Engineered reporter phages for detection of Escherichia coli, Enterococcus, and Klebsiella in urine

A saccharides regulated fluorescence ratio sensing array for bacterial recognition based on lectin response

Array sensing employs cross-identification among analytes and various sensing units to identify substances or complex systems. This manuscript presents a fluorescence ratio sensing array based on lectin responses for the accurate identification of different bacteria. This strategy uses a saccharide-sensitive polymer as the sensing unit within the sensor. By incorporating various saccharides, it regulates the properties of the single sensing unit at the molecular level, altering its interaction with the analyte. This modulation leads to the generation of multiple distinct detection signals for the target, effectively facilitating the goal of array sensing. This approach streamlines the design and construction of the array sensor, while simultaneously enhancing detection efficiency. Not only does this sensing strategy achieve the differentiation and quantification of various types of lectins, but it also enables the identification of different bacterial species based on their unique lectin response profiles. This research introduces a novel approach that simplifies the construction of array sensors and simultaneously furnishes a potent tool for diagnosing and assessing bacterial infections within clinical settings.

Engineering Phages to Fight Multidrug-Resistant Bacteria

Facing the global "superbug" crisis due to the emergence and selection for antibiotic resistance, phages are among the most promising solutions. Fighting multidrug-resistant bacteria requires precise diagnosis of bacterial pathogens and specific cell-killing. Phages have several potential advantages over conventional antibacterial agents such as host specificity, self-amplification, easy production, low toxicity as well as biofilm degradation. However, the narrow host range, uncharacterized properties, as well as potential risks from exponential replication and evolution of natural phages, currently limit their applications. Engineering phages can not only enhance the host bacteria range and improve phage efficacy, but also confer new functions. This review first summarizes major phage engineering techniques including both chemical modification and genetic engineering. Subsequent sections discuss the applications of engineered phages for bacterial pathogen detection and ablation through interdisciplinary approaches of synthetic biology and nanotechnology. We discuss future directions and persistent challenges in the ongoing exploration of phage engineering for pathogen control.

Utilizing Golden Gate Assembly to Streamline CRISPR-Cas/NgTET-Based Phage Mutagenesis

Phage engineering is an emerging technology due to the promising potential application of phages in medical and biotechnological settings. Targeted phage mutagenesis tools are required to customize the phages for a specific application and generate, in addition to that, so-called designer phages. CRISPR-Cas technique is used in various organisms to perform targeted mutagenesis. Yet, its efficacy is notably limited for phage mutagenesis due to the highly abundant phage DNA modifications. Addressing this challenge, we have developed a novel approach that involves the temporal removal of phage DNA cytosine modifications, allowing for effective CRISPR-Cas targeting and subsequent introduction of mutations into the phage genome. The removal of cytosine modification relies on the catalytic activity of a eukaryotic ten-eleven translocation methylcytosine (TET) dioxygenase. TET enzymes iteratively de-modify methylated or hydroxymethylated cytosines on phage DNA. The temporal removal of cytosine modification ultimately enables efficient DNA cleavage by Cas enzymes and facilitates mutagenesis. To streamline the application of the coupled TET-CRISPR-Cas system, we use Golden Gate cloning for fast and efficient assembly of a vector that comprises a TET oxidase and a donor DNA required for scarless site-specific phage mutagenesis. Our approach significantly advances the engineering of modified phage genomes, enabling the efficient generation of customized phages for specific applications.

Emerging Combination of Hydrogel and Electrochemical Biosensors

Electrochemical sensors are among the most promising technologies for biomarker research, with outstanding sensitivity, selectivity, and rapid response capabilities that make them important in medical diagnostics and prognosis. Recently, hydrogels have gained attention in the domain of electrochemical biosensors because of their superior biocompatibility, excellent adhesion, and ability to form conformal contact with diverse surfaces. These features provide distinct advantages, particularly in the advancement of wearable biosensors. This review examines the contemporary utilization of hydrogels in electrochemical sensing, explores strategies for optimization and prospective development trajectories, and highlights their distinctive advantages. The objective is to provide an exhaustive overview of the foundational principles of electrochemical sensing systems, analyze the compatibility of hydrogel properties with electrochemical methodologies, and propose potential healthcare applications to further illustrate their applicability. Despite significant advances in the development of hydrogel-based electrochemical biosensors, challenges persist, such as improving material fatigue resistance, interfacial adhesion, and maintaining balanced water content across various environments. Overall, hydrogels have immense potential in flexible biosensors and provide exciting opportunities. However, resolving the current obstacles will necessitate additional research and development efforts.

The rise, fall, and resurgence of phage therapy for urinary tract infection

In the face of rising antimicrobial resistance, bacteriophage therapy, also known as phage therapy, is seeing a resurgence as a potential treatment for bacterial infections including urinary tract infection (UTI). Primarily caused by uropathogenic Escherichia coli, the 400 million UTI cases annually are major global healthcare burdens and a primary cause of antibiotic prescriptions in the outpatient setting. Phage therapy has several potential advantages over antibiotics including the ability to disrupt bacterial biofilms and synergize with antimicrobial treatments with minimal side effects or impacts on the microbiota. Phage therapy for UTI treatment has shown generally favorable results in recent animal models and human case reports. Ongoing clinical trials seek to understand the efficacy of phage therapy in individuals with asymptomatic bacteriuria and uncomplicated cystitis. A possible challenge for phage therapy is the development of phage resistance in bacteria during treatment. While resistance frequently develops in vitro and in vivo, resistance can come with negative consequences for the bacteria, leaving them susceptible to antibiotics and other environmental conditions and reducing their overall virulence. "Steering" bacteria toward phage resistance outcomes that leave them less fit or virulent is especially useful in the context of UTI where poorly adherent or slow-growing bacteria are likely to be flushed from the system. In this article, we describe the history of phage therapy in treating UTI and its current resurgence, the state of its clinical use, and an outlook on how well-designed phage therapy could be used to "steer" bacteria toward less virulent and antimicrobial-susceptible states.

Rapid point-of-care pathogen sensing in the post-pandemic era

In the post-pandemic era, interest in on-site technologies capable of rapidly and accurately diagnosing viral or bacterial pathogens has significantly increased. Advances in functional nanomaterials and bioengineering have propelled the progress of point-of-care (POC) sensors, enhancing their speed, specificity, sensitivity, affordability, ease of use, and accuracy. Notably, biosensors that utilize surface-enhanced Raman scattering (SERS) technology have revolutionized the rapid and sensitive diagnosis of biomarkers in pathogenic infections. This review of current POC diagnostics highlights the growing emphasis on immunoassays for swift pathogen analysis, augmented by the integration of deep learning for swift interpretation of complex signals through tailored algorithms.

Characteristics of the Enterococcus Phage vB_EfS_SE, and the Properties of Its Chimeric Endolysins Harboring a PlySE-Carbohydrate-Binding Domain and a Synthetic Enzymatic Domain

Background/Objectives: The World Health Organization has selected enterococci as one of the priority multidrug-resistant microorganisms for the development of new antibacterial drugs. Bacteriophages are promising antibacterial agents, but the biology of bacteriophages requires deeper understanding. Methods: The vB_EfS_SE phage which is capable of infecting four species of the genus Enterococci was isolated from sewage plant. The complete genome of the vB_EfS_SE phage was sequenced using illumina technology. The endolysin gene was cloned into pBAD18 expression vector. Two chimeric endolysins were engineered using the vB_EfS_SE carbohydrate-binding domain (CBD) and replacing its enzymatically active domain (EAD). Results: The bacteriophage exhibits promising lytic properties and persists at temperatures of 40 °C and below, and under pH conditions ranging from 5 to 11. The genome sequence is 57,904 bp in length. The vB_EfS_SE endolysin PlySE and chimeric endolysins PlyIME-SE and PlySheep-SE were found to have the same range of specificity, but different thermostability properties and a different pH range for enzyme activity. Conclusions: Taking together the results obtained in this work and other published studies, we can highly appreciate the potential of Saphexavirus phages and their endolysins as novel antibacterial compounds.

Interference-resistant gold nanoparticle assay for detecting Enterococcus in fresh and marine waters

Enterococci are common indicators of fecal contamination and are used to assess the quality of fresh and marine water, sand, soil, and sediment. However, samples collected from these environments contain various cells and other factors that can interfere with the assays used to detect enterococci. We developed a novel assay for the sensitive and specific detection of enterococci that is resistant to interference from other cells and environmental factors. Our interference-resistant assay used 30-nm gold nanoparticles (AuNPs), streptavidin, and a biotinylated Enterococcus antibody. Enterococci inhibited the interaction between streptavidin and biotin and led to the disaggregation of AuNPs. The absence of enterococci led to the aggregation of AuNPs, and this difference was easily detected by spectrophotometry. This interference-resistant AuNP assay was able to detect whole cells of Enterococcus in the range of 10 to 107 CFU/mL within 3 h, had high specificity for enterococci, and was unaffected by the presence of other intestinal bacteria, such as Escherichia coli. Our examination of fresh and marine water samples demonstrated no interference from other cells or environmental factors. The interference-resistant AuNP assay described here has the potential to be used as a rapid, simple, and effective method for monitoring enterococci in diverse environmental samples.

Innovations in Phage Therapy for Urinary Tract Infection

Urinary tract infections (UTIs) are among the most common infections. Increasing rates of multidrug-resistant bacteria are complicating treatment, necessitating alternative strategies. Bacteriophages (phages) are viruses that only target and kill bacteria, and this specific lytic activity can be harnessed therapeutically. Bioengineering holds innovative potential for the use of phages as diagnostic and therapeutic tools for rapid targeted treatments. However, phage therapy and phage products are not currently approved by regulatory agencies in the Western world and can only be applied under specific regulatory frameworks in individual countries. Further basic and clinical research is essential to address the challenges of phage therapy and to explore its value in combating UTIs. PATIENT SUMMARY: Urinary tract infections (UTIs) are becoming more difficult to treat because of antibiotic resistance. Bacteriophages are viruses that kill bacteria and have promise for UTI treatment, but more research and regulatory approval are needed before they become more widely available.

Innovative Biosensor Technologies in the Diagnosis of Urinary Tract Infections: A Comprehensive Literature Review

Urinary tract infections (UTIs) are prevalent bacterial infections globally, posing significant challenges due to their frequency, recurrence, and antibiotic resistance. This review delves into the advancements in UTI diagnostics over the past decade, particularly focusing on the development of biosensor technologies. The emergence of biosensors, including microfluidic, optical, electrochemical, immunosensors, and nanotechnology-based sensors, offers enhanced diagnostic accuracy, reduced healthcare costs. Despite these advancements, challenges such as technical limitations, the need for cross-population validation, and economic barriers for widespread implementation persist. The integration of artificial intelligence and smart devices in UTI diagnostics, highlighting the innovative approaches and their implications for patient care. The article envisions a future where multidisciplinary research and innovation overcome current obstacles, fully leveraging the potential of biosensor technologies to transform biosensor-based UTIs diagnosis. The ultimate goal is to achieve rapid, accurate, and non-invasive diagnostics, making healthcare more accessible and effective.

Enzymes in Synergy: Bacteria Specific Molecular Probe for Locoregional Imaging of Urinary Tract Infection in vivo

Uropathogenic Escherichia coli (UPECs) is a leading cause for urinary tract infections (UTI), accounting for 70-90 % of community or hospital-acquired bacterial infections owing to high recurrence, imprecision in diagnosis and management, and increasing prevalence of antibiotic resistance. Current methods for clinical UPECs detection still rely on labor-intensive urine cultures that impede rapid and accurate diagnosis for timely UTI therapeutic management. Herein, we developed a first-in-class near-infrared (NIR) UPECs fluorescent probe (NO-AH) capable of specifically targeting UPECs through its collaborative response to bacterial enzymes, enabling locoregional imaging of UTIs both in vitro and in vivo. Our NO-AH probe incorporates a dual protease activatable moiety, which first reacts with OmpT, an endopeptidase abundantly present on the outer membrane of UPECs, releasing an intermediate amino acid residue conjugated with a NIR hemicyanine fluorophore. Such liberated fragment would be subsequently recognized by aminopeptidase (APN) within the periplasm of UPECs, activating localized fluorescence for precise imaging of UTIs in complex living environments. The peculiar specificity and selectivity of NO-AH, facilitated by the collaborative action of bacterial enzymes, features a timely and accurate identification of UPECs-infected UTIs, which could overcome misdiagnosis in conventional urine tests, thus opening new avenues towards reliable UTI diagnosis and personalized antimicrobial therapy management.

Decolonization and Pathogen Reduction Approaches to Prevent Antimicrobial Resistance and Healthcare-Associated Infections

Antimicrobial resistance in healthcare-associated bacterial pathogens and the infections they cause are major public health threats affecting nearly all healthcare facilities. Antimicrobial-resistant bacterial infections can occur when colonizing pathogenic bacteria that normally make up a small fraction of the human microbiota increase in number in response to clinical perturbations. Such infections are especially likely when pathogens are resistant to the collateral effects of antimicrobial agents that disrupt the human microbiome, resulting in loss of colonization resistance, a key host defense. Pathogen reduction is an emerging strategy to prevent transmission of, and infection with, antimicrobial-resistant healthcare-associated pathogens. We describe the basis for pathogen reduction as an overall prevention strategy, the evidence for its effectiveness, and the role of the human microbiome in colonization resistance that also reduces the risk for infection once colonized. In addition, we explore ideal attributes of current and future pathogen-reducing approaches.

Scientific Advances in Understanding the Pathogenesis, Diagnosis, and Prevention of Urinary Tract Infection in the Past 10 Years

Urinary tract infection (UTI) is a very common disease that is accompanied by various complications in the affected person. UTI triggers diverse inflammatory reactions locally in the infected urinary bladder and kidney, causing tissue destruction and organ failure. Moreover, systemic responses in the entire body carry the risk of urosepsis with far-reaching consequences. Understanding the cell-, organ-, and systemic mechanisms in UTI are crucial for prevention, early intervention, and current therapeutic approaches. This review summarizes the scientific advances over the last 10 years concerning pathogenesis, prevention, rapid diagnosis, and new treatment approaches. We also highlight the impact of the immune system and potential new therapies to reduce progressive and recurrent UTI.

Synthetic phage-based approach for sensitive and specific detection of Escherichia coli O157

Escherichia coli O157 can cause foodborne outbreaks, with infection leading to severe disease such as hemolytic-uremic syndrome. Although phage-based detection methods for E. coli O157 are being explored, research on their specificity with clinical isolates is lacking. Here, we describe an in vitro assembly-based synthesis of vB_Eco4M-7, an O157 antigen-specific phage with a 68-kb genome, and its use as a proof of concept for E. coli O157 detection. Linking the detection tag to the C-terminus of the tail fiber protein, gp27 produces the greatest detection sensitivity of the 20 insertions sites tested. The constructed phage detects all 53 diverse clinical isolates of E. coli O157, clearly distinguishing them from 35 clinical isolates of non-O157 Shiga toxin-producing E. coli. Our efficient phage synthesis methods can be applied to other pathogenic bacteria for a variety of applications, including phage-based detection and phage therapy.

A nanoluciferase-encoded bacteriophage illuminates viral infection dynamics of Pseudomonas aeruginosa cells

Bacteriophages (phages) are increasingly considered for both treatment and early detection of bacterial pathogens given their specificity and rapid infection kinetics. Here, we exploit an engineered phage expressing nanoluciferase to detect signals associated with Pseudomonas aeruginosa lysis spanning single cells to populations. Using several P. aeruginosa strains we found that the latent period, burst size, fraction of infected cells, and efficiency of plating inferred from fluorescent light intensity signals were consistent with inferences from conventional population assays. Notably, imaging-based traits were obtained in minutes to hours in contrast to the use of overnight plaques, which opens the possibility to study infection dynamics in spatial and/or temporal contexts where plaque development is infeasible. These findings support the use of engineered phages to study infection kinetics of virus-cell interactions in complex environments and potentially accelerate the determination of viral host range in therapeutically relevant contexts.

Development of a Replication-Deficient Bacteriophage Reporter Lacking an Essential Baseplate Wedge Subunit

Engineered bacteriophages (phages) can be effective diagnostic reporters for detecting a variety of bacterial pathogens. Although a promising biotechnology, the large-scale use of these reporters may result in the unintentional release of genetically modified viruses. In order to limit the potential environmental impact, the ability of these phages to propagate outside the laboratory was targeted. The phage SEA1 has been previously engineered to facilitate food safety as an accurate and sensitive reporter for Salmonella contamination. In this study, homologous recombination was used to replace the expression of an essential baseplate wedge subunit (gp141) in SEA1 with a luciferase, NanoLuc®. This reporter, referred to as SEA1Δgp141.NL, demonstrated a loss of plaque formation and a failure to increase in titer following infection of Salmonella. SEA1Δgp141.NL was thus incapable of producing infectious progeny in the absence of gp141. In contrast, production of high titer stocks was possible when gp141 was artificially supplied in trans during infection. As a reporter, SEA1Δgp141.NL facilitated rapid, sensitive, and robust detection of Salmonella despite an inability to replicate. These results suggest that replication-deficient reporter phages are an effective method to obtain improved containment without sacrificing significant performance or the ease of production associated with many phage-based diagnostic methods.

Ongoing shuffling of protein fragments diversifies core viral functions linked to interactions with bacterial hosts

Biological modularity enhances evolutionary adaptability. This principle is vividly exemplified by bacterial viruses (phages), which display extensive genomic modularity. Phage genomes are composed of independent functional modules that evolve separately and recombine in various configurations. While genomic modularity in phages has been extensively studied, less attention has been paid to protein modularity-proteins consisting of distinct building blocks that can evolve and recombine, enhancing functional and genetic diversity. Here, we use a set of 133,574 representative phage proteins and highly sensitive homology detection to capture instances of domain mosaicism, defined as fragment sharing between two otherwise unrelated proteins, and to understand its relationship with functional diversity in phage genomes. We discover that unrelated proteins from diverse functional classes frequently share homologous domains. This phenomenon is particularly pronounced within receptor-binding proteins, endolysins, and DNA polymerases. We also identify multiple instances of recent diversification via domain shuffling in receptor-binding proteins, neck passage structures, endolysins and some members of the core replication machinery, often transcending distant taxonomic and ecological boundaries. Our findings suggest that ongoing diversification via domain shuffling is reflective of a co-evolutionary arms race, driven by the need to overcome various bacterial resistance mechanisms against phages.

Neuro-Urology and Biobanking: An Integrated Approach for Advancing Research and Improving Patient Care

Understanding the molecular mechanisms underlying neuro-urological disorders is crucial for the development of targeted therapeutic interventions. Through the establishment of comprehensive biobanks, researchers can collect and store various biological specimens, including urine, blood, tissue, and DNA samples, to study these mechanisms. In the context of neuro-urology, biobanking facilitates the identification of genetic variations, epigenetic modifications, and gene expression patterns associated with neurogenic lower urinary tract dysfunction. These conditions often present as symptoms of neurological diseases such as Alzheimer's disease, multiple sclerosis, Parkinson's disease, spinal cord injury, and many others. Biobanking of tissue specimens from such patients is essential to understand why these diseases cause the respective symptoms and what can be done to alleviate them. The utilization of high-throughput technologies, such as next-generation sequencing and gene expression profiling, enables researchers to explore the molecular landscape of these conditions in an unprecedented manner. The development of specific and reliable biomarkers resulting from these efforts may help in early detection, accurate diagnosis, and effective monitoring of neuro-urological conditions, leading to improved patient care and management. Furthermore, these biomarkers could potentially facilitate the monitoring of novel therapies currently under investigation in neuro-urological clinical trials. This comprehensive review explores the synergistic integration of neuro-urology and biobanking, with particular emphasis on the translation of biobanking approaches in molecular research in neuro-urology. We discuss the advantages of biobanking in neuro-urological studies, the types of specimens collected and their applications in translational research. Furthermore, we highlight the importance of standardization and quality assurance when collecting samples and discuss challenges that may compromise sample quality and impose limitations on their subsequent utilization. Finally, we give recommendations for sampling in multicenter studies, examine sustainability issues associated with biobanking, and provide future directions for this dynamic field.

Enhancing bacteriophage therapeutics through in situ production and release of heterologous antimicrobial effectors

Bacteriophages operate via pathogen-specific mechanisms of action distinct from conventional, broad-spectrum antibiotics and are emerging as promising alternative antimicrobials. However, phage-mediated killing is often limited by bacterial resistance development. Here, we engineer phages for target-specific effector gene delivery and host-dependent production of colicin-like bacteriocins and cell wall hydrolases. Using urinary tract infection (UTI) as a model, we show how heterologous effector phage therapeutics (HEPTs) suppress resistance and improve uropathogen killing by dual phage- and effector-mediated targeting. Moreover, we designed HEPTs to control polymicrobial uropathogen communities through production of effectors with cross-genus activity. Using phage-based companion diagnostics, we identified potential HEPT responder patients and treated their urine ex vivo. Compared to wildtype phage, a colicin E7-producing HEPT demonstrated superior control of patient E. coli bacteriuria. Arming phages with heterologous effectors paves the way for successful UTI treatment and represents a versatile tool to enhance and adapt phage-based precision antimicrobials.