Phage-based detection of bacterial pathogens

Bacteriophages: a potential game changer in food processing industry

In the food industry, despite the widespread use of interventions such as preservatives and thermal and non-thermal processing technologies to improve food safety, incidences of foodborne disease continue to happen worldwide, prompting the search for alternative strategies. Bacteriophages, commonly known as phages, have emerged as a promising alternative for controlling pathogenic bacteria in food. This review emphasizes the potential applications of phages in biological sciences, food processing, and preservation, with a particular focus on their role as biocontrol agents for improving food quality and preservation. By shedding light on recent developments and future possibilities, this review highlights the significance of phages in the food industry. Additionally, it addresses crucial aspects such as regulatory status and safety concerns surrounding the use of bacteriophages. The inclusion of up-to-date literature further underscores the relevance of phage-based strategies in reducing foodborne pathogenic bacteria's presence in both food and the production environment. As we look ahead, new phage products are likely to be targeted against emerging foodborne pathogens. This will further advance the efficacy of approaches that are based on phages in maintaining the safety and security of food.

Sensitive detection of viable Cronobacter sakazakii by bioluminescent reporter phage emitting stable signals with truncated holin

As outbreaks of foodborne illness caused by the opportunistic pathogen Cronobacter sakazakii (Cs) continue to occur, particularly in infants consuming powdered infant formula (PIF), the need for sensitive, rapid, and easy-to-use detection of Cs from food and food processing environments is increasing. Here, we developed bioluminescent reporter bacteriophages for viable Cs-specific, substrate-free, rapid detection by introducing luciferase and its corresponding substrate-providing enzyme complex into the virulent phage ΦC01. Although the reporter phage ΦC01_lux, constructed by replacing non-essential genes for phage infectivity with a luxCDABE reporter operon, produced bioluminescence upon Cs infection, the emitted signal was quickly decayed due to the superior bacteriolytic activity of ΦC01. By truncating the membrane pore-forming protein holin and thus limiting its function, the bacterial lysis was delayed and the resultant engineered reporter phage ΦC01_lux_Δhol could produce a more stable and reliable bioluminescent signal. Accordingly, ΦC01_lux_Δhol was able to detect at least an average of 2 CFU/ml of Cs artificially contaminated PIF and Sunsik and food contact surface models within a total of 7 h of assays, including 5 h of pre-enrichment for Cs amplification. The sensitive, easy-to-use, and specific detection of live Cs with the developed reporter phage could be applied as a novel complementary tool for monitoring Cs in food and food-related environments for food safety and public health.

Phage-Inducible Chromosomal Islands as a Diagnostic Platform to Capture and Detect Bacterial Pathogens

Phage-inducible chromosomal islands (PICIs) are a family of phage satellites that hijack phage components to facilitate their mobility and spread. Recently, these genetic constructs are repurposed as antibacterial drones, enabling a new toolbox for unorthodox applications in biotechnology. To illustrate a new suite of functions, the authors have developed a user-friendly diagnostic system, based upon PICI transduction to selectively enrich bacteria, allowing the detection and sequential recovery of Escherichia coli and Staphylococcus aureus. The system enables high transfer rates and sensitivities in comparison with phages, with detection down to ≈50 CFU mL-1 . In contrast to conventional detection strategies, which often rely on nucleic acid molecular assays, and cannot differentiate between dead and live organisms, this approach enables visual sensing of viable pathogens only, through the expression of a reporter gene encoded in the PICI. The approach extends diagnostic sensing mechanisms beyond cell-free synthetic biology strategies, enabling new synthetic biology/biosensing toolkits.

Recent advances of fluorescent sensors for bacteria detection-A review

Bacterial infections have become a global public health problem. Rapid and sensitive bacterial detection is of great importance for human health. Among various sensor systems, fluorescence sensor is rapid, portable, multiplexed, and cost-efficient. Herein, we reviewed the current trends of fluorescent sensors for bacterial detection from three aspects (response materials, target and recognition way). The fluorescent materials have the advantages of high fluorescent strength, high stability, and good biocompatibility. They provide a new path for bacterial detection. Several recent fluorescent nanomaterials for bacterial detection, including semiconductor quantum dots (QDs), carbon dots (CDs), up-conversion nanoparticles (UCNPs) and metal organic frameworks (MOFs), were introduced. Their optical properties and detection mechanisms were analyzed and compared. For different response targets in the detection process, we studied the fluorescence strategy using DNA, bacteria, and metabolites as the response target. In addition, we classified the recognition way between nanomaterial and target, including specific recognition methods based on aptamers, antibodies, bacteriophages, and non-specific recognition methods based on biological functional materials. The characteristics of different recognition methods were summarized. Finally, the weaknesses and future development of bacterial fluorescence sensor were discussed. This review provides new insights into the application of fluorescent sensing systems as an important tool for bacterial detection.

Fast and specific detection of staphylococcal PJI with bacteriophage-based methods within 104 sonicate fluid samples

The number of prosthetic joint infection (PJI) cases is increasing along with total joint arthroplasties. There is currently no diagnostic test available with 100% sensitivity to identify PJI. The aim of the study was to assess and compare two different bacteriophage K-based methods with standard microbiological culturing methods to detect staphylococci. Samples were retrieved from 104 patients undergoing revision surgery due to suspected PJI. Implants were subjected to sonication and sonicate fluid (SF) was assessed with the methods of qPCR detection of bacteriophage K DNA and adenosine triphosphate (ATP) detection after bacteriophage K lysis. The results were compared with the results of standard microbiological culturing methods. PJI was confirmed in 33 cases according to the PJI definition. Using the methods of ATP and bacteriophage K DNA detection 100% specificity and predictive value were achieved. The sensitivity of qPCR detection was higher (81.25%) than the sensitivity of ATP detection (62.50%) when analyzing SF directly. The sensitivity of the methods significantly improved (to 94.12%) with SF pre-cultivation. Importantly, both methods provided results in 3-4 h when analyzing SF directly, while results from pre-cultivated SF were obtained 19-20 h after sample collection. Our results suggest that bacteriophage-based methods are specific and sensitive and importantly, faster than standard culturing methods. The addition of new bacteriophages to expand the bacterial detection spectrum could lead to the development of a faster, more sensitive, specific, and also economical, and handy method for PJI diagnosis.

Advances in the Development of Phage-Based Probes for Detection of Bio-Species

Bacteriophages, abbreviated as "phages", have been developed as emerging nanoprobes for the detection of a wide variety of biological species, such as biomarker molecules and pathogens. Nanosized phages can display a certain length of exogenous peptides of arbitrary sequence or single-chain variable fragments (scFv) of antibodies that specifically bind to the targets of interest, such as animal cells, bacteria, viruses, and protein molecules. Metal nanoparticles generally have unique plasmon resonance effects. Metal nanoparticles such as gold, silver, and magnetism are widely used in the field of visual detection. A phage can be assembled with metal nanoparticles to form an organic-inorganic hybrid probe due to its nanometer-scale size and excellent modifiability. Due to the unique plasmon resonance effect of this composite probe, this technology can be used to visually detect objects of interest under a dark-field microscope. In summary, this review summarizes the recent advances in the development of phage-based probes for ultra-sensitive detection of various bio-species, outlining the advantages and limitations of detection technology of phage-based assays, and highlighting the commonly used editing technologies of phage genomes such as homologous recombination and clustered regularly interspaced palindromic repeats/CRISPR-associated proteins system (CRISPR-Cas). Finally, we discuss the possible scenarios for clinical application of phage-probe-based detection methods.

Application of Bacteriophages for Mycobacterial Infections, from Diagnosis to Treatment

Mycobacterium tuberculosis and other non-tuberculous mycobacteria are responsible for a variety of different infections affecting millions of patients worldwide. Their diagnosis is often problematic and delayed until late in the course of disease, requiring a high index of suspicion and the combined efforts of clinical and laboratory colleagues. Molecular methods, such as PCR platforms, are available, but expensive, and with limited sensitivity in the case of paucibacillary disease. Treatment of mycobacterial infections is also challenging, typically requiring months of multiple and combined antibiotics, with associated side effects and toxicities. The presence of innate and acquired drug resistance further complicates the picture, with dramatic cases without effective treatment options. Bacteriophages (viruses that infect bacteria) have been used for decades in Eastern Europe for the treatment of common bacterial infections, but there is limited clinical experience of their use in mycobacterial infections. More recently, bacteriophages' clinical utility has been re-visited and their use has been successfully demonstrated both as diagnostic and treatment options. This review will focus specifically on how mycobacteriophages have been used recently in the diagnosis and treatment of different mycobacterial infections, as potential emerging technologies, and as an alternative treatment option.

Recent progress in the optical detection of pathogenic bacteria based on noble metal nanoparticles

Pathogenic bacteria have become a huge threat to social health and economy for their frighteningly infectious and lethal capacity. It is quite important to make a diagnosis in advance to prevent infection or allow a rapid treatment after infection. Noble metal nanoparticles, due to their unique physicochemical properties, especially optical properties, have drawn a great attention during the past decades and have been widely applied into all kinds of fields related to human health. By utilizing these noble metal nanoparticles, optical diagnosis platforms towards pathogenic bacteria have emerged continually, providing highly sensitive, selective, and particularly facile detection tools for clinic or point-of-care diagnosis. This review summarizes the recent development in this field. It begins with a brief introduction of pathogenic bacteria and noble metal nanoparticles. And then, optical detection methods are systematically discussed in three distinct aspects. In addition to these proof-of-concept methods, corresponding algorithms and point-of-care detection devices are also described. Finally, the review ends up with subjective views on present limitations and some appropriate advice for future research directions.

The Bacteriophage pEp_SNUABM_08 Is a Novel Singleton Siphovirus with High Host Specificity for Erwinia pyrifoliae

Species belonging to the genus Erwinia are predominantly plant pathogens. A number of bacteriophages capable of infecting Erwinia have been used for the control of plant diseases such as fire blight. Public repositories provide the complete genome information for such phages, which includes genomes ranging from 30 kb to 350 kb in size. However, limited information is available regarding bacteriophages belonging to the family Siphoviridae. A novel lytic siphophage, pEp_SNUABM_08, which specifically infects Erwinia pyrifoliae, was isolated from the soil of an affected apple orchard in South Korea. A comprehensive genome analysis was performed using the Erwinia-infecting siphophage. The whole genome of pEp_SNUABM_08 comprised 62,784 bp (GC content, 57.24%) with 79 open reading frames. The genomic characteristics confirmed that pEp_SNUABM_08 is a singleton lytic bacteriophage belonging to the family Siphoviridae, and no closely related phages have been reported thus far. Our study not only characterized a unique phage, but also provides insight into the genetic diversity of Erwinia bacteriophages.

Reporter-Phage-Based Detection and Antibiotic Susceptibility Testing of Yersinia pestis for a Rapid Plague Outbreak Response

Pneumonic plague is a lethal infectious disease caused by Yersinia pestis, a Tier-1 biothreat agent. Antibiotic treatment can save infected patients; however, therapy should begin within 24 h of symptom onset. As some Y. pestis strains showed an antibiotic resistance phenotype, an antibiotic susceptibility test (AST) must be performed. Performing the Clinical and Laboratory Standards Institute (CLSI)-recommended standard process, which includes bacterial isolation, enumeration and microdilution testing, lasts several days. Thus, rapid AST must be developed. As previously published, the Y. pestis-specific reporter phage ϕA1122::luxAB can serve for rapid identification and AST (ID-AST). Herein, we demonstrate the ability to use ϕA1122::luxAB to determine minimal inhibitory concentration (MIC) values and antibiotic susceptibility categories for various Y. pestis therapeutic antibiotics. We confirmed the assay by testing several nonvirulent Y. pestis isolates with reduced susceptibility to doxycycline or ciprofloxacin. Moreover, the assay can be performed directly on positive human blood cultures. Furthermore, as Y. pestis may naturally or deliberately be spread in the environment, we demonstrate the compatibility of this direct method for this scenario. This direct phage-based ID-AST shortens the time needed for standard AST to less than a day, enabling rapid and correct treatment, which may also prevent the spread of the disease.

Recent Innovations in Bacterial Infection Detection and Treatment

Bacterial infections are a major threat to human health, exacerbated by increasing antibiotic resistance. These infections can result in tremendous morbidity and mortality, emphasizing the need to identify and treat pathogenic bacteria quickly and effectively. Recent developments in detection methods have focused on electrochemical, optical, and mass-based biosensors. Advances in these systems include implementing multifunctional materials, microfluidic sampling, and portable data-processing to improve sensitivity, specificity, and ease of operation. Concurrently, advances in antibacterial treatment have largely focused on targeted and responsive delivery for both antibiotics and antibiotic alternatives. Antibiotic alternatives described here include repurposed drugs, antimicrobial peptides and polymers, nucleic acids, small molecules, living systems, and bacteriophages. Finally, closed-loop therapies are combining advances in the fields of both detection and treatment. This review provides a comprehensive summary of the current trends in detection and treatment systems for bacterial infections.

Modification of Bacteriophages to Increase Their Association with Lung Epithelium Cells In Vitro

There is currently a renaissance in research on bacteriophages as alternatives to antibiotics. Phage specificity to their bacterial host, in addition to a plethora of other advantages, makes them ideal candidates for a broad range of applications, including bacterial detection, drug delivery, and phage therapy in particular. One issue obstructing phage efficiency in phage therapy settings is their poor localization to the site of infection in the human body. Here, we engineered phage T7 with lung tissue targeting homing peptides. We then used in vitro studies to demonstrate that the engineered T7 phages had a more significant association with the lung epithelium cells than wild-type T7. In addition, we showed that, in general, there was a trend of increased association of engineered phages with the lung epithelium cells but not mouse fibroblast cells, allowing for targeted tissue specificity. These results indicate that appending phages with homing peptides would potentially allow for greater phage concentrations and greater efficacy at the infection site.

A Reusable Column Method Using Glycopolymer-Functionalized Resins for Capture-Detection of Proteins and Escherichia coli

The use of glycopolymer-functionalized resins (Resin-Glc), as a solid support, in column mode for bacterial/protein capture and quantification is explored. The Resin-Glc is synthesized from commercially available chloromethylated polystyrene resin and glycopolymer, and is characterized by fourier transform infrared spectroscopy, thermogravimetry, and elemental analysis. The percentage of glycopolymer functionalized on Resin-Glc is accounted to be 5 wt%. The ability of Resin-Glc to selectively capture lectin, Concanavalin A, over Peanut Agglutinin, reversibly, is demonstrated for six cycles of experiments. The bacterial sequestration study using SYBR (Synergy Brands, Inc.) Green I tagged Escherichia coli/Staphylococcus aureus reveals the ability of Resin-Glc to selectively capture E. coli over S. aureus. The quantification of captured cells in the column is carried out by enzymatic colorimetric assay using methylumbelliferyl glucuronide as the substrate. The E. coli capture studies reveal a consistent capture efficiency of 10⁵  CFU (Colony Forming Units) g^-1 over six cycles. Studies with spiked tap water samples show satisfactory results for E. coli cell densities ranging from 10² to 10⁷  CFU mL^-1 . The method portrayed can serve as a basis for the development of a reusable solid support in capture and detection of proteins and bacteria.

State-of-the-art polymeric nanoparticles as promising therapeutic tools against human bacterial infections

Infectious diseases kill over 17 million people a year, among which bacterial infections stand out. From all the bacterial infections, tuberculosis, diarrhoea, meningitis, pneumonia, sexual transmission diseases and nosocomial infections are the most severe bacterial infections, which affect millions of people worldwide. Moreover, the indiscriminate use of antibiotic drugs in the last decades has triggered an increasing multiple resistance towards these drugs, which represent a serious global socioeconomic and public health risk. It is estimated that 33,000 and 35,000 people die yearly in Europe and the United States, respectively, as a direct result of antimicrobial resistance. For all these reasons, there is an emerging need to find novel alternatives to overcome these issues and reduced the morbidity and mortality associated to bacterial infectious diseases. In that sense, nanotechnological approaches, especially smart polymeric nanoparticles, has wrought a revolution in this field, providing an innovative therapeutic alternative able to improve the limitations encountered in available treatments and capable to be effective by theirselves. In this review, we examine the current status of most dangerous human infections, together with an in-depth discussion of the role of nanomedicine to overcome the current disadvantages, and specifically the most recent and innovative studies involving polymeric nanoparticles against most common bacterial infections of the human body.

Rapid Isolation, Propagation, and Online Analysis of a Small Number of Therapeutic Staphylococcal Bacteriophages from a Complex Matrix

A method for the fast isolation, propagation, and characterization of very low count bacteriophages active against pathogenic bacterial strains is described in this study. Bacteriophages with a count of 10² phage particles were dynamically adhered from the maximum 10 mL blood plasma sample onto the nanostructured part of the fused silica capillary. One-step propagation of phage particles of genus Kayvirus inside the etched capillary on 10⁴ Staphylococcus aureus host cells increased their number to 6 × 10⁴ phage particles. Phage particles were concentrated online and separated by capillary electrophoretic methods. No phage replication occurred when the phage-resistant S. aureus or Escherichia coli cells were used. Two-step phage propagation in the capillary allowed an increase in the total virion count to up to 6 × 10⁵ phage particles and subsequent off-line matrix-assisted laser desorption/ionization time-of-flight mass spectrometry analysis of the phage zone collected after capillary electrophoresis. Relative standard deviations of the phage peak area were at most 2.3%. We expect that the method of isolating bacteriophages from blood plasma and their simultaneous identification will facilitate clinical studies of phage preparations and contribute to pharmacokinetics studies during phage therapy. This approach is also suitable for capturing and enriching new phages from the environment when a susceptible indicator strain is available.

Dark-Field Microscopic Detection of Bacteria using Bacteriophage-Immobilized SiO2@AuNP Core-Shell Nanoparticles

To replace molecular biological and immunological methods, biosensors have recently been developed for the rapid and sensitive detection of bacteria. Among a wide variety of biological materials, bacteriophages have received increasing attention as promising alternatives to antibodies in biosensor applications. Thus, we herein present a rapid and highly selective detection method for pathogenic bacteria, which combines dark-field light scattering imaging with a plasmonic biosensor system. The plasmonic biosensor system employs bacteriophages as the biorecognition element and the aggregation-induced light scattering signal of gold nanoparticle-assembled silica nanospheres as a signal transducer. Using Staphylococcus aureus strain SA27 as a model analyte, we demonstrated that the plasmonic biosensor system detects S. aureus in the presence of excess Escherichia coli in a highly selective manner. After the sample and the S. aureus phage S13'-conjugated plasmon scattering probe were mixed, S. aureus detection was completed within 15-20 min with a detection limit of 8 × 10⁴ colony forming units per milliliter.

Rapid Colorimetric Detection of Bacterial Species through the Capture of Gold Nanoparticles by Chimeric Phages

Rapid, inexpensive, and sensitive detection of bacterial pathogens is an important goal for several aspects of human health and safety. We present a simple strategy for detecting a variety of bacterial species based on the interaction between bacterial cells and the viruses that infect them (phages). We engineer phage M13 to display the receptor-binding protein from a phage that naturally targets the desired bacteria. Thiolation of the engineered phages allows the binding of gold nanoparticles, which aggregate on the phages and act as a signal amplifier, resulting in a visible color change due to alteration of surface plasmon resonance properties. We demonstrate the detection of two strains of Escherichia coli, the human pathogens Pseudomonas aeruginosa and Vibrio cholerae, and two strains of the plant pathogen Xanthomonas campestris. The assay can detect ∼100 cells with no cross-reactivity found among the Gram-negative bacterial species tested here. The assay can be performed in less than an hour and is robust to different media, including seawater and human serum. This strategy combines highly evolved biological materials with the optical properties of gold nanoparticles to achieve the simple, sensitive, and specific detection of bacterial species.

Detecting Biothreat Agents: From Current Diagnostics to Developing Sensor Technologies

Although a fundamental understanding of the pathogenicity of most biothreat agents has been elucidated and available treatments have increased substantially over the past decades, they still represent a significant public health threat in this age of (bio)terrorism, indiscriminate warfare, pollution, climate change, unchecked population growth, and globalization. The key step to almost all prevention, protection, prophylaxis, post-exposure treatment, and mitigation of any bioagent is early detection. Here, we review available methods for detecting bioagents including pathogenic bacteria and viruses along with their toxins. An introduction placing this subject in the historical context of previous naturally occurring outbreaks and efforts to weaponize selected agents is first provided along with definitions and relevant considerations. An overview of the detection technologies that find use in this endeavor along with how they provide data or transduce signal within a sensing configuration follows. Current "gold" standards for biothreat detection/diagnostics along with a listing of relevant FDA approved in vitro diagnostic devices is then discussed to provide an overview of the current state of the art. Given the 2014 outbreak of Ebola virus in Western Africa and the recent 2016 spread of Zika virus in the Americas, discussion of what constitutes a public health emergency and how new in vitro diagnostic devices are authorized for emergency use in the U.S. are also included. The majority of the Review is then subdivided around the sensing of bacterial, viral, and toxin biothreats with each including an overview of the major agents in that class, a detailed cross-section of different sensing methods in development based on assay format or analytical technique, and some discussion of related microfluidic lab-on-a-chip/point-of-care devices. Finally, an outlook is given on how this field will develop from the perspective of the biosensing technology itself and the new emerging threats they may face.

Dodecagonal plasmonic quasicrystals for phage-based biosensing

In this work, we fabricate and characterize a novel sensitive two-dimensional surface enhanced Raman spectroscopy (SERS) substrate made of plasmonic nanocavities in a photonic quasicrystal arrangement characterized by a 12-fold rotational symmetry. Our SERS device is capable of detecting chemisorbed bacteriophages at a femtomolar range. Most importantly, the paper presents for the first time a study on the procedure to functionalize the plasmonic quasicrystal with bacteriophages of the Podoviridae family. The immobilization of the phages on the plasmonic substrate has been studied and verified through SERS measurements. A new stable peak, visible in the SERS spectra at 1326 cm^-1 at a greater than 60 times amplification, confirms the immobilization of the phages on the substrate. This functionalization approach can be used also for other types of phages or plasmonic sensors and hence, our achievements could allow the development of novel systems for the specific detection of different species of bacteria.

Lyophilized Engineered Phages for Escherichia coli Detection in Food Matrices

Ease of use, low cost, and convenient transport are the key requirements for a commercial bacteria detection kit designed for resource-limited settings. Here, we report the colorimetric detection of Escherichia coli (E. coli) in food samples using freeze-dried engineered bacteriophages (phages). In this approach, we have engineered T7 phages to carry the lacZ operon driven by T7 promoter to overexpress reporter enzymes. The engineered phages were freeze-dried in a water-soluble polymer for storage and transportation. When used for the detection of E. coli cells, the intracellular enzyme [β-galactosidase (β-gal)] was overexpressed and released into the surrounding media, providing an enzyme-amplified colorimetric signal. Using this strategy, we were able to detect E. coli cells at the concentration of 10² CFU mL^-1 in food samples without the need for sophisticated instruments or skilled operators.

Recent advances in bacteriophage-based methods for bacteria detection

Fast and reliable bacteria detection is crucial for lowering the socioeconomic burden related to bacterial infections (e.g., in healthcare, industry or security). Bacteriophages (i.e., viruses with bacterial hosts) pose advantages such as great specificity, robustness, toughness and cheap preparation, making them popular biorecognition elements in biosensors and other assays for bacteria detection. There are several possible designs of bacteriophage-based biosensors. Here, we focus on developments based on whole virions as recognition agents. We divide the review into sections dealing with phage lysis as an analytical signal, phages as capturing elements in assays and phage-based sensing layers, putting the main focus on development reported within the past three years but without omitting the fundamentals.

Print to detect: a rapid and ultrasensitive phage-based dipstick assay for foodborne pathogens

Foodborne pathogens are a burden to the economy and a constant threat to public health. The ability to rapidly detect the presence of foodborne pathogens is a vital component of any strategy towards establishing a safe and secure food supply chain. Bacteriophages (phages) are viruses capable of infecting and replicating within bacteria in a strain-specific manner. The ubiquitous and selective nature of phages makes them ideal for the detection and biocontrol of bacteria. Therefore, the objective of this research was to develop and test a phage-based paper dipstick biosensor for the detection of various foodborne pathogens in food matrices. The first step was to identify the best method for immobilizing phages on paper such that their biological activity (infectivity) was preserved. It was found that piezoelectric inkjet printing resulted in lower loss of phage infectivity when compared with other printing methods (namely gravure and blade coating) and that ColorLok paper was ideally suited to create functional sensors. The phage-based bioactive papers developed with use of piezoelectric inkjet printing actively lysed their target bacteria and retained this antibacterial activity for up to 1 week when stored at room temperature and 80% relative humidity. These bioactive paper strips in combination with quantitative real-time PCR were used for quantitative determination of target bacteria in broth and food matrices. A phage dipstick was used to capture and infect Escherichia coli O157:H7, E. coli O45:H2, and Salmonella Newport in spinach, ground beef and chicken homogenates, respectively, and quantitative real-time PCR was used to detect the progeny phages. A detection limit of 10-50 colony-forming units per millilitre was demonstrated with a total assay time of 8 h, which was the duration of a typical work shift in an industrial setting. This detection method is rapid and cost-effective, and may potentially be applied to a broad range of bacterial foodborne pathogens. Graphical abstract ᅟ.

Octupolar Metastructures for a Highly Sensitive, Rapid, and Reproducible Phage-Based Detection of Bacterial Pathogens by Surface-Enhanced Raman Scattering

The development of fast and ultrasensitive methods to detect bacterial pathogens at low concentrations is of high relevance for human and animal health care and diagnostics. In this context, surface-enhanced Raman scattering (SERS) offers the promise of a simplified, rapid, and high-sensitive detection of biomolecular interactions with several advantages over previous assay methodologies. In this work, we have conceived reproducible SERS nanosensors based on tailored multilayer octupolar nanostructures which can combine high enhancement factor and remarkable molecular selectivity. We show that coating novel multilayer octupolar metastructures with proper self-assembled monolayer (SAM) and immobilized phages can provide label-free analysis of pathogenic bacteria via SERS leading to a giant increase in SERS enhancement. The strong relative intensity changes of about 2100% at the maximum scattered SERS wavelength, induced by the Brucella bacterium captured, demonstrate the performance advantages of the bacteriophage sensing scheme. We performed measurements at the single-cell level thus allowing fast identification in less than an hour without any demanding sample preparation process. Our results based on designing well-controlled octupolar coupling platforms open up new opportunities toward the use of bacteriophages as recognition elements for the creation of SERS-based multifunctional biochips for rapid culture and label-free detection of bacteria.

Recent advances in therapeutic delivery systems of bacteriophage and bacteriophage-encoded endolysins

Antibiotics have been the cornerstone of clinical management of bacterial infection since their discovery in the early 20th century. However, their widespread and often indiscriminate use has now led to reports of multidrug resistance becoming globally commonplace. Bacteriophage therapy has undergone a recent revival in battle against pathogenic bacteria, as the self-replicating and co-evolutionary features of these predatory virions offer several advantages over conventional therapeutic agents. In particular, the use of targeted bacteriophage therapy from specialized delivery platforms has shown particular promise owing to the control of delivery location, administration conditions and dosage of the therapeutic cargo. This review presents an overview of the recent formulations and applications of such delivery vehicles as an innovative and elegant tool for bacterial control.

Dense Layer of Bacteriophages Ordered in Alternating Electric Field and Immobilized by Surface Chemical Modification as Sensing Element for Bacteria Detection

Faster and more sensitive environmental monitoring should be developed to face the worldwide problem of bacterial infections. To remedy this issue, we demonstrate a bacteria-sensing element that utilizes dense and ordered layers of bacteriophages specific to the given bacteria strain. We combine (1) the chemical modification of a surface to increase the surface coverage of bacteriophages (2) with an alternating electric field to greatly increase the number of properly oriented bacteriophages at the surface. Usually, in sensing elements, a random orientation of bacteriophages results in steric hindrance, which results in no more than a few percent of all receptors being available. An increased number of properly ordered phages results in the optimal performance of phage receptors, manifesting in up to a 64-fold increase in sensitivity and a limit of detection as low as 100 CFU mL^-1. Our sensing elements can be applied for selective, sensitive, and fast (15 min) bacterial detection. A well-studied pair T4 bacteriophage-bacteria Escherichia coli, was used as a model; however, the method could be adapted to prepare bacteriophage-based sensors for detection of a variety of bacterial strains.

Development of Engineered Bacteriophages for Escherichia coli Detection and High-Throughput Antibiotic Resistance Determination

T7 bacteriophages (phages) have been genetically engineered to carry the lacZ operon, enabling the overexpression of beta-galactosidase (β-gal) during phage infection and allowing for the enhanced colorimetric detection of Escherichia coli (E. coli). Following the phage infection of E. coli, the enzymatic activity of the released β-gal was monitored using a colorimetric substrate. Compared with a control T7 phage, our T7_lacZ phage generated significantly higher levels of β-gal expression following phage infection, enabling a lower limit of detection for E. coli cells. Using this engineered T7_lacZ phage, we were able to detect E. coli cells at 10 CFU·mL^-1 within 7 h. Furthermore, we demonstrated the potential for phage-based sensing of bacteria antibiotic resistance profiling using our T7_lacZ phage, and subsequent β-gal expression to detect antibiotic resistant profile of E. coli strains.

Integrating recognition elements with nanomaterials for bacteria sensing

Pathogenic bacterial contamination is a major threat to human health and safety. In this review, we summarize recent strategies for the integration of recognition elements with nanomaterials for the detection and sensing of pathogenic bacteria. Nanoprobes can provide sensitive and specific detection of bacterial cells, which can be applied across multiple applications and industries.

Bacteriophages and Bacterial Plant Diseases

Losses in crop yields due to disease need to be reduced in order to meet increasing global food demands associated with growth in the human population. There is a well-recognized need to develop new environmentally friendly control strategies to combat bacterial crop disease. Current control measures involving the use of traditional chemicals or antibiotics are losing their efficacy due to the natural development of bacterial resistance to these agents. In addition, there is an increasing awareness that their use is environmentally unfriendly. Bacteriophages, the viruses of bacteria, have received increased research interest in recent years as a realistic environmentally friendly means of controlling bacterial diseases. Their use presents a viable control measure for a number of destructive bacterial crop diseases, with some phage-based products already becoming available on the market. Phage biocontrol possesses advantages over chemical controls in that tailor-made phage cocktails can be adapted to target specific disease-causing bacteria. Unlike chemical control measures, phage mixtures can be easily adapted for bacterial resistance which may develop over time. In this review, we will examine the progress and challenges for phage-based disease biocontrol in food crops.

A reusable supramolecular platform for the specific capture and release of proteins and bacteria

A re-usable supramolecular platform with the capability of high-efficiency capture and on-demand release of specific proteins and bacteria was developed.

Colorimetric Detection of Escherichia coli Based on the Enzyme-Induced Metallization of Gold Nanorods

A novel enzyme-induced metallization colorimetric assay is developed to monitor and measure beta-galactosidase (β-gal) activity, and is further employed for colorimetric bacteriophage (phage)-enabled detection of Escherichia coli (E. coli). This assay relies on enzymatic reaction-induced silver deposition on the surface of gold nanorods (AuNRs). In the presence of β-gal, the substrate p-aminophenyl β-d-galactopyranoside is hydrolyzed to produce p-aminophenol (PAP). Reduction of silver ions by PAP generates a silver shell on the surface of AuNRs, resulting in the blue shift of the longitudinal localized surface plasmon resonance peak and multicolor changes of the detection solution from light green to orange-red. Under optimized conditions, the detection limit for β-gal is 128 pM, which is lower than the conventional colorimetric assay. Additionally, the assay has a broader dynamic range for β-gal detection. The specificity of this assay for the detection of β-gal is demonstrated against several protein competitors. Additionally, this technique is successfully applied to detect E. coli bacteria cells in combination with bacteriophage infection. Due to the simplicity and short incubation time of this enzyme-induced metallization colorimetric method, the assay is well suited for the detection of bacteria in low-resource settings.

Development of a novel bacteriophage based biomagnetic separation method as an aid for sensitive detection of viable Escherichia coli

The application of bacteriophage combined with the use of magnetic separation techniques has emerged as a valuable tool for the sensitive identification and detection of bacteria. In this study, bacteriophage T7 labelled magnetic beads were developed for the detection of viable bacterial cells. Fusion of the biotin acceptor peptide (BAP) with the phage capsid protein gene and the insertion of the biotin ligase (BirA) gene enabled the display of the BAP ligand and the expression protein BirA during the replication cycle of phage infection. The replicated Escherichia coli specific bacteriophage was biotinylated in vivo and coated on magnetic beads via streptavidin-biotin interaction. Immobilization efficiency of the recombinant phage was investigated on magnetic beads and the phage-bead complex was evaluated by detecting E. coli from inoculated broth. When compared to the wild type phage, the recombinant phage T7birA-bap had a high immobilization density on streptavidin-coated magnetic beads and could capture 86.2% of E. coli cells from broth within 20 min. As this phage-based biomagnetic detection approach provided a low detection limit of 10(2) CFU mL(-1) without pre-enrichment, we believe this assay could be further developed to detect other bacteria of interest by applying host-specific phages. This would be of particular use in detecting bacteria which are difficult to grow or replicate slowly in culture.

Phage-protease-peptide: a novel trifecta enabling multiplex detection of viable bacterial pathogens

Bacteriophages represent rapid, readily targeted, and easily produced molecular probes for the detection of bacterial pathogens. Molecular biology techniques have allowed researchers to make significant advances in the bioengineering of bacteriophage to further improve speed and sensitivity of detection. Despite their host specificity, bacteriophages have not been meaningfully leveraged in multiplex detection of bacterial pathogens. We propose a proof-of-principal phage-based scheme to enable multiplex detection. Our scheme involves bioengineering bacteriophage to carry a gene for a specific protease, which is expressed during infection of the target cell. Upon lysis, the protease is released to cleave a reporter peptide, and the signal detected. Here we demonstrate the successful (i) modification of T7 bacteriophage to carry tobacco etch virus (TEV) protease; (ii) expression of TEV protease by Escherichia coli following infection by our modified T7, an average of 2000 units of protease per phage are produced during infection; and (iii) proof-of-principle detection of E. coli in 3 h after a primary enrichment via TEV protease activity using a fluorescent peptide and using a designed target peptide for matrix-assisted laser desorption/ionization time-of-flight mass spectrometry analysis (MALDI-TOF MS) analysis. This proof-of-principle can be translated to other phage-protease-peptide combinations to enable multiplex bacterial detection and readily adopted on multiple platforms, like MALDI-TOF MS or fluorescent readers, commonly found in labs.

Phage & phosphatase: a novel phage-based probe for rapid, multi-platform detection of bacteria

A bacteriophage-based biosensing platform forE. coliis proposed. The bacteriophage T7 was genetically engineered to carry the alkaline phosphatase genephoA. The overexpression of the gene was quantified with colorimetric, fluorescent, and chemiluminescent methods.