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Cui L, Watanabe S, Miyanaga K, Kiga K, Sasahara T, Aiba Y, Tan XE, Veeranarayanan S, Thitiananpakorn K, Nguyen HM, Wannigama DL. A Comprehensive Review on Phage Therapy and Phage-Based Drug Development. Antibiotics (Basel) 2024; 13:870. [PMID: 39335043 DOI: 10.3390/antibiotics13090870] [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: 08/23/2024] [Revised: 09/06/2024] [Accepted: 09/08/2024] [Indexed: 09/30/2024] Open
Abstract
Phage therapy, the use of bacteriophages (phages) to treat bacterial infections, is regaining momentum as a promising weapon against the rising threat of multidrug-resistant (MDR) bacteria. This comprehensive review explores the historical context, the modern resurgence of phage therapy, and phage-facilitated advancements in medical and technological fields. It details the mechanisms of action and applications of phages in treating MDR bacterial infections, particularly those associated with biofilms and intracellular pathogens. The review further highlights innovative uses of phages in vaccine development, cancer therapy, and as gene delivery vectors. Despite its targeted and efficient approach, phage therapy faces challenges related to phage stability, immune response, and regulatory approval. By examining these areas in detail, this review underscores the immense potential and remaining hurdles in integrating phage-based therapies into modern medical practices.
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Affiliation(s)
- Longzhu Cui
- Division of Bacteriology, Department of Infection and Immunity, School of Medicine, Jichi Medical University, Shimotsuke City 329-0498, Japan
| | - Shinya Watanabe
- Division of Bacteriology, Department of Infection and Immunity, School of Medicine, Jichi Medical University, Shimotsuke City 329-0498, Japan
| | - Kazuhiko Miyanaga
- Division of Bacteriology, Department of Infection and Immunity, School of Medicine, Jichi Medical University, Shimotsuke City 329-0498, Japan
| | - Kotaro Kiga
- Division of Bacteriology, Department of Infection and Immunity, School of Medicine, Jichi Medical University, Shimotsuke City 329-0498, Japan
- Research Center for Drug and Vaccine Development, National Institute of Infectious Diseases, Tokyo 162-8640, Japan
| | - Teppei Sasahara
- Division of Bacteriology, Department of Infection and Immunity, School of Medicine, Jichi Medical University, Shimotsuke City 329-0498, Japan
| | - Yoshifumi Aiba
- Division of Bacteriology, Department of Infection and Immunity, School of Medicine, Jichi Medical University, Shimotsuke City 329-0498, Japan
| | - Xin-Ee Tan
- Division of Bacteriology, Department of Infection and Immunity, School of Medicine, Jichi Medical University, Shimotsuke City 329-0498, Japan
| | - Srivani Veeranarayanan
- Division of Bacteriology, Department of Infection and Immunity, School of Medicine, Jichi Medical University, Shimotsuke City 329-0498, Japan
| | - Kanate Thitiananpakorn
- Division of Bacteriology, Department of Infection and Immunity, School of Medicine, Jichi Medical University, Shimotsuke City 329-0498, Japan
| | - Huong Minh Nguyen
- Division of Bacteriology, Department of Infection and Immunity, School of Medicine, Jichi Medical University, Shimotsuke City 329-0498, Japan
| | - Dhammika Leshan Wannigama
- Department of Infectious Diseases and Infection Control, Yamagata Prefectural Central Hospital, Yamagata 990-2292, Japan
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Uberoi A, McCready-Vangi A, Grice EA. The wound microbiota: microbial mechanisms of impaired wound healing and infection. Nat Rev Microbiol 2024; 22:507-521. [PMID: 38575708 DOI: 10.1038/s41579-024-01035-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/27/2024] [Indexed: 04/06/2024]
Abstract
The skin barrier protects the human body from invasion by exogenous and pathogenic microorganisms. A breach in this barrier exposes the underlying tissue to microbial contamination, which can lead to infection, delayed healing, and further loss of tissue and organ integrity. Delayed wound healing and chronic wounds are associated with comorbidities, including diabetes, advanced age, immunosuppression and autoimmune disease. The wound microbiota can influence each stage of the multi-factorial repair process and influence the likelihood of an infection. Pathogens that commonly infect wounds, such as Staphylococcus aureus and Pseudomonas aeruginosa, express specialized virulence factors that facilitate adherence and invasion. Biofilm formation and other polymicrobial interactions contribute to host immunity evasion and resistance to antimicrobial therapies. Anaerobic organisms, fungal and viral pathogens, and emerging drug-resistant microorganisms present unique challenges for diagnosis and therapy. In this Review, we explore the current understanding of how microorganisms present in wounds impact the process of skin repair and lead to infection through their actions on the host and the other microbial wound inhabitants.
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Affiliation(s)
- Aayushi Uberoi
- Departments of Dermatology and Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Amelia McCready-Vangi
- Departments of Dermatology and Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Elizabeth A Grice
- Departments of Dermatology and Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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McDonnell B, Parlindungan E, Vasiliauskaite E, Bottacini F, Coughlan K, Krishnaswami LP, Sassen T, Lugli GA, Ventura M, Mastroleo F, Mahony J, van Sinderen D. Viromic and Metagenomic Analyses of Commercial Spirulina Fermentations Reveal Remarkable Microbial Diversity. Viruses 2024; 16:1039. [PMID: 39066202 PMCID: PMC11281685 DOI: 10.3390/v16071039] [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: 05/21/2024] [Revised: 06/18/2024] [Accepted: 06/25/2024] [Indexed: 07/28/2024] Open
Abstract
Commercially produced cyanobacteria preparations sold under the name spirulina are widely consumed, due to their traditional use as a nutrient-rich foodstuff and subsequent marketing as a superfood. Despite their popularity, the microbial composition of ponds used to cultivate these bacteria is understudied. A total of 19 pond samples were obtained from small-scale spirulina farms and subjected to metagenome and/or virome sequencing, and the results were analysed. A remarkable level of prokaryotic and viral diversity was found to be present in the ponds, with Limnospira sp. and Arthrospira sp. sometimes being notably scarce. A detailed breakdown of prokaryotic and viral components of 15 samples is presented. Twenty putative Limnospira sp.-infecting bacteriophage contigs were identified, though no correlation between the performance of these cultures and the presence of phages was found. The high diversity of these samples prevented the identification of clear trends in sample performance over time, between ponds or when comparing successful and failed fermentations.
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Affiliation(s)
- Brian McDonnell
- School of Microbiology, University College Cork, T12 Y337 Cork, Ireland; (B.M.); (E.V.); (K.C.); (L.P.K.); (J.M.)
- APC Microbiome Ireland, University College Cork, T12 YT20 Cork, Ireland;
| | - Elvina Parlindungan
- School of Microbiology, University College Cork, T12 Y337 Cork, Ireland; (B.M.); (E.V.); (K.C.); (L.P.K.); (J.M.)
- APC Microbiome Ireland, University College Cork, T12 YT20 Cork, Ireland;
| | - Erika Vasiliauskaite
- School of Microbiology, University College Cork, T12 Y337 Cork, Ireland; (B.M.); (E.V.); (K.C.); (L.P.K.); (J.M.)
- APC Microbiome Ireland, University College Cork, T12 YT20 Cork, Ireland;
| | - Francesca Bottacini
- APC Microbiome Ireland, University College Cork, T12 YT20 Cork, Ireland;
- Biological Sciences, Munster Technological University, Bishopstown, T12 P928 Cork, Ireland
| | - Keith Coughlan
- School of Microbiology, University College Cork, T12 Y337 Cork, Ireland; (B.M.); (E.V.); (K.C.); (L.P.K.); (J.M.)
- APC Microbiome Ireland, University College Cork, T12 YT20 Cork, Ireland;
| | - Lakshmi Priyadarshini Krishnaswami
- School of Microbiology, University College Cork, T12 Y337 Cork, Ireland; (B.M.); (E.V.); (K.C.); (L.P.K.); (J.M.)
- APC Microbiome Ireland, University College Cork, T12 YT20 Cork, Ireland;
| | - Tom Sassen
- School of Microbiology, University College Cork, T12 Y337 Cork, Ireland; (B.M.); (E.V.); (K.C.); (L.P.K.); (J.M.)
- APC Microbiome Ireland, University College Cork, T12 YT20 Cork, Ireland;
- Microbiology Unit, Nuclear Medical Applications, Belgian Nuclear Research Centre, SCK CEN, 2400 Mol, Belgium;
| | - Gabriele Andrea Lugli
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, 43124 Parma, Italy; (G.A.L.); (M.V.)
- Interdepartmental Research Centre “Microbiome Research Hub”, University of Parma, 43124 Parma, Italy
| | - Marco Ventura
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, 43124 Parma, Italy; (G.A.L.); (M.V.)
- Interdepartmental Research Centre “Microbiome Research Hub”, University of Parma, 43124 Parma, Italy
| | - Felice Mastroleo
- Microbiology Unit, Nuclear Medical Applications, Belgian Nuclear Research Centre, SCK CEN, 2400 Mol, Belgium;
| | - Jennifer Mahony
- School of Microbiology, University College Cork, T12 Y337 Cork, Ireland; (B.M.); (E.V.); (K.C.); (L.P.K.); (J.M.)
- APC Microbiome Ireland, University College Cork, T12 YT20 Cork, Ireland;
| | - Douwe van Sinderen
- School of Microbiology, University College Cork, T12 Y337 Cork, Ireland; (B.M.); (E.V.); (K.C.); (L.P.K.); (J.M.)
- APC Microbiome Ireland, University College Cork, T12 YT20 Cork, Ireland;
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Morsli M, Salipante F, Magnan C, Dunyach-Remy C, Sotto A, Lavigne JP. Direct metagenomics investigation of non-surgical hard-to-heal wounds: a review. Ann Clin Microbiol Antimicrob 2024; 23:39. [PMID: 38702796 PMCID: PMC11069288 DOI: 10.1186/s12941-024-00698-z] [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: 10/13/2023] [Accepted: 04/22/2024] [Indexed: 05/06/2024] Open
Abstract
BACKGROUND Non-surgical chronic wounds, including diabetes-related foot diseases (DRFD), pressure injuries (PIs) and venous leg ulcers (VLU), are common hard-to-heal wounds. Wound evolution partly depends on microbial colonisation or infection, which is often confused by clinicians, thereby hampering proper management. Current routine microbiology investigation of these wounds is based on in vitro culture, focusing only on a limited panel of the most frequently isolated bacteria, leaving a large part of the wound microbiome undocumented. METHODS A literature search was conducted on original studies published through October 2022 reporting metagenomic next generation sequencing (mNGS) of chronic wound samples. Studies were eligible for inclusion if they applied 16 S rRNA metagenomics or shotgun metagenomics for microbiome analysis or diagnosis. Case reports, prospective, or retrospective studies were included. However, review articles, animal studies, in vitro model optimisation, benchmarking, treatment optimisation studies, and non-clinical studies were excluded. Articles were identified in PubMed, Google Scholar, Web of Science, Microsoft Academic, Crossref and Semantic Scholar databases. RESULTS Of the 3,202 articles found in the initial search, 2,336 articles were removed after deduplication and 834 articles following title and abstract screening. A further 14 were removed after full text reading, with 18 articles finally included. Data were provided for 3,628 patients, including 1,535 DRFDs, 956 VLUs, and 791 PIs, with 164 microbial genera and 116 species identified using mNGS approaches. A high microbial diversity was observed depending on the geographical location and wound evolution. Clinically infected wounds were the most diverse, possibly due to a widespread colonisation by pathogenic bacteria from body and environmental microbiota. mNGS data identified the presence of virus (EBV) and fungi (Candida and Aspergillus species), as well as Staphylococcus and Pseudomonas bacteriophages. CONCLUSION This study highlighted the benefit of mNGS for time-effective pathogen genome detection. Despite the majority of the included studies investigating only 16 S rDNA, ignoring a part of viral, fungal and parasite colonisation, mNGS detected a large number of bacteria through the included studies. Such technology could be implemented in routine microbiology for hard-to-heal wound microbiota investigation and post-treatment wound colonisation surveillance.
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Affiliation(s)
- Madjid Morsli
- Department of Microbiology and Hospital Hygiene, VBIC, INSERM U1047, Univ Montpellier, Platform MICRO&BIO, CHU Nîmes, Nîmes, France
| | - Florian Salipante
- Department of Biostatistics, Clinical Epidemiology, Public Health, and Innovation in Methodology (BESPIM), CHU Nîmes, Nîmes, France
| | - Chloé Magnan
- Department of Microbiology and Hospital Hygiene, VBIC, INSERM U1047, Univ Montpellier, Platform MICRO&BIO, CHU Nîmes, Nîmes, France
| | - Catherine Dunyach-Remy
- Department of Microbiology and Hospital Hygiene, VBIC, INSERM U1047, Univ Montpellier, Platform MICRO&BIO, CHU Nîmes, Nîmes, France
| | - Albert Sotto
- Department of Infectious Diseases, VBIC, INSERM U1047, Univ Montpellier, CHU Nîmes, Nîmes, France
| | - Jean-Philippe Lavigne
- Department of Microbiology and Hospital Hygiene, VBIC, INSERM U1047, Univ Montpellier, Platform MICRO&BIO, CHU Nîmes, Nîmes, France.
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Yang Y, Huang J, Zeng A, Long X, Yu N, Wang X. The role of the skin microbiome in wound healing. BURNS & TRAUMA 2024; 12:tkad059. [PMID: 38444635 PMCID: PMC10914219 DOI: 10.1093/burnst/tkad059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/11/2023] [Revised: 08/05/2023] [Accepted: 11/21/2023] [Indexed: 03/07/2024]
Abstract
The efficient management of skin wounds for rapid and scarless healing represents a major clinical unmet need. Nonhealing skin wounds and undesired scar formation impair quality of life and result in high healthcare expenditure worldwide. The skin-colonizing microbiota contributes to maintaining an intact skin barrier in homeostasis, but it also participates in the pathogenesis of many skin disorders, including aberrant wound healing, in many respects. This review focuses on the composition of the skin microbiome in cutaneous wounds of different types (i.e. acute and chronic) and with different outcomes (i.e. nonhealing and hypertrophic scarring), mainly based on next-generation sequencing analyses; furthermore, we discuss the mechanistic insights into host-microbe and microbe-microbe interactions during wound healing. Finally, we highlight potential therapeutic strategies that target the skin microbiome to improve healing outcomes.
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Affiliation(s)
- Yuyan Yang
- Department of Plastic and Reconstructive Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, No. 1, Shuaifuyuan, Dongcheng District, Beijing, 100005, China
| | - Jiuzuo Huang
- Department of Plastic and Reconstructive Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, No. 1, Shuaifuyuan, Dongcheng District, Beijing, 100005, China
| | - Ang Zeng
- Department of Plastic and Reconstructive Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, No. 1, Shuaifuyuan, Dongcheng District, Beijing, 100005, China
| | - Xiao Long
- Department of Plastic and Reconstructive Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, No. 1, Shuaifuyuan, Dongcheng District, Beijing, 100005, China
| | - Nanze Yu
- Department of Plastic and Reconstructive Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, No. 1, Shuaifuyuan, Dongcheng District, Beijing, 100005, China
| | - Xiaojun Wang
- Department of Plastic and Reconstructive Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, No. 1, Shuaifuyuan, Dongcheng District, Beijing, 100005, China
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Klose SM, Legione AR, Monotti I, Bushell RN, Sugiyama T, Browning GF, Vaz PK. Genomic characterization of Mycoplasma edwardii isolated from a dog bite induced cat wound reveals multiple horizontal gene transfer events and loss of the CRISPR/Cas system. J Med Microbiol 2024; 73. [PMID: 38167305 DOI: 10.1099/jmm.0.001788] [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: 01/05/2024] Open
Abstract
A domestic short hair cat (Felis catus) suffering from a purulent wound infection resulting from a dog bite was sampled for bacterial culture and isolation as the wound had been unresponsive to prolonged antimicrobial treatment. A mycoplasma was isolated from the wound. Whole genome sequencing of the isolate was performed using short-read Illumina and long-read Oxford Nanopore chemistry, and the organism was identified as Mycoplasma edwardii. Comparison of the genome sequence of the isolate to a reference M. edwardii genome sequence (canid isolate) identified the loss of several key bacterial factors involved in genome editing, as well the insertion of several novel ORFs most closely related to those found in other canine mycoplasmas, specifically Mycoplasma canis, M. cynos, M. molare and M. maculosa. This is only the second known report of disease caused by M. edwardii in a non-canid species, and the first report of it infecting and causing clinical disease in a cat.
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Affiliation(s)
- Sara M Klose
- Asia-Pacific Centre for Animal Health, Melbourne Veterinary School, University of Melbourne, VIC, Australia
- Institute of Molecular Medicine and Experimental Immunology, Faculty of Medicine, University of Bonn, NRW, Germany
| | - Alistair R Legione
- Asia-Pacific Centre for Animal Health, Melbourne Veterinary School, University of Melbourne, VIC, Australia
| | - Isobel Monotti
- U-Vet, Department of Veterinary Clinical Sciences, Melbourne Veterinary School, University of Melbourne, VIC, Australia
| | - Rhys N Bushell
- U-Vet, Department of Veterinary Clinical Sciences, Melbourne Veterinary School, University of Melbourne, VIC, Australia
| | - Takanori Sugiyama
- U-Vet, Department of Veterinary Clinical Sciences, Melbourne Veterinary School, University of Melbourne, VIC, Australia
- Present address: Animalius Vet, WA, Australia
| | - Glenn F Browning
- Asia-Pacific Centre for Animal Health, Melbourne Veterinary School, University of Melbourne, VIC, Australia
| | - Paola K Vaz
- Asia-Pacific Centre for Animal Health, Melbourne Veterinary School, University of Melbourne, VIC, Australia
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Morsli M, Salipante F, Gelis A, Magnan C, Guigon G, Lavigne J, Sotto A, Dunyach‐Remy C. Evolution of the urinary microbiota in spinal cord injury patients with decubitus ulcer: A snapshot study. Int Wound J 2024; 21:e14626. [PMID: 38272816 PMCID: PMC10805533 DOI: 10.1111/iwj.14626] [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: 10/05/2023] [Accepted: 12/14/2023] [Indexed: 01/27/2024] Open
Abstract
Current microbiome investigations of patients with pressure ulcers (PU) are mainly based on wound swabs and/or biopsy sequencing, leaving the colonization scenario unclear. Urinary microbiota has been never studied. As a part of the prospective ESCAFLOR study, we studied urinary microbiota of spinal cord injury (SCI) patients with PU without any urinary tract infection at the inclusion, collected at two times (at admission [D0] and after 28 days [D28]) during the patient's care, investigated by 16S rDNA metagenomics next generation sequencing. Subgroup analyses were carried out between patients with wounds showing improved evolution versus stagnated/worsened wounds at D28. Analysis was done using EPISEQ® 16S and R software. Among the 12 studied patients, the urinary microbiota of patients with improved wound evolution at D28 (n = 6) presented a significant decrease of microbial diversity. This modification was associated with the presence of Proteobacteria phylum and an increase of Escherichia-Shigella (p = 0.005), as well as the presence of probiotic anaerobic bacteria Lactobacillus and Bifidobacterium. In contrast, Proteus abundance was significantly increased in urine of patients with stagnated/worsened wound evolution (n = 6) (p = 0.003). This study proposes urinary microbiota as a complementary factor indirectly associated with the wound evolution and patient cure. It opens new perspectives for further investigations based on multiple body microbiome comparison to describe the complete scenario of the transmission dynamics of wound-colonizing microorganisms.
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Affiliation(s)
- Madjid Morsli
- Department of Microbiology and Hospital HygieneCHU Nîmes, Univ MontpellierNîmesFrance
| | - Florian Salipante
- Department of Biostatistics, Epidemiology, Public Health, and Innovation in Methodology (BESPIM)CHU Nîmes, Univ MontpellierNîmesFrance
| | - Anthony Gelis
- Centre Mutualiste Neurologique ProparaMontpellierFrance
| | - Chloé Magnan
- VBIC, INSERM U1047, Department of Microbiology and Hospital HygieneCHU Nîmes, Univ MontpellierNîmesFrance
| | | | - Jean‐Philippe Lavigne
- VBIC, INSERM U1047, Department of Microbiology and Hospital HygieneCHU Nîmes, Univ MontpellierNîmesFrance
| | - Albert Sotto
- VBIC, INSERM U1047, Department of Infectious and Tropical DiseasesCHU Nîmes, Univ MontpellierNîmesFrance
| | - Catherine Dunyach‐Remy
- VBIC, INSERM U1047, Department of Microbiology and Hospital HygieneCHU Nîmes, Univ MontpellierNîmesFrance
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Srinivasan A, Sajeevan A, Rajaramon S, David H, Solomon AP. Solving polymicrobial puzzles: evolutionary dynamics and future directions. Front Cell Infect Microbiol 2023; 13:1295063. [PMID: 38145044 PMCID: PMC10748482 DOI: 10.3389/fcimb.2023.1295063] [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: 09/15/2023] [Accepted: 11/03/2023] [Indexed: 12/26/2023] Open
Abstract
Polymicrobial infections include various microorganisms, often necessitating different treatment methods than a monomicrobial infection. Scientists have been puzzled by the complex interactions within these communities for generations. The presence of specific microorganisms warrants a chronic infection and impacts crucial factors such as virulence and antibiotic susceptibility. Game theory is valuable for scenarios involving multiple decision-makers, but its relevance to polymicrobial infections is limited. Eco-evolutionary dynamics introduce causation for multiple proteomic interactions like metabolic syntropy and niche segregation. The review culminates both these giants to form evolutionary dynamics (ED). There is a significant amount of literature on inter-bacterial interactions that remain unsynchronised. Such raw data can only be moulded by analysing the ED involved. The review culminates the inter-bacterial interactions in multiple clinically relevant polymicrobial infections like chronic wounds, CAUTI, otitis media and dental carries. The data is further moulded with ED to analyse the niche colonisation of two notoriously competitive bacteria: S.aureus and P.aeruginosa. The review attempts to develop a future trajectory for polymicrobial research by following recent innovative strategies incorporating ED to curb polymicrobial infections.
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Affiliation(s)
| | | | | | | | - Adline Princy Solomon
- Quorum Sensing Laboratory, Centre for Research in Infectious Diseases (CRID), School of Chemical and Biotechnology, SASTRA Deemed to be University, Thanjavur, India
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Mageiros L, Megremis S, Papadopoulos NG. The virome in allergy and asthma: A nascent, ineffable player. J Allergy Clin Immunol 2023; 152:1347-1351. [PMID: 37778473 DOI: 10.1016/j.jaci.2023.09.022] [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: 06/08/2023] [Revised: 08/28/2023] [Accepted: 09/19/2023] [Indexed: 10/03/2023]
Abstract
Allergic diseases can be affected by virus-host interactions and are increasingly linked with the tissue-specific microbiome. High-throughput metagenomic sequencing has offered the opportunity to study the presence of viruses as an ecologic system, namely, the virome. Even though virome studies are technically challenging conceptually and analytically, they are already producing novel data expanding our understanding of the pathophysiologic mechanisms related to chronic inflammation and allergy. The importance of interspecies and intraspecies interactions is becoming apparent, as they can significantly, directly or indirectly, affect the host's response and antigenic state. Here, we emphasize the challenges and potential insights related to study of the virome in the context of allergy and asthma. We review the limited number of studies that have investigated the virome in these conditions, underlining the need for prospective, repeated sampling designs to unravel the virome's impact on disease development and its interplay with microbiota and immunity. The potential therapeutic use of bacteriophages, which are highly complex components of the virome, is discussed. There is clearly a need for further in-depth investigation of the virome as a system in allergic diseases.
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Affiliation(s)
- Leonardos Mageiros
- Allergy Department, 2nd Pediatric Clinic, National and Kapodistrian University of Athens, Athens, Greece
| | | | - Nikolaos G Papadopoulos
- Allergy Department, 2nd Pediatric Clinic, National and Kapodistrian University of Athens, Athens, Greece; University of Manchester, Manchester, United Kingdom.
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Li R, Rouse M, Pace BT, Grey SF, Mclaughlin K, Schobel SA, Simons MP. Host CD3 + T-cells can significantly modulate phage treatment effects on bacterial bioburden in mouse models. Front Microbiol 2023; 14:1240176. [PMID: 37766890 PMCID: PMC10520710 DOI: 10.3389/fmicb.2023.1240176] [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: 06/14/2023] [Accepted: 08/03/2023] [Indexed: 09/29/2023] Open
Abstract
Wound healing is a complex system including such key players as host, microbe, and treatments. However, little is known about their dynamic interactions. Here we explored the interplay between: (1) bacterial bioburden and host immune responses, (2) bacterial bioburden and wound size, and (3) treatments and wound size, using murine models and various treatment modalities: Phosphate buffer saline (PBS or vehicle, negative control), doxycycline, and two doses of A. baumannii phage mixtures. We uncovered that the interplay between bacterial bioburden and host immune system may be bidirectional, and that there is an interaction between host CD3+ T-cells and phage dosage, which significantly impacts bacterial bioburden. Furthermore, the bacterial bioburden and wound size association is significantly modulated by the host CD3+ T-cells. When the host CD3+ T-cells (x on log10 scale) are in the appropriate range (1.35 < x < = 1.5), we observed a strong association between colony forming units (CFU) and wound size, indicating a hallmark of wound healing. On the basis of the findings and our previous work, we proposed an integrated parallel systems biology model.
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Affiliation(s)
- Renhua Li
- Uniformed Services University of the Health Sciences, Bethesda, MD, United States
- Surgical Critical Care Initiative (SC2i), Uniformed Services University (USU), Bethesda, MD, United States
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc, Bethesda, MD, United States
| | - Michael Rouse
- Uniformed Services University of the Health Sciences, Bethesda, MD, United States
- Surgical Critical Care Initiative (SC2i), Uniformed Services University (USU), Bethesda, MD, United States
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc, Bethesda, MD, United States
- Walter Reed National Military Medical Center, Bethesda, MD, United States
| | - Brendon T. Pace
- Uniformed Services University of the Health Sciences, Bethesda, MD, United States
- Eastern Virginia Medical School, Norfolk, VA, United States
| | - Scott F. Grey
- Uniformed Services University of the Health Sciences, Bethesda, MD, United States
- Surgical Critical Care Initiative (SC2i), Uniformed Services University (USU), Bethesda, MD, United States
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc, Bethesda, MD, United States
| | - Kimberly Mclaughlin
- Uniformed Services University of the Health Sciences, Bethesda, MD, United States
- Surgical Critical Care Initiative (SC2i), Uniformed Services University (USU), Bethesda, MD, United States
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc, Bethesda, MD, United States
| | - Seth A. Schobel
- Uniformed Services University of the Health Sciences, Bethesda, MD, United States
- Surgical Critical Care Initiative (SC2i), Uniformed Services University (USU), Bethesda, MD, United States
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc, Bethesda, MD, United States
| | - Mark P. Simons
- Uniformed Services University of the Health Sciences, Bethesda, MD, United States
- Naval Medical Research Center, Silver Spring, MD, United States
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Chen X, Shi X, Xiao H, Xiao D, Xu X. Research hotspot and trend of chronic wounds: A bibliometric analysis from 2013 to 2022. Wound Repair Regen 2023; 31:597-612. [PMID: 37552080 DOI: 10.1111/wrr.13117] [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: 03/30/2023] [Revised: 06/29/2023] [Accepted: 07/31/2023] [Indexed: 08/09/2023]
Abstract
Chronic wounds have been confirmed as a vital health problem facing people in the global population aging process. While significant progress has been achieved in the study of chronic wounds, the treatment effect should be further improved. The number of publications regarding chronic wounds has been rising rapidly. In this study, bibliometric analysis was conducted to explore the hotspots and trends in the research on chronic wounds. All relevant studies on chronic wounds between 2013 and 2022 were collected from the PubMed database of the Web of Science (WOS) and the National Center for Biotechnology Information (NCBI). The data were processed and visualised using a series of software. On that basis, more insights can be gained into hotspots and trends of this research field. Wound Repair and Regeneration has the highest academic achievement in the field of chronic wound research. The United States has been confirmed as the most productive country, and the University of California System ranks high among other institutions. Augustin, M. is the author of the most published study, and Frykberg, RG et al. published the most cited study. Furthermore, the hotspots of wound research over the last decade were identified (e.g., bandages, infection and biofilms, pathophysiology and therapy). This study will help researchers gain insights into chronic wound research's hotspots and trends accurately and quickly. Moreover, the exploration of bacterial biofilm and the pathophysiological mechanism of the chronic wound will lay a solid foundation and clear direction for treating chronic wounds.
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Affiliation(s)
- Xinghan Chen
- Department of Burns and Plastic Surgery, West China Hospital, Sichuan University, Chengdu, Sichuan, China
- Research Institute of Tissue Engineering and Stem Cells, Nanchong Central Hospital, the Second Clinical College of North Sichuan Medical College, Nanchong, Sichuan, China
| | - Xiujun Shi
- Research Institute of Tissue Engineering and Stem Cells, Nanchong Central Hospital, the Second Clinical College of North Sichuan Medical College, Nanchong, Sichuan, China
| | - Haitao Xiao
- Department of Burns and Plastic Surgery, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Dongqin Xiao
- Research Institute of Tissue Engineering and Stem Cells, Nanchong Central Hospital, the Second Clinical College of North Sichuan Medical College, Nanchong, Sichuan, China
| | - Xuewen Xu
- Department of Burns and Plastic Surgery, West China Hospital, Sichuan University, Chengdu, Sichuan, China
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Haddock NL, Barkal LJ, Bollyky PL. Bacteriophage populations mirror those of bacterial pathogens at sites of infection. mSystems 2023; 8:e0049723. [PMID: 37526425 PMCID: PMC10469793 DOI: 10.1128/msystems.00497-23] [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: 05/17/2023] [Accepted: 06/19/2023] [Indexed: 08/02/2023] Open
Abstract
Bacteriophages, viruses that parasitize bacteria, are known to be abundant at sites of bacterial colonization, but the relationship between phages and bacteria at sites of infection is unclear. Bacteriophages are highly specific to their bacterial host species, and so we hypothesize that phage populations would mirror those of bacterial pathogens within infected tissues. To test this, here we study publicly available cell-free DNA (cfDNA) generated using next-generation sequencing of infected bodily fluids, including urine, joint fluid, peritoneal fluid, bronchoalveolar lavage fluid, cerebrospinal fluid, and abscess fluid, as well as uninfected control samples. These were analyzed using a computational pipeline for identifying bacteriophage sequences in cfDNA. We find that bacteriophage sequences are present in both infected and uninfected bodily fluids and represent a variety of bacteriophage morphologies and bacterial hosts. Additionally, phages from Escherichia coli, Streptococcus, and Staphylococcus aureus are overrepresented both in terms of proportion and diversity in fluids infected with these same pathogens. These data indicate that phages reflect the relative abundance of their bacterial hosts at sites of infection. Bacteriophage sequences may help inform future investigative and diagnostic approaches that utilize cell-free DNA to study the microbiome within infected tissues. IMPORTANCE Bacteriophages are an active area of investigation in microbiome research, but most studies have focused on phage populations at sites of bacterial colonization. Little is known about bacteriophage ecology at sites of active infection. To address this gap in knowledge, we utilized a publicly available data set to study bacteriophage populations in cell-free DNA collected from sites of infection. We find that phages reflect the relative abundance of their bacterial hosts at sites of infection. These studies may lead to future investigative and diagnostic approaches that incorporate phages as well as bacterial cell-free DNA.
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Affiliation(s)
- N. L. Haddock
- Immunology Program, School of Medicine, Stanford University, Stanford, California, USA
| | - L. J. Barkal
- Division of Pulmonary, Allergy, and Critical Care Medicine, School of Medicine, Stanford University, Stanford, California, USA
| | - P. L. Bollyky
- Division of Infectious Diseases and Geographic Medicine, School of Medicine, Stanford University, Stanford, California, USA
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13
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The Efficiency and Safety of Platelet-Rich Plasma Dressing in the Treatment of Chronic Wounds: A Systematic Review and Meta-Analysis of Randomized Controlled Trials. J Pers Med 2023; 13:jpm13030430. [PMID: 36983611 PMCID: PMC10053387 DOI: 10.3390/jpm13030430] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 02/13/2023] [Accepted: 02/22/2023] [Indexed: 03/04/2023] Open
Abstract
Recently, many clinical trials have applied platelet-rich plasma (PRP) dressings to treat wounds that have stopped healing, which are also called chronic wounds. However, the clinical efficiency of PRP dressings in treating chronic wounds is still controversial. Therefore, we conducted this study to compare PRP dressings with normal saline dressings in treating chronic wounds. Relevant randomized controlled trials focusing on utilizing PRP dressings in treating chronic wounds were extracted from bibliographic databases. Finally, 330 patients with chronic wounds, reported in eight randomized controlled trials, were included in this study. In total, 169 out of 330 (51.21%) were treated with PRP dressings, and 161 out of 330 (48.79%) were treated with normal saline dressings. The pooled results showed that the complete healing rate of the PRP group was significantly higher than that of saline group at 8 weeks and 12 weeks, respectively. In addition, there were no significant differences in wound infection and adverse events. Compared with normal saline dressing, the PRP dressing could effectively enhance the prognosis of chronic wounds. Furthermore, the PRP did not increase wound infection rate or occurrence of adverse events as an available treatment for chronic wounds.
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Gupta S, Poret AJ, Hashemi D, Eseonu A, Yu SH, D'Gama J, Neel VA, Lieberman TD. Cutaneous Surgical Wounds Have Distinct Microbiomes from Intact Skin. Microbiol Spectr 2023; 11:e0330022. [PMID: 36541798 PMCID: PMC9927587 DOI: 10.1128/spectrum.03300-22] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 11/29/2022] [Indexed: 12/24/2022] Open
Abstract
Infections are relatively rare following cutaneous surgical procedures, despite the potential for wound exposure to pathogens both during surgery and throughout the healing process. Although gut commensals are believed to reduce the risk of intestinal infections, an analogous role for skin commensals has not been described. In fact, the microbiome of normally healing surgical skin wounds has not yet been profiled using culture-independent techniques. We characterized the wound microbiome in 53 patients who underwent skin cancer surgery and healed without signs or symptoms of infection. A week after surgery, several bacterial species displayed significant differences in relative abundance when compared to control, nonoperated skin from the same patient. The relative abundance of the most common bacterium found on intact skin, Cutibacterium acnes, was reduced in wounds 5-fold. Staphylococcus aureus, a frequent cause of postoperative skin infections, was enriched 6.4-fold in clinically noninfected wounds, suggesting active suppression of pathogenicity. Finally, members of the Corynebacterium genus were the dominant organism in postoperative wounds, making up 37% of the average wound microbiome. The enrichment of these bacteria in normally healing wounds suggests that they might be capable of providing colonization resistance. Future studies focused on the biological and clinical significance of the wound microbiome may shed light on normal wound healing and potential therapeutic opportunities to mitigate infection risk. IMPORTANCE Commensal bacteria on skin may limit the ability of pathogenic bacteria to cause clinically significant infections. The bacteria on healing acute wounds, which might provide such a protective effect, have not been described using culture-independent approaches in the absence of antibiotics. We compare the microbiome of wounds a week after skin cancer removal surgery with intact skin from the same patient. We find that the potentially pathogenic species S. aureus is common on these healing wounds despite the absence of symptoms or signs of infection. We report that bacteria often considered as potential skin probiotics, including Staphylococcus epidermidis, do not reach high relative abundance in wound microbiomes. In contrast, specific members of the Corynebacterium genus, rarely associated with infections, were significantly enriched in healing wounds compared to intact skin. Future work is needed to see if Corynebacterium species or derivatives thereof could be employed to lower the risk of wound infection.
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Affiliation(s)
- Sameer Gupta
- Department of Dermatology, MGH, Boston, Massachusetts, USA
| | - Alexandra J. Poret
- Institute for Medical Engineering and Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - David Hashemi
- Department of Dermatology, MGH, Boston, Massachusetts, USA
| | | | - Sherry H. Yu
- Department of Dermatology, MGH, Boston, Massachusetts, USA
| | | | - Victor A. Neel
- Department of Dermatology, MGH, Boston, Massachusetts, USA
| | - Tami D. Lieberman
- Institute for Medical Engineering and Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Ragon Institute of MIT, MGH, and Harvard, Cambridge, Massachusetts, USA
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
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15
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Bacteriophages and the Microbiome in Dermatology: The Role of the Phageome and a Potential Therapeutic Strategy. Int J Mol Sci 2023; 24:ijms24032695. [PMID: 36769020 PMCID: PMC9916943 DOI: 10.3390/ijms24032695] [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: 12/30/2022] [Revised: 01/23/2023] [Accepted: 01/30/2023] [Indexed: 02/04/2023] Open
Abstract
Bacteriophages, also known as phages, are viruses that selectively target and infect bacteria. In addition to bacterial dysbiosis, dermatologic conditions such as acne, psoriasis, and atopic dermatitis are characterized by a relative reduction in the abundance of phages and the overgrowth of the corresponding bacteria. Phages often exhibit high specificity for their targeted bacteria, making phage-replacement therapy a promising therapeutic strategy for the control of pathogenic bacteria in dermatologic disease. Novel therapeutic strategies regulating pathogenic bacteria are especially necessary in light of growing antibiotic resistance. In this review, we aimed to review the medical literature assessing phage dysbiosis and therapeutic trials in dermatology. Ultimately, studies have depicted promising results for the treatment of acne, psoriasis, and atopic dermatitis but are limited by low sample sizes and the omission of control groups in some trials. Additional work is necessary to validate the efficacy depicted in proof-of-concept trials and to further determine optimal treatment vehicles, administration mechanisms, and dosing schedules. This review provides the necessary framework for the assessment of phage efficacy in future trials.
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