High-throughput prescreening of pharmaceuticals using a genome-wide bacterial bioreporter array

Discovery of antimicrobials by massively parallelized growth assays (Mex)

The number of newly approved antimicrobial compounds has been steadily decreasing over the past 50 years emphasizing the need for novel antimicrobial substances. Here we present Me^x, a method for the high-throughput discovery of novel antimicrobials, that relies on E. coli self-screening to determine the bioactivity of more than ten thousand naturally occurring peptides. Analysis of thousands of E. coli growth curves using next-generation sequencing enables the identification of more than 1000 previously unknown antimicrobial peptides. Additionally, by incorporating the kinetics of growth inhibition, a first indication of the mode of action is obtained, which has implications for the ultimate usefulness of the peptides in question. The most promising peptides of the screen are chemically synthesized and their activity is determined in standardized susceptibility assays. Ten out of 15 investigated peptides efficiently eradicate bacteria at a minimal inhibitory concentration in the lower µM or upper nM range. This work represents a step-change in the high-throughput discovery of functionally diverse antimicrobials.

Bayesian-based decipherment of in-depth information in bacterial chemical sensing beyond pleasant/unpleasant responses

Chemical sensing is vital to the survival of all organisms. Bacterial chemotaxis is conducted by multiple receptors that sense chemicals to regulate a single signalling system controlling the transition between the direction (clockwise vs. counterclockwise) of flagellar rotation. Such an integrated system seems better suited to judge chemicals as either favourable or unfavourable, but not for identification purposes though differences in their affinities to the receptors may cause difference in response strength. Here, an experimental setup was developed to monitor behaviours of multiple cells stimulated simultaneously as well as a statistical framework based on Bayesian inferences. Although responses of individual cells varied substantially, ensemble averaging of the time courses seemed characteristic to attractant species, indicating we can extract information of input chemical species from responses of the bacterium. Furthermore, two similar, but distinct, beverages elicited attractant responses of cells with profiles distinguishable with the Bayesian procedure. These results provide a basis for novel bio-inspired sensors that could be used with other cell types to sense wider ranges of chemicals.

Screening of metallic pollution in complex environmental samples through a transcriptomic fingerprint method

Characterizing waste ecotoxicity is laborious because of both the undefined nature of environmental samples and the diversity of contaminants that can be present. With regard to these limitations, traditional approaches do not provide information about the nature of the pollution encountered. To improve such assessments, a fluorescent library of 1870 transcriptomic reporters from Escherichia coli K12 MG1655 was used to report the ecotoxic status of environmental samples. The reliability of the approach was evaluated with 6 metallic pollutants (As, Cu, Cd, Hg, Pb, Zn) used alone and in mixture in pure and complex matrices. A total of 18 synthetic samples were used to characterize the specificity of the resulting metallic contamination fingerprints. Metallic contamination impacted 4.5 to 10.2% of the whole transcriptomic fingerprint of E. coli. The analysis revealed that a subset of 175 transcriptomic reporters is sufficient to characterize metallic contamination, regardless of the nature of the sample. A statistical model distinguished patterns due to metallic contamination and provided information about the level of toxicity with 93 to 98% confidence. The use of the transcriptomic assessment was validated for 17 complex matrices with various toxicities and metal contaminants, such as activated sludge, wastewater effluent, soil, wood and river water. The presence of metals and their associated toxicity, which seems linked to their bioavailabilities, were thereby determined. This method constitutes a possible tool to screen unknown complex samples for their metallic status and identify those for which a deeper characterization must be achieved by the use of traditional biosensors and analytical methods.

The polyaminosaccharide-based buffers as a new type of zwitterionic buffering macromolecules for biochemical applications

A new type of biocompatible buffers based on zwitterionic polyaminosaccharides is reported. The carboxy- and amino-groups containing carboxymethyl chitosan (CM-CS) was synthesized and reacted with hydrochloric/acetic acid resulting in CM-CS-HCl and CM-CS-HAc buffers with buffering capacity of 20.6 and 15.2 mM/pH. The new buffers were comprehensively characterized for their physicochemical properties and checked on enzymatic reactions of acetylcholinesterase (AChE) and alkaline phosphatase (ALP). Their performance was compared to the phosphate and Tris buffers. The chloride-free, CM-CS-HAc demonstrated excellent buffering activity with Michaelis constants of 0.50 and 1.00 mM and maximum reaction rates of 5.62 and 2.26 μmol/min/mL for AChE and ALP reactions, respectively. Toxicity studies on stress-sensitive bioreporter bacteria verified nontoxicity of CM-CS-HAc. Zwitterionic polyaminosaccharides overcome drawbacks of monomeric buffers, such as interference with enzyme active sites, cell membrane injury and purification difficulties. Therefore, they may become the next generation of effective buffers for biological and biochemical applications.

Technologies for High-Throughput Identification of Antibiotic Mechanism of Action

There are two main strategies for antibiotic discovery: target-based and phenotypic screening. The latter has been much more successful in delivering first-in-class antibiotics, despite the major bottleneck of delayed Mechanism-of-Action (MOA) identification. Although finding new antimicrobial compounds is a very challenging task, identifying their MOA has proven equally challenging. MOA identification is important because it is a great facilitator of lead optimization and improves the chances of commercialization. Moreover, the ability to rapidly detect MOA could enable a shift from an activity-based discovery paradigm towards a mechanism-based approach. This would allow to probe the grey chemical matter, an underexplored source of structural novelty. In this study we review techniques with throughput suitable to screen large libraries and sufficient sensitivity to distinguish MOA. In particular, the techniques used in chemical genetics (e.g., based on overexpression and knockout/knockdown collections), promoter-reporter libraries, transcriptomics (e.g., using microarrays and RNA sequencing), proteomics (e.g., either gel-based or gel-free techniques), metabolomics (e.g., resourcing to nuclear magnetic resonance or mass spectrometry techniques), bacterial cytological profiling, and vibrational spectroscopy (e.g., Fourier-transform infrared or Raman scattering spectroscopy) were discussed. Ultimately, new and reinvigorated phenotypic assays bring renewed hope in the discovery of a new generation of antibiotics.

Simultaneous elucidation of antibiotic mechanism of action and potency with high-throughput Fourier-transform infrared (FTIR) spectroscopy and machine learning

The low rate of discovery and rapid spread of resistant pathogens have made antibiotic discovery a worldwide priority. In cell-based screening, the mechanism of action (MOA) is identified after antimicrobial activity. This increases rediscovery, impairs low potency candidate detection, and does not guide lead optimization. In this study, high-throughput Fourier-transform infrared (FTIR) spectroscopy was used to discriminate the MOA of 14 antibiotics at pathway, class, and individual antibiotic level. For that, the optimal combinations and parametrizations of spectral preprocessing were selected with cross-validated partial least squares discriminant analysis, to which various machine learning algorithms were applied. This coherently resulted in very good accuracies, independently of the algorithms, and at all levels of MOA. Particularly, an ensemble of subspace discriminants predicted the known pathway (98.6%), antibiotic classes (100%), and individual antibiotics (97.8%) with exceptional accuracy, and similar results were obtained for simulated novel MOA. Even at very low concentrations (1 μg/mL) and growth inhibition (15%), over 70% pathway and class accuracy was achieved, suggesting FTIR spectroscopy can probe the grey chemical matter. Prediction of inhibitory effect was also examined, for which a squared exponential Gaussian process regression yielded a root mean square error of 0.33 and a R² of 0.92, indicating that metabolic alterations leading to growth inhibition are intrinsically reflected on FTIR spectra beyond cell density. KEY POINTS: • Antibiotic MOA and potency estimated with high-throughput FTIR spectroscopy • Sub-inhibitory MOA identification suggests ability to explore grey chemical matter • Data analysis optimization improved MOA identification at antibiotic level by 38.

Different bacterial host-based lux reporter array for fast identification and toxicity indication of multiple metal ions

Although luminescent bacteria-based bioluminescence inhibition assay has been widely used in the toxicity assessment of environmental pollutants, the response of a luminescent bacterium usually lacks specificity to a target analyte. Recently, some specific analyte inductive promoters were fused to the lux genes for the purpose of selective bioluminescent sensing, and suits of specific promoters were fused to lux genes to compose a bioluminescent array sensor for simultaneous identification of multiple analytes. However, specific promoter-based methods still suffer from drawbacks including limited selectivity, slow responding time, expensive to construct different promoters involved plasmids, and laborious to find new promoters. Herein, we proposed a novel strategy to construct a lux reporter array sensor by directly transforming the natural lux genes in different bacterial hosts without the involvement of any specific promoters. Due to the distinct pathways of signal production, the responding time of the current different bacterial host (DBH)-based lux reporter array has nearly an order of magnitude faster than with specific promoter-based methods. The DBH-based lux reporter array was successfully used for simultaneous identification, quantification, and toxicity/bioactivity assessment of multiple metal ions. Obviously, all the chemical synthetic material-based metal ion sensing methods cannot simultaneously achieve analysis and toxicity evaluation. This approach possessed additional advantages of facile construction, easy operation, high selectivity, fast response, and strong adaptability to other analytes. A different bacterial host-based lux reporter array was established for simultaneous analysis and toxicity assessment of multiple metal ions.

Aminated Polysaccharide-Based Nanoassemblies as Stable Biocompatible Vehicles Enabling Crossing of Biological Barriers: An Effective Transdermal Delivery of Diclofenac Medicine

A series of stable polysaccharide derivatives that spontaneously self-assemble into nanocarriers was synthesized by applying a reductive amination on chitosan. The prepared nanocarriers were comprehensively studied and found to allow encapsulation of molecular cargo in both aqueous and lipidic media and deliver this cargo across biological barriers. The nanocarriers have demonstrated effective transdermal delivery of diclofenac (Voltaren), a nonsteroidal anti-inflammatory drug, by increasing its skin permeation up to 100 vs the tested control. The modified polysaccharides were studied with a panel of three types of bioreporter bacteria sensitive to genotoxic and cytotoxic stresses. These studies showed the general safety of the prepared nanocarriers and provided insights concerning their activity in collaboration with the aliphatic side chain length. The described nanocarriers could be applied as tunable biocompatible vehicles for the delivery of medicines, cosmetic agents, and in other applications.

Development of a green fluorescence protein (GFP)-based bioassay for detection of antibiotics and its application in milk

Antibiotics are one of the most widely used types of drugs in pharmaceutics. However, efficiency of these drugs has decreased recently owing to the threat of antibiotic resistance. One of the important factors causing antibiotic resistance is the excessive use of antibacterials in animals. Therefore, detection of antibiotics in foods of animal origin is crucial. The aim of this study was to develop a novel whole-cell based bioassay to be used for detection of some antibiotics. Green fluorescent protein (GFP)-expressing Escherichia coli cells were used as a recognition agent, and antibiotic detection was carried out by pursuing the inhibition rate of fluorescence intensity as a result of the inhibition of viable cells by the time of progress. The performance of bioassay was tested for different antibiotics, and the obtained results showed that the developed method can be used successfully for detection of ampicillin, benzylpenicillin, gentamicin, neomycin, and tetracycline with the limit of detection (LOD) values of 3.33, 0.29, 28.00, 618.36, and 33.17 µg/L, respectively. The assay was also tested with antibiotic spiked milk samples (skimmed UHT, full-fat UHT, and whole raw milk). According to obtained recovery values, developed method was successful for all samples. The precision and bias values of the method were found between the range of 1.30% to 7.54% and -8.00% to 0.64%, respectively. The developed method, which is inexpensive and simple with detection limits in line with the regulatory limits, is promising for use in milk quality monitoring. Method has potential to be used as a screening method after comprehensive validation. PRACTICAL APPLICATION: This method could be used in animal husbandry to check whether the antibiotic prescribed for the treatment of sick animals is still present in their milk as residual. For dairy industry, detection of residual antibiotics in milk is crucial because of their inhibition effects on the fermentation processes. Therefore, the proposed method can be used for routine analysis of raw milk reception in dairy industries. In addition, it is considered to have a wide range of applications for all foods.

Chemical genomics reveals mechanistic hypotheses for uncharacterized bioactive molecules in bacteria

In an effort to combat the perpetual emergence of new antibiotic-resistant human pathogens, research in industry and academe aims to find new means of controlling infection. The discovery of new antimicrobial chemicals is not the bottleneck in an era where high-throughput screening rapidly uncovers new bioactive compounds. Rather, the rate-limiting step in antimicrobial discovery pipelines is identifying mechanisms of action (MOA) of bioactive molecules produced by these increasingly large-scale efforts. Chemical genomics has proven to be of high value in providing mechanistic hypotheses for novel bioactive chemical matter. Several techniques fall under this blanket term, including interactions with deletion or transposon libraries, fluorescent or luminescent reporter library profiles, or deep sequencing approaches. Each of these provide unique and complementary outputs, and have high value in generating target lists for chemical screens, or assisting in downstream MOA discovery. We review here the broad usefulness of this technique to aid in MOA determination, to identify targets for new lead molecules, and to expand our mechanistic understanding of existing drugs.

Chemically individual armoured bioreporter bacteria used for the in vivo sensing of ultra-trace toxic metal ions

A chemically engineered mesoporous silica armour is developed for simultaneously improving bioreporter bacterial vitality and shielding infectivity.

Toxicity evaluation of e-juice and its soluble aerosols generated by electronic cigarettes using recombinant bioluminescent bacteria responsive to specific cellular damages

Electronic-cigarettes (e-cigarette) are widely used as an alternative to traditional cigarettes but their safety is not well established. Herein, we demonstrate and validate an analytical method to discriminate the deleterious effects of e-cigarette refills (e-juice) and soluble e-juice aerosol (SEA) by employing stress-specific bioluminescent recombinant bacterial cells (RBCs) as whole-cell biosensors. These RBCs carry luxCDABE-operon tightly controlled by promoters that specifically induced to DNA damage (recA), superoxide radicals (sodA), heavy metals (copA) and membrane damage (oprF). The responses of the RBCs following exposure to various concentrations of e-juice/SEA was recorded in real-time that showed dose-dependent stress specific-responses against both the e-juice and vaporized e-juice aerosols produced by the e-cigarette. We also established that high doses of e-juice (4-folds diluted) lead to cell death by repressing the cellular machinery responsible for repairing DNA-damage, superoxide toxicity, ion homeostasis and membrane damage. SEA also caused the cellular damages but the cells showed enhanced bioluminescence expression without significant growth inhibition, indicating that the cells activated their global defense system to repair these damages. DNA fragmentation assay also revealed the disintegration of total cellular DNA at sub-toxic doses of e-juice. Despite their state of matter, the e-juice and its aerosols induce cytotoxicity and alter normal cellular functions, respectively that raises concerns on use of e-cigarettes as alternative to traditional cigarette. The ability of RBCs in detecting both harmful effects and toxicity mechanisms provided a fundamental understanding of biological response to e-juice and aerosols.

Recent Advances in Genetic Technique of Microbial Report Cells and Their Applications in Cell Arrays

Microbial cell arrays have attracted consistent attention for their ability to provide unique global data on target analytes at low cost, their capacity for readily detectable and robust cell growth in diverse environments, their high degree of convenience, and their capacity for multiplexing via incorporation of molecularly tailored reporter cells. To highlight recent progress in the field of microbial cell arrays, this review discusses research on genetic engineering of reporter cells, technologies for patterning live cells on solid surfaces, cellular immobilization in different polymers, and studies on their application in environmental monitoring, disease diagnostics, and other related fields. On the basis of these results, we discuss current challenges and future prospects for novel microbial cell arrays, which show promise for use as potent tools for unraveling complex biological processes.