopie * MeSH
• molekulární sondy chemie   chemická syntéza   metabolismus   MeSH
• molekulární struktura MeSH
• proteiny z Escherichia coli metabolismus   antagonisté a inhibitory   chemie   MeSH
• vazba proteinů MeSH
• vazebná místa MeSH
• vztahy mezi strukturou a aktivitou MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• karbazoly * MeSH
• molekulární sondy MeSH
• proteiny z Escherichia coli MeSH

Integral membrane proteins carry out essential functions in the cell, and their activities are often modulated by specific protein-lipid interactions in the membrane. Here, we elucidate the intricate role of cardiolipin (CDL), a regulatory lipid, as a stabilizer of membrane proteins and their complexes. Using the in silico-designed model protein TMHC4_R (ROCKET) as a scaffold, we employ a combination of molecular dynamics simulations and native mass spectrometry to explore the protein features that facilitate preferential lipid interactions and mediate stabilization. We find that the spatial arrangement of positively charged residues as well as local conformational flexibility are factors that distinguish stabilizing from non-stabilizing CDL interactions. However, we also find that even in this controlled, artificial system, a clear-cut distinction between binding and stabilization is difficult to attain, revealing that overlapping lipid contacts can partially compensate for the effects of binding site mutations. Extending our insights to naturally occurring proteins, we identify a stabilizing CDL site within the E. coli rhomboid intramembrane protease GlpG and uncover its regulatory influence on enzyme substrate preference. In this work, we establish a framework for engineering functional lipid interactions, paving the way for the design of proteins with membrane-specific properties or functions.

• Klíčová slova
• E. coli, lipid binding, mass spectrometry, membrane protein, molecular biophysics, structural biology,
• MeSH
• DNA vazebné proteiny MeSH
• endopeptidasy metabolismus   chemie   genetika   MeSH
• Escherichia coli metabolismus   genetika   MeSH
• kardiolipiny * metabolismus   chemie   MeSH
• membránové proteiny * metabolismus   chemie   genetika   MeSH
• proteinové inženýrství * MeSH
• proteiny z Escherichia coli * metabolismus   chemie   genetika   MeSH
• simulace molekulární dynamiky MeSH
• vazba proteinů MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• DNA vazebné proteiny MeSH
• endopeptidasy MeSH
• GlpG protein, E coli MeSH Prohlížeč
• kardiolipiny * MeSH
• membránové proteiny * MeSH
• proteiny z Escherichia coli * MeSH

The RNA chaperone Hfq plays crucial roles in bacterial gene expression and is a major facilitator of small regulatory RNA (sRNA) action. The toroidal architecture of the Hfq hexamer presents three well-characterized surfaces that allow it to bind sRNAs to stabilize them and engage target transcripts. Hfq-interacting sRNAs are categorized into two classes based on the surfaces they use to bind Hfq. By characterizing a systematic alanine mutant library of Hfq to identify amino acid residues that impact survival of Escherichia coli experiencing nitrogen (N) starvation, we corroborated the important role of the three RNA-binding surfaces for Hfq function. We uncovered two, previously uncharacterized, conserved residues, V22 and G34, in the hydrophobic core of Hfq, to have a profound impact on Hfq's RNA-binding activity in vivo. Transcriptome-scale analysis revealed that V22A and G34A Hfq mutants cause widespread destabilization of both sRNA classes, to the same extent as seen in bacteria devoid of Hfq. However, the alanine substitutions at these residues resulted in only modest alteration in stability and structure of Hfq. We propose that V22 and G34 have impact on Hfq function, especially critical under cellular conditions when there is an increased demand for Hfq, such as N starvation.

• MeSH
• bakteriální RNA * metabolismus   genetika   MeSH
• dusík metabolismus   MeSH
• Escherichia coli genetika   metabolismus   MeSH
• hydrofobní a hydrofilní interakce MeSH
• konzervovaná sekvence MeSH
• malá nekódující RNA * metabolismus   genetika   MeSH
• molekulární chaperony genetika   metabolismus   chemie   MeSH
• mutace MeSH
• protein hostitelského faktoru 1 * genetika   chemie   metabolismus   MeSH
• proteiny z Escherichia coli * genetika   chemie   metabolismus   MeSH
• regulace genové exprese u bakterií MeSH
• stabilita RNA * MeSH
• stanovení celkové genové exprese MeSH
• transkriptom MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• bakteriální RNA * MeSH
• dusík MeSH
• Hfq protein, E coli MeSH Prohlížeč
• malá nekódující RNA * MeSH
• molekulární chaperony MeSH
• protein hostitelského faktoru 1 * MeSH
• proteiny z Escherichia coli * MeSH

The adherence of bladder uroepithelial cells, subsequent expression, and regulation of type 1 fimbrial genes (key mediator of attachment) in clinical multidrug-resistant uropathogenic Escherichia coli (MDR-UPECs) isolated from individuals with asymptomatic bacteriuria (ABU) remain unexplored till date. Therefore, this study aimed to investigate the underlying molecular mechanisms associated with the adherence of clinical MDR-ABU-UPECs to human a uroepithelial cell line (HTB-4), both in the absence and presence of D-Mannose. These investigations focused on phase variation, expression, and regulation of type 1 fimbriae and were compared to a prototype ABU-strain (E. coli 83972) and symptomatic MDR-UPECs. Discordant to the ABU prototype strain, MDR-ABU-UPECs exhibited remarkable adhesive capacity that was significantly reduced after D-mannose exposure, fairly like the MDR symptomatic UPECs. The type 1 fimbrial phase variation, determined by the fim switch analysis, asserted the statistically significant incidence of "both OFF and ON" orientation among the adherent MDR-ABU-UPECs with a significant reduction in phase-ON colonies post-D-mannose exposure, akin to the symptomatic ones. This was indicative of an operative and alternating type 1 fimbrial phase switch. The q-PCR assay revealed a coordinated action of the regulatory factors; H-NS, IHF, and Lrp on the expression of FimB and FimE recombinases, which further controlled the function of fimH and fimA genes in ABU-UPECs, similar to symptomatic strains. Therefore, this study is the first of its kind to provide an insight into the regulatory crosstalk of different cellular factors guiding the adhesion of ABU-UPECs to the host. Additionally, it also advocated for the need to accurately characterize ABU-UPECs.

• Klíčová slova
• Adhesive capacity, Asymptomatic uropathogenic Escherichia coli, FimBE recombinases, Symptomatic uropathogenic Escherichia coli, Type 1 fimbriae-regulating factors, Type 1 fimbrial phase variation,
• MeSH
• adheziny Escherichia coli genetika   metabolismus   MeSH
• bakteriální adheze * MeSH
• bakteriální fimbrie * genetika   metabolismus   MeSH
• bakteriurie mikrobiologie   MeSH
• buněčné linie MeSH
• epitelové buňky * mikrobiologie   MeSH
• infekce vyvolané Escherichia coli * mikrobiologie   MeSH
• lidé MeSH
• mannosa metabolismus   farmakologie   MeSH
• mnohočetná bakteriální léková rezistence * genetika   MeSH
• proteiny fimbrií * genetika   metabolismus   MeSH
• proteiny z Escherichia coli genetika   metabolismus   MeSH
• regulace genové exprese u bakterií MeSH
• uropatogenní Escherichia coli * genetika   účinky léků   izolace a purifikace   MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• adheziny Escherichia coli MeSH
• mannosa MeSH
• proteiny fimbrií * MeSH
• proteiny z Escherichia coli MeSH

Cytochrome b562 is a small redox-active heme protein that has served as an important model system for understanding biological electron transfer processes. Here, we present a comprehensive theoretical study of electron transport mechanisms in protein-metal junctions incorporating cytochrome b562 using a multi-scale computational approach. Employing molecular dynamics (MD) simulations, we generated junction geometries for both vacuum-dried and solvated conditions, with the protein covalently bound to gold contacts in various configurations. Coherent tunneling, described by the Landauer-Buttiker formalism within the density functional theory (DFT) framework, is compared to the incoherent hopping charge transport mechanism captured by the semi-classical Marcus theory. The tunneling was identified as the dominant mechanism explaining the experimental data measured on the cytochrome b562 junctions, exhibiting exponential yet very shallow distance dependence. While the structural orientations and protein contacts with the electrodes influence the junction conductance significantly, the solvation effects are relatively small, affecting the electronic properties mostly via the adsorption arrangement. On the other hand, the considerable temperature dependence of the conductance was found strong only for hopping, while the tunneling current magnitudes remain practically unaffected and are a good indicator of the coherent mechanism in this case.

• MeSH
• cytochromy typu b chemie   metabolismus   MeSH
• proteiny z Escherichia coli MeSH
• rozpouštědla * chemie   MeSH
• simulace molekulární dynamiky * MeSH
• teorie funkcionálu hustoty MeSH
• teplota * MeSH
• transport elektronů MeSH
• zlato chemie   MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• cytochrome b562, E coli MeSH Prohlížeč
• cytochromy typu b MeSH
• proteiny z Escherichia coli MeSH
• rozpouštědla * MeSH
• zlato MeSH

Analysis of 594 isolates of Escherichia coli sequence type (ST)131 and its single locus variants carrying carbapenemase genes from 17 European Union/European Economic Area countries revealed acquisition of 18 carbapenemase variants, mainly in ST131 clades A and C. Most frequent were bla OXA-244 (n = 230) and bla OXA-48 (n = 224), detected in 14 and 12 countries, respectively. Isolates carrying bla OXA-244 have increased rapidly since 2021. The increasing detection of carbapenemase genes in the E. coli high-risk lineage ST131 is a public health concern.

• Klíčová slova
• Carbapenem-resistant Enterobacterales, Escherichia coli, antibiotics, antimicrobial resistance, carbapenemase, cross-border spread, surveillance, whole genome sequencing,
• MeSH
• antibakteriální látky farmakologie   terapeutické užití   MeSH
• bakteriální proteiny * genetika   MeSH
• beta-laktamasy * genetika   MeSH
• Escherichia coli * genetika   izolace a purifikace   MeSH
• Evropská unie * MeSH
• infekce vyvolané Escherichia coli * epidemiologie   mikrobiologie   MeSH
• lidé MeSH
• mikrobiální testy citlivosti MeSH
• multilokusová sekvenční typizace MeSH
• proteiny z Escherichia coli genetika   MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• Geografické názvy
• Evropa epidemiologie   MeSH
• Názvy látek
• antibakteriální látky MeSH
• bakteriální proteiny * MeSH
• beta-laktamasy * MeSH
• carbapenemase MeSH Prohlížeč
• proteiny z Escherichia coli MeSH

RNA 5'-modification with NAD+/NADH (oxidized/reduced nicotinamide adenine dinucleotide) has been found in bacteria, eukaryotes and viruses. 5'-NAD is incorporated into RNA by RNA polymerases (RNAPs) during the initiation of synthesis. It is unknown (i) which factors and physiological conditions permit substantial NAD incorporation into RNA in vivo and (ii) how 5'-NAD impacts gene expression and the fate of RNA in bacteria. Here we show in Escherichia coli that RNA NADylation is stimulated by low cellular concentration of the competing substrate ATP, and by weakening ATP contacts with RNAP active site. Additionally, RNA NADylation may be influenced by DNA supercoiling. RNA NADylation does not interfere with posttranscriptional RNA processing by major ribonuclease RNase E. It does not impact the base-pairing between RNAI, the repressor of plasmid replication, and its antisense target, RNAII. Leaderless NADylated model mRNA cI-lacZ is recognized by the 70S ribosome and is translated with the same efficiency as triphosphorylated cI-lacZ mRNA. Translation exposes the 5'-NAD of this mRNA to de-capping by NudC enzyme. We suggest that NADylated mRNAs are rapidly degraded, consistent with their low abundance in published datasets. Furthermore, we observed that ppGpp inhibits NudC de-capping activity, contributing to the growth phase-dependency of NADylated RNA levels.

• MeSH
• adenosintrifosfát metabolismus   MeSH
• bakteriální RNA metabolismus   genetika   MeSH
• DNA řízené RNA-polymerasy metabolismus   genetika   MeSH
• endoribonukleasy metabolismus   genetika   MeSH
• Escherichia coli * genetika   metabolismus   MeSH
• messenger RNA metabolismus   genetika   MeSH
• NAD * metabolismus   MeSH
• posttranskripční úpravy RNA MeSH
• proteiny z Escherichia coli metabolismus   genetika   MeSH
• proteosyntéza MeSH
• RNA čepičky * metabolismus   MeSH
• stochastické procesy MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• adenosintrifosfát MeSH
• bakteriální RNA MeSH
• DNA řízené RNA-polymerasy MeSH
• endoribonukleasy MeSH
• messenger RNA MeSH
• NAD * MeSH
• proteiny z Escherichia coli MeSH
• ribonuclease E MeSH Prohlížeč
• RNA čepičky * MeSH

Balanced bacterial metabolism is essential for cell homeostasis and growth and can be impacted by various stress factors. In particular, bacteria exposed to metals, including the nanoparticle form, can significantly alter their metabolic processes. It is known that the extensive and intensive use of food and feed supplements, including zinc, in human and animal nutrition alters the intestinal microbiota and this may negatively impact the health of the host. This study examines the effects of zinc (zinc oxide and zinc oxide nanoparticles) on key metabolic pathways of Escherichia coli. Transcriptomic and proteomic analyses along with quantification of intermediates of tricarboxylic acid (TCA) were employed to monitor and study the bacterial responses. Multi-omics analysis revealed that extended zinc exposure induced mainly oxidative stress and elevated expression/production of enzymes of carbohydrate metabolism, especially enzymes for synthesis of trehalose. After the zinc withdrawal, E. coli metabolism returned to a baseline state. These findings shed light on the alteration of TCA and on importance of trehalose synthesis in metal-induced stress and its broader implications for bacterial metabolism and defense and consequently for the balance and health of the human and animal microbiome.

• Klíčová slova
• Carbohydrate metabolism, Nanoparticles, Proteome, Transcriptome, Trehalose synthesis, Tricarboxylic acid cycle, Virulence, Zinc, Zinc oxide,
• MeSH
• citrátový cyklus * účinky léků   MeSH
• Escherichia coli * metabolismus   genetika   účinky léků   MeSH
• fyziologická adaptace MeSH
• metabolické sítě a dráhy účinky léků   MeSH
• oxid zinečnatý metabolismus   farmakologie   MeSH
• oxidační stres MeSH
• proteiny z Escherichia coli metabolismus   genetika   MeSH
• proteomika MeSH
• regulace genové exprese u bakterií účinky léků   MeSH
• stanovení celkové genové exprese MeSH
• transkriptom MeSH
• trehalosa * metabolismus   MeSH
• zinek * metabolismus   MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• oxid zinečnatý MeSH
• proteiny z Escherichia coli MeSH
• trehalosa * MeSH
• zinek * MeSH