Activation of multiple antibiotic resistance in uropathogenic Escherichia coli strains by aryloxoalcanoic acid compounds

RND Efflux Pump Induction: A Crucial Network Unveiling Adaptive Antibiotic Resistance Mechanisms of Gram-Negative Bacteria

The rise of multi-drug-resistant (MDR) pathogenic bacteria presents a grave challenge to global public health, with antimicrobial resistance ranking as the third leading cause of mortality worldwide. Understanding the mechanisms underlying antibiotic resistance is crucial for developing effective treatments. Efflux pumps, particularly those of the resistance-nodulation-cell division (RND) superfamily, play a significant role in expelling molecules from bacterial cells, contributing to the emergence of multi-drug resistance. These are transmembrane transporters naturally produced by Gram-negative bacteria. This review provides comprehensive insights into the modulation of RND efflux pump expression in bacterial pathogens by numerous and common molecules (bile, biocides, pharmaceuticals, additives, plant extracts, etc.). The interplay between these molecules and efflux pump regulators underscores the complexity of antibiotic resistance mechanisms. The clinical implications of efflux pump induction by non-antibiotic compounds highlight the challenges posed to public health and the urgent need for further investigation. By addressing antibiotic resistance from multiple angles, we can mitigate its impact and preserve the efficacy of antimicrobial therapies.

Combined metabolomics and transcriptomics analysis reveals the mechanism of antibiotic resistance of Salmonella enterica serovar Typhimurium after acidic stress

Drug-resistant Salmonella is widely distributed in the meat production chain, endangering food safety and public health. Acidification of meat products during processing can induce acid stress, which may alter antibiotic resistance. Our study investigated the effects of acid stress on the antibiotic resistance and metabolic profile of Salmonella Typhimurium, and explored the underlying mechanisms using metabolomic and transcriptomic analysis. We found that acid-stressed 14028s was more sensitive to small molecule hydrophobic antibiotics (SMHA) while more resistant to meropenem (MERO). Metabolomic analysis revealed that enhanced sensitivity to SMHA was correlated with increased purine metabolism and tricarboxylic acid cycle. Transcriptomic analysis revealed the downregulation of chemotaxis-related genes, which are also associated with SMHA sensitivity. We also found a significant downregulation of the ompF gene, which encodes a major outer membrane protein OmpF of Salmonella. The decreased expression of OmpF porin hindered the influx of MERO, leading to enhanced resistance of the bacteria to the drug. Our findings contribute to greatly improve the understanding of the relationship between Salmonella metabolism, gene expression, and changes in drug resistance after acid stress, while providing a structural framework for exploring the relationship between bacterial stress responses and antibiotic resistance.

Effects of acid, alkaline, cold, and heat environmental stresses on the antibiotic resistance of the Salmonella enterica serovar Typhimurium

Antibiotic resistance in Salmonella enterica serovar Typhimurium (S. ser. Typhimurium) has become a critical safety hazard in food. Sublethal environmental stresses can influence resistance in Salmonella during food processing. This study simulated environmental stresses in food processing. The antibiotic resistance of three strains of S. ser. Typhimurium (the ATCC 14028 strain and two wild-type isolates from chicken and pork product processing) was evaluated under different pH levels (5.0, 5.5, 6.0, 8.0, and 9.0). Also, dynamic changes in resistance with treatment duration under cold (4 °C, -20 °C) and heat (55 °C) treatment were studied. The results showed that acid and alkaline stresses reduced the resistance of S. ser. Typhimurium to eight antibiotics; meanwhile, the resistance of meropenem (MERO) increased. The minimal inhibitory concentration (MIC) of MERO was increased 16- to 64-fold. With acid or alkaline stress, the extracellular ATP content increased, and the scanning electron microscopy (SEM) result clearly revealed the appearance of wrinkles and holes on the outer membrane of Salmonella. These observations imply changes in membrane permeability, which may decrease the antibiotic resistance of Salmonella. Cold or heat stress increased the resistance of S. ser. Typhimurium to tetracycline, cefotaxime, ceftazidime, nalidixic acid, azithromycin, and ampicillin; the MIC increased 2- to 4-fold. The antibiotic resistance only changed when cold and heat stresses occurred over a certain period of time and remained unchanged when the stress persisted. This study reports on the ability of S. ser. Typhimurium to develop antibiotic resistance after environmental stresses. It can provide valuable information for meat processing to improve interventions and risk management.

High-throughput laboratory evolution reveals evolutionary constraints in Escherichia coli

Understanding the constraints that shape the evolution of antibiotic resistance is critical for predicting and controlling drug resistance. Despite its importance, however, a systematic investigation of evolutionary constraints is lacking. Here, we perform a high-throughput laboratory evolution of Escherichia coli under the addition of 95 antibacterial chemicals and quantified the transcriptome, resistance, and genomic profiles for the evolved strains. Utilizing machine learning techniques, we analyze the phenotype-genotype data and identified low dimensional phenotypic states among the evolved strains. Further analysis reveals the underlying biological processes responsible for these distinct states, leading to the identification of trade-off relationships associated with drug resistance. We also report a decelerated evolution of β-lactam resistance, a phenomenon experienced by certain strains under various stresses resulting in higher acquired resistance to β-lactams compared to strains directly selected by β-lactams. These findings bridge the genotypic, gene expression, and drug resistance gap, while contributing to a better understanding of evolutionary constraints for antibiotic resistance.

An Intertwined Network of Regulation Controls Membrane Permeability Including Drug Influx and Efflux in Enterobacteriaceae

The transport of small molecules across membranes is a pivotal step for controlling the drug concentration into the bacterial cell and it efficiently contributes to the antibiotic susceptibility in Enterobacteriaceae. Two types of membrane transports, passive and active, usually represented by porins and efflux pumps, are involved in this process. Importantly, the expression of these transporters and channels are modulated by an armamentarium of tangled regulatory systems. Among them, Helix-turn-Helix (HTH) family regulators (including the AraC/XylS family) and the two-component systems (TCS) play a key role in bacterial adaptation to environmental stresses and can manage a decrease of porin expression associated with an increase of efflux transporters expression. In the present review, we highlight some recent genetic and functional studies that have substantially contributed to our better understanding of the sophisticated mechanisms controlling the transport of small solutes (antibiotics) across the membrane of Enterobacteriaceae. This information is discussed, taking into account the worrying context of clinical antibiotic resistance and fitness of bacterial pathogens. The localization and relevance of mutations identified in the respective regulation cascades in clinical resistant strains are discussed. The possible way to bypass the membrane/transport barriers is described in the perspective of developing new therapeutic targets to combat bacterial resistance.

Prolonged exposure of Stenotrophomonas maltophilia biofilms to trace levels of clofibric acid alters antimicrobial tolerance and virulence

The presence of pharmaceuticals in water sources, including in drinking water (DW), is increasingly being recognized as an emerging and global concern for the environment and public health. Based on the principles of the "One Health" initiative, the present work aims to understand the effects of clofibric acid (CA), a lipid regulator, on the behavior of a selected bacterium isolated from drinking water (DW). Biofilms of the opportunistic pathogen Stenotrophomonas maltophilia were exposed to CA for 12 weeks at 170 and 17000 ng/L. The effects of CA were evaluated on planktonic S. maltophilia susceptibility to chlorine and antibiotics (amoxicillin, ciprofloxacin, erythromycin, kanamycin, levofloxacin, oxacillin, spectinomycin, tetracycline and trimethoprim-sulfamethoxazole), biofilm formation, motility, siderophores production and on the adhesion and internalization of the human colon adenocarcinoma cell line (HT-29). It was found that CA did not affect planktonic S. maltophilia tolerance to chlorine exposure. Additionally, no effects were observed on biofilm formation, motility and siderophores production. However, biofilms formed after CA exposure were more tolerant to chlorine disinfection and lower CFU reductions were obtained. Of additional concern was the effect of CA exposure on S. maltophilia increased tolerance to erythromycin. CA exposure also slightly reduced S. maltophilia ability to invade HT-29 cells. In conclusion, this work reinforces the importance of studying the effects of non-antibiotic contaminants on the behavior of environmental microorganisms, particularly their role as drivers affecting resistance evolution and selection.

Virulence Gene Regulation in Escherichia coli

Escherichia colicauses three types of illnesses in humans: diarrhea, urinary tract infections, and meningitis in newborns. The acquisition of virulence-associated genes and the ability to properly regulate these, often horizontally transferred, loci distinguishes pathogens from the normally harmless commensal E. coli found within the human intestine. This review addresses our current understanding of virulence gene regulation in several important diarrhea-causing pathotypes, including enteropathogenic, enterohemorrhagic,enterotoxigenic, and enteroaggregativeE. coli-EPEC, EHEC, ETEC and EAEC, respectively. The intensely studied regulatory circuitry controlling virulence of uropathogenicE. coli, or UPEC, is also reviewed, as is that of MNEC, a common cause of meningitis in neonates. Specific topics covered include the regulation of initial attachment events necessary for infection, environmental cues affecting virulence gene expression, control of attaching and effacing lesionformation, and control of effector molecule expression and secretion via the type III secretion systems by EPEC and EHEC. How phage control virulence and the expression of the Stx toxins of EHEC, phase variation, quorum sensing, and posttranscriptional regulation of virulence determinants are also addressed. A number of important virulence regulators are described, including the AraC-like molecules PerA of EPEC, CfaR and Rns of ETEC, and AggR of EAEC;the Ler protein of EPEC and EHEC;RfaH of UPEC;and the H-NS molecule that acts to silence gene expression. The regulatory circuitry controlling virulence of these greatly varied E. colipathotypes is complex, but common themes offerinsight into the signals and regulators necessary forE. coli disease progression.

Metabolic Regulation of a Bacterial Cell System with Emphasis on Escherichia coli Metabolism

It is quite important to understand the overall metabolic regulation mechanism of bacterial cells such as Escherichia coli from both science (such as biochemistry) and engineering (such as metabolic engineering) points of view. Here, an attempt was made to clarify the overall metabolic regulation mechanism by focusing on the roles of global regulators which detect the culture or growth condition and manipulate a set of metabolic pathways by modulating the related gene expressions. For this, it was considered how the cell responds to a variety of culture environments such as carbon (catabolite regulation), nitrogen, and phosphate limitations, as well as the effects of oxygen level, pH (acid shock), temperature (heat shock), and nutrient starvation.

The functionally active Mistic-fused histidine kinase receptor, EnvZ

Mistic is a small Bacillus subtilis protein which is of current interest to the field of structural biology and biochemistry because of its unique ability to increase integral membrane protein yields in Escherichia coli expression. Using the osmosensing histidine kinase receptor, EnvZ, an E. coli two-component system, and its cytoplasmic cognate response regulator, OmpR, we provide the first evidence that a Mistic-fused integral membrane protein maintains functionality both in vitro and in vivo. When the purified and detergent-solubilized receptor EnvZ is fused to Mistic, it maintains the ability to autophosphorylate on residue His(243) and phosphotransfers to residue Asp(55) located on OmpR. Functionality was also observed in vivo by means of a β-galactosidase assay in which RU1012 [Φ(ompC-lacZ)10-15, ΔenvZ::Km(r)] cells transformed with Mistic-fused EnvZ led to an increase in downstream signal transduction events detected by the activation of ompC gene expression. These findings illustrate that Mistic preserves the functionality of the Mistic-fused cargo protein and thus provides a beneficial alternate approach to study integral membrane proteins not only by improving expression levels but also for direct use in functional characterization.

Role for tandem duplication and lon protease in AcrAB-TolC- dependent multiple antibiotic resistance (Mar) in an Escherichia coli mutant without mutations in marRAB or acrRAB

A spontaneous mutant (M113) of Escherichia coli AG100 with an unstable multiple antibiotic resistance (Mar) phenotype was isolated in the presence of tetracycline. Two mutations were found: an insertion in the promoter of lon (lon3::IS186) that occurred first and a subsequent large tandem duplication, dupIS186, bearing the genes acrAB and extending from the lon3::IS186 to another IS186 present 149 kb away from lon. The decreased amount of Lon protease increased the amount of MarA by stabilization of the basal quantities of MarA produced, which in turn increased the amount of multidrug effux pump AcrAB-TolC. However, in a mutant carrying only a lon mutation, the overproduced pump mediated little, if any, increased multidrug resistance, indicating that the Lon protease was required for the function of the pump. This requirement was only partial since resistance was mediated when amounts of AcrAB in a lon mutant were further increased by a second mutation. In M113, amplification of acrAB on the duplication led to increased amounts of AcrAB and multidrug resistance. Spontaneous gene duplication represents a new mechanism for mediating multidrug resistance in E. coli through AcrAB-TolC.

Analysis of outer membrane proteome ofEscherichia coli related to resistance to ampicillin and tetracycline

The elucidation of the molecular details of antibiotic resistance will lead to improvements in extending the efficacy of current antimicrobials. In the current study, proteomic methodologies were applied to characterize functional outer membrane proteins (Omps) of E. coli K-12 responded to tetracycline and ampicillin resistance for understanding of universal pathways that form barriers for antimicrobial agents. For this purpose, E. coli K-12 expressional outer membrane proteome was characterized and identified with the use of 2-DE and MALDI-TOF/MS methods. Then, differential Omps due to tetracycline or ampcilin resistance were determined by comparison between tetracycline minimum inhibitory concentration (MIC)10, ampicillin MIC10, control0 and control10, showing 9 proteins with 11 spots for tetracycline and 8 protein with 9 spots for ampicillin, showing a difference in only 1 protein (decreased LamB in tetracyclin) between the two antibiotics. Among the proteins, 3 were known as antibiotic-resistant proteins, including TolC, OmpC and YhiU, while FimD precursor, LamB, Tsx, YfiO, OmpW, NlpB were first reported here to be antibiotic-resistance-related proteins. Our findings will be helpful for further understanding of antibiotic-resistant mechanism(s). This study also shows that the combination of Omp purification methods certainly contributes the sensitivity of Omp detection.

Enhanced active efflux, repression of porin synthesis and development of Mar phenotype by diazepam in two enterobacteria strains

The aim of this work was to determine whether diazepam could induce the multiple antibiotic resistance (Mar) phenotype in Klebsiella pneumoniae and Escherichia coli strains. The Mar phenotype is characterized by decreased susceptibility to multiple antibiotics due to the loss of porins and/or increased expression of active efflux systems. The effect of subinhibitory concentrations of diazepam on the susceptibility of different antimicrobial agents, outer-membrane protein expression and norfloxacin intracellular accumulation was studied. The results revealed that diazepam concentrations equal or twice adult dosage induced the same Mar phenotype as two well known E. coli marRAB inducers, sodium salicylate and sodium benzoate. Susceptibility to norfloxacin in a K. pneumoniae clinical isolate and E. coli strain Ag100 decreased due to enhanced active efflux and loss of porin expression. A decreased susceptibility to chloramphenicol, tetracycline, nalidixic acid and β-lactam antibiotics was also observed. In conclusion, like sodium salicylate or sodium benzoate, diazepam may induce the Mar phenotype.

MicF: an antisense RNA gene involved in response of Escherichia coli to global stress factors

The micF gene is a stress response gene found in Escherichia coli and related bacteria that post-transcriptionally controls expression of the outer membrane porin gene ompF. The micF gene encodes a non-translated 93 nt antisense RNA that binds its target ompF mRNA and regulates ompF expression by inhibiting translation and inducing degradation of the message. In addition, other factors, such as the RNA chaperone protein StpA also play a role in this regulatory system. Expression of micF is controlled by both environmental and internal stress factors. Four transcriptional regulators are known to bind the micF promoter region and activate micF expression. The crystal structure of one these transcriptional activators, Rob, complexed with the micF promoter has been reported. Here, we review new developments in the micF regulatory network.