Exploiting lung adaptation and phage steering to clear pan-resistant Pseudomonas aeruginosa infections in vivo

Optimizing Performance of Inhalable Bacteriophage Powders using Human Serum Albumin (HSA)

In response to the growing threat of antibiotic resistance in pulmonary infections, bacteriophage therapy is emerging as a promising alternative to traditional antibiotics. We aimed to develop novel dry powder formulations for the pulmonary delivery of bacteriophages, using the Pseudomonas aeruginosa-specific phage PEV2 as a model. Our formulations combined human serum albumin (HSA) and lactose to enhance both phage stability and aerosol performance. A Box-Behnken experimental design was conducted to investigate the effects of HSA/lactose ratio, solute concentration of feed solution, and spray-drying inlet temperature. Our results demonstrated that incorporating 60% w/w HSA significantly improved aerosol performance by achieving a fine particle fraction above 50% and effectively delayed lactose recrystallization by maintaining an amorphous state at relative humidity levels of 80% or higher. Importantly, the optimized formulation (60% HSA/40% lactose) preserved phage viability with less than a 0.8 log10 reduction. Possible mechanisms contributing to stabilizing the phage powder formulations in HSA-lactose were discussed. These findings underscore the potential of a balanced HSA-lactose system as a robust powder formulation platform for pulmonary phage therapy.

Aldehyde-modified sodium alginate/gelatin-based bacteriophage-loaded multifunctional hydrogel for promoting the healing of multidrug-resistant bacterial-infected wounds

Multidrug-resistant bacterial infections in skin injuries are hard to repair. There is an urgent need to develop new antibacterials, antibiofilm formation, and immunomodulatory wound dressing. In this study, we produced a bacteriophage-loaded multifunctional hydrogel consisting of aldehyde-modified sodium alginate (ADA), gelatin (GEL), and carboxymethyl chitosan (CMCS) through a Schiff base reaction and borax complexation. These post-reactive ADA/GEL/CMCS/Phage (AGCP) hydrogels, particularly the AGCP3 hydrogel, boast a porous structure, high swelling rate, effective hemostasis, controlled degradation, good rheological properties, and strong antibacterial activity. Furthermore, the hydrogel developed in this study can sustainably release various bacteriophages targeting the bacteria responsible for major skin infections, thereby enhancing antibacterial activity and preventing bacterial biofilm formation. Besides, cytotoxicity and cell proliferation demonstrated that the hydrogel, comprising three polysaccharides, ADA, GEL, and CMCS, facilitates skin tissue regeneration by enhancing cellular proliferation and migration. The AGCP hydrogel enhanced healing and controlled inflammation in bacterial-infected wounds, as evidenced by wound closure, collagen deposition, and quantitative reverse transcription polymerase chain reaction results. In conclusion, the AGCP3 hydrogel exhibits strong antibacterial properties, excellent expands, biocompatibility, hemostatic properties, and a controlled release of bacteriophages, making it ideal for universal bacteriophage delivery systems and wound dressings for skin wounds infected with multidrug-resistant bacteria.

Globotriaosylceramide as a potential biomarker for auxiliary detection of lower respiratory tract infections of Pseudomonas aeruginosa

Lower respiratory tract infections (LRTIs) caused by Pseudomonas aeruginosa (PA) are a significant health concern, notably among vulnerable populations. The glycosphingolipid receptor globotriaosylceramide (Gb3) has been implicated in PA pathogenicity, however, its clinical implications remain underexplored. The present study aimed to investigate the clinical value of Gb3 concentrations in serum and bronchoalveolar lavage fluid (BALF) as a biomarker for PA-induced LRTIs. In the current prospective study, 54 PA-infected patients and 54 healthy individuals were enrolled as controls. Gb3 levels were measured using a Gb3 ELISA kit and the levels of inflammatory markers were assessed. The diagnostic accuracy of Gb3 was evaluated using receiver operating characteristic (ROC) curve analysis. The patients with PA-induced LRTIs exhibited significantly higher Gb3 concentration levels in both serum and BALF compared with those noted in healthy controls, with more pronounced elevations noted in BALF. The area under the ROC curve was 0.899 for serum Gb3 and 0.812 for BALF Gb3, indicating high sensitivity and specificity for diagnosis of PA infection. Gb3 levels were also found to be correlated with C-reactive protein and procalcitonin levels, suggesting its potential in reflecting infection severity. Overall, the present findings revealed a significant association between Gb3 levels and PA-induced LRTIs, proposing Gb3 as a promising biomarker for early detection and diagnosis. Further research is warranted to validate the role of Gb3 in various patient populations and to explore its dynamics over the course of infection.

Characterization of Pseudomonas phage MME: a novel tool for combatting multidrug-resistant Pseudomonas aeruginosa and disinfection

AIM

Combatting Pseudomonas aeruginosa, known for its robust biofilm formation, presents significant challenges in healthcare, food, and industry. Phages offer promising alternatives against this resilient pathogen. We aim to demonstrate their viability as alternative therapeutic and decontamination options.

METHODS AND RESULTS

We introduce the lytic activity and decontamination efficacy of Pseudomonas phage MME, isolated from sewage, on solid surfaces, as well as on its biological and genomic characterization. The phage showed lytic activity against both antibiotic-resistant clinical strains and reference strains. About 90% of the phage adsorbed to its host within 20 min, with an average burst size of ∼53 PFU per infected cell. The bactericidal effect on the host at the 8th hour showed a 95% killing efficiency. Additionally, phage MME effectively reduced bacterial loads on glass, plastic, and metal surfaces, simulating hospital environments. Confocal laser scanning microscopy demonstrated the phage's bactericidal activity on glass surfaces at the 8th and 12th hours, preventing biofilm formation. Bioinformatic analysis confirmed that phage MME represents a new species within the Bruynoghevirus genus. Comparative genomic analysis revealed no virulence factors within the phage MME genome.

CONCLUSIONS

These findings highlight the potent lytic activity of phage MME against P. aeruginosa, underscoring its potential as a valuable tool in combatting this pathogen and its suitability for diverse applications, including as a decontaminating agent.

Mutations in mexT bypass the stringent response dependency of virulence in Pseudomonas aeruginosa

Pseudomonas aeruginosa produces a wealth of virulence factors whose production is controlled via an intricate regulatory systems network. Here, we uncover a major player in the evolution and regulation of virulence that enhances host colonization and antibiotic resistance. By characterizing a collection of mutants lacking the stringent response (SR), a system key for virulence, we show that the loss of the central regulator MexT bypasses absence of the SR, restoring full activation of virulence pathways. Notably, mexT mutations were associated with resistance to aminoglycosides and the last-resort antibiotic, colistin. Analysis of thousands of P. aeruginosa genomes revealed that mexT mutations are widespread in isolates linked to aggressive antibiotic treatment. Furthermore, in vivo experiments in a murine pulmonary model revealed that mexT mutants display a hypervirulent phenotype associated with bacteremia. Altogether, these findings uncover a key regulator that acts as a genetic switch in the regulation of virulence and antimicrobial resistance.

PHIStruct: improving phage-host interaction prediction at low sequence similarity settings using structure-aware protein embeddings

MOTIVATION

Recent computational approaches for predicting phage-host interaction have explored the use of sequence-only protein language models to produce embeddings of phage proteins without manual feature engineering. However, these embeddings do not directly capture protein structure information and structure-informed signals related to host specificity.

RESULTS

We present PHIStruct, a multilayer perceptron that takes in structure-aware embeddings of receptor-binding proteins, generated via the structure-aware protein language model SaProt, and then predicts the host from among the ESKAPEE genera. Compared against recent tools, PHIStruct exhibits the best balance of precision and recall, with the highest and most stable F1 score across a wide range of confidence thresholds and sequence similarity settings. The margin in performance is most pronounced when the sequence similarity between the training and test sets drops below 40%, wherein, at a relatively high-confidence threshold of above 50%, PHIStruct presents a 7%-9% increase in class-averaged F1 over machine learning tools that do not directly incorporate structure information, as well as a 5%-6% increase over BLASTp.

AVAILABILITY AND IMPLEMENTATION

The data and source code for our experiments and analyses are available at https://github.com/bioinfodlsu/PHIStruct.

A blueprint for broadly effective bacteriophage-antibiotic cocktails against bacterial infections

Bacteriophage (phage) therapy is a promising therapeutic modality for multidrug-resistant bacterial infections, but its application is mainly limited to personalized therapy due to the narrow host range of individual phages. While phage cocktails targeting all possible bacterial receptors could theoretically confer broad coverage, the extensive diversity of bacteria and the complexity of phage-phage interactions render this approach challenging. Here, using screening protocols for identifying "complementarity groups" of phages using non-redundant receptors, we generate effective, broad-range phage cocktails that prevent the emergence of bacterial resistance. We also discover characteristic interactions between phage complementarity groups and particular antibiotic classes, facilitating the prediction of phage-antibiotic as well as phage-phage interactions. Using this strategy, we create three phage-antibiotic cocktails, each demonstrating efficacy against ≥96% of 153 Pseudomonas aeruginosa clinical isolates, including biofilm cultures, and demonstrate comparable efficacy in an in vivo wound infection model. We similarly develop effective Staphylococcus aureus phage-antibiotic cocktails and demonstrate their utility of combined cocktails against polymicrobial (mixed P. aeruginosa/S. aureus) cultures, highlighting the broad applicability of this approach. These studies establish a blueprint for the development of effective, broad-spectrum phage-antibiotic cocktails, paving the way for off-the-shelf phage-based therapeutics to combat multidrug-resistant bacterial infections.

Unraveling the genomic diversity of the Pseudomonas putida group: exploring taxonomy, core pangenome, and antibiotic resistance mechanisms

The genus Pseudomonas is characterized by its rich genetic diversity, with over 300 species been validly recognized. This reflects significant progress made through sequencing and computational methods. Pseudomonas putida group comprises highly adaptable species that thrive in diverse environments and play various ecological roles, from promoting plant growth to being pathogenic in immunocompromised individuals. By leveraging the GRUMPS computational pipeline, we scrutinized 26 363 genomes labeled as Pseudomonas in the NCBI GenBank, categorizing all Pseudomonas spp. genomes into 435 distinct species-level clusters or cliques. We identified 224 strains deposited under the taxonomic identifier "Pseudomonas putida" distributed within 31 of these species-level clusters, challenging prior classifications. Nine of these 31 cliques contained at least six genomes labeled as "Pseudomonas putida" and were analysed in depth, particularly clique_1 (P. alloputida) and clique_2 (P. putida). Pangenomic analysis of a set of 413 P. putida group strains revealed over 2.2 million proteins and more than 77 000 distinct protein families. The core genome of these 413 strains includes 2226 protein families involved in essential biological processes. Intraspecific genetic homogeneity was observed within each clique, each possessing a distinct genomic identity. These cliques exhibit distinct core genes and diverse subgroups, reflecting adaptation to specific environments. Contrary to traditional views, nosocomial infections by P. alloputida, P. putida, and P. monteilii have been reported, with strains showing varied antibiotic resistance profiles due to diverse mechanisms. This review enhances the taxonomic understanding of key P. putida group species using advanced population genomics approaches and provides a comprehensive understanding of their genetic diversity, ecological roles, interactions, and potential applications.

A review of bacteriophage and their application in domestic animals in a post-antibiotic era

Bacteriophages (phages for short) are the most abundant biological entities on Earth and are natural enemies of bacteria. Genomics and molecular biology have identified subtle and complex relationships among phages, bacteria and their animal hosts. This review covers composition, diversity and factors affecting gut phage, their lifecycle in the body, and interactions with bacteria and hosts. In addition, research regarding phage in poultry, aquaculture and livestock are summarized, and application of phages in antibiotic substitution, phage therapy and food safety are reviewed.

Challenges and opportunities of phage therapy for Klebsiella pneumoniae infections

Traditional antibiotics have been effective in many cases. However, the rise in multidrug-resistant bacteria has diminished their therapeutic efficacy, signaling the dawn of an era beyond antibiotics. The challenge of multidrug resistance in Klebsiella pneumoniae is particularly critical, with increasing global mortality and resistance rates. Therefore, the development of alternative therapies to antibiotics is urgently needed. Phages, which are natural predators of bacteria, have inherent advantages. However, comprehensive information on K. pneumoniae phages is lacking in current literature. This review aims to analyze and summarize relevant studies, focusing on the present state of phage therapy for K. pneumoniae infections. This includes an examination of treatment methodologies, associated challenges, strategies, new phage technologies, clinical trial safety and efficacy, regulatory issues, and future directions for phage therapy development. Enhancing phage technology is crucial for addressing the evolving threat of multidrug-resistant K. pneumoniae.

Phage therapy: an alternative treatment modality for MDR bacterial infections

The increasing global incidence of multidrug-resistant (MDR) bacterial infections threatens public health and compromises various aspects of modern medicine. Recognising the urgency of this issue, the World Health Organisation has prioritised the development of novel antimicrobials to combat ESKAPEE pathogens. Comprising Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, Enterobacter spp. and Escherichia coli, such pathogens represent a spectrum of high to critical drug resistance, accounting for a significant proportion of hospital-acquired infections worldwide. In response to the waning efficacy of antibiotics against these resilient pathogens, phage therapy (PT) has emerged as a promising therapeutic strategy. This review provides a comprehensive summary of clinical research on PT and explores the translational journey of phages from laboratory settings to clinical applications. It examines recent advancements in pre-clinical and clinical developments, highlighting the potential of phages and their proteins, alone or in combination with antibiotics. Furthermore, this review underlines the importance of establishing safe and approved routes of phage administration to patients. In conclusion, the evolving landscape of phage therapy offers a beacon of hope in the fight against MDR bacterial infections, emphasising the imperative for continued research, innovation and regulatory diligence to realise its full potential in clinical practice.

Phage Therapy: An Alternative Approach to Combating Multidrug-Resistant Bacterial Infections in Cystic Fibrosis

Patients with cystic fibrosis (CF) are prone to developing life-threatening lung infections with a variety of pathogens that are difficult to eradicate, such as Burkholderia cepacia complex (Bcc), Hemophilus influenzae, Mycobacterium abscessus (Mab), Pseudomonas aeruginosa, and Staphylococcus aureus. These infections still remain an important issue, despite the therapy for CF having considerably improved in recent years. Moreover, prolonged exposure to antibiotics in combination favors the development and spread of multi-resistant bacteria; thus, the development of alternative strategies is crucial to counter antimicrobial resistance. In this context, phage therapy, i.e., the use of phages, viruses that specifically infect bacteria, has become a promising strategy. In this review, we aim to address the current status of phage therapy in the management of multidrug-resistant infections, from compassionate use cases to ongoing clinical trials, as well as the challenges this approach presents in the particular context of CF patients.

The past, present and future of polymicrobial infection research: Modelling, eavesdropping, terraforming and other stories

Over the last two centuries, great advances have been made in microbiology as a discipline. Much of this progress has come about as a consequence of studying the growth and physiology of individual microbial species in well-defined laboratory media; so-called "axenic growth". However, in the real world, microbes rarely live in such "splendid isolation" (to paraphrase Foster) and more often-than-not, share the niche with a plethora of co-habitants. The resulting interactions between species (and even between kingdoms) are only very poorly understood, both on a theoretical and experimental level. Nevertheless, the last few years have seen significant progress, and in this review, we assess the importance of polymicrobial infections, and show how improved experimental traction is advancing our understanding of these. A particular focus is on developments that are allowing us to capture the key features of polymicrobial infection scenarios, especially as those associated with the human airways (both healthy and diseased).

Peptide Extract from Red Kidney Beans, Phaseolus vulgaris (Fabaceae), Shows Promising Antimicrobial, Antibiofilm, and Quorum Sensing Inhibitory Effects

The rapid spread of multidrug-resistant bacteria has led to an increased risk of infectious diseases. Pseudomonas aeruginosa, in particular, poses a significant obstacle due to its propensity to rapidly acquire resistance to conventional antibiotics. This has resulted in an urgent need for the development of new classes of antibiotics that do not induce resistance. Antimicrobial peptides (AMPs) have been studied as potential small-molecule antibiotics due to their unique mode of action. In this study, peptides were extracted from the seeds of Phaseolus vulgaris (Fabaceae), and the antimicrobial activities of the extract were evaluated using microbroth dilution against five different microorganisms. The extract showed antimicrobial activity against all tested organisms with minimum inhibitory concentrations (MIC) of 2.5 mg/mL, except for Candida albicans and Pseudomonas aeruginosa, which had MICs of 1.25 mg/mL. The extract was also bacteriostatic for all tested organisms. The crude peptide extract from Phaseolus vulgaris was further studied for its antibiofilm activity against Pseudomonas aeruginosa, a common nosocomial pathogen associated with biofilm formation. The extract showed good antibiofilm activity at 1/2 MIC. The extract also inhibited the expression of pyocyanin and pyoverdine (virulence factors of P. aeruginosa whose expression is mediated by quorum sensing) by 82% and 66%, respectively. These results suggest that the peptide mix from Phaseolus vulgaris may inhibit biofilm formation and virulence factor expression by interfering with cell-to-cell communication in Pseudomonas aeruginosa. The ability of the extract to inhibit the growth and biofilm formation of all tested organisms indicates its potential as an antimicrobial agent that could be further studied for drug discovery.