Phage Paride can kill dormant, antibiotic-tolerant cells of Pseudomonas aeruginosa by direct lytic replication

Unraveling persistent bacteria: Formation, niches, and eradication strategies

Persistent bacteria (persisters) are phenotypic variants that emerge either randomly or in response to a range of adverse environmental conditions. Persistence represents a state whereby a subpopulation of microorganisms can spontaneously enter a "dormant" state in response to environmental factors, while simultaneously exhibiting elevated tolerance to antimicrobial agents. This review provides the current definition of bacterial persistence and summarizes the mechanisms of persisters formation as well as the various niches of bacterial persistence encountered in clinical practice. Strategies targeting persisters are outlined, including but not limited to direct killing, awakening of persistent bacteria, combined clearance, and inhibition of persistence formation, and we conclude by proposing challenges and solutions for addressing bacterial persistence in current clinical practice.

Phage therapy: A novel approach to combat drug-resistant pathogens

Antibiotic-resistant infections, such as those caused by the overuse of antibiotics, have greatly strained healthcare systems. Among them, drug-resistant bacteria ESKAPE (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter species) are typical and common. Enterococcus faecalis and Escherichia coli are of equal concern. These pathogens often have higher pathogenicity than the same strains, and resistance has reduced treatment options, so new treatment options are needed to address these pathogens. This review analyzes recent studies related to phage therapy for the treatment of bacterial infections in various parts of the human body (e.g., alcoholic liver disease, skin, and soft tissues, respiratory tract, gastrointestinal tract, urinary system, etc.), to better understand the potential role of phage therapy as a non-antibiotic strategy for the treatment of infections caused by drug-resistant bacteria. In addition, this review introduces a series of products related to phage therapy and points out potential research directions for phage therapy in clinical applications. This paper elucidates the basic mechanism of human infection by some drug-resistant bacteria and the therapeutic effect of phage therapy against drug-resistant bacteria. It popularizes the understanding of phage therapy and provides a reference for research on its use for drug-resistant bacterial infections.

Adjunctive phage therapy improves antibiotic treatment of ventilator-associated-pneumonia with Pseudomonas aeruginosa

Bacterial multidrug resistance poses an urgent challenge for the treatment of critically ill patients developing ventilator-associated pneumonia (VAP). Phage therapy, a potential alternative when conventional antibiotics fail, has been unsuccessful in first clinical trials when used alone. Whether combining antibiotics with phages may enhance effectiveness remains to be tested in experimental models. Here, we use a murine model of Pseudomonas-induced VAP to compare the efficacy of adjunctive phage cocktail for antibiotic therapy to either meropenem or phages alone. Combined treatment in murine VAP results in faster clinical improvement and prevents lung epithelial cell damage. Using human primary epithelial cells to dissect these synergistic effects, we find that adjunctive phage therapy reduces the minimum effective concentration of meropenem and prevents resistance development against both treatments. These findings suggest adjunctive phage therapy represents a promising treatment for MDR-induced VAP, enhancing the effectiveness of both antibiotics and phages while reducing adverse effects.

Phage Therapy for Urinary Tract Infections: Progress and Challenges Ahead

INTRODUCTION AND HYPOTHESIS

Urinary tract infection (UTI) treatment is a growing public health concern owing to increasing antimicrobial resistance. Phage therapy, an alternative or adjunctive treatment to antibiotics, has the potential to address this challenge. However, clinical use of phage therapy is hindered by knowledge gaps and inconsistent reporting. The objective was to review the current state of phage therapy for UTIs and highlight research priorities that can optimize phage clinical efficacy.

METHODS

Current literature on UTI phage therapy was examined, focusing on the lack of standardized phage susceptibility testing, phage characterization, and microbiological assessments during and after treatment.

RESULTS

Critical areas requiring further investigation include appropriate phage dosing, optimal routes of administration, and the dynamics of phage-host and phage-patient interactions. The influence of the urinary microbiome, including endogenous phages, on treatment outcomes also needs to be better understood. Suggested data collection and reporting standards should be developed and implemented to improve clinical impact of studies examining phage therapy for UTI. Randomized clinical trials are needed to establish efficacy and determine the best practices for clinical use.

CONCLUSION

Phage therapy is a promising alternative to antibiotics for managing UTIs, especially in the face of rising antimicrobial resistance. To fully realize its potential, however, future research must focus on standardized protocols, dosing strategies, and the role of the urinary microbiome, with an emphasis on rigorously conducted clinical trials. These steps are essential for integrating phage therapy into mainstream UTI treatment regimens.

[Basic knowledge of phages and their therapeutic application]

Phages (bacteriophages) are viruses that specifically infect and kill bacteria. They are very abundant in nature, playing a highly relevant role in microbial ecosystems. In medicine, they are investigated as a potential alternative or supplement to antibiotics and can be used to treat wound, urinary tract and lung infections, for example. Single phages or so-called "phage cocktails" are applied.This overview article on basic knowledge of phages sheds light on well-known keywords from classical knowledge of phage biology and on state-of-the-art research focuses. Mechanisms of phage activity are presented as a basis for therapeutic application. Particularly, the phage-host interaction, lysis mechanisms, phage morphologies and specific methods for visualisation are discussed. Being part of the human microbiome, phages contribute to immune defence, especially in the mucosa. Temperate phages that are able to reside in bacterial genomes as prophages and therefore not suitable for therapy use as well as the CrAss phages (Crassvirales) and Lak megaphages discovered in recent years are also introduced. Further topics are bacterial phage defence, phage resistance and phage-antibiotic synergies. An outlook on future research is given, emphasising the importance of a coordinated collection of scientific results.Phages should not replace antibiotics, but they can even improve their efficiency. Currently, the licensing processes for phage therapy are still challenging. However, trust in phage preparations must be based on quality, which has to be guaranteed by harmonised standards.

Completing the BASEL phage collection to unlock hidden diversity for systematic exploration of phage-host interactions

Research on bacteriophages, the viruses infecting bacteria, has fueled the development of modern molecular biology and inspired their therapeutic application to combat bacterial multidrug resistance. However, most work has so far focused on a few model phages which impedes direct applications of these findings in clinics and suggests that a vast potential of powerful molecular biology has remained untapped. We have therefore recently composed the BASEL collection of Escherichia coli phages (BActeriophage SElection for your Laboratory), which made a relevant diversity of phages infecting the E. coli K-12 laboratory strain accessible to the community. These phages are widely used, but their assorted diversity has remained limited by the E. coli K-12 host. We have therefore now genetically overcome the two major limitations of E. coli K-12, its lack of O-antigen glycans and the presence of resident bacterial immunity. Restoring O-antigen expression resulted in the isolation of diverse additional viral groups like Kagunavirus, Nonanavirus, Gordonclarkvirinae, and Gamaleyavirus, while eliminating all known antiviral defenses of E. coli K-12 additionally enabled us to isolate phages of Wifcevirus genus. Even though some of these viral groups appear to be common in nature, no phages from any of them had previously been isolated using E. coli laboratory strains, and they had thus remained largely understudied. Overall, 37 new phage isolates have been added to complete the BASEL collection. These phages were deeply characterized genomically and phenotypically with regard to host receptors, sensitivity to antiviral defense systems, and host range. Our results highlighted dominant roles of the O-antigen barrier for viral host recognition and of restriction-modification systems in bacterial immunity. We anticipate that the completed BASEL collection will propel research on phage-host interactions and their molecular mechanisms, deepening our understanding of viral ecology and fostering innovations in biotechnology and antimicrobial therapy.

Antibiotic resistance genes in anaerobic digestion: Unresolved challenges and potential solutions

Antimicrobial resistance (AMR) threatens public health, necessitating urgent efforts to mitigate the global impact of antibiotic resistance genes (ARGs). Anaerobic digestion (AD), known for volatile solid reduction and energy generation, also presents a feasible approach for the removal of ARGs. This review encapsulates the existing understanding of ARGs and antibiotic-resistant bacteria (ARB) during the AD process, highlighting unresolved challenges pertaining to their detection and quantification. The questions raised and discussed include: Do current ARGs detection methods meet qualitative and quantitative requirements? How can we conduct risk assessments of ARGs? What happens to ARGs when they come into co-exposure with other emerging pollutants? How can the application of internal standards bolster the reliability of the AD resistome study? What are the potential future research directions that could enhance ARG elimination? Investigating these subjects will assist in shaping more efficient management strategies that employ AD for effective ARG control.

Zinc Oxide-Enhanced Copper Sulfide Nanozymes Promote the Healing of Infected Wounds by Activating Immune and Inflammatory Responses

Bacterial infection and an excessive inflammatory response are two major factors that affect the healing of infected wounds. The zinc oxide/copper sulfide (ZnO-CuS) microspheres (MSs) developed in this work can kill bacteria and resist inflammation. ZnO-CuS exhibits different enzyme-like activities depending on pH. In acidic environments, ZnO-CuS exhibits peroxidase-like (POD-like) activity and can convert hydrogen peroxide (H2O2) into hydroxyl radicals (•OH) for sterilization. Under neutral conditions, ZnO-CuS removes reactive oxygen species (ROS) and can convert excess ROS into water and oxygen. The in vitro results of the antibacterial test demonstrate the pronounced disruption effect of ZnO-CuS on the bacterial biofilm and cell membrane. The transcriptome sequencing results of wounded animal tissue reveal that ZnO-CuS MSs increase the expression of proteins produced by immune cells, and reduce the expression levels of inflammatory factors at the wound site. Therefore, antimicrobial activity and rapid wound healing can be achieved by regulating the immune response and reducing the inflammatory response. The results from hemolysis, routine blood and blood biochemistry analyses demonstrate the excellent biosecurity of the ZnO-CuS MSs.

Phage-phage competition and biofilms affect interactions between two virulent bacteriophages and Pseudomonas aeruginosa

Virulent bacteriophages (or phages) are viruses that specifically infect and lyse a bacterial host. When multiple phages co-infect a bacterial host, the extent of lysis and dynamics of bacteria-phage and phage-phage interactions are expected to vary. The objective of this study is to identify the factors influencing the interaction of two virulent phages with different Pseudomonas aeruginosa growth states (planktonic, an infected epithelial cell line, and biofilm) by measuring the bacterial time-kill and individual phage replication kinetics. A single administration of phages effectively reduced P. aeruginosa viability in planktonic conditions and infected human lung cell cultures, but phage-resistant variants subsequently emerged. In static biofilms, the phage combination displayed initial inhibition of biofilm dispersal, but sustained control was achieved only by combining phages and the meropenem antibiotic. In contrast, adherent biofilms showed tolerance to phage and/or meropenem, suggesting a spatio-temporal variation in the phage-bacterial interaction. The kinetics of adsorption of each phage to P. aeruginosa during single or co-administration were comparable. However, the phage with the shorter lysis time depleted bacterial resources early and selected a specific nucleotide polymorphism that conferred a competitive disadvantage and cross-resistance to the second phage. The extent and strength of this phage-phage competition and genetic loci conferring phage resistance are, however, P. aeruginosa genotype-dependent. Nevertheless, adding phages sequentially resulted in their unimpeded replication with no significant increase in bacterial host lysis. These results highlight the interrelatedness of phage-phage competition, phage resistance, and specific bacterial growth state (planktonic/biofilm) in shaping the interplay among P. aeruginosa and virulent phages.

Use of adjuvants to improve antibiotic efficacy and reduce the burden of antimicrobial resistance

INTRODUCTION

The increase in antibiotic resistance, together with the absence of novel antibiotics, makes mandatory the introduction of novel strategies to optimize the use of existing antibiotics. Among these strategies, the use of molecules that increase their activity looks promising.

AREAS COVERED

Different categories of adjuvants have been reviewed. Anti-resistance adjuvants increase the activity of antibiotics by inhibiting antibiotic resistance determinants. Anti-virulence approaches focus on the infection process itself; reducing virulence in combination with an antibiotic can improve therapeutic efficacy. Combination of phages with antibiotics can also be useful, since they present different mechanisms of action and targets. Finally, combining antibiotics with adjuvants in the same molecule may serve to improve antibiotics' efficacy and to overcome potential problems of differential pharmacokinetics/pharmacodynamics.

EXPERT OPINION

The successful combination of inhibitors of β-lactamases with β-lactams has shown that adjuvants can improve the efficacy of current antibiotics. In this sense, novel anti-resistance adjuvants able to inhibit efflux pumps are still needed, as well as anti-virulence compounds that improve the efficacy of antibiotics by interfering with the infection process. Although adjuvants may present different pharmacodynamics/pharmacokinetics than antibiotics, conjugates containing both compounds can solve this problem. Finally, already approved drugs can be a promising source of antibiotic adjuvants.

Isolation and Characterization of Lytic Bacteriophages Capable of Infecting Diverse Multidrug-Resistant Strains of Pseudomonas aeruginosa: PaCCP1 and PaCCP2

BACKGROUND/OBJECTIVES

Antimicrobial resistance (AMR) is a major public health threat, which is exacerbated by the lack of new antibiotics and the emergence of multidrug-resistant (MDR) superbugs. Comprehensive efforts and alternative strategies to combat AMR are urgently needed to prevent social, medical, and economic consequences. Pseudomonas aeruginosa is a pathogen responsible for a wide range of infections, from soft tissue infections to life-threatening conditions such as bacteremia and pneumonia. Bacteriophages have been considered as a potential therapeutic option to treat bacterial infections. Our aim was to isolate phages able to infect MDR P. aeruginosa strains.

METHODS

We isolated two lytic phages, using the conventional double layer agar technique (DLA), from samples obtained from the influent of a wastewater treatment plant in Concepción, Chile. The phages, designated as PaCCP1 and PaCCP2, were observed by electron microscopy and their host range was determined against multiple P. aeruginosa strains using DLA. Moreover, their genomes were sequenced and analyzed.

RESULTS

Phage PaCCP1 is a member of the Septimatrevirus genus and phage PaCCP2 is a member of the Pbunavirus genus. Both phages are tailed and contain dsDNA. The genome of PaCCP1 is 43,176 bp in length with a GC content of 54.4%, encoding 59 ORFs, one of them being a tRNA gene. The genome of PaCCP2 is 66,333 bp in length with a GC content of 55.6%, encoding 102 non-tRNA ORFs. PaCCP1 is capable of infecting five strains of P. aeruginosa, whereas phage PaCCP2 is capable of infecting three strains of P. aeruginosa. Both phages do not contain bacterial virulence or AMR genes and contain three and six putative Anti-CRISPR proteins.

CONCLUSIONS

Phages PaCCP1 and PaCCP2 show promise as effective treatments for MDR P. aeruginosa strains, offering a potential strategy for controlling this clinically important pathogen through phage therapy.

Transmission Dynamics and Novel Treatments of High Risk Carbapenem-Resistant Klebsiella pneumoniae: The Lens of One Health

The rise of antibiotic resistance and the dwindling antimicrobial pipeline have emerged as significant threats to public health. The emergence of carbapenem-resistant Klebsiella pneumoniae (CRKP) poses a global threat, with limited options available for targeted therapy. The CRKP has experienced various changes and discoveries in recent years regarding its frequency, transmission traits, and mechanisms of resistance. In this comprehensive review, we present an in-depth analysis of the global epidemiology of K. pneumoniae, elucidate resistance mechanisms underlying its spread, explore evolutionary dynamics concerning carbapenem-resistant hypervirulent strains as well as KL64 strains of K. pneumoniae, and discuss recent therapeutic advancements and effective control strategies while providing insights into future directions. By going through up-to-date reports, we found that the ST11 KL64 CRKP subclone with high risk demonstrated significant potential for expansion and survival benefits, likely due to genetic influences. In addition, it should be noted that phage and nanoparticle treatments still pose significant risks for resistance development; hence, innovative infection prevention and control initiatives rooted in One Health principles are advocated as effective measures against K. pneumoniae transmission. In the future, further imperative research is warranted to comprehend bacterial resistance mechanisms by focusing particularly on microbiome studies' application and implementation of the One Health strategy.

Artificial Phages with Biocatalytic Spikes for Synergistically Eradicating Antibiotic-Resistant Biofilms

Antibiotic-resistant pathogens have become a global public health crisis, especially biofilm-induced refractory infections. Efficient, safe, and biofilm microenvironment (BME)-adaptive therapeutic strategies are urgently demanded to combat antibiotic-resistant biofilms. Here, inspired by the fascinating biological structures and functions of phages, the de novo design of a spiky Ir@Co3O4 particle is proposed to serve as an artificial phage for synergistically eradicating antibiotic-resistant Staphylococcus aureus biofilms. Benefiting from the abundant nanospikes and highly active Ir sites, the synthesized artificial phage can simultaneously achieve efficient biofilm accumulation, extracellular polymeric substance (EPS) penetration, and superior BME-adaptive reactive oxygen species (ROS) generation, thus facilitating the in situ ROS delivery and enhancing the biofilm eradication. Moreover, metabolomics found that the artificial phage obstructs the bacterial attachment to EPS, disrupts the maintenance of the BME, and fosters the dispersion and eradication of biofilms by down-regulating the associated genes for the biosynthesis and preservation of both intra- and extracellular environments. The in vivo results demonstrate that the artificial phage can treat the biofilm-induced recalcitrant infected wounds equivalent to vancomycin. It is suggested that the design of this spiky artificial phage with synergistic "penetrate and eradicate" capability to treat antibiotic-resistant biofilms offers a new pathway for bionic and nonantibiotic disinfection.

Phage SEP1 hijacks Staphylococcus epidermidis stationary cells' metabolism to replicate

In nature, bacteria often survive in a stationary state with low metabolic activity. Phages use the metabolic machinery of the host cell to replicate, and, therefore, their efficacy against non-dividing cells is usually limited. Nevertheless, it was previously shown that the Staphylococcus epidermidis phage SEP1 has the remarkable capacity to actively replicate in stationary-phase cells, reducing their numbers. Here, we studied for the first time the transcriptomic profiles of both exponential and stationary cells infected with SEP1 phage using RNA-seq to gain a better understanding of this rare phenomenon. We showed that SEP1 successfully takes over the transcriptional apparatus of both exponential and stationary cells. Infection was, however, delayed in stationary cells, with genes within the gp142-gp154 module putatively implicated in host takeover. S. epidermidis responded to SEP1 infection by upregulating three genes involved in a DNA modification system, with this being observed already 5 min after infection in exponential cells and later in stationary cells. In stationary cells, a significant number of genes involved in translation and RNA metabolic and biosynthetic processes were upregulated after 15 and 30 min of SEP1 infection in comparison with the uninfected control, showing that SEP1 activates metabolic and biosynthetic pathways necessary to its successful replication.IMPORTANCEMost phage-host interaction studies are performed with exponentially growing cells. However, this cell state is not representative of what happens in natural environments. Additionally, most phages fail to replicate in stationary cells. The Staphylococcus epidermidis phage SEP1 is one of the few phages reported to date to be able to infect stationary cells. Here, we unveiled the interaction of SEP1 with its host in both exponential and stationary states of growth at the transcriptomic level. The findings of this study provide valuable insights for a better implementation of phage therapy since phages able to infect stationary cells could be more efficient in the treatment of recalcitrant infections.

Improvement of antibacterial activity of polysaccharides via chemical modification: A review

Antibiotic residue and bacterial resistance induced by antibiotic abuse have seriously threatened food safety and human healthiness. Thus, the development and application of safe, high-efficiency, and environmentally friendly antibiotic alternatives are urgently necessary. Apart from antitumor, antivirus, anti-inflammatory, gut microbiota regulation, immunity improvement, and growth promotion activities, polysaccharides also have antibacterial activity, but such activity is relatively low, which cannot satisfy the requirements of food preservation, clinical sterilization, livestock feeding, and agricultural cultivation. Chemical modification not only provides polysaccharides with better antibacterial activity, but also promotes easy operation and large-scale production. Herein, the enhancement of the antibacterial activity of polysaccharides via acetylation, sulfation, phosphorylation, carboxymethylation, selenation, amination, acid graft, and other chemical modifications is reviewed. Meanwhile, a new trend on the application of loading chemically modified polysaccharides into nanostructures is discussed. Furthermore, possible limitations and future recommendations for the development and application of chemically modified polysaccharides with better antibacterial activity are suggested.

Phage Therapy for Respiratory Infections: Opportunities and Challenges

We are entering the post-antibiotic era. Antimicrobial resistance (AMR) is a critical problem in chronic lung infections resulting in progressive respiratory failure and increased mortality. In the absence of emerging novel antibiotics to counter AMR infections, bacteriophages (phages), viruses that infect bacteria, have become a promising option for chronic respiratory infections. However, while personalized phage therapy is associated with improved outcomes in individual cases, clinical trials demonstrating treatment efficacy are lacking, limiting the therapeutic potential of this approach for respiratory infections. In this review, we address the current state of phage therapy for managing chronic respiratory diseases. We then discuss how phage therapy may address major microbiologic obstacles which hinder disease resolution of chronic lung infections with current antibiotic-based treatment practices. Finally, we highlight the challenges that must be addressed for successful phage therapy clinical trials. Through this discussion, we hope to expand on the potential of phages as an adjuvant therapy in chronic lung infections, as well as the microbiologic challenges that need to be addressed for phage therapy to expand beyond personalized salvage therapy.

Complete genome sequence of Pseudomonas aeruginosa phage Knedl

Bacteriophage Knedl is the first reported Pseudomonas aeruginosa phage that targets the Psl exopolysaccharide as receptor. Here, we report the genome of Knedl, demonstrating that it belongs to the genus Iggyvirus of the Queuovirinae subfamily. Future studies on the infection mechanism of Knedl could inform phage-based approaches to eradicate biofilms.

Characterization and genome-informatic analysis of a novel lytic mendocina phage vB_PmeS_STP12 suitable for phage therapy pseudomonas or biocontrol

BACKGROUND

A novel lytic bacteriophage (phage) was isolated with Pseudomonas mendocina strain STP12 (P. mendocina) from the untreated site of Sewage Treatment Plant of Lovely Professional University, India. P. mendocina is a Gram-negative, rod-shaped, aerobic bacterium belonging to the family Pseudomonadaceae and has been reported in fifteen (15) cases of economically important diseases worldwide.

METHODS AND RESULTS

Here, a novel phage specifically infecting and killing P. mendocina strain STP12 was isolated from sewage sample using enrichment, spot test and double agar overlay (DAOL) method and was designated as vB_PmeS_STP12. The phage vB-PmeS-STP12 was viable at wide range of pH and temperature ranging from 4 to10 and - 20 to 70 °C respectively. Host range and efficiency of plating (EOP) analysis indicated that phage vB-PmeS-STP12 was capable of infecting and killing P. mendocina strain STP6 with EOP of 0.34. Phage vB_PmeS_STP12 was found to have a significant bacterial reduction (p < 0.005) at all the doses administered, particularly at optimal MOI of 1 PFU/CFU, compared to the control. Morphological analysis using high resolution transmission electron microscopy (HR-TEM) revealed an icosahedral capsid of ~ 55 nm in diameter on average with a short, non-contractile tail. The genome of vB_PmeS_STP12 is a linear, dsDNA containing 36,212 bp in size with a GC content of 58.87% harbouring 46 open reading frames (ORFs). The 46 predicted ORFs encode proteins with functional information categorized as lysis, replication, packaging, regulation, assembly, infection, immune, and hypothetical. However, the genome of vB_PmeS_STP12 appeared to be devoid of tRNAs, integrase gene, toxins genes, virulence factors, antimicrobial resistance genes (ARGs) and CRISPR arrays. The blast analysis with phylogeny revealed that vB_PmeS_STP12 is genetically similar to Pseudomonas phage PMBT14, Pseudomonas phage Almagne and Serratia phage Serbin with a highest identity of 74.00%, 74.93% and 59.48% respectively.

CONCLUSIONS

Taken together, characterization, morphological analysis and genome-informatics indicated that vB_PmeS_STP12 is podovirus morphotype belonging to the class Caudoviticetes, family Zobellviridae which appeared to be devoid of integrase gene, ARGs, CRISPR arrays, virulence factors and toxins genes, exhibiting stability and infectivity at wide range of pH (4 to10) and temperature (-20 to 70 °C), thereby making vB_PmeS_STP12 suitable for phage therapy or biocontrol. Based on the bibliometric analysis and data availability with respect to sequences deposited in GenBank, this is the first report of a phage infecting Pseudomonas mendocina.