Antimicrobial Peptides as Probes in Biosensors Detecting Whole Bacteria: A Review

Detection strategies of infectious diseases via peptide-based electrochemical biosensors

Infectious diseases have threatened human life for as long as humankind has existed. One of the most crucial aspects of fighting against these infections is diagnosis to prevent disease spread. However, traditional diagnostic methods prove insufficient and time-consuming in the face of a pandemic. Therefore, studies focusing on detecting viruses causing these diseases have increased, with a particular emphasis on developing rapid, accurate, specific, user-friendly, and portable electrochemical biosensor systems. Peptides are used integral components in biosensor fabrication for several reasons, including various and adaptable synthesis protocols, long-term stability, and specificity. Here, we discuss peptide-based electrochemical biosensor systems that have been developed over the last decade for the detection of infectious diseases. In contrast to other reports on peptide-based biosensors, we have emphasized the following points i) the synthesis methods of peptides for biosensor applications, ii) biosensor fabrication approaches of peptide-based electrochemical biosensor systems, iii) the comparison of electrochemical biosensors with other peptide-based biosensor systems and the advantages and limitations of electrochemical biosensors, iv) the pros and cons of peptides compared to other biorecognition molecules in the detection of infectious diseases, v) different perspectives for future studies with the shortcomings of the systems developed in the past decade.

Nanozyme colourimetry based on temperate bacteriophage for rapid and sensitive detection of Staphylococcus aureus in food matrices

Although bacteriophage-based biosensors are promising tools for rapid, convenient, and sensitive detection of Staphylococcus aureus in food products, the effect of biosensors using temperate phages as biorecognition elements to detect viable S. aureus isolates remains unclear. In this study, three temperate S. aureus phages were isolated and their biological features (one-step growth, host range, pH stability, temperature stability, and adsorption rate) were evaluated as the biological element. The selected phage SapYZUs8 was immobilized on the nanozyme Cu-MOF via electrostatic interactions to generate SapYZUs8@Cu-MOF, and its detection performance in real food (skim milk and pork) was then evaluated. Compared with phages SapYZUm7 and SapYZUs16, phage SapYZUs8 exhibited a broader host range, greater pH stability (3-12), and a better absorption rate (92 %, 8 min) suitable for S. aureus detection, which is likely the result of the DNA replication (DNA helicase) and phage tail protein genes in the SapYZUs8 genome. Therefore, phage SapYZUs8 was fixed on Cu-MOF to generate SapYZUs8@Cu-MOF, which exhibited good sensitivity and specificity for rapid colourimetric detection of viable S. aureus. The method took <0.5 h, and the detection limit was 1.09 × 102 CFU/mL. In addition, SapYZUs8@Cu-MOF was successfully employed for the colourimetric detection of S. aureus in food samples without interference from different food additives, NaCl concentrations, or pH values. With these benefits, it allows rapid visual assessment of S. aureus levels.

Detection of Microorganisms Using Artificial Siderophore-FeIII Complex-Modified Substrates

Four FeIII complexes of typical artificial siderophore ligands containing catecholate and/or hydroxamate groups of tricatecholate, biscatecholate-monohydroxamate, monocatecholate-bishydroxamate, and trihydroxamate type artificial siderophores (K3[FeIIILC3], K2[FeIIILC2H1], K[FeIIILC1H2], and [FeIIILH3]) were modified on Au substrate surfaces. Their abilities to adsorb microorganisms were investigated using scanning electron microscopy, quartz crystal microbalance, and AC impedance methods. The artificial siderophore-iron complexes modified on Au substrates (FeLC3/Au, FeLC2H1/Au, FeLC1H2/Au, and FeLH3/Au) showed the selective immobilization behavior for various microorganisms, depending on the structural features of the artificial siderophores (the number of catecholate and hydroxamate arms). Their specificities corresponded well with the structural characteristics of natural siderophores released by microorganisms and used for FeIII ion uptake. These findings suggest that they were generated via specific interactions between the artificial siderophore-FeIII complexes and the receptors on microorganism surfaces. Our observations revealed that the FeL/Au systems may be potentially used as effective microbe-capturing probes that can enable rapid and simple detection and identification of various microorganisms.

[Microorganism Immobilization Device Using Artificial Siderophores]

Inspired by the mechanism by which microorganisms utilize siderophores to ingest iron, four different FeIII complexes of typical artificial siderophore ligands containing catecholate and/or hydroxamate groups, K3[FeIII-LC3], K2[FeIII-LC2H1], K[FeIII-LC1H2], and [FeIII-LH3], were prepared. They were modified on an Au substrate surface (Fe-L/Au) and applied as microorganism immobilization devices for fast, sensitive, selective detection of microorganisms, where H6LC3, H5LC2H1, H4LC1H2, and H3LH3 denote the tri-catecholate, biscatecholate-monohydroxamate, monocatecholate-bishydroxamate, and tri-hydroxamate type of artificial siderophores, respectively. Their adsorption properties for the several microorganisms were investigated using scanning electron microscopy (SEM), quartz crystal microbalance (QCM), and electric impedance spectroscopy (EIS) methods. The artificial siderophore-iron complexes modified on the Au substrates Fe-LC3/Au, Fe-LC2H1/Au, Fe-LC1H2/Au, and Fe-LH3/Au showed specific microorganism immobilization behavior with selectivity based on the structure of the artificial siderophores. Their specificities corresponded well with the structural characteristics of natural siderophores that microorganisms release from the cell and/or use to take up an iron. These findings suggest that release and uptake are achieved through specific interactions between the artificial siderophore-FeIII complexes and receptors on the cell surfaces of microorganisms. This study revealed that Fe-L/Au systems have specific potential to serve as effective immobilization probes of microorganisms for rapid, selective detection and identification of a variety of microorganisms.

In-silico selection of peptides for the recognition of imidacloprid

The sensitive detection of pesticides using low-cost receptors designed from peptides can widen their uses in the environmental surveillance for emerging pollutants. In-silico selection of peptides can help accelerate the design of receptor sequence banks for a given target of interest. In this work, we started from Lymnaea stagnalis acetylcholine-binding protein Q55R mutant receptor-imidacloprid complex, available in the PDB databank, to select three primary short peptides (YSP09, DMR12, WQW13 respectively having 9, 12 and 13 amino acids (AA) in length) from the pesticide interacting zones with the A, B and C chains of the nicotinic receptor. Using molecular docking and molecular dynamics (MD) simulations, we showed that the three peptides can form complexes with the target imidacloprid, having energies close to that obtained from a reference RNR12 peptide. Combination of these peptides allowed preparing a new set of longer peptides (YSM21, PSM22, PSW31 and WQA34) that have higher stability and affinity as shown by the MM-PBSA calculations. In particular, the WQA34 peptide displayed an average binding free energy of -6.44±0.27 kcal/mol, which is three times higher than that of the reference RNR12 peptide (-2.29±0.25 kcal/mol) and formed a stable complex with imidacloprid. Furthermore, the dissociation constants (Kd), calculated from the binding free energy, showed that WQA32 (40 μM) has three orders of magnitude lower Kd than the reference RNR12 peptide (3.4 × 104 μM). Docking and RMSD scores showed that the WQA34 peptide is potentially selective to the target imidacloprid with respect to acetamiprid and clothianidin. Therefore, this peptide can be used in wet-lab experiments to prepare a biosensor to selectively detect imidacloprid.

Microbial nanowires with genetically modified peptide ligands to sustainably fabricate electronic sensing devices

Nanowires have substantial potential as the sensor component in electronic sensing devices. However, surface functionalization of traditional nanowire and nanotube materials with short peptides that increase sensor selectivity and sensitivity requires complex chemistries with toxic reagents. In contrast, microorganisms can assemble pilin monomers into protein nanowires with intrinsic conductivity from renewable feedstocks, yielding an electronic material that is robust and stable in applications, but also biodegradable. Here we report that the sensitivity and selectivity of protein nanowire-based sensors can be modified with a simple plug and play genetic approach in which a short peptide sequence, designed to bind the analyte of interest, is incorporated into the pilin protein that is microbially assembled into nanowires. We employed a scalable Escherichia coli chassis to fabricate protein nanowires that displayed either a peptide previously demonstrated to effectively bind ammonia, or a peptide known to bind acetic acid. Sensors comprised of thin films of the nanowires amended with the ammonia-specific peptide had a ca. 100-fold greater response to ammonia than sensors made with unmodified protein nanowires. Protein nanowires with the peptide that binds acetic acid yielded a 4-fold higher response than nanowires without the peptide. The protein nanowire-based sensors had greater responses than previously reported sensors fabricated with other nanomaterials. The results demonstrate that protein nanowires with enhanced sensor response for analytes of interest can be fabricated with a flexible genetic strategy that sustainably eliminates the energy, environmental, and health concerns associated with other common nanomaterials.

Recent Advances on Peptide-Based Biosensors and Electronic Noses for Foodborne Pathogen Detection

Foodborne pathogens present a serious issue around the world due to the remarkably high number of illnesses they cause every year. In an effort to narrow the gap between monitoring needs and currently implemented classical detection methodologies, the last decades have seen an increased development of highly accurate and reliable biosensors. Peptides as recognition biomolecules have been explored to develop biosensors that combine simple sample preparation and enhanced detection of bacterial pathogens in food. This review first focuses on the selection strategies for the design and screening of sensitive peptide bioreceptors, such as the isolation of natural antimicrobial peptides (AMPs) from living organisms, the screening of peptides by phage display and the use of in silico tools. Subsequently, an overview on the state-of-the-art techniques in the development of peptide-based biosensors for foodborne pathogen detection based on various transduction systems was given. Additionally, limitations in classical detection strategies have led to the development of innovative approaches for food monitoring, such as electronic noses, as promising alternatives. The use of peptide receptors in electronic noses is a growing field and the recent advances of such systems for foodborne pathogen detection are presented. All these biosensors and electronic noses are promising alternatives for the pathogen detection with high sensitivity, low cost and rapid response, and some of them are potential portable devices for on-site analyses.

Multifunctional Composite Hydrogels for Bacterial Capture, Growth/Elimination, and Sensing Applications

Hydrogels are cross-linked networks of hydrophilic polymer chains with a three-dimensional structure. Owing to their unique features, the application of hydrogels for bacterial/antibacterial studies and bacterial infection management has grown in importance in recent years. This trend is likely to continue due to the rise in bacterial infections and antimicrobial resistance. By exploiting their physicochemical characteristics and inherent nature, hydrogels have been developed to achieve bacterial capture and detection, bacterial growth or elimination, antibiotic delivery, or bacterial sensing. Traditionally, the development of hydrogels for bacterial/antibacterial studies has focused on achieving a single function such as antibiotic delivery, antibacterial activity, bacterial growth, or bacterial detection. However, recent studies demonstrate the fabrication of multifunctional hydrogels, where a single hydrogel is capable of performing more than one bacterial/antibacterial function, or composite hydrogels consisting of a number of single functionalized hydrogels, which exhibit bacterial/antibacterial function synergistically. In this review, we first highlight the hydrogel features critical for bacterial studies and infection management. Then, we specifically address unique hydrogel properties, their surface/network functionalization, and their mode of action for bacterial capture, adhesion/growth, antibacterial activity, and bacterial sensing, respectively. Finally, we provide insights into different strategies for developing multifunctional hydrogels and how such systems can help tackle, manage, and understand bacterial infections and antimicrobial resistance. We also note that the strategies highlighted in this review can be adapted to other cell types and are therefore likely to find applications beyond the field of microbiology.

Technique Evolutions for Microorganism Detection in Complex Samples: A Review

Rapid detection of microorganisms is a major challenge in the medical and industrial sectors. In a pharmaceutical laboratory, contamination of medical products may lead to severe health risks for patients, such as sepsis. In the specific case of advanced therapy medicinal products, contamination must be detected as early as possible to avoid late production stop and unnecessary costs. Unfortunately, the conventional methods used to detect microorganisms are based on time-consuming and labor-intensive approaches. Therefore, it is important to find new tools to detect microorganisms in a shorter time frame. This review sums up the current methods and represents the evolution in techniques for microorganism detection. First, there is a focus on promising ligands, such as aptamers and antimicrobial peptides, cheaper to produce and with a broader spectrum of detection. Then, we describe methods achieving low limits of detection, thanks to Raman spectroscopy or precise handling of samples through microfluids devices. The last part is dedicated to techniques in real-time, such as surface plasmon resonance, preventing the risk of contamination. Detection of pathogens in complex biological fluids remains a scientific challenge, and this review points toward important areas for future research.

In silico screening for oligopeptides useful as capture and reporting probes for interleukin-6 biosensing

IL-6 is an important interleukin associated with inflammation and several diseases such as cancer. Evaluation of its levels in human blood sera is a critical step for an accurate diagnosis of the diseases. Our goal is to design peptides that can selectively bind in different poses with good affinities to IL-6. For this purpose, we started from the crystal structures of different IL-6/protein complexes available in the Protein Data Bank (PDB) to select short peptides in the interaction zones, in which we intentionally introduced point mutations to increase their stability and affinity. To examine their usefulness as capture and reporting probes for the IL-6 biosensing, the five peptides and their interaction with IL-6 were studied in saline aqueous solution. Molecular docking, MD, and MM-PBSA were used to investigate the affinity and stability of these complexes. The conformational changes, the distance between the mass centers, the gyration radii, and the numbers of hydrogen bonds were analyzed to select the most suitable candidates. Three peptides, namely CTE17, CAY15 and CSE25, have the highest affinities presenting significant numbers of residues that have contact frequencies greater than 50% of simulation run time and are the most promising candidates. CTE17 and CSE25 showed they can form a stable sandwich with the target protein. For sake of comparison, we examined the previously known peptides (FND20, INL19 and CEK17) having affinity to IL-6 and the affinity of the lead i.e. CSE25 to two other interleukin family members (IL-4 and to IL-10).

In silico design by docking and molecular dynamics of short peptides that can selectively recognize IL-6 for biosensing purposes.

Antimicrobial peptides: Promising alternatives over conventional capture ligands for biosensor-based detection of pathogenic bacteria

The detection of pathogenic bacteria using biosensing techniques could be a potential alternative to traditional culture based methods. However, the low specificity and sensitivity of conventional biosensors, critically related to the choice of bio-recognition elements, limit their practical applicability. Mammalian antibodies have been widely investigated as biorecognition ligands due to high specificity and technological advancement in antibody production. However, antibody-based biosensors are not considered as an efficient approach due to the batch-to-batch inconsistencies as well as low stability. In recent years, antimicrobial peptides (AMPs) have been increasingly investigated as ligands as they have demonstrated high stability and possessed multiple sites for capturing bacteria. The conjugation of chemo-selective groups with AMPs has allowed effective immobilization of peptides on biosensor surface. However, the specificity of AMPs is a major concern for consideration as an efficient ligand. In this article, we have reviewed the advances and concerns, particularly the selectivity of AMPs for specific detection of pathogenic bacteria. This review also focuses the state-of-the-art mechanisms, challenges and prospects for designing potential AMP conjugated biosensors. The application of AMP in different biosensing transducers such as electrochemical, optical and piezoelectric varieties has been widely discussed. We argue that this review would provide insights to design and construct AMP conjugated biosensors for the pathogenic bacteria detection.

New analytical methods using carbon-based nanomaterials for detection of Salmonella species as a major food poisoning organism in water and soil resources

Salmonella is one of the most prevalent causing agents of food- and water-borne illnesses, posing an ongoing public health threat. These food-poisoning bacteria contaminate the resources at different stages such as production, aggregation, processing, distribution, as well as marketing. According to the high incidence of salmonellosis, effective strategies for early-stage detection are required at the highest priority. Since traditional culture-dependent methods and polymerase chain reaction are labor-intensive and time-taking, identification of early and accurate detection of Salmonella in food and water samples can prevent significant health economic burden and lessen the costs. The immense potentiality of biosensors in diagnosis, such as simplicity in operation, the ability of multiplex analysis, high sensitivity, and specificity, have driven research in the evolution of nanotechnology, innovating newer biosensors. Carbon nanomaterials enhance the detection sensitivity of biosensors while obtaining low levels of detection limits due to their possibility to immobilize huge amounts of bioreceptor units at insignificant volume. Moreover, conjugation and functionalization of carbon nanomaterials with metallic nanoparticles or organic molecules enables surface functional groups. According to these remarkable properties, carbon nanomaterials are widely exploited in the development of novel biosensors. To be specific, carbon nanomaterials such as carbon nanotubes, graphene and fullerenes function as transducers in the analyte recognition process or surface immobilizers for biomolecules. Herein the potential application of carbon nanomaterials in the development of novel Salmonella biosensors platforms is reviewed comprehensively. In addition, the current problems and critical analyses of the future perspectives of Salmonella biosensors are discussed.

Antimicrobial peptide-based materials: opportunities and challenges

The multifunctional properties of antimicrobial peptides (AMPs) make them attractive candidates for the treatment of various diseases. AMPs are considered alternatives to antibiotics due to the rising number of multidrug-resistant...

Antimicrobial Peptides: A Potent Alternative to Antibiotics

Antimicrobial peptides constitute one of the most promising alternatives to antibiotics since they could be used to treat bacterial infections, especially those caused by multidrug-resistant pathogens. Many antimicrobial peptides, with various activity spectra and mechanisms of actions, have been described. This review focuses on their use against ESKAPE bacteria, especially in biofilm treatments, their synergistic activity, and their application as prophylactic agents. Limitations and challenges restricting therapeutic applications are highlighted, and solutions for each challenge are evaluated to analyze whether antimicrobial peptides could replace antibiotics in the near future.

Electrochemical-based ''antibiotsensor'' for the whole-cell detection of the vancomycin-susceptible bacteria

In this study, we aim to develop an antibiotic-based biosensor platform 'Antibiotsensor' for the specific detection of gram-positive bacteria using vancomycin modified Screen Printed Gold Electrodes (SPGEs). Through this pathway, vancomycin molecules were first functionalized with thiol groups and characterized with quadrupole time of flight (q-TOF) mass spectroscopy analysis. Immobilization of thiolated vancomycin molecules (HS-Van) onto SPGEs was carried out based on self-assembled monolayer (SAM) phenomenon. Electrochemical impedance spectroscopy (EIS) was employed to test the detection and showed a considerable change in impedance value upon the binding of HS-Van molecules onto the electrode surface. Atomic Force Microscopy analysis indicated that SPGE was successfully modified upon the treatment with HS-Van molecules based on the shift in surface roughness from 173 ± 2 nm to 301 ± 3 nm. Fourier Transform Infrared Spectroscopy (FTIR) spectroscopy proved the EIS and AFM results as well by showing characteristic peaks of immobilized HS-Van molecule. As a proof-of-concept, EIS-based susceptibility testing was performed using Escherichia coli, Staphylococcus aureus and Mycobacterium smegmatis bacteria to prove the specificity of obtained SPGE-Van. EIS data showed that the charge transfer resistance (R_ct) values changed from 1.08, 1.18 to 26.5, respectively, indicating that vancomycin susceptible S. aureus was successfully attached onto SPGE-Van surface strongly, while vancomycin resistance E. coli and M. smegmatis did not show any significant attachment properties. In addition, different concentration (10⁸-10 CFU/mL) of S. aureus was performed to investigate sensitivity of proposed sensor platform. Limit of detection and limit of quantitation was calculated as 10^1.58 and 10^4.81 CFU/mL, respectively. Scanning electron microscopy (SEM) analysis also confirmed that only S. aureus bacteria was attached to the surface in a dense monolayer distribution. We believe that the proposed approach is selective and sensitive towards the whole-cell detection of vancomycin-susceptible bacteria and can be modified for different purposes in the future.

New Detection Platform for Screening Bacteria in Liquid Samples

The development of sensitive methods for the determination of potential bacterial contamination is of upmost importance for environmental monitoring and food safety. In this study, we present a new method combining a fast pre-enrichment step using a microporous cryogel and a detection and identification step using antimicrobial peptides (AMPs) and labelled antibodies, respectively. The experimental method consists of: (i) the capture of large amounts of bacteria from liquid samples by using a highly porous and functionalized cryogel; (ii) the detection and categorisation of Gram-positive and Gram-negative bacteria by determining their affinities toward a small set of AMPs; and (iii) the identification of the bacterial strain by using labelled detection antibodies. As proof of concept, the assessment of the three steps of the analysis was performed by using Escherichia coli and Bacillus sp. as models for Gram-negative and Gram-positive bacteria, respectively. The use of AMPs with broad specificity combined with labelled antibodies enabled the detection and potential categorization of a large spectrum of unknown or unexpected bacteria.

Infrared Metasurface Augmented by Deep Learning for Monitoring Dynamics between All Major Classes of Biomolecules

Insights into the fascinating molecular world of biological processes are crucial for understanding diseases, developing diagnostics, and effective therapeutics. These processes are complex as they involve interactions between four major classes of biomolecules, i.e., proteins, nucleic acids, carbohydrates, and lipids, which makes it important to be able to discriminate between all these different biomolecular species. In this work, a deep learning-augmented, chemically-specific nanoplasmonic technique that enables such a feat in a label-free manner to not disrupt native processes is presented. The method uses a highly sensitive multiresonant plasmonic metasurface in a microfluidic device, which enhances infrared absorption across a broadband mid-IR spectrum and in water, despite its strongly overlapping absorption bands. The real-time format of the optofluidic method enables the collection of a vast amount of spectrotemporal data, which allows the construction of a deep neural network to discriminate accurately between all major classes of biomolecules. The capabilities of the new method are demonstrated by monitoring of a multistep bioassay containing sucrose- and nucleotides-loaded liposomes interacting with a small, lipid membrane-perforating peptide. It is envisioned that the presented technology will impact the fields of biology, bioanalytics, and pharmacology from fundamental research and disease diagnostics to drug development.

Environmental Management of Legionella in Domestic Water Systems: Consolidated and Innovative Approaches for Disinfection Methods and Risk Assessment

Legionella is able to remain in water as free-living planktonic bacteria or to grow within biofilms that adhere to the pipes. It is also able to enter amoebas or to switch into a viable but not culturable (VBNC) state, which contributes to its resistance to harsh conditions and hinders its detection in water. Factors regulating Legionella growth, such as environmental conditions, type and concentration of available organic and inorganic nutrients, presence of protozoa, spatial location of microorganisms, metal plumbing components, and associated corrosion products are important for Legionella survival and growth. Finally, water treatment and distribution conditions may affect each of these factors. A deeper comprehension of Legionella interactions in water distribution systems with the environmental conditions is needed for better control of the colonization. To this purpose, the implementation of water management plans is the main prevention measure against Legionella. A water management program requires coordination among building managers, health care providers, and Public Health professionals. The review reports a comprehensive view of the state of the art and the promising perspectives of both monitoring and disinfection methods against Legionella in water, focusing on the main current challenges concerning the Public Health sector.

Proximity ligation assay: an ultrasensitive method for protein quantification and its applications in pathogen detection

It is of great significance to establish sensitive and accurate pathogen detection methods, considering the continuous emergence or re-emergence of infectious diseases seriously influences the safety of human and animals. Proximity ligation assay (PLA) is developed for the sensitive protein detection and also can be used for the detection of pathogens. PLA employs aptamer or monoclonal/polyclonal antibody-nucleic acid complexes as proximity probes. When the paired proximity probes bind to the same target protein or protein complex, they will be adjacent to each other and form an amplifiable DNA sequence through ligation. Combining the specificity of enzyme-linked immunosorbent assay (ELISA) and sensitivity of polymerase chain reaction (PCR), PLA transforms the detection of protein into the detection of DNA nucleic acid sequence. Therefore, as an ultrasensitive protein assay, PLA has great potential for quantification, localization of protein, and clinical diagnostics. In this review, we summarize the basic principles of PLA and its applications in pathogen detection. KEY POINTS: • Different forms of proximity ligation assay are introduced. • Applications of proximity ligation assay in pathogen detection are summarized. • Proximity ligation assay is an ultrasensitive method to quantify protein and pathogen.