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1.
J Med Microbiol ; 73(5)2024 May.
Article En | MEDLINE | ID: mdl-38743467

Introduction . Acinetobacter baumannii is a critical priority pathogen for novel antimicrobials (World Health Organization) because of the rise in nosocomial infections and its ability to evolve resistance to last resort antibiotics. A. baumannii is thus a priority target for phage therapeutics. Two strains of a novel, virulent bacteriophage (LemonAid and Tonic) able to infect carbapenem-resistant A. baumannii (strain NCTC 13420), were isolated from environmental water samples collected through a citizen science programme.Gap statement. Phage-host coevolution can lead to emergence of host resistance, with a concomitant reduction in the virulence of host bacteria; a potential benefit to phage therapy applications.Methodology. In vitro and in vivo assays, genomics and microscopy techniques were used to characterize the phages; determine mechanisms and impact of phage resistance on host virulence, and the efficacy of the phages against A. baumannii.Results. A. baumannii developed resistance to both viruses, LemonAid and Tonic. Resistance came at a cost to virulence, with the resistant variants causing significantly reduced mortality in a Galleria mellonella larval in vivo model. A replicated 8 bp insertion increased in frequency (~40 % higher frequency than in the wild-type) within phage-resistant A. baumannii mutants, putatively resulting in early truncation of a protein of unknown function. Evidence from comparative genomics and an adsorption assay suggests this protein acts as a novel phage receptor site in A. baumannii. We find no evidence linking resistance to changes in capsule structure, a known virulence factor. LemonAid efficiently suppressed growth of A. baumanni in vitro across a wide range of titres. However, in vivo, while survival of A. baumannii infected larvae significantly increased with both remedial and prophylactic treatment with LemonAid (107 p.f.u. ml-1), the effect was weak and not sufficient to save larvae from morbidity and mortality.Conclusion. While LemonAid and Tonic did not prove effective as a treatment in a Galleria larvae model, there is potential to harness their ability to attenuate virulence in drug-resistant A. baumannii.


Acinetobacter Infections , Acinetobacter baumannii , Bacteriophages , Acinetobacter baumannii/virology , Acinetobacter baumannii/drug effects , Acinetobacter baumannii/pathogenicity , Acinetobacter baumannii/genetics , Bacteriophages/genetics , Bacteriophages/physiology , Virulence , Acinetobacter Infections/microbiology , Animals , Moths/microbiology , Moths/virology , Phage Therapy , Anti-Bacterial Agents/pharmacology , Drug Resistance, Bacterial , Larva/microbiology , Larva/virology
2.
PLoS One ; 19(5): e0301292, 2024.
Article En | MEDLINE | ID: mdl-38743671

Enterococcus faecalis, a Gram-positive bacterium, poses a significant clinical challenge owing to its intrinsic resistance to a broad spectrum of antibiotics, warranting urgent exploration of innovative therapeutic strategies. This study investigated the viability of phage therapy as an alternative intervention for antibiotic-resistant E. faecalis, with a specific emphasis on the comprehensive genomic analysis of bacteriophage SAM-E.f 12. The investigation involved whole-genome sequencing of SAM-E.f 12 using Illumina technology, resulting in a robust dataset for detailed genomic characterization. Bioinformatics analyses were employed to predict genes and assign functional annotations. The bacteriophage SAM-E.f 12, which belongs to the Siphoviridae family, exhibited substantial potential, with a burst size of 5.7 PFU/infected cells and a latent period of 20 min. Host range determination experiments demonstrated its effectiveness against clinical E. faecalis strains, positioning SAM-E.f 12 as a precise therapeutic agent. Stability assays underscore resilience across diverse environmental conditions. This study provides a comprehensive understanding of SAM-E.f 12 genomic composition, lytic lifecycle parameters, and practical applications, particularly its efficacy in murine wound models. These results emphasize the promising role of phage therapy, specifically its targeted approach against antibiotic-resistant E. faecalis strains. The nuanced insights derived from this research will contribute to the ongoing pursuit of efficacious phage therapies and offer valuable implications for addressing the clinical challenges associated with E. faecalis infections.


Bacteriophages , Enterococcus faecalis , Genome, Viral , Enterococcus faecalis/virology , Enterococcus faecalis/genetics , Bacteriophages/genetics , Animals , Mice , Phage Therapy , Host Specificity/genetics , Gram-Positive Bacterial Infections/microbiology , Gram-Positive Bacterial Infections/therapy , Whole Genome Sequencing , Genomics/methods , Siphoviridae/genetics
3.
Vet Q ; 44(1): 1-9, 2024 Dec.
Article En | MEDLINE | ID: mdl-38726795

Antibiotic-resistant pathogens are a growing global issue, leading to untreatable infectious diseases in both humans and animals. Personalized bacteriophage (phage) therapy, the use of specific anti-bacterial viruses, is currently a leading approach to combat antibiotic-resistant infections. The implementation of phage therapy has primarily been focused on humans, almost neglecting the impact of such infections on the health and welfare of companion animals. Pets also have the potential to spread resistant infections to their owners or the veterinary staff through zoonotic transmission. Here, we showcase personalized phage-antibiotic treatment of a cat with a multidrug-resistant Pseudomonas aeruginosa implant-associated infection post-arthrodesis surgery. The treatment encompassed a tailored combination of an anti-P. aeruginosa phage and ceftazidime, precisely matched to the pathogen. The phage was topically applied to the surgical wound while the antibiotic was administered intramuscularly. After two treatment courses spanning 7 and 3 weeks, the surgical wound, which had previously remained open for five months, fully closed. To the best of our knowledge, this is the first case of personalized phage therapy application in felines, which provides further evidence of the effectiveness of this approach. The successful outcome paves the way for personalized phage-antibiotic treatments against persistent infections therapy in veterinary practice.


Anti-Bacterial Agents , Cat Diseases , Phage Therapy , Pseudomonas Infections , Pseudomonas aeruginosa , Animals , Cats , Phage Therapy/veterinary , Pseudomonas Infections/veterinary , Pseudomonas Infections/drug therapy , Pseudomonas Infections/therapy , Cat Diseases/therapy , Cat Diseases/drug therapy , Cat Diseases/microbiology , Pseudomonas aeruginosa/drug effects , Anti-Bacterial Agents/therapeutic use , Ceftazidime/therapeutic use , Drug Resistance, Multiple, Bacterial , Bacteriophages
4.
PLoS One ; 19(5): e0303056, 2024.
Article En | MEDLINE | ID: mdl-38713691

With the global challenge of antimicrobial resistance (AMR), interest in the development of antibiotic alternatives has surged worldwide. While phage therapy is not a new phenomenon, technological and socio-economic factors have limited its implementation in the Western world. There is now a resurged effort, especially in the UK, to address these challenges. In this study, we collect survey data on UK general practitioners (n = 131) and other healthcare professionals (n = 103), as well as interviews with medical professionals (n = 4) and a focus group with medical students (n = 6) to explore factors associated with their willingness to prescribe phage therapy to patients. The interviews with medical professionals show support for the expansion of bacteriophage clinical trials and highlight their role as a viable alternative to antibiotics. A conjoint experiment reveals that success rate, side effect rate, and patient attitude to treatment are the decisive factors when it comes to phage therapy prescription; in contrast, the effects of administration route, type of treatment, and severity of infection were not statistically significant. Moreover, we show that general practitioners overall are more likely to recommend phage treatment to patients, compared to other healthcare professionals. The results of the study suggest that phage therapy has a potential to be widely accepted and used by healthcare workers in the UK.


Phage Therapy , Humans , United Kingdom , Phage Therapy/methods , Female , Male , Health Personnel/psychology , Adult , Surveys and Questionnaires , Middle Aged , Practice Patterns, Physicians'/statistics & numerical data , Attitude of Health Personnel
5.
Vet Res ; 55(1): 59, 2024 May 07.
Article En | MEDLINE | ID: mdl-38715095

Klebsiella pneumoniae has become one of the most intractable gram-negative pathogens infecting humans and animals due to its severe antibiotic resistance. Bacteriophages and protein products derived from them are receiving increasing amounts of attention as potential alternatives to antibiotics. In this study, we isolated and investigated the characteristics of a new lytic phage, P1011, which lyses K5 K. pneumoniae specifically among 26 serotypes. The K5-specific capsular polysaccharide-degrading depolymerase dep1011 was identified and expressed. By establishing murine infection models using bovine strain B16 (capable of supporting phage proliferation) and human strain KP181 (incapable of sustaining phage expansion), we explored the safety and efficacy of phage and dep1011 treatments against K5 K. pneumoniae. Phage P1011 resulted in a 60% survival rate of the mice challenged with K. pneumoniae supporting phage multiplication, concurrently lowering the bacterial burden in their blood, liver, and lungs. Unexpectedly, even when confronted with bacteria impervious to phage multiplication, phage therapy markedly decreased the number of viable organisms. The protective efficacy of the depolymerase was significantly better than that of the phage. The depolymerase achieved 100% survival in both treatment groups regardless of phage propagation compatibility. These findings indicated that P1011 and dep1011 might be used as potential antibacterial agents to control K5 K. pneumoniae infection.


Bacteriophages , Klebsiella Infections , Klebsiella pneumoniae , Animals , Klebsiella pneumoniae/virology , Klebsiella pneumoniae/physiology , Mice , Klebsiella Infections/therapy , Klebsiella Infections/veterinary , Klebsiella Infections/microbiology , Bacteriophages/physiology , Disease Models, Animal , Phage Therapy , Female , Glycoside Hydrolases/metabolism , Cattle
6.
Front Cell Infect Microbiol ; 14: 1382145, 2024.
Article En | MEDLINE | ID: mdl-38736748

Carbapenem-resistant Acinetobacter baumannii (CRAB) has become a new threat in recent years, owing to its rapidly increasing resistance to antibiotics and new effective therapies are needed to combat this pathogen. Phage therapy is considered to be the most promising alternative for treating CRAB infections. In this study, a novel phage, Ab_WF01, which can lyse clinical CRAB, was isolated and characterized from hospital sewage. The multiplicity of infection, morphology, one-step growth curve, stability, sensitivity, and lytic activity of the phage were also investigated. The genome of phage Ab_WF01 was 41, 317 bp in size with a GC content of 39.12% and encoded 51 open reading frames (ORFs). tRNA, virulence, and antibiotic resistance genes were not detected in the phage genome. Comparative genomic and phylogenetic analyses suggest that phage Ab_WF01 is a novel species of the genus Friunavirus, subfamily Beijerinckvirinae, and family Autographiviridae. The in vivo results showed that phage Ab_WF01 significantly increased the survival rate of CRAB-infected Galleria mellonella (from 0% to 70% at 48 h) and mice (from 0% to 60% for 7 days). Moreover, after day 3 post-infection, phage Ab_WF01 reduced inflammatory response, with strongly ameliorated histological damage and bacterial clearance in infected tissue organs (lungs, liver, and spleen) in mouse CRAB infection model. Taken together, these results show that phage Ab_WF01 holds great promise as a potential alternative agent with excellent stability for against CRAB infections.


Acinetobacter Infections , Acinetobacter baumannii , Bacteriophages , Carbapenems , Genome, Viral , Phage Therapy , Phylogeny , Sewage , Acinetobacter baumannii/virology , Acinetobacter baumannii/drug effects , Sewage/virology , Sewage/microbiology , Animals , Carbapenems/pharmacology , Bacteriophages/genetics , Bacteriophages/physiology , Bacteriophages/classification , Bacteriophages/isolation & purification , Acinetobacter Infections/microbiology , Mice , Anti-Bacterial Agents/pharmacology , Open Reading Frames , Disease Models, Animal , Moths/virology , Moths/microbiology , Base Composition
7.
Urologiia ; (1): 114-118, 2024 Mar.
Article Ru | MEDLINE | ID: mdl-38655779

Clinical cases of three patients with neurogenic lower urinary tract dysfunction, complicated by chronic urinary tract infection are presented in the article. All patients underwent clean intermittent catheterization and, in order to prevent symptomatic lower urinary tract infections, received bacteriophage therapy with a clinically proven positive effect. During 3 months follow-up, there were no episodes of urinary tract infection. A change in the concentration of uropathogens and restoration of sensitivity to a number of antimicrobial drugs were observed. Although phage therapy in urology requires further clinical research, it provides an additional strategy to treat urinary tract infections considering an increase in antibiotic resistance.


Phage Therapy , Urinary Tract Infections , Humans , Urinary Tract Infections/therapy , Urinary Tract Infections/etiology , Male , Phage Therapy/methods , Middle Aged , Female , Bacteriophages , Urinary Bladder, Neurogenic/therapy , Adult , Aged , Recurrence
8.
Cell Biochem Funct ; 42(3): e4022, 2024 Apr.
Article En | MEDLINE | ID: mdl-38655589

Over the years, the administration of antibiotics for the purpose of addressing bacterial infections has become increasingly challenging due to the increased prevalence of antimicrobial resistance exhibited by various strains of bacteria. Multidrug-resistant (MDR) bacterial species are rising due to the unavailability of novel antibiotics, leading to higher mortality rates. With these conditions, there is a need for alternatives in which phage therapy has made promising results. Phage-derived endolysins, phage cocktails, and bioengineered phages are effective and have antimicrobial properties against MDR and extensively drug-resistant strains. Despite these, it has been observed that phages can give antimicrobial activity to more than one bacterial species. Thus, phage cocktail against resistant strains provides broad spectrum treatment and magnitude of effectivity, which is many folds higher than antibiotics. Many commercially available endolysins such as Staphefekt SA.100, Exebacase (CF-301), and N-Rephasin®SAL200 are used in biofilm penetration and treating plant diseases. The role of CMP1 phage endolysin in transgenic tomato plants in preventing Clavibacter michiganensis infection and the effectiveness of phage in protecting Atlantic salmon from vibriosis have been reported. Furthermore, phage-derived endolysin therapy, such as TSPphg phage exogenous treatment, can aid in disrupting cell walls, leading to bacterial cell lysis. As animals in aquaculture and slaughterhouses are highly susceptible to bacterial infections, effective phage therapy instead of antibiotics can help treat poultry animals, preserve them, and facilitate disease-free trade. Using bioengineered phages and phage cocktails enhances the effectiveness by providing a broad spectrum of phages and target specificity. Research is currently being conducted on clinical trials to confirm the efficacy of engineered phages and phage cocktails in humans. Although obtaining commercial approval may be time-consuming, it will be beneficial in the postantibiotic era. This review provides an overview of the significance of phage therapy as a potential alternative to antibiotics in combating resistant bacterial strains and its application to various fields and emphasizes the importance of safeguarding and ensuring treatment efficacy.


Anti-Bacterial Agents , Bacteriophages , Endopeptidases , Phage Therapy , Anti-Bacterial Agents/pharmacology , Humans , Animals , Bacterial Infections/therapy , Bacterial Infections/drug therapy , Bacterial Infections/microbiology , Bacteria/drug effects , Bacteria/virology
10.
Sci Rep ; 14(1): 9251, 2024 04 22.
Article En | MEDLINE | ID: mdl-38649443

The increasing prevalence of methicillin-resistant Staphylococcus aureus (MRSA) emphasises the urgent need for novel antimicrobial agents as alternatives to antibiotics. Bacteriophage therapy is one of the most promising antimicrobial strategies. Here, we isolated and comprehensively characterized a novel Staphylococcus phage, vB_SauM_VL10 (VL10), from urban sewage. The VL10 genome displays 141,746 bp of linear double-stranded DNA, containing 193 open reading frames and lacking tRNA, virulence, or antibiotic resistance genes. Phylogenetic analysis categorizes VL10 as a novel species within the Silviavirus genus, Twortvirinae subfamily. VL10 exhibits lytic behaviour characterized by efficient adsorption, a short latent period, and substantial burst size, with environmental stability. It demonstrates lytic activity against 79.06% of tested S. aureus strains, highlighting its species specificity. Additionally, VL10 effectively targets MRSA biofilms, reducing biomass and viable cells. In MRSA-infected G. mellonella larvae, VL10 enhances survival rates, supporting its potential for phage therapy applications. Moreover, the emergence of VL10-resistant S. aureus strains associated with fitness trade-offs, including reduced growth, biofilm formation, and virulence. Altogether, these findings emphasize VL10 as a promising candidate for developing therapeutic agents against MRSA infections, providing insights into phage biology and resistance dynamics.


Biofilms , Genome, Viral , Methicillin-Resistant Staphylococcus aureus , Phylogeny , Staphylococcus Phages , Methicillin-Resistant Staphylococcus aureus/drug effects , Methicillin-Resistant Staphylococcus aureus/virology , Staphylococcus Phages/genetics , Biofilms/drug effects , Staphylococcal Infections/microbiology , Staphylococcal Infections/therapy , Staphylococcal Infections/drug therapy , Phage Therapy , Sewage/microbiology , Sewage/virology , Animals , Humans , Anti-Bacterial Agents/pharmacology
11.
Sci Rep ; 14(1): 9399, 2024 04 24.
Article En | MEDLINE | ID: mdl-38658654

Edwardsiella piscicida causes significant economic losses to the aquaculture industry worldwide. Phage-based biocontrol methods are experiencing a renaissance because of the spread of drug-resistant genes and bacteria resulting from the heavy use of antibiotics. Here, we showed that the novel Edwardsiella phage EPP-1 could achieve comparable efficacy to florfenicol using a zebrafish model of Edwardsiella piscicida infection and could reduce the content of the floR resistance gene in zebrafish excreta. Specifically, phage EPP-1 inhibited bacterial growth in vitro and significantly improved the zebrafish survival rate in vivo (P = 0.0035), achieving an efficacy comparable to that of florfenicol (P = 0.2304). Notably, integrating the results of 16S rRNA sequencing, metagenomic sequencing, and qPCR, although the effects of phage EPP-1 converged with those of florfenicol in terms of the community composition and potential function of the zebrafish gut microbiota, it reduced the floR gene content in zebrafish excreta and aquaculture water. Overall, our study highlights the feasibility and safety of phage therapy for edwardsiellosis control, which has profound implications for the development of antibiotic alternatives to address the antibiotic crisis.


Anti-Bacterial Agents , Bacteriophages , Edwardsiella , Enterobacteriaceae Infections , Thiamphenicol/analogs & derivatives , Zebrafish , Animals , Zebrafish/microbiology , Edwardsiella/genetics , Enterobacteriaceae Infections/microbiology , Enterobacteriaceae Infections/veterinary , Enterobacteriaceae Infections/therapy , Bacteriophages/genetics , Bacteriophages/physiology , Anti-Bacterial Agents/pharmacology , Drug Resistance, Bacterial/genetics , Gastrointestinal Microbiome , Phage Therapy/methods , RNA, Ribosomal, 16S/genetics , Fish Diseases/microbiology , Fish Diseases/therapy , Fish Diseases/prevention & control , Thiamphenicol/pharmacology , Aquaculture/methods
13.
PLoS Biol ; 22(4): e3002566, 2024 Apr.
Article En | MEDLINE | ID: mdl-38652717

Phage therapy is a therapeutic approach to treat multidrug-resistant (MDR) infections that employs lytic bacteriophages (phages) to eliminate bacteria. Despite the abundant evidence for its success as an antimicrobial in Eastern Europe, there is scarce data regarding its effects on the human host. Here, we aimed to understand how lytic phages interact with cells of the airway epithelium, the tissue site that is colonized by bacterial biofilms in numerous chronic respiratory disorders. Using a panel of Pseudomonas aeruginosa phages and human airway epithelial cells (AECs) derived from a person with cystic fibrosis (CF), we determined that interactions between phages and epithelial cells depend on specific phage properties as well as physiochemical features of the microenvironment. Although poor at internalizing phages, the airway epithelium responds to phage exposure by changing its transcriptional profile and secreting antiviral and proinflammatory cytokines that correlate with specific phage families. Overall, our findings indicate that mammalian responses to phages are heterogenous and could potentially alter the way that respiratory local defenses aid in bacterial clearance during phage therapy. Thus, besides phage receptor specificity in a particular bacterial isolate, the criteria to select lytic phages for therapy should be expanded to include mammalian cell responses.


Cystic Fibrosis , Cytokines , Epithelial Cells , Pseudomonas aeruginosa , Humans , Pseudomonas aeruginosa/virology , Epithelial Cells/virology , Epithelial Cells/metabolism , Epithelial Cells/immunology , Cytokines/metabolism , Cystic Fibrosis/therapy , Cystic Fibrosis/immunology , Cystic Fibrosis/metabolism , Phage Therapy , Bacteriophages/physiology , Bacteriophages/genetics , Respiratory Mucosa/virology , Respiratory Mucosa/metabolism , Respiratory Mucosa/immunology , Pseudomonas Infections/therapy , Pseudomonas Infections/immunology , Pseudomonas Phages/metabolism , Biofilms
14.
Antimicrob Agents Chemother ; 68(5): e0143923, 2024 May 02.
Article En | MEDLINE | ID: mdl-38591854

Phage therapy has (re)emerged as a serious possibility for combating multidrug-resistant bacterial infections, including those caused by vancomycin-resistant Enterococcus faecium strains. These opportunistic pathogens belong to a specific clonal complex 17, against which relatively few phages have been screened. We isolated a collection of 21 virulent phages growing on these vancomycin-resistant isolates. Each of these phages harbored a typical narrow plaquing host range, lysing at most 5 strains and covering together 10 strains of our panel of 14 clinical isolates. To enlarge the host spectrum of our phages, the Appelmans protocol was used. We mixed four out of our most complementary phages in a cocktail that we iteratively grew on eight naive strains from our panel, of which six were initially refractory to at least three of the combined phages. Fifteen successive passages permitted to significantly improve the lytic activity of the cocktail, from which phages with extended host ranges within the E. faecium species could be isolated. A single evolved phage able to kill up to 10 of the 14 initial E. faecium strains was obtained, and it barely infected nearby species. All evolved phages had acquired point mutations or a recombination event in the tail fiber genetic region, suggesting these genes might have driven phage evolution by contributing to their extended host spectra.


Bacteriophages , Enterococcus faecium , Host Specificity , Vancomycin-Resistant Enterococci , Enterococcus faecium/drug effects , Bacteriophages/genetics , Vancomycin-Resistant Enterococci/drug effects , Phage Therapy/methods , Gram-Positive Bacterial Infections/microbiology , Vancomycin Resistance , Vancomycin/pharmacology , Humans , Anti-Bacterial Agents/pharmacology
15.
Microbiol Spectr ; 12(5): e0322123, 2024 May 02.
Article En | MEDLINE | ID: mdl-38526142

The emergence of antibiotic-resistant bacteria (ARB) has necessitated the development of alternative therapies to deal with this global threat. Bacteriophages (viruses that target bacteria) that kill ARB are one such alternative. Although phages have been used clinically for decades with inconsistent results, a number of recent advances in phage selection, propagation, and purification have enabled a reevaluation of their utility in contemporary clinical medicine. In most phage therapy cases, phages are administered in combination with antibiotics to ensure that patients receive the standard-of-care treatment. Some phages may work cooperatively with antibiotics to eradicate ARB, as often determined using non-standardized broth assays. We sought to develop a solid media-based assay to assess cooperativity between antibiotics and phages to offer a standardized platform for such testing. We modeled the interactions that occur between antibiotics and phages on solid medium to measure additive, antagonistic, and synergistic interactions. We then tested the method using different bacterial isolates and identified a number of isolates where synergistic interactions were identified. These interactions were not dependent on the specific organism, phage family, or antibiotic used. A priori susceptibility to the antibiotic or the specific phage were not requirements to observe synergistic interactions. Our data also confirm the potential for the restoration of vancomycin to treat vancomycin-resistant Enterococcus (VRE) when used in combination with phages. Solid media assays for the detection of cooperative interactions between antibiotics and phages can be an accessible technique adopted by clinical laboratories to evaluate antibiotic and phage choices in phage therapy.IMPORTANCEBacteriophages have become an important alternative treatment for individuals with life-threatening antibiotic-resistant bacteria (ARB) infections. Because antibiotics represent the standard-of-care for treatment of ARB, antibiotics and phages often are delivered together without evidence that they work cooperatively. Testing for cooperativity can be difficult due to the equipment necessary and a lack of standardized means for performing the testing in liquid medium. We developed an assay using solid medium to identify interactions between antibiotics and phages for gram-positive and gram-negative bacteria. We modeled the interactions between antibiotics and phages on solid medium, and then tested multiple replicates of vancomycin-resistant Enterococcus (VRE) and Stenotrophomonas in the assay. For each organism, we identified synergy between different phage and antibiotic combinations. The development of this solid media assay for assessing synergy between phages and antibiotics will better inform the use of these combinations in the treatment of ARB infections.


Anti-Bacterial Agents , Bacteriophages , Phage Therapy , Bacteriophages/physiology , Bacteriophages/isolation & purification , Anti-Bacterial Agents/pharmacology , Phage Therapy/methods , Humans , Culture Media/chemistry , Microbial Sensitivity Tests/methods , Bacteria/virology , Bacteria/drug effects , Drug Resistance, Bacterial
16.
Mol Biol Rep ; 51(1): 419, 2024 Mar 14.
Article En | MEDLINE | ID: mdl-38483683

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.


Bacteriophages , Phage Therapy , Humans , Bacteriophages/genetics , Pseudomonas , Sewage , Genome, Viral , Informatics , Integrases , Virulence Factors , Phylogeny
17.
Nat Commun ; 15(1): 2274, 2024 Mar 13.
Article En | MEDLINE | ID: mdl-38480702

One of the hopes for overcoming the antibiotic resistance crisis is the use of bacteriophages to combat bacterial infections, the so-called phage therapy. This therapeutic approach is generally believed to be safe for humans and animals as phages should infect only prokaryotic cells. Nevertheless, recent studies suggested that bacteriophages might be recognized by eukaryotic cells, inducing specific cellular responses. Here we show that in chickens infected with Salmonella enterica and treated with a phage cocktail, bacteriophages are initially recognized by animal cells as viruses, however, the cGAS-STING pathway (one of two major pathways of the innate antiviral response) is blocked at the stage of the IRF3 transcription factor phosphorylation. This inhibition is due to the inability of RNA polymerase III to recognize phage DNA and to produce dsRNA molecules which are necessary to stimulate a large protein complex indispensable for IRF3 phosphorylation, indicating the mechanism of the antiviral response impairment.


Bacteriophages , Phage Therapy , Humans , Animals , Bacteriophages/physiology , Chickens , Immunity , Antiviral Agents
18.
Proc Natl Acad Sci U S A ; 121(12): e2313574121, 2024 Mar 19.
Article En | MEDLINE | ID: mdl-38478693

This study supports the development of predictive bacteriophage (phage) therapy: the concept of phage cocktail selection to treat a bacterial infection based on machine learning (ML) models. For this purpose, ML models were trained on thousands of measured interactions between a panel of phage and sequenced bacterial isolates. The concept was applied to Escherichia coli associated with urinary tract infections. This is an important common infection in humans and companion animals from which multidrug-resistant (MDR) bloodstream infections can originate. The global threat of MDR infection has reinvigorated international efforts into alternatives to antibiotics including phage therapy. E. coli exhibit extensive genome-level variation due to horizontal gene transfer via phage and plasmids. Associated with this, phage selection for E. coli is difficult as individual isolates can exhibit considerable variation in phage susceptibility due to differences in factors important to phage infection including phage receptor profiles and resistance mechanisms. The activity of 31 phage was measured on 314 isolates with growth curves in artificial urine. Random Forest models were built for each phage from bacterial genome features, and the more generalist phage, acting on over 20% of the bacterial population, exhibited F1 scores of >0.6 and could be used to predict phage cocktails effective against previously untested strains. The study demonstrates the potential of predictive ML models which integrate bacterial genomics with phage activity datasets allowing their use on data derived from direct sequencing of clinical samples to inform rapid and effective phage therapy.


Bacteriophages , Escherichia coli Infections , Phage Therapy , Urinary Tract Infections , Humans , Animals , Escherichia coli/genetics , Escherichia coli Infections/microbiology , Bacteriophages/genetics , Anti-Bacterial Agents/pharmacology , Urinary Tract Infections/drug therapy
19.
Viruses ; 16(3)2024 Mar 12.
Article En | MEDLINE | ID: mdl-38543808

Bacteriophage therapy is a promising approach to treating bacterial infections. Research and development of bacteriophage therapy is intensifying due to the increase in antibiotic resistance and the faltering development of new antibiotics. Bacteriophage therapy uses bacteriophages (phages), i.e., prokaryotic viruses, to specifically target and kill pathogenic bacteria. The legal handling of this type of therapy raises several questions. These include whether phage therapeutics belong to a specially regulated class of medicinal products, and which legal framework should be followed with regard to the various technical ways in which phage therapeutics can be manufactured and administered. The article shows to which class of medicinal products phage therapeutics from wild type phages and from genetically modified (designer) phages do or do not belong. Furthermore, the article explains which legal framework is relevant for the manufacture and administration of phage therapeutics, which are manufactured in advance in a uniform, patient-independent manner, and for tailor-made patient-specific phage therapeutics. For the systematically coherent, successful translation of phage therapy, the article considers pharmaceutical law and related legal areas, such as genetic engineering law. Finally, the article shows how the planned legislative revisions of Directive 2001/83/EC and Regulation (EC) No 726/2004 may affect the legal future of phage therapy.


Bacterial Infections , Bacteriophages , Phage Therapy , Humans , Bacteriophages/physiology , Bacteria , Bacterial Infections/therapy , Anti-Bacterial Agents , Pharmaceutical Preparations
20.
Commun Biol ; 7(1): 294, 2024 Mar 09.
Article En | MEDLINE | ID: mdl-38461214

The continuing emergence of new strains of antibiotic-resistant bacteria has renewed interest in phage therapy; however, there has been limited progress in applying phage therapy to multi-drug resistant Mycobacterium tuberculosis (Mtb) infections. In this study, we show that bacteriophage strains D29 and DS6A can efficiently lyse Mtb H37Rv in 7H10 agar plates. However, only phage DS6A efficiently kills H37Rv in liquid culture and in Mtb-infected human primary macrophages. We further show in subsequent experiments that, after the humanized mice were infected with aerosolized H37Rv, then treated with DS6A intravenously, the DS6A treated mice showed increased body weight and improved pulmonary function relative to control mice. Furthermore, DS6A reduces Mtb load in mouse organs with greater efficacy in the spleen. These results demonstrate the feasibility of developing phage therapy as an effective therapeutic against Mtb infection.


Mycobacterium tuberculosis , Phage Therapy , Tuberculosis , Animals , Mice , Humans , Tuberculosis/therapy , Tuberculosis/microbiology , Macrophages/microbiology
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