Efficacy and potential of phage therapy against multidrug resistant Shigella spp

A Review on Recent Trends in Bacteriophages for Post-Harvest Food Decontamination

Infectious diseases resulting from unsafe food consumption are a global concern. Despite recent advances and control measures in the food industry aimed at fulfilling the growing consumer demand for high-quality and safe food products, infection outbreaks continue to occur. This review stands out by providing an overview of post-harvest food decontamination methods against some of the most important bacterial foodborne pathogens, with particular focus on the advantages and challenges of using phages, including their most recent post-harvest applications directly to food and integration into active food packaging systems, highlighting their potential in providing safer and healthier food products. The already approved commercial phage products and the numerous available studies demonstrate their antibacterial efficacy against some of the most problematic foodborne pathogens in different food products, reinforcing their possible use in the future as a current practice in the food industry for food decontamination. Moreover, the incorporation of phages into packaging materials holds particular promise, providing protection against harsh conditions and enabling their controlled and continuous release into the food matrix. The effectiveness of phage-added packaging materials in reducing the growth of pathogens in food systems has been well-demonstrated. However, there are still some challenges associated with the development of phage-based packaging systems that need to be addressed with future research.

An insight into the applications of bacteriophages against food-borne pathogens

Novel and emerging pathogens, enduring contamination, antibiotic resistance, an environment that is always changing, and the complexity of food production systems all contribute to the worsening of foodborne illness. It has been proposed that bacteriophages can serve as both fast food-borne pathogen detection tools and natural food preservatives in a variety of foods. Phages, like many other antimicrobial interventions used in food production systems, are not a cure-all for issues related to food safety, though. Consequently, phage-based biocontrol has a generally narrower antibacterial spectrum than most antibiotics, even though it can be promising in the fight against foodborne infections. Among the difficulties phage-based biocontrol techniques encounter are forming phage-insensitive single-cell variations and creating potent cocktails. To better understand when and where phage-based applications can be successfully implemented at the production and processing levels, this review focuses on phage-based applications at crucial control points in food production systems.

A Concise Overview of Studies on Successful Real-World Applications of Bacteriophages in Aquaculture

Increasing antibiotic resistance poses an urgent global public health threat and a serious concern worldwide. Bacteriophage (phage) therapy has been identified as a promising alternative to antibiotics for treating bacterial diseases in both humans and animals. The excessive use of antibiotics in aquaculture is a major threat to sustainable aquaculture, promoting the spread of antibiotic resistance in the aquaculture environment and the contamination of aquaculture products with antibiotic residues. Consequently, interest in alternative approaches that reduce reliance on antibiotics has grown within the aquaculture sector. As a promising alternative, extensive phage research targeted at aquaculture has demonstrated the protective efficacy of phages against diseases in aquatic animals. Although numerous studies have employed in vitro models, research supported by in vivo experiments remains scarce. Without in vivo evidence, phage therapy cannot fulfill the requirements of aquaculturists. The first part of this review outlines the bacterial diseases severely affecting the health and survival of aquatic animals. The second part provides updates on phage applications for the therapy and prophylaxis of pathogenic bacterial infection in aquatic animals, including administration routes and key accomplishments. Therefore, this review provides insights into effective real-world phage biocontrol strategies that enable sustainable aquaculture.

A game of resistance: War between bacteria and phages and how phage cocktails can be the solution

While phages hold promise as an antibiotic alternative, they encounter significant challenges in combating bacterial infections, primarily due to the emergence of phage-resistant bacteria. Bacterial defence mechanisms like superinfection exclusion, CRISPR, and restriction-modification systems can hinder phage effectiveness. Innovative strategies, such as combining different phages into cocktails, have been explored to address these challenges. This review delves into these defence mechanisms and their impact at each stage of the infection cycle, their challenges, and the strategies phages have developed to counteract them. Additionally, we examine the role of phage cocktails in the evolving landscape of antibacterial treatments and discuss recent studies that highlight the effectiveness of diverse phage cocktails in targeting essential bacterial receptors and combating resistant strains.

Use of Bacteriophages to Target Intracellular Pathogens

Bacteriophages (phages) have shown great potential as natural antimicrobials against extracellular pathogens (eg, Escherichia coli or Klebsiella pneumoniae), but little is known about how they interact with intracellular targets (eg, Shigella spp., Salmonella spp., Mycobacterium spp.) in the mammalian host. Recent research has demonstrated that phages can enter human cells. However, for the design of successful clinical applications, further investigation is required to define their subcellular behavior and to understand the complex biological processes that underlie the interaction with their bacterial targets. In this review, we summarize the molecular evidence of phage internalization in eucaryotic cells, with specific focus on proof of phage activity against their bacterial targets within the eucaryotic host, and the current proposed strategies to overcome poor penetrance issues that may impact therapeutic use against the most clinically relevant intracellular pathogens.

Bacteriophages and Their Host Range in Multidrug-Resistant Bacterial Disease Treatment

The rapid emergence of multidrug-resistant (MDR) bacteria in recent times has prompted the search for new and more potent antibiotics. Bacteriophages (commonly known as phages) are viruses that target and infect their bacterial hosts. As such, they are also a potential alternative to antibiotics. These phages can be broadly categorized into monovalent (with a narrow host range spectrum and specific to a single bacterial genus) and polyvalent (with a broad host range and specific to more than two genera). However, there is still much ambiguity in the use of these terms, with researchers often describing their phages differently. There is considerable research on the use of both narrow- and broad-host range phages in the treatment of infections and diseases caused by MDR bacteria, including tuberculosis, cystic fibrosis, and carbapenem-resistant Enterobacterales (CRE) infectious diseases. From this, it is clear that the host range of these phages plays a vital role in determining the effectiveness of any phage therapy, and this factor is usually analyzed based on the advantages and limitations of different host ranges. There have also been efforts to expand phage host ranges via phage cocktail development, phage engineering and combination therapies, in line with current technological advancements. This literature review aims to provide a more in-depth understanding of the role of phage host ranges in the effectiveness of treating MDR-bacterial diseases, by exploring the following: phage biology, the importance of phages in MDR bacteria diseases treatment, the importance of phage host range and its advantages and limitations, current findings and recent developments, and finally, possible future directions for wide host range phages.

The Safety of Bacteriophages in Treatment of Diseases Caused by Multidrug-Resistant Bacteria

Given the urgency due to the rapid emergence of multidrug-resistant (MDR) bacteria, bacteriophages (phages), which are viruses that specifically target and kill bacteria, are rising as a potential alternative to antibiotics. In recent years, researchers have begun to elucidate the safety aspects of phage therapy with the aim of ensuring safe and effective clinical applications. While phage therapy has generally been demonstrated to be safe and tolerable among animals and humans, the current research on phage safety monitoring lacks sufficient and consistent data. This emphasizes the critical need for a standardized phage safety assessment to ensure a more reliable evaluation of its safety profile. Therefore, this review aims to bridge the knowledge gap concerning phage safety for treating MDR bacterial infections by covering various aspects involving phage applications, including phage preparation, administration, and the implications for human health and the environment.

Recent Advances in Electrochemical Biosensors for the Detection of Foodborne Pathogens: Current Perspective and Challenges

Foodborne pathogens cause many diseases and significantly impact human health and the economy. Foodborne pathogens mainly include Salmonella spp., Escherichia coli, Staphylococcus aureus, Shigella spp., Campylobacter spp. and Listeria monocytogenes, which are present in agricultural products, dairy products, animal-derived foods and the environment. Various pathogens in many different types of food and water can cause potentially life-threatening diseases and develop resistance to various types of antibiotics. The harm of foodborne pathogens is increasing, necessitating effective and efficient methods for early monitoring and detection. Traditional methods, such as real-time polymerase chain reaction (RT-PCR), enzyme-linked immunosorbent assay (ELISA) and culture plate, are time-consuming, labour-intensive and expensive and cannot satisfy the demands of rapid food testing. Therefore, new fast detection methods are urgently needed. Electrochemical biosensors provide consumer-friendly methods to quickly detect foodborne pathogens in food and the environment and achieve extensive accuracy and reproducible results. In this paper, by focusing on various mechanisms of electrochemical transducers, we present a comprehensive overview of electrochemical biosensors for the detection of foodborne pathogens. Furthermore, the review introduces the hazards of foodborne pathogens, risk analysis methods and measures of control. Finally, the review also emphasizes the recent research progress and solutions regarding the use of electrochemical biosensors to detect foodborne pathogens in food and the environment, evaluates limitations and challenges experienced during the development of biosensors to detect foodborne pathogens and discusses future possibilities.

Bacteriophages and food safety: An updated overview

Despite significant advances in pathogen survival and food cleaning measures, foodborne diseases continue to be the main reason for hospitalization or other fatality globally. Conventional antibacterial techniques including pasteurization, pressurized preparation, radioactivity, as well as synthetic antiseptics could indeed decrease bacterial activity in nutrition to variable levels, despite their serious downsides like an elevated upfront outlay, the possibility of accessing malfunctions due to one corrosiveness, as well as an adverse effect upon those the foodstuffs' organoleptic properties and maybe their nutritional significance. Greatest significantly, these cleansing methods eliminate all contaminants, including numerous (often beneficial) bacteria found naturally in food. A huge amount of scientific publication that discussed the application of virus bioremediation to treat a multitude of pathogenic bacteria in meals spanning between prepared raw food to fresh fruit and vegetables although since initial idea through using retroviruses on meals. Furthermore, the quantity of widely viable bacteriophage-containing medicines licensed for use in health and safety purposes has continuously expanded. Bacteriophage bio-control, a leafy and ordinary technique that employs lytic bacteriophages extracted from the atmosphere to selectively target pathogenic bacteria and remove meaningfully decrease their stages meals, is one potential remedy that solves some of these difficulties. It has been suggested that applying bacteriophages to food is a unique method for avoiding bacterial development in vegetables. Because of their selectivity, security, stability, and use, bacteriophages are desirable. Phages have been utilized in post-harvest activities, either alone or in combination with antimicrobial drugs, since they are effective, strain-specific, informal to split and manipulate. In this review to ensure food safety, it may be viable to use retroviruses as a spontaneous treatment in the thread pollution of fresh picked fruits and vegetables, dairy, and convenience foods.

Alternatives Therapeutic Approaches to Conventional Antibiotics: Advantages, Limitations and Potential Application in Medicine

Resistance to antimicrobials and particularly multidrug resistance is one of the greatest challenges in the health system nowadays. The continual increase in the rates of antimicrobial resistance worldwide boosted by the ongoing COVID-19 pandemic poses a major public health threat. Different approaches have been employed to minimize the effect of resistance and control this threat, but the question still lingers as to their safety and efficiency. In this context, new anti-infectious approaches against multidrug resistance are being examined. Use of new antibiotics and their combination with new β-lactamase inhibitors, phage therapy, antimicrobial peptides, nanoparticles, and antisense antimicrobial therapeutics are considered as one such promising approach for overcoming bacterial resistance. In this review, we provide insights into these emerging alternative therapies that are currently being evaluated and which may be developed in the future to break the progression of antimicrobial resistance. We focus on their advantages and limitations and potential application in medicine. We further highlight the importance of the combination therapy approach, wherein two or more therapies are used in combination in order to more effectively combat infectious disease and increasing access to quality healthcare. These advances could give an alternate solution to overcome antimicrobial drug resistance. We eventually hope to provide useful information for clinicians who are seeking solutions to the problems caused by antimicrobial resistance.

High-resolution cryo-EM structure of the Shigella virus Sf6 genome delivery tail machine

Sf6 is a bacterial virus that infects the human pathogen Shigella flexneri. Here, we describe the cryo-electron microscopy structure of the Sf6 tail machine before DNA ejection, which we determined at a 2.7-angstrom resolution. We built de novo structures of all tail components and resolved four symmetry-mismatched interfaces. Unexpectedly, we found that the tail exists in two conformations, rotated by ~6° with respect to the capsid. The two tail conformers are identical in structure but differ solely in how the portal and head-to-tail adaptor carboxyl termini bond with the capsid at the fivefold vertex, similar to a diamond held over a five-pronged ring in two nonidentical states. Thus, in the mature Sf6 tail, the portal structure does not morph locally to accommodate the symmetry mismatch but exists in two energetic minima rotated by a discrete angle. We propose that the design principles of the Sf6 tail are conserved across P22-like Podoviridae.

Bacteriophages and Food Production: Biocontrol and Bio-Preservation Options for Food Safety

Food safety and sustainable food production is an important part of the Sustainable Development goals aiming to safeguard the health and wellbeing of humans, animals and the environment. Foodborne illness is a major cause of morbidity and mortality, particularly as the global crisis of antimicrobial resistance proliferates. In order to actively move towards sustainable food production, it is imperative that green biocontrol options are implemented to prevent and mitigate infectious disease in food production. Replacing current chemical pesticides, antimicrobials and disinfectants with green, organic options such as biopesticides is a step towards a sustainable future. Bacteriophages, virus which infect and kill bacteria are an area of great potential as biocontrol agents in agriculture and aquaculture. Lytic bacteriophages offer many advantages over traditional chemical-based solutions to control microbiological contamination in the food industry. The innate specificity for target bacterial species, their natural presence in the environment and biocompatibility with animal and humans means phages are a practical biocontrol candidate at all stages of food production, from farm-to-fork. Phages have demonstrated efficacy as bio-sanitisation and bio-preservation agents against many foodborne pathogens, with activity against biofilm communities also evident. Additionally, phages have long been recognised for their potential as therapeutics, prophylactically and metaphylactically. Further investigation is warranted however, to overcome their limitations such as formulation and stability issues, phage resistance mechanisms and transmission of bacterial virulence factors.

Gene sequencing analysis of tailed phages identified diverse (Kayfunavirus and Berlinvirus) coliphages in aquatic niche against AMR Escherichia coli

Escherichia coli has been recognized as a pathogen of concern in the antimicrobial resistance (AMR) perspective. Globally initiatives were taken to control AMR. Bacteriophages are recognized as promising alternative to antibiotics. Harnessing broad-spectrum bacteriophages for augmenting phage repositories is being prioritized across continents for future health care needs. In this context, a study was conducted to isolate coliphages against a collection of AMR E. coli isolated from diverse aquatic niche. Thirty pooled water samples (5 each from rivers, aquaculture ponds, lake, sewage treatment plant, domestic waste and canals) were analysed, and fifty-four lytic coliphages were isolated against the wide range of E. coli host strains. Broad host-spectrum phages were isolated predominantly from sewage water samples. Enriched phages were quantified, and the concentrations ranged from 10⁶ to 10⁷ PFU/mL. Ten phages, viz. ФEC-S-18, ФEC-S-21, ФEC-S-22, ФEC-S-23, ФEC-S-24, ФEC-S-25, ФEC-S-28, ФEC-S-30, ФEC-S-39 and ФEC-S-49, exhibited lytic activity against more than ten AMR strains of E. coli. PCR analysis of the 54 phages using the major capsid protein (MCP) specific primers coupled with gene sequence analysis identified two phages related to Berlinvirus and 35 phages to Kayfunavirus of Autographiviridae. However, the remaining 17 phages did not show amplification using the MCP primers. The study has demonstrated that aquatic environment harboured phages with broad host spectrum that can potentially be used as agents for biological control of E. coli for infection control and food safety.

Aggregation-Induced Emission-Active Poly(phenyleneethynylene)s for Fluorescence and Raman Dual-Modal Imaging and Drug-Resistant Bacteria Killing

Poly(phenyleneethynylene) (PPE) is a widely used functional conjugated polymer with applications ranging from organic optoelectronics and fluorescence sensors to optical imaging and theranostics. However, the fluorescence efficiency of PPE in aggregate states is generally not as good as their solution states, which greatly compromises their performance in fluorescence-related applications. Herein, a series of PPE derivatives with typical aggregation-induced emission (AIE) properties is designed and synthesized. In these PPEs, the diethylamino-substituted tetraphenylethene units function as the long-wavelength AIE source and the alkyl side chains serve as the functionalization site. The obtained AIE-active PPEs with large π-conjugation show strong aggregate-state fluorescence, interesting self-assembly behaviors, inherently enhanced alkyne vibrations in the Raman-silent region of cells, and efficient antibacterial activities. The PPE nanoparticles with good cellular uptake capability can clearly and sensitively visualize the tumor region and residual tumors via their fluorescence and Raman signals, respectively, to benefit the precise tumor resection surgery. After post-functionalization, the obtained PPE-based polyelectrolyte can preferentially image bacteria over mammalian cells and possesses efficient photodynamic killing capability against Gram-positive and drug-resistant bacteria. This work provides a feasible design strategy for developing functional conjugated polymers with multimodal imaging capability as well as photodynamic antimicrobial ability.

Molecular Characteristics of Novel Phage vB_ShiP-A7 Infecting Multidrug-Resistant Shigella flexneri and Escherichia coli, and Its Bactericidal Effect in vitro and in vivo

In recent years, increasing evidence has shown that bacteriophages (phages) can inhibit infection caused by multidrug-resistant (MDR) bacteria. Here, we isolated a new phage, named vB_ShiP-A7, using MDR Shigella flexneri as the host. vB_ShiP-A7 is a novel member of Podoviridae, with a latency period of approximately 35 min and a burst size of approximately 100 phage particles/cell. The adsorption rate constant of phage vB_ShiP-A7 to its host S. flexneri was 1.405 × 10^–8 mL/min. The vB_ShiP-A7 genome is a linear double-stranded DNA composed of 40,058 bp with 177 bp terminal repeats, encoding 43 putative open reading frames. Comparative genomic analysis demonstrated that the genome sequence of vB_ShiP-A7 is closely related to 15 different phages, which can infect different strains. Mass spectrometry analysis revealed that 12 known proteins and 6 hypothetical proteins exist in the particles of phage vB_ShiP-A7. Our results confirmed that the genome of vB_ShiP-A7 is free of lysogen-related genes, bacterial virulence genes, and antibiotic resistance genes. vB_ShiP-A7 can significantly disrupt the growth of some MDR clinical strains of S. flexneri and Escherichia coli in liquid culture and biofilms in vitro. In addition, vB_ShiP-A7 can reduce the load of S. flexneri by approximately 3–10 folds in an infection model of mice. Therefore, vB_ShiP-A7 is a stable novel phage with the potential to treat infections caused by MDR strains of S. flexneri and E. coli.

Applications of bacteriophages against intracellular bacteria

Infectious diseases pose a significant threat to both human and animal populations. Intracellular bacteria are a group of pathogens that invade and survive within the interior of eukaryotic cells, which in turn protect them from antibacterial drugs and the host immune system. Limited penetration of antibacterials into host cells results in insufficient bacterial clearance and treatment failure. Bacteriophages have, over the decades, been proved to play an important role in combating bacterial infections (phage therapy), making them an important alternative to classical antibiotic strategies today. Phages have been found to be effective at killing various species of extracellular bacteria, but little is still known about how phages control intracellular infections. With advances in phage genomics and mechanisms of delivery and cell uptake, the development of phage-based antibacterial strategies to address the treatment of intracellular bacteria has general potential. In this review, we present the current state of knowledge regarding the application of bacteriophages against intracellular bacteria. We cover phage deployment against the most common intracellular pathogens with special attention to therapeutic and preventive strategies.

Community-acquired pneumonia: aetiology, antibiotic resistance and prospects of phage therapy

Bacteria are the most common aetiological agents of community-acquired pneumonia (CAP) and use a variety of mechanisms to evade the host immune system. With the emerging antibiotic resistance, CAP-causing bacteria have now become resistant to most antibiotics. Consequently, significant morbimortality is attributed to CAP despite their varying rates depending on the clinical setting in which the patients being treated. Therefore, there is a pressing need for a safe and effective alternative or supplement to conventional antibiotics. Bacteriophages could be a ray of hope as they are specific in killing their host bacteria. Several bacteriophages had been identified that can efficiently parasitize bacteria related to CAP infection and have shown a promising protective effect. Thus, bacteriophages have shown immense possibilities against CAP inflicted by multidrug-resistant bacteria. This review provides an overview of common antibiotic-resistant CAP bacteria with a comprehensive summarization of the promising bacteriophage candidates for prospective phage therapy.

Shigella: Antibiotic-Resistance Mechanisms And New Horizons For Treatment

Shigella spp. are a common cause of diarrheal disease and have remained an important pathogen responsible for increased rates of morbidity and mortality caused by dysentery each year around the globe. Antibiotic treatment of Shigella infections plays an essential role in reducing prevalence and death rates of the disease. However, treatment of these infections remains a challenge, due to the global rise in broad-spectrum resistance to many antibiotics. Drug resistance in Shigella spp. can result from many mechanisms, such as decrease in cellular permeability, extrusion of drugs by active efflux pumps, and overexpression of drug-modifying and -inactivating enzymes or target modification by mutation. Therefore, there is an increasing need for identification and evolution of alternative therapeutic strategies presenting innovative avenues against Shigella infections, as well as paying further attention to this infection. The current review focuses on various antibiotic-resistance mechanisms of Shigella spp. with a particular emphasis on epidemiology and new mechanisms of resistance and their acquisition, and also discusses the status of novel strategies for treatment of Shigella infection and vaccine candidates currently under evaluation in preclinical or clinical phases.