An RGB-emitting molecular cocktail for the detection of bacterial fingerprints

Metabolism-triggered sensor array aided by machine learning for rapid identification of pathogens

Chemical-nose strategy has achieved certain success in the discrimination and identification of pathogens. However, this strategy usually relies on non-specific interactions, which are prone to be significantly disturbed by the change of environment thus limiting its practical usefulness. Herein, we present a novel chemical-nose sensing approach leveraging the difference in the dynamic metabolic variation during peptidoglycan metabolism among different species for rapid pathogen discrimination. Pathogens were first tethered with clickable handles through metabolic labeling at two different acidities (pH = 5 and 7) for 20 and 60 min, respectively, followed by click reaction with fluorescence up-conversion nanoparticles to generate a four-dimensional signal output. This discriminative multi-dimensional signal allowed eight types of model bacteria to be successfully classified within the training set into strains, genera, and Gram phenotypes. As the difference in signals of the four sensing channels reflects the difference in the amount/activity of enzymes involved in metabolic labeling, this strategy has good anti-interference capability, which enables precise pathogen identification within 2 h with 100% accuracy in spiked urinary samples and allows classification of unknown species out of the training set into the right phenotype. The robustness of this approach holds significant promise for its widespread application in pathogen identification and surveillance.

Chemical Nose Strategy with Metabolic Labeling and "Antibiotic-Responsive Spectrum" Enables Accurate and Rapid Pathogen Identification

The worldwide antimicrobial resistance (AMR) dilemma urgently requires rapid and accurate pathogen phenotype discrimination and antibiotic resistance identification. The conventional protocols are either time-consuming or depend on expensive instrumentations. Herein, we demonstrate a metabolic-labeling-assisted chemical nose strategy for phenotyping classification and antibiotic resistance identification of pathogens based on the "antibiotic-responsive spectrum" of different pathogens. d-Amino acids with click handles were metabolically incorporated into the cell wall of pathogens for further clicking with dibenzocyclooctyne-functionalized upconversion nanoparticles (DBCO-UCNPs) in the presence/absence of six types of antibiotics, which generates seven-channel sensing responses. With the assistance of machine learning algorithms, eight types of pathogens, including three types of antibiotic-resistant bacteria, can be well classified and discriminated in terms of microbial taxonomies, Gram phenotypes, and antibiotic resistance. The present metabolic-labeling-assisted strategy exhibits good anti-interference capability and improved discrimination ability rooted in the unique sensing mechanism. Sensitive identification of pathogens with 100% accuracy from artificial urinary tract infection samples at a concentration as low as 105 CFU/mL was achieved. Pathogens outside of the training set can also be discriminated well. This clearly demonstrated the potential of the present strategy in the identification of unknown pathogens in clinical samples.

Synthetic engineered bacteria for cancer therapy

INTRODUCTION

Cancer mortality worldwide highlights the urgency for advanced therapeutic methods to fill the gaps in conventional cancer therapies. Bacteriotherapy is showing great potential in tumor regression due to the motility and colonization tendencies of bacteria. However, the complicated in vivo environment and tumor pathogenesis hamper the therapeutic outcomes. Synthetic engineering methods endow bacteria with flexible abilities both at the extracellular and intracellular levels to meet treatment requirements. In this review, we introduce synthetic engineering methods for bacterial modifications. We highlight the recent progress in engineered bacteria and explore how these synthetic methods endow bacteria with superior abilities in cancer therapy. The current clinical translations are further discussed. Overall, this review may shed light on the advancement of engineered bacteria for cancer therapy.

AREAS COVERED

Recent progress in synthetic methods for bacterial engineering and specific examples of their applications in cancer therapy are discussed in this review.

EXPERT OPINION

Bacteriotherapy bridges the gaps of conventional cancer therapies through the natural motility and colonization tendency of bacteria, as well as their synthetic engineering. Nevertheless, to fulfill the bacteriotherapy potential and move into clinical trials, more research focusing on its safety concerns should be conducted.

Portable biosensor-based oral pathogenic bacteria detection for community and family applications

Detection of oral pathogens is essential in the management of oral diseases, as their occurrence and progression are closely linked to an imbalance in these microorganisms. Detection techniques such as microbial cultures, enzyme-linked immunosorbent assays and polymerase chain reactions are highly dependent on complex testing procedures and specialized laboratory equipment, making prevention and early diagnosis of oral diseases difficult. To comprehensively implement oral disease prevention and early diagnosis in social groups, there is an urgent need for portable testing methods for oral pathogenic bacteria that can be applied in community and home settings. In this review, several common portable biosensors for pathogenic bacteria are first described. Based on the goal of achieving primary prevention and diagnosis of oral diseases, we elaborate and summarize portable biosensors for common oral pathogenic bacteria in terms of how to achieve portability of the technique. This review aims to reflect the current status of portable biosensors for common oral pathogens and to lay the foundation for the further realization of portable detection of oral pathogens.

Decorated bacteria and the application in drug delivery

The use of living bacteria either as therapeutic agents or drug carriers has shown great potential in treating a multitude of intractable diseases. However, cells are often fragile to unfriendly environmental stressors and limited by inadequately therapeutic responses, leading to unwanted cell death and a decline in treatment efficacy. Surface decoration of bacteria has emerged as a simple yet useful strategy that not only confers bacteria with extra capacity to resist environmental threats but also endows them with exogenous characteristics that are neither inherent nor naturally achievable. In this review, we systematically introduce the advancements of physicochemical and biological technologies for surface modification of bacteria, especially the single-cell surface decoration strategies of individual bacteria. We highlight the recent progress on surface decoration that aims to improve the bioavailability and efficacy of therapeutic bacterial agents and also to achieve enhanced and targeted delivery of conventional drugs. The promises along with challenges of surface-decorated bacteria as drug delivery systems for applications in cancer therapy, intestinal disease treatment, bioimaging, and diagnosis are further discussed with respect to future clinical translation. This review offers an overview of the advances of decorated bacteria for drug delivery applications and would contribute to the development of the next generation of advanced bacterial-based therapies.

One-Component Multichannel Sensor Array for Rapid Identification of Bacteria

Bacterial infections routinely cause serious problems to public health. To mitigate the impact of bacterial infections, sensing systems are urgently required for the detection and subsequent epidemiological control of pathogenic organisms. Most conventional approaches are time-consuming and highly instrument- and professional operator-dependent. Here, we developed a novel one-component multichannel array constructed with complex systems made from three modified polyethyleneimine as well as negatively charged graphene oxide, which provided an information-rich multimode response to successfully identify 10 bacteria within minutes via electrostatic interactions and hydrophobic interactions. Furthermore, the concentration of bacteria (from OD₆₀₀ = 0.025 to 1) and the ratio of mixed bacteria were successfully achieved with our smart sensing system. Our designed sensor array also exhibited huge potential in biological samples, such as in urine (OD₆₀₀ = 0.125, 94% accuracy). The way to construct a sensor array with minimal sensor element with abundant signal outputs tremendously saves cost and time, providing a powerful tool for the diagnosis and assessment of bacterial infections in the clinic.

Rapid Identification of Fupenzi (Rubus chingii Hu) and Its Adulteration by AuNP Visualization

Fupenzi (Rubus chingii Hu) is a dried and immature fruit in East China, which has effects of nourishing kidneys, solidifying essence, and otherwise. Because Fupenzi was often adulterated and replaced with inferior things, this paper had researched Fupenzi and its adulterant raspberry. A new type of visible sensor was constructed by using Au nanoparticles (AuNPs), which was modified by the surface-active agent and combined with the ultraviolet-visible (UV-vis) spectrum technology. It was found that the change in particle size after the interaction of AuNPs and adulterants will lead to color change. In this paper, the RGB (red, green, and blue) values of the solution were extracted to correlate the color with the concentration of adulterants, and the relationship between the absorption peak intensity and the concentration of adulterants was established. The results showed that the intensity of an absorption peak is related to adulteration concentration, and the color of the solution changed from red to gray as the particle size changed. The visual sensor constructed based on the above principle is a fast and precise method to detect adulteration with different concentrations, which has a potential application value in real-time and rapid detection of Fupenzi’s quality.

Metabolism-Triggered Colorimetric Sensor Array for Fingerprinting and Antibiotic Susceptibility Testing of Bacteria

The rapid identification and antibiotic susceptibility testing (AST) of bacteria would help us to accurately identify the infectious sources as well as guide the use of antibiotics, which are crucial for improving the survival rate and antimicrobial resistance. Herein, a colorimetric sensor array for bacteria fingerprinting was constructed with d-amino acid (d-AA)-modified gold nanoparticles (AuNPs) as probes (Au/d-AA). Bacteria can metabolize the d-AA, triggering the aggregation of AuNPs. Making use of different metabolic capabilities of bacteria toward different d-AA, eight kinds of bacteria including antibiotic-resistant bacteria and strains of the same bacterial species are successfully differentiated via learning the response patterns. Meanwhile, the sensor array also performs well in quantitative analysis of single bacterium and differentiation of bacteria mixtures. More interestingly, a rapid colorimetric AST approach has been developed based on the Au/d-AA nanoprobes by monitoring the d-AA metabolic activity of bacteria toward various antibiotic treatments. In this regard, the outlined work here would promote clinical practicability and facilitate antibiotic stewardship.

Engineering bacterial surface interactions using DNA as a programmable material

The diverse surface interactions and functions of a bacterium play an important role in cell signaling, host infection, and colony formation. To understand and synthetically control the biological functions of individual cells as well as the whole community, there is growing attention on the development of chemical and biological tools that can integrate artificial functional motifs onto the bacterial surface to replace the native interactions, enabling a variety of applications in biosynthesis, environmental protection, and human health. Among all these functional motifs, DNA emerges as a powerful tool that can precisely control bacterial interactions at the bio-interface due to its programmability and biorecognition properties. Compared with conventional chemical and genetic approaches, the sequence-specific Watson-Crick interaction enables almost unlimited programmability in DNA nanostructures, realizing one base-pair spatial control and bio-responsive properties. This highlight aims to provide an overview on this emerging research topic of DNA-engineered bacterial interactions from the aspect of synthetic chemists. We start with the introduction of native bacterial surface ligands and established synthetic approaches to install artificial ligands, including direct modification, metabolic engineering, and genetic engineering. A brief overview of DNA nanotechnology, reported DNA-bacteria conjugation chemistries, and several examples of DNA-engineered bacteria are included in this highlight. The future perspectives and challenges in this field are also discussed, including the development of dynamic bacterial surface chemistry, assembly of programmable multicellular community, and realization of bacteria-based theranostic agents and synthetic microbiota as long-term goals.

Single Probe-Based Chemical-Tongue Sensor Array for Multiple Bacterial Identification and Photothermal Sterilization in Real Time

Simple and efficient identification of multiple bacteria and sterilization in real time is of considerable significance for clinical diagnostics and quality control in food. Herein, a novel chemical-tongue sensor array with 3,3',5,5'-tetramethylbenzidine (TMB) as a single probe was developed for bacterial identification and photothermal elimination. The synthesized bimetallic palladium/platinum nanoparticles (Pd/Pt_NPs) present excellent catalytic capability that can catalyze TMB into oxidized TMB (oxTMB) with four feature absorption peaks. Bacteria have different ability on inhibiting the reaction between TMB and Pd/Pt_NPs. With the absorbance intensity of oxTMB at the four feature peaks as readout, nine kinds of bacteria including two drug-resistant bacteria can be successfully distinguished via linear discriminant analysis. Remarkably, oxTMB exhibits excellent photothermal properties and can effectively kill bacteria in real time under near-infrared laser irradiation. The strategy of selecting TMB as a single probe simplifies the experimental operation and reduces the time cost. Furthermore, the developed sensing system was used to promote the wound healing process of MRSA-infected mice in vivo. The investigation provides a promising simple and efficient strategy for bacterial identification and sterilization with a universal platform, which has great potential application in clinical diagnosis and therapy.

Machine Learning-Assisted Pattern Recognition of Amyloid Beta Aggregates with Fluorescent Conjugated Polymers and Graphite Oxide Electrostatic Complexes

Five fluorescent positively charged poly(para-aryleneethynylene) (P1-P5) were designed to construct electrostatic complexes C1-C5 with negatively charged graphene oxide (GO). The fluorescence of conjugated polymers was quenched by the quencher GO. Three electrostatic complexes were enough to distinguish between 12 proteins with 100% accuracy. Furthermore, using these sensor arrays, we could identify the levels of Aβ40 and Aβ42 aggregates (monomers, oligomers, and fibrils) via employing machine learning algorithms, making it an attractive strategy for early diagnosis of Alzheimer's disease.

A multifunctional colorimetric sensor array for bacterial identification and real-time bacterial elimination to prevent bacterial contamination

The constructed sensor array has simple operation and successfully integrates bacterial identification and inactivation.

Customized materials-assisted microorganisms in tumor therapeutics

Microorganisms have been extensively applied as active biotherapeutic agents or drug delivery vehicles for antitumor treatment because of their unparalleled bio-functionalities. Taking advantage of the living attributes of microorganisms, a new avenue has been opened in anticancer research. The integration of customized functional materials with living microorganisms has demonstrated unprecedented potential in solving existing questions and even conferring microorganisms with updated antitumor abilities and has also provided an innovative train of thought for enhancing the efficacy of microorganism-based tumor therapy. In this review, we have summarized the emerging development of customized materials-assisted microorganisms (MAMO) (including bacteria, viruses, fungi, microalgae, as well as their components) in tumor therapeutics with an emphasis on the rational utilization of chosen microorganisms and tailored materials, the ingenious design of biohybrid systems, and the efficacious antitumor mechanisms. The future perspectives and challenges in this field are also discussed.

Fast label-free identification of bacteria by synchronous fluorescence of amino acids

Fast identification of pathogenic bacteria is an essential need for patient's diagnostic in hospitals and environmental monitoring of water and air quality. Bacterial cells consist of a very high amount of biological molecules whose content changes in response to different environmental conditions. The similarity between the molecular compositions of different bacterial cells limits the possibility to find unique markers to enable differentiation among species. Although many biological molecules in the cells absorb at the UV-Vis region, only a few of them can be detected in whole cells by their intrinsic fluorescence. Among these molecules are the amino acids phenylalanine, tyrosine, and tryptophan. In this work, we develop a rapid method for bacterial identification by synchronous fluorescence. We show that we can quantify the concentration for the 3 amino acids without any significant interference from other fluorophores in the cells and that we can differentiate among 6 pathogenic bacterial species by using the concentrations of their amino acids as a bacterial fingerprint. Fluorescent amino acids exist in all living cells. Therefore, this method has the potential to be applicative for the rapid identification of cells from all kinds of organisms.

Antibacterial AIE polycarbonates endowed with selective imaging capabilities by adjusting the electrostaticity of the mixed-charge backbone

Combining rapid microbial discrimination with antibacterial properties, multi-functional biomacromolecules allow the timely diagnosis and effective treatment of infectious diseases. Through a two-step approach involving organocatalytic ring-opening copolymerization and thiol-ene modification, aggregation-induced emission (AIE) polycarbonates decorated with tertiary amines were prepared. After being ionized using acetic acid, the obtained cationic AIE polycarbonate with excellent water solubility showed bacteria imaging capabilities and antibacterial activities toward both Gram-positive S. aureus and Gram-negative E. coli. It was indicated via scanning electron microscope images that the bactericidal mechanism involved membrane lysis, consistent with most cationic polymers. Through further co-grafting carboxyl and tertiary amine groups, mixed-charge AIE polycarbonates were obtained. The isoelectric points of such mixed-charge AIE polycarbonates could be simply tuned based on the grafting ratio of positive and negative moieties. Compared with the cationic AIE polycarbonate, mixed-charge AIE polycarbonates allowed the rapid and selective imaging of S. aureus, but not E. coli. The selectivity probably arose from the lower binding forces between the mixed-charge AIE polycarbonates and the low-negative-charge components of the E. coli surface. Therefore, these biodegradable polycarbonates, which integrated selective bacteria imaging and antibiotic abilities, potentially suggest a precision medicine approach for infectious diseases. The overall synthesis approach and mixed-charge AIE polycarbonates provide new references for the design and application of bio-related AIE polymers.

Surface-Enhanced Raman Spectroscopy of Bacterial Metabolites for Bacterial Growth Monitoring and Diagnosis of Viral Infection

Bacterial metabolites are intermediate products of bacterial metabolism and their production reflects metabolic activity. Herein, we report the use of surface-enhanced Raman spectroscopy (SERS) for detection of both volatile and nonvolatile metabolites and the application of this approach for bacterial growth quantification and diagnosis of viral infection. The time-dependent SERS signal of the volatile metabolite dimethyl disulfide in the headspace above bacteria growing on an agar plate was detected and quantified. In addition, SERS signals arising from the plate reflected nutrient consumption and production of nonvolatile metabolites. The measurement of metabolite accumulation can be used for bacterial quantification. In the presence of bacteriophage virus, bacterial metabolism is suppressed, and the relative decrease in SERS intensity reflects the initial virus concentration. Using multivariate analysis, we detect viral infection with a prediction accuracy of 93%. Our SERS-based approach for metabolite production monitoring provides new insights toward viral infection diagnosis.

Theranostic platforms for specific discrimination and selective killing of bacteria

Bacterial infections are serious threats to public health due to lack of advanced techniques to rapidly and accurately diagnose these infections in clinics. Although bacterial infections can be treated with broad-spectrum antibiotics based on empirical judgment, the emergence of antimicrobial resistance has attracted global attention due to long-term misuse and abuse of antibiotics by humans in recent decades. Therefore, it is imperative to selectively discriminate and precisely eliminate pathogenic bacteria. Herein, in addition to the conventional methods for bacterial identification, we comprehensively reviewed the recently developed theranostic platforms for specific discrimination and selective killing of bacteria according to their different interactions with the target bacteria, such as electrostatic and hydrophobic interactions, molecular recognition, microenvironment response, metabolic labeling, bacteriophage targeting, and others. These theranostic agents not only benefit from improved therapeutic efficiency but also present limited susceptibility to induce bacterial resistance. The strategies summarized in this review will open up new avenues in developing effective antimicrobial materials to accurately diagnose and treat bacterial infections in the post-antibiotic era. STATEMENT OF SIGNIFICANCE: Bacterial infections are difficult to be rapidly and accurately diagnosed, and are generally treated with broad-spectrum antibiotics, which leads to the development of drug resistance. By integrating imaging modalities and therapeutic methods in a single treatment, various theranostic agents have been developed to address the abovementioned issues. Therefore, the emerging theranostic platforms for selective identification and elimination of bacteria based on the distinct interactions of the theranostic agents with the target bacteria are summarized in this review. We believe that the information provided in this review will guide researchers in designing advanced antibacterial theranostics for practical applications in the post-antibiotic era.

Engineering diformyl diaryldipyrromethane into a molecular keypad lock

A diaryldipyrromethane-based acyclic system acts as a photolabile sequential chemosensor for both anions and cations via ESIDPT and deprotonation, which is engineered into a fluorescent molecular keypad lock system.