Genomic and biological characterization of bacteriophages against Enterobacter cloacae, a high-priority pathogen.

Enterobacter cloacae is a clinically significant pathogen due to its multi-resistance to antibiotics, presenting a challenge in the treatment of infections. As concerns over antibiotic resistance escalate, novel therapeutic approaches have been explored. Bacteriophages, characterized by their remarkable specificity and ability to self-replicate within target bacteria, are emerging as a promising alternative therapy. In this study, we isolated and partially characterized nine lytic bacteriophages targeting E. cloacae, with two selected for comprehensive genomic analysis based on their host range and bacteriolytic activity. All identified phages exhibited a narrow host range, demonstrated stability within a temperature range of 30-60 °C, displayed pH tolerance from 3 to 10, and showed an excellent bacteriolytic capacity for up to 18 h. Notably, the fully characterized phage genomes revealed an absence of lysogenic, virulence, or antibiotic-resistance genes, positioning them as promising candidates for therapeutic intervention against E. cloacae-related diseases. Nonetheless, translating this knowledge into practical therapeutic applications mandates a deeper understanding of bacteriophage interactions within complex biological environments.

CRISPRals: A Web Database for Assessing the CRISPR Defense System in the Ralstonia solanacearum Species Complex to Avoid Phage Resistance.

Clustered regularly interspaced short palindromic repeats (CRISPR) has been widely characterized as a defense system against phages and other invading elements in bacteria and archaea. A low percentage of Ralstonia solanacearum species complex (RSSC) strains possess the CRISPR array and the CRISPR-associated proteins (Cas) that would confer immunity against various phages. To provide a wide-range screen of the CRISPR presence in the RSSC, we analyzed 378 genomes of RSSC strains to find the CRISPR locus. We found that 20.1, 14.3, and 54.5% of the R. solanacearum, R. pseudosolanacearum, and R. syzygii strains, respectively, possess the CRISPR locus. In addition, we performed further analysis to identify the respective phages that are restricted by the CRISPR arrays. We found 252 different phages infecting different strains of the RSSC, by means of the identification of similarities between the protospacers in phages and spacers in bacteria. We compiled this information in a database with web access called CRISPRals (https://crisprals.yachaytech.edu.ec/). Additionally, we made available a number of tools to detect and identify CRISPR array and Cas genes in genomic sequences that could be uploaded by users. Finally, a matching tool to relate bacteria spacer with phage protospacer sequences is available. CRISPRals is a valuable resource for the scientific community that contributes to the study of bacteria-phage interaction and a starting point that will help to design efficient phage therapy strategies.

Phage Delivery Strategies for Biocontrolling Human, Animal, and Plant Bacterial Infections: State of the Art.

This review aims at presenting the main strategies that are currently available for the delivery of bacteriophages to combat bacterial infections in humans, animals, and plants. It can be seen that the main routes for phage delivery are topical, oral, systemic, and airways for humans. In animals, the topical and oral routes are the most used. To combat infections in plant species, spraying the plant's phyllosphere or drenching the soil are the most commonly used methods. In both phage therapy and biocontrol using phages, very promising results have been obtained so far. However, more experiments are needed to establish forms of treatment and phage doses, among other parameters. Furthermore, in general, there is a lack of specific standards for the use of phages to combat bacterial infections.

Phage therapy: resurrecting a historical solution for the contemporary challenge of rising antibiotic resistance in Latin America.

INTRODUCTION: Antimicrobial resistance in Latin America is a growing concern in both human and non-human animal populations. The economic burden that is likely to be imposed through increased resistance will cause further strains on public health systems and the population at large. AREAS COVERED: We propose the rapid adoption and implementation of phage therapy as a necessary addition to the medical arsenal to help mitigate antimicrobial resistance, with an emphasis on considering the potential benefits that highly biodiverse countries such as Ecuador may have on phage discovery. However, programs may count on limited government support and/or facilitation, which could slow progress. EXPERT OPINION: We highlight the need for educational campaigns to be implemented in parallel with the development of phage therapy programs, particularly to implement these novel treatments in rural and indigenous communities.

Characterization and biocontrol efficacy of lytic phage (KPP-1) that infects multidrug resistant Klebsiella variicola.

Klebsiella variicola strain was identified from a natural water stream. Novel phage (KPP-1) infecting K. variicola was isolated and characterized. The biocontrol efficacy of KPP-1 against K. variicola-infected adult zebrafish was also investigated. The host K. variicola strain was resistant to six of the antibiotics tested and comprised the virulence genes kfuBC, fim, ureA, and Wza-Wzb-Wzccps. Morphological analysis by transmission electron microscopy revealed that KPP-1 has icosahedron head and tail structures. The latent period and burst size of KPP-1 were 20 min and 88 PFU per infected cell, respectively, at a multiplicity of infection of 0.1. KPP-1 was stable over a broad pH range (3-11), temperature (4-50 °C), and salinity (0.1-3%). KPP-1 inhibits the growth of K. variicola in vitro and in vivo. In the zebrafish infection model, treatment with KPP-1-infected K. variicola demonstrated 56% of cumulative survival. This suggests the possibility of developing KPP-1 as a potential biocontrol agent against multidrug-resistant K. variicola that belongs to the K. pneumoniae complex.

Cytotoxic Evaluation in HaCaT Cells of the Pa.7 Bacteriophage from Cutibacterium (Propionibacterium) acnes, Free and Encapsulated Within Liposomes.

Introduction: Acne is a multifactorial disease involving the colonization of skin follicles by Cutibacterium (formerly Propionibacterium) acnes. A combination of different retinoid-derived products, antibiotics, and hormonal antiandrogens are used to treat the disease, but these treatments require extended periods, may have secondary effects, are expensive, and not always effective. Owing to antibiotic resistance, the use of bacteriophages has been proposed as an alternative treatment. However, if they are intended for a cosmetic or pharmaceutical use, it is necessary to evaluate the safety of the phages and the preparations containing them. Materials and Methods: In this study, the cytotoxicity of Pa.7 bacteriophage was evaluated in HaCaT cells, along with a liposome suitable for their encapsulation, using 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide and trypan blue assays. Results: We found that Pa.7 was not cytotoxic for HaCaT cells. Also, 30 mM of liposomes, or below are considered noncytotoxic concentrations. Conclusion: Phages encapsulated in the liposomes presented in this study can be used safely for skin treatments.

Bacteriophages potentiate the effect of antibiotics by eradication of persister cells and killing of biofilm-forming cells.

Persister cells and biofilms are associated with chronic urinary infections which are more critical when generated by multi-drug resistant bacteria. In this context, joint administration of phages and antibiotics has been proposed as an alternative approach, since it may decrease the probability to generate resistant mutants to both agents. In this work, we exposed cultures of uropathogenic Escherichia coli conjunctly to antibiotics and phages. We determined that MLP2 combined with antibiotics eradicates persister cells. Similarly, MLP1 and MLP3 impact viability of biofilm-forming cells when administered with ampicillin. Our findings suggest a feasible prophylactic and therapeutic use of these non-transducing phages.

Current knowledge in the use of bacteriophages to combat infections caused by Pseudomonas aeruginosa in cystic fibrosis.

Pseudomonas aeruginosa (PA) is considered the first causal agent of morbidity and mortality in people with cystic fibrosis (CF) disease. Multi-resistant strains have emerged due to prolonged treatment with specific antibiotics, so new alternatives have been sought for their control. In this context, there is a renewed interest in therapies based on bacteriophages (phages) supported by several studies suggesting that therapy based on lytic phages and biofilm degraders may be promising for the treatment of lung infections in CF patients. However, there is little clinical data about phage studies in CF and the effectiveness and safety in patients with this disease has not been clear. Therefore, studies regarding on phage characterization, selection, and evaluation in vitro and in vivo models will provide reliable information for designing effective cocktails, either using mixed phages or in combination with antibiotics, making a great progress in clinical research. Hence, this review focuses on the most relevant and recent findings on the activity of lytic phages against PA strains isolated from CF patients and hospital environments, and discusses perspectives on the use of phage therapy on the treatment of PA in CF patients.

A Broad-Host-Range Phage Cocktail Selectively and Effectively Eliminates Vibrio Species from Shrimp Aquaculture Environment.

The protective effects of a phage cocktail composed of vB_Vc_SrVc2 and vB_Vc_SrVc9 were tested in Pacific white shrimp (Litopenaeus vannamei) postlarvae, which were originally isolated from diseased shrimps and selected due to their broad-host-range properties against several pathogenic Vibsrio species. We used culture-dependent and culture-independent approaches to explore its effect on bacterial communities associated with shrimp postlarvae. Both methods revealed that the levels of Vibrio species were significantly reduced after phage cocktail administration. Phage-treated shrimp also exhibisuppted lesser damage and higher lipid accumulation in B cells of the hepatopancreas, as revealed by histopathological examination. Taken together, this study provides clear evidence that phage therapy can selectively and effectively reduce Vibrio species, thereby providing an environmentally safe alternative to the prophylactic use of antibiotics in shrimp aquaculture.

Resistance against two lytic phage variants attenuates virulence and antibiotic resistance in Pseudomonas aeruginosa.

Background: Bacteriophage therapy is becoming part of mainstream Western medicine since antibiotics of clinical use tend to fail. It involves applying lytic bacteriophages that self-replicate and induce cell lysis, thus killing their hosts. Nevertheless, bacterial killing promotes the selection of resistant clones which sometimes may exhibit a decrease in bacterial virulence or antibiotic resistance. Methods: In this work, we studied the Pseudomonas aeruginosa lytic phage φDCL-PA6 and its variant φDCL-PA6α. Additionally, we characterized and evaluated the production of virulence factors and the virulence in a Galleria mellonella model of resistant mutants against each phage for PA14 and two clinical strains. Results: Phage φDCL-PA6α differs from the original by only two amino acids: one in the baseplate wedge subunit and another in the tail fiber protein. According to genomic data and cross-resistance experiments, these changes may promote the change of the phage receptor from the O-antigen to the core lipopolysaccharide. Interestingly, the host range of the two phages differs as determined against the Pseudomonas aeruginosa reference strains PA14 and PAO1 and against nine multidrug-resistant isolates from ventilator associated pneumonia. Conclusions: We show as well that phage resistance impacts virulence factor production. Specifically, phage resistance led to decreased biofilm formation, swarming, and type III secretion; therefore, the virulence towards Galleria mellonella was dramatically attenuated. Furthermore, antibiotic resistance decreased for one clinical strain. Our study highlights important potential advantages of phage therapy's evolutionary impact that may be exploited to generate robust therapy schemes.

Phage Therapies: Lessons (Not) Learned from the "Antibiotic Era".

The use of phages as therapeutic or prophylactic approaches is gaining increased interest amid the growing menace of antibiotic resistance. Phages, along with other new anti-infective strategies, are certainly welcome as much needed additions to the medicinal arsenal. However, we can easily make with phages the same mistakes we made with antibiotics, which caused the current resistance crisis. The oversimplification of the ecological role of antibiotics, neglecting ancient resistance and the role of horizontal gene transfer; the active search for wide spectrum, and the massive agricultural abuse; and, most importantly, the financial greed behind the development and use of antibiotics; these are all trends that are now visible in phage research. Should we bring phages to the same track that wasted antibiotics, we could be looking at a "postphage era" in our near future.

The immunomodulatory potential of phage therapy to treat acne: a review on bacterial lysis and immunomodulation.

Background: Characterized by an inflammatory pathogenesis, acne is the most common skin disorder worldwide. Altered sebum production, abnormal proliferation of keratinocytes, and microbiota dysbiosis represented by disbalance in Cutibacterium acnes population structure, have a synergic effect on inflammation of acne-compromised skin. Although the role of C. acnes as a single factor in acne development is still under debate, it is known that skin and skin-resident immune cells recognize this bacterium and produce inflammatory markers as a result. Control of the inflammatory response is frequently the target for acne treatment, using diverse chemical or physical agents including antibiotics. However, some of these treatments have side effects that compromise patient adherence and drug safety and in the case of antibiotics, it has been reported C. acnes resistance to these molecules. Phage therapy is an alternative to treat antibiotic-resistant bacterial strains and have been recently proposed as an immunomodulatory therapy. Here, we explore this perspective about phage therapy for acne, considering the potential immunomodulatory role of phages. Methodology: Literature review was performed using four different databases (Europe PubMed Central-ePMC, Google Scholar, PubMed, and ScienceDirect). Articles were ordered and selected according to their year of publication, number of citations, and quartile of the publishing journal. Results: The use of lytic bacteriophages to control bacterial infections has proven its promising results, and anti-inflammatory effects have been found for some bacteriophages and phage therapy. These effects can be related to bacterial elimination or direct interaction with immune cells that result in the regulation of pro-inflammatory cytokines. Studies on C. acnes bacteriophages have investigated their lytic activity, genomic structure, and stability on different matrices. However, studies exploring the potential of immunomodulation of these bacteriophages are still scarce. Conclusions: C. acnes bacteriophages, as well as other phages, may have direct immunomodulatory effects that are yet to be fully elucidated. To our knowledge, to the date that this review was written, there are only two studies that investigate anti-inflammatory properties for C. acnes bacteriophages. In those studies, it has been evidenced reduction of pro-inflammatory response to C. acnes inoculation in mice after bacteriophage application. Nevertheless, these studies were conducted in mice, and the interaction with the immune response was not described. Phage therapy to treat acne can be a suitable therapeutic alternative to C. acnes control, which in turn can aid to restore the skin's balance of microbiota. By controlling C. acnes colonization, C. acnes bacteriophages can reduce inflammatory reactions triggered by this bacterium.

Characterization of Xanthomonas arboricola pv. juglandis Bacteriophages against Bacterial Walnut Blight and Field Evaluation.

Xanthomonas arboricola pv. juglandis (hereafter X. juglandis) is the etiological agent of walnut blight, the most important bacterial disease affecting walnut production worldwide. Currently, the disease is treated mainly with copper-derived compounds (e.g., CuSO4) despite the evidence of genetic resistance in these strains. Regarding the effectiveness and sustainability, the use of a bacteriophage appears to be a biocontrol alternative to reduce X. juglandis load and symptomatology of walnut blight. Here, the phages f20-Xaj, f29-Xaj, and f30-Xaj were characterized, and their effectiveness in walnut orchards against walnut blight was determined. These bacteriophages showed a specific lytic infection in X. juglandis strains isolated from Chile and France. Phylogenetic analysis of the complete genome of f20-Xaj and f30-Xaj indicates that these phages belong to the Pradovirus genus. In the field, the cocktail of these bacteriophages showed similar effectivity to CuSO4 in the reduction of incidence and severity in walnut tissue. Moreover, the bacterial load of X. juglandis was significantly reduced in the presence of bacteriophages in contrast to a CuSO4 treatment. These results show that the use of bacteriophages can be an alternative to combat the symptoms of walnut blight caused by X. juglandis.

Phage Therapy in the Era of Multidrug Resistance in Bacteria: A Systematic Review.

Bacteriophages offer an alternative for the treatment of multidrug-resistant bacterial diseases as their mechanism of action differs from that of antibiotics. However, their application in the clinical field is limited to specific cases of patients with few or no other alternative therapies. This systematic review assesses the effectiveness and safety of phage therapy against multidrug-resistant bacteria through the evaluation of studies published over the past decade. To that end, a bibliographic search was carried out in the PubMed, Science Direct, and Google Scholar databases. Of the 1500 studies found, 27 met the inclusion criteria, with a total of 165 treated patients. Treatment effectiveness, defined as the reduction in or elimination of the bacterial load, was 85%. Except for two patients who died from causes unrelated to phage therapy, no serious adverse events were reported. This shows that phage therapy could be an alternative treatment for patients with infections associated with multidrug-resistant bacteria. However, owing to the phage specificity required for the treatment of various bacterial strains, this therapy must be personalized in terms of bacteriophage type, route of administration, and dosage.

Genomic and biological characterization of the novel phages vB_VpaP_AL-1 and vB_VpaS_AL-2 infecting Vibrio parahaemolyticus associated with acute hepatopancreatic necrosis disease (AHPND).

Acute hepatopancreatic necrosis disease (AHPND) is a life-threatening disease to recently stocked shrimp. This disease is mainly caused by Vibrio parahaemolyticus and, to date, it has not been effectively controlled. Bacteriophages are a promising method to control bacterial diseases in aquaculture and multiple phages that infect Asian strains of V. parahaemolyticus have been described. However, few studies have characterized the bacteriophages that infect Latin American strains. Here, two lytic Vibrio phages (vB_VpaP_AL-1 and vB_VpaS_AL-2) were isolated from estuary water in Sinaloa, Mexico. The host ranges were tested using ten AHPND-causing strains isolated from Mexico and phage AL-1 was able to infect two strains while AL-2 infected four. One-step growth curve showed that AL-1 produced 85 PFU/cell and AL-2 produced 68 PFU/cell in 30 and 40 min, respectively. Both phages were able to tolerate temperatures ranging from 20 to 50 °C and pH values ranging from 4 to 10. Phages AL-1 and AL-2 have double-stranded DNA genomes of 42,854 bp and 58,457 bp, respectively. In total, 53 putative ORFs associated with the phage structure, packing, host lysis, DNA metabolism, and additional functions were predicted in the AL-1 genome, while 92 ORFs associated with the same functions as the AL-1 and 1 tRNA were predicted in the AL-2 genome. The lifecycle was classified as virulent for both phages. Morphology, phylogeny, and comparative genomic analyses assigned phage AL-1 as a new member of the genus Maculvirus in the Autographiviridae family, and phage AL-2 as a new member of the Siphoviridae family. These findings suggest that vB_VpaP_AL-1 and vB_VpaS_AL-2 are potential biocontrol agents against AHPND-causing V. parahaemolyticus from Mexico.

Phage Therapy for Crops: Concepts, Experimental and Bioinformatics Approaches to Direct Its Application.

Phage therapy consists of applying bacteriophages, whose natural function is to kill specific bacteria. Bacteriophages are safe, evolve together with their host, and are environmentally friendly. At present, the indiscriminate use of antibiotics and salt minerals (Zn2+ or Cu2+) has caused the emergence of resistant strains that infect crops, causing difficulties and loss of food production. Phage therapy is an alternative that has shown positive results and can improve the treatments available for agriculture. However, the success of phage therapy depends on finding effective bacteriophages. This review focused on describing the potential, up to now, of applying phage therapy as an alternative treatment against bacterial diseases, with sustainable improvement in food production. We described the current isolation techniques, characterization, detection, and selection of lytic phages, highlighting the importance of complementary studies using genome analysis of the phage and its host. Finally, among these studies, we concentrated on the most relevant bacteriophages used for biocontrol of Pseudomonas spp., Xanthomonas spp., Pectobacterium spp., Ralstonia spp., Burkholderia spp., Dickeya spp., Clavibacter michiganensis, and Agrobacterium tumefaciens as agents that cause damage to crops, and affect food production around the world.

Characterization of a Coliphage AS1 isolated from sewage effluent in Pakistan / Caracterização de um colifago AS1 isolado de efluente de esgoto no Paquistão

The emergence of multi-drug resistant (MDR) bacterial strains, which are posing a global health threat has developed the interest of scientists to use bacteriophages instead of conventional antibiotics therapy. In light of an increased interest in the use of phage as a bacterial control agent, the study aimed to isolate and characterize lytic phages from sewage effluent. During the current study, bacteriophage AS1 was isolated from sewage effluent against E.coli S2. The lytic activity of phageAS1 was limited to E.coli S2 strain showing monovalent behavior. The calculated phage titer was 3.5×109 pfu/ml. PhageAS1 was stable at a wide range of pH and temperature. The maximum stability was recorded at 37ºC and pH 7.0, while showing its normal lytic activity at temperature 60ºC and from pH 5.0 to 11.0 respectively. At temperature 70ºC, phage activity was somewhat reduced whereas, further increase in temperature and decrease or increase in pH completely inactivated the phage. From the current study, it was concluded that waste water is a best source for finding bacteriophages against multi-drug resistant bacterial strains and can be used as bacterial control agent.(AU)

O surgimento de cepas bacterianas multirresistentes (MDR), que representam uma ameaça global à saúde, desenvolveu o interesse dos cientistas em usar bacteriófagos em vez da terapia convencional com antibióticos. Diante do crescente interesse no uso de fago como agente de controle bacteriano, o estudo visou isolar e caracterizar fagos líticos de efluente de esgoto. Durante o estudo atual, o bacteriófago AS1 foi isolado de efluente de esgoto contra E. coli S2. A atividade lítica de phageAS1 foi limitada à cepa E. coli S2, apresentando comportamento monovalente. O título de fago calculado foi de 3,5 x 109 ufp/ml. PhageAS1 foi estável em uma ampla faixa de pH e temperatura. A estabilidade máxima foi registrada a 37ºC e pH 7,0, enquanto mostrou atividade lítica normal em temperatura de 60ºC e pH 5,0 a 11,0, respectivamente. Na temperatura de 70ºC, a atividade do fago foi um pouco reduzida, enquanto o aumento adicional da temperatura e a diminuição ou aumento do pH inativaram completamente o fago. Com base no estudo atual, concluiu-se que a água residual é a melhor fonte para encontrar bacteriófagos contra cepas bacterianas multirresistentes e pode ser usada como agente de controle bacteriano.(AU)

Characterization of a Coliphage AS1 isolated from sewage effluent in Pakistan / Caracterização de um colifago AS1 isolado de efluente de esgoto no Paquistão

The emergence of multi-drug resistant (MDR) bacterial strains, which are posing a global health threat has developed the interest of scientists to use bacteriophages instead of conventional antibiotics therapy. In light of an increased interest in the use of phage as a bacterial control agent, the study aimed to isolate and characterize lytic phages from sewage effluent. During the current study, bacteriophage AS1 was isolated from sewage effluent against E.coli S2. The lytic activity of phageAS1 was limited to E.coli S2 strain showing monovalent behavior. The calculated phage titer was 3.5×109 pfu/ml. PhageAS1 was stable at a wide range of pH and temperature. The maximum stability was recorded at 37ºC and pH 7.0, while showing its normal lytic activity at temperature 60ºC and from pH 5.0 to 11.0 respectively. At temperature 70ºC, phage activity was somewhat reduced whereas, further increase in temperature and decrease or increase in pH completely inactivated the phage. From the current study, it was concluded that waste water is a best source for finding bacteriophages against multi-drug resistant bacterial strains and can be used as bacterial control agent.

O surgimento de cepas bacterianas multirresistentes (MDR), que representam uma ameaça global à saúde, desenvolveu o interesse dos cientistas em usar bacteriófagos em vez da terapia convencional com antibióticos. Diante do crescente interesse no uso de fago como agente de controle bacteriano, o estudo visou isolar e caracterizar fagos líticos de efluente de esgoto. Durante o estudo atual, o bacteriófago AS1 foi isolado de efluente de esgoto contra E. coli S2. A atividade lítica de phageAS1 foi limitada à cepa E. coli S2, apresentando comportamento monovalente. O título de fago calculado foi de 3,5 x 109 ufp/ml. PhageAS1 foi estável em uma ampla faixa de pH e temperatura. A estabilidade máxima foi registrada a 37ºC e pH 7,0, enquanto mostrou atividade lítica normal em temperatura de 60ºC e pH 5,0 a 11,0, respectivamente. Na temperatura de 70ºC, a atividade do fago foi um pouco reduzida, enquanto o aumento adicional da temperatura e a diminuição ou aumento do pH inativaram completamente o fago. Com base no estudo atual, concluiu-se que a água residual é a melhor fonte para encontrar bacteriófagos contra cepas bacterianas multirresistentes e pode ser usada como agente de controle bacteriano.