Advances in bacteriophage-mediated strategies for combating polymicrobial biofilms

Optimizing phage therapy for carbapenem-resistant Enterobacter cloacae bacteremia: insights into dose and timing

The increase in multidrug-resistant (MDR) Enterobacter cloacae complex (ECC) infections, particularly those resistant to carbapenems, underscores the urgent need for alternative therapies. Phage therapy, with its specific bactericidal action, offers a promising solution. However, there remains a shortage of well-characterized ECC-targeting phages, and dosing and timing optimization for ECC-specific phage cocktails is largely unexplored. In this study, we isolated and characterized three novel lytic phages with diverse genome sizes and host ranges. Notably, ФEBU8 demonstrated broad-spectrum activity, lysing both Enterobacter species and Acinetobacter baumannii. ФECL22 displayed stability across a wide temperature range (4-50°C), pH tolerance (6-10), and a burst size of 19 PFU/cell, with OmpA identified as its receptor. Our formulated phage cocktail, comprising ФEBU8, ФECL22, and ФECL30, effectively rescued mice with E. cloacae bacteremia in a dose-dependent manner, with a mid-dose regimen showing particularly strong efficacy. Immediate phage administration achieved full survival, whereas a combined prophylactic and therapeutic regimen ("-24 + 6") also resulted in 100% survival. These findings highlight the critical roles of dosing and timing in optimizing phage therapy for carbapenem-resistant Enterobacter infections, with prophylactic use providing a valuable window for delayed treatment and a promising strategy for combating severe bacterial infections.

Exploring the antimicrobial potential of lactobacilli against early-stage and mature biofilms of Staphylococcus aureus and Pseudomonas aeruginosa

Bacterial biofilms are dynamic, complex, and very adaptive, and they can cause health problems in both humans and animals while also posing a serious threat to various industries. This study explores the potential of cell-free preparations of lactobacilli isolated from breast milk (HM; n = 11) and infant fecal (IF; n = 15) samples to impact the growth of Staphylococcus aureus and Pseudomonas aeruginosa biofilms. The anti-biofilm activity of three distinct cell-free preparations, namely, untreated cell-free supernatant (CFS), pH-neutralized CFS (N-CFS), and heat-treated CFS (H-CFS), was examined against both early-stage and mature biofilms. The post-incubation strategy examined the impact on mature biofilms, while the co-incubation treatment assessed the impact of CFS on adhesion and initial colonization. Compared to post-incubation treatment (HM3, 67.12%), the CFSs exhibited greater inhibitory activity during co-incubation (IF9, 85.19%). Based on the findings, untreated CFS exhibited the most promising biofilm inactivation, although its activity was not completely lost upon pH neutralization and heat treatment. Treatment with H-CFSs and N-CFSs moderately reduced the population of S. aureus and P. aeruginosa bacterial cells within the biofilm by 40%-60%. Microscopic observations showed that after CFS treatment, the integrity of the biofilm conformation was disrupted. According to principal component analysis (PCA) (significance level at p < 0.05), the most promising anti-biofilm activity against both test pathogens was found in the CFS of Lacticaseibacillus paracasei HM1.

Isolation, characterization, and genomic analysis of a novel bacteriophage vB_Kp_XP4 targeting hypervirulent and multidrug-resistant Klebsiella pneumoniae

Introduction

Hypervirulent and multidrug-resistant Klebsiella pneumoniae (hvKP and MDR-KP) are significant public health threats. This study aimed to isolate a lytic bacteriophage targeting these high-risk strains, systematically characterize its biological properties, genomic features, and therapeutic efficacy, and establish a foundation for clinical phage therapy and novel antimicrobial development.

Methods

The phage vB_Kp_XP4 was isolated from river water using the double-layer agar plate method with the clinically isolated strain P4 as the host. Morphology was analyzed via transmission electron microscopy (TEM). Host range, pH, and thermal stability were assessed using spot assays and OD630 measurements. One-step growth curves determined the latent period and burst size. Whole-genome sequencing and phylogenetic analysis were performed. Therapeutic efficacy and safety were evaluated in a Galleria mellonella infection model.

Results

TEM revealed Phage vB_Kp_XP4 as a tailed phage with an icosahedral head and a long, flexible tail. It lysed an hvKP strain (carrying rmp, peg, iuc, iro genes) and an MDR-KP strain (resistant to carbapenems, fluoroquinolones, etc.), with an optimal MOI of 0.1 and latent period <10 minutes. Stability was maintained at pH 4-11 and ≤70°C. Whole-genome sequencing revealed a linear double-stranded DNA genome of 44,344 bp with a G+C content of 53.80%. The genome comprised 54 coding sequences and lacked lysogenic, virulence, or antibiotic resistance genes. Phylogenetic analysis positioned phage vB_Kp_XP4 as a novel species within the genus Drulisvirus, family Autographiviridae. In the Galleria mellonella model, vB_Kp_XP4 prolonged survival of P4-infected larvae (P < 0.001).

Conclusion

Phage vB_Kp_XP4 exhibits high stability, specificity, potent lytic activity, and no undesirable genes, demonstrating effective in vivo therapeutic efficacy, suggest its potential for clinical applications against Klebsiella pneumoniae infections. The presence of multiple halos during plaque formation further enhances its research value. The complete genome sequence has been submitted to GenBank under accession number PP663283.

Isolation and characterization of a broad-spectrum bacteriophage against multi-drug resistant Escherichia coli from waterfowl field

Escherichia coli (E. coli) is a significant pathogen responsible for intestinal infections and foodborne diseases. The rise of antibiotic resistance poses a significant challenge to global public health. Traditional antibiotic therapy is becoming increasingly ineffective, highlighting the urgent need for innovative control strategies. This study explores the potential of bacteriophages as a sustainable alternative to traditional antibiotics. From 2021 to 2022, a total of 183 non-repetitive duck source fecal samples were collected from Mianyang City, Sichuan Province, and 126 strains of E. coli were isolated. The minimum inhibitory concentration (MIC) test showed that these strains exhibited high resistance to piperacillin (96.8%), tetracycline (88.9%), and chloramphenicol (86.5%). It is concerning that 93.7% of the isolates are classified as multidrug-resistant (MDR), posing a significant threat to existing treatment options. 20 bacteriophages were isolated from fecal and soil samples, among which 5 bacteriophages were selected for further analysis. Bacteriophage YP6 showed excellent lytic effects on MDR strains, especially strain MY104, as well as representative serotypes O1 (E. coli MY51) and O18 (E. coli MY106). The identification of YP6 as a member of the Myoviridae family was conducted using transmission electron microscopy, and it was found to have an optimal infection factor of 0.1. Bacteriophages exhibit significant thermal and pH stability, maintaining survival at temperatures up to 60 °C and pH ranges of 4 to 10. Whole genome sequencing confirmed that YP6 has a double stranded DNA genome of 139,323 base pairs (bp), and no antibiotic resistance or virulence genes were found, indicating a low possibility of horizontal gene transfer. In addition, YP6 effectively inhibits the formation of E. coli biofilm, which is a key factor in chronic infections. The in vivo experiments using Galleria mellonella (G. mellonella) larvae have shown that it has a significant protective effect against MDR E. coli infection. In summary, bacteriophage YP6 is expected to become a therapeutic agent against MDR E. coli infection due to its broad host range, environmental stability, and biofilm inhibition properties. Future research should optimize bacteriophage preparations, evaluate the safety and efficacy of animal models, and establish clinical application plans in the field of food safety.

Microbial Dynamics in Endodontic Pathology-From Bacterial Infection to Therapeutic Interventions-A Narrative Review

Endodontic infection is a penetration of microorganisms into the dental pulp. Bacteria are the most common entities that induce an infection. This state is associated with significant pain and discomfort. Therapeutic intervention involves removal of infected pulp from the tooth and roots, which eliminates viable tissue, thus creating a tooth less resistant to mechanical pressure. Studies suggest that there are several types of bacteria most commonly associated with endodontic infections. Furthermore, it is considered that different types of pathogens could play a major role in primary and secondary endodontic infections. The aim of this review is to summarize major bacteria involved in the process of endodontic infection. Furthermore, we discuss the bacterial properties that allow them to penetrate dental pulp and hypothesize about possible future treatment strategies.

Comprehensive Approaches to Combatting Acinetobacter baumannii Biofilms: From Biofilm Structure to Phage-Based Therapies

Acinetobacter baumannii-a multidrug-resistant (MDR) pathogen that causes, for example, skin and soft tissue wounds; urinary tract infections; pneumonia; bacteremia; and endocarditis, particularly due to its ability to form robust biofilms-poses a significant challenge in clinical settings. This structure protects the bacteria from immune responses and antibiotic treatments, making infections difficult to eradicate. Given the rise in antibiotic resistance, alternative therapeutic approaches are urgently needed. Bacteriophage-based strategies have emerged as a promising solution for combating A. baumannii biofilms. Phages, which are viruses that specifically infect bacteria, offer a targeted and effective means of disrupting biofilm and lysing bacterial cells. This review explores the current advancements in bacteriophage therapy, focusing on its potential for treating A. baumannii biofilm-related infections. We described the mechanisms by which phages interact with biofilms, the challenges in phage therapy implementation, and the strategies being developed to enhance its efficacy (phage cocktails, engineered phages, combination therapies with antibiotics). Understanding the role of bacteriophages in both biofilm disruption and in inhibition of its forming could pave the way for innovative treatments in combating MDR A. baumannii infections as well as the prevention of their development.

"Stop, Little Pot" as the Motto of Suppressive Management of Various Microbial Consortia

The unresolved challenges in the development of highly efficient, stable and controlled synthetic microbial consortia, as well as the use of natural consortia, are very attractive for science and technology. However, the consortia management should be done with the knowledge of how not only to accelerate but also stop the action of such "little pots". Moreover, there are a lot of microbial consortia, the activity of which should be suppressively controlled. The processes, catalyzed by various microorganisms being in complex consortia which should be slowed down or completely cancelled, are typical for the environment (biocorrosion, landfill gas accumulation, biodegradation of building materials, water sources deterioration etc.), industry (food and biotechnological production), medical practice (vaginitis, cystitis, intestinal dysbiosis, etc.). The search for ways to suppress the functioning of heterogeneous consortia in each of these areas is relevant. The purpose of this review is to summarize the general trends in these studies regarding the targets and new means of influence used. The analysis of the features of the applied approaches to solving the main problem confirms the possibility of obtaining a combined effect, as well as selective influence on individual components of the consortia. Of particular interest is the role of viruses in suppressing the functioning of microbial consortia of different compositions.

Gut phageome: challenges in research and impact on human microbiota

The human gut microbiome plays a critical role in maintaining our health. Fluctuations in the diversity and structure of the gut microbiota have been implicated in the pathogenesis of several metabolic and inflammatory conditions. Dietary patterns, medication, smoking, alcohol consumption, and physical activity can all influence the abundance of different types of microbiota in the gut, which in turn can affect the health of individuals. Intestinal phages are an essential component of the gut microbiome, but most studies predominantly focus on the structure and dynamics of gut bacteria while neglecting the role of phages in shaping the gut microbiome. As bacteria-killing viruses, the distribution of bacteriophages in the intestine, their role in influencing the intestinal microbiota, and their mechanisms of action remain elusive. Herein, we present an overview of the current knowledge of gut phages, their lifestyles, identification, and potential impact on the gut microbiota.

Stability study in selected conditions and biofilm-reducing activity of phages active against drug-resistant Acinetobacter baumannii

Acinetobacter baumannii is currently a serious threat to human health, especially to people with immunodeficiency as well as patients with prolonged hospital stays and those undergoing invasive medical procedures. The ever-increasing percentage of strains characterized by multidrug resistance to widely used antibiotics and their ability to form biofilms make it difficult to fight infections with traditional antibiotic therapy. In view of the above, phage therapy seems to be extremely attractive. Therefore, phages with good storage stability are recommended for therapeutic purposes. In this work, we present the results of studies on the stability of 12 phages specific for A. baumannii under different conditions (including temperature, different pH values, commercially available disinfectants, essential oils, and surfactants) and in the urine of patients with urinary tract infections (UTIs). Based on our long-term stability studies, the most optimal storage method for the A. baumannii phage turned out to be - 70 °C. In contrast, 60 °C caused a significant decrease in phage activity after 1 h of incubation. The tested phages were the most stable at a pH from 7.0 to 9.0, with the most inactivating pH being strongly acidic. Interestingly, ethanol-based disinfectants caused a significant decrease in phage titers even after 30 s of incubation. Moreover, copper and silver nanoparticle solutions also caused a decrease in phage titers (which was statistically significant, except for the Acba_3 phage incubated in silver solution), but to a much lesser extent than disinfectants. However, bacteriophages incubated for 24 h in essential oils (cinnamon and eucalyptus) can be considered stable.