Oxidative stress induction of the MexXY multidrug efflux genes and promotion of aminoglycoside resistance development in Pseudomonas aeruginosa

Pyrite from acid mine drainage promotes the removal of antibiotic resistance genes and mobile genetic elements in karst watershed with abundant calcium carbonate

More information is needed to fully comprehend how acid mine drainage (AMD) affects the phototransformation of antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARGs) in karst water and sewage-irrigated farmland soil with abundant carbonate rocks (CaCO3) due to increasing pollution of AMD formed from pyrite (FeS2). The results showed FeS2 accelerated the inactivation of ARB with an inactivation of 8.7 log. Notably, extracellular and intracellular ARGs and mobile genetic elements (MGEs) also experienced rapid degradation. Additionally, the pH of the solution buffered by CaCO3 significantly influenced the photo-inactivation of ARB. The Fe2+ in neutral solution was present in Fe(II) coordination with strong reducing potential and played a crucial role in generating •OH (7.0 μM), which caused severe damage to ARB, ARGs, and MGEs. The •OH induced by photo-Fenton of FeS2 posed pressure to ARB, promoting oxidative stress response and increasing generation of reactive oxygen species (ROS), ultimately damaging cell membranes, proteins and DNA. Moreover, FeS2 contributed to a decrease in MIC of ARB from 24 mg/L to 4 mg/L. These findings highlight the importance of AMD in influencing karst water and sewage-irrigated farmland soil ecosystems. They are also critical in advancing the utilization of FeS2 to inactivate pathogenic bacteria.

Response mechanisms of resistance in L-form bacteria to different target antibiotics: Implications from oxidative stress to metabolism

Due to the specific action on bacterial cell wall, β-lactam antibiotics have gained widespread usage as they exhibit a high degree of specificity in targeting bacteria, but causing minimal toxicity to host cells. Under antibiotic pressure, bacteria may opt to shed their cell walls and transform into L-form state as a means to evade the antibiotic effects. In this study, we explored and identified diverse optimal conditions for both Gram-negative bacteria (E. coli DH5α (CTX)) and Gram-positive bacteria (B. subtilis ATCC6633), which were induced to L-form bacteria using lysozyme (0.5 ppm) and meropenem (64 ppm). Notably, when bacteria transformed into L-form state, both bacterial strains showed varying degrees of increased resistance to antibiotics polymyxin E, meropenem, rifampicin, and tetracycline. E. coli DH5α (CTX) exhibited the most significant enhancement in resistance to tetracycline, with a 128-fold increase, while B. subtilis ATCC6633 showed a 32-fold increase in resistance to tetracycline and polymyxin E. Furthermore, L-form bacteria maintained their normal metabolic activity, combined with enhanced oxidative stress, served as an adaptive strategy promoting the sustained survival of L-form bacteria. This study provided a theoretical basis for comprehending antibiotic resistance mechanisms, developing innovative treatment strategies, and confronting global antibiotic resistance challenges.

Antibiotic influx and efflux in Pseudomonas aeruginosa: Regulation and therapeutic implications

Pseudomonas aeruginosa is a notorious multidrug-resistant pathogen that poses a serious and growing threat to the worldwide public health. The expression of resistance determinants is exquisitely modulated by the abundant regulatory proteins and the intricate signal sensing and transduction systems in this pathogen. Downregulation of antibiotic influx porin proteins and upregulation of antibiotic efflux pump systems owing to mutational changes in their regulators or the presence of distinct inducing molecular signals represent two of the most efficient mechanisms that restrict intracellular antibiotic accumulation and enable P. aeruginosa to resist multiple antibiotics. Treatment of P. aeruginosa infections is extremely challenging due to the highly inducible mechanism of antibiotic resistance. This review comprehensively summarizes the regulatory networks of the major porin proteins (OprD and OprH) and efflux pumps (MexAB-OprM, MexCD-OprJ, MexEF-OprN, and MexXY) that play critical roles in antibiotic influx and efflux in P. aeruginosa. It also discusses promising therapeutic approaches using safe and efficient adjuvants to enhance the efficacy of conventional antibiotics to combat multidrug-resistant P. aeruginosa by controlling the expression levels of porins and efflux pumps. This review not only highlights the complexity of the regulatory network that induces antibiotic resistance in P. aeruginosa but also provides important therapeutic implications in targeting the inducible mechanism of resistance.

Enhanced Antimicrobial Activity through Synergistic Effects of Cold Atmospheric Plasma and Plant Secondary Metabolites: Opportunities and Challenges

The emergence of antibiotic resistant microorganisms possesses a great threat to human health and the environment. Considering the exponential increase in the spread of antibiotic resistant microorganisms, it would be prudent to consider the use of alternative antimicrobial agents or therapies. Only a sustainable, sustained, determined, and coordinated international effort will provide the solutions needed for the future. Plant secondary metabolites show bactericidal and bacteriostatic activity similar to that of conventional antibiotics. However, to effectively eliminate infection, secondary metabolites may need to be activated by heat treatment or combined with other therapies. Cold atmospheric plasma therapy is yet another novel approach that has proven antimicrobial effects. In this review, we explore the physiochemical mechanisms that may give rise to the improved antimicrobial activity of secondary metabolites when combined with cold atmospheric plasma therapy.

Light-Based Anti-Biofilm and Antibacterial Strategies

Biofilm formation and antimicrobial resistance pose significant challenges not only in clinical settings (i.e., implant-associated infections, endocarditis, and urinary tract infections) but also in industrial settings and in the environment, where the spreading of antibiotic-resistant bacteria is on the rise. Indeed, developing effective strategies to prevent biofilm formation and treat infections will be one of the major global challenges in the next few years. As traditional pharmacological treatments are becoming inadequate to curb this problem, a constant commitment to the exploration of novel therapeutic strategies is necessary. Light-triggered therapies have emerged as promising alternatives to traditional approaches due to their non-invasive nature, precise spatial and temporal control, and potential multifunctional properties. Here, we provide a comprehensive overview of the different biofilm formation stages and the molecular mechanism of biofilm disruption, with a major focus on the quorum sensing machinery. Moreover, we highlight the principal guidelines for the development of light-responsive materials and photosensitive compounds. The synergistic effects of combining light-triggered therapies with conventional treatments are also discussed. Through elegant molecular and material design solutions, remarkable results have been achieved in the fight against biofilm formation and antibacterial resistance. However, further research and development in this field are essential to optimize therapeutic strategies and translate them into clinical and industrial applications, ultimately addressing the global challenges posed by biofilm and antimicrobial resistance.

Drug resistance and physiological roles of RND multidrug efflux pumps in Salmonella enterica, Escherichia coli and Pseudomonas aeruginosa

Drug efflux pumps transport antimicrobial agents out of bacteria, thereby reducing the intracellular antimicrobial concentration, which is associated with intrinsic and acquired bacterial resistance to these antimicrobials. As genome analysis has advanced, many drug efflux pump genes have been detected in the genomes of bacterial species. In addition to drug resistance, these pumps are involved in various essential physiological functions, such as bacterial adaptation to hostile environments, toxin and metabolite efflux, biofilm formation and quorum sensing. In Gram-negative bacteria, efflux pumps in the resistance–nodulation–division (RND) superfamily play a clinically important role. In this review, we focus on Gram-negative bacteria, including Salmonella enterica , Escherichia coli and Pseudomonas aeruginosa , and discuss the role of RND efflux pumps in drug resistance and physiological functions.

Identification of a Czc-like operon of the periodontal pathobiont P. gingivalis involved in metal ion efflux

OBJECTIVE

The study aimed to investigate the role of the PGN2012 gene of the periodontitis contributing pathobiont Porphyromonas gingivalis. PGN2012 is a homolgue of TolC and is a gene our group previously showed was overexpressed in hyperinvasive cells.

METHODS

The study used a combination of bioinformatics, knockout mutagenesis, growth experiments, biofilm assays and human cell invation assays to investigate PGN2012 function.

RESULTS

Bioinformatics identified that PGN2012 is part of one of four TolC containing gene loci in P. gingivalis that we predicted may encode a metal resistance RND family tripartite pump, similar to those present in other Gram-negative bacteria, but which are not well understood in anaerobic bacteria. A ΔPGN2012 deletion displayed slightly reduced growth in liquid culture but did not effect biofilm formation or human cell invasion. When metal ions were included in the medium the mutant displayed significantly increased sensitivity to the divalent metal ions Zn²⁺ (500 μM), Co²⁺ (2 mM), and Cd²⁺(0.1 mM) but not Cu²⁺.

CONCLUSIONS

We propose to rename the PGN2012-2014 genes czcCBA, which we suggest plays a role in intracellular stress resistance where zinc is often employed by host cells in antibacterial defence with implications for chronic infection in humans.

Functional Characterization of TetR-like Transcriptional Regulator PA3973 from Pseudomonas aeruginosa

Pseudomonas aeruginosa, a human opportunistic pathogen, is a common cause of nosocomial infections. Its ability to survive under different conditions relies on a complex regulatory network engaging transcriptional regulators controlling metabolic pathways and capabilities to efficiently use the available resources. P. aeruginosa PA3973 encodes an uncharacterized TetR family transcriptional regulator. In this study, we applied a transcriptome profiling (RNA-seq), genome-wide identification of binding sites using ChIP-seq, as well as the phenotype analyses to unravel the biological role of PA3973. Transcriptional profiling of P. aeruginosa PAO1161 overexpressing PA3973 showed changes in the mRNA level of 648 genes. Concomitantly, ChIP-seq analysis identified more than 300 PA3973 binding sites in the P. aeruginosa genome. A 13 bp sequence motif was indicated as the binding site of PA3973. The PA3973 regulon encompasses the PA3972-PA3971 genes encoding a probable acyl-CoA dehydrogenase and a thioesterase. In vitro analysis showed PA3973 binding to PA3973p. Accordingly, the lack of PA3973 triggered increased expression of PA3972 and PA3971. The ∆PA3972-71 PAO1161 strain demonstrated impaired growth in the presence of stress-inducing agents hydroxylamine or hydroxyurea, thus suggesting the role of PA3972-71 in pathogen survival upon stress. Overall our results showed that TetR-type transcriptional regulator PA3973 has multiple binding sites in the P. aeruginosa genome and influences the expression of diverse genes, including PA3972-PA3971, encoding proteins with a proposed role in stress response.

New Multidrug Efflux Systems in a Microcystin-Degrading Bacterium Blastomonas fulva and Its Genomic Feature

A microcystin-degrading bacterial strain, Blastomonas fulva T2, was isolated from the culture of a microalgae Microcystis. The strain B. fulva T2 is Gram-stain-negative, non-motile, aerobic, non-spore-forming and phototrophic. The cells of B. fulva T2 are able to grow in ranges of temperature from 15 to 37 °C, with a pH of 6 to 8 and a salinity of 0 to 1% NaCl. Here, we sequenced the complete genome of B. fulva T2, aiming to better understand the evolutionary biology and the function of the genus Blastomonas at the molecular level. The complete genome of B. fulva T2 contained a circular chromosome (3,977,381 bp) with 64.3% GC content and a sizable plasmid (145.829 bp) with 60.7% GC content which comprises about 3.5% of the total genetic content. A total of 3842 coding genes, including 46 tRNAs and 6 rRNAs, were predicted in the genome. The genome contains genes for glycolysis, citric acid cycle, Entner–Doudoroff pathways, photoreaction center and bacteriochlorophylla synthesis. A 7.9 K gene cluster containing mlrA, mlrB, mlrC and mlrD_1,2,3,4 of microcystin-degrading enzymes was identified. Notably, eight different efflux pumps categorized into RND, ABC and MFS types have been identified in the genome of strain T2. Our findings should provide new insights of the alternative reaction pathway as well as the enzymes which mediated the degradation of microcystin by bacteria, as well as the evolution, architectures, chemical mechanisms and physiological roles of the new bacterial multidrug efflux system.

Response mechanisms of different antibiotic-resistant bacteria with different resistance action targets to the stress from photocatalytic oxidation

The stress response of antibiotic-resistant bacteria (ARB) and the spread of antibiotic resistance genes (ARGs) pose a serious threat to the aquatic environment and human beings. This study mainly explored the effect of the heterogeneous photocatalytic oxidation (UVA-TiO₂ system) on the stress response mechanism of ARB with different antibiotic resistance action targets, including the cell wall, proteins, DNA, RNA, folate and the cell membrane. Results indicate that the stress response mechanism of tetracycline- and sulfamethoxazole-resistant E. coli DH5α, which targets the synthesis of protein and folate, could rapidly induce global regulators by the overexpression of relative antibiotic resistance action target genes. Different stress response systems were mediated via cross-protection mechanism, causing stronger tolerance to an adverse environment than other ARB. Moreover, the photocatalytic inactivation mechanism of bacterial cells and a graded response of cellular stress mechanism caused differences in the intensity of the stress mechanism of antibiotic resistance action targets. E. coli DH5α resistant to cefotaxime and polymyxin, targeting synthesis of the cell wall and cell membrane, respectively, could confer greater advantages to bacterial survival and higher conjugative transfer frequency than E. coli DH5α resistant to nalidixic acid and rifampicin, which target the synthesis of DNA and RNA, respectively. This new perspective provides detailed information on the practical application of photocatalytic oxidation for inactivating ARB and hampering the spreading of ARGs in the aquatic environment.

Electrochemical flow-through disinfection reduces antibiotic resistance genes and horizontal transfer risk across bacterial species

Antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARGs), as emerging pollutants, are released into environment, increasing the risk of horizontal gene transfer (HGT). However, a limited number of studies quantified the effects of ARB disinfection on the HGT risk. This study investigated the inactivation of E. coli 10667 (sul) and the release and removal of ARGs using an electrochemical flow-through reactor (EFTR). Furthermore, the transfer frequencies and potential mechanisms of HGT after disinfection were explored using non-resistant E. coli GMCC 13373 as the recipient and E. coli DH5α carrying plasmid RP4 as the donor. A threshold of current density (0.25 mA/cm²) was observed to destroy cells and release intracellular ARGs (iARGs) to increase extracellular ARGs (eARGs) concentration. The further increase in the current density to 1 mA/cm² resulted in the decline of eARGs concentration due to the higher degradation rate of eARGs than the release rate of iARGs. The performance of ARGs degradation and HGT frequency by EFTR were compared with those of conventional disinfection processes, including chlorination and ultraviolet radiation (UV). A higher ARGs degradation (83.46%) was observed by EFTR compared with that under chlorination (10.23%) and UV (27.07%). Accordingly, EFTR reduced the HGT frequency (0.69) of released ARGs into the recipient (Forward transfer), and the value was lower than that by chlorination (2.69) and UV (1.73). Meanwhile, the surviving injured E. coli 10667 (sul) with increased cell permeability was transferred by plasmid RP4 from the donor (Reverse transfer) with a higher frequency of 0.33 by EFTR compared with that under chlorination (0.26) and UV (0.16). In addition, the sul3 gene was the least resistant to EFTR than sul1 and sul2 gene. These findings provide important insights into the mechanism of HGT between the injured E. coli 10667 (sul) and environmental bacteria. EFTR is a promising disinfection technology for preventing the spread of antibiotic resistance.

Involvement of the SCO3366 efflux pump from S. coelicolor in rifampicin resistance and its regulation by a TetR regulator

Overexpression of efflux pumps represents a key mechanism of resistance in bacteria. Soil bacteria such as Streptomyces harbour a vast array of efflux genes that are transcriptionally silent under laboratory conditions. However, dissemination of many of these genes into clinical pathogens via horizontal gene transfer results in conferring resistance to multiple drugs. In this study, we have identified the role of a MFS transporter, SCO3366 from Streptomyces coelicolor, in governing multidrug resistance. Overexpression and knockout studies revealed that SCO3366 provides resistance to several structurally unrelated drugs including ciprofloxacin, chloramphenicol, rifampicin and EtBr, with rifampicin being the major substrate. Beyond multidrug resistance, SCO3366 was efficient in providing tolerance towards oxidative stress. A combinatorial mechanism of increased oxidative stress tolerance decreased intracellular drug levels and decreased permeability act synergistically to provide resistance towards rifampicin. Shedding light on the regulation of SCO3366, we find the pump to be directly regulated by the TetR regulator SCO3367 in a negative manner and the repression was found to be relieved in presence of different compounds recognized as substrates of SCO3366. KEY POINTS: • First reported rifampicin efflux pump in Streptomyces coelicolor • Resistance to rifampicin is the result of a synergistic action of increased efflux with increased oxidative stress tolerance and decreased permeability, which can potentially arise in clinically relevant bacteria • SCO3366-SCO3367 to be a novel system that operates to protect the bacteria under varied environmental stress conditions.

Mobility of antibiotic resistance and its co-occurrence with metal resistance in pathogens under oxidative stress

The bacterial communities are challenged with oxidative stress during their exposure to bactericidal antibiotics, metals, and different levels of dissolved oxygen (DO) encountered in diverse environmental habitats. The frequency of antibiotic resistance genes (ARGs) and metal resistance genes (MRGs) co-selection is increased by selective pressure posed by oxidative stress. Hence, study of resistance acquisition is important from an evolutionary perspective. To understand the dependence of oxidative stress on the dissemination of ARGs and MRGs through a pathogenic bacterial population, 12 metagenomes belonging to gut, water and soil habitats were evaluated. The metagenome-wide analysis showed the chicken gut to pose the most diverse pool of ARGs (30.4 ppm) and pathogenic bacteria (Simpson diversity = 0.98). The most common types of resistances found in all the environmental samples were efflux pumps (13.22 ppm) and genes conferring resistance to vancomycin (12.4 ppm), tetracycline (12.1 ppm), or beta-lactam (9.4 ppm) antibiotics. Additionally, limiting DO level in soil was observed to increase the abundance of excision nucleases (uvrA and uvrB), DNA polymerase (polA), catalases (katG), and other oxidative stress response genes (OSGs). This was further evident from major variations occurred in antibiotic efflux genes due to the effect of DO concentration on two human pathogens, namely Salmonella enterica and Shigella sonnei found in all the selected habitats. In conclusion, the microbial community, when challenged with oxidative stress caused by environmental variations in oxygen level, tends to accumulate higher amounts of ARGs with increased dissemination potential through triggering non-lethal mutagenesis. Furthermore, the genetic linkage or co-occurrence of ARGs and MRGs provides evidence for selecting ARGs under high concentrations of heavy metals.

The role of chemotaxis and efflux pumps on nitrate reduction in the toxic regions of a ciprofloxacin concentration gradient

Spatial concentration gradients of antibiotics are prevalent in the natural environment. Yet, the microbial response in these heterogeneous systems remains poorly understood. We used a microfluidic reactor to create an artificial microscopic ecosystem that generates diffusive gradients of solutes across interconnected microenvironments. With this reactor, we showed that chemotaxis toward a soluble electron acceptor (nitrate) allowed Shewanella oneidensis MR-1 to inhabit and sustain metabolic activity in highly toxic regions of the antibiotic ciprofloxacin (>80× minimum inhibitory concentration, MIC). Acquired antibiotic resistance was not observed for cells extracted from the reactor, so we explored the role of transient adaptive resistance by probing multidrug resistance (MDR) efflux pumps, ancient elements that are important for bacterial physiology and virulence. Accordingly, we constructed an efflux pump deficient mutant (∆mexF) and used resistance-nodulation-division (RND) efflux pump inhibitors (EPIs). While batch results showed the importance of RND efflux pumps for microbial survival, microfluidic studies indicated that these pumps were not necessary for survival in antibiotic gradients. Our work contributes to an emerging body of knowledge deciphering the effects of antibiotic spatial heterogeneity on microorganisms and highlights differences of microbial response in these systems versus well-mixed batch conditions.

Oxidative Stress Response in Pseudomonas aeruginosa

Pseudomonas aeruginosa is a Gram-negative environmental and human opportunistic pathogen highly adapted to many different environmental conditions. It can cause a wide range of serious infections, including wounds, lungs, the urinary tract, and systemic infections. The high versatility and pathogenicity of this bacterium is attributed to its genomic complexity, the expression of several virulence factors, and its intrinsic resistance to various antimicrobials. However, to thrive and establish infection, P. aeruginosa must overcome several barriers. One of these barriers is the presence of oxidizing agents (e.g., hydrogen peroxide, superoxide, and hypochlorous acid) produced by the host immune system or that are commonly used as disinfectants in a variety of different environments including hospitals. These agents damage several cellular molecules and can cause cell death. Therefore, bacteria adapt to these harsh conditions by altering gene expression and eliciting several stress responses to survive under oxidative stress. Here, we used PubMed to evaluate the current knowledge on the oxidative stress responses adopted by P. aeruginosa. We will describe the genes that are often differently expressed under oxidative stress conditions, the pathways and proteins employed to sense and respond to oxidative stress, and how these changes in gene expression influence pathogenicity and the virulence of P. aeruginosa. Understanding these responses and changes in gene expression is critical to controlling bacterial pathogenicity and developing new therapeutic agents.

Impact of spent engine oil contamination on the antibiotic resistome of a tropical agricultural soil

Profiling of hydrocarbon-contaminated soils for antibiotic resistance genes (ARGs) is becoming increasingly important due to emerging realities of their preponderance in hydrocarbon-inundated matrices. In this study, the antibiotic resistome of an agricultural soil (1S) and agricultural soil contaminated with spent engine oil (AB1) were evaluated via functional annotation of the open reading frames (ORFs) of their metagenomes using the comprehensive antibiotic database (CARD) and KEGG KofamKOALA. CARD analysis of AB1 metagenome revealed the detection of 24 AMR (antimicrobial resistance) gene families, 66 ARGs, and the preponderance (69.7%) of ARGs responsible for antibiotic efflux in AB1 metagenome. CARD analysis of 1S metagenome revealed four AMR gene families and five ARGs. Functional annotation of the two metagenomes using KofamKOALA showed 171 ARGs in AB1 and 29 ARGs in 1S, respectively. Majority of the detected ARGs in AB1 (121; 70.8%) and 1S (16; 55.2%) using KofamKOALA are responsible for antibiotic efflux while ARGs for other resistance mechanisms were also detected. All the five major antibiotic efflux pump systems were detected in AB1 metagenome, though majority of the ARGs for antibiotic efflux belong to the RND (resistance-nodulation-cell division) and MFS (major facilitator superfamily) efflux systems. Significant differences observed in the ARGs recovered from 1S and AB1 metagenomes were statistically validated (P < 0.05). SEO contamination is believed to be responsible for ARGs increase in AB1 metagenome via mechanisms of cross-resistance especially with efflux pumps. The detection of these ARGs is of great public health concern in this era of multidrug resistant isolates resurgence.

The Effects of Natural Products and Environmental Conditions on Antimicrobial Resistance

Due to the extensive application of antibiotics in medical and farming practices, the continued diversification and development of antimicrobial resistance (AMR) has attracted serious public concern. With the emergence of AMR and the failure to treat bacterial infections, it has led to an increased interest in searching for novel antibacterial substances such as natural antimicrobial substances, including microbial volatile compounds (MVCs), plant-derived compounds, and antimicrobial peptides. However, increasing observations have revealed that AMR is associated not only with the use of antibacterial substances but also with tolerance to heavy metals existing in nature and being used in agriculture practice. Additionally, bacteria respond to environmental stresses, e.g., nutrients, oxidative stress, envelope stress, by employing various adaptive strategies that contribute to the development of AMR and the survival of bacteria. Therefore, we need to elucidate thoroughly the factors and conditions affecting AMR to take comprehensive measures to control the development of AMR.

Roles of FadRACB system in formaldehyde detoxification, oxidative stress alleviation and antibiotic susceptibility in Stenotrophomonas maltophilia

BACKGROUND

Formaldehyde toxicity is invariably stressful for microbes. Stenotrophomonas maltophilia, a human opportunistic pathogen, is widely distributed in different environments and has evolved an array of systems to alleviate various stresses.

OBJECTIVES

To characterize the role of the formaldehyde detoxification system FadRACB of S. maltophilia in formaldehyde detoxification, oxidative stress alleviation and antibiotic susceptibility.

METHODS

Presence of the fadRACB operon was verified by RT-PCR. Single or combined deletion mutants of the fadRACB operon were constructed for functional assays. Formaldehyde, menadione and quinolone susceptibilities were assessed by observing cell viability in formaldehyde-, menadione- and quinolone-containing media, respectively. Susceptibility to hydrogen peroxide was evaluated by disc diffusion assay. The agar dilution method was used to assess bacterial antibiotic susceptibilities. Expression of fadRACB was assessed by quantitative RT-PCR.

RESULTS

The fadR, fadA, fadC and fadB genes were arranged in an operon. Mutants of fadA and/or fadB were more susceptible to formaldehyde and oxidative stress than the WT KJ strain of S. maltophilia. No significant difference was observed in the ability of a fadC single mutant to ameliorate formaldehyde and oxidative stress; however, simultaneous inactivation of fadA, fadB and fadC further enhanced susceptibility to formaldehyde and oxidative stress. In addition, compared with WT KJ, the triple mutant KJΔFadACB was more susceptible to quinolones and more resistant to aminoglycosides. FadR functions as a repressor for the fadRACB operon. The FadRACB operon has moderate expression in aerobically grown WT KJ and is further derepressed by formaldehyde challenge or oxidative stress, but not by antibiotics.

CONCLUSIONS

The FadACB system contributes to mitigation of formaldehyde toxicity and oxidative stress and cross-protects S. maltophilia from quinolones.

Role of AzoR, a LysR-type transcriptional regulator, in SmeVWX pump-mediated antibiotic resistance in Stenotrophomonas maltophilia

BACKGROUND

The SmeVWX efflux pump of Stenotrophomonas maltophilia contributes to menadione (MD) tolerance and resistance to chloramphenicol, quinolones and tetracycline. The components of the SmeVWX efflux pump are encoded by a five-gene operon, smeU1VWU2X. We have previously demonstrated that the smeU1VWU2X operon is intrinsically unexpressed and inducibly expressed by MD via a SoxR- and SmeRv-involved regulatory circuit in S. maltophilia KJ. We also inferred that there should be other regulator(s) involved in MD-mediated smeU1VWU2X expression in addition to SoxR and SmeRv.

OBJECTIVES

To identify novel regulator(s) involved in the regulation of MD-mediated smeU1VWU2X expression and elucidate the regulatory circuit.

METHODS

A possible regulator candidate involved in the regulation of MD-mediated smeU1VWU2X expression was identified by a homologue search using the helix-turn-helix domain of SmeRv as a query. Gene expression was assessed using the promoter-xylE transcriptional fusion assay and quantitative RT-PCR. The impact of the regulator on SmeVWX pump-mediated functions was investigated via mutant construction and functional tests (antibiotic susceptibility and MD tolerance).

RESULTS

AzoR (Smlt3089), a LysR-type transcriptional regulator, was investigated. In unstressed logarithmically grown cells, AzoR was abundantly expressed and functioned as a repressor, inhibiting the expression of the smeU1VWU2X operon. MD challenge attenuated azoR expression, thus derepressing the expression of the smeU1VWU2X operon in S. maltophilia KJ. AzoR down-regulation-mediated smeU1VWU2X expression was observed in quinolone-resistant and SmeVWX-overexpressing S. maltophilia clinical isolates.

CONCLUSIONS

AzoR negatively regulates the expression of the smeU1VWU2X operon and SmeVWX pump-mediated antibiotic resistance in S. maltophilia.

Overexpression of the MexXY Multidrug Efflux System Correlates with Deficient Pyoverdine Production in Pseudomonas aeruginosa

Multidrug-resistant Pseudomonas aeruginosa poses a serious problem due to hospital- and healthcare-associated infections. A major drug resistance mechanism of P. aeruginosa involves active efflux via resistance nodulation cell division (RND)-type multidrug efflux pumps of which MexXY is increasingly recognized as a primary determinant of aminoglycoside resistance in P. aeruginosa. MexXY overexpression is often observed in drug-resistant P. aeruginosa clinical isolates. MexXY deficiency increased pyoverdine production in all four P. aeruginosa strains we tested. MexXY-overproducing multidrug-resistant P. aeruginosa PA7 exhibited the greatest effect among the strains. Complementation with a MexXY-expressing plasmid restored low-level pyoverdine production in a MexXY-deficient P. aeruginosa mutant from PA7, indicating that MexXY expression decreases pyoverdine production. Because P. aeruginosa produces pyoverdine to acquire iron, MexXY-deficient mutants might be more susceptible to iron deficiency than MexXY-producing strains or might require extra iron. High-risk clones of multidrug-resistant P. aeruginosa reportedly tend to be MexXY overproducers but defective pyoverdine producers. This study suggests that P. aeruginosa reduces production of a virulence factor after acquiring a drug resistance factor.

Antimicrobial and biofilm-disrupting nanostructured TiO2 coating demonstrating photoactivity and dark activity

Antimicrobial materials are tools used to reduce the transmission of infectious microorganisms. Photo-illuminated titania (TiO2) is a known antimicrobial material. Used as a coating on door handles and similar surfaces, it may reduce viability and colonization by pathogens and limit their spread. We tested the survival of Escherichia coli, Pseudomonas aeruginosa, Staphylococcus aureus and Saccharomyces cerevisiae on a nano-structured TiO2-based thin film, called 'NsARC', and on stainless steel under a variety of light wavelengths and intensities. There was significantly less survival (P <0.001) of all the organisms tested on NsARC compared to inert uncoated stainless steel under all conditions. NsARC was active in the dark and possible mechanisms for this are suggested. NsARC inhibited biofilm formation as confirmed by scanning electron microscopy. These results suggest that NsARC can be used as a self-cleaning and self-sterilizing antimicrobial surface coating for the prevention and reduction in the spread of potentially infectious microbes.

Physiological Functions of Bacterial "Multidrug" Efflux Pumps

Bacterial multidrug efflux pumps have come to prominence in human and veterinary pathogenesis because they help bacteria protect themselves against the antimicrobials used to overcome their infections. However, it is increasingly realized that many, probably most, such pumps have physiological roles that are distinct from protection of bacteria against antimicrobials administered by humans. Here we undertake a broad survey of the proteins involved, allied to detailed examples of their evolution, energetics, structures, chemical recognition, and molecular mechanisms, together with the experimental strategies that enable rapid and economical progress in understanding their true physiological roles. Once these roles are established, the knowledge can be harnessed to design more effective drugs, improve existing microbial production of drugs for clinical practice and of feedstocks for commercial exploitation, and even develop more sustainable biological processes that avoid, for example, utilization of petroleum.

Decreased Antibiotic Susceptibility in Pseudomonas aeruginosa Surviving UV Irradition

Given its excellent performance against the pathogens, UV disinfection has been applied broadly in different fields. However, only limited studies have comprehensively investigated the response of bacteria surviving UV irradiation to the environmental antibiotic stress. Here, we investigated the antibiotic susceptibility of Pseudomonas aeruginosa suffering from the UV irradiation. Our results revealed that UV exposure may decrease the susceptibility to tetracycline, ciprofloxacin, and polymyxin B in the survival P. aeruginosa. Mechanistically, UV exposure causes oxidative stress in P. aeruginosa and consequently induces dysregulation of genes contributed to the related antibiotic resistance genes. These results revealed that the insufficient ultraviolet radiation dose may result in the decreased antibiotic susceptibility in the pathogens, thus posing potential threats to the environment and human health.

Over-Expression of Hypochlorite Inducible Major Facilitator Superfamily (MFS) Pumps Reduces Antimicrobial Drug Susceptibility by Increasing the Production of MexXY Mediated by ArmZ in Pseudomonas aeruginosa

Pseudomonas aeruginosa, a well-known cause of nosocomial infection, is frequently antibiotic resistant and this complicates treatment. Links between oxidative stress responses inducing antibiotic resistance through over-production of RND-type efflux pumps have been reported in P. aeruginosa, but this has not previously been associated with MFS-type efflux pumps. Two MFS efflux pumps encoded by mfs1 and mfs2 were selected for study because they were found to be sodium hypochlorite (NaOCl) inducible. Antibiotic susceptibility testing was used to define the importance of these MFS pumps in antibiotic resistance and proteomics was used to characterize the resistance mechanisms involved. The results revealed that mfs1 is NaOCl inducible whereas mfs2 is NaOCl, N-Ethylmaleimide and t-butyl hydroperoxide inducible. Deletion of mfs1 or mfs2 did not affect antibiotic or paraquat susceptibility. However, over-production of Mfs1 and Mfs2 reduced susceptibility to aminoglycosides, quinolones, and paraquat. Proteomics, gene expression analysis and targeted mutagenesis showed that over-production of the MexXY RND-type efflux pump in a manner dependent upon armZ, but not amgRS, is the cause of reduced antibiotic susceptibility upon over-production of Mfs1 and Mfs2. mexXY operon expression analysis in strains carrying various lengths of mfs1 and mfs2 revealed that at least three transmembrane domains are necessary for mexXY over-expression and decreased antibiotic susceptibility. Over-expression of the MFS-type efflux pump gene tetA(C) did not give the same effect. Changes in paraquat susceptibility were independent of mexXY and armZ suggesting that it is a substrate of Mfs1 and Mfs2. Altogether, this is the first evidence of cascade effects where the over-production of an MFS pump causes over-production of an RND pump, in this case MexXY via increased armZ expression.

Transcriptomics Uncovers the Response of Anammox Bacteria to Dissolved Oxygen Inhibition and the Subsequent Recovery Mechanism

Understanding the recovery of anaerobic ammonium-oxidizing (anammox) bacteria after inhibition by dissolved oxygen (DO) is critical for the successful applications of anammox-based processes. Therefore, the effects of oxygen exposure (2 mg L^-1 DO for 90 min) and subsequent recovery treatments [N₂ purging or nano zero-valent iron (nZVI) addition] on the activity and gene expression in a Kuenenia stuttgartiensis enrichment culture were examined. Combining the self-organizing map clustering and enrichment analysis, we proposed the oxidative stress response of anammox bacteria based on the existing concepts of oxidative stress in microbes: the DO exposure triggered a stringent response in K. stuttgartiensis, which downregulated the transcription levels of genes involved in the central metabolism and diverted energy to a flagellar assembly and metal transport modules; these changes possibly promoted survival during the inhibition of anammox activity. According to the cotranscription with central catabolism genes, putative reactive oxygen species (ROS) scavenger genes (kat and sod) were presumed to detoxify the anammox intermediates rather than ROS. In addition, both activity and mRNA profiles with appropriate amount of nZVI addition (5 and 25 mg L^-1) were close to that of control, which proved the effectiveness of nZVI addition in anammox recovery. These results would be relevant to the physio-biochemistry development of anammox bacteria and further enhancement of nitrogen removal in wastewater treatment.

Insights Into Mechanisms of Antimicrobial Photodynamic Action Toward Biofilms Using Phenalen-1-One Derivatives as Photosensitizers

Introduction

In view of increasing resistance against antibiotics and antiseptics, antimicrobial photodynamic therapy (aPDT) may be a promising approach for use in dentistry. The aim of this study was to investigate the mechanism of action of aPDT with the phenalene-1-one derivatives SAPYR and SA-PN-05 as photosensitizers by evaluating bacterial ability to replicate, membrane integrity, metabolic activity, and formation of reactive oxygen species (ROS) in biofilms of Actinomyces naeslundii, Streptococcus mutans, and Escherichia coli.

Materials and Methods

Single-species biofilms (A. naeslundii, S. mutans, and E. coli) were cultured under aerobic conditions for 48 h followed by treatment with the photosensitizers SAPYR and SA-PN-05 at various concentrations (0, 50, 100, 500 μM) and different incubation periods of 5, 10, 20, and 30 min and subsequent irradiation for 10 min (Waldmann PIB 3000; λ_em = 360–600 nm; 50 mW/cm²; 30 J/cm²). Control samples were treated with dH₂O and kept in dark for the same periods. Bacterial ability to replicate was evaluated by colony forming unit (CFU) assay. The cytoplasmic membrane integrity was investigated by flow cytometry using SYBR Green and propidium iodide and visualized by scanning and transmission electron microscopy. For SAPYR, metabolic activity and formation of intracellular ROS after irradiation were evaluated via luminescence and fluorometric assays, respectively.

Results

SAPYR showed antimicrobial effects (>3 log₁₀ CFU reduction) on S. mutans after 5 min and on A. naeslundii after 20 min incubation and light activation. For E. coli, CFU reduction was >2 log₁₀ after 30 min of incubation. SA-PN-05 showed an antimicrobial effect after 5 min for all bacteria. Membrane damage upon aPDT with SAPYR was observed for E. coli, but not for S. mutans and A. naeslundii. Following treatment with SA-PN-05, irradiated samples and dark controls of all three species showed loss of membrane integrity. Luminescence and fluorometric assays showed a reduction in metabolic activity and an increase in formation of intracellular ROS in all three species upon aPDT treatment with SAPYR.

Conclusion

The observed loss in ability to replicate upon aPDT with SAPYR in single-species biofilms may be due to an increase in formation of intracellular ROS upon photodynamic treatment.

Mutation rate and efflux response of bacteria exposed to a novel antimicrobial iodo-thiocyanate complex

OBJECTIVES

Antimicrobials, at sub-lethal concentrations, can act as selectors and promoters of resistance by increasing mutation rates. We measured the rate of Escherichia coli mutation from levofloxacin (LVX) sensitivity to resistance when it was grown under the near-lethal challenge of the novel biocidal iodo-thiocyanate complex (ITC). Another relevant factor affecting the emergence of antimicrobial resistance is the role of efflux pumps. Consequently, we evaluated whether ITC could potentially be a substrate for efflux pumps, and thus that efflux-mediated resistance could arise towards ITC.

METHODS

The mutation rate was measured by fluctuation analysis, when multiple parallel E. coli cultures were grown in the absence and presence of ITC. Then the mutational events, which occurred independently in each culture, were scored by plating the fraction of the culture in LVX-selective solid media and compared with the total cell number. To detect if ITC is a substrate for efflux pumps, minimum inhibitory concentrations (MICs) were determined against Pseudomonas aeruginosa in the absence and presence of the efflux pump inhibitor (EPI).

RESULTS

We have found that the E. coli exposed to the near-lethal level of ITC had a slight, but not significant, increase in mutation rate compared with unexposed cultures. Furthermore, the presence of EPI decreased the MIC of ITC by a modest 2-fold, showing that ITC was not a target for efflux pumps.

CONCLUSIONS

ITC usage most likely will not promote resistance development via increased mutation rates, and efflux-mediated resistance emergence to it is less likely than for some other antimicrobials.

Impacts on antibiotic-resistant bacteria and their horizontal gene transfer by graphene-based TiO2&Ag composite photocatalysts under solar irradiation

In recent years, photocatalysis has been considered as a promising method, which provides measures to environmental pollution. Antibiotic resistant bacteria (ARB) and their antibiotic resistance genes (ARGs), as the emerging environmental pollutants, are released into the environment, resulting in antibiotic resistance spread. TiO₂-based nanocomposites, as the most common photocatalytic material, may influence ARB and ARGs under photocatalytic conditions. However, the research on this aspect is rare. A novel nanocomposite synthesized from Ag, TiO₂ and graphene oxide (GO), was selected as a representative of nanomaterials for investigation. The experimental results indicated that TiO₂/Ag/GO nanocomposites significantly affected ARB vitality. 100 mg/L TiO₂/Ag/GO will reduce bacterial survival to 12.2% in 10 min under simulated sunlight irradiation. Chloramphenicol as the most representative antibiotic in the water, reduces the effect of ARB inactivation under photocatalytic conditions. The addition of TiO₂/Ag/GO could affect tetracycline antibiotic resistance. The level of bacterial tolerance to tetracycline had a significant reduction. The horizontal gene transfer was promoted from 1 to 2 folds with the addition of TiO₂/Ag/GO. Even high TiO₂/Ag/GO concentration (100 mg/L) sample had a limited promotion, suggesting that TiO₂/Ag/GO will not increase the risk of antibiotic resistance spread compared to other nano materials.

Species Interaction and Selective Carbon Addition During Antibiotic Exposure Enhances Bacterial Survival

Biofilms are multifaceted and robust microbiological systems that enable microorganisms to withstand a multitude of environmental stresses and expand their habitat range. We have shown previously that nutritional status alters antibiotic susceptibility in a mixed-species biofilm. To further elucidate the effects of nutrient addition on inter-species dynamics and whole-biofilm susceptibility to high-dose streptomycin exposures, a CO₂ Evolution Measurement System was used to monitor the metabolic activity of early steady state pure-culture and mixed-species biofilms containing Pseudomonas aeruginosa and Stenotrophomonas maltophilia, with and without added carbon. Carbon supplementation was needed for biofilm recovery from high-dose streptomycin exposures when P. aeruginosa was either the dominant community member in a mixed-species biofilm (containing predominantly P. aeruginosa and S. maltophilia) or as a pure culture. By contrast, S. maltophilia biofilms could recover from high-dose streptomycin exposures without the need for carbon addition during antibiotic exposure. Metagenomic analysis revealed that even when inocula were dominated by Pseudomonas, the relative abundance of Stenotrophomonas increased upon biofilm development to ultimately become the dominant species post-streptomycin exposure. The combined metabolic and metagenomic results demonstrated the relevance of inter-species influence on survival and that nutritional status has a strong influence on the survival of P. aeruginosa dominated biofilms.

Cinnamaldehyde Induces Expression of Efflux Pumps and Multidrug Resistance in Pseudomonas aeruginosa

Essential oils or their components are increasingly used to fight bacterial infections. Cinnamaldehyde (CNA), the main constituent of cinnamon bark oil, has demonstrated interesting properties in vitro against various pathogens, including Pseudomonas aeruginosa In the present study, we investigated the mechanisms and possible therapeutic consequences of P. aeruginosa adaptation to CNA. Exposure of P. aeruginosa PA14 to subinhibitory concentrations of CNA caused a strong albeit transient increase in the expression of operons that encode the efflux systems MexAB-OprM, MexCD-OprJ, MexEF-OprN, and MexXY/OprM. This multipump activation enhanced from 2- to 8-fold the resistance (MIC) of PA14 to various antipseudomonal antibiotics, including meropenem, ceftazidime, tobramycin, and ciprofloxacin. CNA-induced production of pump MexAB-OprM was found to play a major role in the adaption of P. aeruginosa to the electrophilic biocide, through the NalC regulatory pathway. CNA was progressively transformed by bacteria into the less toxic metabolite cinnamic alcohol (CN-OH), via yet undetermined detoxifying mechanisms. In conclusion, the use of cinnamon bark oil or cinnamaldehyde as adjunctive therapy to treat P. aeruginosa infections may potentially have antagonistic effects if combined with antibiotics because of Mex pump activation.

Interaction of ArmZ with the DNA-binding domain of MexZ induces expression of mexXY multidrug efflux pump genes and antimicrobial resistance in Pseudomonas aeruginosa

Multidrug efflux pumps play an important role in antibiotic resistance in bacteria. In Pseudomonas aeruginosa, MexXY pump provides intrinsic resistance to many antimicrobials, including aminoglycosides. The expression of mexXY operon is negatively regulated by MexZ repressor. The repression is alleviated in response to the antibiotic-induced ribosome stress, which results in increased synthesis of anti-repressor ArmZ, interacting with MexZ. The molecular mechanism of MexZ inactivation by ArmZ is not known. Here, we showed that the N-terminal part of MexZ, encompassing the DNA-binding domain, is required for interaction with ArmZ. Using the bacterial two hybrid system based mutant screening and pull-down analyses we identified substitutions in MexZ that diminished (R3S, K6E, R13H) or completely impaired (K53E) the interaction with ArmZ without blocking MexZ activity as a transcriptional repressor. Introduction of corresponding mexZ missense mutations into P aeruginosa PAO1161 chromosome impaired (mexZ K6E, mexZ R13H) or blocked (mexZ K53E) tetracycline mediated induction of mexY expression. Concomitantly, PAO1161 mexZ K53E strain was more susceptible to aminoglycosides. The identified residues are highly conserved in MexZ-like transcriptional regulators found in bacterial genomes encoding both MexX/MexY/MexZ and ArmZ/PA5470 orthologs, suggesting that a similar mechanism may contribute to induction of efflux mediated resistance in other bacterial species. Overall, our data shed light on the molecular mechanism of ArmZ mediated induction of intrinsic antimicrobial resistance in P. aeruginosa.

Natural Alkaloid Berberine Activity against Pseudomonas aeruginosa MexXY-Mediated Aminoglycoside Resistance: In Silico and in Vitro Studies

The multidrug efflux system MexXY-OprM, inside the resistance-nodulation-division family, is a major determinant of aminoglycoside resistance in Pseudomonas aeruginosa. In the fight aimed to identify potential efflux pump inhibitors among natural compounds, the alkaloid berberine emerged as a putative inhibitor of MexXY-OprM. In this work, we elucidated its interaction with the extrusor protein MexY and assessed its synergistic activity with aminoglycosides. In particular, we built an in silico model for the MexY protein in its trimeric association using both AcrB (E. coli) and MexB (P. aeruginosa) as 3D templates. This model has been stabilized in the bacterial cytoplasmic membrane using a molecular dynamics approach and used for ensemble docking to obtain the binding site mapping. Then, through dynamic docking, we assessed its binding affinity and its synergism with aminoglycosides focusing on tobramycin, which is widely used in the treatment of pulmonary infections. In vitro assays validated the data obtained: the results showed a 2-fold increase of the inhibitory activity and 2-4 log increase of the killing activity of the association berberine-tobramycin compared to those of tobramycin alone against 13/28 tested P. aeruginosa clinical isolates. From hemolytic assays, we preliminarily assessed berberine's low toxicity.

Biofilms: The Microbial "Protective Clothing" in Extreme Environments

Microbial biofilms are communities of aggregated microbial cells embedded in a self-produced matrix of extracellular polymeric substances (EPS). Biofilms are recalcitrant to extreme environments, and can protect microorganisms from ultraviolet (UV) radiation, extreme temperature, extreme pH, high salinity, high pressure, poor nutrients, antibiotics, etc., by acting as "protective clothing". In recent years, research works on biofilms have been mainly focused on biofilm-associated infections and strategies for combating microbial biofilms. In this review, we focus instead on the contemporary perspectives of biofilm formation in extreme environments, and describe the fundamental roles of biofilm in protecting microbial exposure to extreme environmental stresses and the regulatory factors involved in biofilm formation. Understanding the mechanisms of biofilm formation in extreme environments is essential for the employment of beneficial microorganisms and prevention of harmful microorganisms.

Chlorine injury enhances antibiotic resistance in Pseudomonas aeruginosa through over expression of drug efflux pumps

Adaption to adverse environments plays an important role in bacterial survival and is receiving increasing globe attention now. Here, cultivable chlorine-injured Pseudomonas aeruginosa, produced on the chlorination process, was investigated about their resistance to antibiotics. Then, global transcriptional analyses, quantitative PCR (qPCR) validation and antioxidant enzymes measurement were performed to explore the underlying mechanisms. The results showed that chlorine injury enhanced antibiotic resistance in P. aeruginosa and cultivable chlorine-injured P. aeruginosa exposed to 4 mg/L sodium hypochlorite (half of the lethal dose) improved antibiotic resistance against ceftazidime, chloramphenicol and ampicillin by 1.4-5.6 fold. This increase in antibiotic resistance was not hereditable and over expression of the MexEF-OprN efflux pump resulting from oxidative stress contributed to it. These results demonstrate temporal physiological persistence to antibiotics in cultivable chlorine-injured pathogens, suggesting their survival from adverse environments with antibiotic exposure and thereby posing lasting hazards to human health.

Molecular Mechanism of Antibiotic Resistance: The Untouched Area of Future Hope

The treatment of bacterial infections is becoming increasingly ineffective due to rapid mutation which leads to antibiotic resistant and resistant bacteria become more prevalent. As a result the existing antibiotics are gradually obsolete and again new drugs are needed to be designed for the same threat. However, the prediction of evolutionary processes/antibiotic resistance is uncertain. Still, the understanding of mode of evolution of resistance in bacteria is a determining step in the preclinical development of new antibiotics, because drug developers assess the risk of resistance arising against a drug during preclinical development. Multidrug efflux pump systems play an important role for making multidrug resistance to a range of clinically important antibiotics in gram-negative bacteria like Pseudomonas aeruginosa, which lower the intracellular drug concentration by exporting incoming antibiotics across the membranes. We tried to show that the wild type susceptible bacteria P. aeruginosa modified its genetic makeup at mutational hotspots under stress. This strain may either become multidrug resistant or remain susceptible depending on position of amino acid changes in regulatory proteins of efflux pump. Multidrug resistant strain made significant changes at the amino acid positions, 103rd (G → A) and 126th (E → V) through the mutation on the nucleotide position of 308th (G → C); both 377th (A → T) and 378th (G → T), respectively in mexR, a repressor of mexAB-oprM efflux pump. This mutant protein showed low affinity with their operator. But the alteration at 103th position (G → A) in mexR may provide almost similar structural and functional stability as wild type. It was found that mutation was seemed to be well regulated within the limit and position specific under stress which might be back to its original form by supplying counter stress unless addition or deletion takes place.

Upregulation of peroxide scavenging enzymes and multidrug efflux proteins highlight an active sodium hypochlorite response in Pseudomonas fluorescens biofilms

The oxidative biocide sodium hypochlorite is among the most commonly used antimicrobial agents in the control of surface-attached microbial communities (biofilms). Clarifying the genetic response of microorganisms in biofilms to hypochlorite may contribute to improved biofilm control strategies. Here, RNA-seq was used to investigate the differential gene expression response of industrially relevant Pseudomonas fluorescens biofilms to sub-lethal concentrations of sodium hypochlorite. Pseudomonas biofilms responded to hypochlorite exposure with increased transcription of genes encoding peroxide scavenging enzymes (e.g., alkyl hydroperoxide reductase (Ahp) and hydroperoxide resistance protein (Ohr)), oxidative stress repair enzymes (e.g., the periplasmic sulfoxide reductase YedYZ complex), and multidrug efflux (e.g., MexEF pumps). In addition, genes involved in amino acid synthesis and energy metabolism were down-regulated following hypochlorite exposure. This work improves the current understanding of genetic response mechanisms to biocides and contributes to the optimization of biocides and application strategies.

Antibiotic-resistance gene transfer in antibiotic-resistance bacteria under different light irradiation: Implications from oxidative stress and gene expression

Due to the significant public health risks, there is substantial scientific interest in the increasing abundance of antibiotic-resistance bacteria (ARB) and the spread of antibiotic-resistance genes (ARGs) in aquatic environments. To clearly understand the mechanism of ARG transfer, this study examined the conjugative transfer of genes encoding resistance to cephalosporin (bla_CTX) and polymyxin (mcr-1) from two antibiotic-resistant donor strains, namely E. coli DH5α (CTX) and E. coli DH5α (MCR), and to a streptomycin-resistant receptor strain (E. coli C600 (Sm)). Conjugative transfer was specifically studied under different light irradiation conditions including visible light (VL), simulated sunlight (SS) and ultraviolet light (UV_254nm). Results show that the conjugative transfer frequency was not affected by VL irradiation, while it was slightly improved (2-10 fold) by SS irradiation and extremely accelerated (up to 100 fold) by UV irradiation. Furthermore, this study also explored the link between ARG transfer and stress conditions. This was done by studying physiological and biochemical changes; oxidative stress response; and functional gene expression of co-cultured AR-E. coli strains under stress conditions. When correlated with the transfer frequency results, we found that VL irradiation did not affect the physiological and biochemical characteristics of the bacteria, or induce oxidative stress and gene expression. For SS irradiation, oxidative stress occurred slowly, with a slight increase in the expression of target genes in the bacterial cells. In contrast, UV irradiation, rapidly inactivated the bacteria, the degree of oxidative stress was very severe and the expression of the target genes was markedly up-regulated. Our study could provide new insight into the underlying mechanisms and links between accelerated conjugative transfer and oxidative stress, as well as the altered expression of genes relevant to conjugation and other stress responses in bacterial cells.

Cold plasma effect on the proteome of Pseudomonas aeruginosa - Role for bacterioferritin

Cold atmospheric-pressure plasma (CAP) is a relatively new method used for bacterial inactivation. CAP is ionized gas that can be generated by applying an electric current to air or a feeding gas. It contains reactive species and emits UV radiation, which have antibacterial activity. Previous data suggests that CAP is effective in microbial inactivation and can decontaminate and sterilize surfaces, but its exact mode of action is still under debate. This study demonstrates the effect of CAP on the whole proteome of Pseudomonas aeruginosa PAO1 biofilms, which is a dominant pathogen in cystic fibrosis and medical device-related infections. Liquid chromatography-mass spectrometry (LC-MS) was used to identify differentially regulated proteins of whole cell P. aeruginosa extracts. A total of 16 proteins were identified to be affected by plasma treatment compared to the control. Eight of the identified proteins have functions in transcription and translation and their expression changes are likely to be part of a general physiological response instead of a CAP-specific adaptation. However, CAP also affected bacterioferritin (Bfr), Isocitrate dehydrogenase (Idh), Trigger factor (Tig) and a chemotaxis protein, which may be involved in P. aeruginosa’s specific response to CAP. We confirm that bacterioferritin B plays a role in the bacterial response to CAP because ΔbfrB mutants of both PAO1 and PA14 are more susceptible to plasma-induced cell-death than their corresponding wild-type strains. To our knowledge, this is the first study showing the effect of plasma on the whole proteome of a pathogenic microorganism. It will help our understanding of the mode of action of CAP-mediated bacterial inactivation and thus support a safe and effective routine use of CAP in clinical and industrial settings.

Mutations causing low level antibiotic resistance ensure bacterial survival in antibiotic-treated hosts

In 474 genome sequenced Pseudomonas aeruginosa isolates from 34 cystic fibrosis (CF) patients, 40% of these harbor mutations in the mexZ gene encoding a negative regulator of the MexXY-OprM efflux pump associated with aminoglycoside and fluoroquinolone resistance. Surprisingly, resistance to aminoglycosides and fluoroquinolones of mexZ mutants was far below the breakpoint of clinical resistance. However, the fitness increase of the mutant bacteria in presence of the relevant antibiotics, as demonstrated in competition experiments between mutant and ancestor bacteria, showed that 1) very small phenotypic changes cause significant fitness increase with severe adaptive consequences, and 2) standardized phenotypic tests fail to detect such low-level variations. The frequent appearance of P. aeruginosa mexZ mutants in CF patients is directly connected to the intense use of the target antibiotics, and low-level antibiotic resistance, if left unnoticed, can result in accumulation of additional genetic changes leading to high-level resistance.

Role of smeU1VWU2X Operon in Alleviation of Oxidative Stresses and Occurrence of Sulfamethoxazole-Trimethoprim-Resistant Mutants in Stenotrophomonas maltophilia

Overexpression of resistance-nodulation-division (RND)-type efflux pumps is an important mechanism for bacteria to combat antimicrobials. RND efflux pumps are also critical for bacterial physiology, such as oxidative stress tolerance. Stenotrophomonas maltophilia, a multidrug-resistant opportunistic pathogen, harbors eight RND-type efflux pump operons. Of these, the smeU1VWU2X operon is unique for its possession of two additional genes, smeU1 and smeU2, which encode proteins of the short-chain dehydrogenase/reductase (SDR) family. Overexpression of the SmeVWX pump is known to contribute to the acquired resistance to chloramphenicol, quinolone, and tetracycline; however, SmeU1 and SmeU2 are little involved in this phenotype. In the study described in this article, we further linked the smeU1VWU2X operon to oxidative stress alleviation and sulfamethoxazole-trimethoprim (SXT)-resistant mutant occurrence. The smeU1VWU2X operon was inducibly expressed upon challenge with menadione (MD), plumbagin (PL), and hydrogen peroxide (H₂O₂), as verified by the use of the chromosomal smeU1VWU2X-xylE transcriptional fusion construct and quantitative real-time PCR (qRT-PCR). The MD-mediated smeU1VWU2X upexpression was totally dependent on SoxR and partially relied on SmeRv but was less relevant to OxyR. SmeRv, but not SoxR and OxyR, played a regulatory role in the H₂O₂-mediated smeU1VWU2X upexpression. The significance of smeU1VWU2X upexpression was investigated with respect to oxidative stress alleviation and SXT-resistant mutant occurrence. Overexpression of the smeU1VWU2X operon contributed to the alleviation of MD-mediated oxidative stress. Of the encoded proteins, the SmeVWX pump and SmeU2, rather than SmeU1, participated in MD tolerance. Furthermore, we also demonstrated that the MD-mediated expression of the smeU1VWU2X operon decreased the SXT resistance frequency when S. maltophilia was grown in a reactive oxygen species (ROS)-rich environment.

At the Nexus of Antibiotics and Metals: The Impact of Cu and Zn on Antibiotic Activity and Resistance

Environmental influences on antibiotic activity and resistance can wreak havoc with in vivo antibiotic efficacy and, ultimately, antimicrobial chemotherapy. In nature, bacteria encounter a variety of metal ions, particularly copper (Cu) and zinc (Zn), as contaminants in soil and water, as feed additives in agriculture, as clinically-used antimicrobials, and as components of human antibacterial responses. Importantly, there is a growing body of evidence for Cu/Zn driving antibiotic resistance development in metal-exposed bacteria, owing to metal selection of genetic elements harbouring both metal and antibiotic resistance genes, and metal recruitment of antibiotic resistance mechanisms. Many classes of antibiotics also form complexes with metal cations, including Cu and Zn, and this can hinder (or enhance) antibiotic activity. This review highlights the ways in which Cu/Zn influence antibiotic resistance development and antibiotic activity, and in so doing impact in vivo antibiotic efficacy.

Vitamin K3 Induces the Expression of the Stenotrophomonas maltophilia SmeVWX Multidrug Efflux Pump

Stenotrophomonas maltophilia is an opportunistic pathogen with increasing prevalence, which is able to cause infections in immunocompromised patients or in those with a previous pathology. The treatment of the infections caused by this bacterium is often complicated due to the several intrinsic antibiotic resistance mechanisms that it presents. Multidrug efflux pumps are among the best-studied mechanisms of S. maltophilia antibiotic resistance. Some of these efflux pumps have a basal expression level but, in general, their expression is often low and only reaches high levels when the local regulator is mutated or bacteria are in the presence of an effector. In the current work, we have developed a yellow fluorescent protein (YFP)-based sensor with the aim to identify effectors able to trigger the expression of SmeVWX, an efflux pump that confers resistance to quinolones, chloramphenicol, and tetracycline when it is expressed at high levels. With this purpose in mind, we tested a variety of different compounds and analyzed the fluorescence signal given by the expression of YFP under the control of the smeVWX promoter. Among the tested compounds, vitamin K₃, which is a compound belonging to the 2-methyl-1,4-naphthoquinone family, is produced by plants in defense against infection, and has increasing importance in human therapy, was able to induce the expression of the SmeVWX efflux pump. In addition, a decrease in the susceptibility of S. maltophilia to ofloxacin and chloramphenicol was observed in the presence of vitamin K₃, in both wild-type and smeW-deficient strains.

Competitive Growth Enhances Conditional Growth Mutant Sensitivity to Antibiotics and Exposes a Two-Component System as an Emerging Antibacterial Target in Burkholderia cenocepacia

Chemogenetic approaches to profile an antibiotic mode of action are based on detecting differential sensitivities of engineered bacterial strains in which the antibacterial target (usually encoded by an essential gene) or an associated process is regulated. We previously developed an essential-gene knockdown mutant library in the multidrug-resistant Burkholderia cenocepacia by transposon delivery of a rhamnose-inducible promoter. In this work, we used Illumina sequencing of multiplex-PCR-amplified transposon junctions to track individual mutants during pooled growth in the presence of antibiotics. We found that competition from nontarget mutants magnified the hypersensitivity of a clone underexpressing gyrB to novobiocin by 8-fold compared with hypersensitivity measured during clonal growth. Additional profiling of various antibiotics against a pilot library representing most categories of essential genes revealed a two-component system with unknown function, which, upon depletion of the response regulator, sensitized B. cenocepacia to novobiocin, ciprofloxacin, tetracycline, chloramphenicol, kanamycin, meropenem, and carbonyl cyanide 3-chlorophenylhydrazone, but not to colistin, hydrogen peroxide, and dimethyl sulfoxide. We named the gene cluster esaSR for enhanced sensitivity to antibiotics sensor and response regulator. Mutational analysis and efflux activity assays revealed that while esaS is not essential and is involved in antibiotic-induced efflux, esaR is an essential gene and regulates efflux independently of antibiotic-mediated induction. Furthermore, microscopic analysis of cells stained with propidium iodide provided evidence that depletion of EsaR has a profound effect on the integrity of cell membranes. In summary, we unraveled a previously uncharacterized two-component system that can be targeted to reduce antibiotic resistance in B. cenocepacia.

Calcium induces tobramycin resistance in Pseudomonas aeruginosa by regulating RND efflux pumps

Pseudomonas aeruginosa is an opportunistic multidrug resistant pathogen causing severe chronic infections. Our previous studies showed that elevated calcium (Ca²⁺) enhances production of several virulence factors and plant infectivity of the pathogen. Here we show that Ca²⁺ increases resistance of P. aeruginosa PAO1 to tobramycin, antibiotic commonly used to treat Pseudomonas infections. LC-MS/MS-based comparative analysis of the membrane proteomes of P aeruginosa grown at elevated versus not added Ca²⁺, determined that the abundances of two RND (resistance-nodulation-cell division) efflux pumps, MexAB-OprM and MexVW-OprM, were increased in the presence of elevated Ca²⁺. Analysis of twelve transposon mutants with disrupted RND efflux pumps showed that six of them (mexB, muxC, mexY, mexJ, czcB, and mexE) contribute to Ca²⁺-induced tobramycin resistance. Transcriptional analyses by promoter activity and RT-qPCR showed that the expression of mexAB, muxABC, mexXY, mexJK, czcCBA, and mexVW is increased by elevated Ca²⁺. Disruption of mexJ, mexC, mexI, and triA significantly decreased Ca²⁺-induced plant infectivity of the pathogen. Earlier, our group showed that PAO1 maintains intracellular Ca²⁺ (Ca²⁺_in) homeostasis, which mediates Ca²⁺ regulation of P. aeruginosa virulence, and identified four putative Ca²⁺ transporters involved in this process (Guragain et al., 2013). Here we show that three of these transporters (PA2435, PA2092, PA4614) play role in Ca²⁺-induced tobramycin resistance and one of them (PA2435) contributes to Ca²⁺ regulation of mexAB-oprM promoter activity. Furthermore, mexJ, czcB, and mexE contribute to the maintenance of Ca²⁺_in homeostasis. This provides the first evidence that Ca²⁺_in homeostasis mediates Ca²⁺ regulation of RND transport systems, which contribute to Ca²⁺-enhanced tobramycin resistance and plant infectivity in P. aeruginosa.

Difference of Type 3 secretion system (T3SS) effector gene genotypes (exoU and exoS) and its implication to antibiotics resistances in isolates of Pseudomonas aeruginosa from chronic otitis media

OBJECTIVE

Type 3 secretion system (T3SS) is the most important virulence factor in Pseudomonas aeruginosa infection. Of the various T3SS effector genes, exoS and exoU showed mutually exclusive distributions, and these two genes showed varied virulence. In many pseudomonal infections, the distribution of these genes showed different pattern and it influenced severity of infection. This study was aimed to evaluate differences of virulence factors and antibiotics resistance between chronic otitis media and other body infection caused by P. aeruginosa.

METHODS

To estimate the prevalence of effector genes of T3SS, especially the distributions of exoS and exoU genes and their association with antibiotic resistance in COM, we compared the prevalence of T3SS genes in isolates from COM with those from lower respiratory infection and bacteremia. Other virulence genes, including groEL, pilA, ndvB, lasB, rhlI, and apr, were also studied to evaluate prevalence. These isolates were tested for antibiotic susceptibility, and we examined the association between antibiotic susceptibility and the prevalence of T3SS effector genes.

RESULTS

The COM group showed a significantly higher exoU-positive rate than the control group (70.6% vs. 6.7%; P<0.01). Furthermore, COM patients with exoU showed significant antibiotic resistance to ciprofloxacin and tobramycin (P=0.035), whereas there was no significant difference in the control group.

CONCLUSIONS

The high incidence of exoU-positive P. aeruginosa and ciprofloxacin resistance can explain the chronicity and intractability of infection in COM. Elucidation of this pathogenicity will facilitate the development of new treatment options for COM patients.