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Horwitz EK, Strobel HM, Haiso J, Meyer JR. More evolvable bacteriophages better suppress their host. Evol Appl 2024; 17:e13742. [PMID: 38975285 PMCID: PMC11224127 DOI: 10.1111/eva.13742] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 04/09/2024] [Accepted: 06/10/2024] [Indexed: 07/09/2024] Open
Abstract
The number of multidrug-resistant strains of bacteria is increasing rapidly, while the number of new antibiotic discoveries has stagnated. This trend has caused a surge in interest in bacteriophages as anti-bacterial therapeutics, in part because there is near limitless diversity of phages to harness. While this diversity provides an opportunity, it also creates the dilemma of having to decide which criteria to use to select phages. Here we test whether a phage's ability to coevolve with its host (evolvability) should be considered and how this property compares to two previously proposed criteria: fast reproduction and thermostability. To do this, we compared the suppressiveness of three phages that vary by a single amino acid yet differ in these traits such that each strain maximized two of three characteristics. Our studies revealed that both evolvability and reproductive rate are independently important. The phage most able to suppress bacterial populations was the strain with high evolvability and reproductive rate, yet this phage was unstable. Phages varied due to differences in the types of resistance evolved against them and their ability to counteract resistance. When conditions were shifted to exaggerate the importance of thermostability, one of the stable phages was most suppressive in the short-term, but not over the long-term. Our results demonstrate the utility of biological therapeutics' capacities to evolve and adjust in action to resolve complications like resistance evolution. Furthermore, evolvability is a property that can be engineered into phage therapeutics to enhance their effectiveness.
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Affiliation(s)
- Elijah K. Horwitz
- Department of Ecology, Behavior and EvolutionUniversity of California San DiegoLa JollaCaliforniaUSA
| | - Hannah M. Strobel
- Department of Ecology, Behavior and EvolutionUniversity of California San DiegoLa JollaCaliforniaUSA
| | - Jason Haiso
- Department of Ecology, Behavior and EvolutionUniversity of California San DiegoLa JollaCaliforniaUSA
| | - Justin R. Meyer
- Department of Ecology, Behavior and EvolutionUniversity of California San DiegoLa JollaCaliforniaUSA
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Ulrich L, Steiner LX, Giez C, Lachnit T. Optimizing bacteriophage treatment of resistant Pseudomonas. mSphere 2024:e0070723. [PMID: 38934592 DOI: 10.1128/msphere.00707-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Accepted: 04/15/2024] [Indexed: 06/28/2024] Open
Abstract
Phage therapy is increasing in relevance as an alternative treatment to combat antibiotic resistant bacteria. Phage cocktails are the state-of-the-art method of administering phages in clinical settings, preferred over monophage treatment because of their ability to eliminate multiple bacterial strains and reduce resistance formation. In our study, we compare monophage applications and phage cocktails to our chosen method of phage sequential treatments. To do so, we isolated four novel bacteriophages capable of infecting Pseudomonas alcaligenes T3, a close relative of P. aeruginosa, and characterized them using sequencing and transmission electron microscopy. While investigating monophage treatments, we observed that different phage concentrations had a strong impact on the timing and amount of resistance formation. When using phage cocktails, we observed that P. alcaligenes were capable of forming resistance in the same timespan it took them to become resistant to single phages. We isolated mutants resistant to each single phage as well as mutants exposed to phage cocktails, resulting in bacteria resistant to all four phages at once. Sequencing these mutants showed that different treatments yielded unique single nucleotide polymorphism mutation patterns. In order to combat resistance formation, we added phages one by one in intervals of 24 h, thus managing to delay resistance development and keeping bacterial growth significantly lower compared to phage cocktails.IMPORTANCEWHO declared antimicrobial resistance a top threat to global health; while antibiotics have stood at the forefront in the fight against bacterial infection, the increasing number of multidrug-resistant bacteria highlights a need to branch out in order to address the threat of antimicrobial resistance. Bacteriophages, viruses solely infecting bacteria, could present a solution due to their abundance, versatility, and adaptability. For this study, we isolated new phages infecting a fast-mutating Pseudomonas alcaligenes strain capable of forming resistance within 30 h. By using a sequential treatment approach of adding one phage after another, we were able to curb bacterial growth significantly more compared to state-of-the-art phage cocktails.
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Affiliation(s)
- Laura Ulrich
- Zoological Institute, Christian-Albrechts Universität zu Kiel, Kiel, Germany
| | - Leon X Steiner
- RD3 Marine Ecology, RU Marine Symbioses, GEOMAR Helmholtz Centre for Ocean Research, Kiel, Germany
| | - Christoph Giez
- Zoological Institute, Christian-Albrechts Universität zu Kiel, Kiel, Germany
| | - Tim Lachnit
- Zoological Institute, Christian-Albrechts Universität zu Kiel, Kiel, Germany
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3
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Barrio-Pujante A, Bleriot I, Blasco L, Fernández-Garcia L, Pacios O, Ortiz-Cartagena C, Cuenca FF, Oteo-Iglesias J, Tomás M. Regulation of anti-phage defense mechanisms by using cinnamaldehyde as a quorum sensing inhibitor. Front Microbiol 2024; 15:1416628. [PMID: 38989015 PMCID: PMC11233531 DOI: 10.3389/fmicb.2024.1416628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Accepted: 06/12/2024] [Indexed: 07/12/2024] Open
Abstract
Background Multidrug-resistant bacteria and the shortage of new antibiotics constitute a serious health problem. This problem has led to increased interest in the use of bacteriophages, which have great potential as antimicrobial agents but also carry the risk of inducing resistance. The objective of the present study was to minimize the development of phage resistance in Klebsiella pneumoniae strains by inhibiting quorum sensing (QS) and thus demonstrate the role of QS in regulating defense mechanisms. Results Cinnamaldehyde (CAD) was added to K. pneumoniae cultures to inhibit QS and thus demonstrate the role of the signaling system in regulating the anti-phage defense mechanism. The QS inhibitory activity of CAD in K. pneumoniae was confirmed by a reduction in the quantitative expression of the lsrB gene (AI-2 pathway) and by proteomic analysis. The infection assays showed that the phage was able to infect a previously resistant K. pneumoniae strain in the cultures to which CAD was added. The results were confirmed using proteomic analysis. Thus, anti-phage defense-related proteins from different systems, such as cyclic oligonucleotide-based bacterial anti-phage signaling systems (CBASS), restriction-modification (R-M) systems, clustered regularly interspaced short palindromic repeat-Cas (CRISPR-Cas) system, and bacteriophage control infection (BCI), were present in the cultures with phage but not in the cultures with phage and CAD. When the QS and anti-phage defense systems were inhibited by the combined treatment, proteins related to phage infection and proliferation, such as the tail fiber protein, the cell division protein DamX, and the outer membrane channel protein TolC, were detected. Conclusion Inhibition of QS reduces phage resistance in K. pneumoniae, resulting in the infection of a previously resistant strain by phage, with a significant increase in phage proliferation and a significant reduction in bacterial growth. QS inhibitors could be considered for therapeutic application by including them in phage cocktails or in phage-antibiotic combinations to enhance synergistic effects and reduce the emergence of antimicrobial resistance.
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Affiliation(s)
- Antonio Barrio-Pujante
- Grupo de Microbiología Traslacional y Multidisciplinar (MicroTM)-Servicio de Microbiología Instituto de Investigación Biomédica A Coruña (INIBIC), Hospital A Coruña (CHUAC), Universidad de A Coruña (UDC), A Coruña, Spain
- Study Group on Mechanisms of Action and Resistance to Antimicrobials (GEMARA) the Behalf of the Spanish Society of Infectious Diseases and Clinical Microbiology (SEIMC), Madrid, Spain
| | - Inés Bleriot
- Grupo de Microbiología Traslacional y Multidisciplinar (MicroTM)-Servicio de Microbiología Instituto de Investigación Biomédica A Coruña (INIBIC), Hospital A Coruña (CHUAC), Universidad de A Coruña (UDC), A Coruña, Spain
- Study Group on Mechanisms of Action and Resistance to Antimicrobials (GEMARA) the Behalf of the Spanish Society of Infectious Diseases and Clinical Microbiology (SEIMC), Madrid, Spain
| | - Lucía Blasco
- Grupo de Microbiología Traslacional y Multidisciplinar (MicroTM)-Servicio de Microbiología Instituto de Investigación Biomédica A Coruña (INIBIC), Hospital A Coruña (CHUAC), Universidad de A Coruña (UDC), A Coruña, Spain
- Study Group on Mechanisms of Action and Resistance to Antimicrobials (GEMARA) the Behalf of the Spanish Society of Infectious Diseases and Clinical Microbiology (SEIMC), Madrid, Spain
| | - Laura Fernández-Garcia
- Grupo de Microbiología Traslacional y Multidisciplinar (MicroTM)-Servicio de Microbiología Instituto de Investigación Biomédica A Coruña (INIBIC), Hospital A Coruña (CHUAC), Universidad de A Coruña (UDC), A Coruña, Spain
- Study Group on Mechanisms of Action and Resistance to Antimicrobials (GEMARA) the Behalf of the Spanish Society of Infectious Diseases and Clinical Microbiology (SEIMC), Madrid, Spain
| | - Olga Pacios
- Grupo de Microbiología Traslacional y Multidisciplinar (MicroTM)-Servicio de Microbiología Instituto de Investigación Biomédica A Coruña (INIBIC), Hospital A Coruña (CHUAC), Universidad de A Coruña (UDC), A Coruña, Spain
- Study Group on Mechanisms of Action and Resistance to Antimicrobials (GEMARA) the Behalf of the Spanish Society of Infectious Diseases and Clinical Microbiology (SEIMC), Madrid, Spain
| | - Concha Ortiz-Cartagena
- Grupo de Microbiología Traslacional y Multidisciplinar (MicroTM)-Servicio de Microbiología Instituto de Investigación Biomédica A Coruña (INIBIC), Hospital A Coruña (CHUAC), Universidad de A Coruña (UDC), A Coruña, Spain
- Study Group on Mechanisms of Action and Resistance to Antimicrobials (GEMARA) the Behalf of the Spanish Society of Infectious Diseases and Clinical Microbiology (SEIMC), Madrid, Spain
| | - Felipe Fernández Cuenca
- Unidad Clínica de Enfermedades Infecciosas y Microbiología Clínica, Hospital Universitario Virgen Macarena, Instituto de Biomedicina de Sevilla (Hospital Universitario Virgen Macarena/CSIC/Universidad de Sevilla), Sevilla, Spain
- CIBER de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
- MEPRAM, Proyecto de Medicina de Precisión Contra las Resistencias Antimicrobianas, Madrid, Spain
| | - Jesús Oteo-Iglesias
- CIBER de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
- MEPRAM, Proyecto de Medicina de Precisión Contra las Resistencias Antimicrobianas, Madrid, Spain
- Laboratorio de Referencia e Investigación de Resistencias a Antibióticos e Infecciones Sanitarias, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
| | - María Tomás
- Grupo de Microbiología Traslacional y Multidisciplinar (MicroTM)-Servicio de Microbiología Instituto de Investigación Biomédica A Coruña (INIBIC), Hospital A Coruña (CHUAC), Universidad de A Coruña (UDC), A Coruña, Spain
- Study Group on Mechanisms of Action and Resistance to Antimicrobials (GEMARA) the Behalf of the Spanish Society of Infectious Diseases and Clinical Microbiology (SEIMC), Madrid, Spain
- MEPRAM, Proyecto de Medicina de Precisión Contra las Resistencias Antimicrobianas, Madrid, Spain
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4
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Lewis JM, Williams J, Sagona AP. Making the leap from technique to treatment - genetic engineering is paving the way for more efficient phage therapy. Biochem Soc Trans 2024; 52:1373-1384. [PMID: 38716972 DOI: 10.1042/bst20231289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 03/30/2024] [Accepted: 04/29/2024] [Indexed: 06/27/2024]
Abstract
Bacteriophages (phages) are viruses specific to bacteria that target them with great efficiency and specificity. Phages were first studied for their antibacterial potential in the early twentieth century; however, their use was largely eclipsed by the popularity of antibiotics. Given the surge of antimicrobial-resistant strains worldwide, there has been a renaissance in harnessing phages as therapeutics once more. One of the key advantages of phages is their amenability to modification, allowing the generation of numerous derivatives optimised for specific functions depending on the modification. These enhanced derivatives could display higher infectivity, expanded host range or greater affinity to human tissues, where some bacterial species exert their pathogenesis. Despite this, there has been a noticeable discrepancy between the generation of derivatives in vitro and their clinical application in vivo. In most instances, phage therapy is only used on a compassionate-use basis, where all other treatment options have been exhausted. A lack of clinical trials and numerous regulatory hurdles hamper the progress of phage therapy and in turn, the engineered variants, in becoming widely used in the clinic. In this review, we outline the various types of modifications enacted upon phages and how these modifications contribute to their enhanced bactericidal function compared with wild-type phages. We also discuss the nascent progress of genetically modified phages in clinical trials along with the current issues these are confronted with, to validate it as a therapy in the clinic.
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Affiliation(s)
- Jessica M Lewis
- School of Life Sciences, University of Warwick, Coventry, U.K
| | - Joshua Williams
- School of Life Sciences, University of Warwick, Coventry, U.K
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5
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Ziller L, Blum PC, Buhl EM, Krüttgen A, Horz HP, Tagliaferri TL. Newly isolated Drexlerviridae phage LAPAZ is physically robust and fosters eradication of Klebsiella pneumoniae in combination with meropenem. Virus Res 2024; 347:199417. [PMID: 38880333 DOI: 10.1016/j.virusres.2024.199417] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 06/11/2024] [Accepted: 06/13/2024] [Indexed: 06/18/2024]
Abstract
Due to the spread of multidrug resistance there is a renewed interest in using bacteriophages (briefly: phages) for controlling bacterial pathogens. The objective of this study was the characterization of a newly isolated phage (i.e. phage LAPAZ, vB_KpnD-LAPAZ), its antimicrobial activity against multidrug resistant Klebsiella pneumoniae and potential synergistic interactions with antibiotics. LAPAZ belongs to the family Drexlerviridae (genus: Webervirus) and lysed 30 % of tested strains, whereby four distinct capsular types can be infected. The genome consists of 51,689 bp and encodes 84 ORFs. The latent period is 30 min with an average burst size of 27 PFU/cell. Long-term storage experiments show that LAPAZ is significantly more stable in wastewater compared to laboratory media. A phage titre of 90 % persists up to 30 min at 50 ˚C and entire phage loss was seen only at temperatures > 66 ˚C. Besides stability against UV-C, antibacterial activity in liquid culture medium was consistent at pH values ranging from 4 to 10. Unlike exposure to phage or antibiotic alone, synergistic interactions and a complete bacterial eradication was achieved when combining LAPAZ with meropenem. In addition, synergism with the co-presence of ciprofloxacin was observed and phage resistance emergence could be delayed. Without co-addition of the antibiotic, phage resistant mutants readily emerged and showed a mixed pattern of drug sensitivity alterations. Around 88 % became less sensitive towards ceftazidime, meropenem and gentamicin. Conversely, around 44 % showed decreased resistance levels against ciprofloxacin. Whole genome analysis of a phage-resistant mutant with a 16-fold increased sensitivity towards ciprofloxacin revealed one de novo frameshift mutation leading to a gene fusion affecting two transport proteins belonging to the major facilitator-superfamily (MFS). Apparently, this mutation compromises ciprofloxacin efflux efficiency and further studies are warranted to understand how the non-mutated protein might be involved in phage-host adsorption.
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Affiliation(s)
- Leonie Ziller
- Institute of Medical Microbiology, RWTH Aachen University Hospital, 52074 Aachen, Germany
| | | | - Eva Miriam Buhl
- Electron Microscopy Facility, RWTH Aachen University Hospital, 52074 Aachen, Germany
| | - Alex Krüttgen
- Laboratory Diagnostic Center, RWTH Aachen University Hospital, 52074 Aachen, Germany
| | - Hans-Peter Horz
- Institute of Medical Microbiology, RWTH Aachen University Hospital, 52074 Aachen, Germany.
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6
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Bernabéu-Gimeno M, Pardo-Freire M, Chan BK, Turner PE, Gil-Brusola A, Pérez-Tarazona S, Carrasco-Hernández L, Quintana-Gallego E, Domingo-Calap P. Neutralizing antibodies after nebulized phage therapy in cystic fibrosis patients. MED 2024:S2666-6340(24)00221-6. [PMID: 38917792 DOI: 10.1016/j.medj.2024.05.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Revised: 04/02/2024] [Accepted: 05/30/2024] [Indexed: 06/27/2024]
Abstract
BACKGROUND Cystic fibrosis (CF) patients are prone to recurrent multi-drug-resistant (MDR) bacterial lung infections. Under this scenario, phage therapy has been proposed as a promising tool. However, the limited number of reported cases hampers the understanding of clinical outcomes. Anti-phage immune responses have often been overlooked and only described following invasive routes of administration. METHODS Three monophage treatments against Staphylococcus aureus and/or Pseudomonas aeruginosa lung infections were conducted in cystic fibrosis patients. In-house phage preparations were nebulized over 10 days with standard-of-care antibiotics. Clinical indicators, bacterial counts, phage and antibiotic susceptibility, phage detection, and immune responses were monitored. FINDINGS Bacterial load was reduced by 3-6 log in two of the treatments. No adverse events were described. Phages remained in sputum up to 33 days after completion of the treatment. In all cases, phage-neutralizing antibodies were detected in serum from 10 to 42 days post treatment, with this being the first report of anti-phage antibodies after nebulized therapy. CONCLUSIONS Nebulized phage therapy reduced bacterial load, improving quality of life even without bacterial eradication. The emergence of antibodies emphasizes the importance of long-term monitoring to better understand clinical outcomes. These findings encourage the use of personalized monophage therapies in contrast to ready-to-use cocktails, which might induce undesirable antibody generation. FUNDING This study was supported by the Spanish Ministry of Science, Innovation and Universities; Generalitat Valenciana; and a crowdfunding in collaboration with the Spanish Cystic Fibrosis Foundation.
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Affiliation(s)
- Mireia Bernabéu-Gimeno
- Institute for Integrative Systems Biology, University of Valencia-CSIC, 46980 Paterna, Spain
| | - Marco Pardo-Freire
- Institute for Integrative Systems Biology, University of Valencia-CSIC, 46980 Paterna, Spain
| | - Benjamin K Chan
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520, USA; Center for Phage Biology and Therapy, Yale University, New Haven, CT 06520, USA
| | - Paul E Turner
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520, USA; Center for Phage Biology and Therapy, Yale University, New Haven, CT 06520, USA; Program in Microbiology, Yale School of Medicine, New Haven, CT 06520, USA
| | - Ana Gil-Brusola
- Microbiology Department, La Fe University and Polytechnic Hospital, 46026 Valencia, Spain; Severe Infection Research Group, Health Research Institute La Fe, 46026 Valencia, Spain
| | - Santiago Pérez-Tarazona
- Pediatric Pulmonology Unit, La Fe University and Polytechnic Hospital, 46026 Valencia, Spain
| | - Laura Carrasco-Hernández
- Medical-Surgical Unit of Respiratory Diseases, Virgen del Rocío University Hospital, 41013 Sevilla, Spain; CIBER Respiratory Diseases (CIBERES), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Esther Quintana-Gallego
- Medical-Surgical Unit of Respiratory Diseases, Virgen del Rocío University Hospital, 41013 Sevilla, Spain; CIBER Respiratory Diseases (CIBERES), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Pilar Domingo-Calap
- Institute for Integrative Systems Biology, University of Valencia-CSIC, 46980 Paterna, Spain.
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7
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Al-Anany AM, Fatima R, Nair G, Mayol JT, Hynes AP. Temperate phage-antibiotic synergy across antibiotic classes reveals new mechanism for preventing lysogeny. mBio 2024; 15:e0050424. [PMID: 38757974 DOI: 10.1128/mbio.00504-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Accepted: 04/18/2024] [Indexed: 05/18/2024] Open
Abstract
A recent demonstration of synergy between a temperate phage and the antibiotic ciprofloxacin suggested a scalable approach to exploiting temperate phages in therapy, termed temperate phage-antibiotic synergy, which specifically interacted with the lysis-lysogeny decision. To determine whether this would hold true across antibiotics, we challenged Escherichia coli with the phage HK97 and a set of 13 antibiotics spanning seven classes. As expected, given the conserved induction pathway, we observed synergy with classes of drugs known to induce an SOS response: a sulfa drug, other quinolones, and mitomycin C. While some β-lactams exhibited synergy, this appeared to be traditional phage-antibiotic synergy, with no effect on the lysis-lysogeny decision. Curiously, we observed a potent synergy with antibiotics not known to induce the SOS response: protein synthesis inhibitors gentamicin, kanamycin, tetracycline, and azithromycin. The synergy results in an eightfold reduction in the effective minimum inhibitory concentration of gentamicin, complete eradication of the bacteria, and, when administered at sub-optimal doses, drastically decreases the frequency of lysogens emerging from the combined challenge. However, lysogens exhibit no increased sensitivity to the antibiotic; synergy was maintained in the absence of RecA; and the antibiotic reduced the initial frequency of lysogeny rather than selecting against formed lysogens. Our results confirm that SOS-inducing antibiotics broadly result in temperate-phage-specific synergy, but that other antibiotics can interact with temperate phages specifically and result in synergy. This is the first report of a means of chemically blocking entry into lysogeny, providing a new means for manipulating the key lysis-lysogeny decision.IMPORTANCEThe lysis-lysogeny decision is made by most bacterial viruses (bacteriophages, phages), determining whether to kill their host or go dormant within it. With over half of the bacteria containing phages waiting to wake, this is one of the most important behaviors in all of biology. These phages are also considered unusable for therapy because of this behavior. In this paper, we show that many antibiotics bias this behavior to "wake" the dormant phages, forcing them to kill their host, but some also prevent dormancy in the first place. These will be important tools to study this critical decision point and may enable the therapeutic use of these phages.
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Affiliation(s)
- Amany M Al-Anany
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Rabia Fatima
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Gayatri Nair
- Department of Medicine, McMaster University, Hamilton, Ontario, Canada
| | - Jordan T Mayol
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Alexander P Hynes
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
- Department of Medicine, McMaster University, Hamilton, Ontario, Canada
- Farncombe Family Digestive Health Research Institute, McMaster University, Hamilton, Ontario, Canada
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada
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8
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Zeng X, Liang S, Dong J, Gao G, Hu Y, Sun Y. The trade-off of Vibrio parahaemolyticus between bacteriophage resistance and growth competitiveness. Front Microbiol 2024; 15:1346251. [PMID: 38919495 PMCID: PMC11196418 DOI: 10.3389/fmicb.2024.1346251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Accepted: 04/10/2024] [Indexed: 06/27/2024] Open
Abstract
Vibrio parahaemolyticus is a food-borne pathogen, which is often isolated from various seafood products. In this study, two kinds of bacteriophages was isolated from the offshore sediments samples. The anti-phage mutant strain were obtained after seventeen rounds of co-culture of Vibrio parahaemolyticus and mixed bacteriophage, multigroup sequencing was carried out on spontaneous the anti-phage mutant strain and the wild-type strain. We used the Sanger sequencing to verify the accuracy of the mutation sites. Biolog GEN III MicroPlates were used to evaluate the metabolic capacity of wild-type strains and the anti-phage mutant strain. In this study, we found that with flaG gene (slight homology to N terminus of multiple flagellins) mutated, making the bacteriophage unable to absorb to the cell surface of the host. And, the growth competitiveness of the anti-phage mutant strain is lower than the wild-type strain. These results indicated that the fitness cost, including loss of the growth competitiveness, constitutes a barrier to the prevalence of these defense mechanisms. And the selection pressure on different anti-phage strategies depends on the trade-off between mortality imposed by bacteriophages and fitness cost of the defense strategy under the given environmental conditions. In conclusion, this study provides valuable insights into the phage-host interaction and phage resistance in Vibrio parahaemolyticus. Our study provided knowledge for the evolutionary adaption of bacteria against the bacteriophage, which could add more information to understand the phage resistance mechanism before applying in the industry.
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Affiliation(s)
- Xiuxiu Zeng
- Guoke Ningbo Life Science and Health Industry Research Institute, Ningbo, Zhejiang, China
| | | | - Jiayi Dong
- Guoke Ningbo Life Science and Health Industry Research Institute, Ningbo, Zhejiang, China
| | | | - Yaoren Hu
- Ningbo Hospital, Ningbo, Zhejiang, China
| | - Yuechao Sun
- Guoke Ningbo Life Science and Health Industry Research Institute, Ningbo, Zhejiang, China
- Ningbo Hospital, Ningbo, Zhejiang, China
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9
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Pirnay JP, Djebara S, Steurs G, Griselain J, Cochez C, De Soir S, Glonti T, Spiessens A, Vanden Berghe E, Green S, Wagemans J, Lood C, Schrevens E, Chanishvili N, Kutateladze M, de Jode M, Ceyssens PJ, Draye JP, Verbeken G, De Vos D, Rose T, Onsea J, Van Nieuwenhuyse B, Soentjens P, Lavigne R, Merabishvili M. Personalized bacteriophage therapy outcomes for 100 consecutive cases: a multicentre, multinational, retrospective observational study. Nat Microbiol 2024; 9:1434-1453. [PMID: 38834776 PMCID: PMC11153159 DOI: 10.1038/s41564-024-01705-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Accepted: 04/19/2024] [Indexed: 06/06/2024]
Abstract
In contrast to the many reports of successful real-world cases of personalized bacteriophage therapy (BT), randomized controlled trials of non-personalized bacteriophage products have not produced the expected results. Here we present the outcomes of a retrospective observational analysis of the first 100 consecutive cases of personalized BT of difficult-to-treat infections facilitated by a Belgian consortium in 35 hospitals, 29 cities and 12 countries during the period from 1 January 2008 to 30 April 2022. We assessed how often personalized BT produced a positive clinical outcome (general efficacy) and performed a regression analysis to identify functional relationships. The most common indications were lower respiratory tract, skin and soft tissue, and bone infections, and involved combinations of 26 bacteriophages and 6 defined bacteriophage cocktails, individually selected and sometimes pre-adapted to target the causative bacterial pathogens. Clinical improvement and eradication of the targeted bacteria were reported for 77.2% and 61.3% of infections, respectively. In our dataset of 100 cases, eradication was 70% less probable when no concomitant antibiotics were used (odds ratio = 0.3; 95% confidence interval = 0.127-0.749). In vivo selection of bacteriophage resistance and in vitro bacteriophage-antibiotic synergy were documented in 43.8% (7/16 patients) and 90% (9/10) of evaluated patients, respectively. We observed a combination of antibiotic re-sensitization and reduced virulence in bacteriophage-resistant bacterial isolates that emerged during BT. Bacteriophage immune neutralization was observed in 38.5% (5/13) of screened patients. Fifteen adverse events were reported, including seven non-serious adverse drug reactions suspected to be linked to BT. While our analysis is limited by the uncontrolled nature of these data, it indicates that BT can be effective in combination with antibiotics and can inform the design of future controlled clinical trials. BT100 study, ClinicalTrials.gov registration: NCT05498363 .
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Affiliation(s)
- Jean-Paul Pirnay
- Laboratory for Molecular and Cellular Technology, Queen Astrid Military Hospital, Brussels, Belgium.
- European Society of Clinical Microbiology and Infectious Diseases (ESCMID) Study Group for Non-traditional Antibacterial Therapy (ESGNTA), Basel, Switzerland.
| | - Sarah Djebara
- Center for Infectious Diseases, Queen Astrid Military Hospital, Brussels, Belgium
| | - Griet Steurs
- Laboratory for Molecular and Cellular Technology, Queen Astrid Military Hospital, Brussels, Belgium
| | - Johann Griselain
- Laboratory for Molecular and Cellular Technology, Queen Astrid Military Hospital, Brussels, Belgium
| | - Christel Cochez
- Laboratory for Molecular and Cellular Technology, Queen Astrid Military Hospital, Brussels, Belgium
| | - Steven De Soir
- Laboratory for Molecular and Cellular Technology, Queen Astrid Military Hospital, Brussels, Belgium
| | - Tea Glonti
- Laboratory for Molecular and Cellular Technology, Queen Astrid Military Hospital, Brussels, Belgium
| | - An Spiessens
- Center for Infectious Diseases, Queen Astrid Military Hospital, Brussels, Belgium
| | - Emily Vanden Berghe
- Center for Infectious Diseases, Queen Astrid Military Hospital, Brussels, Belgium
| | - Sabrina Green
- Laboratory of Gene Technology, Department of Biosystems, KU Leuven, Leuven, Belgium
| | - Jeroen Wagemans
- Laboratory of Gene Technology, Department of Biosystems, KU Leuven, Leuven, Belgium
| | - Cédric Lood
- Laboratory of Gene Technology, Department of Biosystems, KU Leuven, Leuven, Belgium
| | | | - Nina Chanishvili
- Eliava Institute of Bacteriophages, Microbiology and Virology, Tbilisi, Georgia
| | - Mzia Kutateladze
- Eliava Institute of Bacteriophages, Microbiology and Virology, Tbilisi, Georgia
| | | | | | - Jean-Pierre Draye
- Laboratory for Molecular and Cellular Technology, Queen Astrid Military Hospital, Brussels, Belgium
| | - Gilbert Verbeken
- Laboratory for Molecular and Cellular Technology, Queen Astrid Military Hospital, Brussels, Belgium
| | - Daniel De Vos
- Laboratory for Molecular and Cellular Technology, Queen Astrid Military Hospital, Brussels, Belgium
| | - Thomas Rose
- Laboratory for Molecular and Cellular Technology, Queen Astrid Military Hospital, Brussels, Belgium
| | - Jolien Onsea
- Department of Trauma Surgery, University Hospitals Leuven; Department of Development and Regeneration, KU Leuven, Leuven, Belgium
| | - Brieuc Van Nieuwenhuyse
- Institute of Experimental and Clinical Research, Pediatric Department, UCLouvain, Brussels, Belgium
| | - Patrick Soentjens
- Center for Infectious Diseases, Queen Astrid Military Hospital, Brussels, Belgium
| | - Rob Lavigne
- Laboratory of Gene Technology, Department of Biosystems, KU Leuven, Leuven, Belgium
| | - Maya Merabishvili
- Laboratory for Molecular and Cellular Technology, Queen Astrid Military Hospital, Brussels, Belgium
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10
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De Meester L, Vázquez-Domínguez E, Kassen R, Forest F, Bellon MR, Koskella B, Scherson RA, Colli L, Hendry AP, Crandall KA, Faith DP, Starger CJ, Geeta R, Araki H, Dulloo EM, Souffreau C, Schroer S, Johnson MTJ. A link between evolution and society fostering the UN sustainable development goals. Evol Appl 2024; 17:e13728. [PMID: 38884021 PMCID: PMC11178947 DOI: 10.1111/eva.13728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 05/16/2024] [Accepted: 05/17/2024] [Indexed: 06/18/2024] Open
Abstract
Given the multitude of challenges Earth is facing, sustainability science is of key importance to our continued existence. Evolution is the fundamental biological process underlying the origin of all biodiversity. This phylogenetic diversity fosters the resilience of ecosystems to environmental change, and provides numerous resources to society, and options for the future. Genetic diversity within species is also key to the ability of populations to evolve and adapt to environmental change. Yet, the value of evolutionary processes and the consequences of their impairment have not generally been considered in sustainability research. We argue that biological evolution is important for sustainability and that the concepts, theory, data, and methodological approaches used in evolutionary biology can, in crucial ways, contribute to achieving the UN Sustainable Development Goals (SDGs). We discuss how evolutionary principles are relevant to understanding, maintaining, and improving Nature Contributions to People (NCP) and how they contribute to the SDGs. We highlight specific applications of evolution, evolutionary theory, and evolutionary biology's diverse toolbox, grouped into four major routes through which evolution and evolutionary insights can impact sustainability. We argue that information on both within-species evolutionary potential and among-species phylogenetic diversity is necessary to predict population, community, and ecosystem responses to global change and to make informed decisions on sustainable production, health, and well-being. We provide examples of how evolutionary insights and the tools developed by evolutionary biology can not only inspire and enhance progress on the trajectory to sustainability, but also highlight some obstacles that hitherto seem to have impeded an efficient uptake of evolutionary insights in sustainability research and actions to sustain SDGs. We call for enhanced collaboration between sustainability science and evolutionary biology to understand how integrating these disciplines can help achieve the sustainable future envisioned by the UN SDGs.
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Affiliation(s)
- Luc De Meester
- Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB) Berlin Germany
- Laboratory of Aquatic Ecology, Evolution and Conservation KU Leuven Leuven Belgium
- Institute of Biology Freie University Berlin Berlin Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB) Berlin Germany
| | - Ella Vázquez-Domínguez
- Departamento de Ecología de la Biodiversidad, Instituto de Ecología, Universidad Nacional Autónoma de México Ciudad Universitaria Ciudad de México Mexico
- Conservation and Evolutionary Genetics Group Estación Biológica de Doñana (EBD-CSIC) Sevilla Spain
| | - Rees Kassen
- Department of Biology McGill University Montreal Quebec Canada
| | | | - Mauricio R Bellon
- Comisión Nacional Para el Conocimiento y Uso de la Biodiversidad (CONABIO) México City Mexico
- Swette Center for Sustainable Food Systems Arizona State University Tempe Arizona USA
| | - Britt Koskella
- Department of Integrative Biology University of California Berkeley California USA
| | - Rosa A Scherson
- Laboratorio Evolución y Sistemática, Departamento de Silvicultura y Conservación de la Naturaleza Universidad de Chile Santiago Chile
| | - Licia Colli
- Dipartimento di Scienze Animali, Della Nutrizione e Degli Alimenti, BioDNA Centro di Ricerca Sulla Biodiversità e Sul DNA Antico, Facoltà di Scienze Agrarie, Alimentari e Ambientali Università Cattolica del Sacro Cuore Piacenza Italy
| | - Andrew P Hendry
- Redpath Museum & Department of Biology McGill University Montreal Quebec Canada
| | - Keith A Crandall
- Department of Biostatistics and Bioinformatics George Washington University Washington DC USA
- Department of Invertebrate Zoology, US National Museum of Natural History Smithsonian Institution Washington DC USA
| | | | - Craig J Starger
- School of Global Environmental Sustainability Colorado State University Fort Collins Colorado USA
| | - R Geeta
- Department of Botany University of Delhi New Delhi India
| | - Hitoshi Araki
- Research Faculty of Agriculture Hokkaido University Sapporo Japan
| | - Ehsan M Dulloo
- Effective Genetic Resources Conservation and Use Alliance of Bioversity International and CIAT Rome Italy
| | - Caroline Souffreau
- Laboratory of Aquatic Ecology, Evolution and Conservation KU Leuven Leuven Belgium
| | - Sibylle Schroer
- Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB) Berlin Germany
| | - Marc T J Johnson
- Department of Biology & Centre for Urban Environments University of Toronto Mississauga Mississauga Ontario Canada
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11
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Khosravi A, Chen Q, Echterhof A, Koff JL, Bollyky PL. Phage Therapy for Respiratory Infections: Opportunities and Challenges. Lung 2024; 202:223-232. [PMID: 38772946 DOI: 10.1007/s00408-024-00700-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Accepted: 04/13/2024] [Indexed: 05/23/2024]
Abstract
We are entering the post-antibiotic era. Antimicrobial resistance (AMR) is a critical problem in chronic lung infections resulting in progressive respiratory failure and increased mortality. In the absence of emerging novel antibiotics to counter AMR infections, bacteriophages (phages), viruses that infect bacteria, have become a promising option for chronic respiratory infections. However, while personalized phage therapy is associated with improved outcomes in individual cases, clinical trials demonstrating treatment efficacy are lacking, limiting the therapeutic potential of this approach for respiratory infections. In this review, we address the current state of phage therapy for managing chronic respiratory diseases. We then discuss how phage therapy may address major microbiologic obstacles which hinder disease resolution of chronic lung infections with current antibiotic-based treatment practices. Finally, we highlight the challenges that must be addressed for successful phage therapy clinical trials. Through this discussion, we hope to expand on the potential of phages as an adjuvant therapy in chronic lung infections, as well as the microbiologic challenges that need to be addressed for phage therapy to expand beyond personalized salvage therapy.
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Affiliation(s)
- Arya Khosravi
- Division of Infectious Diseases, School of Medicine, Stanford University, Stanford, CA, USA.
- Division of Infectious Diseases, Department of Medicine, Stanford University, 279 Campus Drive, Beckman Center, Room B237, Stanford, CA, 94305, USA.
| | - Qingquan Chen
- Division of Infectious Diseases, School of Medicine, Stanford University, Stanford, CA, USA
| | - Arne Echterhof
- Division of Infectious Diseases, School of Medicine, Stanford University, Stanford, CA, USA
| | - Jonathan L Koff
- Section of Pulmonary, Critical Care & Sleep Medicine, School of Medicine, Yale University, New Haven, CT, USA
| | - Paul L Bollyky
- Division of Infectious Diseases, School of Medicine, Stanford University, Stanford, CA, USA
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12
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Kovacs CJ, Rapp EM, McKenzie SM, Mazur MZ, Mchale RP, Brasko B, Min MY, Burpo FJ, Barnhill JC. Disruption of Biofilm by Bacteriophages in Clinically Relevant Settings. Mil Med 2024; 189:e1294-e1302. [PMID: 37847552 DOI: 10.1093/milmed/usad385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 07/29/2023] [Accepted: 09/19/2023] [Indexed: 10/18/2023] Open
Abstract
INTRODUCTION Antibiotic-resistant bacteria are a growing threat to civilian and military health today. Although infections were once easily treatable by antibiotics and wound cleaning, the frequent mutation of bacteria has created strains impermeable to antibiotics and physical attack. Bacteria further their pathogenicity because of their ability to form biofilms on wounds, medical devices, and implant surfaces. Methods for treating biofilms in clinical settings are limited, and when formed by antibiotic-resistant bacteria, can generate chronic infections that are recalcitrant to available therapies. Bacteriophages are natural viral predators of bacteria, and their ability to rapidly destroy their host has led to increased attention in potential phage therapy applications. MATERIALS AND METHODS The present article sought to address a knowledge gap in the available literature pertaining to the usage of bacteriophage in clinically relevant settings and the resolution of infections particular to military concerns. PRISMA guidelines were followed for a systematic review of available literature that met the criteria for analysis and inclusion. The research completed for this review article originated from the U.S. Military Academy's library "Scout" search engine, which complies results from 254 available databases (including PubMed, Google Scholar, and SciFinder). The search criteria included original studies that employed bacteriophage use against biofilms, as well as successful phage therapy strategies for combating chronic bacterial infections. We specifically explored the use of bacteriophage against antibiotic- and treatment-resistant bacteria. RESULTS A total of 80 studies were identified that met the inclusion criteria following PRISMA guidelines. The application of bacteriophage has been demonstrated to robustly disrupt biofilm growth in wounds and on implant surfaces. When traditional therapies have failed to disrupt biofilms and chronic infections, a combination of these treatments with phage has proven to be effective, often leading to complete wound healing without reinfection. CONCLUSIONS This review article examines the available literature where bacteriophages have been utilized to treat biofilms in clinically relevant settings. Specific attention is paid to biofilms on implant medical devices, biofilms formed on wounds, and clinical outcomes, where phage treatment has been efficacious. In addition to the clinical benefit of phage therapies, the military relevance and treatment of combat-related infections is also examined. Phages offer the ability to expand available treatment options in austere environments with relatively low cost and effort, allowing the impacted warfighter to return to duty quicker and healthier.
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Affiliation(s)
- Christopher J Kovacs
- Department of Chemistry and Life Science, United States Military Academy, West Point, NY 10996, USA
- Defense Threat Reduction Agency, Fort Belvoir, VA 22060, USA
| | - Erika M Rapp
- Department of Chemistry and Life Science, United States Military Academy, West Point, NY 10996, USA
| | - Sophia M McKenzie
- Department of Chemistry and Life Science, United States Military Academy, West Point, NY 10996, USA
| | - Michael Z Mazur
- Department of Chemistry and Life Science, United States Military Academy, West Point, NY 10996, USA
| | - Riley P Mchale
- Department of Chemistry and Life Science, United States Military Academy, West Point, NY 10996, USA
| | - Briana Brasko
- Department of Chemistry and Life Science, United States Military Academy, West Point, NY 10996, USA
| | - Michael Y Min
- Department of Chemistry and Life Science, United States Military Academy, West Point, NY 10996, USA
| | - F John Burpo
- Department of Chemistry and Life Science, United States Military Academy, West Point, NY 10996, USA
| | - Jason C Barnhill
- Department of Chemistry and Life Science, United States Military Academy, West Point, NY 10996, USA
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13
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Wang B, Du L, Dong B, Kou E, Wang L, Zhu Y. Current Knowledge and Perspectives of Phage Therapy for Combating Refractory Wound Infections. Int J Mol Sci 2024; 25:5465. [PMID: 38791502 PMCID: PMC11122179 DOI: 10.3390/ijms25105465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Revised: 05/09/2024] [Accepted: 05/15/2024] [Indexed: 05/26/2024] Open
Abstract
Wound infection is one of the most important factors affecting wound healing, so its effective control is critical to promote the process of wound healing. However, with the increasing prevalence of multi-drug-resistant (MDR) bacterial strains, the prevention and treatment of wound infections are now more challenging, imposing heavy medical and financial burdens on patients. Furthermore, the diminishing effectiveness of conventional antimicrobials and the declining research on new antibiotics necessitate the urgent exploration of alternative treatments for wound infections. Recently, phage therapy has been revitalized as a promising strategy to address the challenges posed by bacterial infections in the era of antibiotic resistance. The use of phage therapy in treating infectious diseases has demonstrated positive results. This review provides an overview of the mechanisms, characteristics, and delivery methods of phage therapy for combating pathogenic bacteria. Then, we focus on the clinical application of various phage therapies in managing refractory wound infections, such as diabetic foot infections, as well as traumatic, surgical, and burn wound infections. Additionally, an analysis of the potential obstacles and challenges of phage therapy in clinical practice is presented, along with corresponding strategies for addressing these issues. This review serves to enhance our understanding of phage therapy and provides innovative avenues for addressing refractory infections in wound healing.
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Affiliation(s)
- Bo Wang
- Department of Dermatology, Naval Medical Center, Naval Medical University, Shanghai 200052, China
| | - Lin Du
- Department of Dermatology, Naval Medical Center, Naval Medical University, Shanghai 200052, China
| | - Baiping Dong
- Department of Dermatology, Naval Medical Center, Naval Medical University, Shanghai 200052, China
| | - Erwen Kou
- Department of Dermatology, Naval Medical Center, Naval Medical University, Shanghai 200052, China
| | - Liangzhe Wang
- Department of Dermatology, Naval Medical Center, Naval Medical University, Shanghai 200052, China
| | - Yuanjie Zhu
- Department of Dermatology, Naval Medical Center, Naval Medical University, Shanghai 200052, China
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14
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Fujiki J, Nakamura K, Ishiguro Y, Iwano H. Using phage to drive selections toward restoring antibiotic sensitivity in Pseudomonas aeruginosa via chromosomal deletions. Front Microbiol 2024; 15:1401234. [PMID: 38812675 PMCID: PMC11133617 DOI: 10.3389/fmicb.2024.1401234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Accepted: 05/03/2024] [Indexed: 05/31/2024] Open
Abstract
Phage therapy has re-emerged in modern medicine as a robust antimicrobial strategy in response to the increasing prevalence of antimicrobial-resistant bacteria. However, bacterial resistance to phages can also arise via a variety of molecular mechanisms. In fact, several clinical studies on phage therapy have reported the occurrence of phage-resistant variants, representing a significant concern for the successful development of phage-based therapies. In this context, the fitness trade-offs between phage and antibiotic resistance have revealed new avenues in the field of phage therapy as a countermeasure against phage resistance. This strategy forces to restore the antibiotic susceptibility of antimicrobial-resistant bacteria as compensation for the development of phage resistance. Here, we present the key achievements of these fitness trade-offs, notably focusing on the enhancement of antibiotic sensitivity through the induction of large chromosomal deletions by bacteriophage infection. We also describe the challenges of this strategy that need to be overcome to promote favorable therapeutic outcomes and discuss future directions. The insights gained from the trade-offs between phage and antibiotic sensitivity will help maximize the potential of phage therapy for the treatment of infectious diseases.
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Affiliation(s)
- Jumpei Fujiki
- School of Veterinary Medicine, Rakuno Gakuen University, Ebetsu, Japan
| | - Keisuke Nakamura
- School of Veterinary Medicine, Rakuno Gakuen University, Ebetsu, Japan
| | - Yuko Ishiguro
- School of Veterinary Medicine, Rakuno Gakuen University, Ebetsu, Japan
| | - Hidetomo Iwano
- School of Veterinary Medicine, Rakuno Gakuen University, Ebetsu, Japan
- Phage Therapy Institute, Waseda University, Tokyo, Japan
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15
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Duan S, Zhang Z, Wang X, Sun Y, Dong Y, Ren L, Geng L, Xiu Z. Co-production of 1,3-propanediol and phage phiKpS2 from the glycerol fermentation by Klebsiella pneumoniae. BIORESOUR BIOPROCESS 2024; 11:44. [PMID: 38722416 PMCID: PMC11082122 DOI: 10.1186/s40643-024-00760-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Accepted: 04/18/2024] [Indexed: 05/12/2024] Open
Abstract
As an alternative to antibiotics in response to antimicrobial-resistant infections, bacteriophages (phages) are garnering renewed interest in recent years. However, the massive preparation of phage is restricted using traditional pathogens as host cells, which incurs additional costs and contamination. In this study, an opportunistic pathogen, Klebsiella pneumoniae used to convert glycerol to 1,3-propanediol (1,3-PDO), was reused to prepare phage after fermentation. The phage infection showed that the fed-batch fermentation broth containing 71.6 g/L 1,3-PDO can be directly used for preparation of phage with a titer of 1 × 108 pfu/mL. Then, the two-step salting-out extraction was adopted to remove most impurities, e.g. acetic acid (93.5%), ethanol (91.5%) and cells (99.4%) at the first step, and obtain 1,3-PDO (56.6%) in the top phase as well as phage (97.4%) in the middle phase at the second step. This integrated process provides a cheap and environment-friendly manner for coproduction of 1,3-PDO and phage.
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Affiliation(s)
- Suyang Duan
- School of Bioengineering, Dalian University of Technology, Linggong Road 2, Dalian, 116024, P. R. China
| | - Zhirong Zhang
- School of Bioengineering, Dalian University of Technology, Linggong Road 2, Dalian, 116024, P. R. China
| | - Xiaoli Wang
- School of Bioengineering, Dalian University of Technology, Linggong Road 2, Dalian, 116024, P. R. China
| | - Yaqin Sun
- School of Bioengineering, Dalian University of Technology, Linggong Road 2, Dalian, 116024, P. R. China
| | - Yuesheng Dong
- School of Bioengineering, Dalian University of Technology, Linggong Road 2, Dalian, 116024, P. R. China
| | - Lina Ren
- Department of Respiratory, Affiliated Dalian Municipal Central Hospital of Dalian University of Technology, Dalian, 116033, Liaoning, P. R. China
| | - Lili Geng
- Department of Respiratory, Affiliated Dalian Municipal Central Hospital of Dalian University of Technology, Dalian, 116033, Liaoning, P. R. China
| | - Zhilong Xiu
- School of Bioengineering, Dalian University of Technology, Linggong Road 2, Dalian, 116024, P. R. China.
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16
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Li H, Xu H. Mechanisms of bacterial resistance to environmental silver and antimicrobial strategies for silver: A review. ENVIRONMENTAL RESEARCH 2024; 248:118313. [PMID: 38280527 DOI: 10.1016/j.envres.2024.118313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 01/22/2024] [Accepted: 01/23/2024] [Indexed: 01/29/2024]
Abstract
The good antimicrobial properties of silver make it widely used in food, medicine, and environmental applications. However, the release and accumulation of silver-based antimicrobial agents in the environment is increasing with the extensive use of silver-based antimicrobials, and the prevalence of silver-resistant bacteria is increasing. To prevent the emergence of superbugs, it is necessary to exercise rational and strict control over drug use. The mechanism of bacterial resistance to silver has not been fully elucidated, and this article provides a review of the progress of research on the mechanism of bacterial resistance to silver. The results indicate that bacterial resistance to silver can occur through inducing silver particles aggregation and Ag+ reduction, inhibiting silver contact with and entry into cells, efflux of silver particles and Ag+ in cells, and activation of damage repair mechanisms. We propose that the bacterial mechanism of silver resistance involves a combination of interrelated systems. Finally, we discuss how this information can be used to develop the next generation of silver-based antimicrobials and antimicrobial therapies. And some antimicrobial strategies are proposed such as the "Trojan Horse" - camouflage, using efflux pump inhibitors to reduce silver efflux, working with "minesweeper", immobilization of silver particles.
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Affiliation(s)
- Hui Li
- State Key Laboratory of Food Science and Resources, Nanchang University, Nanchang 330047, China
| | - Hengyi Xu
- State Key Laboratory of Food Science and Resources, Nanchang University, Nanchang 330047, China.
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17
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Yang QE, Ma X, Li M, Zhao M, Zeng L, He M, Deng H, Liao H, Rensing C, Friman VP, Zhou S, Walsh TR. Evolution of triclosan resistance modulates bacterial permissiveness to multidrug resistance plasmids and phages. Nat Commun 2024; 15:3654. [PMID: 38688912 PMCID: PMC11061290 DOI: 10.1038/s41467-024-48006-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Accepted: 04/17/2024] [Indexed: 05/02/2024] Open
Abstract
The horizontal transfer of plasmids has been recognized as one of the key drivers for the worldwide spread of antimicrobial resistance (AMR) across bacterial pathogens. However, knowledge remain limited about the contribution made by environmental stress on the evolution of bacterial AMR by modulating horizontal acquisition of AMR plasmids and other mobile genetic elements. Here we combined experimental evolution, whole genome sequencing, reverse genetic engineering, and transcriptomics to examine if the evolution of chromosomal AMR to triclosan (TCS) disinfectant has correlated effects on modulating bacterial pathogen (Klebsiella pneumoniae) permissiveness to AMR plasmids and phage susceptibility. Herein, we show that TCS exposure increases the evolvability of K. pneumoniae to evolve TCS-resistant mutants (TRMs) by acquiring mutations and altered expression of several genes previously associated with TCS and antibiotic resistance. Notably, nsrR deletion increases conjugation permissiveness of K. pneumoniae to four AMR plasmids, and enhances susceptibility to various Klebsiella-specific phages through the downregulation of several bacterial defense systems and changes in membrane potential with altered reactive oxygen species response. Our findings suggest that unrestricted use of TCS disinfectant imposes a dual impact on bacterial antibiotic resistance by augmenting both chromosomally and horizontally acquired AMR mechanisms.
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Affiliation(s)
- Qiu E Yang
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Xiaodan Ma
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Minchun Li
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Mengshi Zhao
- Fujian Key Laboratory of Traditional Chinese Veterinary Medicine and Animal Health, College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Lingshuang Zeng
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Minzhen He
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Hui Deng
- Fujian Key Laboratory of Traditional Chinese Veterinary Medicine and Animal Health, College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Hanpeng Liao
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Christopher Rensing
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Ville-Petri Friman
- Department of Microbiology, University of Helsinki, 00014, Helsinki, Finland
| | - Shungui Zhou
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
| | - Timothy R Walsh
- Ineos Oxford Institute for Antimicrobial Research, Department of Biology, University of Oxford, Oxford, OX1 3RE, UK.
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18
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Maffei E, Manner C, Jenal U, Harms A. Complete genome sequence of Pseudomonas aeruginosa phage Knedl. Microbiol Resour Announc 2024; 13:e0117423. [PMID: 38393330 PMCID: PMC11008142 DOI: 10.1128/mra.01174-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 02/13/2024] [Indexed: 02/25/2024] Open
Abstract
Bacteriophage Knedl is the first reported Pseudomonas aeruginosa phage that targets the Psl exopolysaccharide as receptor. Here, we report the genome of Knedl, demonstrating that it belongs to the genus Iggyvirus of the Queuovirinae subfamily. Future studies on the infection mechanism of Knedl could inform phage-based approaches to eradicate biofilms.
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Affiliation(s)
- Enea Maffei
- Biozentrum, University of Basel, Basel, Switzerland
- Institute of Food, Nutrition and Health, ETH Zurich, Zurich, Switzerland
| | | | - Urs Jenal
- Biozentrum, University of Basel, Basel, Switzerland
| | - Alexander Harms
- Biozentrum, University of Basel, Basel, Switzerland
- Institute of Food, Nutrition and Health, ETH Zurich, Zurich, Switzerland
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19
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Wang X, Tang Y, Yue X, Wang S, Yang K, Xu Y, Shen Q, Friman VP, Wei Z. The role of rhizosphere phages in soil health. FEMS Microbiol Ecol 2024; 100:fiae052. [PMID: 38678007 PMCID: PMC11065364 DOI: 10.1093/femsec/fiae052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2023] [Revised: 03/22/2024] [Accepted: 04/25/2024] [Indexed: 04/29/2024] Open
Abstract
While the One Health framework has emphasized the importance of soil microbiomes for plant and human health, one of the most diverse and abundant groups-bacterial viruses, i.e. phages-has been mostly neglected. This perspective reviews the significance of phages for plant health in rhizosphere and explores their ecological and evolutionary impacts on soil ecosystems. We first summarize our current understanding of the diversity and ecological roles of phages in soil microbiomes in terms of nutrient cycling, top-down density regulation, and pathogen suppression. We then consider how phages drive bacterial evolution in soils by promoting horizontal gene transfer, encoding auxiliary metabolic genes that increase host bacterial fitness, and selecting for phage-resistant mutants with altered ecology due to trade-offs with pathogen competitiveness and virulence. Finally, we consider challenges and avenues for phage research in soil ecosystems and how to elucidate the significance of phages for microbial ecology and evolution and soil ecosystem functioning in the future. We conclude that similar to bacteria, phages likely play important roles in connecting different One Health compartments, affecting microbiome diversity and functions in soils. From the applied perspective, phages could offer novel approaches to modulate and optimize microbial and microbe-plant interactions to enhance soil health.
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Affiliation(s)
- Xiaofang Wang
- Jiangsu provincial key lab for solid organic waste utilization, Key lab of organic-based fertilizers of China,Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing 210095, China
| | - Yike Tang
- Jiangsu provincial key lab for solid organic waste utilization, Key lab of organic-based fertilizers of China,Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiufeng Yue
- Jiangsu provincial key lab for solid organic waste utilization, Key lab of organic-based fertilizers of China,Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing 210095, China
| | - Shuo Wang
- Jiangsu provincial key lab for solid organic waste utilization, Key lab of organic-based fertilizers of China,Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing 210095, China
| | - Keming Yang
- Jiangsu provincial key lab for solid organic waste utilization, Key lab of organic-based fertilizers of China,Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing 210095, China
| | - Yangchun Xu
- Jiangsu provincial key lab for solid organic waste utilization, Key lab of organic-based fertilizers of China,Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing 210095, China
| | - Qirong Shen
- Jiangsu provincial key lab for solid organic waste utilization, Key lab of organic-based fertilizers of China,Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing 210095, China
| | - Ville-Petri Friman
- Jiangsu provincial key lab for solid organic waste utilization, Key lab of organic-based fertilizers of China,Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing 210095, China
- Department of Microbiology, University of Helsinki, 00014 Helsinki, Finland
| | - Zhong Wei
- Jiangsu provincial key lab for solid organic waste utilization, Key lab of organic-based fertilizers of China,Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing 210095, China
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20
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Elfadadny A, Ragab RF, AlHarbi M, Badshah F, Ibáñez-Arancibia E, Farag A, Hendawy AO, De los Ríos-Escalante PR, Aboubakr M, Zakai SA, Nageeb WM. Antimicrobial resistance of Pseudomonas aeruginosa: navigating clinical impacts, current resistance trends, and innovations in breaking therapies. Front Microbiol 2024; 15:1374466. [PMID: 38646632 PMCID: PMC11026690 DOI: 10.3389/fmicb.2024.1374466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Accepted: 03/05/2024] [Indexed: 04/23/2024] Open
Abstract
Pseudomonas aeruginosa, a Gram-negative bacterium, is recognized for its adaptability and opportunistic nature. It poses a substantial challenge in clinical settings due to its complicated antibiotic resistance mechanisms, biofilm formation, and capacity for persistent infections in both animal and human hosts. Recent studies revealed a potential zoonotic transmission of P. aeruginosa between animals, the environment, and human populations which highlights awareness of this microbe. Implementation of the One Health approach, which underscores the connection between human, animal, and environmental health, we aim to offer a comprehensive perspective on the current landscape of P. aeruginosa management. This review presents innovative strategies designed to counteract P. aeruginosa infections. Traditional antibiotics, while effective in many cases, are increasingly compromised by the development of multidrug-resistant strains. Non-antibiotic avenues, such as quorum sensing inhibition, phage therapy, and nanoparticle-based treatments, are emerging as promising alternatives. However, their clinical application encounters obstacles like cost, side effects, and safety concerns. Effectively addressing P. aeruginosa infections necessitates persistent research efforts, advancements in clinical development, and a comprehension of host-pathogen interactions to deal with this resilient pathogen.
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Affiliation(s)
- Ahmed Elfadadny
- Laboratory of Internal Medicine, Cooperative Division of Veterinary Sciences, Tokyo University of Agriculture and Technology, Fuchu, Japan
- Department of Internal Medicine, Faculty of Veterinary Medicine, Damanhour University, Damanhour, Egypt
| | - Rokaia F. Ragab
- Laboratory of Internal Medicine, Cooperative Division of Veterinary Sciences, Tokyo University of Agriculture and Technology, Fuchu, Japan
- Department of Biochemistry, Faculty of Veterinary Medicine, Damanhour University, Damanhour, Egypt
| | - Maha AlHarbi
- Department of Biology, College of Science, Princess Nourah Bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Farhad Badshah
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Science, Chinese Academy of Agricultural Science, Beijing, China
| | - Eliana Ibáñez-Arancibia
- PhD Program in Sciences Mentioning Applied Molecular and Cell Biology, La Frontera University, Temuco, Chile
- Laboratory of Engineering, Biotechnology and Applied Biochemistry – LIBBA, Department of Chemical Engineering, Faculty of Engineering and Science, La Frontera University, Temuco, Chile
- Department of Biological and Chemical Sciences, Faculty of Natural Resources, Catholic University of Temuco, Temuco, Chile
| | - Ahmed Farag
- Department of Surgery, Anesthesiology, and Radiology, Faculty of Veterinary Medicine, Zagazig University, Zagazig, Egypt
| | - Amin Omar Hendawy
- Department of Animal and Poultry Production, Faculty of Agriculture, Damanhour University, Damanhour, Egypt
| | - Patricio R. De los Ríos-Escalante
- Department of Biological and Chemical Sciences, Faculty of Natural Resources, Catholic University of Temuco, Temuco, Chile
- Nucleus of Environmental Sciences, Faculty of Natural Resources, Catholic University of Temuco, Temuco, Chile
| | - Mohamed Aboubakr
- Department of Pharmacology, Faculty of Veterinary Medicine, Benha University, Moshtohor, Toukh, Qaliobiya, Egypt
| | - Shadi A. Zakai
- Department of Clinical Microbiology and Immunology, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Wedad M. Nageeb
- Department of Medical Microbiology and Immunology, Faculty of Medicine, Suez Canal University, Ismailia, Egypt
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21
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Alseth EO, Custodio R, Sundius SA, Kuske RA, Brown SP, Westra ER. The impact of phage and phage resistance on microbial community dynamics. PLoS Biol 2024; 22:e3002346. [PMID: 38648198 PMCID: PMC11034675 DOI: 10.1371/journal.pbio.3002346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Accepted: 03/19/2024] [Indexed: 04/25/2024] Open
Abstract
Where there are bacteria, there will be bacteriophages. These viruses are known to be important players in shaping the wider microbial community in which they are embedded, with potential implications for human health. On the other hand, bacteria possess a range of distinct immune mechanisms that provide protection against bacteriophages, including the mutation or complete loss of the phage receptor, and CRISPR-Cas adaptive immunity. While our previous work showed how a microbial community may impact phage resistance evolution, little is known about the inverse, namely how interactions between phages and these different phage resistance mechanisms affect the wider microbial community in which they are embedded. Here, we conducted a 10-day, fully factorial evolution experiment to examine how phage impact the structure and dynamics of an artificial four-species bacterial community that includes either Pseudomonas aeruginosa wild-type or an isogenic mutant unable to evolve phage resistance through CRISPR-Cas. Additionally, we used mathematical modelling to explore the ecological interactions underlying full community behaviour, as well as to identify general principles governing the impacts of phage on community dynamics. Our results show that the microbial community structure is drastically altered by the addition of phage, with Acinetobacter baumannii becoming the dominant species and P. aeruginosa being driven nearly extinct, whereas P. aeruginosa outcompetes the other species in the absence of phage. Moreover, we find that a P. aeruginosa strain with the ability to evolve CRISPR-based resistance generally does better when in the presence of A. baumannii, but that this benefit is largely lost over time as phage is driven extinct. Finally, we show that pairwise data alone is insufficient when modelling our microbial community, both with and without phage, highlighting the importance of higher order interactions in governing multispecies dynamics in complex communities. Combined, our data clearly illustrate how phage targeting a dominant species allows for the competitive release of the strongest competitor while also contributing to community diversity maintenance and potentially preventing the reinvasion of the target species, and underline the importance of mapping community composition before therapeutically applying phage.
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Affiliation(s)
- Ellinor O. Alseth
- Environment and Sustainability Institute, Biosciences, University of Exeter, Penryn, United Kingdom
- Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, Georgia, United States of America
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | - Rafael Custodio
- Environment and Sustainability Institute, Biosciences, University of Exeter, Penryn, United Kingdom
| | - Sarah A. Sundius
- Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, Georgia, United States of America
- School of Math, Georgia Institute of Technology, Atlanta, Georgia, United States of America
- Interdisciplinary Program in Quantitative Biosciences, Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | - Rachel A. Kuske
- Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, Georgia, United States of America
- School of Math, Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | - Sam P. Brown
- Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, Georgia, United States of America
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | - Edze R. Westra
- Environment and Sustainability Institute, Biosciences, University of Exeter, Penryn, United Kingdom
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22
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Longo M, Lelchat F, Le Baut V, Rioual S, Faÿ F, Lescop B, Hellio C. Tracking of Bacteriophage Predation on Pseudomonas aeruginosa Using a New Radiofrequency Biofilm Sensor. SENSORS (BASEL, SWITZERLAND) 2024; 24:2042. [PMID: 38610253 PMCID: PMC11013890 DOI: 10.3390/s24072042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Revised: 03/15/2024] [Accepted: 03/21/2024] [Indexed: 04/14/2024]
Abstract
Confronting the challenge of biofilm resistance and widespread antimicrobial resistance (AMR), this study emphasizes the need for innovative monitoring methods and explores the potential of bacteriophages against bacterial biofilms. Traditional methods, like optical density (OD) measurements and confocal microscopy, crucial in studying biofilm-virus interactions, often lack real-time monitoring and early detection capabilities, especially for biofilm formation and low bacterial concentrations. Addressing these gaps, we developed a new real-time, label-free radiofrequency sensor for monitoring bacteria and biofilm growth. The sensor, an open-ended coaxial probe, offers enhanced monitoring of bacterial development stages. Tested on a biological model of bacteria and bacteriophages, our results indicate the limitations of traditional OD measurements, influenced by factors like sedimented cell fragments and biofilm formation on well walls. While confocal microscopy provides detailed 3D biofilm architecture, its real-time monitoring application is limited. Our novel approach using radio frequency measurements (300 MHz) overcomes these shortcomings. It facilitates a finer analysis of the dynamic interaction between bacterial populations and phages, detecting real-time subtle changes. This method reveals distinct phases and breakpoints in biofilm formation and virion interaction not captured by conventional techniques. This study underscores the sensor's potential in detecting irregular viral activity and assessing the efficacy of anti-biofilm treatments, contributing significantly to the understanding of biofilm dynamics. This research is vital in developing effective monitoring tools, guiding therapeutic strategies, and combating AMR.
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Affiliation(s)
- Matthieu Longo
- Univ Brest, Lab-STICC, CNRS, UMR 6285, F-29200 Brest, France; (M.L.); (S.R.)
- Univ Brest, BIODIMAR/LEMAR, CNRS, UMR 6539, F-29200 Brest, France;
| | - Florian Lelchat
- Leo Viridis, 245 Rue René Descartes, F-29280 Plouzané, France; (F.L.); (V.L.B.)
| | - Violette Le Baut
- Leo Viridis, 245 Rue René Descartes, F-29280 Plouzané, France; (F.L.); (V.L.B.)
| | - Stéphane Rioual
- Univ Brest, Lab-STICC, CNRS, UMR 6285, F-29200 Brest, France; (M.L.); (S.R.)
| | - Fabienne Faÿ
- Laboratoire de Biotechnologie et Chimie Marines, Centre de Recherche Saint Maudé, Université Européenne de Bretagne, Université de Bretagne-Sud, F-56321 Lorient, France;
| | - Benoit Lescop
- Univ Brest, Lab-STICC, CNRS, UMR 6285, F-29200 Brest, France; (M.L.); (S.R.)
| | - Claire Hellio
- Univ Brest, BIODIMAR/LEMAR, CNRS, UMR 6539, F-29200 Brest, France;
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23
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Dicks LMT, Vermeulen W. Bacteriophage-Host Interactions and the Therapeutic Potential of Bacteriophages. Viruses 2024; 16:478. [PMID: 38543843 PMCID: PMC10975011 DOI: 10.3390/v16030478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Revised: 03/15/2024] [Accepted: 03/18/2024] [Indexed: 05/23/2024] Open
Abstract
Healthcare faces a major problem with the increased emergence of antimicrobial resistance due to over-prescribing antibiotics. Bacteriophages may provide a solution to the treatment of bacterial infections given their specificity. Enzymes such as endolysins, exolysins, endopeptidases, endosialidases, and depolymerases produced by phages interact with bacterial surfaces, cell wall components, and exopolysaccharides, and may even destroy biofilms. Enzymatic cleavage of the host cell envelope components exposes specific receptors required for phage adhesion. Gram-positive bacteria are susceptible to phage infiltration through their peptidoglycan, cell wall teichoic acid (WTA), lipoteichoic acids (LTAs), and flagella. In Gram-negative bacteria, lipopolysaccharides (LPSs), pili, and capsules serve as targets. Defense mechanisms used by bacteria differ and include physical barriers (e.g., capsules) or endogenous mechanisms such as clustered regularly interspaced palindromic repeat (CRISPR)-associated protein (Cas) systems. Phage proteins stimulate immune responses against specific pathogens and improve antibiotic susceptibility. This review discusses the attachment of phages to bacterial cells, the penetration of bacterial cells, the use of phages in the treatment of bacterial infections, and the limitations of phage therapy. The therapeutic potential of phage-derived proteins and the impact that genomically engineered phages may have in the treatment of infections are summarized.
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Affiliation(s)
- Leon M. T. Dicks
- Department of Microbiology, Stellenbosch University, Stellenbosch 7600, South Africa;
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24
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Hong Q, Chang RYK, Assafiri O, Morales S, Chan HK. Optimizing in vitro phage-ciprofloxacin combination formulation for respiratory therapy of multi-drug resistant Pseudomonas aeruginosa infections. Int J Pharm 2024; 652:123853. [PMID: 38280500 DOI: 10.1016/j.ijpharm.2024.123853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2023] [Revised: 01/21/2024] [Accepted: 01/23/2024] [Indexed: 01/29/2024]
Abstract
Respiratory infection caused by multi-drug resistant (MDR) Pseudomonas aeruginosa is challenging to treat. In this study, we investigate the optimal dose of anti-pseudomonas phage PEV31 (103, 105, and 108 PFU/mL) combined with ciprofloxacin (ranging from 1/8× MIC to 8× MIC) to treat the MDR P. aeruginosa strain FADD1-PA001 using time-kill studies. We determined the impact of phage growth kinetics in the presence of ciprofloxacin through one-step growth analysis. Single treatments with either phage PEV31 or ciprofloxacin (except at 8× MIC) showed limited bactericidal efficiency, with bacterial regrowth observed at 48 h. The most effective treatments were PEV31 at multiplicity of infection (MOI) of 0.1 and 100 combined with ciprofloxacin at concentrations above 1× MIC, resulting in a >4 log10 reduction in bacterial counts. While the burst size of phage PEV31 was decreased with increasing ciprofloxacin concentration, robust antimicrobial effects were still maintained in the combination treatment. Aerosol samples collected from vibrating mesh nebulization of the combination formulation at phage MOI of 100 with 2× MIC effectively inhibited bacterial density. In summary, our combination treatments eradicated in vitro bacterial growth and sustained antimicrobial effects for 48 h. These results indicated the potential application of nebulization-based strategies for the combination treatment against MDR lung infections.
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Affiliation(s)
- Qixuan Hong
- Advanced Drug Delivery Group, School of Pharmacy, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2006, Australia
| | - Rachel Yoon Kyung Chang
- Advanced Drug Delivery Group, School of Pharmacy, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2006, Australia
| | - Omar Assafiri
- Advanced Drug Delivery Group, School of Pharmacy, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2006, Australia
| | | | - Hak-Kim Chan
- Advanced Drug Delivery Group, School of Pharmacy, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2006, Australia.
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25
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Murray TS, Stanley G, Koff JL. Novel Approaches to Multidrug-Resistant Infections in Cystic Fibrosis. Infect Dis Clin North Am 2024; 38:149-162. [PMID: 38280761 DOI: 10.1016/j.idc.2023.12.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2024]
Abstract
Patients with cystic fibrosis (CF) often develop respiratory tract infections with pathogenic multidrug-resistant organisms (MDROs) such as methicillin-resistant Staphylococcus aureus, and a variety of gram-negative organisms that include Pseudomonas aeruginosa, Burkholderia sp., Stenotrophomonas maltophilia, Achromobacter xylosoxidans, and nontuberculous mycobacteria (NTM). Despite the introduction of new therapies to address underlying cystic fibrosis transmembrane conductance regulator (CFTR) dysfunction, MDRO infections remain a problem and novel antimicrobial interventions are still needed. Therapeutic approaches include improving the efficacy of existing drugs by adjusting the dose based on differences in CF patient pharmacokinetics/pharmacodynamics, the development of inhaled formulations to reduce systemic adverse events, and the use of newer beta-lactam/beta-lactamase combinations. Alternative innovative therapeutic approaches include the use of gallium and bacteriophages to treat MDRO pulmonary infections including those with extreme antibiotic resistance. However, additional clinical trials are required to determine the optimal dosing and efficacy of these different strategies and to identify patients with CF most likely to benefit from these new treatment options.
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Affiliation(s)
- Thomas S Murray
- Department of Pediatrics, Section Infectious Diseases and Global Health, Yale University School of Medicine, PO Box 208064, 333 Cedar Street, New Haven, CT 06520-8064, USA.
| | - Gail Stanley
- Department of Internal Medicine, Section Pulmonary, Critical Care and Sleep Medicine, Yale University School of Medicine, PO Box 208057, 300 Cedar Street TAC-441 South, New Haven, CT 06520-8057, USA; Adult Cystic Fibrosis Program; Yale University Center for Phage Biology & Therapy.
| | - Jonathan L Koff
- Adult Cystic Fibrosis Program; Yale University Center for Phage Biology & Therapy; Department of Internal Medicine, Section Pulmonary, Critical Care and Sleep Medicine, Yale University School of Medicine, PO Box 208057, 300 Cedar Street TAC-455A South, New Haven, CT 06520-8057, USA.
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26
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Wang M, Zhang J, Wei J, Jiang L, Jiang L, Sun Y, Zeng Z, Wang Z. Phage-inspired strategies to combat antibacterial resistance. Crit Rev Microbiol 2024; 50:196-211. [PMID: 38400715 DOI: 10.1080/1040841x.2023.2181056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 02/07/2023] [Indexed: 02/25/2023]
Abstract
Antimicrobial resistance (AMR) in clinically priority pathogensis now a major threat to public health worldwide. Phages are bacterial parasites that efficiently infect or kill specific strains and represent the most abundant biological entities on earth, showing great attraction as potential antibacterial therapeutics in combating AMR. This review provides a summary of phage-inspired strategies to combat AMR. We firstly cover the phage diversity, and then explain the biological principles of phage therapy that support the use of phages in the post-antimicrobial era. Furthermore, we state the versatility methods of phage therapy both from direct access as well as collateral access. Among the direct access approaches, we discuss the use of phage cocktail therapy, phage-encoded endolysins and the bioengineering for function improvement of used phages or endolysins. On the other hand, we introduce the collateral access, including the phages antimicrobial immunity combined therapy and phage-based novel antibacterial mimic molecules. Nowadays, more and more talented and enthusiastic scientist, doctors, pharmacists, media, authorities, and industry are promoting the progress of phage therapy, and proposed more phages-inspired strategy to make them more tractable to combat AMR and benefit more people, more animal and diverse environment in "one health" framework.
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Affiliation(s)
- Mianzhi Wang
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
| | - Junxuan Zhang
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Jingyi Wei
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
| | - Lei Jiang
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
| | - Li Jiang
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
| | - Yongxue Sun
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Zhenling Zeng
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Zhiqiang Wang
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
- International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou, China
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27
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Ashworth EA, Wright RCT, Shears RK, Wong JKL, Hassan A, Hall JPJ, Kadioglu A, Fothergill JL. Exploiting lung adaptation and phage steering to clear pan-resistant Pseudomonas aeruginosa infections in vivo. Nat Commun 2024; 15:1547. [PMID: 38378698 PMCID: PMC10879199 DOI: 10.1038/s41467-024-45785-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 02/05/2024] [Indexed: 02/22/2024] Open
Abstract
Pseudomonas aeruginosa is a major nosocomial pathogen that causes severe disease including sepsis. Carbapenem-resistant P. aeruginosa is recognised by the World Health Organisation as a priority 1 pathogen, with urgent need for new therapeutics. As such, there is renewed interest in using bacteriophages as a therapeutic. However, the dynamics of treating pan-resistant P. aeruginosa with phage in vivo are poorly understood. Using a pan-resistant P. aeruginosa in vivo infection model, phage therapy displays strong therapeutic potential, clearing infection from the blood, kidneys, and spleen. Remaining bacteria in the lungs and liver displays phage resistance due to limiting phage adsorption. Yet, resistance to phage results in re-sensitisation to a wide range of antibiotics. In this work, we use phage steering in vivo, pre-exposing a pan resistant P. aeruginosa infection with a phage cocktail to re-sensitise bacteria to antibiotics, clearing the infection from all organs.
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Affiliation(s)
- Eleri A Ashworth
- Department of Clinical Infection, Microbiology and Immunology, University of Liverpool, Liverpool, UK
| | - Rosanna C T Wright
- Division of Evolution & Genomic Sciences, School of Biological Sciences, University of Manchester, Manchester, UK
| | - Rebecca K Shears
- Department of Clinical Infection, Microbiology and Immunology, University of Liverpool, Liverpool, UK
- Centre for Bioscience, Manchester Metropolitan University, Manchester, M1 5DG, UK
| | - Janet K L Wong
- Department of Clinical Infection, Microbiology and Immunology, University of Liverpool, Liverpool, UK
| | - Akram Hassan
- Department of Clinical Infection, Microbiology and Immunology, University of Liverpool, Liverpool, UK
| | - James P J Hall
- Department of Evolution, Ecology and Behaviour, University of Liverpool, Liverpool, UK
| | - Aras Kadioglu
- Department of Clinical Infection, Microbiology and Immunology, University of Liverpool, Liverpool, UK.
| | - Joanne L Fothergill
- Department of Clinical Infection, Microbiology and Immunology, University of Liverpool, Liverpool, UK.
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28
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Samananda Singh L. Nano-emulsion encapsulation for the efficient delivery of bacteriophage therapeutics. Biologicals 2024; 85:101725. [PMID: 37951140 DOI: 10.1016/j.biologicals.2023.101725] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 10/20/2023] [Accepted: 10/31/2023] [Indexed: 11/13/2023] Open
Abstract
Antibiotic resistance has become the major concern for global public health. Phage therapy is being considered as an alternative for antibiotics to treat the multidrug resistant bacterial infections. Bacteriophage therapeutic developments has faced many challenges, including the drug formulations for sustainable phage delivery. The nano-emulsion platform has been described as the best approach to retain phage efficacy, shelf life and stability. Encapsulated phage drugs ensure stable delivery of phages to the target site and integrate in the system. In this review, our main focus is on the nano-emulsion encapsulation of bacteriophages and its effects towards the phage therapeutic development.
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29
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Würstle S, Lee A, Kortright KE, Winzig F, An W, Stanley GL, Rajagopalan G, Harris Z, Sun Y, Hu B, Blazanin M, Hajfathalian M, Bollyky PL, Turner PE, Koff JL, Chan BK. Optimized preparation pipeline for emergency phage therapy against Pseudomonas aeruginosa at Yale University. Sci Rep 2024; 14:2657. [PMID: 38302552 PMCID: PMC10834462 DOI: 10.1038/s41598-024-52192-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 01/15/2024] [Indexed: 02/03/2024] Open
Abstract
Bacteriophage therapy is one potential strategy to treat antimicrobial resistant or persistent bacterial infections, and the year 2021 marked the centennial of Felix d'Hérelle's first publication on the clinical applications of phages. At the Center for Phage Biology & Therapy at Yale University, a preparatory modular approach has been established to offer safe and potent phages for single-patient investigational new drug applications while recognizing the time constraints imposed by infection(s). This study provides a practical walkthrough of the pipeline with an Autographiviridae phage targeting Pseudomonas aeruginosa (phage vB_PaeA_SB, abbreviated to ΦSB). Notably, a thorough phage characterization and the evolutionary selection pressure exerted on bacteria by phages, analogous to antibiotics, are incorporated into the pipeline.
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Affiliation(s)
- Silvia Würstle
- Yale Center for Phage Biology and Therapy, Yale University, 165 Prospect Street, New Haven, CT, 06520, USA
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, 06520, USA
- Department of Internal Medicine, Section of Pulmonary, Critical Care, and Sleep Medicine, Yale School of Medicine, New Haven, CT, 06519, USA
- Technical University of Munich, 81675, Munich, Germany
| | - Alina Lee
- Yale Center for Phage Biology and Therapy, Yale University, 165 Prospect Street, New Haven, CT, 06520, USA
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, 06520, USA
| | - Kaitlyn E Kortright
- Yale Center for Phage Biology and Therapy, Yale University, 165 Prospect Street, New Haven, CT, 06520, USA
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, 06520, USA
| | - Franziska Winzig
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, 06520, USA
- Technical University of Munich, 81675, Munich, Germany
| | - William An
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, 06520, USA
| | - Gail L Stanley
- Yale Center for Phage Biology and Therapy, Yale University, 165 Prospect Street, New Haven, CT, 06520, USA
- Department of Internal Medicine, Section of Pulmonary, Critical Care, and Sleep Medicine, Yale School of Medicine, New Haven, CT, 06519, USA
| | - Govindarajan Rajagopalan
- Yale Center for Phage Biology and Therapy, Yale University, 165 Prospect Street, New Haven, CT, 06520, USA
- Department of Internal Medicine, Section of Pulmonary, Critical Care, and Sleep Medicine, Yale School of Medicine, New Haven, CT, 06519, USA
| | - Zach Harris
- Department of Internal Medicine, Section of Pulmonary, Critical Care, and Sleep Medicine, Yale School of Medicine, New Haven, CT, 06519, USA
| | - Ying Sun
- Department of Internal Medicine, Section of Pulmonary, Critical Care, and Sleep Medicine, Yale School of Medicine, New Haven, CT, 06519, USA
| | - Buqu Hu
- Department of Internal Medicine, Section of Pulmonary, Critical Care, and Sleep Medicine, Yale School of Medicine, New Haven, CT, 06519, USA
| | - Michael Blazanin
- Yale Center for Phage Biology and Therapy, Yale University, 165 Prospect Street, New Haven, CT, 06520, USA
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, 06520, USA
| | - Maryam Hajfathalian
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University, Stanford, CA, 94305, USA
| | - Paul L Bollyky
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University, Stanford, CA, 94305, USA
| | - Paul E Turner
- Yale Center for Phage Biology and Therapy, Yale University, 165 Prospect Street, New Haven, CT, 06520, USA
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, 06520, USA
- Department of Internal Medicine, Section of Pulmonary, Critical Care, and Sleep Medicine, Yale School of Medicine, New Haven, CT, 06519, USA
- Program in Microbiology, Yale School of Medicine, New Haven, CT, 06520, USA
| | - Jonathan L Koff
- Yale Center for Phage Biology and Therapy, Yale University, 165 Prospect Street, New Haven, CT, 06520, USA.
- Department of Internal Medicine, Section of Pulmonary, Critical Care, and Sleep Medicine, Yale School of Medicine, New Haven, CT, 06519, USA.
| | - Benjamin K Chan
- Yale Center for Phage Biology and Therapy, Yale University, 165 Prospect Street, New Haven, CT, 06520, USA.
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, 06520, USA.
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Kumari K, Sharma PK, Singh RP. Unravelling the transcriptome response of Enterobacter sp. S-33 under varying temperature. Arch Microbiol 2024; 206:81. [PMID: 38294553 DOI: 10.1007/s00203-023-03792-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 11/22/2023] [Accepted: 12/11/2023] [Indexed: 02/01/2024]
Abstract
Enterobacter genus includes the bacteria occupying every aspect of environment, however, their adaptability at varying temperature is not clear. In the present study, we analyzed the transcriptome response of Enterobacter sp. S-33 and their functional genes under various temperatures (30-45 ℃) that were expressed and accumulated in cells under temperature-stress. During a temperature shift from 37 to 45 ℃, 165 genes showed differential expression including 112 up-regulated and 53 down-regulated. In particular, heat-shock genes such as CspA, 16 kDa heat shock protein A/B and transcriptional regulators such as LysR, TetR, and LuxR were differentially expressed, indicating the role of complex molecular mechanism of Enterobacter adapting to temperature stress. Similarly, genes associated to signal transduction, ABC transporters, iron homeostasis, and quorum sensing were also induced. The Gene ontology enrichment analysis of differentially expressed genes (DEGs) were categorized into "transmembrane transport", "tRNA binding", "hydrogen sulfide biosynthetic process" and "sulfate assimilation" terms. In addition, Kyoto Encyclopedia of Genes and Genomes pathways showed that ABC transporter as well as quorum sensing pathways were significantly enriched. Overall, current study has contributed to explore the adaptive molecular mechanisms of Enterobacter spp. upon temperature change, which further opens new avenues for future in-depth functional studies.
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Affiliation(s)
- Kiran Kumari
- Department of Bioengineering and Biotechnology, Birla Institute of Technology, Mesra, Ranchi, Jharkhand, 835215, India
| | - Parva Kumar Sharma
- Department of Plant Sciences and Landscape Architecture, University of Maryland, College Park, MD, 20742, USA
| | - Rajnish Prakash Singh
- Department of Biotechnology, Jaypee Institute of Information Technology, Noida, India.
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Echterhof A, Dharmaraj T, McBride R, Berry J, Hopkins M, Selvakumar H, Miesel L, Chia JH, Lin KY, Shen CC, Lee YL, Yeh YC, Liao WT, Suh G, Blankenberg FG, Frymoyer AR, Bollyky PL. The contribution of neutrophils to bacteriophage clearance and pharmacokinetics in vivo. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.25.577154. [PMID: 38328123 PMCID: PMC10849746 DOI: 10.1101/2024.01.25.577154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
With the increasing prevalence of antimicrobial-resistant bacterial infections, there is great interest in using lytic bacteriophages (phages) to treat such infections. However, the factors that govern bacteriophage pharmacokinetics in vivo remain poorly understood. Here, we have examined the contribution of neutrophils, the most abundant phagocytes in the body, to the pharmacokinetics of intravenously administered bacteriophage in uninfected mice. A single dose of LPS-5, an antipseudomonal bacteriophage recently used in human clinical trials, was administered intravenously to both wild-type BALB/c and neutropenic ICR mice. Phage concentrations were assessed in peripheral blood and spleen at 0.5, 1, 2, 4, 8, 12, and 24 hours after administration by plaque assay and qPCR. We observed that the phage clearance is only minimally affected by neutropenia. Indeed, the half-life of phages in blood in BALB/c and ICR mice is 3.45 and 3.66 hours, respectively. These data suggest that neutrophil-mediated phagocytosis is not a major determinant of phage clearance. Conversely, we observed a substantial discrepancy in circulating phage levels over time when measured by qPCR versus plaque assay, suggesting that substantial functional inactivation of circulating phages occurs over time. These data indicate that circulating factors, but not neutrophils, inactivate intravenously administered phages.
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Yin C, Alam MZ, Fallon JT, Huang W. Advances in Development of Novel Therapeutic Strategies against Multi-Drug Resistant Pseudomonas aeruginosa. Antibiotics (Basel) 2024; 13:119. [PMID: 38391505 PMCID: PMC10885988 DOI: 10.3390/antibiotics13020119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 01/19/2024] [Accepted: 01/23/2024] [Indexed: 02/24/2024] Open
Abstract
Pseudomonas aeruginosa (P. aeruginosa) with multi-drug resistance (MDR) is a major cause of serious healthcare-associated infections, leading to high morbidity and mortality. This opportunistic pathogen is responsible for various infectious diseases, such as those seen in cystic fibrosis, ventilator-associated pneumonia, urinary tract infection, otitis externa, and burn and wound injuries. Due to its relatively large genome, P. aeruginosa has great diversity and can use various molecular mechanisms for antimicrobial resistance. For example, outer membrane permeability can contribute to antimicrobial resistance and is determined by lipopolysaccharide (LPS) and porin proteins. Recent findings on the regulatory interaction between peptidoglycan and LPS synthesis provide additional clues against pathogenic P. aeruginosa. This review focuses on recent advances in antimicrobial agents and inhibitors targeting LPS and porin proteins. In addition, we explore current and emerging treatment strategies for MDR P. aeruginosa, including phages, vaccines, nanoparticles, and their combinatorial therapies. Novel strategies and their corresponding therapeutic agents are urgently needed for combating MDR pathogens.
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Affiliation(s)
- Changhong Yin
- Department of Pathology and Laboratory Medicine, Brody School of Medicine, East Carolina University, Greenville, NC 27834, USA
| | - Md Zahidul Alam
- Department of Pathology and Laboratory Medicine, Brody School of Medicine, East Carolina University, Greenville, NC 27834, USA
| | - John T Fallon
- Department of Pathology and Laboratory Medicine, Brody School of Medicine, East Carolina University, Greenville, NC 27834, USA
| | - Weihua Huang
- Department of Pathology and Laboratory Medicine, Brody School of Medicine, East Carolina University, Greenville, NC 27834, USA
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Bae HW, Choi SY, Cho YH. An outer membrane determinant for RNA phage genome entry in Pseudomonas aeruginosa. iScience 2024; 27:108675. [PMID: 38213628 PMCID: PMC10783630 DOI: 10.1016/j.isci.2023.108675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 11/06/2023] [Accepted: 12/05/2023] [Indexed: 01/13/2024] Open
Abstract
Host range of a phage is determined at the various life cycle stages during phage infection. We reported the limited phage-receptor interaction between the RNA phage, PP7 and its host Pseudomonas aeruginosa strains: PAO1 has susceptible type IV pilus (TFP) pilin, whereas PA14 has resistant pilin. Here, we have created a PA14 derivative (PA14P) with the PAO1 pilin gene and found that other determinants than TFP pilin could limit PP7 infectivity in PA14P. Transposon mutant screens revealed that PP7 infectivity was restored in the PA14P mutants (htrB2) lacking a secondary acyltransferase in lipid A biosynthesis. The lack of this enzyme increased the RNA phage entry, which is deemed attributed to the loosened lipopolysaccharide (LPS) structure. Polymyxin B treatment also selectively increased the RNA phage entry. These results demonstrated that LPS structures could limit the entry stage of RNA phages, providing another determinant for the host range in diverse P. aeruginosa strains.
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Affiliation(s)
- Hee-Won Bae
- Department of Pharmacy, College of Pharmacy and Institute of Pharmaceutical Sciences, CHA University, Gyeonggi-do 13488, Korea
| | - Shin-Yae Choi
- Department of Pharmacy, College of Pharmacy and Institute of Pharmaceutical Sciences, CHA University, Gyeonggi-do 13488, Korea
| | - You-Hee Cho
- Department of Pharmacy, College of Pharmacy and Institute of Pharmaceutical Sciences, CHA University, Gyeonggi-do 13488, Korea
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García-Cruz JC, Rebollar-Juarez X, Limones-Martinez A, Santos-Lopez CS, Toya S, Maeda T, Ceapă CD, Blasco L, Tomás M, Díaz-Velásquez CE, Vaca-Paniagua F, Díaz-Guerrero M, Cazares D, Cazares A, Hernández-Durán M, López-Jácome LE, Franco-Cendejas R, Husain FM, Khan A, Arshad M, Morales-Espinosa R, Fernández-Presas AM, Cadet F, Wood TK, García-Contreras R. Resistance against two lytic phage variants attenuates virulence and antibiotic resistance in Pseudomonas aeruginosa. Front Cell Infect Microbiol 2024; 13:1280265. [PMID: 38298921 PMCID: PMC10828002 DOI: 10.3389/fcimb.2023.1280265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2023] [Accepted: 12/22/2023] [Indexed: 02/02/2024] Open
Abstract
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.
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Affiliation(s)
- Juan Carlos García-Cruz
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México (UNAM), Mexico City, Mexico
| | - Xareni Rebollar-Juarez
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México (UNAM), Mexico City, Mexico
| | - Aldo Limones-Martinez
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México (UNAM), Mexico City, Mexico
| | - Cristian Sadalis Santos-Lopez
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México (UNAM), Mexico City, Mexico
- Universidad Univer Milenium, Toluca de Lerdo, Mexico
| | - Shotaro Toya
- Department of Biological Functions Engineering, Graduate School of Life Science and Systems Engineering, Kyushu Institute of Technology, Kitakyushu, Japan
| | - Toshinari Maeda
- Department of Biological Functions Engineering, Graduate School of Life Science and Systems Engineering, Kyushu Institute of Technology, Kitakyushu, Japan
| | - Corina Diana Ceapă
- Microbiology Laboratory, Chemistry Institute, Universidad Nacional Autónoma de México (UNAM), Mexico City, Mexico
| | - Lucia Blasco
- Microbiología Traslacional y Multidisciplinar (MicroTM), Instituto de Investigación Biomédica (INIBIC), Universidad de A Coruña (UDC), A Coruña, Spain
- Servicio de Microbiología, Hospital A Coruña (CHUAC), Universidad de A Coruña (UDC), A Coruña, Spain
| | - María Tomás
- Microbiología Traslacional y Multidisciplinar (MicroTM), Instituto de Investigación Biomédica (INIBIC), Universidad de A Coruña (UDC), A Coruña, Spain
- Servicio de Microbiología, Hospital A Coruña (CHUAC), Universidad de A Coruña (UDC), A Coruña, Spain
| | - Clara Estela Díaz-Velásquez
- Laboratorio Nacional en Salud, Diagnóstico Molecular y Efecto Ambiental en Enfermedades Crónico-Degenerativas, Facultad de Estudios Superiores (FES) Iztacala, Universidad Nacional Autónoma de México, Tlalnepantla de Baz, Estado de México, Mexico
| | - Felipe Vaca-Paniagua
- Laboratorio Nacional en Salud, Diagnóstico Molecular y Efecto Ambiental en Enfermedades Crónico-Degenerativas, Facultad de Estudios Superiores (FES) Iztacala, Universidad Nacional Autónoma de México, Tlalnepantla de Baz, Estado de México, Mexico
- Subdirección de Investigación Básica, Instituto Nacional de Cancerología, Ciudad de México, Mexico
| | - Miguel Díaz-Guerrero
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México (UNAM), Mexico City, Mexico
| | - Daniel Cazares
- Department of Biology, University of Oxford, Oxford, United Kingdom
| | - Adrián Cazares
- Parasites and Microbes Programme, Wellcome Sanger Institute, Hinxton, United Kingdom
| | - Melisa Hernández-Durán
- Laboratorio de Microbiología Clínica, División de Infectología, Instituto Nacional de Rehabilitación, Luis Guillermo Ibarra Ibarra, Mexico, Mexico
| | - Luis Esaú López-Jácome
- Laboratorio de Microbiología Clínica, División de Infectología, Instituto Nacional de Rehabilitación, Luis Guillermo Ibarra Ibarra, Mexico, Mexico
- Departamento de Biología, Facultad de Química, Universidad Nacional Autónoma de México (UNAM), Mexico City, Mexico
| | - Rafael Franco-Cendejas
- Subdirección de Investigación Biomédica, Instituto Nacional de Rehabilitación Luis Guillermo Ibarra Ibarra, Mexico, Mexico
| | - Fohad Mabood Husain
- Department of Food Science and Nutrition, King Saud University, Riyadh, Saudi Arabia
| | - Altaf Khan
- Department of Pharmacology, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Mohammed Arshad
- Dental Health Department, College of Applied Medical Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Rosario Morales-Espinosa
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México (UNAM), Mexico City, Mexico
| | - Ana María Fernández-Presas
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México (UNAM), Mexico City, Mexico
| | - Frederic Cadet
- PEACCEL, Artificial Intelligence Department, AI for Biologics, Paris, France
| | - Thomas K. Wood
- Department of Chemical Engineering, Pennsylvania State University, University Park, PA, United States
| | - Rodolfo García-Contreras
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México (UNAM), Mexico City, Mexico
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Gliźniewicz M, Miłek D, Olszewska P, Czajkowski A, Serwin N, Cecerska-Heryć E, Dołęgowska B, Grygorcewicz B. Advances in bacteriophage-mediated strategies for combating polymicrobial biofilms. Front Microbiol 2024; 14:1320345. [PMID: 38249486 PMCID: PMC10797108 DOI: 10.3389/fmicb.2023.1320345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Accepted: 12/04/2023] [Indexed: 01/23/2024] Open
Abstract
Bacteria and fungi tend to coexist within biofilms instead of in planktonic states. Usually, such communities include cross-kingdom microorganisms, which make them harder to remove from abiotic surfaces or infection sites. Additionally, the produced biofilm matrix protects embedded microorganisms from antibiotics, disinfectants, or the host immune system. Therefore, classic therapies based on antibiotics might be ineffective, especially when multidrug-resistant bacteria are causative factors. The complexities surrounding the eradication of biofilms from diverse surfaces and the human body have spurred the exploration of alternative therapeutic modalities. Among these options, bacteriophages and their enzymatic counterparts have emerged as promising candidates, either employed independently or in synergy with antibiotics and other agents. Phages are natural bacteria killers because of mechanisms of action that differ from antibiotics, phages might answer worldwide problems with bacterial infections. In this review, we report the attempts to use bacteriophages in combating polymicrobial biofilms in in vitro studies, using different models, including the therapeutical use of phages. In addition, we sum up the advantages, disadvantages, and perspectives of phage therapy.
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Affiliation(s)
- Marta Gliźniewicz
- Faculty of Pharmacy, Medical Biotechnology and Laboratory Medicine, Pomeranian Medical University in Szczecin, Szczecin, Poland
| | - Dominika Miłek
- Faculty of Pharmacy, Medical Biotechnology and Laboratory Medicine, Pomeranian Medical University in Szczecin, Szczecin, Poland
| | - Patrycja Olszewska
- Faculty of Pharmacy, Medical Biotechnology and Laboratory Medicine, Pomeranian Medical University in Szczecin, Szczecin, Poland
| | - Artur Czajkowski
- Faculty of Pharmacy, Medical Biotechnology and Laboratory Medicine, Pomeranian Medical University in Szczecin, Szczecin, Poland
| | - Natalia Serwin
- Faculty of Pharmacy, Medical Biotechnology and Laboratory Medicine, Pomeranian Medical University in Szczecin, Szczecin, Poland
| | - Elżbieta Cecerska-Heryć
- Faculty of Pharmacy, Medical Biotechnology and Laboratory Medicine, Pomeranian Medical University in Szczecin, Szczecin, Poland
| | - Barbara Dołęgowska
- Faculty of Pharmacy, Medical Biotechnology and Laboratory Medicine, Pomeranian Medical University in Szczecin, Szczecin, Poland
| | - Bartłomiej Grygorcewicz
- Faculty of Pharmacy, Medical Biotechnology and Laboratory Medicine, Pomeranian Medical University in Szczecin, Szczecin, Poland
- Department of Chemical Technology and Engineering, Institute of Chemical Engineering and Environmental Protection Processes, West Pomeranian University of Technology, Szczecin, Poland
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36
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Vo L, Avgidis F, Mattingly HH, Balasubramanian R, Shimizu TS, Kazmierczak BI, Emonet T. Non-genetic adaptation by collective migration. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.02.573956. [PMID: 38260286 PMCID: PMC10802332 DOI: 10.1101/2024.01.02.573956] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Collective behaviors require coordination of individuals. Thus, a population must adjust its phenotypic distribution to adapt to changing environments. How can a population regulate its phenotypic distribution? One strategy is to utilize specialized networks for gene regulation and maintaining distinct phenotypic subsets. Another involves genetic mutations, which can be augmented by stress-response pathways. Here, we studied how a migrating bacterial population regulates its phenotypic distribution to traverse across diverse environments. We generated isogenic Escherichia coli populations with varying distributions of swimming behaviors and observed their phenotype distributions during migration in liquid and porous environments. Surprisingly, we found that during collective migration, the distributions of swimming phenotypes adapt to the environment without mutations or gene regulation. Instead, adaptation is caused by the dynamic and reversible enrichment of high-performing swimming phenotypes within each environment. This adaptation mechanism is supported by a recent theoretical study, which proposed that the phenotypic composition of a migrating population results from a balance between cell growth generating diversity and collective migration eliminating the phenotypes that are unable to keep up with the migrating group. Furthermore, by examining chemoreceptor abundance distributions during migration towards different attractants, we found that this mechanism acts on multiple chemotaxis-related traits simultaneously. Our findings reveal that collective migration itself can enable cell populations with continuous, multi-dimensional phenotypes to flexibly and rapidly adapt their phenotypic composition to diverse environmental conditions. Significance statement Conventional cell adaptation mechanisms, like gene regulation and random phenotypic switching, act swiftly but are limited to a few traits, while mutation-driven adaptations unfold slowly. By quantifying phenotypic diversity during bacterial collective migration, we discovered an adaptation mechanism that rapidly and reversibly adjusts multiple traits simultaneously. By dynamically balancing the elimination of phenotypes unable to keep pace with generation of diversity through growth, this process enables populations to tune their phenotypic composition based on the environment, without the need for gene regulation or mutations. Given the prevalence of collective migration in microbes, cancers, and embryonic development, non-genetic adaptation through collective migration may be a universal mechanism for populations to navigate diverse environments, offering insights into broader applications across various fields.
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Kulshrestha M, Tiwari M, Tiwari V. Bacteriophage therapy against ESKAPE bacterial pathogens: Current status, strategies, challenges, and future scope. Microb Pathog 2024; 186:106467. [PMID: 38036110 DOI: 10.1016/j.micpath.2023.106467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 10/19/2023] [Accepted: 11/24/2023] [Indexed: 12/02/2023]
Abstract
The ESKAPE pathogens are the primary threat due to their constant spread of drug resistance worldwide. These pathogens are also regarded as opportunistic pathogens and could potentially cause nosocomial infections. Most of the ESKAPE pathogens have developed resistance to almost all the antibiotics that are used against them. Therefore, to deal with antimicrobial resistance, there is an urgent requirement for alternative non-antibiotic strategies to combat this rising issue of drug-resistant organisms. One of the promising alternatives to this scenario is implementing bacteriophage therapy. This under-explored mode of treatment in modern medicine has posed several concerns, such as preferable phages for the treatment, impact on the microbiome (or gut microflora), dose optimisation, safety, etc. The review will cover a rationale for phage therapy, clinical challenges, and propose phage therapy as an effective therapeutic against bacterial coinfections during pandemics. This review also addresses the expected uncertainties for administering the phage as a treatment against the ESKAPE pathogens and the advantages of using lytic phage over temperate, the immune response to phages, and phages in combinational therapies. The interaction between bacteria and bacteriophages in humans and countless animal models can also be used to design novel and futuristic therapeutics like personalised medicine or bacteriophages as anti-biofilm agents. Hence, this review explores different aspects of phage therapy and its potential to emerge as a frontline therapy against the ESKAPE bacterial pathogen.
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Affiliation(s)
- Mukta Kulshrestha
- Department of Biochemistry, Central University of Rajasthan, Ajmer, 305817, India
| | - Monalisa Tiwari
- Department of Biochemistry, Central University of Rajasthan, Ajmer, 305817, India
| | - Vishvanath Tiwari
- Department of Biochemistry, Central University of Rajasthan, Ajmer, 305817, India.
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38
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Zhao Y, Shu M, Zhang L, Zhong C, Liao N, Wu G. Phage-driven coevolution reveals trade-off between antibiotic and phage resistance in Salmonella anatum. ISME COMMUNICATIONS 2024; 4:ycae039. [PMID: 38616926 PMCID: PMC11014889 DOI: 10.1093/ismeco/ycae039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 03/07/2024] [Accepted: 03/18/2024] [Indexed: 04/16/2024]
Abstract
Phage therapy faces challenges against multidrug-resistant (MDR) Salmonella due to rapid phage-resistant mutant emergence. Understanding the intricate interplay between antibiotics and phages is essential for shaping Salmonella evolution and advancing phage therapy. In this study, MDR Salmonella anatum (S. anatum) 2089b coevolved with phage JNwz02 for 30 passages (60 days), then the effect of coevolution on the trade-off between phage and antibiotic resistance in bacteria was investigated. Our results demonstrated antagonistic coevolution between bacteria and phages, transitioning from arms race dynamics (ARD) to fluctuating selection dynamics (FSD). The fitness cost of phage resistance, manifested as reduced competitiveness, was observed. Bacteria evolved phage resistance while simultaneously regaining sensitivity to amoxicillin, ampicillin, and gentamicin, influenced by phage selection pressure and bacterial competitiveness. Moreover, the impact of phage selection pressure on the trade-off between antibiotic and phage resistance was more pronounced in the ARD stage than in the FSD stage. Whole genome analysis revealed mutations in the btuB gene in evolved S. anatum strains, with a notably higher mutation frequency in the ARD stage compared to the FSD stage. Subsequent knockout experiments confirmed BtuB as a receptor for phage JNwz02, and the deletion of btuB resulted in reduced bacterial competitiveness. Additionally, the mutations identified in the phage-resistant strains were linked to multiple single nucleotide polymorphisms (SNPs) associated with membrane components. This correlation implies a potential role of these SNPs in reinstating antibiotic susceptibility. These findings significantly advance our understanding of phage-host interactions and the impact of bacterial adaptations on antibiotic resistance.
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Affiliation(s)
- Yuanyang Zhao
- College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang 330045, Jiangxi, PR China
- College of Food Science and Engineering, Jiangxi Agricultural University, Nanchang 330045, Jiangxi, PR China
| | - Mei Shu
- College of Food Science and Engineering, Jiangxi Agricultural University, Nanchang 330045, Jiangxi, PR China
| | - Ling Zhang
- College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang 330045, Jiangxi, PR China
| | - Chan Zhong
- College of Food Science and Engineering, Jiangxi Agricultural University, Nanchang 330045, Jiangxi, PR China
| | - Ningbo Liao
- College of Food Science and Engineering, Jiangxi Agricultural University, Nanchang 330045, Jiangxi, PR China
| | - Guoping Wu
- College of Food Science and Engineering, Jiangxi Agricultural University, Nanchang 330045, Jiangxi, PR China
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Laanto E. Overcoming Bacteriophage Resistance in Phage Therapy. Methods Mol Biol 2024; 2738:401-410. [PMID: 37966611 DOI: 10.1007/978-1-0716-3549-0_23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2023]
Abstract
Antibiotic resistance among pathogenic bacteria is one of the most severe global challenges. It is predicted that over ten million lives will be lost annually by 2050. Phage therapy is a promising alternative to antibiotics. However, the ease of development of phage resistance during therapy is a concern. This review focuses on the possible ways to overcome phage resistance in phage therapy.
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Affiliation(s)
- Elina Laanto
- Department of Biological and Environmental Science and Nanoscience Center, University of Jyvaskyla, Jyväskylä, Finland.
- Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland.
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40
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Zurabov F, Petrova M, Zurabov A, Gurkova M, Polyakov P, Cheboksarov D, Chernevskaya E, Yuryev M, Popova V, Kuzovlev A, Yakovlev A, Grechko A. Adaptive Phage Therapy for the Prevention of Recurrent Nosocomial Pneumonia: Novel Protocol Description and Case Series. Antibiotics (Basel) 2023; 12:1734. [PMID: 38136768 PMCID: PMC10741035 DOI: 10.3390/antibiotics12121734] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 12/05/2023] [Accepted: 12/11/2023] [Indexed: 12/24/2023] Open
Abstract
Nowadays there is a growing interest worldwide in using bacteriophages for therapeutic purposes to combat antibiotic-resistant bacterial strains, driven by the increasing ineffectiveness of drugs against bacterial infections. Despite this fact, no novel commercially available therapeutic phage products have been developed in the last two decades, as it is extremely difficult to register them under the current legal regulations. This paper presents a description of the interaction between a bacteriophage manufacturer and a clinical institution, the specificity of which is the selection of bacteriophages not for an individual patient, but for the entire spectrum of bacteria circulating in the intensive care unit with continuous clinical and microbiological monitoring of efficacy. The study presents the description of three clinical cases of patients who received bacteriophage complex via inhalation for 28 days according to the protocol without antibiotic use throughout the period. No adverse effects were observed and the elimination of multidrug-resistant microorganisms from the bronchoalveolar lavage contents was detected in all patients. A decrease in such inflammatory markers as C-reactive protein (CRP) and procalcitonin was also noted. The obtained results demonstrate the potential of an adaptive phage therapy protocol in intensive care units for reducing the amount of antibiotics used and preserving their efficacy.
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Affiliation(s)
- Fedor Zurabov
- Research and Production Center “MicroMir”, 107031 Moscow, Russia; (A.Z.); (M.G.); (V.P.)
| | - Marina Petrova
- Federal Research and Clinical Center of Intensive Care Medicine and Rehabilitology, 10703 Moscow, Russia; (M.P.); (P.P.); (D.C.); (E.C.); (M.Y.); (A.K.); (A.Y.); (A.G.)
| | - Alexander Zurabov
- Research and Production Center “MicroMir”, 107031 Moscow, Russia; (A.Z.); (M.G.); (V.P.)
| | - Marina Gurkova
- Research and Production Center “MicroMir”, 107031 Moscow, Russia; (A.Z.); (M.G.); (V.P.)
| | - Petr Polyakov
- Federal Research and Clinical Center of Intensive Care Medicine and Rehabilitology, 10703 Moscow, Russia; (M.P.); (P.P.); (D.C.); (E.C.); (M.Y.); (A.K.); (A.Y.); (A.G.)
| | - Dmitriy Cheboksarov
- Federal Research and Clinical Center of Intensive Care Medicine and Rehabilitology, 10703 Moscow, Russia; (M.P.); (P.P.); (D.C.); (E.C.); (M.Y.); (A.K.); (A.Y.); (A.G.)
| | - Ekaterina Chernevskaya
- Federal Research and Clinical Center of Intensive Care Medicine and Rehabilitology, 10703 Moscow, Russia; (M.P.); (P.P.); (D.C.); (E.C.); (M.Y.); (A.K.); (A.Y.); (A.G.)
| | - Mikhail Yuryev
- Federal Research and Clinical Center of Intensive Care Medicine and Rehabilitology, 10703 Moscow, Russia; (M.P.); (P.P.); (D.C.); (E.C.); (M.Y.); (A.K.); (A.Y.); (A.G.)
| | - Valentina Popova
- Research and Production Center “MicroMir”, 107031 Moscow, Russia; (A.Z.); (M.G.); (V.P.)
| | - Artem Kuzovlev
- Federal Research and Clinical Center of Intensive Care Medicine and Rehabilitology, 10703 Moscow, Russia; (M.P.); (P.P.); (D.C.); (E.C.); (M.Y.); (A.K.); (A.Y.); (A.G.)
| | - Alexey Yakovlev
- Federal Research and Clinical Center of Intensive Care Medicine and Rehabilitology, 10703 Moscow, Russia; (M.P.); (P.P.); (D.C.); (E.C.); (M.Y.); (A.K.); (A.Y.); (A.G.)
| | - Andrey Grechko
- Federal Research and Clinical Center of Intensive Care Medicine and Rehabilitology, 10703 Moscow, Russia; (M.P.); (P.P.); (D.C.); (E.C.); (M.Y.); (A.K.); (A.Y.); (A.G.)
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Cobián Güemes AG, Ghatbale P, Blanc AN, Morgan CJ, Garcia A, Leonard J, Huang L, Kovalick G, Proost M, Chiu M, Kuo P, Oh J, Karthikeyan S, Knight R, Pogliano J, Schooley RT, Pride DT. Jumbo phages are active against extensively drug-resistant eyedrop-associated Pseudomonas aeruginosa infections. Antimicrob Agents Chemother 2023; 67:e0065423. [PMID: 37931230 PMCID: PMC10720484 DOI: 10.1128/aac.00654-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 09/08/2023] [Indexed: 11/08/2023] Open
Abstract
Antibiotic-resistant bacteria present an emerging challenge to human health. Their prevalence has been increasing across the globe due in part to the liberal use of antibiotics that has pressured them to develop resistance. Those bacteria that acquire mobile genetic elements are especially concerning because those plasmids may be shared readily with other microbes that can then also become antibiotic resistant. Serious infections have recently been related to the contamination of preservative-free eyedrops with extensively drug-resistant (XDR) isolates of Pseudomonas aeruginosa, already resulting in three deaths. These drug-resistant isolates cannot be managed with most conventional antibiotics. We sought to identify alternatives to conventional antibiotics for the lysis of these XDR isolates and identified multiple bacteriophages (viruses that attack bacteria) that killed them efficiently. We found both jumbo phages (>200 kb in genome size) and non-jumbo phages that were active against these isolates, the former killing more efficiently. Jumbo phages effectively killed the three separate XDR P. aeruginosa isolates both on solid and liquid medium. Given the ongoing nature of the XDR P. aeruginosa eyedrop outbreak, the identification of phages active against them provides physicians with several novel potential alternatives for treatment.
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Affiliation(s)
| | - Pooja Ghatbale
- Department of Pathology, University of California San Diego, La Jolla, California, USA
| | - Alisha N. Blanc
- Department of Pathology, University of California San Diego, La Jolla, California, USA
| | - Chase J. Morgan
- Department of Biology, University of California San Diego, La Jolla, California, USA
| | - Andrew Garcia
- Department of Pathology, University of California San Diego, La Jolla, California, USA
| | - Jesse Leonard
- Department of Pathology, University of California San Diego, La Jolla, California, USA
| | - Lina Huang
- Department of Pathology, University of California San Diego, La Jolla, California, USA
| | - Grace Kovalick
- Department of Pathology, University of California San Diego, La Jolla, California, USA
| | - Marissa Proost
- Department of Pathology, University of California San Diego, La Jolla, California, USA
| | - Megan Chiu
- Department of Pathology, University of California San Diego, La Jolla, California, USA
| | - Peiting Kuo
- Department of Pathology, University of California San Diego, La Jolla, California, USA
| | - Joseph Oh
- Department of Pathology, University of California San Diego, La Jolla, California, USA
| | - Smruthi Karthikeyan
- Department of Environmental Science and Engineering, Division of Engineering and Applied Science, California Institute of Technology, Pasadena, California, USA
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Rob Knight
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
- Center for Microbiome Innovation, University of California San Diego, La Jolla, California, USA
- Department of Bioengineering, University of California San Diego, La Jolla, California, USA
- Department of Computer Sciences & Engineering, University of California San Diego, La Jolla, California, USA
| | - Joe Pogliano
- Department of Biology, University of California San Diego, La Jolla, California, USA
- Howard Hughes Medical Institute, University of California San Diego, La Jolla, California, USA
| | - Robert T. Schooley
- Department of Medicine, University of California San Diego, La Jolla, California, USA
| | - David T. Pride
- Department of Pathology, University of California San Diego, La Jolla, California, USA
- Howard Hughes Medical Institute, University of California San Diego, La Jolla, California, USA
- Department of Medicine, University of California San Diego, La Jolla, California, USA
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42
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Fujiki J, Schnabl B. Phage therapy: Targeting intestinal bacterial microbiota for the treatment of liver diseases. JHEP Rep 2023; 5:100909. [PMID: 37965159 PMCID: PMC10641246 DOI: 10.1016/j.jhepr.2023.100909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 08/16/2023] [Accepted: 08/22/2023] [Indexed: 11/16/2023] Open
Abstract
Phage therapy has been overshadowed by antibiotics for decades. However, it is being revisited as a powerful approach against antimicrobial-resistant bacteria. As bacterial microbiota have been mechanistically linked to gastrointestinal and liver diseases, precise editing of the gut microbiota via the selective bactericidal action of phages has prompted renewed interest in phage therapy. In this review, we summarise the basic virological properties of phages and the latest findings on the composition of the intestinal phageome and the changes associated with liver diseases. We also review preclinical and clinical studies assessing phage therapy for the treatment of gastrointestinal and liver diseases, as well as future prospects and challenges.
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Affiliation(s)
- Jumpei Fujiki
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
- Department of Veterinary Medicine, Rakuno Gakuen University, Ebetsu, Hokkaido, Japan
| | - Bernd Schnabl
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
- Department of Medicine, VA San Diego Healthcare System, San Diego, CA, USA
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43
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Dharmaraj T, Kratochvil MJ, Pourtois JD, Chen Q, Hajfathalian M, Hargil A, Lin YH, Evans Z, Oromí-Bosch A, Berry JD, McBride R, Haddock NL, Holman DR, van Belleghem JD, Chang TH, Barr JJ, Lavigne R, Heilshorn SC, Blankenberg FG, Bollyky PL. Rapid assessment of changes in phage bioactivity using dynamic light scattering. PNAS NEXUS 2023; 2:pgad406. [PMID: 38111822 PMCID: PMC10726995 DOI: 10.1093/pnasnexus/pgad406] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/28/2023] [Accepted: 11/02/2023] [Indexed: 12/20/2023]
Abstract
Extensive efforts are underway to develop bacteriophages as therapies against antibiotic-resistant bacteria. However, these efforts are confounded by the instability of phage preparations and a lack of suitable tools to assess active phage concentrations over time. In this study, we use dynamic light scattering (DLS) to measure changes in phage physical state in response to environmental factors and time, finding that phages tend to decay and form aggregates and that the degree of aggregation can be used to predict phage bioactivity. We then use DLS to optimize phage storage conditions for phages from human clinical trials, predict bioactivity in 50-y-old archival stocks, and evaluate phage samples for use in a phage therapy/wound infection model. We also provide a web application (Phage-Estimator of Lytic Function) to facilitate DLS studies of phages. We conclude that DLS provides a rapid, convenient, and nondestructive tool for quality control of phage preparations in academic and commercial settings.
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Affiliation(s)
- Tejas Dharmaraj
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Beckman Center for Molecular and Genetic Medicine, Stanford, CA 94305, USA
- Sarafan ChEM-H, Stanford University, Stanford, CA 94305, USA
| | - Michael J Kratochvil
- Department of Materials Science and Engineering, Stanford University, Stanford, CA 94305, USA
| | - Julie D Pourtois
- Department of Biology, Hopkins Marine Station, Stanford University, Pacific Grove, CA 93950, USA
| | - Qingquan Chen
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Beckman Center for Molecular and Genetic Medicine, Stanford, CA 94305, USA
| | - Maryam Hajfathalian
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Beckman Center for Molecular and Genetic Medicine, Stanford, CA 94305, USA
| | - Aviv Hargil
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Beckman Center for Molecular and Genetic Medicine, Stanford, CA 94305, USA
| | - Yung-Hao Lin
- Department of Chemical Engineering, Stanford University, Stanford, CA 94305, USA
| | - Zoe Evans
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Beckman Center for Molecular and Genetic Medicine, Stanford, CA 94305, USA
| | | | - Joel D Berry
- Felix Biotechnology, South SanFrancisco, CA 94080, USA
| | | | - Naomi L Haddock
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Beckman Center for Molecular and Genetic Medicine, Stanford, CA 94305, USA
| | - Derek R Holman
- Division of Gastroenterology and Hepatology, Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Jonas D van Belleghem
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Beckman Center for Molecular and Genetic Medicine, Stanford, CA 94305, USA
| | - Tony H Chang
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Beckman Center for Molecular and Genetic Medicine, Stanford, CA 94305, USA
| | - Jeremy J Barr
- School of Biological Sciences, Monash University, Clayton, VIC 3800, Australia
| | - Rob Lavigne
- Department of Biosystems, KU Leuven, Leuven 3001, Belgium
| | - Sarah C Heilshorn
- Department of Materials Science and Engineering, Stanford University, Stanford, CA 94305, USA
| | - Francis G Blankenberg
- Division of Pediatric Radiology and Nuclear Medicine, Department of Radiology, Lucile Packard Children's Hospital, Stanford, CA 94305, USA
| | - Paul L Bollyky
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Beckman Center for Molecular and Genetic Medicine, Stanford, CA 94305, USA
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44
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Blumstein DT, Johnson NA, Katz ND, Kharpatin S, Ortiz‐Ross X, Parra E, Reshke A. Biological lessons for strategic resistance management. Evol Appl 2023; 16:1861-1871. [PMID: 38143901 PMCID: PMC10739074 DOI: 10.1111/eva.13616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 10/28/2023] [Indexed: 12/26/2023] Open
Abstract
Biological resistance to pesticides, vaccines, antibiotics, and chemotherapies creates huge costs to society, including extensive morbidity and mortality. We simultaneously face costly resistance to social changes, such as those required to resolve human-wildlife conflicts and conserve biodiversity and the biosphere. Viewing resistance as a force that impedes change from one state to another, we suggest that an analysis of biological resistance can provide unique and potentially testable insights into understanding resistance to social changes. We review key insights from managing biological resistance and develop a framework that identifies seven strategies to overcome resistance. We apply this framework to consider how it might be used to understand social resistance and generate potentially novel hypotheses that may be useful to both enhance the development of strategies to manage resistance and modulate change in socio-ecological systems.
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Affiliation(s)
- Daniel T. Blumstein
- Department of Ecology and Evolutionary BiologyUniversity of California Los AngelesLos AngelesCaliforniaUSA
| | - Norman A. Johnson
- Department of BiologyUniversity of MassachusettsAmherstMassachusettsUSA
| | - Nurit D. Katz
- Department of Ecology and Evolutionary BiologyUniversity of California Los AngelesLos AngelesCaliforniaUSA
| | - Samuel Kharpatin
- Department of Ecology and Evolutionary BiologyUniversity of California Los AngelesLos AngelesCaliforniaUSA
| | - Xochitl Ortiz‐Ross
- Department of Ecology and Evolutionary BiologyUniversity of California Los AngelesLos AngelesCaliforniaUSA
| | - Eliseo Parra
- Department of Ecology and Evolutionary BiologyUniversity of California Los AngelesLos AngelesCaliforniaUSA
| | - Amanda Reshke
- Department of Ecology and Evolutionary BiologyUniversity of California Los AngelesLos AngelesCaliforniaUSA
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45
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El Ghali A, Stamper K, Kunz Coyne AJ, Holger D, Kebriaei R, Alexander J, Lehman SM, Rybak MJ. Ciprofloxacin in combination with bacteriophage cocktails against multi-drug resistant Pseudomonas aeruginosa in ex vivo simulated endocardial vegetation models. Antimicrob Agents Chemother 2023; 67:e0072823. [PMID: 37877697 PMCID: PMC10649104 DOI: 10.1128/aac.00728-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 08/18/2023] [Indexed: 10/26/2023] Open
Abstract
Pseudomonas aeruginosa-associated infective endocarditis represents difficult-to-treat, deep-seated infections. Phage-antibiotic combinations have shown to eradicate multi-drug resistant (MDR) P. aeruginosa, limit the development of phage resistance, and restore antibiotic sensitivity. The objective of this study was to evaluate the activity of phage-ciprofloxacin (CIP) combinations in 4-day ex vivo simulated endocardial vegetation (SEV) models against drug-resistant P. aeruginosa isolates. Two P. aeruginosa isolates, extensively drug-resistant AR351 and MDR I0003-1, were selected for their drug resistance and sensitivity to phage. Three phages [LL-5504721-AH (LL), E2005-C (EC), and 109] and CIP were evaluated alone and in combination for their activity and influence on drug and phage resistance using 24-h time-kill analysis. The three-phage cocktail (q24h) in combination with CIP (400 mg q12h) was then tested in dynamic 4-day ex vivo SEV models, with reduction of log10 CFU/mL compared using ANOVA with Bonferroni analysis. Compared to other combinations, CIP-LL-EC-109 demonstrated synergistic and bactericidal activity from starting CFU/g against AR351 and I0003-1 (-Δ5.65 and 6.60 log10 CFU/g, respectively; P < 0.001). Additionally, CIP-LL-EC-109 mitigated phage resistance, while all other therapies had a high degree of resistance to >1 phages, and all phage-containing regimens prevented CIP mean inhibitory concentration increases compared to CIP alone for both AR351 and I0003-1 at 96 h.
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Affiliation(s)
- Amer El Ghali
- Anti-Infective Research Laboratory, Department of Pharmacy Practice, Eugene Applebaum College of Pharmacy and Health Sciences, Detroit, Michigan, USA
| | - Kyle Stamper
- Anti-Infective Research Laboratory, Department of Pharmacy Practice, Eugene Applebaum College of Pharmacy and Health Sciences, Detroit, Michigan, USA
| | - Ashlan J. Kunz Coyne
- Anti-Infective Research Laboratory, Department of Pharmacy Practice, Eugene Applebaum College of Pharmacy and Health Sciences, Detroit, Michigan, USA
| | - Dana Holger
- Anti-Infective Research Laboratory, Department of Pharmacy Practice, Eugene Applebaum College of Pharmacy and Health Sciences, Detroit, Michigan, USA
| | - Razieh Kebriaei
- Anti-Infective Research Laboratory, Department of Pharmacy Practice, Eugene Applebaum College of Pharmacy and Health Sciences, Detroit, Michigan, USA
| | - Jose Alexander
- Department of Microbiology, Virology and Immunology, AdventHealth Central Florida, Orlando, Florida, USA
| | - Susan M. Lehman
- Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, Maryland, USA
| | - Michael J. Rybak
- Anti-Infective Research Laboratory, Department of Pharmacy Practice, Eugene Applebaum College of Pharmacy and Health Sciences, Detroit, Michigan, USA
- Department of Medicine, Division of Infectious Diseases, Wayne State University, Detroit, Michigan, USA
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46
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Wang M, Ning Y, Jiao X, Liu J, Qiao J. Bacteriophages and their derived enzymes as promising alternatives for the treatment of Acinetobacter baumannii infections. Arch Virol 2023; 168:288. [PMID: 37947926 DOI: 10.1007/s00705-023-05910-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2023] [Accepted: 09/11/2023] [Indexed: 11/12/2023]
Abstract
Nosocomial infections with the opportunistic bacterium Acinetobacter baumannii pose a severe challenge to clinical treatment, which is aggravated by the increasing occurrence of multi-drug resistance, especially resistance to carbapenems. The use of phage therapy as an alternative and supplement to the current antibiotics has become an important research topic in the post-antibiotic era. This review summarizes in vivo and in vitro studies on phage therapy against multi-drug-resistant A. baumannii infection that have used different approaches, including treatment with a single phage, combination with other phages or non-phage agents, and administration of phage-derived enzymes. We also briefly discuss the current challenges of phage-based therapy as well as promising approaches for the treatment of A. baumannii infection in the future.
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Affiliation(s)
- Menglu Wang
- Department of Medical Laboratory, Weifang Medical University, Weifang, 261053, Shandong, People's Republic of China
| | - Yu Ning
- Department of Medical Laboratory, Weifang Medical University, Weifang, 261053, Shandong, People's Republic of China
| | - Xin Jiao
- Department of Medical Laboratory, Weifang Medical University, Weifang, 261053, Shandong, People's Republic of China
| | - Jiayi Liu
- Department of Medical Laboratory, Weifang Medical University, Weifang, 261053, Shandong, People's Republic of China
- Department of Basic Medicine, Weifang Nursing Vocational College, Weifang, 262500, Shandong, People's Republic of China
| | - Jinjuan Qiao
- Department of Medical Laboratory, Weifang Medical University, Weifang, 261053, Shandong, People's Republic of China.
- Institutional Key Laboratory of Clinical Laboratory Diagnostics, 12th 5-Year Project of Shandong Province, Weifang Medical University, Weifang, 261053, Shandong, People's Republic of China.
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47
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Bosco K, Lynch S, Sandaradura I, Khatami A. Therapeutic Phage Monitoring: A Review. Clin Infect Dis 2023; 77:S384-S394. [PMID: 37932121 DOI: 10.1093/cid/ciad497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2023] Open
Abstract
With the global rise in antimicrobial resistance, there has been a renewed interest in the application of therapeutic phages to treat bacterial infections. Therapeutic phage monitoring (TPM) is proposed as an essential element of phage therapy (PT) protocols to generate data and fill knowledge gaps regarding the in vivo efficacy of therapeutic phages, patients' immune responses to PT, and the wider ecological effects of PT. By monitoring phage concentrations in blood and tissues, together with immune responses and possible ecological changes during PT, TPM may enable the optimization of dosing and the implementation of precision medicine approaches. Furthermore, TPM can validate diagnostic surrogates of efficacy, direct research efforts, and establish quality assurance indicators for therapeutic phage products. Thus, TPM holds great potential for enhancing our understanding of the multidirectional phage-bacteria-host interactions and advancing "best practice" PT, ultimately improving patient care.
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Affiliation(s)
- Kiran Bosco
- Centre for Infectious Diseases and Microbiology, Westmead Institute for Medical Research, Westmead, New South Wales, Australia
- Faculty of Medicine and Health, Sydney Medical School, University of Sydney, Sydney, New South Wales, Australia
| | - Stephanie Lynch
- Centre for Infectious Diseases and Microbiology, Westmead Institute for Medical Research, Westmead, New South Wales, Australia
- Faculty of Medicine and Health, Sydney Medical School, University of Sydney, Sydney, New South Wales, Australia
| | - Indy Sandaradura
- Centre for Infectious Diseases and Microbiology, Westmead Institute for Medical Research, Westmead, New South Wales, Australia
- Faculty of Medicine and Health, Sydney Medical School, University of Sydney, Sydney, New South Wales, Australia
- Department of Infectious Diseases and Microbiology, The Children's Hospital at Westmead, Westmead, New South Wales, Australia
- Institute of Clinical Pathology and Medical Research, New South Wales Health Pathology, Westmead Hospital, Westmead, New South Wales, Australia
| | - Ameneh Khatami
- Faculty of Medicine and Health, Sydney Medical School, University of Sydney, Sydney, New South Wales, Australia
- Department of Infectious Diseases and Microbiology, The Children's Hospital at Westmead, Westmead, New South Wales, Australia
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48
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Fajardo-Lubian A, Venturini C. Use of Bacteriophages to Target Intracellular Pathogens. Clin Infect Dis 2023; 77:S423-S432. [PMID: 37932114 DOI: 10.1093/cid/ciad515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2023] Open
Abstract
Bacteriophages (phages) have shown great potential as natural antimicrobials against extracellular pathogens (eg, Escherichia coli or Klebsiella pneumoniae), but little is known about how they interact with intracellular targets (eg, Shigella spp., Salmonella spp., Mycobacterium spp.) in the mammalian host. Recent research has demonstrated that phages can enter human cells. However, for the design of successful clinical applications, further investigation is required to define their subcellular behavior and to understand the complex biological processes that underlie the interaction with their bacterial targets. In this review, we summarize the molecular evidence of phage internalization in eucaryotic cells, with specific focus on proof of phage activity against their bacterial targets within the eucaryotic host, and the current proposed strategies to overcome poor penetrance issues that may impact therapeutic use against the most clinically relevant intracellular pathogens.
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Affiliation(s)
- Alicia Fajardo-Lubian
- Faculty of Medicine and Health, Sydney ID Institute, University of Sydney, Sydney, New South Wales, Australia
- Centre for Infectious Diseases and Microbiology, Westmead Institute for Medical Research, Westmead, New South Wales, Australia
| | - Carola Venturini
- Centre for Infectious Diseases and Microbiology, Westmead Institute for Medical Research, Westmead, New South Wales, Australia
- Faculty of Science, Sydney School of Veterinary Science, University of Sydney, Sydney, New South Wales, Australia
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49
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Suh GA, Ferry T, Abdel MP. Phage Therapy as a Novel Therapeutic for the Treatment of Bone and Joint Infections. Clin Infect Dis 2023; 77:S407-S415. [PMID: 37932115 DOI: 10.1093/cid/ciad533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2023] Open
Abstract
Solutions for bone and joint infection (BJI) are needed where conventional treatments are inadequate. Bacteriophages (phages) are naturally occurring viruses that infect bacteria and have been harnessed for refractory bone and joint infections (BJI) in many case reports. Here we examine the safety and efficacy of English-language published cases of BJI since 2010 with phage therapy. From 33 reported cases of BJI treated with phage therapy, 29 (87%) achieved microbiological or clinical success, 2 (5.9%) relapsed with the same organisms, and 2 (5.9%) with a different organism. Of these 4 relapses, all but 1 had eventual clinical resolution with additional surgery or phage treatments. Eight out of 33 cases (24%) reported mild, transient adverse events with no serious events reported. Further work is needed to understand the true efficacy of phages and the role of phages in BJI. Opportunities lay ahead for thoughtfully designed clinical trials adapted to individualized therapies.
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Affiliation(s)
- Gina A Suh
- Division of Infectious Diseases, Department of Medicine, Mayo Clinic, Rochester Minnesota, USA
| | - Tristan Ferry
- Department of Infectious and Tropical Diseases, Hospital de la Croix-Rousse, Hospices Civils de Lyon, Lyon, France
| | - Matthew P Abdel
- Department of Orthopedic Surgery, Mayo Clinic, Rochester Minnesota, USA
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50
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Miele L, Evans RML, Cunniffe NJ, Torres-Barceló C, Bevacqua D. Evolutionary Epidemiology Consequences of Trait-Dependent Control of Heterogeneous Parasites. Am Nat 2023; 202:E130-E146. [PMID: 37963120 DOI: 10.1086/726062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2023]
Abstract
AbstractDisease control can induce both demographic and evolutionary responses in host-parasite systems. Foreseeing the outcome of control therefore requires knowledge of the eco-evolutionary feedback between control and system. Previous work has assumed that control strategies have a homogeneous effect on the parasite population. However, this is not true when control targets those traits that confer to the parasite heterogeneous levels of resistance, which can additionally be related to other key parasite traits through evolutionary trade-offs. In this work, we develop a minimal model coupling epidemiological and evolutionary dynamics to explore possible trait-dependent effects of control strategies. In particular, we consider a parasite expressing continuous levels of a trait-determining resource exploitation and a control treatment that can be either positively or negatively correlated with that trait. We demonstrate the potential of trait-dependent control by considering that the decision maker may want to minimize both the damage caused by the disease and the use of treatment, due to possible environmental or economic costs. We identify efficient strategies showing that the optimal type of treatment depends on the amount applied. Our results pave the way for the study of control strategies based on evolutionary constraints, such as collateral sensitivity and resistance costs, which are receiving increasing attention for both public health and agricultural purposes.
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