The depressed central carbon and energy metabolisms is associated to the acquisition of levofloxacin resistance in Vibrio alginolyticus

Enhanced fatty acid biosynthesis by Sigma28 in stringent responses contributes to multidrug resistance and biofilm formation in Helicobacter pylori

The metabolic state of bacteria significantly contributes to their resistance to antibiotics; however, the specific metabolic mechanisms conferring antimicrobial resistance in Helicobacter pylori remain largely understudied. Employing transcriptomic and non-targeted metabolomics, we characterized the metabolic reprogramming of H. pylori when challenged with antibiotic agents. We observed a notable increase in both genetic and key proteomic components involved in fatty acid biosynthesis. Inhibition of this pathway significantly enhanced the antibiotic susceptibility of the sensitive and multidrug-resistant H. pylori strains while also disrupting their biofilm-forming capacities. Further analysis revealed that antibiotic treatment induced a stringent response, triggering the expression of the hp0560-hp0557 operon regulated by Sigma28 (σ28). This activation in turn stimulated the fatty acid biosynthetic pathway, thereby enhancing the antibiotic tolerance of H. pylori. Our findings reveal a novel adaptive strategy employed by H. pylori to withstand antibiotic stress.

Edwardsiella tarda Attenuates Virulence upon Oxytetracycline Resistance

The relationship between antibiotic resistance and bacterial virulence has not yet been fully explored. Here, we use Edwardsiella tarda as the research model to investigate the proteomic change upon oxytetracycline resistance (LTB4-ROTC). Compared to oxytetracycline-sensitive E. tarda (LTB4-S), LTB4-ROTC has 234 differentially expressed proteins, of which the abundance of 84 proteins is downregulated and 15 proteins are enriched to the Type III secretion system, Type VI secretion system, and flagellum pathways. Functional analysis confirms virulent phenotypes, including autoaggregation, biofilm formation, hemolysis, swimming, and swarming, are impaired in LTB4-ROTC. Furthermore, the in vivo bacterial challenge in both tilapia and zebrafish infection models suggests that the virulence of LTB4-ROTC is attenuated. Analysis of immune gene expression shows that LTB4-ROTC induces a stronger immune response in the spleen but a weaker response in the head kidney than that induced by LTB4-S, suggesting it's a potential vaccine candidate. Zebrafish and tilapia were challenged with a sublethal dose of LTB4-ROTC as a live vaccine followed by LTB4-S challenge. The relative percentage of survival of zebrafish is 60% and that of tilapia is 75% after vaccination. Thus, our study suggests that bacteria that acquire antibiotic resistance may attenuate virulence, which can be explored as a potential live vaccine to tackle bacterial infection in aquaculture.

Elevated Membrane Potential as a Tetracycline Resistance Mechanism in Escherichia coli

The metabolic environment is responsible for antibiotic resistance, which highlights the way in which the antibiotic resistance mechanism works. Here, GC-MS-based metabolomics with iTRAQ-based proteomics was used to characterize a metabolic state in tetracycline-resistant Escherichia coli K12 (E. coli-RTET) compared with tetracycline-sensitive E. coli K12. The repressed pyruvate cycle against the elevation of the proton motive force (PMF) and ATP constructed the most characteristic feature as a consequence of tetracycline resistance. To understand the role of the elevated PMF in tetracycline resistance, PMF inhibitor carbonyl cyanide 3-chlorophenylhydrazone (CCCP) and the pH gradient were used to investigate how the elevation influences bacterial viability and intracellular antibiotic concentration. A strong synergy was detected between CCCP and tetracycline to the viability, which was consistent with increasing intracellular drug and decreasing external pH. Furthermore, E. coli-RTET and E. coli-RGEN with high and low PMF concentrations were susceptible to gentamicin and tetracycline, respectively. The elevated PMF in E. coli-RTET was attributed to the activation of other metabolic pathways, except for the pyruvate cycle, including a malate-oxaloacetate-phosphoenolpyruvate-pyruvate-malate cycle. These results not only revealed a PMF-dependent mechanism for tetracycline resistance but also provided a solution to tetracycline-resistant pathogens by aminoglycosides and aminoglycoside-resistant bacteria by tetracyclines.

Microbial-mediated conversion of soil organic carbon co-regulates the evolution of antibiotic resistance

The influence of organic carbon on the proliferation of antibiotic resistance genes (ARGs) in the soil has been widely documented. However, it is unclear how soil organic carbon (SOC) interacts with the evolution of antibiotic resistance in bacteria. Here, we examined the variations in ARGs abundance during SOC mineralization and explored the microbiological mechanisms and key metabolic pathways involved in their coevolution. The results showed that the SOC mineralization rate was closely correlated with ARGs abundance (p < 0.05). High organic carbon (OC) mineralization was conducive to the occurrence of multidrug resistance genes. For example, multidrug_transporter and mexB increased 2.26 and 7.83 times from the initial level. The competitor (stress) evolutionary strategy model revealed that higher OC inputs drive environmental microorganisms to evolve from stress tolerant to high resistance and strong adaptation. Meta-genomic and transcriptomic analyses revealed that the conversion process of pyruvate to acetyl-CoA to acetate was the critical metabolic pathway for the co-regulation of antibiotic resistance. Gene deletion validation trials have demonstrated that the key functional genes (ackA and pta) involved in this process can modulate the development of vancomycin and multidrug resistance. This outcome provides a preliminary framework for microbial mechanisms that target the co-regulation of microbial OC conversion and the evolution of antibiotic resistance.

Laboratory Evolution of Antimicrobial Resistance in Bacteria to Develop Rational Treatment Strategies

Laboratory evolution studies, particularly with Escherichia coli, have yielded invaluable insights into the mechanisms of antimicrobial resistance (AMR). Recent investigations have illuminated that, with repetitive antibiotic exposures, bacterial populations will adapt and eventually become tolerant and resistant to the drugs. Through intensive analyses, these inquiries have unveiled instances of convergent evolution across diverse antibiotics, the pleiotropic effects of resistance mutations, and the role played by loss-of-function mutations in the evolutionary landscape. Moreover, a quantitative analysis of multidrug combinations has shed light on collateral sensitivity, revealing specific drug combinations capable of suppressing the acquisition of resistance. This review article introduces the methodologies employed in the laboratory evolution of AMR in bacteria and presents recent discoveries concerning AMR mechanisms derived from laboratory evolution. Additionally, the review outlines the application of laboratory evolution in endeavors to formulate rational treatment strategies.

Exogenous pyruvate promotes gentamicin uptake to kill antibiotic-resistant Vibrio alginolyticus

OBJECTIVES

Elucidating antibiotic resistance mechanisms is necessary for developing novel therapeutic strategies. The increasing incidence of antibiotic-resistant Vibrio alginolyticus infection threatens both human health and aquaculture, but the mechanism has not been fully elucidated.

METHODS

Here, an isobaric tags for relative and absolute quantification (iTRAQ) functional proteomics analysis was performed on gentamicin-resistant V. alginolyticus (VA-RGEN) and a gentamicin-sensitive strain in order to characterize the global protein expression changes upon gentamicin resistance. Then, the bacterial killing assay and bacterial gentamicin pharmacokinetics were performed.

RESULTS

Proteomics analysis demonstrated a global metabolic downshift in VA-RGEN, where the pyruvate cycle (the P cycle) was severely compromised. Exogenous pyruvate restored the P cycle activity, disrupting the redox state and increasing the membrane potential. It thereby potentiated gentamicin-mediated killing by approximately 3000- and 150-fold in vitro and in vivo, respectively. More importantly, bacterial gentamicin pharmacokinetics indicated that pyruvate enhanced gentamicin influx to a degree that exceeded the gentamicin expelled by the bacteria, increasing the intracellular gentamicin.

CONCLUSION

Thus, our study suggests a metabolism-based approach to combating gentamicin-resistant V. algonolyticus, which paves the way for combating other types of antibiotic-resistant bacterial pathogens.

Fructose promotes ampicillin killing of antibiotic-resistant Streptococcus agalactiae

Streptococcus agalactiae (GBS) is an important pathogenic bacteria that infected both aquatic animals and human beings, causing huge economic loss. The increasing cases of antibiotic-resistant GBS impose challenges to treat such infection by antibiotics. Thus, it is highly demanded for the approach to tackle antibiotic resistance in GBS. In this study, we adopt a metabolomic approach to identify the metabolic signature of ampicillin-resistant GBS (AR-GBS) that ampicillin is the routine choice to treat infection by GBS. We find glycolysis is significantly repressed in AR-GBS, and fructose is the crucial biomarker. Exogenous fructose not only reverses ampicillin resistance in AR-GBS but also in clinic isolates including methicillin-resistant Staphylococcus aureus (MRSA) and NDM-1 expressing Escherichia coli. The synergistic effect is confirmed in a zebrafish infection model. Furthermore, we demonstrate that the potentiation by fructose is dependent on glycolysis that enhances ampicillin uptake and the expression of penicillin-binding proteins, the ampicillin target. Our study demonstrates a novel approach to combat antibiotic resistance in GBS.

A glucose-mediated antibiotic resistance metabolic flux from glycolysis, the pyruvate cycle, and glutamate metabolism to purine metabolism

Introduction

Bacterial metabolic environment influences antibiotic killing efficacy. Thus, a full understanding for the metabolic resistance mechanisms is especially important to combat antibiotic-resistant bacteria.

Methods

Isobaric tags for relative and absolute quantification-based proteomics approach was employed to compare proteomes between ceftazidime-resistant and -sensitive Edwarsiella tarda LTB4 (LTB4-RCAZ and LTB4-S, respectively).

Results

This analysis suggested the possibility that the ceftazidime resistance mediated by depressed glucose is implemented through an inefficient metabolic flux from glycolysis, the pyruvate cycle, glutamate metabolism to purine metabolism. The inefficient flux was demonstrated by the reduced expression of genes and the decreased activity of enzymes in the four metabolic pathways. However, supplement upstream glucose and downstream guanosine separately restored ceftazidime killing, which not only supports the conclusion that the inefficient metabolic flux is responsible for the resistance, but also provides an effective approach to reverse the resistance. In addition, the present study showed that ceftazidime is bound to pts promoter in E. tarda.

Discussion

Our study highlights the way in fully understanding metabolic resistance mechanisms and establishing metabolites-based metabolic reprogramming to combat antibiotic resistance.

Gentamicin resistance to Escherichia coli related to fatty acid metabolism based on transcriptome analysis

Antibiotic overuse and misuse have promoted the emergence and spread of antibiotic-resistant bacteria. Increasing bacterial resistance to antibiotics is a major healthcare problem, necessitating elucidation of antibiotic resistance mechanisms. In this study, we explored the mechanism of gentamicin resistance by comparing the transcriptomes of antibiotic-sensitive and -resistant Escherichia coli. A total of 410 differentially expressed genes were identified, of which 233 (56.83%) were up-regulated and 177 (43.17%) were down-regulated in the resistant strain compared with the sensitive strain. Gene Ontology (GO) analysis classifies differential gene expression into three main categories: biological processes, cellular components, and molecular functions. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis indicated that the up-regulated genes were enriched in eight metabolic pathways, including fatty acid metabolism, which suggests that fatty acid metabolism may be involved in the development of gentamicin resistance in E. coli. This was demonstrated by measuring the acetyl-CoA carboxylase activity, plays a fundamental role in fatty acid metabolism, was increased in gentamicin-resistant E. coli. Treatment of fatty acid synthesis inhibitor, triclosan, promoted gentamicin-mediated killing efficacy to antibiotic-resistant bacteria. We also found that exogenous addition of oleic acid, which involved in fatty acid metabolism, reduced E. coli sensitivity to gentamicin. Overall, our results provide insight into the molecular mechanism of gentamicin resistance development in E. coli.

L-leucine increases the sensitivity of drug-resistant Salmonella to sarafloxacin by stimulating central carbon metabolism and increasing intracellular reactive oxygen species level

Introduction

The overuse of antibiotics has made public health and safety face a serious cisis. It is urgent to develop new clinical treatment methods to combat drug resistant bacteria to alleviate the health crisis. The efficiency of antibiotics is closely related to the metabolic state of bacteria. However, studies on fluoroquinolone resistant Salmonella are relatively rare.

Methods

CICC21484 were passaged in medium with and without sarafloxacin and obtain sarafloxacin- susceptible Salmonella Typhimurium (SAR-S) and sarafloxacin resistant Salmonella Typhimurium (SAR-R), respectively. Non-targeted metabolomics was used to analyze the metabolic difference between SAR-S and SAR-R. Then we verified that exogenous L-leucine promoted the killing effect of sarafloxacin in vitro, and measured the intracellular ATP, NADH and reactive oxygen species levels of bacteria. Gene expression was determined using Real Time quantitative PCR.

Results

We confirmed that exogenous L-leucine increased the killing effect of sarafloxacin on SAR-R and other clinically resistant Salmonella serotypes. Exogenous L-leucine stimulated the metabolic state of bacteria, especially the TCA cycle, which increased the working efficiency of the electron transfer chain and increased the intracellular NADH, ATP concentration, and reactive oxygen species level. Our results suggest that when the metabolism of drug-resistant bacteria is reprogrammed, the bactericidal effect of antibiotics improves.

Discussion

This study further enhances research in the anti-drug resistance field at the metabolic level and provides theoretical support for solving the current problem of sarafloxacin drug resistance, a unique fluoroquinolone drug for animals and indicating the potential of L-leucine as a new antibiotic adjuvant.

Quantitative proteomics reveals reduction in central carbon and energy metabolisms contributes to gentamicin resistance in Staphylococcus aureus

The emergence of antibiotic resistance greatly increases the difficulty of treating bacterial infections. In order to develop effective treatments, the underlying mechanisms of antibiotic resistance must be understood. In this study, Staphylococcus aureus ATCC6538 strain was passaged in medium with and without gentamicin and obtained lab-evolved gentamicin-resistant S. aureus (R_GEN) and gentamicin-sensitive S. aureus (S_GEN) strains, respectively. Data-Independent Acquisition (DIA)-based proteomics approach was applied to compare the two strains. A total of 1426 proteins were identified, of which 462 were significantly different: 126 were upregulated and 336 were downregulated in R_GEN compared to S_GEN. Further analysis found that reduced protein biosynthesis was a characteristic feature in R_GEN, related to metabolic suppression. The most differentially expressed proteins were involved in metabolic pathways. In R_GEN, central carbon metabolism was dysregulated and energy metabolism decreased. After verification, it was found that the levels of NADH, ATP, and reactive oxygen species (ROS) decreased, and superoxide dismutase and catalase activities increased. These findings suggest that inhibition of central carbon and energy metabolic pathways may play an important role in the resistance of S. aureus to gentamicin, and that gentamicin resistance is associated with oxidative stress. Significance: The overuse and misuse of antibiotics have led to bacterial antibiotic resistance, which is a serious threat to human health. Understanding the mechanisms of antibiotic resistance will help better control these antibiotic-resistant pathogens in the future. The present study characterized the differential proteome of gentamicin-resistant Staphylococcus aureus using the most advanced DIA-based proteomics technology. Many of the differential expressed proteins were related to metabolism, specifically, reduced central carbon and energy metabolism. Lower levels of NADH, ROS, and ATP were detected as a consequence of the reduced metabolism. These results reveal that downregulation of protein expression affecting central carbon and energy metabolisms may play an important role in the resistance of S. aureus to gentamicin.

Ampicillin-controlled glucose metabolism manipulates the transition from tolerance to resistance in bacteria

The mechanism(s) of how bacteria acquire tolerance and then resistance to antibiotics remains poorly understood. Here, we show that glucose abundance decreases progressively as ampicillin-sensitive strains acquire resistance to ampicillin. The mechanism involves that ampicillin initiates this event via targeting pts promoter and pyruvate dehydrogenase (PDH) to promote glucose transport and inhibit glycolysis, respectively. Thus, glucose fluxes into pentose phosphate pathway to generate reactive oxygen species (ROS) causing genetic mutations. Meanwhile, PDH activity is gradually restored due to the competitive binding of accumulated pyruvate and ampicillin, which lowers glucose level, and activates cyclic adenosine monophosphate (cAMP)/cAMP receptor protein (CRP) complex. cAMP/CRP negatively regulates glucose transport and ROS but enhances DNA repair, leading to ampicillin resistance. Glucose and Mn²⁺ delay the acquisition, providing an effective approach to control the resistance. The same effect is also determined in the intracellular pathogen Edwardsiella tarda. Thus, glucose metabolism represents a promising target to stop/delay the transition of tolerance to resistance.

Alanine-Dependent TCA Cycle Promotion Restores the Zhongshengmycin-Susceptibility in Xanthomonas oryzae

Xanthomonas oryzae pv. oryzicola (Xoo) is a plant pathogenic bacterium that can cause rice bacterial blight disease, which results in a severe reduction in rice production. Antimicrobial-dependent microbial controlling is a useful way to control the spread and outbreak of plant pathogenic bacteria. However, the abuse and long-term use of antimicrobials also cause microbial antimicrobial resistance. As far as known, the mechanism of antimicrobial resistance in agricultural plant pathogenic bacteria still lacks prospecting. In this study, we explore the mechanism of Zhongshengmycin (ZSM)-resistance in Xoo by GC-MS-based metabolomic analysis. The results showed that the down-regulation of the TCA cycle was characteristic of antimicrobial resistance in Xoo, which was further demonstrated by the reduction of activity and gene expression levels of key enzymes in the TCA cycle. Furthermore, alanine was proven to reverse the ZSM resistance in Xoo by accelerating the TCA cycle in vivo. Our results are essential for understanding the mechanisms of ZSM resistance in Xoo and may provide new strategies for controlling this agricultural plant pathogen at the metabolic level.

Functional proteomics identify mannitol metabolism in serum resistance and therapeutic implications in Vibrio alginolyticus

Serum resistance is recognized as one of the most important pathogenic traits of bacterial pathogens, and no control measure is available. Based on our previous discovery that pathogenic Escherichia coli represses glycine, serine, and threonine metabolism to confer serum resistance and that the reactivation of this pathway by exogenous glycine could restore serum sensitivity, we further investigate the mechanism underlying the action of glycine in Vibrio alginolyticus. Thus, V. alginolyticus is treated with glycine, and the proteomic change is profiled with tandem mass tag-based quantitative proteomics. Compared to the control group, glycine treatment influences the expression of a total of 291 proteins. Among them, a trap-type mannitol/chloroaromatic compound transport system with periplasmic component, encoded by N646_0992, is the most significantly increased protein. In combination with the pathway enrichment analysis showing the altered fructose and mannitol metabolism, mannitol has emerged as a possible metabolite in enhancing the serum killing activity. To demonstrate this, exogenous mannitol reduces bacterial viability. This synergistic effect is further confirmed in a V. alginolyticus-Danio rerio infection model. Furthermore, the mechanism underlying mannitol-enabled serum killing is dependent on glycolysis and the pyruvate cycle that increases the deposition of complement components C3b and C5b-9 on the bacterial surface, whereas inhibiting glycolysis or the pyruvate cycle significantly weakened the synergistic effects and complement deposition. These data together suggest that mannitol is a potent metabolite in reversing the serum resistance of V. alginolyticus and has promising use in aquaculture.

Enhanced Biosynthesis of Fatty Acids Contributes to Ciprofloxacin Resistance in Pseudomonas aeruginosa

Antibiotic-resistant Pseudomonas aeruginosa is insensitive to antibiotics and difficult to deal with. An understanding of the resistance mechanisms is required for the control of the pathogen. In this study, gas chromatography-mass spectrometer (GC-MS)-based metabolomics was performed to identify differential metabolomes in ciprofloxacin (CIP)-resistant P. aeruginosa strains that originated from P. aeruginosa ATCC 27853 and had minimum inhibitory concentrations (MICs) that were 16-, 64-, and 128-fold (PA-R16_CIP, PA-R64_CIP, and PA-R128_CIP, respectively) higher than the original value, compared to CIP-sensitive P. aeruginosa (PA-S). Upregulation of fatty acid biosynthesis forms a characteristic feature of the CIP-resistant metabolomes and fatty acid metabolome, which was supported by elevated gene expression and enzymatic activity in the metabolic pathway. The fatty acid synthase inhibitor triclosan potentiates CIP to kill PA-R128_CIP and clinically multidrug-resistant P. aeruginosa strains. The potentiated killing was companied with reduced gene expression and enzymatic activity and the returned abundance of fatty acids in the metabolic pathway. Consistently, membrane permeability was reduced in the PA-R and clinically multidrug-resistant P. aeruginosa strains, which were reverted by triclosan. Triclosan also stimulated the uptake of CIP. These findings highlight the importance of the elevated biosynthesis of fatty acids in the CIP resistance of P. aeruginosa and provide a target pathway for combating CIP-resistant P. aeruginosa.

Vibrio alginolyticus Survives From Ofloxacin Stress by Metabolic Adjustment

Antibiotic-resistant Vibrio alginolyticus becomes a worldwide challenge threatening both human health and food safety. The approach in managing such infection is largely absent, despite the fact that the mechanisms of antibiotic resistance have been extensively investigated. Metabolic modulation has been documented to be a novel approach in improving antibiotic efficacy. In this study, we characterize the metabolic signature of V. alginolyticus exposed to 0.3 or 0.5 μg/ml of ofloxacin (OFX). By profiling the metabolome, we find that bacteria treated by the two different concentrations of OFX generate different metabolic signatures. While a part of these metabolites was shared by both groups, the other metabolites represent their own signatures. The pathway enrichment analysis demonstrates that the pyruvate cycle is disrupted in the bacteria treated by the 0.3 μg/ml OFX as compared to those by the 0.5 μg/ml. Importantly, the disruption of pyruvate cycle confers the capability of bacteria to survive under 0.5 μg/ml of antibiotic stress. Further analysis identifies that the fatty acid biosynthesis is elevated in bacteria treated by 0.3 μg/ml OFX, and inhibition on fatty acid completely prevents the bacteria from survival even under such dose of antibiotic stress. Our study suggests that bacteria adapt to antibiotic stress by modulating the metabolic flux for survival, which could be targeted to increase antibiotic efficacy.

Repressed Central Carbon Metabolism and Its Effect on Related Metabolic Pathways in Cefoperazone/Sulbactam-Resistant Pseudomonas aeruginosa

Metabolic shift and antibiotic resistance have been reported in Pseudomonas aeruginosa. However, the global metabolic characteristics remain largely unknown. The present study characterizes the central carbon metabolism and its effect on other metabolic pathways in cefoperazone-sulbactam (SCF)-resistant P. aeruginosa (PA-R_SCF). GC-MS-based metabolomics shows a repressed central carbon metabolism in PA-R_SCF, which is confirmed by measuring expression of genes and activity of enzymes in the metabolism. Furthermore, expression of the genes that encode the enzymes for the first step of fatty acid biosynthesis, glutamate metabolism, and electron transport chain is reduced, confirmed by their enzymatic activity assay, and the key enzyme for riboflavin metabolism is also reduced, indicating the decreased metabolic flux to the four related metabolic pathways. Moreover, the role of the reduced riboflavin metabolism, being related to ROS generation, in SCF resistance is explored. Exogenous H₂O₂ potentiates SCF-mediated killing in a dose-dependent manner, suggesting that the decreased ROS resulted from the reduced riboflavin metabolism that contributed to the resistance. These results indicate that the repressed central carbon metabolism and related riboflavin metabolism contribute to SCF resistance, but increasing ROS can restore SCF sensitivity. These findings characterize the repressed central carbon metabolism and its effect on other metabolic pathways as the global metabolic features in PA-R_SCF.

Glucose-Potentiated Amikacin Killing of Cefoperazone/Sulbactam Resistant Pseudomonas aeruginosa

Multidrug-resistant Pseudomonas aeruginosa has become one of global threat pathogens for human health due to insensitivity to antibiotics. Recently developed reprogramming metabolomics can identify biomarkers, and then, the biomarkers were used to revert the insensitivity and elevate antibiotic-mediated killing. Here, the methodology was used to study cefoperazone/sulbactam (SCF)-resistant P. aeruginosa (PA-R_SCF) and identified reduced glycolysis and pyruvate cycle, a recent clarified cycle providing respiratory energy in bacteria, as the most key enriched pathways and the depressed glucose as one of the most crucial biomarkers. Further experiments showed that the depression of glucose was attributed to reduction of glucose transport. However, exogenous glucose reverted the reduction to elevate intracellular glucose via activating glucose transport. The elevated glucose fluxed to the glycolysis, pyruvate cycle, and electron transport chain to promote downstream proton motive force (PMF). Consistently, exogenous glucose did not promote SCF-mediated elimination but potentiated aminoglycosides-mediated killing since aminoglycosides uptake is PMF-dependent, where amikacin was the best one. The glucose-potentiated amikacin-mediated killing was effective to both lab-evolved PA-R_SCF and clinical multidrug-resistant P. aeruginosa. These results reveal the depressed glucose uptake causes the reduced intracellular glucose and expand the application of metabolome-reprogramming on selecting conventional antibiotics to achieve the best killing efficacy.

Exogenous Alanine Reverses the Bacterial Resistance to Zhongshengmycin with the Promotion of the P Cycle in Xanthomonas oryzae

Microbial antibiotic resistance has become a worldwide concern, as it weakens the efficiency of the control of pathogenic microbes in both the fields of medicine and plant protection. A better understanding of antibiotic resistance mechanisms is helpful for the development of efficient approaches to settle this issue. In the present study, GC-MS-based metabolomic analysis was applied to explore the mechanisms of Zhongshengmycin (ZSM) resistance in Xanthomonas oryzae (Xoo), a bacterium that causes serious disease in rice. Our results show that the decline in the pyruvate cycle (the P cycle) was a feature for ZSM resistance in the metabolome of ZSM-resistant strain (Xoo-ZSM), which was further demonstrated as the expression level of genes involved in the P cycle and two enzyme activities were reduced. On the other hand, alanine was considered a crucial metabolite as it was significantly decreased in Xoo-ZSM. Exogenous alanine promoted the P cycle and enhanced the ZSM-mediated killing efficiency in Xoo-ZSM. Our study highlights that the depressed P cycle is a feature in Xoo-ZSM for the first time. Additionally, exogenous alanine is a candidate enhancer and can be applied with ZSM to improve the antibiotic-mediated killing efficiency in the control of infection caused by Xoo.

Proteomics in antibiotic resistance and tolerance research: Mapping the resistome and the tolerome of bacterial pathogens

Antibiotic resistance, the ability of a microbial pathogen to evade the effects of antibiotics thereby allowing them to grow under elevated drug concentrations, is an alarming health problem worldwide and has attracted the attention of scientists for decades. On the other hand, the clinical importance of persistence and tolerance as alternative mechanisms for pathogens to survive prolonged lethal antibiotic doses has recently become increasingly appreciated. Persisters and high-tolerance populations are thought to cause the relapse of infectious diseases, and provide opportunities for the pathogens to evolve resistance during the course of antibiotic therapy. Although proteomics and other omics methodology have long been employed to study resistance, its applications in studying persistence and tolerance are still limited. However, due to the growing interest in the topic and recent progress in method developments to study them, there have been some proteomic studies that yield fresh insights into the phenomenon of persistence and tolerance. Combined with the studies on resistance, these collectively guide us to novel molecular targets for the potential drugs for the control of these dangerous pathogens. In this review, we surveyed previous proteomic studies to investigate resistance, persistence, and tolerance mechanisms, and discussed emerging experimental strategies for studying these phenotypes with a combination of adaptive laboratory evolution and high-throughput proteomics. This article is protected by copyright. All rights reserved.

Cell Membrane Remodeling Mediates Polymyxin B Resistance in Klebsiella pneumoniae: An Integrated Proteomics and Metabolomics Study

Polymyxin B (PB) is introduced into the clinic as the last-line therapy against carbapenem-resistant Klebsiella pneumoniae (CRKP). Unfortunately, increased resistance to PB in Klebsiella pneumoniae (K. pneumoniae) has threatened global health. Resistance of K. pneumoniae to PB was induced by passaging in serial concentrations of PB and determined by microbroth dilution method. Growth characteristics of induced strains including growth curve, reversibility of resistance, and biofilm formation (crystal violet staining method) were measured. This study employed TMT-labeled quantitative proteomics and LC-MS/MS metabolomics analysis to investigate the key biological processes associated with PB resistance in K. pneumoniae. A total of 315 differentially expressed proteins (DEPs) were identified, of which 133 were upregulated and 182 were downregulated in the PB-resistant K. pneumoniae. KEGG enrichment analysis revealed that the DEPs were mainly involved in ATP-binding cassette (ABC) transporters and cationic antimicrobial peptide (CAMP) resistance. Proteins related to central carbon metabolism were inhibited in the PB-resistant K. pneumoniae, but proteins mediating LPS modification were activated. Transcriptional levels of CAMP resistance-related proteins were significantly different between PB-susceptible and -resistant K. pneumoniae. PB treatment led to an increase in reactive oxygen species (ROS) levels of K. pneumoniae. Metabolomics data demonstrated that 23 metabolites were significantly upregulated in PB-resistant K. pneumoniae and 5 were downregulated. The differential metabolites were mainly lipids, including glycerophospholipids, sphingolipids, and fatty acids. Exposure to PB resulted in increased level of phospholipid transport gene mlaF in K. pneumoniae. Our study suggested that membrane remodeling and inhibited central carbon metabolism are conducive to the development of PB resistance in K. pneumoniae.

ToxR modulates biofilm formation in fish pathogen Vibrio harveyi

Vibrio harveyi is a common aquaculture pathogen causing diseases in a variety of aquatic animals. toxR, a conserved virulence-associated gene in vibrios, is identified in V. harveyi 345, a pathogenic strain isolated from diseased fish. In this study, to gain insight into function of ToxR in V. harveyi, an in-frame deletion of the toxR gene was constructed to reveal the role of ToxR in the physiology and virulence of V. harveyi. The statistical analysis showed no significant differences in the growth ability, motility, extracellular protease secretion, antibiotic susceptibility, virulence by intraperitoneal injection and the ability of V. harveyi to colonize the spleen and liver tissues of the pearl gentian grouper between the wild-type (WT) and the toxR mutant. However, the deletion of toxR increased the biofilm formation. The structure of the V. harveyi biofilm was further analysed by using scanning electron microscopy (SEM) and confocal laser scanning microscopy, and the results showed that deletion of toxR increased the number and density of V. harveyi biofilm. Since biofilm production is flagella, exopolysaccharide (EPS) and lipopolysaccharide dependent, 16 of V. harveyi biofilm-related genes were selected for further analysis. Based on quantitative real-time reverse transcription-PCR, the expression levels of these genes, including genes flrB, motY and mshA, flaE, flrA and gmhD, were significantly up-regulated in the ΔtoxR⁺ strain as compared with the WT⁺ and C-ΔtoxR strains during the early and mid-exponential, while epsG, flaA, flaE, flgD, flgE, flrB, flrC, lpxB, motY, mshA and scrG genes were inhibited because of deletion of the toxR gene in the stationary growth phase. Our results indicate that ToxR plays an important role in controlling the biofilm in V. harveyi.

Allyl Isothiocyanate in the Volatiles of Brassica juncea Inhibits the Growth of Root Rot Pathogens of Panax notoginseng by Inducing the Accumulation of ROS

The cultivation of Panax notoginseng is often seriously hindered by root rot disease caused by the accumulation of soil-borne pathogens. Here, the inhibitory activity of Brassica juncea volatiles on P. notoginseng root rot pathogens was assessed and compounds in volatiles were identified. Furthermore, the antimicrobial activity and mechanism of allyl isothiocyanate (AITC) were deciphered by integrated transcriptome and metabolome analyses. The volatiles of B. juncea showed dose-dependent antimicrobial activity against root rot pathogens. AITC, identified as the main volatile compound, not only significantly inhibited pathogen growth in vitro but also suppressed root rot disease in the field. Integrated transcriptomic and metabolomics analysis revealed that AITC inhibited Fusarium solani by interfering with energy production and induced the accumulation of ROS by decreasing the content of glutathione (GSH). In summary, B. juncea releases AITC to inhibit soil-borne pathogens and could be used as a rotation crop or soil fumigant to alleviate root rot disease.

Elevation of Fatty Acid Biosynthesis Metabolism Contributes to Zhongshengmycin Resistance in Xanthomonas oryzae

Xanthomonas oryzae severely impacts the yield and quality of rice. Antibiotics are the most common control measure for this pathogen; however, the overuse of antibiotics in past decades has caused bacterial resistance to these antibiotics. The agricultural context is of particular importance as antibiotic-resistant bacteria are prevalent, but the resistance mechanism largely remains unexplored. Herein, using gas chromatography-mass spectrometry (GC-MS), we demonstrated that zhongshengmycin-resistant X. oryzae (Xoo-Rzs) and zhongshengmycin-sensitive X. oryzae (Xoo-S) have distinct metabolic profiles. We found that the resistance to zhongshengmycin (ZS) in X. oryzae is related to increased fatty acid biosynthesis. This was demonstrated by measuring the Acetyl-CoA carboxylase (ACC) activity, the expression levels of enzyme genes involved in the fatty acid biosynthesis and degradation pathways, and adding exogenous materials, i.e., triclosan and fatty acids. Our work provides a basis for the subsequent control of the production of antibiotic-resistant strains of X. oryzae and the development of coping strategies.

Enhanced Biosynthesis of Fatty Acids Is Associated with the Acquisition of Ciprofloxacin Resistance in Edwardsiella tarda

Misuse and overuse of antibiotics drive the selection and spread of antibiotic-resistant bacteria. Although genetic mutations have been well defined for different types of antibiotic resistance, ways to revert antibiotic resistance are largely unexplored. Here, we adopted a proteomics approach to investigate the mechanism underlying ciprofloxacin resistance in Edwardsiella tarda, a representative pathogen that infects both economic animal species and human beings. By comparing the protein expression profiles of ciprofloxacin-sensitive and -resistant E. tarda, a total of 233 proteins of differential abundance were identified, where 53 proteins belong to the functional categories of metabolism, featuring a disrupted pyruvate cycle and decreased energy metabolism but increased fatty acid biosynthesis. The altered pyruvate cycle and energy metabolism were confirmed by gene expression and biochemical assays. Furthermore, the role of fatty acid biosynthesis and quinolone resistance were explored. The expression level and enzymatic activity of acetyl coenzyme A (acetyl-CoA) carboxylase, the first step of fatty acid biosynthesis, were increased in ciprofloxacin-resistant E. tarda. Treatment of ciprofloxacin-resistant E. tarda with acetyl-CoA carboxylase and 3-oxoacyl-[acyl carrier protein] synthase II inhibitors, 2-aminooxazole and triclosan, respectively, reduced the expression of fatty acid biosynthesis and promoted quinolone-mediated killing efficacy to antibiotic-resistant bacteria. Similar results were obtained in clinically isolated E. tarda strains. Our study suggests that energy metabolism has been reprogramed in ciprofloxacin-resistant bacteria that favor the biosynthesis of fatty acid, presenting a novel target to tackle antibiotic-resistant bacteria.

IMPORTANCEEdwardsiella tarda is the causative agent of edwardsiellosis, which imposes huge challenges on clinics and aquaculture. Due to the overuse of antibiotics, the emergence and spread of antibiotic-resistant E. tarda threaten human health and animal farming. However, the mechanism of ciprofloxacin resistance in E. tarda is still lacking. Here, iTRAQ (isobaric tags for relative and absolute quantification)-based proteomics was performed to identify a differential proteome between ciprofloxacin-sensitive and -resistant E. tarda. The fluctuated pyruvate cycle and reduced energy metabolism and elevated fatty acid biosynthesis are metabolic signatures of ciprofloxacin resistance. Moreover, inhibition of biosynthesis of fatty acids promotes quinolone-mediated killing efficacy in both lab-evolved and clinically isolated strains. This study reveals that a ciprofloxacin resistance mechanism is mediated by the elevated biosynthesis of fatty acids and the depressed pyruvate metabolism and energy metabolism in E. tarda. These findings provide a novel understanding for the ciprofloxacin resistance mechanism in E. tarda.

Transcriptome of Edwardsiella anguillarum in vivo and in vitro revealed two-component system, ABC transporter and flagellar assembly are three pathways pathogenic to European eel (Anguilla anguilla)

Edwardsiella anguillarum is one of the common bacterial pathogens for the cultivated eels in China. The aim of this study was to reveal the cause of E. anguillarum pathogenic to European eel (Anguilla anguilla) from the perspective of the transcriptome. In this study, we first prepared E. anguillarum cultured in vitro and analysed the whole transcriptome after extracting the total RNA. Then, eels were i.p injected with E. anguillarum, and total RNA were extracted from the liver of European eels 48 h after the infection. After sequencing the transcriptome, we obtained average 1.97 × 10⁸ clean reads cultured in vitro and 1.36 × 10⁵ clean reads located in vivo after annotating all reads into the genome of E. anguillarum. The whole transcriptome showed, compared to the E. anguillarum cultured in vitro, 503 significantly up and 657 significantly down-regulated different expressed genes (DEGs) were observed. KEGG analysis showed that 38 DEGs of Two-Component System, 41 DEGs of ABC transporter, and 10 DEGs flagellar assembly pathways were highly upregulated in E. anguillarum located in vivo. Then, we designed primers to analyse the up-regulated DEGs through qRT-PCR and confirmed some up-regulated DEGs. The results of this study provide important reference for the further study of pathogen-host interaction between E. anguillarum and European eel.

Malate enhances survival of zebrafish against Vibrio alginolyticus infection in the same manner as taurine

Development of low-cost and eco-friendly approaches to fight bacterial pathogens is especially needed in aquaculture. We previously showed that exogenous malate reprograms zebrafish’s metabolome to potentiate zebrafish survival against Vibrio alginolyticus infection. However, the underlying mechanism is unknown. Here, we use GC-MS based metabolomics to identify the malate-triggered metabolic shift. An activated TCA cycle and elevated taurine are identified as the key metabolic pathways and the most crucial biomarker of the reprogrammed metabolome, respectively. Taurine elevation is attributed to the activated TCA cycle, which is further supported by the increased expression of genes in the metabolic pathway of taurine biosynthesis from the isocitrate of the TCA cycle to taurine. Exogenous taurine increases the survival of zebrafish against V. alginolyticus infection as malate did. Moreover, exogenous taurine and malate regulate the expression of innate immunity genes and promote the generation of reactive oxygen species and nitrogen oxide in a similar way. The two metabolites can alleviate the excessive immune response to bacterial challenge, which protects fish from bacterial infection. These results indicate that malate enhances the survival of zebrafish to V. alginolyticus infection via taurine. Thus, our study highlights a metabolic approach to enhance a host’s ability to fight bacterial infection.

Combating Antibiotic Tolerance Through Activating Bacterial Metabolism

The emergence of antibiotic tolerance enables genetically susceptible bacteria to withstand the killing by clinically relevant antibiotics. As is reported, an increasing body of evidence sheds light on the critical and underappreciated role of antibiotic tolerance in the disease burden of bacterial infections. Considering this tense situation, new therapeutic strategies are urgently required for combating antibiotic tolerance. Herein, we provide an insightful illustration to distinguish between antibiotic resistance and tolerance, and highlight its clinical significance and complexities of drug-tolerant bacteria. Then, we discuss the close relationship between antibiotic tolerance and bacterial metabolism. As such, a bacterial metabolism-based approach was proposed to counter antibiotic tolerance. These exogenous metabolites including amino acids, tricarboxylic acid cycle (TCA cycle) metabolites, and nucleotides effectively activate bacterial metabolism and convert the tolerant cells to sensitive cells, and eventually restore antibiotic efficacy. A better understanding of molecular mechanisms of antibiotic tolerance particularly in vivo would substantially drive the development of novel strategies targeting bacterial metabolism.

Metabolic mechanism of colistin resistance and its reverting in Vibrio alginolyticus

Colistin is a last-line antibiotic against Gram-negative multidrug-resistant bacteria, but the increased resistance poses a huge challenge to this drug. However, the mechanisms underlying such resistance are largely unexplored. The present study first identified the mutations of two genes encoding AceF subunit of pyruvate dehydrogenase (PDH) and TetR family transcriptional regulator in colistin-resistant Vibrio alginolyticus (VA-R_CT ) through genome sequencing. Then, gas chromatography-mass spectroscopy-based metabolomics was adopted to investigate metabolic responses since PDH plays a role in central carbon metabolism. Colistin resistance was associated with the reduction of the central carbon metabolism and energy metabolism, featuring the alteration of the pyruvate cycle, a recently characterized energy-producing cycle. Metabolites in the pyruvate cycle reprogramed colistin-resistant metabolome to colistin-sensitive metabolome, resulting in increased gene expression, enzyme activity or protein abundance of the cycle and sodium-translocating nicotinamide adenine dinucleotide-ubiquinone oxidoreductase. This reprogramming promoted the production of the proton motive force that enhances the binding between colistin and lipid A in lipopolysaccharide. Moreover, this metabolic approach was effective against VA-R_CT in vitro and in vivo as well as other clinical isolates. These findings reveal a previously unknown mechanism of colistin resistance and develop a metabolome-reprogramming approach to promote colistin efficiency to combat with colistin-resistant bacteria.

TonB-Dependent Receptors Affect the Spontaneous Oxytetracycline Resistance Evolution in Aeromonas hydrophila

It is well known that most microbial populations develop their intrinsic antibiotics resistance at low concentrations in antibiotics environments, but the factors influencing spontaneous resistance are still largely unknown. In this study, Aeromonas hydrophila strains with different resistance levels to oxytetracycline (OXY) were induced by sublethal antibiotic selection pressure, and differential expression of proteins was compared among them using iTRAQ-based quantitative proteomics. Our following bioinformatic analysis showed that energy metabolism-related proteins were downregulated, while several iron-related proteins were upregulated in high OXY-resistant strains. To further investigate the role of spontaneous OXY resistance evolution, four TonB-dependent receptor-coded genes were deleted, and their OXY susceptibility capabilities and antibiotic evolutionary assays were performed, respectively. Our results showed that the deletion of these genes did not affect the susceptibility to OXY, but showed different evolution rates in the spontaneous OXY evolution compared with wild-type strain, especially for AHA_0971 and AHA_4251. Therefore, this study indicates the important role of TonB-dependent receptor proteins during the bacterial antibiotics resistance evolution and may provide a new prophylactic strategy against the development of antibiotic resistance.

Bacterial metabolism-inspired molecules to modulate antibiotic efficacy

The decreasing antibiotic susceptibility of bacterial pathogens calls for novel antimicrobial therapies. Traditional screening pathways based on drug-target interaction have gradually reached the stage of diminishing returns. Thus, novel strategies are urgently needed in the fight against antibiotic-refractory bacteria, particularly for tolerant bacteria. Recently, evidence has accumulated demonstrating that microbial changes caused by bacterial metabolic processes significantly modulate antibiotic killing. A better understanding of these bacterial metabolic processes is indicating a need to screen novel metabolic modulators as potential antibiotic adjuvants. In this review, we describe the state of our current knowledge about how these bacterial metabolism-inspired molecules affect antibiotic efficacy, including potentiation and inhibition activity. In addition, the challenges faced and prospects for bringing them into clinic are also discussed. These examples may provide candidates or targets for the development of novel antibiotic adjuvants.

Reduced ROS-mediated antibiotic resistance and its reverting by glucose in Vibrio alginolyticus

Antibiotic-resistant Vibrio alginolyticus poses a big challenge to human health and food safety. It is urgently needed to understand the mechanisms underlying antibiotic resistance to develop effective approaches for the control. Here we explored the metabolic difference between gentamicin-resistant V. alginolyticus (VA-R_GEN ) and gentamicin-sensitive V. alginolyticus (VA-S), and found that the reactive oxygen species (ROS) generation was altered. Compared with VA-S, the ROS content in VA-R_GEN was reduced due to the decreased generation and increased breakdown of ROS. The decreased production of ROS was attributed to the decreased central carbon metabolism, which is associated with the resistance to gentamicin. As such a mechanism, we exogenously administrated VA-R_GEN with the glucose that activated the central carbon metabolism and promoted the generation of ROS, but decreased the breakdown of ROS in VA-R_GEN . The gentamicin-mediated killing was increased with the elevation of the ROS level by a synergistic effect between gentamicin and exogenous glucose. The synergistic effect was inhibited by thiourea, a scavenger of ROS. These results reveal a reduced ROS-mediated antibiotic resistance mechanism and its reversal by exogenous glucose.

Metabolic modulation of redox state confounds fish survival against Vibrio alginolyticus infection

Vibrio alginolyticus threatens both humans and marine animals, but hosts respond to V. alginolyticus infection is not fully understood. Here, functional metabolomics was adopted to investigate the metabolic differences between the dying and surviving zebrafish upon V. alginolyticus infection. Tryptophan was identified as the most crucial metabolite, whose abundance was decreased in the dying group but increased in the survival group as compared to control group without infection. Concurrently, the dying zebrafish displayed excessive immune response and produced higher level of reactive oxygen species (ROS). Interestingly, exogenous tryptophan reverted dying rate through metabolome re‐programming, thereby enhancing the survival from V. alginolyticus infection. It is preceded by the following mechanism: tryptophan fluxed into the glycolysis and tricarboxylic acid cycle (TCA cycle), promoted adenosine triphosphate (ATP) production and further increased the generation of NADPH. Meanwhile, tryptophan decreased NADPH oxidation. These together ameliorate ROS, key molecules in excessive immune response. This is further supported by the event that the inhibition of pyruvate metabolism and TCA cycle by inhibitors decreased D. reiro survival. Thus, our data indicate that tryptophan is a key metabolite for the host to fight against V. alginolyticus infection, representing an alternative strategy to treat bacterial infection in an antibiotic‐independent way.

The depressed P cycle contributes to the acquisition of ampicillin resistance in Edwardsiella piscicida

Antibiotic-resistant bacteria are an increasingly serious threat to human health and aquaculture. To further explore bacterial antibiotic resistance mechanism, iTRAQ is used to identify a differential proteome in ampicillin-resistant LTB4 (LTB4-R_AMP), a strain of Edwardsiella piscicida. A total of 102 differentially proteins with 50 upregulation and 52 downregulation are identified. Since many of these changes are related to metabolism, interactive pathways explorer(iPath) is used to understand a global differentially metabolic response in LTB4-R_AMP. This analysis identifies a global depressed metabolic modulation as the most characteristic feature of LTB4-R_AMP. Lower membrane potential and ATP in LTB4-R_AMP than control support that the central carbon metabolism and energy metabolism are reduced. Since the pyruvate cycle (the P cycle) plays a key role in the central carbon metabolism and energy metabolism, further investigation focuses on the P cycle and shows that expression of genes and activity of enzymes in the P cycle are decreased in LTB4-R_AMP. These results support the conclusion that the depressed P cycle contributes to the acquisition of ampicillin resistance in E.piscicida. These findings indicate that the combination of proteomics and iPath analysis can provide a global metabolic profile, which helps us better understand the correlation between ampicillin resistance and cellular metabolism. SIGNIFICANCE: The present study uses iTRAQ to explore ampicillin resistance mechanism in Edwardsiella piscicida and finds many of these differential abundances of proteins are related to metabolism. IPath further identifies a global depressed metabolic modulation and characterizes the reduced pyruvate cycle as the most characteristic feature of the ampicillin-resistant E. piscicida, which is supported by reduced expression of genes and activity of enzymes in the pyruvate cycle. Consisitently, lower membrane potential and ATP are detetced. These results reveal the metabolic mechanism of ampicillin resistance and provide a solid proof to revert the resistance by reprogramming metabolomics.

Proteomics approach to understand bacterial antibiotic resistance strategies

Introduction: The understanding of novel antibiotic resistance mechanisms is essential to develop strategies against antibiotic-resistant pathogens, which has become an urgent task due to the worldwide emergence of antibiotic resistance. Areas covered: In this review, the authors summarize the recent progress on antibiotic resistance caused by lab-evolved bacteria and clinical multidrug-resistant bacterial pathogens from the proteomics perspective. Expert opinion: Proteomics provides a new platform for a comprehensive understanding of change in protein pathways that are engaged in antibiotics resistance, which is different from a genetic view that focuses on the role of an individual gene or protein. Further work is required to understand why and how the involved pathways are integrated for surviving antibiotic-mediated killing, to use other OMICs for better comprehension of antibiotic resistance mechanisms, and to develop reprogramming proteomics, which reverts an 'antibiotic resistance proteome' to an 'antibiotic sensitive or antibiotic sensitive-like' proteome, for the control of antibiotic-resistant pathogens.

Glucose-Induced Cyclic Lipopeptides Resistance in Bacteria via ATP Maintenance through Enhanced Glycolysis

Cyclic lipopeptide (CLP) antibiotics have a mechanism that causes membrane malfunction. Thus mechanisms of bacterial resistance to CLPs are thought to modify cell surfaces. However, we found that bacterial resistance to CLPs was strongly related to energy metabolism. Using polymyxin B (PB) as a model of CLPs, we showed that PB causes malfunction of respiration and serious depletion of ATP, contributing to PB-induced cell death and carbon starvation. Glucose addition could maintain the intracellular ATP level and reverse the carbon starvation response resulting from PB treatment. Another study revealed that glycolysis was stimulated by the presence of PB and glucose. The mechanism underlying glucose-enabled CLPs' resistance suggests that glucose could maintain the ATP level in PB-treated bacteria by enhancing glycolysis. Similar results were observed in Staphylococcus aureus, where daptomycin resistance was enhanced by glucose. These findings provide insight into the mode of action of CLPs and resistance to these antibiotics.

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Glucose induces the drug resistance to CLPs

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CLPs significantly inhibit energy metabolism and result in ATP depletion

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Glucose maintains the intracellular ATP level in CLP-treated bacteria

Elevated biosynthesis of palmitic acid is required for zebrafish against Edwardsiella tarda infection

Mechanisms by which vaccines enhance immunity to combat bacterial pathogens are not fully understood. Recently, we have found that live Edwardsiella tarda vaccine enhances ability against the bacterial challenge by metabolic modulation in zebrafish. Here we first explored the metabolic modulation promoted by inactivated E. tarda to eliminate the pathogen. Inactivated E. tarda vaccine modulated a similar metabolome to combat with the pathogen in zebrafish as live E. tarda vaccine did. Specifically, both vaccines promoted biosynthesis of unsaturated fatty acids and the TCA cycle. However, due to relatively higher activated TCA cycle in inactivated vaccine than live vaccine, live vaccine promoted higher abundance of palmitate than inactivated vaccine. Consistently, the protection against E. tarda challenge was palmitate dose-dependent. Live vaccine activated higher expression of IL-1β, IL-8,Cox-2 genes and lower expression of IL-15, IL-21 genes than inactivated vaccine, which is similar to the results stimulated by high and low doses of palmitate, respectively. These findings indicate live and inactivated E. tarda vaccines stimulate differential abundances of palmitate that contribute to differential innate immunities against bacterial infection. Thus, metabolic environment contributes to immune response.

Comparative metabolomics shows the metabolic profiles fluctuate in multi-drug resistant Escherichia coli strains

In this study, two susceptible strains and two multi-drug resistant clinical Escherichia coli strains were obtained by Kirby-Bauer method, and then a GC-MS-based metabolomics method was used to compare the differential expression of metabolites between two drug sensitive (CK1 and CK2) and two multidrug-resistant (MDR1 and MDR2) clinical strains of E. coli. We characterized a total of 273 metabolites, including 77 commonly altered metabolites, between MDR vs. antibiotic sensitive strains. Interestingly, the PCA score plot clearly discriminated drug sensitive and MDR strains. The following bioinformatics analysis showed that biosynthesis of amino acids, biosynthesis of phenylpropanoids and purine metabolism were commonly enriched in MDR strains. Moreover, microbial metabolism in diverse environments, carbon metabolism，and pyrimidine metabolism pathways were more likely to be enriched MDR1 strain, while ABC transporters, and cysteine and methionine metabolism pathways were enriched in MDR2 strains. The enzyme activities in several involved metabolic pathways were further measured and metabolite candidates were validated by GC-MS-SIM method. These results indicated that antibiotic resistance affects the metabolite profiles of bacteria. In general, our study provides evidence on the study and prediction of MDR characteristics and mechanisms in bacteria at the metabolite level. BIOLOGICAL SIGNIFICANCE: Overuse and abuse of antibiotics has led to the emergence of antibiotic-resistant strains of bacteria; however, relatively little is known about their resistance mechanisms. In this study, metabolomics method was used to compare the differential expression of metabolites between sensitive and multidrug-resistant clinical strains of E. coli. Results show that the PCA score plot clearly discriminated sensitive and MDR strains, indicating that they had different metabolic profiles. Further, bioinformatics analysis showed that biosynthesis of amino acids, biosynthesis of phenylpropanoids and purine metabolism may be related to resistance. Finally, the enzyme activities in several involved metabolic pathways were further measured and metabolite candidates were validated by GC-MS-SIM method. In general, our study provides evidence on the study and prediction of MDR characteristics and mechanisms in bacteria at the metabolite level.

Glycine, serine and threonine metabolism confounds efficacy of complement-mediated killing

Serum resistance is a poorly understood but common trait of some difficult-to-treat pathogenic strains of bacteria. Here, we report that glycine, serine and threonine catabolic pathway is down-regulated in serum-resistant Escherichia coli, whereas exogenous glycine reverts the serum resistance and effectively potentiates serum to eliminate clinically-relevant bacterial pathogens in vitro and in vivo. We find that exogenous glycine increases the formation of membrane attack complex on bacterial membrane through two previously unrecognized regulations: 1) glycine negatively and positively regulates metabolic flux to purine biosynthesis and Krebs cycle, respectively. 2) α-Ketoglutarate inhibits adenosine triphosphate synthase, which in together promote the formation of cAMP/CRP regulon to increase the expression of complement-binding proteins HtrE, NfrA, and YhcD. The results could lead to effective strategies for managing the infection with serum-resistant bacteria, an especially valuable approach for treating individuals with weak acquired immunity but a normal complement system.

Serum-resistant bacteria can escape complement killing in the bloodstream. Here, using metabolomics and metabolite perturbations, the authors describe an altered metabolic state in serum-resistant Escherichia coli and show that exogenous glycine potentiates elimination of pathogenic bacteria in vivo.

Antimicrobial Tolerance and Metabolic Adaptations in Microbial Biofilms

Active bacterial metabolism is a prerequisite for optimal activity of many classes of antibiotics. Hence, bacteria have developed strategies to reduce or modulate metabolic pathways to become tolerant. This review describes the tight relationship between metabolism and tolerance in bacterial biofilms, and how physicochemical properties of the microenvironment at the host-pathogen interface (such as oxygen and nutritional content) are key to this relationship. Understanding how metabolic adaptations lead to tolerance brings us to novel approaches to tackle antibiotic-tolerant biofilms. We describe the use of hyperbaric oxygen therapy, metabolism-stimulating metabolites, and alternative strategies to redirect bacterial metabolism towards an antibiotic-susceptible phenotype.

Comparative Extracellular Proteomics of Aeromonas hydrophila Reveals Iron-Regulated Secreted Proteins as Potential Vaccine Candidates

In our previous study, several iron-related outer membrane proteins in Aeromonas hydrophila, a serious pathogen of farmed fish, conferred high immunoprotectivity to fish, and were proposed as potential vaccine candidates. However, the protective efficacy of these extracellular proteins against A. hydrophila remains largely unknown. Here, we identified secreted proteins that were differentially expressed in A. hydrophila LP-2 in response to iron starvation using an iTRAQ-based quantitative proteomics method. We identified 341 proteins, of which 9 were upregulated in response to iron starvation and 24 were downregulated. Many of the differently expressed proteins were associated with protease activity. We confirmed our proteomics results with Western blotting and qPCR. We constructed three mutants by knocking out three genes encoding differentially expressed proteins (Δorf01830, Δorf01609, and Δorf03641). The physiological characteristics of these mutants were investigated. In all these mutant strains, protease activity decreased, and Δorf01609, and Δorf01830 were less virulent in zebrafish. This indicated that the proteins encoded by these genes may play important roles in bacterial infection. We next evaluated the immune response provoked by the six iron-related recombinant proteins (ORF01609, ORF01830, ORF01839, ORF02943, ORF03355, and ORF03641) in zebrafish as well as the immunization efficacy of these proteins. Immunization with these proteins significantly increased the zebrafish immune response. In addition, the relative percent survival (RPS) of the immunized zebrafish was 50-80% when challenged with three virulent A. hydrophila strains, respectively. Thus, these extracellular secreted proteins might be effective vaccine candidates against A. hydrophila infection in fish.

Metabolic mechanism of ceftazidime resistance in Vibrio alginolyticus

Background

Microbial metabolism confounds antibiotic efficacy. However, information regarding effect of metabolism on cephalosporin antibiotics-mediated killing and Vibrio spp is largely absence, although the drugs are widely used in clinic and the bacteria are pathogens to both human and aquaculture animals.

Purpose

This study explores the metabolome of cephalosporin antibiotic-resistant Vibrio alginolyticus and analyzes the role of bacterial metabolism in drug and multidrug-resistance.

Results

The metabolomes of isogenic ceftazidime-resistant V. alginolyticus (VA-R_CAZ) and ceftazidime-sensitive V. alginolyticus (VA-S) were analyzed using gas chromatography -mass spectrometry. The metabolome of VA-R_CAZ is characterized by inefficient respiration, an inefficient pyruvate cycle (P cycle), increased biosynthesis of fatty acids and decreased membrane proton motive force. This hypothesis was confirmed by the fact that furfural and malonate, inhibitors of pyruvate dehydrogenase and succinate dehydrogenase (P cycle enzymes), respectively, increased resistance of VA-R_CAZ to antibiotics, while exposure to triclosan, to inhibit biosynthesis of fatty acids, decreased resistance.

Conclusion

These results contribute to our understanding of mechanisms of bacterial antibiotic-resistance and may lead to more effective approaches to treat, manage or prevent infections caused by antibiotic-resistant pathogens including those of the Vibrio species.