Quinolones: from antibiotics to autoinducers

Iridium-Catalyzed Borylation of 6-Fluoroquinolines: Access to 6-Fluoroquinolones

The Ir-catalyzed C–H borylation of fluoroquinolines has been realized. The quinoline boronic ester formed undergoes a range of important transformations of relevance to medicinal chemistry. Judicious choice of the substituent at C4 on the quinoline facilitated the unmasking of a fluoroquinolone—the core structure of many antibiotics.

Tackling Multiple-Drug-Resistant Bacteria With Conventional and Complex Phytochemicals

Emerging antibiotic resistance in bacteria endorses the failure of existing drugs with chronic illness, complicated treatment, and ever-increasing expenditures. Bacteria acquire the nature to adapt to starving conditions, abiotic stress, antibiotics, and our immune defense mechanism due to its swift evolution. The intense and inappropriate use of antibiotics has led to the development of multidrug-resistant (MDR) strains of bacteria. Phytochemicals can be used as an alternative for complementing antibiotics due to their variation in metabolic, genetic, and physiological fronts as well as the rapid evolution of resistant microbes and lack of tactile management. Several phytochemicals from diverse groups, including alkaloids, phenols, coumarins, and terpenes, have effectively proved their inhibitory potential against MDR pathogens through their counter-action towards bacterial membrane proteins, efflux pumps, biofilms, and bacterial cell-to-cell communications, which are important factors in promoting the emergence of drug resistance. Plant extracts consist of a complex assortment of phytochemical elements, against which the development of bacterial resistance is quite deliberate. This review emphasizes the antibiotic resistance mechanisms of bacteria, the reversal mechanism of antibiotic resistance by phytochemicals, the bioactive potential of phytochemicals against MDR, and the scientific evidence on molecular, biochemical, and clinical aspects to treat bacterial pathogenesis in humans. Moreover, clinical efficacy, trial, safety, toxicity, and affordability investigations, current status and developments, related demands, and future prospects are also highlighted.

PqsE Expands and Differentially Modulates the RhlR Quorum Sensing Regulon in Pseudomonas aeruginosa

In the opportunistic pathogen Pseudomonas aeruginosa, many virulence traits are finely regulated by quorum sensing (QS), an intercellular communication system that allows the cells of a population to coordinate gene expression in response to cell density. The key aspects underlying the functionality of the complex regulatory network governing QS in P. aeruginosa are still poorly understood, including the interplay between the effector protein PqsE and the transcriptional regulator RhlR in controlling the QS regulon. Different studies have focused on the characterization of PqsE- and RhlR-controlled genes in genetic backgrounds in which RhlR activity can be modulated by PqsE and pqsE expression is controlled by RhlR, thus hampering identification of the distinct regulons controlled by PqsE and RhlR. In this study, a P. aeruginosa PAO1 mutant strain with deletion of multiple QS elements and inducible expression of pqsE and/or rhlR was generated and validated. Transcriptomic analyses performed on this genetic background allowed us to unambiguously define the regulons controlled by PqsE and RhlR when produced alone or in combination. Transcriptomic data were validated via reverse transcription-quantitative PCR (RT-qPCR) and transcriptional fusions. Overall, our results showed that PqsE has a negligible effect on the P. aeruginosa transcriptome in the absence of RhlR, and that multiple RhlR subregulons exist with distinct dependency on PqsE. Overall, this study contributes to untangling the regulatory link between the pqs and rhl QS systems mediated by PqsE and RhlR and clarifying the impact of these QS elements on the P. aeruginosa transcriptome. IMPORTANCE The ability of Pseudomonas aeruginosa to cause difficult-to-treat infections relies on its capacity to fine-tune the expression of multiple virulence traits via the las, rhl, and pqs QS systems. Both the pqs effector protein PqsE and the rhl transcriptional regulator RhlR are required for full production of key virulence factors in vitro and pathogenicity in vivo. While it is known that PqsE can stimulate the ability of RhlR to control some virulence factors, no data are available to allow clear discrimination of the PqsE and RhlR regulons. The data produced in this study demonstrate that PqsE mainly impacts the P. aeruginosa transcriptome via an RhlR-dependent pathway and splits the RhlR regulon into PqsE-dependent and PqsE-independent subregulons. Besides contributing to untangling of the complex QS network of P. aeruginosa, our data confirm that both PqsE and RhlR are suitable targets for the development of antivirulence drugs.

Pseudomonas aeruginosa Ld-08 isolated from Lilium davidii exhibits antifungal and growth-promoting properties

A plant growth-promoting and antifungal endophytic bacteria designated as Ld-08 isolated from the bulbs of Lilium davidii was identified as Pseudomonas aeruginosa based on phenotypic, microscopic, and 16S rRNA gene sequence analysis. Ld-08 exhibited antifungal effects against Fusarium oxysporum, Botrytis cinerea, Botryosphaeria dothidea, and Fusarium fujikuroi. Ld-08 showed the highest growth inhibition, i.e., 83.82±4.76% against B. dothidea followed by 74.12±3.87%, 67.56±3.35%, and 63.67±3.39% against F. fujikuroi, B. cinerea, and F. oxysporum, respectively. The ethyl acetate fraction of Ld-08 revealed the presence of several bioactive secondary metabolites. Prominent compounds were quinolones; 3,9-dimethoxypterocarpan; cascaroside B; dehydroabietylamine; epiandrosterone; nocodazole; oxolinic acid; pyochelin; rhodotulic acid; 9,12-octadecadienoic acid; di-peptides; tri-peptides; ursodiol, and venlafaxine. The strain Ld-08 showed organic acids, ACC deaminase, phosphate solubilization, IAA, and siderophore. The sterilized bulbs of a Lilium variety, inoculated with Ld-08, were further studied for plant growth-promoting traits. The inoculated plants showed improved growth than the control plants. Importantly, some growth parameters such as plant height, leaf length, bulb weight, and root length were significantly (P ≤0.05) increased in the inoculated plants than in the control un-inoculated plants. Further investigations are required to explore the potential of this strain to be used as a plant growth-promoting and biocontrol agent in sustainable agriculture.

Zeolite 4A as a jammer of bacterial communication in Chromobacterium violaceum and Pseudomonas aeruginosa

Aim: To investigate the hypothesis that zeolites interfere with quorum-sensing (QS) systems of Chromobacterium violaceum and Pseudomonas aeruginosa by adsorbing N-acyl homoserine lactone (AHL) signal molecules. Methods: QS inhibition by zeolite 4A was investigated using an AHL-based bioreporter assay. The adsorption of the AHLs was evaluated by performing inductively coupled plasma-optical emission spectroscopy and confirmed by Monte Carlo and molecular dynamic simulations. Results: Zeolite 4A reduced the violacein production in C. violaceum by over 90% and the biofilm formation, elastase and pyocyanin production in P. aeruginosa by 87, 68 and 98%, respectively. Conclusion: Zeolite 4A disrupts the QS systems of C. violaceum and P. aeruginosa by means of adsorbing 3-oxo-C6-AHL and 3-oxo-C12-AHL signaling molecules and can be developed as a novel QS jammer to combat P. aeruginosa-related infections.

Enhanced wastewater treatment performance by understanding the interaction between algae and bacteria based on quorum sensing

In order to further obtain sustainable wastewater treatment technology, in-depth analysis based on algal-bacterial symbiosis, quorum sensing signal molecules and algal-bacterial relationship will lay the foundation for the synergistic algal-bacterial wastewater treatment process. The methods of enhancing algae and bacteria wastewater treatment technology were systematically explored, including promoting symbiosis, reducing algicidal behavior, eliminating the interference of quorum sensing inhibitor, and developing algae and bacteria granular sludge. These findings can provide guidance for sustainable economic and environmental development, and facilitate carbon emissions reduction by using algae and bacteria synergistic wastewater treatment technology in further attempts. The future work should be carried out in the following four aspects: (1) Screening of dominant microalgae and bacteria; (2) Coordination of stable (emerging) contaminants removal; (3) Utilization of algae to produce fertilizers and feed (additives), and (4) Constructing recombinant algae and bacteria for reducing carbon emissions and obtaining high value-added products.

Bioactive Compounds for Quorum Sensing Signal-Response Systems in Marine Phycosphere

Quorum sensing in the phycosphere refers to a sensor system in which bacteria secrete bioactive compounds to coordinate group behavior relying on cell density. It is an important way for algae and bacteria to communicate with each other and achieve interactions. It has been determined that quorum sensing is widely presented in the marine phycosphere, which involves a variety of bioactive compounds. Focused on these compounds in marine phycosphere, this review summarizes the types and structures of the compounds, describes the methods in detection and functional evaluation, discusses the ecological functions regulated by the compounds, such as modulating microbial colonization, achieving algae–bacteria mutualism or competition and contributing to marine biogeochemical cycles. Meanwhile, the application prospects of the compounds are also proposed, including controlling harmful algal blooms and producing biofuel. Future research should focus on improving detection techniques, developing more model systems and investigating the effects of climate change on the quorum-sensing pathway to further understand the mechanism and application potential of quorum sensing compounds. This review aims to present an overview of current research carried out in order to provide the reader with perspective on bioactive compounds involved in quorum sensing.

Rhodaelectro-Catalyzed peri-Selective Direct Alkenylations with Weak O-Coordination Enabled by the Hydrogen Evolution Reaction (HER)

Direct C-H functionalizations by electrocatalysis is dominated by strongly coordinating N(sp2 )-directing groups. In sharp contrast, direct electrocatalytic transformations of weakly-coordinating phenols remain underdeveloped. Herein, electrooxidative peri C-H alkenylations of challenging 1-naphthols were achieved by versatile rhodium(III) catalysis via user-friendly constant current electrolysis. The rhodaelectrocatalysis employed readily-available alkenes and a protic reaction medium and features ample scope, good functional group tolerance and high site- and stereoselectivity. The strategy was successfully applied to high-value, nitrogen-containing heterocycles, thereby providing direct access to uncommon heterocyclic motifs based on the dihydropyranoquinoline skeleton.

Biofilm-mediated bioremediation is a powerful tool for the removal of environmental pollutants

Biofilm-mediated bioremediation is an attractive approach for the elimination of environmental pollutants, because of its wide adaptability, biomass, and excellent capacity to absorb, immobilize, or degrade contaminants. Biofilms are assemblages of individual or mixed microbial cells adhering to a living or non-living surface in an aqueous environment. Biofilm-forming microorganisms have excellent survival under exposure to harsh environmental stressors, can compete for nutrients, exhibit greater tolerance to pollutants compared to free-floating planktonic cells, and provide a protective environment for cells. Biofilm communities are thus capable of sorption and metabolization of organic pollutants and heavy metals through a well-controlled expression pattern of genes governed by quorum sensing. The involvement of quorum sensing and chemotaxis in biofilms can enhance the bioremediation kinetics with the help of signaling molecules, the transfer of genetic material, and metabolites. This review provides in-depth knowledge of the process of biofilm formation in microorganisms, their regulatory mechanisms of interaction, and their importance and application as powerful bioremediation agents in the biodegradation of environmental pollutants, including hydrocarbons, pesticides, and heavy metals.

Structural insights into inhibition of the drug target dihydroorotate dehydrogenase by bacterial hydroxyalkylquinolines

Hydroxyalkylquinolines (HAQs) are ubiquitious natural products but their interactions with associated protein targets remain elusive. We report X-ray crystal structures of two HAQs in complex with dihydroorotate dehydrogenase (DHODH). Our results reveal the structural basis of DHODH inhibition by HAQs and open the door to downstream structure-activity relationship studies.

Simultaneous electrochemical removal of Microcystis aeruginosa and sulfamethoxazole and its ecologic impacts on Vallisneria spiralis

In this study, the simultaneous removal effects of electrochemical oxidation with boron-doped diamond anodes at different current densities were tested on Microcystis aeruginosa and sulfamethoxazole. Flow cytometry and non-invasive micro-test technology were applied to study the physiological states of M. aeruginosa and Vallisneria spiralis leaf cells. As the current density increased, the degradation effect of electrochemical oxidation on sulfamethoxazole and microcystin-LR increased and exceeded 60% within 6 h. In addition, population density of M. aeruginosa, fluorescence response of chlorophyll a, and cytoplasmic membrane integrity decreased, whereas the proportion of cells with excessive accumulation of intracellular reactive oxygen species (ROS) increased. The effect of electrochemical oxidation on the cell population of M. aeruginosa continued after the power was turned off. The physiological state of V. spiralis leaf cells was not severely affected at 10 mA/cm² for 24 h. Higher current intensity and longer electrolysis time would induce apoptosis or necrosis. In order to achieve a higher target pollutant removal effect and simultaneously avoid damage to the lake ecosystem, the current intensity of the electrochemical oxidation device should not exceed 10 mA/cm², and a single electrolysis treatment should range from 6 h to 24 h.

The Effect of CFTR Modulators on Airway Infection in Cystic Fibrosis

The advent of Cystic fibrosis transmembrane receptor (CFTR) modulators in 2012 was a critical event in the history of cystic fibrosis (CF) treatment. Unlike traditional therapies that target downstream effects of CFTR dysfunction, CFTR modulators aim to correct the underlying defect at the protein level. These genotype-specific therapies are now available for an increasing number of CF patients, transforming the way we view the condition from a life-limiting disease to one that can be effectively managed. Several studies have demonstrated the vast improvement CFTR modulators have on normalization of sweat chloride, CFTR function, clinical endpoints, and frequency of pulmonary exacerbation. However, their impact on other aspects of the disease, such as pathogenic burden and airway infection, remain under explored. Frequent airway infections as a result of increased susceptibility and impaired innate immune response are a serious problem within CF, often leading to accelerated decline in lung function and disease progression. Current evidence suggests that CFTR modulators are unable to eradicate pathogenic organisms in those with already established lung disease. However, this may not be the case for those with relatively low levels of disease progression and conserved microbial diversity, such as young patients. Furthermore, it remains unknown whether the restorative effects exerted by CFTR modulators extend to immune cells, such as phagocytes, which have the potential to modulate the response of people with CF (pwCF) to infection. Throughout this review, we look at the potential impact of CFTR modulators on airway infection in CF and their ability to shape impaired pulmonary defences to pathogens.

Systemic quinolones and risk of retinal detachment III: a nested case-control study using a US electronic health records database

Background

Quinolones are popular antibiotics that are known for their potency, broad coverage, and reasonable safety. Concerns have been raised about a possible association between quinolones and retinal detachment (RD).

Methods

We conducted a nested case–control study using electronic health records (EHR) from the Health Facts® Database. The initial cohort included all patients who were admitted between 2000 and 2016, with no history of eye disease, and had a minimum medical history of one year. Eligible cases comprised inpatients who were first admitted with a primary diagnosis of RD between 2010 and 2015. Each eligible case was matched without replacement to five unique controls by sex, race, age, and period-at-risk. We used conditional logistic regression to calculate RD risk, adjusting for exposure to other medications, and major risk factors.

Results

We identified 772 cases and 3860 controls. Whereas our primary analysis of all subjects revealed no quinolone-associated RD risk, elevated but non-significant risks were noted in African Americans (ciprofloxacin and levofloxacin), those aged 56–70 years old (moxifloxacin), and women (ciprofloxacin).

Conclusion

Our study did not identify an elevated RD risk within 30 days following systemic administration of quinolone antibiotics. Suggestions of increased risk observed in some population subgroups warrant further investigation.

Supplementary Information

The online version contains supplementary material available at 10.1007/s00228-021-03260-4.

Photodegradation of norfloxacin in ice: Role of the fluorine substituent

Ice is an important medium in cold regions, because it regulates the environmental behaviors and the fate of pollutants. The photodegradation of fluoroquinolone (FQ) antibiotics as emerging contaminants of concern in ice remains poorly understood. Here, the photodegradation of fluorine-containing norfloxacin (NOR) as one model of FQs in ice formed from freezing solutions was investigated. Pipemidic acid (PPA) as a structural analogue of NOR was selected to compare the effect of molecular structure on the antibiotic photodegradation in the ice. Results suggested that the photodegradation rate constant of NOR in ice relative to pure water increased by 40.0%. Both the absorbance in the absorption spectra and quantum yields of NOR in ice over water increased by 1.4 times. Direct photodegradation mainly caused the defluorination of NOR, which was more important than cleavage and oxidation of the piperazine ring by self-sensitized photooxidation in ice. The defluorination rate of NOR in the ice relative to water increased by about 12.7%. The fluorine substituent played a more important role in the NOR photodegradation in the ice, resulting in a 1.6-fold increase in the photodegradation rate constant of NOR relative to PPA. This work provides a new insight into the role of fluorine substituents in the photodegradation of fluorinated pharmaceuticals in cold regions.

Metrics of Antifungal Effects of Ciprofloxacin on Aspergillus fumigatus Planktonic Growth and Biofilm Metabolism; Effects of Iron and Siderophores

Pseudomonas aeruginosa and Aspergillus fumigatus frequently coexist in the airways of immunocompromised patients or individuals with cystic fibrosis. Ciprofloxacin (CIP) is a synthetic quinolone antibiotic commonly used to treat bacterial infections, such as those produced by Pseudomonas aeruginosa. CIP binds iron, and it is unclear what effect this complex would have on the mycobiome. The effects of CIP on Aspergillus were dependent on the iron levels present, and on the presence of Aspergillus siderophores. We found that CIP alone stimulated wildtype planktonic growth, but not biofilm metabolism. At high concentrations, CIP antagonized a profungal effect of iron on wildtype Aspergillus metabolism, presumably owing to iron chelation. CIP interfered with the metabolism and growth of an Aspergillus siderophore mutant, with the effect on metabolism being antagonized by iron. CIP acted synergistically with iron on the growth of the mutant, and, to a lesser extent, the wildtype. In summary, CIP can increase fungal growth or affect fungal metabolism, depending on the local iron concentration and available siderophores. Therefore, high local CIP concentrations during treatment of Pseudomonas–Aspergillus co-infections may increase the fungal burden.

Camphorsulfonic Acid-Mediated One-Pot Tandem Consecutive via the Ugi Four-Component Reaction for the Synthesis of Functionalized Indole and 2-Quinolone Derivatives by Switching Solvents

A camphorsulfonic acid-mediated one-pot tandem consecutive approach was developed to synthesize functionalized indole and 2-quinolone derivatives from the Ugi four-component reaction by switching solvents. A reaction of the Ugi adduct in an aprotic solvent undergoes 5-exo-trig cyclization to form an indole ring. In a protic solvent, however, the Ugi adduct undergoes an alkyne-carbonyl metathesis reaction to form a 2-quinolone ring.

Environmental structure impacts microbial composition and secondary metabolism

Determining the drivers of microbial community assembly is a central theme of microbial ecology, and chemical ecologists seek to characterize how secondary metabolites mediate these assembly patterns. Environmental structure affects how communities assemble and what metabolic pathways aid in that assembly. Here, we bridged these two perspectives by addressing the chemical drivers of community assembly within a spatially structured landscape with varying oxygen availability. We hypothesized that structured environments would favor higher microbial diversity and metabolite diversity. We anticipated that the production of a compound would be more advantageous in a structured environment (less mixing) compared to an unstructured environment (more mixing), where the molecule would have a diminished local effect. We observed this to be partially true in our experiments: structured environments had similar microbial diversity compared to unstructured environments but differed significantly in the metabolites produced. We also found that structured environments selected for communities with higher evenness, rather than communities with higher richness. This supports the idea that when characterizing the drivers of community assembly, it matters less about who is there and more about what they are doing. Overall, these data contribute to a growing effort to approach microbial community assembly with interdisciplinary tools and perspectives.

Systematic review and meta-analysis of environmental Vibrio species - antibiotic resistance

Adequate comprehension of the genomics of microbial resistance to an antimicrobial agent will advance knowledge on the management of associated pathologies and public health safety. However, continued emergences and reemergence of pathogens, including Vibrio species, hallmarks a potential knowledge gap. A clear understanding of the process and forecast of the next trend should be in place to nip in the bud, microbial acquisition of resistance to antibiotics. Therefore, this two-decade (1 January 2000 to 31 December 2019) systematic review and meta-analytical study articulated the prevalence and incidence of antibiotics resistance genes in Vibrio species isolated from environmental samples. Articles from the Web of Science and PubMed electronic databases was engaged. Heterogeneity of the data and bias were analyzed with random effect model meta-analysis and funnel plot. A total of 1920 Vibrio sp. were reported by the ten selected articles included in this study; out of which 32.39% of identified isolates displayed antimicrobial resistance and associated genes. The distribution of antibiotics resistance genes in Vibrio sp., reported within six countries was 21% tetracycline (tet), and 20% sulphonamide (sul) and β-lactamase (bla) respectively. The quinolone, tetracycline and sulfonamide resistance genes showed 32.97% (95% CI 0.18–0.53) prevalence while chloramphenicol, macrolides and aminoglycoside resistance genes are expressed in percentages as 28.67% (95% CI 0.15–0.47) and β-lactamase resistance genes 27.93% (95% CI 0.11–0.56) respectively. The Vibrio antibiotics resistance genes (V-ARG) distribution depicts no regular trend or pattern from the analyzed data. Consequently, more studies would be required to articulate the structure of cohesion in the distribution of the resistance determinants in microbes.

Methotrexate Disposition, Anti-Folate Activity, and Metabolomic Profiling to Identify Molecular Markers of Disease Activity and Drug Response in the Collagen-Induced Arthritis Mouse Model

Methotrexate (MTX) is widely used in the treatment of autoimmune arthritis but is limited by its unpredictable and variable response profile. Currently, no biomarkers exist to predict or monitor early therapeutic responses to MTX. Using a collagen-induced arthritis (CIA) mouse model, this study aimed to identify biochemical pathways and biomarkers associated with MTX efficacy in autoimmune arthritis. Following arthritis disease induction, DBA/1J mice were treated with subcutaneous MTX (20 mg/kg/week) and disease activity was assessed based on disease activity scores (DAS) and paw volume (PV) measurements. Red blood cell (RBC) and plasma samples were collected at the end of the study and were assessed for folate and MTX content. Plasma samples were analyzed by semitargeted global metabolomic profiling and analyzed by univariate and multivariate analysis. Treatment with MTX was associated with significant reductions in disease activity based on both DAS (p = 0.0006) and PV (p = 0.0006). MTX therapy resulted in significant reductions in 5-methyltetrahydrofolate (5mTHF) levels in plasma (p = 0.02) and RBCs (p = 0.001). Reductions in both RBC and plasma 5mTHF were associated with lower DAS (p = 0.0007, p = 0.01, respectively) and PV (p = 0.001, p = 0.005, respectively). Increases in RBC MTX were associated with lower DAS (p = 0.003) but not PV (p = 0.23). Metabolomic analysis identified N-methylisoleucine (NMI) and quinolone as metabolites significantly altered in disease mice, which were corrected towards healthy control levels in mice treated with MTX. Reductions in plasma NMI were associated with lower DAS (p = 0.0002) and PV (p = 9.5 × 10^-6). Increases in plasma quinolone were associated with lower DAS (p = 0.02) and PV (p = 0.01). Receiver-operating characteristic curve analysis identified plasma NMI (AUC = 1.00, p = 2.4 × 10^-8), RBC 5mTHF (AUC = 0.99, p = 2.4 × 10^-5), and plasma quinolone (AUC = 0.89, p = 0.01) as top discriminating metabolites of MTX treatment. Our data support a relationship between MTX efficacy and its effect on circulating folates and identified 5mTHF, NMI, and quinolone as potential therapeutic biomarkers of disease activity and MTX response in the CIA mouse model of autoimmune arthritis.

Biological Effects of Quinolones: A Family of Broad-Spectrum Antimicrobial Agents

Broad antibacterial spectrum, high oral bioavailability and excellent tissue penetration combined with safety and few, yet rare, unwanted effects, have made the quinolones class of antimicrobials one of the most used in inpatients and outpatients. Initially discovered during the search for improved chloroquine-derivative molecules with increased anti-malarial activity, today the quinolones, intended as antimicrobials, comprehend four generations that progressively have been extending antimicrobial spectrum and clinical use. The quinolone class of antimicrobials exerts its antimicrobial actions through inhibiting DNA gyrase and Topoisomerase IV that in turn inhibits synthesis of DNA and RNA. Good distribution through different tissues and organs to treat Gram-positive and Gram-negative bacteria have made quinolones a good choice to treat disease in both humans and animals. The extensive use of quinolones, in both human health and in the veterinary field, has induced a rise of resistance and menace with leaving the quinolones family ineffective to treat infections. This review revises the evolution of quinolones structures, biological activity, and the clinical importance of this evolving family. Next, updated information regarding the mechanism of antimicrobial activity is revised. The veterinary use of quinolones in animal productions is also considered for its environmental role in spreading resistance. Finally, considerations for the use of quinolones in human and veterinary medicine are discussed.

Sub-Inhibitory Antibiotic Exposure and Virulence in Pseudomonas aeruginosa

Pseudomonas aeruginosa is a prime opportunistic pathogen, one of the most important causes of hospital-acquired infections and the major cause of morbidity and mortality in cystic fibrosis lung infections. One reason for the bacterium's pathogenic success is the large array of virulence factors that it can employ. Another is its high degree of intrinsic and acquired resistance to antibiotics. In this review, we first summarise the current knowledge about the regulation of virulence factor expression and production. We then look at the impact of sub-MIC antibiotic exposure and find that the virulence-antibiotic interaction for P. aeruginosa is antibiotic-specific, multifaceted, and complex. Most studies undertaken to date have been in vitro assays in batch culture systems, involving short-term (<24 h) antibiotic exposure. Therefore, we discuss the importance of long-term, in vivo-mimicking models for future work, particularly highlighting the need to account for bacterial physiology, which by extension governs both virulence factor expression and antibiotic tolerance/resistance.

A Metagenomic Nanopore Sequence Analysis Combined with Conventional Screening and Spectroscopic Methods for Deciphering the Antimicrobial Metabolites Produced by Alcaligenes faecalis Soil Isolate MZ921504

The continuous development of multidrug resistance pathogens with limited therapeutic options has become a great problem globally that impose sever health hazards. Accordingly, searching for of new antimicrobials became an urgent demand and great challenge. Soil significantly have been associated with several species that are antibiotic producers. In this study, combination of conventional screening methods with Liquid chromatography- Mass spectroscopy (LC/MS) and metagenomic nanopore sequence analysis have been conducted for the deciphering the active metabolites produced by soil isolate(s). Preliminary soil screening resulted in a Gram-negative isolate identified via 16S ribosomal RNA as Alcaligenes faecalis isolate MZ921504 with promising antimicrobial activities against wide range of MDR gram-positive and gram-negative pathogens. The LC/MS analysis of the metabolites of A. faecalis isolate MZ921504 confirmed the presence of ectoine, bacillibactin, quinolobactin and burkholderic acid. Metagenomics sequence analysis of the soil sample (NCBI GenBank accession PRJNA771993) revealed the presence of conserved biosynthetic gene clusters of ectoine, bacteriocin, bacillibactin, quinolobactin, terpene and burkholderic acid of A. faecalis. In conclusion, A. faecalis isolate MZ921504 is a promising source for antimicrobial metabolites. LC/MS spectral analysis and third generation sequencing tools followed by secondary metabolite gene clusters analysis are useful methods to predict the nature of the antimicrobial metabolites.

Prediction of antimicrobial resistance based on whole-genome sequencing and machine learning

MOTIVATION

Antimicrobial resistance (AMR) is one of the biggest global problems threatening human and animal health. Rapid and accurate AMR diagnostic methods are thus very urgently needed. However, traditional antimicrobial susceptibility testing (AST) is time-consuming, low throughput and viable only for cultivable bacteria. Machine learning methods may pave the way for automated AMR prediction based on genomic data of the bacteria. However, comparing different machine learning methods for the prediction of AMR based on different encodings and whole-genome sequencing data without previously known knowledge remains to be done.

RESULTS

In this study, we evaluated logistic regression (LR), support vector machine (SVM), random forest (RF) and convolutional neural network (CNN) for the prediction of AMR for the antibiotics ciprofloxacin, cefotaxime, ceftazidime and gentamicin. We could demonstrate that these models can effectively predict AMR with label encoding, one-hot encoding and frequency matrix chaos game representation (FCGR encoding) on whole-genome sequencing data. We trained these models on a large AMR dataset and evaluated them on an independent public dataset. Generally, RFs and CNNs perform better than LR and SVM with AUCs up to 0.96. Furthermore, we were able to identify mutations that are associated with AMR for each antibiotic.

AVAILABILITY AND IMPLEMENTATION

Source code in data preparation and model training are provided at GitHub website (https://github.com/YunxiaoRen/ML-iAMR).

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Cysteamine Inhibits Glycine Utilisation and Disrupts Virulence in Pseudomonas aeruginosa

Pseudomonas aeruginosa is a major opportunistic human pathogen which employs a myriad of virulence factors. In people with cystic fibrosis (CF) P. aeruginosa frequently colonises the lungs and becomes a chronic infection that evolves to become less virulent over time, but often adapts to favour persistence in the host with alginate-producing mucoid, slow-growing, and antibiotic resistant phenotypes emerging. Cysteamine is an endogenous aminothiol which has been shown to prevent biofilm formation, reduce phenazine production, and potentiate antibiotic activity against P. aeruginosa, and has been investigated in clinical trials as an adjunct therapy for pulmonary exacerbations of CF. Here we demonstrate (for the first time in a prokaryote) that cysteamine prevents glycine utilisation by P. aeruginosa in common with previously reported activity blocking the glycine cleavage system in human cells. Despite the clear inhibition of glycine metabolism, cysteamine also inhibits hydrogen cyanide (HCN) production by P. aeruginosa, suggesting a direct interference in the regulation of virulence factor synthesis. Cysteamine impaired chemotaxis, lowered pyocyanin, pyoverdine and exopolysaccharide production, and reduced the toxicity of P. aeruginosa secreted factors in a Galleria mellonella infection model. Thus, cysteamine has additional potent anti-virulence properties targeting P. aeruginosa, further supporting its therapeutic potential in CF and other infections.

Functions of elements in soil microorganisms

The soil microbial community fulfils various functions, such as nutrient cycling and carbon (C) sequestration, therefore contributing to maintenance of soil fertility and mitigation of global warming. In this context, a major focus of research has been on C, nitrogen (N) and phosphorus (P) cycling. However, from aquatic and other environments, it is well known that other elements beyond C, N, and P are essential for microbial functioning. Nonetheless, for soil microorganisms this knowledge has not yet been synthesised. To gain a better mechanistic understanding of microbial processes in soil systems, we aimed at summarising the current knowledge on the function of a range of essential or beneficial elements, which may affect the efficiency of microbial processes in soil. This knowledge is discussed in the context of microbial driven nutrient and C cycling. Our findings may support future investigations and data evaluation, where other elements than C, N, and P affect microbial processes.

Novel detection of specific bacterial quorum sensing molecules in saliva: Potential non-invasive biomarkers for pulmonary Pseudomonas aeruginosa in cystic fibrosis

Pseudomonas aeruginosa produces specific signalling molecules, 2-alkyl-4-quinolones (AQs) that are detectable in the sputum of adults with cystic fibrosis (CF) and who have pulmonary infection with this opportunistic pathogen. This study aimed to determine whether AQs could be detected in saliva of patients with CF and known infection with Pseudomonas aeruginosa. Saliva and sputum samples were obtained from 89 adults with CF and analyzed using liquid chromatography-tandem mass spectrometry. AQs were detected in 39/89 (43.8%) saliva samples and 70/77(90.9%) sputum samples. Salivary AQs had a sensitivity of 50% (95%CI; 37.8; 62.2), specificity of 100% (95%CI; 47.8; 100), when compared to a molecular microbiological measure of P. aeruginosa in sputum as measured using polymerase chain reaction. Specific AQs produced by P. aeruginosa can be detected in the saliva and warrant investigation as potential non-invasive biomarkers of pulmonary P. aeruginosa.

Phytochemicals: A Promising Weapon in the Arsenal against Antibiotic-Resistant Bacteria

The extensive usage of antibiotics and the rapid emergence of antimicrobial-resistant microbes (AMR) are becoming important global public health issues. Many solutions to these problems have been proposed, including developing alternative compounds with antimicrobial activities, managing existing antimicrobials, and rapidly detecting AMR pathogens. Among all of them, employing alternative compounds such as phytochemicals alone or in combination with other antibacterial agents appears to be both an effective and safe strategy for battling against these pathogens. The present review summarizes the scientific evidence on the biochemical, pharmacological, and clinical aspects of phytochemicals used to treat microbial pathogenesis. A wide range of commercial products are currently available on the market. Their well-documented clinical efficacy suggests that phytomedicines are valuable sources of new types of antimicrobial agents for future use. Innovative approaches and methodologies for identifying plant-derived products effective against AMR are also proposed in this review.

Impact of artificial sputum media formulation on Pseudomonas aeruginosa secondary metabolite production

In vitro culture media are being developed to understand how host site-specific nutrient profiles influence microbial pathogenicity and ecology. To mimic the cystic fibrosis (CF) lung environment, a variety of artificial sputum media (ASM) have been created. However, the composition of these ASM vary in the concentration of key nutrients, including amino acids, lipids, DNA, and mucin. In this work, we used feature-based molecular networking (FBMN) to perform comparative metabolomics of Pseudomonas aeruginosa, the predominant opportunistic pathogen infecting the lungs of people with CF, cultured in nine different ASM. We found that the concentration of aromatic amino acids and iron from mucin added to the media contributes to differences in the production of P. aeruginosa virulence-associated secondary metabolites.

IMPORTANCE Different media formulations aiming to replicate in vivo infection environments contain different nutrients, which affects interpretation of experimental results. Inclusion of undefined components, such as commercial porcine gastric mucin (PGM), in an otherwise chemically defined medium can alter the nutrient content of the medium in unexpected ways and influence experimental outcomes.

Bacterial Long-Range Warfare: Aerial Killing of Legionella pneumophila by Pseudomonas fluorescens

Legionella pneumophila, the causative agent of Legionnaires’ disease, is mostly found in man-made water systems and is one of the most closely monitored waterborne pathogens. With the aim of finding natural ways to control waterborne pathogens and thus further reduce the impact of disinfection by-products on human health, some studies have demonstrated the ability of bacteria to kill Legionella through the production of secondary metabolites or antimicrobial compounds. Here, we describe an unexpected growth inhibition of L. pneumophila when exposed to a physically separated strain of Pseudomonas fluorescens, designated as MFE01. Most of the members of the Legionellaceae family are sensitive to the volatile substances emitted by MFE01, unlike other bacteria tested. Using headspace solid-phase microextraction GC-MS strategy, a volatilome comparison revealed that emission of 1-undecene, 2-undecanone, and 2-tridecanone were mainly reduced in a Tn5-transposon mutant unable to inhibit at distance the growth of L. pneumophila strain Lens. We showed that 1-undecene was mainly responsible for the inhibition at distance in vitro, and led to cell lysis in small amounts, as determined by gas chromatography-mass spectrometry (GC-MS). Collectively, our results provide new insights into the mode of action of bacterial volatiles and highlight them as potent anti-Legionella agents to focus research on novel strategies to fight legionellosis.

IMPORTANCE Microbial volatile compounds are molecules whose activities are increasingly attracting the attention of researchers. Indeed, they can act as key compounds in long-distance intrakingdom and interkingdom communication, but also as antimicrobials in competition and predation. In fact, most studies to date have focused on their antifungal activities and only a few have reported on their antibacterial properties. Here, we describe that 1-undecene, naturally produced by P. fluorescens, is a volatile with potent activity against bacteria of the genus Legionella. In small amounts, it is capable of inducing cell lysis even when the producing strain is physically separated from the target. This is the first time that such activity is described. This molecule could therefore constitute an efficient compound to counter bacterial pathogens whose treatment may fail, particularly in pulmonary diseases. Indeed, inhalation of these volatiles should be considered as a possible route of therapy in addition to antibiotic treatment.

Exploring Phytochemicals for Combating Antibiotic Resistance in Microbial Pathogens

Antibiotic resistance or microbial drug resistance is emerging as a serious threat to human healthcare globally, and the multidrug-resistant (MDR) strains are imposing major hurdles to the progression of drug discovery programs. Newer antibiotic-resistance mechanisms in microbes contribute to the inefficacy of the existing drugs along with the prolonged illness and escalating expenditures. The injudicious usage of the conventional and commonly available antibiotics in human health, hygiene, veterinary and agricultural practices is proving to be a major driver for evolution, persistence and spread of antibiotic-resistance at a frightening rate. The drying pipeline of new and potent antibiotics is adding to the severity. Therefore, novel and effective new drugs and innovative therapies to treat MDR infections are urgently needed. Apart from the different natural and synthetic drugs being tested, plant secondary metabolites or phytochemicals are proving efficient in combating the drug-resistant strains. Various phytochemicals from classes including alkaloids, phenols, coumarins, terpenes have been successfully demonstrated their inhibitory potential against the drug-resistant pathogens. Several phytochemicals have proved effective against the molecular determinants responsible for attaining the drug resistance in pathogens like membrane proteins, biofilms, efflux pumps and bacterial cell communications. However, translational success rate needs to be improved, but the trends are encouraging. This review highlights current knowledge and developments associated challenges and future prospects for the successful application of phytochemicals in combating antibiotic resistance and the resistant microbial pathogens.

Mobile Genetic Elements of Vibrio cholerae and the Evolution of Its Antimicrobial Resistance

Vibrio cholerae (VC) is the causative agent of the severe dehydrating diarrheal disease cholera. The primary treatment for cholera is oral rehydration therapy (ORT). However, in case of moderate to severe dehydration, antibiotics are administered to reduce morbidity. Due to the emergence of multidrug resistant (MDR) strains of VC routinely used antibiotics fail to be effective in cholera patients. Antimicrobial resistance (AMR) is encoded in the genome of bacteria and is usually acquired from other organisms cohabiting in the environment or in the gut with which it interacts in the gut or environmental niche. The antimicrobial resistance genes (ARGs) are usually borne on mobile genetic elements (MGEs) like plasmids, transposons, integrons and SXT constin. Horizontal gene transfer (HGT) helps in the exchange of ARGs among bacteria leading to dissemination of AMR. In VC the acquisition and loss of AMR to many antibiotics have been found to be a dynamic process. This review describes the different AMR determinants and mechanisms of resistance that have been discovered in VC. These ARGs borne usually on MGEs have been recovered from isolates associated with past and present epidemics worldwide. These are responsible for resistance of VC to common antibiotics and are periodically lost and gained contributing to its genetic evolution. These resistance markers can be routinely used for AMR surveillance in VC. The review also presents a precise perspective on the importance of the gut microbiome in the emergence of MDR VC and concludes that the gut microbiome is a potential source of molecular markers and networks which can be manipulated for the interception of AMR in the future.

How Do Quorum-Sensing Signals Mediate Algae-Bacteria Interactions?

Quorum sensing (QS) describes a process by which bacteria can sense the local cell density of their own species, thus enabling them to coordinate gene expression and physiological processes on a community-wide scale. Small molecules called autoinducers or QS signals, which act as intraspecies signals, mediate quorum sensing. As our knowledge of QS has progressed, so too has our understanding of the structural diversity of QS signals, along with the diversity of bacteria conducting QS and the range of ecosystems in which QS takes place. It is now also clear that QS signals are more than just intraspecies signals. QS signals mediate interactions between species of prokaryotes, and between prokaryotes and eukaryotes. In recent years, our understanding of QS signals as mediators of algae-bacteria interactions has advanced such that we are beginning to develop a mechanistic understanding of their effects. This review will summarize the recent efforts to understand how different classes of QS signals contribute to the interactions between planktonic microalgae and bacteria in our oceans, primarily N-acyl-homoserine lactones, their degradation products of tetramic acids, and 2-alkyl-4-quinolones. In particular, this review will discuss the ways in which QS signals alter microalgae growth and metabolism, namely as direct effectors of photosynthesis, regulators of the cell cycle, and as modulators of other algicidal mechanisms. Furthermore, the contribution of QS signals to nutrient acquisition is discussed, and finally, how microalgae can modulate these small molecules to dampen their effects.

Intestinal interplay of quorum sensing molecules and human receptors

Human gut is in permanent contact with microorganisms that play an important role in many physiological processes including metabolism and immunologic activity. These microorganisms communicate and manage themself by the quorum sensing system (QS) that helps to coordinate optimal growth and subsistence by activating signaling pathways that regulate bacterial gene expression. Diverse QS molecules produced by pathogenic as well as resident microbiota have been found throughout the human gut. However, even a host can by affected by these molecules. Intestinal and immune cells possess a range of molecular targets for QS. Our present knowledge on bacteria-cell communication encompasses G-protein-coupled receptors, nuclear receptors and receptors for bacterial cell-wall components. The QS of commensal bacteria has been approved as a protective factor with favourable effects on intestinal homeostasis and immunity. Signaling molecules of QS interacting with above-mentioned receptors thus parcipitate on maintaining of barrier functions, control of inflammation processes and increase of resistance to pathogen colonization in host organisms. Pathogens QS molecules can have a dual function. Host cells are able to detect the ongoing infection by monitoring the presence and changes in concentrations of QS molecules. Such information can help to set the most effective immune defence to prevent or overcome the infection. Contrary, pathogens QS signals can target the host receptors to deceive the immune system to get the best conditions for growth. However, our knowledge about communication mediated by QS is still limited and detailed understanding of molecular mechanisms of QS signaling is desired.

Presence of the Hmq System and Production of 4-Hydroxy-3-Methyl-2-Alkylquinolines Are Heterogeneously Distributed between Burkholderia cepacia Complex Species and More Prevalent among Environmental than Clinical Isolates

The Burkholderia cepacia complex (Bcc) comprises several species of closely related, versatile bacteria. Some Bcc strains produce 4-hydroxy-3-methyl-2-alkylquinolines (HMAQs), analogous to the 4-hydroxy-2-alkylquinolines of Pseudomonas aeruginosa. Using in silico analyses, we previously estimated that the hmqABCDEFG operon, which encodes enzymes involved in the biosynthesis of HMAQs, is carried by about one-third of Bcc strains, with considerable inter- and intraspecies variability. In the present study, we investigated by PCR, using consensus primers, the distribution of hmqABCDEFG in a collection of 312 Bcc strains (222 of clinical and 90 of environmental origins) belonging to 18 Bcc species. We confirmed that this operon is not distributed evenly among Bcc species. Among the 30% of strains bearing the hmqABCDEFG operon, we found that 92% of environmental isolates and 82% of clinically isolated Bcc strains produce levels of HMAQs detectable by liquid chromatography-mass spectrometry in at least one of the tested culture conditions. Among the hmqABCDEFG-positive but HMAQ-negative strains, none expressed the hmqA gene under the specified culture conditions. Interestingly, the hmqABCDEFG operon is more prevalent among plant root environment species (e.g., Burkholderia ambifaria and Burkholderia cepacia) and absent in species commonly found in chronically colonized individuals with cystic fibrosis (e.g., Burkholderia cenocepacia and Burkholderia multivorans), suggesting a role for the Hmq system in niche adaptation. We investigated the impact of the Hmq system on plant growth promotion and found that Pisum sativum root development by B. ambifaria required a functional HMAQ system.

IMPORTANCE Environmental bacteria belonging to the various closely related species forming the Burkholderia cepacia complex (Bcc) can infect plants and animals, including humans. Their pathogenicity is regulated by intercellular communication, or quorum sensing, allowing them to collaborate instead of acting individually. Bcc organisms generally exploit interacting quorum sensing systems based on N-acyl-homoserine lactones as signaling molecules. Several Bcc strains also carry an hmqABCDEFG operon responsible for the biosynthesis of 4-hydroxy-3-methyl-2-alkylquinolines (HMAQs), molecules analogous to the Pseudomonas quinolone signal (PQS) system of P. aeruginosa. Our finding that the prevalences of the Hmq system and HMAQ production are very different between various Bcc species suggests a key role in niche adaptation or pathogenicity. This is supported by a significant reduction in plant growth promotion in the absence of HMAQ production for a beneficial Bcc strain.

Catalyst-Free [3 + 3] Annulation/Oxidation of Cyclic Amidines with Activated Olefins: When the Substrate Olefin Is Also an Oxidant

Herein we describe a catalyst-free regioselective [3 + 3] annulation/oxidation reaction of cyclic amidines such as DBU (1,8-diazabicyclo(5.4.0)undec-7-ene) and DBN (1,5-diazabicyclo(4.3.0)non-5-ene) with activated olefins, i.e., 2-arylidenemalononitriles and 2-cyano-3-aryl acrylates, to afford tricyclic 2-pyridones and pyridin-2(1H)-imines, respectively. The mechanism has been proposed based on DFT calculations. In the reaction, the cyclic amidines serve as C,N-bisnucleophiles for the cyclization, while the olefins play a dual role by acting as both reactants and oxidants.

Growing emergence of drug-resistant Pseudomonas aeruginosa and attenuation of its virulence using quorum sensing inhibitors: A critical review

A perilous increase in the number of bacterial infections has led to developing throngs of antibiotics for increasing the quality and expectancy of life. Pseudomonas aeruginosa is becoming resistant to all known conventional antimicrobial agents thereby posing a deadly threat to the human population. Nowadays, targeting virulence traits of infectious agents is an alternative approach to antimicrobials that is gaining much popularity to fight antimicrobial resistance. Quorum sensing (QS) involves interspecies communication via a chemical signaling pathway. Under this mechanism, cells work in a concerted manner, communicate with each other with the help of signaling molecules called auto-inducers (AI). The virulence of these strains is driven by genes, whose expression is regulated by AI, which in turn acts as transcriptional activators. Moreover, the problem of antibiotic-resistance in case of infections caused by P. aeruginosa becomes more alarming among immune-compromised patients, where the infectious agents easily take over the cellular machinery of the host while hidden in the QS mediated biofilms. Inhibition of the QS circuit of P. aeruginosa by targeting various signaling pathways such as LasR, RhlR, Pqs, and QScR transcriptional proteins will help in blocking downstream signal transducers which could result in reducing the bacterial virulence. The anti-virulence agent does not pose an immediate selective pressure on growing bacterium and thus reduces the pathogenicity without harming the target species. Here, we review exclusively, the growing emergence of multi-drug resistant (MDR) P. aeruginosa and the critical literature survey of QS inhibitors with their potential application of blocking P. aeruginosa infections.

Efficient Killing of Multidrug-Resistant Internalized Bacteria by AIEgens In Vivo

Bacteria infected cells acting as "Trojan horses" not only protect bacteria from antibiotic therapies and immune clearance, but also increase the dissemination of pathogens from the initial sites of infection. Antibiotics are hard and insufficient to treat such hidden internalized bacteria, especially multidrug-resistant (MDR) bacteria. Herein, aggregation-induced emission luminogens (AIEgens) such as N,N-diphenyl-4-(7-(pyridin-4-yl) benzo [c] [1,2,5] thiadiazol-4-yl) aniline functionalized with 1-bromoethane (TBP-1) and (3-bromopropyl) trimethylammonium bromide (TBP-2) (TBPs) show potent broad-spectrum bactericidal activity against both extracellular and internalized Gram-positive pathogens. TBPs trigger reactive oxygen species (ROS)-mediated membrane damage to kill bacteria, regardless of light irradiation. TBPs effectively kill bacteria without the development of resistance. Additionally, such AIEgens activate mitochondria dependent autophagy to eliminate internalized bacteria in host cells. Compared to the routinely used vancomycin in clinic, TBPs demonstrate comparable efficacy against methicillin-resistant Staphylococcus aureus (MRSA) in vivo. The studies suggest that AIEgens are promising new agents for the treatment of MDR bacteria associated infections.

Molecular Modifications of the Pseudomonas Quinolone Signal in the Intermicrobial Competition with Aspergillus

The Pseudomonas quinolone signal (PQS) is an important quorum-sensing molecule for Pseudomonas aeruginosa that regulates virulence factors, chelates iron, and is an important factor in interactions with eukaryotes, including fungi and mammalian hosts. It was previously shown to inhibit or boost Aspergillus, depending on the milieu iron concentration. We studied several molecular modifications of the PQS molecule, and their effects on Aspergillus biofilm metabolism and growth in vitro, and the effects of iron supplementation. We found that most molecules inhibited Aspergillus at concentrations similar to that of PQS, but with relatively flat dose-responses, and all were less potent than PQS. The inhibition was reversible by iron, suggesting interference with fungal iron metabolism. Stimulation of Aspergillus was not noted. We conclude that the critical Aspergillus-inhibiting moeities of the PQS molecule were partially, but not completely, interfered with by molecular modifications at several sites on the PQS molecule. The mechanism, as with PQS, appears to relate to fungal iron metabolism.

Inhibitor Mimetic Mutations in the Pseudomonas aeruginosa PqsE Enzyme Reveal a Protein-Protein Interaction with the Quorum-Sensing Receptor RhlR That Is Vital for Virulence Factor Production

Pseudomonas aeruginosa is an opportunistic human pathogen that causes fatal infections. There exists an urgent need for new antimicrobial agents to combat P. aeruginosa. We conducted a screen for molecules that bind the virulence-controlling protein PqsE and characterized hit compounds for inhibition of PqsE enzymatic activity. The binding conformations of two inhibitory molecules, BB391 and BB393, were identified by crystallography, and inhibitor binding was mimicked by the substitution of PqsE residues E182 and S285 with tryptophan. Comparison of the inhibitor-mimetic mutations to the catalytically inactive PqsE D73A protein demonstrated that catalysis is not responsible for the role PqsE plays in driving virulence factor production. Rather, the PqsE E182W protein fails to interact with the quorum-sensing receptor, RhlR, and our results suggest that it is this interaction that is responsible for promoting virulence factor production in P. aeruginosa. These findings provide a new route for drug discovery efforts targeting PqsE.

An Overview of Biological and Computational Methods for Designing Mechanism-Informed Anti-biofilm Agents

Bacterial biofilms are complex and highly antibiotic-resistant aggregates of microbes that form on surfaces in the environment and body including medical devices. They are key contributors to the growing antibiotic resistance crisis and account for two-thirds of all infections. Thus, there is a critical need to develop anti-biofilm specific therapeutics. Here we discuss mechanisms of biofilm formation, current anti-biofilm agents, and strategies for developing, discovering, and testing new anti-biofilm agents. Biofilm formation involves many factors and is broadly regulated by the stringent response, quorum sensing, and c-di-GMP signaling, processes that have been targeted by anti-biofilm agents. Developing new anti-biofilm agents requires a comprehensive systems-level understanding of these mechanisms, as well as the discovery of new mechanisms. This can be accomplished through omics approaches such as transcriptomics, metabolomics, and proteomics, which can also be integrated to better understand biofilm biology. Guided by mechanistic understanding, in silico techniques such as virtual screening and machine learning can discover small molecules that can inhibit key biofilm regulators. To increase the likelihood that these candidate agents selected from in silico approaches are efficacious in humans, they must be tested in biologically relevant biofilm models. We discuss the benefits and drawbacks of in vitro and in vivo biofilm models and highlight organoids as a new biofilm model. This review offers a comprehensive guide of current and future biological and computational approaches of anti-biofilm therapeutic discovery for investigators to utilize to combat the antibiotic resistance crisis.

Infrared MALDI Mass Spectrometry with Laser-Induced Postionization for Imaging of Bacterial Colonies

Ultraviolet matrix-assisted laser desorption ionization mass spectrometry imaging (UV-MALDI-MSI) is a powerful tool to visualize bacterial metabolites in microbial colonies and in biofilms. However, a challenge for the method is the efficient extraction of analytes from deeper within the bacterial colonies and from the cytoplasm of individual cells during the matrix coating step. Here, we used a pulsed infrared (IR) laser of 2.94 μm wavelength to disrupt and ablate bacterial cells without a prior coating with a MALDI matrix. Instead, tissue water or, in some experiments, in addition a small amount of glycerol was exploited for the deposition of the IR laser energy and for supporting the ionization of the analytes. Compared to water, glycerol exhibits a lower vapor pressure, which prolonged the available measurement time window within an MSI experiment. Mass spectra were acquired with a hybrid Synapt G2-S HDMS instrument at a pixel size of 120 μm. A frequency-quadrupled q-switched Nd:YAG laser with 266 nm wavelength served for laser-induced postionization (MALDI-2). In this way, the ion abundances of numerous small molecules such as nucleobases, 2-alkyl-quinolones, a prominent class of Pseudomonas aeruginosa signaling molecules involved in one of the three quorum-sensing pathways, and also the signals of various bacterial phospholipids were boosted, partially by orders of magnitude. We analyzed single and cocultured colonies of Gram-negative P. aeruginosa and of Gram-positive Bacillus subtilis and Staphylococcus aureus as exemplary bacterial systems. To enable a rapid (within 5 s) MSI-compatible steam inactivation in a custom-made autoclave filled with hot water steam, bacterial cultures were grown on porous polyamide membranes. Compared to a UV-MALDI-2-MS measurement of the same systems, mass spectra with a reduced low mass background were generally generated. This resulted in the unequivocal detection of numerous metabolites only with the IR laser. In a fundamental part of our study, and to optimize the IR-MALDI-2 approach for the highest analytical sensitivity, we characterized the expansion dynamics of the particle plume as generated by the IR laser. Here, we recorded the total ion count and the intensities of selected signals registered from P. aeruginosa samples as a function of the interlaser delay and buffer gas pressure in the ion source. The data revealed that the IR-MALDI-2 ion signals are primarily generated from slow particles having mean velocities of ∼10 m/s. Interestingly, two different pressure/delay time regimes of the optimized ionization efficiency for phospholipids and smaller metabolites, respectively, were revealed, a result pointing to yet-unknown convoluted reaction cascades. The described IR-MALDI-2 method could be a helpful new tool for a microbial mass spectrometry imaging of small molecules requiring little sample preparation.