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Sikora M, Wąsik S, Semaniak J, Drulis-Kawa Z, Wiśniewska-Wrona M, Arabski M. Chitosan-based matrix as a carrier for bacteriophages. Appl Microbiol Biotechnol 2024; 108:6. [PMID: 38165478 PMCID: PMC10761466 DOI: 10.1007/s00253-023-12838-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 09/21/2023] [Accepted: 10/03/2023] [Indexed: 01/03/2024]
Abstract
Wound healing is a dynamic and complex process where infection prevention is essential. Chitosan, thanks to its bactericidal activity against gram-positive and gram-negative bacteria, as well as anti-inflammatory and hemostatic properties, is an excellent candidate to design dressings for difficult-to-heal wound treatment. The great advantage of this biopolymer is its capacity to be chemically modified, which allows for the production of various functional forms, depending on the needs and subsequent use. Moreover, chitosan can be an excellent polymer matrix for bacteriophage (phage) packing as a novel alternative/supportive antibacterial therapy approach. This study is focused on the preparation and characteristics of chitosan-based material in the form of a film with the addition of Pseudomonas lytic phages (KTN4, KT28, and LUZ19), which would exhibit antibacterial activity as a potential dressing that accelerates the wound healing. We investigated the method of producing a polymer based on microcrystalline chitosan (MKCh) to serve as the matrix for phage deposition. We described some important parameters such as average molar mass, swelling capacity, surface morphology, phage release profile, and antibacterial activity tested in the Pseudomonas aeruginosa bacterial model. The chitosan polysaccharide turned out to interact with phage particles immobilizing them within a material matrix. Nevertheless, with the high hydrophilicity and swelling features of the prepared material, the external solution of bacterial culture was absorbed and phages went in direct contact with bacteria causing their lysis in the polymer matrix. KEY POINTS: • A novel chitosan-based matrix with the addition of active phages was prepared • Phage interactions with the chitosan matrix were determined as electrostatic • Phages in the matrix work through direct contact with the bacterial cells.
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Affiliation(s)
- Monika Sikora
- Department of Medical Biology, Institute of Biology, Jan Kochanowski University in Kielce, Kielce, Poland
- Lukasiewicz Research Network-Lodz Institute of Technology, Lodz, Poland
| | - Sławomir Wąsik
- Institute of Physics, Jan Kochanowski University in Kielce, Kielce, Poland
- Central Office of Measures, Warsaw, Poland
| | - Jacek Semaniak
- Institute of Physics, Jan Kochanowski University in Kielce, Kielce, Poland
- Central Office of Measures, Warsaw, Poland
| | - Zuzanna Drulis-Kawa
- Department of Pathogen Biology and Immunology, University of Wroclaw, Wroclaw, Poland
| | | | - Michał Arabski
- Department of Medical Biology, Institute of Biology, Jan Kochanowski University in Kielce, Kielce, Poland.
- Central Office of Measures, Warsaw, Poland.
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Aparicio-Blanco J, Vishwakarma N, Lehr CM, Prestidge CA, Thomas N, Roberts RJ, Thorn CR, Melero A. Antibiotic resistance and tolerance: What can drug delivery do against this global threat? Drug Deliv Transl Res 2024; 14:1725-1734. [PMID: 38341386 DOI: 10.1007/s13346-023-01513-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/23/2023] [Indexed: 02/12/2024]
Abstract
Antimicrobial resistance and tolerance (AMR&T) are urgent global health concerns, with alarmingly increasing numbers of antimicrobial drugs failing and a corresponding rise in related deaths. Several reasons for this situation can be cited, such as the misuse of traditional antibiotics, the massive use of sanitizing measures, and the overuse of antibiotics in agriculture, fisheries, and cattle. AMR&T management requires a multifaceted approach involving various strategies at different levels, such as increasing the patient's awareness of the situation and measures to reduce new resistances, reduction of current misuse or abuse, and improvement of selectivity of treatments. Also, the identification of new antibiotics, including small molecules and more complex approaches, is a key factor. Among these, novel DNA- or RNA-based approaches, the use of phages, or CRISPR technologies are some potent strategies under development. In this perspective article, emerging and experienced leaders in drug delivery discuss the most important biological barriers for drugs to reach infectious bacteria (bacterial bioavailability). They explore how overcoming these barriers is crucial for producing the desired effects and discuss the ways in which drug delivery systems can facilitate this process.
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Affiliation(s)
- Juan Aparicio-Blanco
- Department of Pharmaceutics and Food Technology, Faculty of Pharmacy, Complutense University of Madrid, 28040, Madrid, Spain
| | - Nikhar Vishwakarma
- Department of Pharmacy, Gyan Ganga Institute of Technology and Sciences, Jabalpur, 482003, Madhya Pradesh, India
| | - Claus-Michael Lehr
- Department Drug Delivery across Biological Barriers (DDEL), Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Saarbrücken, Germany
- Department of Pharmacy, Saarland University, Campus Building E8 1, 66123, Saarbrücken, Germany
| | - Clive A Prestidge
- Centre for Pharmaceutical Innovation, Clinical and Health Sciences, University of South Australia, Adelaide, SA, 5000, Australia
| | - Nicky Thomas
- Centre for Pharmaceutical Innovation, Clinical and Health Sciences, University of South Australia, Adelaide, SA, 5000, Australia
| | | | - Chelsea R Thorn
- Biotherapeutics Pharmaceutical Research and Development, Pfizer, Inc., 1 Burtt Road, Andover, MA, 01810, USA.
| | - Ana Melero
- Department of Pharmacy and Pharmaceutical Technology and Parasitology, Faculty of Pharmacy, University of Valencia, 46100, Burjassot, Spain.
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Wu Y, Gao N, Sun C, Feng T, Liu Q, Chen WH. A compendium of ruminant gastrointestinal phage genomes revealed a higher proportion of lytic phages than in any other environments. Microbiome 2024; 12:69. [PMID: 38576042 PMCID: PMC10993611 DOI: 10.1186/s40168-024-01784-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 02/29/2024] [Indexed: 04/06/2024]
Abstract
BACKGROUND Ruminants are important livestock animals that have a unique digestive system comprising multiple stomach compartments. Despite significant progress in the study of microbiome in the gastrointestinal tract (GIT) sites of ruminants, we still lack an understanding of the viral community of ruminants. Here, we surveyed its viral ecology using 2333 samples from 10 sites along the GIT of 8 ruminant species. RESULTS We present the Unified Ruminant Phage Catalogue (URPC), a comprehensive survey of phages in the GITs of ruminants including 64,922 non-redundant phage genomes. We characterized the distributions of the phage genomes in different ruminants and GIT sites and found that most phages were organism-specific. We revealed that ~ 60% of the ruminant phages were lytic, which was the highest as compared with those in all other environments and certainly will facilitate their applications in microbial interventions. To further facilitate the future applications of the phages, we also constructed a comprehensive virus-bacteria/archaea interaction network and identified dozens of phages that may have lytic effects on methanogenic archaea. CONCLUSIONS The URPC dataset represents a useful resource for future microbial interventions to improve ruminant production and ecological environmental qualities. Phages have great potential for controlling pathogenic bacterial/archaeal species and reducing methane emissions. Our findings provide insights into the virome ecology research of the ruminant GIT and offer a starting point for future research on phage therapy in ruminants. Video Abstract.
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Affiliation(s)
- Yingjian Wu
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-Imaging, Center for Artificial Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, Hubei, China
| | - Na Gao
- Department of Laboratory Medicine, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, 430071, China
| | - Chuqing Sun
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-Imaging, Center for Artificial Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, Hubei, China
| | - Tong Feng
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-Imaging, Center for Artificial Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, Hubei, China
| | - Qingyou Liu
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and Engineering, Foshan University, Foshan, 528225, China.
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, 530005, China.
| | - Wei-Hua Chen
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-Imaging, Center for Artificial Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, Hubei, China.
- Institution of Medical Artificial Intelligence, Binzhou Medical University, Yantai, 264003, China.
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Yeh HY, Cox NA, Hinton A, Berrang ME. Detection and Distribution of Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs) in Campylobacter jejuni Isolates from Chicken Livers. J Food Prot 2024; 87:100250. [PMID: 38382707 DOI: 10.1016/j.jfp.2024.100250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 02/12/2024] [Accepted: 02/15/2024] [Indexed: 02/23/2024]
Abstract
Campylobacter jejuni is the leading foodborne bacterial pathogen that causes human gastroenteritis worldwide linked to the consumption of undercooked broiler livers. Application of bacteriophages during poultry production has been used as an alternative approach to reduce contamination of poultry meat by Campylobacter. To make this approach effective, understanding the presence of the bacteriophage sequences in the CRISPR spacers in C. jejuni is critical as they may confer bacterial resistance to bacteriophage treatment. Therefore, in this study, we explored the distribution of the CRISPR arrays from 178 C. jejuni isolated from chicken livers between January and July 2018. Genomic DNA of C. jejuni isolates was extracted, and CRISPR type 1 sequences were amplified by PCR. Amplicons were purified and sequenced by the Sanger dideoxy sequencing method. Direct repeats (DRs) and spacers of CRISPR sequences were identified using the CRISPRFinder program. Further, spacer sequences were submitted to the CRISPRTarget to identify potential homology to bacteriophage types. Even though CRISPR-Cas is reportedly not an active system in Campylobacter, a total of 155 (87%) C. jejuni isolates were found to harbor CRISPR sequences; one type of DR was identified in all 155 isolates. The CRISPR loci lengths ranged from 97 to 431 nucleotides. The numbers of spacers ranged from one to six. A total of 371 spacer sequences were identified in the 155 isolates that could be grouped into 51 distinctive individual sequences. Further comparison of these 51 spacer sequences with those in databases showed that most spacer sequences were homologous to Campylobacter bacteriophage DA10. The results of our study provide important information relative to the development of an effective bacteriophage treatment to mitigate Campylobacter during poultry production.
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Affiliation(s)
- Hung-Yueh Yeh
- U.S. National Poultry Research Center, Agricultural Research Service, United States Department of Agriculture, 950 College Station Road, Athens, GA 30605-2720, USA.
| | - Nelson A Cox
- U.S. National Poultry Research Center, Agricultural Research Service, United States Department of Agriculture, 950 College Station Road, Athens, GA 30605-2720, USA
| | - Arthur Hinton
- U.S. National Poultry Research Center, Agricultural Research Service, United States Department of Agriculture, 950 College Station Road, Athens, GA 30605-2720, USA
| | - Mark E Berrang
- U.S. National Poultry Research Center, Agricultural Research Service, United States Department of Agriculture, 950 College Station Road, Athens, GA 30605-2720, USA
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Li Z, Guo X, Liu B, Huang T, Liu R, Liu X. Metagenome sequencing reveals shifts in phage-associated antibiotic resistance genes from influent to effluent in wastewater treatment plants. Water Res 2024; 253:121289. [PMID: 38341975 DOI: 10.1016/j.watres.2024.121289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 01/12/2024] [Accepted: 02/07/2024] [Indexed: 02/13/2024]
Abstract
Antibiotic resistance poses a significant threat to global health, and the microbe-rich activated sludge environment may contribute to the dissemination of antibiotic resistance genes (ARGs). ARGs spread across various bacterial populations via multiple dissemination routes, including horizontal gene transfer mediated by bacteriophages (phages). However, the potential role of phages in spreading ARGs in wastewater treatment systems remains unclear. This study characterized the core resistome, mobile genetic elements (MGEs), and virus-associated ARGs (vir_ARGs) in influents (Inf) and effluents (Eff) samples from nine WWTPs in eastern China. The abundance of ARGs in the Inf samples was higher than that in the Eff samples. A total of 21 core ARGs were identified, accounting for 38.70 %-83.70 % of the different samples. There was an increase in MGEs associated with phage-related processes from influents to effluents (from 12.68 % to 21.10 %). These MGEs showed strong correlations in relative abundance and composition with the core ARGs in the Eff samples. Across the Inf and Eff samples, 58 unique vir_ARGs were detected, with the Eff samples exhibiting higher diversity of vir_ARGs than the Inf samples. Statistical analyses indicated a robust relationship between core ARG profile, MGEs associated with phage-related processes, and vir_ARG composition in the Eff samples. Additionally, the co-occurrence of MGEs and ARGs in viral genomes was observed, ranging from 22.73 % to 68.75 %. This co-occurrence may exacerbate the persistence and spread of ARGs within WWTPs. The findings present new information on the changes in core ARGs, MGEs, and phage-associated ARGs from influents to effluents in WWTPs and provide new insights into the role of phage-associated ARGs in these systems.
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Affiliation(s)
- Zong Li
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China; Binzhou Institute of Technology, Binzhou 256212, China
| | - Xiaoxiao Guo
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China; Binzhou Institute of Technology, Binzhou 256212, China
| | - Bingxin Liu
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ting Huang
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ruyin Liu
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China; Binzhou Institute of Technology, Binzhou 256212, China.
| | - Xinchun Liu
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China; Binzhou Institute of Technology, Binzhou 256212, China.
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Chepchumba B, Asudi GO, Katana J, Ngayo MO, Khayeli JA. Isolation of phages against Streptococcus species in the oral cavity for potential control of dental diseases and associated systemic complications. Arch Microbiol 2024; 206:175. [PMID: 38493441 DOI: 10.1007/s00203-024-03897-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2023] [Revised: 02/07/2024] [Accepted: 02/12/2024] [Indexed: 03/19/2024]
Abstract
Dental infections and systemic complications caused by Streptococcus species in the oral cavity are increasingly exhibiting resistance to commonly used antibiotics, posing a potential threat to global public health. Phage therapy may offer a superior alternative, given that bacteriophages can be easily isolated and rapidly replicate in large numbers. In this study, six Streptococcus species from the oral cavity were characterized. Bacteriophages isolated from wastewater using five of these species as hosts produced plaques ranging from 0.2 to 2.4 mm in size. The phages demonstrated stability within a temperature range of 4 ℃ to 37 ℃. However, at temperatures exceeding 45 ℃, a noticeable reduction in bacteriophage titer was observed. Similarly, the phages showed greater stability within a pH range of 5 to 10. The isolated phages exhibited latency periods ranging from 15 to 20 min and had burst sizes varying from 10 to 200 viral particles. This study supports the potential use of bacteriophages in controlling infections caused by Streptococcus species.
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Affiliation(s)
- Beatrice Chepchumba
- Department of Biochemistry, Microbiology and Biotechnology, Kenyatta University, Nairobi, Kenya.
| | - George O Asudi
- Department of Biochemistry, Microbiology and Biotechnology, Kenyatta University, Nairobi, Kenya
| | - Japhet Katana
- Center for Microbiology Research, Kenya Medical Research Institute, Nairobi, Kenya
| | - Musa O Ngayo
- Center for Microbiology Research, Kenya Medical Research Institute, Nairobi, Kenya
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Xiong X, Gong J, Lu T, Yuan L, Lan Y, Tu X. Characteristics of intestinal bacteriophages and their relationship with Bacteria and serum metabolites during quail sexual maturity transition. BMC Vet Res 2024; 20:93. [PMID: 38459523 PMCID: PMC10921806 DOI: 10.1186/s12917-024-03945-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 02/20/2024] [Indexed: 03/10/2024] Open
Abstract
BACKGROUND Bacteriophages are prokaryotic viruses that rank among the most abundant microbes in the gut but remain among the least understood, especially in quails. In this study, we surveyed the gut bacteriophage communities in 22 quails at different ages (days 20 and 70) using shotgun metagenomic sequencing. We then systematically evaluated the relationships with gut bacteria and host serum metabolites. RESULTS We discovered that Myoviridae and Siphoviridae were the dominant bacteriophage families in quails. Through a random forest and LEfSe analysis, we identified 23 differential bacteriophages with overlapping presence. Of these, 21 bacteriophages (e.g., Enterococcus phage IME-EFm5 and Enterococcus phage IME-EFm1) showed higher abundances in the day 20 group, while two bacteriophages (Bacillus phage Silence and Bacillus virus WPh) were enriched in the day 70 group. These key bacteriophages can serve as biomarkers for quail sexual maturity. Additionally, the differential bacteriophages significantly correlated with specific bacterial species and shifts in the functional capacities of the gut microbiome. For example, Enterococcus phages (e.g., Enterococcus phage EFP01, Enterococcus phage IME-EFm5, and Enterococcus phage IME-EFm1) were significantly (P < 0.001, FDR) and positively correlated with Enterococcus faecalis. However, the relationships between the host serum metabolites and either bacteriophages or bacterial species varied. None of the bacteriophages significantly (P > 0.05, FDR) correlated with nicotinamide riboside and triacetate lactone. In contrast, some differential bacterial species (e.g., Christensenella massiliensis and Bacteroides neonati) significantly (P < 0.05, FDR) correlated with nicotinamide riboside and triacetate lactone. Furthermore, characteristic successional alterations in gut bacteriophages, bacteria, and host serum metabolites across different ages highlighted a sexual maturity transition coexpression network. CONCLUSION This study improves our understanding of the gut bacteriophage characteristics in quails and offers profound insights into the interactions among gut bacteriophages, bacteria, and host serum metabolites during the quail's sexual maturity transition.
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Affiliation(s)
- Xinwei Xiong
- Jiangxi Provincial Key Laboratory of Poultry Genetic Improvement, Nanchang Normal University, Nanchang, Jiangxi, 330032, China.
| | - Jishang Gong
- Jiangxi Provincial Key Laboratory of Poultry Genetic Improvement, Nanchang Normal University, Nanchang, Jiangxi, 330032, China
| | - Tian Lu
- Jiangxi Provincial Key Laboratory of Poultry Genetic Improvement, Nanchang Normal University, Nanchang, Jiangxi, 330032, China
| | - Liuying Yuan
- Jiangxi Provincial Key Laboratory of Poultry Genetic Improvement, Nanchang Normal University, Nanchang, Jiangxi, 330032, China
| | - Yuehang Lan
- Jiangxi Provincial Key Laboratory of Poultry Genetic Improvement, Nanchang Normal University, Nanchang, Jiangxi, 330032, China
| | - Xutang Tu
- Jiangxi Provincial Key Laboratory of Poultry Genetic Improvement, Nanchang Normal University, Nanchang, Jiangxi, 330032, China.
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Shanmugasundaram S, Nayak N, Puzhankara L, Kedlaya MN, Rajagopal A, Karmakar S. Bacteriophages: the dawn of a new era in periodontal microbiology? Crit Rev Microbiol 2024; 50:212-223. [PMID: 36883683 DOI: 10.1080/1040841x.2023.2182667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 01/02/2023] [Accepted: 02/15/2023] [Indexed: 03/09/2023]
Abstract
The oral microbiome, populated by a diverse range of species, plays a critical role in the initiation and progression of periodontal disease. The most dominant yet little-discussed players in the microbiome, the bacteriophages, influence the health and disease of the host in various ways. They, not only contribute to periodontal health by preventing the colonization of pathogens and disrupting biofilms but also play a role in periodontal disease by upregulating the virulence of periodontal pathogens through the transfer of antibiotic resistance and virulence factors. Since bacteriophages selectively infect only bacterial cells, they have an enormous scope to be used as a therapeutic strategy; recently, phage therapy has been successfully used to treat antibiotic-resistant systemic infections. Their ability to disrupt biofilms widens the scope against periodontal pathogens and dental plaque biofilms in periodontitis. Future research focussing on the oral phageome and phage therapy's effectiveness and safety could pave way for new avenues in periodontal therapy. This review explores our current understanding of bacteriophages, their interactions in the oral microbiome, and their therapeutic potential in periodontal disease.
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Affiliation(s)
- Shashikiran Shanmugasundaram
- Department of Periodontology, Manipal College of Dental Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Namratha Nayak
- Department of Periodontology, Manipal College of Dental Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Lakshmi Puzhankara
- Department of Periodontology, Manipal College of Dental Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Madhurya N Kedlaya
- Department of Periodontology, Manipal College of Dental Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Anjale Rajagopal
- Department of Periodontology, Manipal College of Dental Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Shaswata Karmakar
- Department of Periodontology, Manipal College of Dental Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, India
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Kelishomi FZ, Nikkhahi F, Amereh S, Ghayyaz F, Marashi SMA, Javadi A, Shahbazi G, Khakpour M. Evaluation of the therapeutic effect of a novel bacteriophage in the healing process of infected wounds with Klebsiella pneumoniae in mice. J Glob Antimicrob Resist 2024; 36:371-378. [PMID: 38307250 DOI: 10.1016/j.jgar.2024.01.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 07/23/2023] [Accepted: 01/25/2024] [Indexed: 02/04/2024] Open
Abstract
OBJECTIVE Bacterial wound infections have recently become a threat to public health. The emergence of multidrug-resistant (MDR) strains of Klebsiella pneumoniae highlights the need for a new treatment method. The effectiveness of bacteriophages has been observed for several infections in animal models and human trials. In this study, we assessed the effectiveness of bacteriophages in the treatment of wound infections associated with MDR and biofilm-producing K. pneumoniae and compared its effectiveness with that of gentamicin. METHODS A lytic phage against MDR K. pneumoniae was isolated and identified. The effectiveness of phages in the treatment of wound infection in mice was investigated and its effectiveness was compared with gentamicin. RESULTS The results showed that the isolated phage belonged to the Drexlerviridae family. This phage acts like gentamicin and effectively eliminates bacteria from wounds. In addition, mice in the phage therapy group were in better physical condition. CONCLUSION Our results demonstrated the success of phage therapy in the treatment of mice wounds infected with K. pneumoniae. These results indicate the feasibility of topical phage therapy for the safe treatment of wound infections.
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Affiliation(s)
| | - Farhad Nikkhahi
- Medical Microbiology Research Center, Qazvin University of Medical Sciences, Qazvin, Iran.
| | - Samira Amereh
- Medical Microbiology Research Center, Qazvin University of Medical Sciences, Qazvin, Iran
| | - Fatemeh Ghayyaz
- Medical Microbiology Research Center, Qazvin University of Medical Sciences, Qazvin, Iran
| | | | - Amir Javadi
- Department of Community Medicine, School of Medicine, Qazvin University of medical Sciences, Qazvin, Iran
| | - Gholamhassan Shahbazi
- Medical Microbiology Research Center, Qazvin University of Medical Sciences, Qazvin, Iran
| | - Mohadeseh Khakpour
- Medical Microbiology Research Center, Qazvin University of Medical Sciences, Qazvin, Iran
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Hassannia M, Naderifar M, Salamy S, Akbarizadeh MR, Mohebi S, Moghadam MT. Engineered phage enzymes against drug-resistant pathogens: a review on advances and applications. Bioprocess Biosyst Eng 2024; 47:301-312. [PMID: 37962644 DOI: 10.1007/s00449-023-02938-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Accepted: 10/16/2023] [Indexed: 11/15/2023]
Abstract
In recent decades, the expansion of multi and extensively drug-resistant (MDR and XDR) bacteria has reached an alarming rate, causing serious health concerns. Infections caused by drug-resistant bacteria have been associated with morbidity and mortality, making tackling bacterial resistance an urgent and unmet challenge that needs to be addressed properly. Endolysins are phage-encoded enzymes that can specifically degrade the bacterial cell wall and lead to bacterial death. There is remarkable evidence that corroborates the unique ability of endolysins to rapidly digest the peptidoglycan particular bonds externally without the assistance of phage. Thus, their modulation in therapeutic approaches has opened new options for therapeutic applications in the fight against bacterial infections in the human and veterinary sectors, as well as within the agricultural and biotechnology areas. The use of genetically engineered phage enzymes (EPE) promises to generate endolysin variants with unique properties for prophylactic and therapeutic applications. These approaches have gained momentum to accelerate basic as well as translational phage research and the potential development of therapeutics in the near future. This review will focus on the novel knowledge into EPE and demonstrate that EPE has far better performance than natural endolysins and phages in dealing with antibiotic-resistant infections. Therefore, it provides essential information for clinical trials involving EPE.
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Affiliation(s)
- Mohadeseh Hassannia
- Department of Genetic, Faculty of Science, Islamic Azad University, Tehran, Iran
| | - Mahin Naderifar
- School of Medicine, Zabol University of Medical Sciences, Zabol, Iran
| | - Shakiba Salamy
- Department of Microbiology, Faculty of Pharmacy, Islamic Azad University, Tehran, Iran
| | | | - Samane Mohebi
- Department of Bacteriology and Virology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
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He J, Wong CW, Schultze DM, Wang S. Inactivation of Salmonella enteritidis in liquid egg yolk and egg white using bacteriophage cocktails. Curr Res Food Sci 2024; 8:100703. [PMID: 38444729 PMCID: PMC10912847 DOI: 10.1016/j.crfs.2024.100703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 02/13/2024] [Accepted: 02/17/2024] [Indexed: 03/07/2024] Open
Abstract
Salmonella Enteritidis (SE) is a significant global cause of foodborne illness, often linked to egg contamination. This study evaluated the inhibitory effects of eight bacteriophages (phages) against three SE strains isolated from poultry environments. The most effective phages were selected to formulate different phage cocktails, to enhance the efficacy and prolong inhibition. Four phage cocktails were tested at a multiplicity of infection (MOI) of 100 in tryptic soy broth (TSB), and at MOIs of 100 and 1000 in liquid egg white (EW) and egg yolk (EY) with storage at 8 °C for up to 30 days (d). The effectiveness of the phage cocktails varied significantly among bacterial strains, yet all demonstrated significant reductions compared to the positive control in liquid culture (P < 0.05). Similarly, the tested SE strains in both EW and EY showed significant reductions with phage treatments (P < 0.005), although the effectiveness was influenced by the MOI and medium composition. Treating EY proved to be more challenging, with lower magnitudes of reduction and longer treatment durations required, compared to EW. Reductions ranged from 1 to greater than 4 log CFU/mL in EW and EY after 30 d, with consistently higher reductions achieved at MOI 1000. Phage titers decreased initially, but remained stable following SE inoculation in broth and liquid eggs at 8 °C, indicating that lysis from without mechanisms may have contributed to the inhibitory effect. Notably, phages exhibited stronger attachment to SE in EW, which can be attributed to be less viscous nature of EW compared to EY. This study demonstrated that phage applications in both EW and EY effectively reduced SE counts at 8 °C, with no regrowth during long-term storage. These findings contribute to the development of biocontrol methods that enhance food safety and reduce foodborne outbreaks associated with contaminated egg products.
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Affiliation(s)
- Jiangning He
- Food, Nutrition and Health, The University of British Columbia, 2205 East Mall, Vancouver, BC, V6R 1Z4, Canada
| | - Catherine W.Y. Wong
- Food, Nutrition and Health, The University of British Columbia, 2205 East Mall, Vancouver, BC, V6R 1Z4, Canada
| | - Danielle M. Schultze
- Food, Nutrition and Health, The University of British Columbia, 2205 East Mall, Vancouver, BC, V6R 1Z4, Canada
| | - Siyun Wang
- Food, Nutrition and Health, The University of British Columbia, 2205 East Mall, Vancouver, BC, V6R 1Z4, Canada
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12
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Atrashkevich A, Alum A, Stirling R, Abbaszadegan M, Garcia-Segura S. Approaching easy water disinfection for all: Can in situ electrochlorination outperform conventional chlorination under realistic conditions? Water Res 2024; 250:121014. [PMID: 38128307 DOI: 10.1016/j.watres.2023.121014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 11/29/2023] [Accepted: 12/11/2023] [Indexed: 12/23/2023]
Abstract
Electrochlorination has gained research interest for its potential application as decentralized water treatment. A number of studies have displayed promising efficiency for water disinfection. However, a comprehensive comparison of in situ electrodisinfection to existing disinfection techniques, particularly under realistic water composition and flow rates, still needs additional research efforts. The aim of this study is to evaluate in situ electrochlorination while comparing the treatment with conventional chemical chlorination for point-of-entry decentralized disinfection at the household level. An electrochemical flow cell reactor was operated in a single pass mode considering water flow and water consumption for a household of four family members. Disinfection efficiency assessment of both electrochemical and chemical chlorination was conducted using bacterial and viral surrogates, E. coli and MS2 bacteriophage. Furthermore, a techno-economic analysis was conducted, using the levelized cost of water, to compare two electrochemical chlorination scenarios (i.e., electrical grid energy use, and solar panel powered system) and benchmarked against the baseline treatment of chemical chlorination. The findings revealed increased inactivation efficiency of in situ electrochlorination over conventional chlorination (p-value < 0.05). The synergetic impact of radicals and chlorine, and/or contribution of high chlorine concentration at acidic pH near anode surface were identified as key factors that could enhance disinfection performance of in situ electrochlorination. The techno-economic analysis demonstrated that electrochemical treatment, when operated using renewable energy sources, is not only a more environmentally sustainable approach, but also emerges as a more economically feasible solution for decentralized water treatment application. The results highlight that in situ electrochlorination is a more advanced alternative to decentralized water chlorination. However, further fundamental research on products and by-products formation under various water matrices is required.
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Affiliation(s)
- Aksana Atrashkevich
- School of Sustainable Engineering and the Built Environment, Arizona State University, Tempe, AZ 85287-3005, USA; Nanosystems Engineering Research Center for Nanotechnology-Enabled Water Treatment, Tempe, AZ 85287-3005, USA
| | - Absar Alum
- School of Sustainable Engineering and the Built Environment, Arizona State University, Tempe, AZ 85287-3005, USA; Water and Environmental Technology Center, Arizona State University, Tempe, AZ 85281, USA
| | - Robert Stirling
- School of Sustainable Engineering and the Built Environment, Arizona State University, Tempe, AZ 85287-3005, USA; Nanosystems Engineering Research Center for Nanotechnology-Enabled Water Treatment, Tempe, AZ 85287-3005, USA
| | - Morteza Abbaszadegan
- School of Sustainable Engineering and the Built Environment, Arizona State University, Tempe, AZ 85287-3005, USA; Water and Environmental Technology Center, Arizona State University, Tempe, AZ 85281, USA
| | - Sergi Garcia-Segura
- School of Sustainable Engineering and the Built Environment, Arizona State University, Tempe, AZ 85287-3005, USA; Nanosystems Engineering Research Center for Nanotechnology-Enabled Water Treatment, Tempe, AZ 85287-3005, USA.
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13
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Sánchez C, Garde S, Landete JM, Calzada J, Baker DJ, Evans R, Narbad A, Mayer MJ, Ávila M. Identification, activity and delivery of new LysFA67 endolysin to target cheese spoilage Clostridium tyrobutyricum. Food Microbiol 2024; 117:104401. [PMID: 37919009 DOI: 10.1016/j.fm.2023.104401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 10/03/2023] [Accepted: 10/07/2023] [Indexed: 11/04/2023]
Abstract
Bacteriophages and their endolysins are potential biocontrol agents for the anaerobic spoilage organism Clostridium tyrobutyricum, which causes cheese late blowing defect. This study sequenced and compared the genomes of eight bacteriophages from Spanish dairy farms that were active against C. tyrobutyricum, to identify novel species and phage proteins. Phages vB_CtyS-FA67 and vB_CtyS-FA70 shared >94% intergenomic similarity to each other but neither phage had significant similarity to ΦCTP1, the unique C. tyrobutyricum phage sequenced to date. Taxonomic analysis indicated that both phages belong to the class Caudoviricetes and are related to dsDNA viruses with long non-contractile tails. vB_CtyS-FA67 had no other close relatives and encoded a novel endolysin, LysFA67, predicted to belong to the glycoside hydrolase GH24 family. LysFA67 lysed 93% of C. tyrobutyricum cells after 4 min in turbidity reduction assays, retaining lytic activity at pHs 4.2-8.1 and at 30-45 °C. The endolysin remained stable after 30 d storage at 4, 12 and 25 °C, while its activity decreased at -20 °C. LysFA67 lysed several clostridia species, while common dairy bacteria were not affected. Lactococcus lactis INIA 437, used as a cheese starter, was engineered to deliver LysFA67 and red fluorescent LysFA67-mCherry to dairy products. We demonstrated that these engineered strains were able to maintain lytic activity and fluorescence without affecting their technological properties in milk.
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Affiliation(s)
- Carmen Sánchez
- Departamento de Tecnología de Alimentos, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Carretera de La Coruña km 7, 28040, Madrid, Spain
| | - Sonia Garde
- Departamento de Tecnología de Alimentos, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Carretera de La Coruña km 7, 28040, Madrid, Spain.
| | - José María Landete
- Departamento de Tecnología de Alimentos, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Carretera de La Coruña km 7, 28040, Madrid, Spain
| | - Javier Calzada
- Departamento de Tecnología de Alimentos, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Carretera de La Coruña km 7, 28040, Madrid, Spain
| | - Dave J Baker
- Science Operations, Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, UK
| | - Rhiannon Evans
- Science Operations, Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, UK
| | - Arjan Narbad
- Food, Microbiome and Health Institute Strategic Programme, Quadram Institute Bioscience, Colney, Norwich, NR4 7UA, UK
| | - Melinda J Mayer
- Food, Microbiome and Health Institute Strategic Programme, Quadram Institute Bioscience, Colney, Norwich, NR4 7UA, UK.
| | - Marta Ávila
- Departamento de Tecnología de Alimentos, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Carretera de La Coruña km 7, 28040, Madrid, Spain.
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14
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Bichet MC, Gardette M, Das Neves B, Challant J, Erbs A, Roman V, Robin M, La Carbona S, Gantzer C, Boudaud N, Bertrand I. A new understanding of somatic coliphages belonging to the Microviridae family in urban wastewater. Water Res 2024; 249:120916. [PMID: 38043350 DOI: 10.1016/j.watres.2023.120916] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 11/08/2023] [Accepted: 11/22/2023] [Indexed: 12/05/2023]
Abstract
Somatic coliphages (SC) and F-specific RNA coliphages (FRNAPH) have been included in regulations or guidelines by several developed countries as a way of monitoring water safety and the microbiological quality of shellfish harvesting waters. SC are highly diverse in their morphology, size and genome. The Microviridae family contains three genera of phages (Alphatrevirus, Gequatrovirus, and Sinsheimervirus), all having a capsid of similar morphology (icosahedral) and size (25-30 nm in diameter) to that of common pathogenic enteric viruses. Three PCR assays specific for each genus of Microviridae were designed to study these phages in raw and treated wastewater (WW) in order to gain knowledge about the diversity and prevalence of Microviridae among SC, as well as their inactivation and removal during WW treatments. Among the four wastewater treatment plants (WWTPs) monitored here, two WWTPs applied disinfection by UV light as tertiary treatment. First, we noticed that Microviridae represented 10 to 30 % of infectious SC in both raw and treated WW. Microviridae appeared to behave in the same way as all SC during these WW treatments. As expected, the highest inactivation, at least 4 log10, was achieved for infectious Microviridae and SC in both WWTPs using UV disinfection. PCR assays showed that the highest removal of Microviridae reached about 4 log10, but the phage removal can vary greatly between WWTPs using similar treatments. This work forms the basis for a broader evaluation of Microviridae as a viral indicator of water treatment efficiency and WW reuse.
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Affiliation(s)
- Marion C Bichet
- Food Safety Department, ACTALIA, Saint-Lô F-50000, France; Université de Lorraine, CNRS, LCPME, F-54000 Nancy, France
| | - Marion Gardette
- Food Safety Department, ACTALIA, Saint-Lô F-50000, France; Université de Lorraine, CNRS, LCPME, F-54000 Nancy, France
| | | | - Julie Challant
- Université de Lorraine, CNRS, LCPME, F-54000 Nancy, France
| | - Anaïs Erbs
- Food Safety Department, ACTALIA, Saint-Lô F-50000, France; Université de Lorraine, CNRS, LCPME, F-54000 Nancy, France
| | - Véronica Roman
- Université de Lorraine, CNRS, LCPME, F-54000 Nancy, France
| | - Maëlle Robin
- Food Safety Department, ACTALIA, Saint-Lô F-50000, France
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15
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Samson R, Dharne M, Khairnar K. Bacteriophages: Status quo and emerging trends toward one health approach. Sci Total Environ 2024; 908:168461. [PMID: 37967634 DOI: 10.1016/j.scitotenv.2023.168461] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 10/30/2023] [Accepted: 11/07/2023] [Indexed: 11/17/2023]
Abstract
The alarming rise in antimicrobial resistance (AMR) among the drug-resistant pathogens has been attributed to the ESKAPEE group (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumanii, Pseudomonas aeruginosa, Enterobacter sp., and Escherichia coli). Recently, these AMR microbes have become difficult to treat, as they have rendered the existing therapeutics ineffective. Thus, there is an urgent need for effective alternatives to lessen or eliminate the current infections and limit the spread of emerging diseases under the "One Health" framework. Bacteriophages (phages) are naturally occurring biological resources with extraordinary potential for biomedical, agriculture/food safety, environmental protection, and energy production. Specific unique properties of phages, such as their bactericidal activity, host specificity, potency, and biocompatibility, make them desirable candidates in therapeutics. The recent biotechnological advancement has broadened the repertoire of phage applications in nanoscience, material science, physical chemistry, and soft-matter research. Herein, we present a comprehensive review, coupling the substantial aspects of phages with their applicability status and emerging opportunities in several interdependent areas under one health concept. Consolidating the recent state-of-the-art studies that integrate human, animal, plant, and environment health, the following points have been highlighted: (i) The biomedical and pharmacological advantages of phages and their antimicrobial derivatives with particular emphasis on in-vivo and clinical studies. (ii) The remarkable potential of phages to be altered, improved, and applied for drug delivery, biosensors, biomedical imaging, tissue engineering, energy, and catalysis. (iii) Resurgence of phages in biocontrol of plant, food, and animal-borne pathogens. (iv) Commercialization of phage-based products, current challenges, and perspectives.
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Affiliation(s)
- Rachel Samson
- National Collection of Industrial Microorganisms (NCIM), Biochemical Sciences Division, CSIR-National Chemical Laboratory (NCL), Pune 411008, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201002, India
| | - Mahesh Dharne
- National Collection of Industrial Microorganisms (NCIM), Biochemical Sciences Division, CSIR-National Chemical Laboratory (NCL), Pune 411008, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201002, India.
| | - Krishna Khairnar
- National Collection of Industrial Microorganisms (NCIM), Biochemical Sciences Division, CSIR-National Chemical Laboratory (NCL), Pune 411008, India; Environmental Virology Cell (EVC), CSIR-National Environmental Engineering Research Institute (NEERI), Nehru Marg, Nagpur 440020, India.
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16
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Aljabali AAA, Aljbaly MBM, Obeid MA, Shahcheraghi SH, Tambuwala MM. The Next Generation of Drug Delivery: Harnessing the Power of Bacteriophages. Methods Mol Biol 2024; 2738:279-315. [PMID: 37966606 DOI: 10.1007/978-1-0716-3549-0_18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2023]
Abstract
The use of biomaterials, such as bacteriophages, as drug delivery vehicles (DDVs) has gained increasing interest in recent years due to their potential to address the limitations of conventional drug delivery systems. Bacteriophages offer several advantages as drug carriers, such as high specificity for targeting bacterial cells, low toxicity, and the ability to be engineered to express specific proteins or peptides for enhanced targeting and drug delivery. In addition, bacteriophages have been shown to reduce the development of antibiotic resistance, which is a major concern in the field of antimicrobial therapy. Many initiatives have been taken to take up various payloads selectively and precisely by surface functionalization of the outside or interior of self-assembling viral protein capsids. Bacteriophages have emerged as a promising platform for the targeted delivery of therapeutic agents, including drugs, genes, and imaging agents. They possess several properties that make them attractive as drug delivery vehicles, including their ability to specifically target bacterial cells, their structural diversity, their ease of genetic manipulation, and their biocompatibility. Despite the potential advantages of using bacteriophages as drug carriers, several challenges and limitations need to be addressed. One of the main challenges is the limited host range of bacteriophages, which restricts their use to specific bacterial strains. However, this can also be considered as an advantage, as it allows for precise and targeted drug delivery to the desired bacterial cells. The use of biomaterials, including bacteriophages, as drug delivery vehicles has shown promising potential to address the limitations of conventional drug delivery systems. Further research is needed to fully understand the potential of these biomaterials and address the challenges and limitations associated with their use.
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Affiliation(s)
- Alaa A A Aljabali
- Department of Pharmaceutics and Pharmaceutical Technology, Faculty of Pharmacy, Yarmouk University, Irbid, Jordan.
| | | | - Mohammad A Obeid
- Department of Pharmaceutics and Pharmaceutical Technology, Faculty of Pharmacy, Yarmouk University, Irbid, Jordan
| | - Seyed Hossein Shahcheraghi
- Department of Medical Genetics, School of Medicine, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | - Murtaza M Tambuwala
- Lincoln Medical School, Brayford Pool Campus, University of Lincoln, Lincoln, UK.
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17
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Ferry T. A Review of Phage Therapy for Bone and Joint Infections. Methods Mol Biol 2024; 2734:207-235. [PMID: 38066372 DOI: 10.1007/978-1-0716-3523-0_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2023]
Abstract
There is a strong rationale for using phages in patients with bone and joint infections (BJIs). Indeed, specific phages can infect and replicate in bacterial pathogens and have also demonstrated their activity in vitro against biofilm produced by different bacteria. However, there is a high variability of the different clinical forms of BJI, and their management is complex and frequently includes surgery followed by the administration of antibiotics. Regardless of the availability of active phages, optimal ways of phage administration in patients with BJIs are unknown. Otherwise, all BJIs are not relevant for phage therapy. Except for diabetic foot infection, a BJI with bone exposure is potentially not a relevant indication for phage therapy. On the counterpart, prosthetic joint infections in patients for whom a multidisciplinary expert team judges a conservative approach as the best option to keep the patient's function seem to be a relevant indication with the hypothesis that phage therapy could increase the rate of infection control. The ESCMID Study Group for Non-traditional Antibacterial Therapy (ESGNTA) was created in 2022. One century after the first use of phages as a therapy, the phage therapy 2.0 era, with the possibility to evaluate personalized phage therapy in modern medicine and orthopedic surgery, is just open.
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Affiliation(s)
- Tristan Ferry
- Service de Maladies Infectieuses et Tropicales, Hôpital de la Croix-Rousse, Hospices Civils de Lyon, Lyon, France.
- Université Claude Bernard Lyon 1, Villeurbanne, France.
- Centre de Références des IOA Complexes de Lyon, CRIOAc Lyon, Lyon, France.
- StaPath team, Centre International de Recherche en Infectiologie, CIRI, Inserm U1111, CNRS UMR5308, ENS de Lyon, UCBL1, Lyon, France.
- Education and Clinical Officer of the ESCMID Study Group for Non-traditional Antibacterial Therapy (ESGNTA), Basel, Switzerland.
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18
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Bloch S, Lewandowska N, Wesołowski W, Łukasiak A, Mach P, Nejman-Faleńczyk B, Węgrzyn G. Analysis of Phage Regulatory RNAs: Sequencing Library Construction from the Fraction of Small Prokaryotic RNAs Less Than 50 Nucleotides in Length. Methods Mol Biol 2024; 2741:25-34. [PMID: 38217647 DOI: 10.1007/978-1-0716-3565-0_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2024]
Abstract
So far, bacterial regulatory sRNAs of length less than 50 nucleotides have been poorly understood, and a low number of such molecules has been identified. The first microRNA-size functional ribonucleic acid occurring in a bacterial cell has been described only recently, and it was found to be encoded by a bacteriophage. One of the reasons for such a scarcity in this field is the lack of procedures intended for the isolation and selection of molecules of this size from bacterial cells. To meet these difficulties, we describe here the few-step procedure of isolation, purification, selection, and sequencing library preparation that is dedicated to the fraction of very small, bacterial RNA molecules.
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Affiliation(s)
- Sylwia Bloch
- Department of Molecular Biology, Faculty of Biology, University of Gdansk, Gdansk, Poland
| | - Natalia Lewandowska
- Department of Molecular Biology, Faculty of Biology, University of Gdansk, Gdansk, Poland
| | - Wojciech Wesołowski
- Department of Molecular Biology, Faculty of Biology, University of Gdansk, Gdansk, Poland
| | - Aleksandra Łukasiak
- Department of Molecular Biology, Faculty of Biology, University of Gdansk, Gdansk, Poland
| | - Paulina Mach
- Department of Molecular Biology, Faculty of Biology, University of Gdansk, Gdansk, Poland
| | | | - Grzegorz Węgrzyn
- Department of Molecular Biology, Faculty of Biology, University of Gdansk, Gdansk, Poland.
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19
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Torres-Franco AF, Leroy-Freitas D, Martinez-Fraile C, Rodríguez E, García-Encina PA, Muñoz R. Partitioning and inactivation of enveloped and nonenveloped viruses in activated sludge, anaerobic and microalgae-based wastewater treatment systems. Water Res 2024; 248:120834. [PMID: 37984037 DOI: 10.1016/j.watres.2023.120834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 11/01/2023] [Accepted: 11/03/2023] [Indexed: 11/22/2023]
Abstract
Anaerobic and microalgae-based technologies for municipal wastewater treatment have emerged as sustainable alternatives to activated sludge systems. However, viruses are a major sanitary concern for reuse applications of liquid and solid byproducts from these technologies. To assess their capacity to reduce viruses during secondary wastewater treatment, enveloped Phi6 and nonenveloped MS2 bacteriophages, typically used as surrogates of several types of wastewater viruses, were spiked into batch bioreactors treating synthetic municipal wastewater (SMWW). The decay of Phi6 and MS2 in anaerobic and microalgae-based reactors was compared with the decay in activated sludge batch reactors for 96 h (Phi6) and 144 h (MS2). In each reactor, bacteriophages in the soluble and solids fractions were titered, allowing the assessment of virus partitioning to biomass over time. Moreover, the influence of abiotic conditions such as agitation, oxygen absence and light excess in activated sludge, anaerobic and microalgae reactors, respectively, was assessed using dedicated SMWW control reactors. All technologies showed Phi6 and MS2 reductions. Phi6 was reduced in at least 4.7 to 6.5 log10 units, with 0 h concentrations ranging from 5.0 to 6.5 log10 PFU mL-1. Similarly, reductions achieved for MS2 were of at least 3.9 to 7.2 log10 units, from starting concentrations of 8.0 to 8.6 log10 PFU mL-1. Log-logistic models adjusted to bacteriophages' decay indicated T90 values in activated sludge and microalgae reactors of 2.2 and 7.9 h for Phi6 and of 1.0 and 11.5 h for MS2, respectively, all within typical hydraulic retention times (HRT) of full-scale operation. In the case of the microalgae technology, T99 values for Phi6 and MS2 of 12.7 h and 13.6 h were also lower than typical operating HRTs (2-10 d), while activated sludge and anaerobic treatment achieved less than 99 % of Phi6 and 50 % of MS2 inactivation within 12 h of typical HRT, respectively. Thus, the microalgae-based treatment exhibited a higher potential to reduce the disinfection requirements of treated wastewater.
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Affiliation(s)
- Andrés F Torres-Franco
- Institute of Sustainable Processes, Dr. Mergelina, s/n, 47011 Valladolid, Spain; Department of Chemical Engineering and Environmental Technology, School of Industrial Engineering, University of Valladolid, Dr. Mergelina. s/n, 47011 Valladolid, Spain.
| | - Deborah Leroy-Freitas
- Institute of Sustainable Processes, Dr. Mergelina, s/n, 47011 Valladolid, Spain; Department of Chemical Engineering and Environmental Technology, School of Industrial Engineering, University of Valladolid, Dr. Mergelina. s/n, 47011 Valladolid, Spain
| | - Cristina Martinez-Fraile
- Institute of Sustainable Processes, Dr. Mergelina, s/n, 47011 Valladolid, Spain; Department of Chemical Engineering and Environmental Technology, School of Industrial Engineering, University of Valladolid, Dr. Mergelina. s/n, 47011 Valladolid, Spain
| | - Elisa Rodríguez
- Institute of Sustainable Processes, Dr. Mergelina, s/n, 47011 Valladolid, Spain; Department of Chemical Engineering and Environmental Technology, School of Industrial Engineering, University of Valladolid, Dr. Mergelina. s/n, 47011 Valladolid, Spain
| | - Pedro A García-Encina
- Institute of Sustainable Processes, Dr. Mergelina, s/n, 47011 Valladolid, Spain; Department of Chemical Engineering and Environmental Technology, School of Industrial Engineering, University of Valladolid, Dr. Mergelina. s/n, 47011 Valladolid, Spain
| | - Raúl Muñoz
- Institute of Sustainable Processes, Dr. Mergelina, s/n, 47011 Valladolid, Spain; Department of Chemical Engineering and Environmental Technology, School of Industrial Engineering, University of Valladolid, Dr. Mergelina. s/n, 47011 Valladolid, Spain.
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20
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Marks TJ, Rowland IR. The Diversity of Bacteriophages in Hot Springs. Methods Mol Biol 2024; 2738:73-88. [PMID: 37966592 DOI: 10.1007/978-1-0716-3549-0_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2023]
Abstract
Bacteriophages are ubiquitous in all environments that support microbial life. This includes hot springs, which can range in temperatures between 40 and 98 °C and pH levels between 1 and 9. Bacteriophages that survive in the higher temperatures of hot springs are known as thermophages. Thermophages have developed distinct adaptations allowing for thermostability in these extreme environments, including increased G + C DNA percentages, reliance upon the pentose phosphate metabolic pathway to avoid oxidative stress, and a codon preference for those with a GNA sequence leading to increased hydrophobic interactions and disulfide bonds. In this review, we discuss the diversity of characterized thermophages in hot spring environments that span five viral families: Myoviridae, Siphoviridae, Tectiviridae, Sphaerolipoviridae, and Inoviridae. Potential industrial and medicinal applications of thermophages will also be addressed.
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Affiliation(s)
- Timothy J Marks
- Department of Pharmaceutical and Clinical Sciences, Campbell University, Buies Creek, NC, USA.
| | - Isabella R Rowland
- Department of Pharmaceutical and Clinical Sciences, Campbell University, Buies Creek, NC, USA
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21
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Tumban E. Bacteriophage Virus-Like Particles: Platforms for Vaccine Design. Methods Mol Biol 2024; 2738:411-423. [PMID: 37966612 DOI: 10.1007/978-1-0716-3549-0_24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2023]
Abstract
Virus-like particles (VLPs) derived from bacteriophages have many applications in biomedical sciences, especially in the development of candidate vaccines against viral and bacterial infections. Bacteriophage VLPs can be manufactured cheaply and in large quantities in bacteria compared to eukaryotic expression systems. In addition to this, bacteriophage VLPs are excellent platforms for vaccine design for the following reason: Humans do not have preexisting antibodies against bacteriophage VLPs. Thus, antigens displayed on bacteriophage VLP platforms are expected to be highly immunogenic. As such, VLPs derived from MS2, PP7, Qβ, AP205, P22 bacteriophages, etc. have been used to develop candidate vaccines against human infectious and noninfectious agents. This mini-review summarizes data from some of the candidate bacteriophage-based VLP peptide vaccines that have been developed. The review also highlights some strategies used to develop the candidate bacteriophage-based VLP peptide vaccines.
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Affiliation(s)
- Ebenezer Tumban
- School of Veterinary Medicine, Texas Tech University, Amarillo, TX, USA.
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22
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Ely B, Lenski J, Mohammadi T. Structural and Genomic Diversity of Bacteriophages. Methods Mol Biol 2024; 2738:3-16. [PMID: 37966589 DOI: 10.1007/978-1-0716-3549-0_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2023]
Abstract
Bacteriophage diversity is a relatively unknown frontier that is rapidly being explored, leading to a wealth of new information. New bacteriophages are being discovered at an astounding rate via both phage isolation studies and metagenomic analyses. In addition, a nucleotide sequence-based viral taxonomic system has been developed to better handle this wealth of new information. As a result of these developments, phage scientists are transitioning from knowing that there must be huge numbers of diverse kinds of phage particles in natural environments to identifying the actual abundance and phage diversity that is present in specific environments. This review documents the beginning of this transition, offering a glimpse into the magnitude of change unfolding in the field. It stands as a testament to the expanding frontiers of phage research, illuminating the remarkable progress made in unraveling the intricate world of bacteriophage diversity and advancing our understanding of these enigmatic viral entities.
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Affiliation(s)
- Bert Ely
- Department of Biological Sciences, University of South Carolina, Columbia, SC, USA.
| | - Jacob Lenski
- Department of Biological Sciences, University of South Carolina, Columbia, SC, USA
| | - Tannaz Mohammadi
- Department of Biological Sciences, University of South Carolina, Columbia, SC, USA
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23
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Sala-Comorera L, Muniesa M, Rodríguez-Rubio L. Detection and Quantification of Bacteriophages in Wastewater Samples by Culture and Molecular Methods. Methods Mol Biol 2024; 2738:155-173. [PMID: 37966598 DOI: 10.1007/978-1-0716-3549-0_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2023]
Abstract
Bacteriophages are promising tools for the detection of fecal pollution in water bodies and particularly for viral pathogen risk assessment. Having similar morphological and biological characteristics, bacteriophages are perfect surrogates for the study of the fate and transport of enteric viruses, generally better than any other group of indicators.Different groups of bacteriophages, such as somatic coliphages, F-specific RNA bacteriophages, and bacteriophages infecting selected strains of Bacteroides, have been comprehensively tested as indicators of fecal pollution. Somatic coliphages and F-specific RNA bacteriophages can be used as indicators of general fecal contamination, whereas Bacteroides phages can be used to detect a particular fecal source, for instance, human, bovine, porcine, or poultry fecal contamination.Feasible and cost-effective protocols standardized by the International Standardization Organization and the United States Environmental Protection Agency for the detection of infectious bacteriophages belonging to these three groups are available. Molecular methods for the detection of some particular phages have also been developed. Here we introduce those methods for the detection, enumeration, and isolation of bacteriophages in wastewater samples.
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Affiliation(s)
- Laura Sala-Comorera
- Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona, Barcelona, Spain
| | - Maite Muniesa
- Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona, Barcelona, Spain
| | - Lorena Rodríguez-Rubio
- Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona, Barcelona, Spain.
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24
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Larsen F, Jakobsen RR, Mao X, Castro-Mejia J, Deng L, Nielsen DS. Purification and Up-Concentration of Bacteriophages and Viruses from Fecal Samples. Methods Mol Biol 2024; 2738:105-110. [PMID: 37966594 DOI: 10.1007/978-1-0716-3549-0_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2023]
Abstract
The viral fraction of human and experimental animal fecal matter is increasingly attracting research interest due to its newfound influence on the gut microbiome and host health. During the past decade, high-throughput sequencing techniques have seen massive improvements, and in recent years, bioinformatics pipelines for virome analysis have also vastly improved with respect to both user-friendliness and output quality. Yet, the shape and quality of such data are highly dependent on how the viruses are isolated and their genomes extracted and processed to build sequencing libraries.Here we describe a simple protocol for virus isolation from fecal samples suitable for further propagation/characterization or sequencing efforts. It is based on two filtration steps: one for removing large particles such as bacteria and one for removing free DNA and up-concentrating phages and other viruses in the solution. The method is highly scalable, adaptable to a long range of sample types including low-input samples, and has a quantifiable output suitable for both plaquing and sequencing.
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Affiliation(s)
- Frej Larsen
- University of Copenhagen, Frederiksberg C, Denmark.
| | | | - Xiaotian Mao
- University of Copenhagen, Frederiksberg C, Denmark
| | | | - Ling Deng
- University of Copenhagen, Frederiksberg C, Denmark
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25
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Cortés P, Cano-Sarabia M, Colom J, Otero J, Maspoch D, Llagostera M. Nano/microformulations for Bacteriophage Delivery. Methods Mol Biol 2024; 2734:117-130. [PMID: 38066365 DOI: 10.1007/978-1-0716-3523-0_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2023]
Abstract
Encapsulation methodologies allow the protection of bacteriophages for overcoming critical environmental conditions. Moreover, they improve the stability and the controlled delivery of bacteriophages which is of great innovative value in bacteriophage therapy. Here, two different encapsulation methodologies of bacteriophages are described using two biocompatible materials: a lipid cationic mixture and a combination of alginate with the antacid CaCO3. To perform bacteriophage encapsulation is necessary to dispose of a purified and highly concentrated lysate (around 1010 to 1011 pfu/mL) and a specific equipment. Both methodologies have been successfully applied for encapsulating Salmonella bacteriophages with different morphologies. Also, the material employed does not modify the antibacterial action of bacteriophages. Moreover, both technologies can be adapted to any bacteriophage and possibly to any delivery route for bacteriophage therapy.
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Affiliation(s)
- Pilar Cortés
- Departament de Genètica i Microbiologia, Universitat Autònoma de Barcelona, Campus de Bellaterra, Cerdanyola del Vallès, Spain
| | - Mary Cano-Sarabia
- Catalan Institute of Nanoscience and Nanotechnology (ICN2), CSIC and The Barcelona Institute of Science and Technology, Campus de Bellaterra, Cerdanyola del Vallès, Spain
| | - Joan Colom
- Deerland Ireland R&D Ltd., Food Science Building, University College Cork, Cork, Ireland
| | - Jennifer Otero
- Departament de Genètica i Microbiologia, Universitat Autònoma de Barcelona, Campus de Bellaterra, Cerdanyola del Vallès, Spain
| | - Daniel Maspoch
- Catalan Institute of Nanoscience and Nanotechnology (ICN2), CSIC and The Barcelona Institute of Science and Technology, Campus de Bellaterra, Cerdanyola del Vallès, Spain
- ICREA, Barcelona, Spain
| | - Montserrat Llagostera
- Departament de Genètica i Microbiologia, Universitat Autònoma de Barcelona, Campus de Bellaterra, Cerdanyola del Vallès, Spain.
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26
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Levrier A, Bowden S, Nash B, Lindner A, Noireaux V. Cell-Free Synthesis and Quantitation of Bacteriophages. Methods Mol Biol 2024; 2760:447-461. [PMID: 38468103 DOI: 10.1007/978-1-0716-3658-9_25] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/13/2024]
Abstract
Cell-free transcription-translation (TXTL) enables achieving an ever-growing number of applications, ranging from the rapid characterization of DNA parts to the production of biologics. As TXTL systems gain in versatility and efficacy, larger DNAs can be expressed in vitro extending the scope of cell-free biomanufacturing to new territories. The demonstration that complex entities such as infectious bacteriophages can be synthesized from their genomes in TXTL reactions opens new opportunities, especially for biomedical applications. Over the last century, phages have been instrumental in the discovery of many ground-breaking biotechnologies including CRISPR. The primary function of phages is to infect bacteria. In that capacity, phages are considered an alternative approach to tackling current societal problems such as the rise of antibiotic-resistant microbes. TXTL provides alternative means to produce phages and with several advantages over in vivo synthesis methods. In this chapter, we describe the basic procedures to purify phage genomes, cell-free synthesize phages, and quantitate them using an all-E. coli TXTL system.
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Affiliation(s)
- Antoine Levrier
- Center for Research and Interdisciplinarity (CRI), Université de Paris, INSERM U1284, Paris, France
- Physics and Nanotechnology, University of Minnesota, Minneapolis, MN, USA
| | - Steven Bowden
- Department of Food Science and Nutrition, University of Minnesota, Saint Paul, MN, USA
| | - Bruce Nash
- Cold Spring Harbor Laboratory, DNA Learning Center, Cold Spring Harbor, NY, USA
| | - Ariel Lindner
- Center for Research and Interdisciplinarity (CRI), Université de Paris, INSERM U1284, Paris, France
| | - Vincent Noireaux
- Physics and Nanotechnology, University of Minnesota, Minneapolis, MN, USA.
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27
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Hou CFD, Li F, Iglesias S, Cingolani G. Use of Localized Reconstruction to Visualize the Shigella Phage Sf6 Tail Apparatus. Methods Mol Biol 2024; 2738:215-228. [PMID: 37966602 PMCID: PMC10655839 DOI: 10.1007/978-1-0716-3549-0_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2023]
Abstract
Cryogenic electron microscopy (cryo-EM) single-particle analysis has revolutionized the structural analysis of icosahedral viruses, including tailed bacteriophages. In recent years, localized (or focused) reconstruction has emerged as a powerful data analysis method to capture symmetry mismatches and resolve asymmetric features in icosahedral viruses. Here, we describe the methods used to reconstruct the 2.65-MDa tail apparatus of the Shigella phage Sf6, a representative member of the Podoviridae superfamily.
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Affiliation(s)
- Chun-Feng David Hou
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA, USA
| | - Fenglin Li
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA, USA
| | - Stephano Iglesias
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA, USA
| | - Gino Cingolani
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA, USA.
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28
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Wan X, Skurnik M. Multidisciplinary Methods for Screening Toxic Proteins from Phages and Their Potential Molecular Targets. Methods Mol Biol 2024; 2793:237-256. [PMID: 38526734 DOI: 10.1007/978-1-0716-3798-2_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/27/2024]
Abstract
This chapter presents a comprehensive methodology for the identification, characterization, and functional analyses of potentially toxic hypothetical proteins of unknown function (toxHPUFs) in phages. The methods begin with in vivo toxicity verification of toxHPUFs in bacterial hosts, utilizing conventional drop tests and following growth curves. Computational methods for structural and functional predictions of toxHPUFs are outlined, incorporating the use of tools such as Phyre2, HHpred, and AlphaFold2. To ascertain potential targets, a comparative genomic approach is described using bioinformatics toolkits for sequence alignment and functional annotation. Moreover, steps are provided to predict protein-protein interactions and visualizing these using PyMOL. The culmination of these methods equips researchers with an effective pipeline to identify and analyze toxHPUFs and their potential targets, laying the groundwork for future experimental confirmations.
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Affiliation(s)
- Xing Wan
- Department of Bacteriology and Immunology, Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland.
- Department of Microbiology, Faculty of Agriculture and Forestry, University of Helsinki, Helsinki, Finland.
| | - Mikael Skurnik
- Department of Bacteriology and Immunology, Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
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29
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Liang T, Jiang T, Liang Z, Zhang N, Dong B, Wu Q, Gu B. Carbohydrate-active enzyme profiles of Lactiplantibacillus plantarum strain 84-3 contribute to flavor formation in fermented dairy and vegetable products. Food Chem X 2023; 20:101036. [PMID: 38059176 PMCID: PMC10696159 DOI: 10.1016/j.fochx.2023.101036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 10/26/2023] [Accepted: 11/24/2023] [Indexed: 12/08/2023] Open
Abstract
Microbes are critical for flavor formation in fermented foods; however, their mechanisms of action are not fully understood. The microbial composition of 51 dairy and 47 vegetable products was functionally annotated and the carbohydrate-active enzyme (CAZyme) profiles of Lactiplantibacillus plantarum 84-3 (Lp84-3), isolated from dairy samples, can promote resistant starch (RS) degradation, were analyzed. Lactobacillus, Streptococcus, and Lactococcus were the predominant genera in dairy products, whereas the major genera in vegetables were Lactobacillus, Weissella, and Carnimonas. Phages from Siphoviridae, Myoviridae, and Herelleviridae were also present in dairy products. Additionally, the glycosyl hydrolase (GHs) family members GH1 and GH13 and the glycosyltransferase (GTs) family members GT2 and GT4 were abundant in Lp84-3. Moreover, Lp84-3 was enriched in butanoate metabolism enzymes and butanoate metabolite compounds. Therefore, fermented food microbes, especially Lp84-3, have an abundant repertoire of enzymes that promote flavor production, as starter improving the flavor of fermented dairy and vegetable products.
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Affiliation(s)
- Tingting Liang
- Guangdong Cardiovascular Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
- Department of Clinical Laboratory Medicine, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Tong Jiang
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Zhuang Liang
- Department of Rehabilitation Hospital Pain Ward, Honghui Hospital, Xi'an Jiaotong University, Xi'an, Shaanxi 710054, China
| | - Ni Zhang
- Department of Clinical Laboratory Medicine, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China
| | - Bo Dong
- Department of Rehabilitation Hospital Pain Ward, Honghui Hospital, Xi'an Jiaotong University, Xi'an, Shaanxi 710054, China
| | - Qingping Wu
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Bing Gu
- Department of Clinical Laboratory Medicine, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China
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30
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Sørensen AN, Kalmár D, Lutz VT, Klein-Sousa V, Taylor NMI, Sørensen MC, Brøndsted L. Agtrevirus phage AV101 recognizes four different O-antigens infecting diverse E. coli. Microlife 2023; 5:uqad047. [PMID: 38234449 PMCID: PMC10791037 DOI: 10.1093/femsml/uqad047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 12/11/2023] [Accepted: 12/19/2023] [Indexed: 01/19/2024]
Abstract
Bacteriophages in the Agtrevirus genus are known for expressing multiple tail spike proteins (TSPs), but little is known about their genetic diversity and host recognition apart from their ability to infect diverse Enterobacteriaceae species. Here, we aim to determine the genetic differences that may account for the diverse host ranges of Agrevirus phages. We performed comparative genomics of 14 Agtrevirus and identified only a few genetic differences including genes involved in nucleotide metabolism. Most notably was the diversity of the tsp gene cluster, specifically in the receptor-binding domains that were unique among most of the phages. We further characterized agtrevirus AV101 infecting nine diverse Extended Spectrum β-lactamase (ESBL) Escherichia coli and demonstrated that this phage encoded four unique TSPs among Agtrevirus. Purified TSPs formed translucent zones and inhibited AV101 infection of specific hosts, demonstrating that TSP1, TSP2, TSP3, and TSP4 recognize O8, O82, O153, and O159 O-antigens of E. coli, respectively. BLASTp analysis showed that the receptor-binding domain of TSP1, TSP2, TSP3, and TSP4 are similar to TSPs encoded by E. coli prophages and distant related virulent phages. Thus, Agtrevirus may have gained their receptor-binding domains by recombining with prophages or virulent phages. Overall, combining bioinformatic and biological data expands the understanding of TSP host recognition of Agtrevirus and give new insight into the origin and acquisition of receptor-binding domains of Ackermannviridae phages.
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Affiliation(s)
- Anders Nørgaard Sørensen
- Department of Veterinary and Animal Sciences, University of Copenhagen, Stigbøjlen 4, 1870 Frederiksberg C, Denmark
| | - Dorottya Kalmár
- Department of Veterinary and Animal Sciences, University of Copenhagen, Stigbøjlen 4, 1870 Frederiksberg C, Denmark
| | - Veronika Theresa Lutz
- Department of Veterinary and Animal Sciences, University of Copenhagen, Stigbøjlen 4, 1870 Frederiksberg C, Denmark
| | - Victor Klein-Sousa
- Structural Biology of Molecular Machines Group, Protein Structure & Function Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Nicholas M I Taylor
- Structural Biology of Molecular Machines Group, Protein Structure & Function Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Martine C Sørensen
- Department of Veterinary and Animal Sciences, University of Copenhagen, Stigbøjlen 4, 1870 Frederiksberg C, Denmark
| | - Lone Brøndsted
- Department of Veterinary and Animal Sciences, University of Copenhagen, Stigbøjlen 4, 1870 Frederiksberg C, Denmark
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31
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Pastuszka A, Rousseau GM, Somerville V, Levesque S, Fiset JP, Goulet A, Doyon Y, Moineau S. Dairy phages escape CRISPR defence of Streptococcus thermophilus via the anti-CRISPR AcrIIA3. Int J Food Microbiol 2023; 407:110414. [PMID: 37778080 DOI: 10.1016/j.ijfoodmicro.2023.110414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2023] [Revised: 08/22/2023] [Accepted: 09/21/2023] [Indexed: 10/03/2023]
Abstract
Bacterial community collapse due to phage infection is a major risk in cheese making processes. As virulent phages are ubiquitous and diverse in milk fermentation factories, the use of phage-resistant lactic acid bacteria (LAB) is essential to obtain high-quality fermented dairy products. The LAB species Streptococcus thermophilus contains two type II-A CRISPR-Cas systems (CRISPR1 and CRISPR3) that can effectively protect against phage infection. However, virulent streptococcal phages carrying anti-CRISPR proteins (ACR) that block the activity of CRISPR-Cas systems have emerged in yogurt and cheese environments. For example, phages carrying AcrIIA5 can impede both CRISPR1 and CRISPR3 systems, while AcrIIA6 stops only CRISPR1. Here, we explore the activity and diversity of a third streptococcal phage anti-CRISPR protein, namely AcrIIA3. We were able to demonstrate that AcrIIA3 is efficiently active against the CRISPR3-Cas system of S. thermophilus. We used AlphaFold2 to infer the structure of AcrIIA3 and we predicted that this new family of functional ACR in virulent streptococcal phages has a new α-helical fold, with no previously identified structural homologs. Because ACR proteins are being explored as modulators in genome editing applications, we also tested AcrIIA3 against SpCas9. We found that AcrIIA3 could block SpCas9 in bacteria but not in human cells. Understanding the diversity and functioning of anti-defence mechanisms will be of importance in the design of long-term stable starter cultures.
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Affiliation(s)
- Adeline Pastuszka
- Département de biochimie, de microbiologie, et de bio-informatique, Faculté des sciences et de génie, Université Laval, Québec, QC, Canada; Groupe de recherche en écologie buccale, Faculté de médecine dentaire, Université Laval, Québec, QC, Canada
| | - Geneviève M Rousseau
- Département de biochimie, de microbiologie, et de bio-informatique, Faculté des sciences et de génie, Université Laval, Québec, QC, Canada; Groupe de recherche en écologie buccale, Faculté de médecine dentaire, Université Laval, Québec, QC, Canada
| | - Vincent Somerville
- Département de biochimie, de microbiologie, et de bio-informatique, Faculté des sciences et de génie, Université Laval, Québec, QC, Canada; Groupe de recherche en écologie buccale, Faculté de médecine dentaire, Université Laval, Québec, QC, Canada; Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland; Agroscope, Bern, Switzerland
| | - Sébastien Levesque
- Centre Hospitalier Universitaire de Québec Research Center, Université Laval, Québec, QC, Canada; Université Laval Cancer Research Centre, Québec, QC, Canada
| | - Jean-Philippe Fiset
- Centre Hospitalier Universitaire de Québec Research Center, Université Laval, Québec, QC, Canada; Université Laval Cancer Research Centre, Québec, QC, Canada
| | - Adeline Goulet
- Laboratoire d'Ingénierie des Systèmes Macromoléculaires, Institut de Microbiologie, Bioénergies et Biotechnologies, CNRS UMR7255, Aix-Marseille Université, Marseille, France
| | - Yannick Doyon
- Centre Hospitalier Universitaire de Québec Research Center, Université Laval, Québec, QC, Canada; Université Laval Cancer Research Centre, Québec, QC, Canada
| | - Sylvain Moineau
- Département de biochimie, de microbiologie, et de bio-informatique, Faculté des sciences et de génie, Université Laval, Québec, QC, Canada; Groupe de recherche en écologie buccale, Faculté de médecine dentaire, Université Laval, Québec, QC, Canada; Félix d'Hérelle Reference Center for Bacterial Viruses, Faculté de médecine dentaire, Université Laval, Québec, QC, Canada.
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32
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Lousada MB, Edelkamp J, Lachnit T, Fehrholz M, Pastar I, Jimenez F, Erdmann H, Bosch TCG, Paus R. Spatial Distribution and Functional Impact of Human Scalp Hair Follicle Microbiota. J Invest Dermatol 2023:S0022-202X(23)03119-6. [PMID: 38070726 DOI: 10.1016/j.jid.2023.11.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 10/17/2023] [Accepted: 11/01/2023] [Indexed: 02/26/2024]
Abstract
Human hair follicles (HFs) constitute a unique microbiota habitat that differs substantially from the skin surface. Traditional HF sampling methods fail to eliminate skin microbiota contaminants or assess the HF microbiota incompletely, and microbiota functions in human HF physiology remain ill explored. Therefore, we used laser-capture microdissection, metagenomic shotgun sequencing, and FISH to characterize the human scalp HF microbiota in defined anatomical compartments. This revealed significant compartment-, tissue lineage-, and donor age-dependent variations in microbiota composition. Greatest abundance variations between HF compartments were observed for viruses, archaea, Staphylococcus epidermidis, Cutibacterium acnes, and Malassezia restricta, with the latter 2 being the most abundant viable HF colonizers (as tested by propidium monoazide assay) and, surprisingly, most abundant in the HF mesenchyme. Transfection of organ-cultured human scalp HFs with S. epidermidis-specific lytic bacteriophages ex vivo downregulated transcription of genes known to regulate HF growth and development, metabolism, and melanogenesis, suggesting that selected microbial products may modulate HF functions. Indeed, HF treatment with butyrate, a metabolite of S. epidermidis and other HF microbiota, delayed catagen and promoted autophagy, mitochondrial activity, and gp100 and dermcidin expression ex vivo. Thus, human HF microbiota show spatial variations in abundance and modulate the physiology of their host, which invites therapeutic targeting.
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Affiliation(s)
- Marta B Lousada
- Monasterium Laboratory, Münster, Germany; Zoological Institute, Christian Albrechts University in Kiel, Kiel, Germany
| | | | - Tim Lachnit
- Zoological Institute, Christian Albrechts University in Kiel, Kiel, Germany
| | | | - Irena Pastar
- Dr Phillip Frost Department of Dermatology and Cutaneous Surgery, University of Miami Miller School of Medicine, Miami, Florida, USA
| | - Francisco Jimenez
- Mediteknia Skin & Hair Lab, Las Palmas de Gran Canaria, Spain; Ciencias de la Salud, Universidad Fernando Pessoa Canarias, Las Palmas de Gran Canaria, Spain
| | | | - Thomas C G Bosch
- Zoological Institute, Christian Albrechts University in Kiel, Kiel, Germany
| | - Ralf Paus
- Monasterium Laboratory, Münster, Germany; Dr Phillip Frost Department of Dermatology and Cutaneous Surgery, University of Miami Miller School of Medicine, Miami, Florida, USA; CUTANEON, Hamburg, Germany.
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33
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Ngoma NFN, Malahlela MN, Marufu MC, Cenci-Goga BT, Grispoldi L, Etter E, Kalake A, Karama M. Antimicrobial growth promoters approved in food-producing animals in South Africa induce shiga toxin-converting bacteriophages from Escherichia coli O157:H7. Gut Pathog 2023; 15:64. [PMID: 38057920 DOI: 10.1186/s13099-023-00590-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 11/23/2023] [Indexed: 12/08/2023] Open
Abstract
In this study, four antimicrobial growth promoters, including virginiamycin, josamycin, flavophospholipol, poly 2-propenal 2-propenoic acid and ultraviolet light, were tested for their capacity to induce stx-bacteriophages in 47 Shiga toxin-producing E. coli O157:H7 isolates. Induced bacteriophages were characterized for shiga toxin subtypes and structural genes by PCR, DNA restriction fragment length polymorphisms (RFLP) and morphological features by electron microscopy. Bacteriophages were induced from 72.3% (34/47) of the STEC O157:H7 isolates tested. Bacteriophage induction rates per induction method were as follows: ultraviolet light, 53.2% (25/47); poly 2-propenal 2-propenoic acid, 42.6% (20/47); virginiamycin, 34.0% (16/47); josamycin, 34.0% (16/47); and flavophospholipol, 29.8% (14/47). A total of 98 bacteriophages were isolated, but only 59 were digestible by NdeI, revealing 40 RFLP profiles which could be subdivided in 12 phylogenetic subgroups. Among the 98 bacteriophages, stx2a, stx2c and stx2d were present in 85.7%, 94.9% and 36.7% of bacteriophages, respectively. The Q, P, CIII, N1, N2 and IS1203 genes were found in 96.9%, 82.7%, 69.4%, 40.8%, 60.2% and 73.5% of the samples, respectively. Electron microscopy revealed four main representative morphologies which included three bacteriophages which all had long tails but different head morphologies: long hexagonal head, oval/oblong head and oval/circular head, and one bacteriophage with an icosahedral/hexagonal head with a short thick contractile tail. This study demonstrated that virginiamycin, josamycin, flavophospholipol and poly 2-propenal 2-propenoic acid induce genetically and morphologically diverse free stx-converting bacteriophages from STEC O157:H7. The possibility that these antimicrobial growth promoters may induce bacteriophages in vivo in animals and human hosts is a public health concern. Policies aimed at minimizing or banning the use of antimicrobial growth promoters should be promoted and implemented in countries where these compounds are still in use in animal agriculture.
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Affiliation(s)
- Nomonde F N Ngoma
- Department of Paraclinical Sciences, Faculty of Veterinary Science, Veterinary Public Health Section, University of Pretoria, Onderstepoort, 0110, South Africa
| | - Mogaugedi N Malahlela
- Department of Paraclinical Sciences, Faculty of Veterinary Science, Veterinary Public Health Section, University of Pretoria, Onderstepoort, 0110, South Africa
| | - Munyaradzi C Marufu
- Department of Veterinary Tropical Diseases, Faculty of Veterinary Science, University of Pretoria, Pretoria, South Africa
| | - Beniamino T Cenci-Goga
- Department of Paraclinical Sciences, Faculty of Veterinary Science, Veterinary Public Health Section, University of Pretoria, Onderstepoort, 0110, South Africa
- Departimento di Medicina Veterinaria, Laboratorio di Ispezione Degli Alimenti di Origine Animale, University of Perugia, Perugia, 06126, Italy
| | - Luca Grispoldi
- Departimento di Medicina Veterinaria, Laboratorio di Ispezione Degli Alimenti di Origine Animale, University of Perugia, Perugia, 06126, Italy
| | - Eric Etter
- CIRAD, UMR ASTRE, Petit-Bourg, F-97170, France
- ASTRE, Université de Montpellier, CIRAD INRAE, Montpellier, France
| | - Alan Kalake
- Gauteng Department of Agriculture and Rural Development, Johannesburg, 2001, South Africa
| | - Musafiri Karama
- Department of Paraclinical Sciences, Faculty of Veterinary Science, Veterinary Public Health Section, University of Pretoria, Onderstepoort, 0110, South Africa.
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Safarirad M, Shahdadi M, Berizi E, Mazloomi SM, Hosseinzadeh S, Montaseri M, Derakhshan Z. A systematic review and modeling of the effect of bacteriophages on E. coli O157:H7 reduction in vegetables. Heliyon 2023; 9:e22961. [PMID: 38058426 PMCID: PMC10696239 DOI: 10.1016/j.heliyon.2023.e22961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 11/21/2023] [Accepted: 11/22/2023] [Indexed: 12/08/2023] Open
Abstract
Prevention and control of food pathogens are important for public health and E. coli O157:H7 infections are known as one of the most important food-borne bacterial diseases transmitted to humans. Vegetables can be a major source of E. coli O157:H7 bacteria. Bacteriophages have been considered in recent years as a natural method for controlling pathogens with minimal damage to the quality of vegetables. The performance of these natural antimicrobial agents is affected by various factors including time, temperature, phage and bacterial dose, method of phage application and origin of phages. The aim of the present study was to conduct a systematic review of the works that have examined the effect of different factors to reduce E. coli O157:H7 bacteria by its specific phages and model their effect. In our study, 10 articles were chosen after applying the inclusion and exclusion criteria mentioned in the methodology. The multivariate regression results showed that time, temperature, and method of phage application revealed a positive influence on the phage function, and with each unit of increase, the E. coli O157:H7 reduction increases by 0.4 %, 3 % and 0.94 % respectively, and 6 % for phage dose, but not statistically significant (P = 0.44). In addition, commercial-type phages were more effective than wild-type phages and this result was statistically significant (Beta = 0.99; P = 0.001). The results of this study indicate that the various factors, such as temperature, time, method of phage application and type of vegetables can play an important role to reduce E. coli O157:H7 in vegetables.
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Affiliation(s)
- Maryam Safarirad
- Student Research Committee, Department of Food Hygiene and Quality Control, School of Nutrition and Food Sciences, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mohsen Shahdadi
- Student Research Committee, Department of Food Hygiene and Quality Control, School of Nutrition and Food Sciences, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Enayat Berizi
- Nutrition Research Center, Department of Food Hygiene and Quality Control, School of Nutrition and Food Sciences, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Seyed Mohammad Mazloomi
- Nutrition Research Center, Department of Food Hygiene and Quality Control, School of Nutrition and Food Sciences, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Saeid Hosseinzadeh
- Department of Food Hygiene and Public Health, School of Veterinary Medicine, Shiraz University, Shiraz, Iran
| | - Maryam Montaseri
- Department of Food Hygiene and Public Health, School of Veterinary Medicine, Shiraz University, Shiraz, Iran
| | - Zahra Derakhshan
- Research Center for Health Sciences, Institute of Health, Shiraz University of Medical Sciences, Shiraz, Iran
- Department of Environmental Health Engineering, School of Health, Shiraz University of Medical Sciences, Shiraz, Iran
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Nolan TM, Sala-Comorera L, Reynolds LJ, Martin NA, Stephens JH, O'Hare GMP, O'Sullivan JJ, Meijer WG. Bacteriophages from faecal contamination are an important reservoir for AMR in aquatic environments. Sci Total Environ 2023; 900:165490. [PMID: 37487901 DOI: 10.1016/j.scitotenv.2023.165490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 07/10/2023] [Accepted: 07/10/2023] [Indexed: 07/26/2023]
Abstract
Bacteriophages have been shown to play an important role in harbouring and propagating antibiotic resistance genes (ARGs). Faecal matter contains high levels of phages, suggesting that faecal contamination of water bodies may lead to increased antimicrobial resistance (AMR) levels due to increased phage loading in aquatic environments. In this study, we assessed whether faecal pollution of three rivers (Rivers Liffey, Tolka, and Dodder) was responsible for increased levels of ARGs in phage particles using established phage-faecal markers, focusing on four ARGs (blaTEM, tet(O), qnrS, and sul1). We observed all four ARGs in phage fractions in all three rivers, with ARGs more frequently observed in agricultural and urban sampling sites compared to their source. These findings highlight the role of faecal pollution in environmental AMR and the impact of agricultural and urban activities on water quality. Furthermore, our results suggest the importance of including phages as indicators when assessing environmental AMR, as they serve as significant reservoirs of resistance genes in aquatic environments. This study provides important insights into the role of faecal pollution and phages in the prevalence of AMR in the environment and the need for their inclusion in future studies to provide a comprehensive understanding of environmental AMR.
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Affiliation(s)
- Tristan M Nolan
- UCD School of Biomolecular and Biomedical Science, UCD Earth Institute and UCD Conway Institute, University College Dublin, Dublin 4, Ireland
| | - Laura Sala-Comorera
- UCD School of Biomolecular and Biomedical Science, UCD Earth Institute and UCD Conway Institute, University College Dublin, Dublin 4, Ireland
| | - Liam J Reynolds
- UCD School of Biomolecular and Biomedical Science, UCD Earth Institute and UCD Conway Institute, University College Dublin, Dublin 4, Ireland
| | - Niamh A Martin
- UCD School of Biomolecular and Biomedical Science, UCD Earth Institute and UCD Conway Institute, University College Dublin, Dublin 4, Ireland
| | - Jayne H Stephens
- UCD School of Biomolecular and Biomedical Science, UCD Earth Institute and UCD Conway Institute, University College Dublin, Dublin 4, Ireland
| | - Gregory M P O'Hare
- School of Computer Science and Statistics, Trinity College Dublin, Dublin 2, Ireland
| | - John J O'Sullivan
- UCD School of Civil Engineering, UCD Dooge Centre for Water Resources Research and UCD Earth Institute, University College Dublin, Dublin 4, Ireland
| | - Wim G Meijer
- UCD School of Biomolecular and Biomedical Science, UCD Earth Institute and UCD Conway Institute, University College Dublin, Dublin 4, Ireland.
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El-Telbany M, Lin CY, Abdelaziz MN, Maung AT, El-Shibiny A, Mohammadi TN, Zayda M, Wang C, Zar Chi Lwin S, Zhao J, Masuda Y, Honjoh KI, Miyamoto T, El M. Potential application of phage vB_EfKS5 to control Enterococcus faecalis and its biofilm in food. AMB Express 2023; 13:130. [PMID: 37985524 PMCID: PMC10661674 DOI: 10.1186/s13568-023-01628-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 10/09/2023] [Indexed: 11/22/2023] Open
Abstract
Contaminated food with antibiotic-resistant Enterococcus spp. could be the vehicle for transmitting Enterococcus to humans and accordingly cause a public health problem. The accumulation of biogenic amines produced by Enterococcus faecalis (E. faecalis) in food may have cytological effects. Bacteriophages (phage in short) are natural antimicrobial agents and can be used alone or in combination with other food preservatives to reduce food microbial contaminants. The aim of this study was to isolate a novel phage against E. faecalis and determine its host range to evaluate its potential application. Bacteriophage, vB_EfKS5, with a broad host range, was isolated to control the growth of E. faecalis. The vB_EfKS5 genome is 59,246 bp in length and has a GC content of 39.7%. The computational analysis of phage vB_EfKS5 genome confirmed that it does not contain any lysogenic, toxic, or virulent genes. Phage vB_EfKS5 exhibited lytic activity against most E. faecalis isolates with different multiplicities of infections and it infected 75.5% (22/29) of E. faecalis isolates and 42.3% (3/7) of E. faecium isolates. It was also able to destroy the biofilm formed by E. faecalis with different MOIs. Phage vB_EfKS5 alone or in combination with nisin could control the growth of E. faecalis in broth and milk. Based on its high productivity, stability, short latent period, and large burst size, phage vB_EfKS5 has a high potential for applications both in food and medical applications.
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Affiliation(s)
- Mohamed El-Telbany
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, Fukuoka, Japan
- Department of Microbiology and Botany, Faculty of Science, Zagazig University, 44519, Zagazig, Egypt
| | - Chen-Yu Lin
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, Fukuoka, Japan
| | - Marwa Nabil Abdelaziz
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, Fukuoka, Japan
| | - Aye Thida Maung
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, Fukuoka, Japan
| | - Ayman El-Shibiny
- Center for Microbiology and Phage Therapy, Zewail City of Science and Technology, 12578, Giza, Egypt
| | - Tahir Noor Mohammadi
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, Fukuoka, Japan
- Teagasc Food Research Center, Moorepark, Fermoy, Cork, Ireland
| | - Mahmoud Zayda
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, Fukuoka, Japan
- Department of Food Hygiene and Control, Faculty of Veterinary Medicine, University of Sadat City, Sadat City, Monofiya Governorate, Egypt
| | - Chen Wang
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, Fukuoka, Japan
| | - Su Zar Chi Lwin
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, Fukuoka, Japan
| | - Junxin Zhao
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, Fukuoka, Japan
| | - Yoshimitsu Masuda
- Department of Bioscience and Biotechnology, Faculty of Agriculture, Graduate School, Kyushu University, 744 Motooka, Nishi-ku, 819-0395, Fukuoka, Japan
| | - Ken-Ichi Honjoh
- Department of Bioscience and Biotechnology, Faculty of Agriculture, Graduate School, Kyushu University, 744 Motooka, Nishi-ku, 819-0395, Fukuoka, Japan.
| | - Takahisa Miyamoto
- Department of Bioscience and Biotechnology, Faculty of Agriculture, Graduate School, Kyushu University, 744 Motooka, Nishi-ku, 819-0395, Fukuoka, Japan
| | - Mohamed El
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, Fukuoka, Japan
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Ghadimi D, Fölster-Holst R, Ebsen M, Röcken C, Dörfer C, Uchiyama J, Matsuzaki S, Bockelmann W. Exploring the Interplay between Nutrients, Bacteriophages, and Bacterial Lipases in Host- and Bacteria-mediated Pathogenesis. Endocr Metab Immune Disord Drug Targets 2023; 24:EMIDDT-EPUB-135990. [PMID: 37957846 DOI: 10.2174/0118715303257321231024094904] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 08/30/2023] [Accepted: 09/15/2023] [Indexed: 11/15/2023]
Abstract
BACKGROUND AND AIMS Pathogenic bacteria and host cells counteract or neutralize each other's effect in two fundamental ways: Direct invasion and secretion of various substances. Among these, lipases secreted by pathogenic bacteria and host cell lysozyme are key actors. Secreted lipases from pathogenic bacterial are suggested as a key player in the pathogen-host interaction. Among the gut microbial energy sources, glucose and fats have been referred to as one of the best inducers and substrates for bacterial lipases. Enrichment of bacterial growth medium with extra glucose or oil has been shown to induce lipase production in pathogenic bacteria. More recently, research has focused on the role of human gut phage alterations in the onset of dysbiosis because the bacteria-phage interactions can be dramatically affected by the nutrient milieu of the gut. However, the reciprocal role of bacterial lipases and phages in this context has not been well studied and there is no data available about how high glucose or fat availability might modulate the cellular milieu of the pathogenic bacteria-phageeukaryotic host cell interface. The purpose of this study was to evaluate the immunologic outcome of pathogenic bacteria-phage interaction under normal, high glucose, and high butter oil conditions to understand how nutrient availability affects lipase activity in pathogenic bacteria and, ultimately, the eukaryotic host cell responses to pathogenic bacteria-phage interaction. MATERIALS AND METHODS 10 groups of co-cultured T84 and HepG2 cells were treated with Pseudomonas aeruginosa strain PAO1 (P.a PAO1) in the presence and absence of its KPP22 phage and incubated in three different growth media (DMEM, DMEM + glucose and DMEM + butter oil). Structural and physiological (barrier function and cell viability), inflammatory (IL-6 and IL-8), metabolic (glucose and triglycerides), and enzymatic (lipases and lysozyme) parameters were determined. RESULTS Excess glucose or butter oil enhanced additively extracellular lipase activity of P.a PAO1. Excess glucose or butter oil treatments also magnified P. a PAO1- induced secretion of inflammatory signal molecules (IL-1β, IL-6) from co-cultured cells, concomitant with the enhancement of intracellular triglycerides in co-cultured HepG2 cells, these effects being abolished by phage KPP22. CONCLUSION The results of the present study imply that KPP22 phage influences the interplay between food substances, gut bacterial lipases, and the gut cellular milieu. This can be applied in two-way interaction: by affecting the microbial uptake of excess free simple sugars and fats from the gut milieu leading to decreased bacterial lipases and by modulating the immune system of the intestinal -liver axis cells. Further studies are needed to see if the biological consequences of these effects also occur in vivo.
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Affiliation(s)
- Darab Ghadimi
- Department of Microbiology and Biotechnology, Max Rubner-Institut, Hermann-Weigmann-Str 1, D-24103 Kiel, Germany
| | - Regina Fölster-Holst
- Clinic of Dermatology, University Hospital Schleswig-Holstein, Schittenhelmstr. 7, D-24105 Kiel, Germany
| | - Michael Ebsen
- Städtisches MVZ Kiel GmbH (Kiel City Hospital), Department of Pathology, Chemnitzstr. 33, 24116 Kiel, Germany
| | - Christoph Röcken
- Institute of Pathology, Kiel University, University Hospital, Schleswig-Holstein, Arnold-Heller-Straße 3/14, D-24105 Kiel, Germany
| | - Christof Dörfer
- Department of Operative Dentistry and Periodontology, University Medical Center Schleswig-Holstein, Campus Kiel, Germany
| | - Jumpei Uchiyama
- Department of Bacteriology, Graduate School of Medicine Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, Japan
| | - Shigenobu Matsuzaki
- Department of Medical Laboratory Science, Faculty of Health Sciences, Kochi Gakuen University, Kochi, Japan
| | - Wilhelm Bockelmann
- Department of Microbiology and Biotechnology, Max Rubner-Institut, Hermann-Weigmann-Str 1, D-24103 Kiel, Germany
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Grigson SR, Giles SK, Edwards RA, Papudeshi B. Knowing and Naming: Phage Annotation and Nomenclature for Phage Therapy. Clin Infect Dis 2023; 77:S352-S359. [PMID: 37932119 PMCID: PMC10627814 DOI: 10.1093/cid/ciad539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2023] Open
Abstract
Bacteriophages, or phages, are viruses that infect bacteria shaping microbial communities and ecosystems. They have gained attention as potential agents against antibiotic resistance. In phage therapy, lytic phages are preferred for their bacteria killing ability, while temperate phages, which can transfer antibiotic resistance or toxin genes, are avoided. Selection relies on plaque morphology and genome sequencing. This review outlines annotating genomes, identifying critical genomic features, and assigning functional labels to protein-coding sequences. These annotations prevent the transfer of unwanted genes, such as antimicrobial resistance or toxin genes, during phage therapy. Additionally, it covers International Committee on Taxonomy of Viruses (ICTV)-an established phage nomenclature system for simplified classification and communication. Accurate phage genome annotation and nomenclature provide insights into phage-host interactions, replication strategies, and evolution, accelerating our understanding of the diversity and evolution of phages and facilitating the development of phage-based therapies.
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Affiliation(s)
- Susanna R Grigson
- Flinders Accelerator for Microbiome Exploration, College of Science and Engineering, Flinders University, Adelaide, Australia
| | - Sarah K Giles
- Flinders Accelerator for Microbiome Exploration, College of Science and Engineering, Flinders University, Adelaide, Australia
| | - Robert A Edwards
- Flinders Accelerator for Microbiome Exploration, College of Science and Engineering, Flinders University, Adelaide, Australia
| | - Bhavya Papudeshi
- Flinders Accelerator for Microbiome Exploration, College of Science and Engineering, Flinders University, Adelaide, Australia
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Panhwar S, Keerio HA, Ilhan H, Boyacı IH, Tamer U. Principles, Methods, and Real-Time Applications of Bacteriophage-Based Pathogen Detection. Mol Biotechnol 2023:10.1007/s12033-023-00926-5. [PMID: 37914863 DOI: 10.1007/s12033-023-00926-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 10/02/2023] [Indexed: 11/03/2023]
Abstract
Bacterial pathogens in water, food, and the environment are spreading diseases around the world. According to a World Health Organization (WHO) report, waterborne pathogens pose the most significant global health risks to living organisms, including humans and animals. Conventional bacterial detection approaches such as colony counting, microscopic analysis, biochemical analysis, and molecular analysis are expensive, time-consuming, less sensitive, and require a pre-enrichment step. However, the bacteriophage-based detection of pathogenic bacteria is a robust approach that utilizes bacteriophages, which are viruses that specifically target and infect bacteria, for rapid and accurate detection of targets. This review shed light on cutting-edge technologies about the novel structure of phages and the immobilization process on the surface of electrodes to detect targeted bacterial cells. Similarly, the purpose of this study was to provide a comprehensive assessment of bacteriophage-based biosensors utilized for pathogen detection, as well as their trends, outcomes, and problems. This review article summaries current phage-based pathogen detection strategies for the development of low-cost lab-on-chip (LOC) and point-of-care (POC) devices using electrochemical and optical methods such as surface-enhanced Raman spectroscopy (SERS).
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Affiliation(s)
- Sallahuddin Panhwar
- Department of Analytical Chemistry, Faculty of Pharmacy, Gazi University, 06330, Ankara, Turkey.
- Department of Civil Engineering, National University of Sciences and Technology, Quetta, 24090, Balochistan, Pakistan.
| | - Hareef Ahmed Keerio
- Department of Civil and Environmental Engineering, Hanyang University, Seoul, Republic of Korea
| | - Hasan Ilhan
- Department of Chemistry, Faculty of Science, Ordu University, Altinordu, 52200, Ordu, Turkey
| | - Ismail Hakkı Boyacı
- Department of Food Engineering, Faculty of Engineering, Hacettepe University, Beytepe, 06800, Ankara, Turkey
| | - Ugur Tamer
- Department of Analytical Chemistry, Faculty of Pharmacy, Gazi University, 06330, Ankara, Turkey.
- Metu MEMS Center, Ankara, Turkey.
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Romero-Calle DX, de Santana VP, Benevides RG, Aliaga MTA, Billington C, Góes-Neto A. Systematic review and meta-analysis: the efficiency of bacteriophages previously patented against pathogenic bacteria on food. Syst Rev 2023; 12:201. [PMID: 37898821 PMCID: PMC10612260 DOI: 10.1186/s13643-023-02352-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Accepted: 09/13/2023] [Indexed: 10/30/2023] Open
Abstract
Food-borne diseases are a global public health issue with 1 in 10 people falling ill after eating contaminated food every year. In response, the food industry has implemented several new pathogen control strategies, such as biotechnological tools using the direct application of bacteriophages for biological control. We have undertaken a systematic review and meta-analysis that evaluated the efficiency of patented phages as a biological control for food-borne pathogens and determined the physical-chemical characteristics of the antimicrobial effect. Included and excluded criteria was developed. Included criteria: Phage patent files with an application in biological control on food and scientific articles and book chapters that used phages patented for food biological control. Excluded criteria: Patent documents, scientific articles, and book chapters that included phage therapy in humans, animals, and biological control on plants but did not have an application on food were not considered in our study. The systematic analysis identified 77 documents, 46 scientific articles, and 31 documents of patents and 23 articles was included in the meta-analysis. Listeria monocytogenes and Salmonella sp. comprised most of the targets identified in the screening, so that we focused on these strains to do the meta-analysis. There are a total of 383 and 192 experiments for Listeria and Salmonella phages for quantitative data analysis.Indexing databases for the bibliographic search (Scopus, Web of Science (WoS) and PubMed (Medline) were addressed by an automated script written in Python 3 Python Core Team (2015) and deposited on GitHub ( https://github.com/glenjasper ).A random-effects meta-analysis revealed (i) significant antimicrobial effect of Listeria phages in apple, apple juice, pear, and pear juice, (ii) significant antimicrobial effect of Salmonella phages in eggs, apple, and ready-to-eat chicken, (iii) no heterogeneity was identified in either meta-analysis, (iv) publication bias was detected for Listeria phages but not for Salmonella phages. (v) ListShield and Felix01 phages showed the best result for Listeria and Salmonella biological control, respectively, (vi) concentration of phage and bacteria, time and food had significant effect in the biological control of Listeria, (vii) temperature and time had a significant effect on the antimicrobial activity of Salmonella phages. The systematic review and meta-analyses to determine the efficiency of bacteriophages previously patented against pathogenic bacteria on dairy products, meat, fruits and vegetables. Besides, the discovering of key factors for efficacy, so that future applications of phage biotechnology in foods can be optimally deployed.
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Affiliation(s)
- Danitza Xiomara Romero-Calle
- Postgraduate Program in Biotechnology, State University of Feira de Santana (UEFS), Av. Transnordestina S/N, Feira de Santana, BA, 44036-900, Brazil.
- Department of Biological Sciences, Feira de Santana State University (UEFS), Feira de Santana, BA, 44036-900, Brazil.
- Biotechnology Area, Institute of Pharmaco-Biochemical Research, Faculty of Pharmaceutical and Biochemical Sciences, Higher San Andres University, P.O. Box 3239, La Paz, Bolivia.
| | - Vinicius Pereira de Santana
- Department of Biological Sciences, Feira de Santana State University (UEFS), Feira de Santana, BA, 44036-900, Brazil
| | - Raquel Guimarães Benevides
- Postgraduate Program in Biotechnology, State University of Feira de Santana (UEFS), Av. Transnordestina S/N, Feira de Santana, BA, 44036-900, Brazil
- Department of Biological Sciences, Feira de Santana State University (UEFS), Feira de Santana, BA, 44036-900, Brazil
| | - Maria Teresa Alvarez Aliaga
- Biotechnology Area, Institute of Pharmaco-Biochemical Research, Faculty of Pharmaceutical and Biochemical Sciences, Higher San Andres University, P.O. Box 3239, La Paz, Bolivia
| | - Craig Billington
- Health & Environment Group, Institute of Environmental Sciences and Research, PO Box 29-181, Christchurch, 8540, New Zealand
| | - Aristóteles Góes-Neto
- Postgraduate Program in Biotechnology, State University of Feira de Santana (UEFS), Av. Transnordestina S/N, Feira de Santana, BA, 44036-900, Brazil
- Department of Biological Sciences, Feira de Santana State University (UEFS), Feira de Santana, BA, 44036-900, Brazil
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Walter N, Mirzaei M, Deng L, Willy C, Alt V, Rupp M. The Potential of Bacteriophage Therapy as an Alternative Treatment Approach for Antibiotic-Resistant Infections. Med Princ Pract 2023; 33:1-9. [PMID: 37879316 PMCID: PMC10896615 DOI: 10.1159/000534717] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Accepted: 10/19/2023] [Indexed: 10/27/2023] Open
Abstract
OBJECTIVE This study aimed to provide a comprehensive overview of the current state of the literature on the therapeutical application of bacteriophages. METHODS First, a bibliometric analysis was performed using the database Web of Science to determine annual number of publications and citations. Second, a systematic literature review was conducted on randomized-controlled trials (RCTs) of phage therapy in PubMed. RESULTS Over the past decade, the number of publications on bacteriophage therapy increased more than fourfold with 212 articles in 2011 and 739 in 2022. The systematic search in PubMed yielded 7 RCTs eligible for inclusion, reporting on a total of 418 participants. Identified indications in this study included bacterial diarrhea, urinary tract infections, infected burn wounds, chronic otitis, chronic venous leg ulcers, and chronic rhinosinusitis. In three studies, mild to moderate adverse events were reported in 10/195 participants (5.1%). Three of the studies reported a statistically significant difference in outcomes comparing phage therapy with standard of care or placebo. CONCLUSION Phage therapy has gained increasing interest over the years. RCTs on different indications suggest the safety of phage therapy; however, reasons why phage therapy is not yet well accepted are limitations in the study designs. For a successful translation into clinical practice researchers and clinicians should learn from the earlier experiences and consider issues such as the quality of phage preparation, sensitivity testing, titer and dosages, as well as access to the infection site and stability for standardized protocols and future trials.
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Affiliation(s)
- Nike Walter
- Department of Trauma Surgery, University Hospital Regensburg, Regensburg, Germany
- Department for Psychosomatic Medicine, University Hospital Regensburg, Regensburg, Germany
| | - Mohammadali Mirzaei
- Helmholtz Centre Munich, German Research Center for Environmental Health, Institute of Virology, Munich, Germany
- Institute of Virology, Technical University of Munich, Munich, Germany
| | - Li Deng
- Institute of Virology, Technical University of Munich, Munich, Germany
- Department Trauma and Orthopedic Surgery, Septic and Reconstructive Surgery, Research and Treatment Center Septic Defect Wounds, Federal Armed Forces of Germany, Military Academic Hospital Berlin, Berlin, Germany
| | - Christian Willy
- Department Trauma and Orthopedic Surgery, Septic and Reconstructive Surgery, Research and Treatment Center Septic Defect Wounds, Federal Armed Forces of Germany, Military Academic Hospital Berlin, Berlin, Germany
| | - Volker Alt
- Department of Trauma Surgery, University Hospital Regensburg, Regensburg, Germany
| | - Markus Rupp
- Department of Trauma Surgery, University Hospital Regensburg, Regensburg, Germany
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Palomo A, Dechesne A, Smets BF, Zheng Y. Narrow host range phages infect essential bacteria for water purification reactions in groundwater-fed rapid sand filters. Water Res 2023; 245:120655. [PMID: 37748347 DOI: 10.1016/j.watres.2023.120655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 09/18/2023] [Accepted: 09/19/2023] [Indexed: 09/27/2023]
Abstract
Biofiltration is used worldwide to provide safe potable water due to its low energy demand and excellent treatment performance. For instance, in Denmark, over 95% of drinking water is supplied through groundwater-fed rapid sand filters (RSF). Bacteriophages, viruses that infect bacteria, have been shown to shape the taxonomic and functional composition of microbial communities across a range of natural and engineering systems. However, phages in the biofiltration systems are rarely studied, despite the central role microbes play in water purification. To probe this, metagenomic data from surface water, groundwater and mixed source water biofiltration units (n = 26 from China, Europe and USA) for drinking water production were analysed to characterize prokaryotic viruses and to identify their potential microbial hosts. The source water type and geographical location are found to exert influence on the composition of the phageome in biofilters. Although the viral abundance (71,676 ± 17,841 RPKM) in biofilters is only 14.4% and 17.0% lower than those of the nutrient-rich wastewater treatment plants and fresh surface waters, the richness (1,441 ± 1,046) and diversity (Inverse Simpson: 91 ± 61) in biofiltration units are significantly less by a factor of 2-5 and 3-4, respectively. In depth analysis of data from 24 groundwater-fed RSFs in Denmark revealed a core phageome shared by most RSFs, which was consistently linked to dominant microbial hosts involved in key biological reactions for water purification. Finally, the high number of specific links detected between phages and bacterial species and the large proportion of lytic phages (77%) led to the conjecture that phages regulate bacterial populations through predation, preventing the proliferation of dominant species and contributing to the established functional redundancy among the dominant microbial groups. In conclusion, bacteriophages are likely to play a significant role in water treatment within biofilters, particularly through interactions with key bacterial species.
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Affiliation(s)
- Alejandro Palomo
- State Environmental Protection Key Laboratory of Integrated Surface Water-Groundwater Pollution Control, School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen 518055, China; Guangdong Provincial Key Laboratory of Soil and Groundwater Pollution Control, School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen 518055, China; Shenzhen Key Laboratory of Precision Measurement and Early Warning Technology for Urban Environmental Health Risks, School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen 518055, China
| | - Arnaud Dechesne
- Department of Environmental and Resource Engineering, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Barth F Smets
- Department of Environmental and Resource Engineering, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Yan Zheng
- State Environmental Protection Key Laboratory of Integrated Surface Water-Groundwater Pollution Control, School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen 518055, China; Guangdong Provincial Key Laboratory of Soil and Groundwater Pollution Control, School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen 518055, China; Shenzhen Key Laboratory of Precision Measurement and Early Warning Technology for Urban Environmental Health Risks, School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen 518055, China.
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Ru J, Xue J, Sun J, Cova L, Deng L. Unveiling the hidden role of aquatic viruses in hydrocarbon pollution bioremediation. J Hazard Mater 2023; 459:132299. [PMID: 37597386 DOI: 10.1016/j.jhazmat.2023.132299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 07/28/2023] [Accepted: 08/12/2023] [Indexed: 08/21/2023]
Abstract
Hydrocarbon pollution poses substantial environmental risks to water and soil. Bioremediation, which utilizes microorganisms to manage pollutants, offers a cost-effective solution. However, the role of viruses, particularly bacteriophages (phages), in bioremediation remains unexplored. This study examines the diversity and activity of hydrocarbon-degradation genes encoded by environmental viruses, focusing on phages, within public databases. We identified 57 high-quality phage-encoded auxiliary metabolic genes (AMGs) related to hydrocarbon degradation, which we refer to as virus-encoded hydrocarbon degradation genes (vHYDEGs). These genes are encoded by taxonomically diverse aquatic phages and highlight the under-characterized global virosphere. Six protein families involved in the initial alkane hydroxylation steps were identified. Phylogenetic analyses revealed the diverse evolutionary trajectories of vHYDEGs across habitats, revealing previously unknown biodegraders linked evolutionarily with vHYDEGs. Our findings suggest phage AMGs may contribute to alkane and aromatic hydrocarbon degradation, participating in the initial, rate-limiting hydroxylation steps, thereby aiding hydrocarbon pollution bioremediation and promoting their propagation. To support future research, we developed vHyDeg, a database containing identified vHYDEGs with comprehensive annotations, facilitating the screening of hydrocarbon degradation AMGs and encouraging their bioremediation applications.
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Affiliation(s)
- Jinlong Ru
- Institute of Virology, Helmholtz Centre Munich - German Research Centre for Environmental Health, Neuherberg 85764, Germany; Chair of Prevention for Microbial Infectious Disease, Central Institute of Disease Prevention and School of Life Sciences, Technical University of Munich, Freising 85354, Germany
| | - Jinling Xue
- Institute of Virology, Helmholtz Centre Munich - German Research Centre for Environmental Health, Neuherberg 85764, Germany; Chair of Prevention for Microbial Infectious Disease, Central Institute of Disease Prevention and School of Life Sciences, Technical University of Munich, Freising 85354, Germany
| | - Jianfeng Sun
- Botnar Research Centre, University of Oxford, Oxford OX3 7LD, UK
| | - Linda Cova
- Institute of Virology, Helmholtz Centre Munich - German Research Centre for Environmental Health, Neuherberg 85764, Germany
| | - Li Deng
- Institute of Virology, Helmholtz Centre Munich - German Research Centre for Environmental Health, Neuherberg 85764, Germany; Chair of Prevention for Microbial Infectious Disease, Central Institute of Disease Prevention and School of Life Sciences, Technical University of Munich, Freising 85354, Germany.
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Cao Y, Feng T, Wu Y, Xu Y, Du L, Wang T, Luo Y, Wang Y, Li Z, Xuan Z, Chen S, Yao N, Gao NL, Xiao Q, Huang K, Wang X, Cui K, Rehman SU, Tang X, Liu D, Han H, Li Y, Chen WH, Liu Q. The multi-kingdom microbiome of the goat gastrointestinal tract. Microbiome 2023; 11:219. [PMID: 37779211 PMCID: PMC10544373 DOI: 10.1186/s40168-023-01651-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 08/14/2023] [Indexed: 10/03/2023]
Abstract
BACKGROUND Goat is an important livestock worldwide, which plays an indispensable role in human life by providing meat, milk, fiber, and pelts. Despite recent significant advances in microbiome studies, a comprehensive survey on the goat microbiomes covering gastrointestinal tract (GIT) sites, developmental stages, feeding styles, and geographical factors is still unavailable. Here, we surveyed its multi-kingdom microbial communities using 497 samples from ten sites along the goat GIT. RESULTS We reconstructed a goat multi-kingdom microbiome catalog (GMMC) including 4004 bacterial, 71 archaeal, and 7204 viral genomes and annotated over 4,817,256 non-redundant protein-coding genes. We revealed patterns of feeding-driven microbial community dynamics along the goat GIT sites which were likely associated with gastrointestinal food digestion and absorption capabilities and disease risks, and identified an abundance of large intestine-enriched genera involved in plant fiber digestion. We quantified the effects of various factors affecting the distribution and abundance of methane-producing microbes including the GIT site, age, feeding style, and geography, and identified 68 virulent viruses targeting the methane producers via a comprehensive virus-bacterium/archaea interaction network. CONCLUSIONS Together, our GMMC catalog provides functional insights of the goat GIT microbiota through microbiome-host interactions and paves the way to microbial interventions for better goat and eco-environmental qualities. Video Abstract.
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Affiliation(s)
- Yanhong Cao
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and Engineering, Foshan University, Foshan, 528225, China
- Guangxi Vocational University of Agriculture, Nanning, Guangxi, 530007, China
| | - Tong Feng
- Department of Bioinformatics and Systems Biology, Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Center for Artificial Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, Hubei, China.
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, 530005, China.
| | - Yingjian Wu
- Department of Bioinformatics and Systems Biology, Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Center for Artificial Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, Hubei, China
| | - Yixue Xu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, 530005, China
| | - Li Du
- Hainan Key Lab of Tropical Animal Reproduction and Breeding and Epidemic Disease Research, College of Animal Science and Technology, Hainan University, Haikou, 570000, Hainan, China
| | - Teng Wang
- Department of Bioinformatics and Systems Biology, Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Center for Artificial Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, Hubei, China
| | - Yuhong Luo
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, 530005, China
| | - Yan Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, 530005, China
| | - Zhipeng Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, 530005, China
| | - Zeyi Xuan
- Animal Husbandry Research Institute of Guangxi Zhuang Autonomous Region, Nanning, 530001, Guangxi, China
| | - Shaomei Chen
- Animal Husbandry Research Institute of Guangxi Zhuang Autonomous Region, Nanning, 530001, Guangxi, China
| | - Na Yao
- Animal Husbandry Research Institute of Guangxi Zhuang Autonomous Region, Nanning, 530001, Guangxi, China
| | - Na L Gao
- Department of Bioinformatics and Systems Biology, Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Center for Artificial Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, Hubei, China
| | - Qian Xiao
- Hainan Key Lab of Tropical Animal Reproduction and Breeding and Epidemic Disease Research, College of Animal Science and Technology, Hainan University, Haikou, 570000, Hainan, China
| | - Kongwei Huang
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and Engineering, Foshan University, Foshan, 528225, China
| | - Xiaobo Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, 530005, China
| | - Kuiqing Cui
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and Engineering, Foshan University, Foshan, 528225, China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, 530005, China
| | - Saif Ur Rehman
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, 530005, China
| | - Xiangfang Tang
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Dewu Liu
- South China Agricultural University, Guangzhou, 510642, China
| | - Hongbing Han
- College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Ying Li
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and Engineering, Foshan University, Foshan, 528225, China
| | - Wei-Hua Chen
- Department of Bioinformatics and Systems Biology, Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Center for Artificial Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, Hubei, China.
- Institution of Medical Artificial Intelligence, Binzhou Medical University, Yantai, 264003, China.
| | - Qingyou Liu
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and Engineering, Foshan University, Foshan, 528225, China.
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, 530005, China.
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Pekkle Lam HY, Lai MJ, Wu WJ, Chin YH, Chao HJ, Chen LK, Peng SY, Chang KC. Isolation and characterization of bacteriophages with activities against multi-drug-resistant Acinetobacter nosocomialis causing bloodstream infection in vivo. J Microbiol Immunol Infect 2023; 56:1026-1035. [PMID: 37586915 DOI: 10.1016/j.jmii.2023.07.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 07/04/2023] [Accepted: 07/31/2023] [Indexed: 08/18/2023]
Abstract
BACKGROUND Acinetobacter nosocomialis (A. nosocomialis) is a glucose non-fermentative, gram-negative bacillus that belongs to the Acinetobacter calcoaceticus-baumannii complex. In recent years, studies have found an increased clinical prevalence of A. nosocomialis. However, given the increasing trend of antibiotic resistance, developing new antibacterial agents is vital. Currently, research regarding bacteriophage therapy against A. nosocomialis is only limited. METHODS Two A. nosocomialis bacteriophages, TCUAN1 and TCUAN2, were isolated from sewage. Experiments such as transmission electron microscopy (TEM), host-range analysis, and sequencing were performed to determine their biological and genomic characteristics. TCUAN2 were further subjected to in vivo experiments and their derived-endolysin were cloned and tested against their bacteria host. RESULTS Transmission electron microscopy revealed that TCUAN1 and TCUAN2 belong to Myoviridae and Podoviridae, respectively. Both phages show a broad host spectrum and rapid adsorption efficiency. Further biological analysis showed that TCUAN2 possesses a shorter latent period and larger burst size compared to TCUAN1. Because TCUAN2 showed a better antibacterial activity, it was injected into A. nosocomialis-infected mice which resulted in a significant decrease in bacterial load levels in the blood and increased the mice's survival. Finally, genomic analysis revealed that the complete nucleotide sequence of TCUAN1 is 49, 691 bps (containing 75 open reading frames) with a G + C content of 39.3%; whereas the complete nucleotide sequence of TCUAN2 is 41, 815 bps (containing 68 open reading frames) with a G + C content of 39.1%. The endolysin gene cloned and purified from TCUAN2 also showed antibacterial activity when used with a chelator EDTA.
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Affiliation(s)
- Ho Yin Pekkle Lam
- Department of Biochemistry, School of Medicine, Tzu Chi University, Hualien, Taiwan
| | - Meng-Jiun Lai
- Department of Laboratory Medicine and Biotechnology, Tzu Chi University, Hualien, Taiwan
| | - Wen-Jui Wu
- Department of Laboratory Medicine and Biotechnology, Tzu Chi University, Hualien, Taiwan
| | - Ying-Hao Chin
- Department of Laboratory Medicine, Hualien Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, Hualien, Taiwan
| | - Huei-Jen Chao
- Department of Laboratory Medicine, Hualien Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, Hualien, Taiwan
| | - Li-Kuang Chen
- Department of Laboratory Medicine, Hualien Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, Hualien, Taiwan
| | - Shih-Yi Peng
- Department of Biochemistry, School of Medicine, Tzu Chi University, Hualien, Taiwan.
| | - Kai-Chih Chang
- Department of Laboratory Medicine and Biotechnology, Tzu Chi University, Hualien, Taiwan; Department of Laboratory Medicine, Hualien Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, Hualien, Taiwan.
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Zhou WY, Wen H, Li YJ, Gao L, Rao SQ, Yang ZQ, Zhu GQ. Acquisition, loss, and replication of functional modules promote the genetic diversity of Salmonella bacteriophages. Microbiol Res 2023; 275:127461. [PMID: 37499310 DOI: 10.1016/j.micres.2023.127461] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 07/13/2023] [Accepted: 07/13/2023] [Indexed: 07/29/2023]
Abstract
Owing to the threats that Salmonella poses to public health and the abuse of antimicrobials, bacteriophage therapy against Salmonella is experiencing a resurgence. Although several phages have been reported as safe and efficient for controlling Salmonella, the genetic diversity and relatedness among Salmonella phages remain poorly understood. In this study, whole-genome sequences of 91 Salmonella bacteriophages were obtained from the National Center for Biological Information genome database. Phylogenetic analysis, mosaic structure comparisons, gene content analysis, and orthologue group clustering were performed. Phylogenetic analysis revealed four singletons and two major lineages (I-II), including five subdividing clades, of which Salmonella phages belonging to morphologically distinct families were clustered in the same clade. Chimeric structures (n = 31), holin genes (n = 18), lysin genes (n = 66), DNA packaging genes (n = 55), and DNA metabolism genes (n = 24) were present in these phages. Moreover, phages from different subdivided clusters harboured distinct genes associated with host cell lysis, DNA packaging, and DNA metabolism. Notably, phages belonging to morphologically distinct families shared common orthologue groups. Although several functional modules of phages SS1 and SE16 shared > 99% nucleotide sequence identity with phages SI2 and SI23, the major differences between these phages were the absence and replication of functional modules. The data obtained herein revealed the genetic diversity of Salmonella phages at genomic, structural, and gene content levels. The genetic diversity of Salmonella phages is likely owing to the acquisition, loss, and replication of functional modules.
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Affiliation(s)
- Wen-Yuan Zhou
- College of Food Science and Engineering, Yangzhou University, Yangzhou, Jiangsu 225127, China; College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Hua Wen
- College of Food Science and Engineering, Yangzhou University, Yangzhou, Jiangsu 225127, China
| | - Ya-Jie Li
- College of Food Science and Engineering, Yangzhou University, Yangzhou, Jiangsu 225127, China
| | - Lu Gao
- College of Food Science and Engineering, Yangzhou University, Yangzhou, Jiangsu 225127, China
| | - Sheng-Qi Rao
- College of Food Science and Engineering, Yangzhou University, Yangzhou, Jiangsu 225127, China
| | - Zhen-Quan Yang
- College of Food Science and Engineering, Yangzhou University, Yangzhou, Jiangsu 225127, China.
| | - Guo-Qiang Zhu
- College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu 225009, China.
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Dedrick RM, Abad L, Storey N, Kaganovsky AM, Smith BE, Aull HA, Cristinziano M, Morkowska A, Murthy S, Loebinger MR, Hatfull GF, Satta G. The problem of Mycobacterium abscessus complex: multi-drug resistance, bacteriophage susceptibility and potential healthcare transmission. Clin Microbiol Infect 2023; 29:1335.e9-1335.e16. [PMID: 37364635 PMCID: PMC10583746 DOI: 10.1016/j.cmi.2023.06.026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 06/13/2023] [Accepted: 06/21/2023] [Indexed: 06/28/2023]
Abstract
OBJECTIVES Mycobacterium abscessus complex is responsible for 2.6-13.0% of all non-tuberculous mycobacterial pulmonary infections and these are notoriously difficult to treat due to the complex regimens required, drug resistance and adverse effects. Hence, bacteriophages have been considered in clinical practice as an additional treatment option. Here, we evaluated antibiotic and phage susceptibility profiles of M. abscessus clinical isolates. Whole-genome sequencing (WGS) revealed the phylogenetic relationships, dominant circulating clones (DCCs), the likelihood of patient-to-patient transmission and the presence of prophages. METHODS Antibiotic susceptibility testing was performed using CLSI breakpoints (n = 95), and plaque assays were used for phage susceptibility testing (subset of n = 88, 35 rough and 53 smooth morphology). WGS was completed using the Illumina platform and analysed using Snippy/snp-dists and Discovery and Extraction of Phages Tool (DEPhT). RESULTS Amikacin and Tigecycline were the most active drugs (with 2 strains resistant to amikacin, and one strain with Tigecycline MIC of 4 μg/mL). Most strains were resistant to all other drugs tested, with Linezolid and Imipenem showing the least resistance, at 38% (36/95) and 55% (52/95), respectively. Rough colony morphotype strains were more phage-susceptible than smooth strains (77%-27/35 versus 48%-25/53 in the plaque assays, but smooth strains are not killed efficiently by those phages in liquid infection assay). We have also identified 100 resident prophages, some of which were propagated lytically. DCC1 (20%-18/90) and DCC4 (22%-20/90) were observed to be the major clones and WGS identified 6 events of possible patient-to-patient transmission. DISCUSSION Many strains of M. abscessus complex are intrinsically resistant to available antibiotics and bacteriophages represent an alternative therapeutic option, but only for strains with rough morphology. Further studies are needed to elucidate the role of hospital-borne M. abscessus transmission.
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Affiliation(s)
- Rebekah M Dedrick
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Lawrence Abad
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Nathaniel Storey
- Department of Microbiology, Virology and Infection Control, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Ari M Kaganovsky
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Bailey E Smith
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Haley A Aull
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Madison Cristinziano
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | | | - Saraswathi Murthy
- Royal Brompton and Harefield Hospitals, Guys and St Thomas's NHS Foundation Trust, London, UK
| | - Michael R Loebinger
- Royal Brompton and Harefield Hospitals, Guys and St Thomas's NHS Foundation Trust, London, UK; National Heart and Lung Institute, Imperial College London, London, UK
| | - Graham F Hatfull
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Giovanni Satta
- Centre for Clinical Microbiology, University College London, London, UK; Infection Division, University College London Hospitals NHS Foundation Trust, London, UK.
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Qu Q, Chen T, He P, Geng H, Zeng P, Luan G. Isolation and characterization of a novel lytic bacteriophage vB_Efm_LG62 infecting Enterococcus faecium. Virus Genes 2023; 59:763-774. [PMID: 37422898 DOI: 10.1007/s11262-023-02016-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 06/11/2023] [Indexed: 07/11/2023]
Abstract
Enterococcus faecium has been classified as a "high priority" pathogen by the World Health Organization. Enterococcus faecium has rapidly evolved as a global nosocomial pathogen with adaptation to the nosocomial environment and the accumulation of resistance to multiple antibiotics. Phage therapy is considered a promising strategy against difficult-to-treat infections and antimicrobial resistance. In this study, we isolated and characterized a novel virulent bacteriophage, vB_Efm_LG62, that specifically infects multidrug-resistant E. faecium. Morphological observations suggested that the phage has siphovirus morphology, with an optimal multiplicity of infection of 0.001. One-step growth tests revealed that its latent growth was at 20 min, with a burst size of 101 PFU/cell. Phage vB_Efm_LG62 was verified to have a double-stranded genome of 42,236 bp (35.21% GC content), containing 66 predicted coding sequences as determined by whole genomic sequencing. No genes were predicted to have functions associated with virulence factors or antibiotic resistance, indicating that the phage vB_Efm_LG62 has good therapeutic potential. Our isolation and characterization of this highly efficient phage aids in expanding our knowledge of E. faecium-targeting phages, and provides additional options for phage cocktail therapy.
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Affiliation(s)
- Qianyu Qu
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Tao Chen
- Medical Laboratory, Xindu District People's Hospital of Chengdu, Chengdu, China
| | - Penggang He
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Huaixin Geng
- Non-Coding RNA and Drug Discovery Key Laboratory of Sichuan Province, Chengdu Medical College, Chengdu, China
| | - Peibin Zeng
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China.
| | - Guangxin Luan
- Non-Coding RNA and Drug Discovery Key Laboratory of Sichuan Province, Chengdu Medical College, Chengdu, China.
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Yang Y, Hu Z, Kang Y, Gao J, Chen H, Liu H, Wang Y, Liu B. Phage SPO1 Protein Gp49 Is a Novel RNA Binding Protein That Is Involved in Host Iron Metabolism. Int J Mol Sci 2023; 24:14318. [PMID: 37762620 PMCID: PMC10531801 DOI: 10.3390/ijms241814318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 09/11/2023] [Accepted: 09/15/2023] [Indexed: 09/29/2023] Open
Abstract
Bacillus subtilis is a model organism for studying Gram-positive bacteria and serves as a cell factory in the industry for enzyme and chemical production. Additionally, it functions as a probiotic in the gastrointestinal tract, modulating the gut microbiota. Its lytic phage SPO1 is also the most studied phage among the genus Okubovrius, including Bacillus phage SPO1 and Camphawk. One of the notable features of SPO1 is the existence of a "host-takeover module", a cluster of 24 genes which occupies most of the terminal redundancy. Some of the gene products from the module have been characterized, revealing their ability to disrupt host metabolism by inhibiting DNA replication, RNA transcription, cell division, and glycolysis. However, many of the gene products which share limited similarity to known proteins remain under researched. In this study, we highlight the involvement of Gp49, a gene product from the module, in host RNA binding and heme metabolism-no observation has been reported in other phages. Gp49 folds into a structure that does not resemble any protein in the database and has a new putative RNA binding motif. The transcriptome study reveals that Gp49 primarily upregulates host heme synthesis which captures cytosolic iron to facilitate phage development.
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Affiliation(s)
- Yanan Yang
- BioBank, The First Affiliated Hospital of Xi’an Jiaotong University, Yanta District, Xi’an 710061, China; (Y.Y.); (Z.H.); (Y.K.); (J.G.); (H.C.); (H.L.)
- Centre for Biobank and Advanced Medical Research of Shaanxi Province, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an 710061, China
| | - Zhenyue Hu
- BioBank, The First Affiliated Hospital of Xi’an Jiaotong University, Yanta District, Xi’an 710061, China; (Y.Y.); (Z.H.); (Y.K.); (J.G.); (H.C.); (H.L.)
- Centre for Biobank and Advanced Medical Research of Shaanxi Province, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an 710061, China
| | - Yue Kang
- BioBank, The First Affiliated Hospital of Xi’an Jiaotong University, Yanta District, Xi’an 710061, China; (Y.Y.); (Z.H.); (Y.K.); (J.G.); (H.C.); (H.L.)
- Centre for Biobank and Advanced Medical Research of Shaanxi Province, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an 710061, China
| | - Juanjuan Gao
- BioBank, The First Affiliated Hospital of Xi’an Jiaotong University, Yanta District, Xi’an 710061, China; (Y.Y.); (Z.H.); (Y.K.); (J.G.); (H.C.); (H.L.)
- Centre for Biobank and Advanced Medical Research of Shaanxi Province, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an 710061, China
| | - Huan Chen
- BioBank, The First Affiliated Hospital of Xi’an Jiaotong University, Yanta District, Xi’an 710061, China; (Y.Y.); (Z.H.); (Y.K.); (J.G.); (H.C.); (H.L.)
- Centre for Biobank and Advanced Medical Research of Shaanxi Province, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an 710061, China
| | - Hui Liu
- BioBank, The First Affiliated Hospital of Xi’an Jiaotong University, Yanta District, Xi’an 710061, China; (Y.Y.); (Z.H.); (Y.K.); (J.G.); (H.C.); (H.L.)
- Centre for Biobank and Advanced Medical Research of Shaanxi Province, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an 710061, China
| | - Yawen Wang
- BioBank, The First Affiliated Hospital of Xi’an Jiaotong University, Yanta District, Xi’an 710061, China; (Y.Y.); (Z.H.); (Y.K.); (J.G.); (H.C.); (H.L.)
- Centre for Biobank and Advanced Medical Research of Shaanxi Province, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an 710061, China
| | - Bing Liu
- BioBank, The First Affiliated Hospital of Xi’an Jiaotong University, Yanta District, Xi’an 710061, China; (Y.Y.); (Z.H.); (Y.K.); (J.G.); (H.C.); (H.L.)
- Centre for Biobank and Advanced Medical Research of Shaanxi Province, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an 710061, China
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Liu Y, Zhao Y, Qian C, Huang Z, Feng L, Chen L, Yao Z, Xu C, Ye J, Zhou T. Study of Combined Effect of Bacteriophage vB3530 and Chlorhexidine on the Inactivation of Pseudomonas aeruginosa. BMC Microbiol 2023; 23:256. [PMID: 37704976 PMCID: PMC10498570 DOI: 10.1186/s12866-023-02976-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Accepted: 08/09/2023] [Indexed: 09/15/2023] Open
Abstract
BACKGROUND Chlorhexidine (CHG) is a disinfectant commonly used in hospitals. However, it has been reported that the excessive use of CHG can cause resistance in bacteria to this agent and even to other clinical antibiotics. Therefore, new methods are needed to alleviate the development of CHG tolerance and reduce its dosage. This study aimed to explore the synergistic effects of CHG in combination with bacteriophage against CHG-tolerant Pseudomonas aeruginosa (P. aeruginosa) and provide ideas for optimizing disinfection strategies in clinical environments as well as for the efficient use of disinfectants. METHODS The CHG-tolerant P. aeruginosa strains were isolated from the First Affiliated Hospital of Wenzhou Medical University in China. The bacteriophage vB3530 was isolated from the sewage inlet of the hospital, and its genome was sequenced. Time-killing curve was used to determine the antibacterial effects of vB3530 and chlorohexidine gluconate (CHG). The phage sensitivity to 16 CHG-tolerant P. aeruginosa strains and PAO1 strain was detected using plaque assay. The emergence rate of resistant bacterial strains was detected to determine the development of phage-resistant and CHG-tolerant strains. Finally, the disinfection effects of the disinfectant and phage combination on the surface of the medical devices were preliminarily evaluated. RESULTS The results showed that (1) CHG combined with bacteriophage vB3530 significantly inhibited the growth of CHG-resistant P. aeruginosa and reduced the bacterial colony forming units (CFUs) after 24 h. (2) The combination of CHG and bacteriophage inhibited the emergence of phage-resistant and CHG-tolerant strains. (3) The combination of CHG and bacteriophage significantly reduced the bacterial load on the surface of medical devices. CONCLUSIONS In this study, the combination of bacteriophage vB3530 and CHG presented a combined inactivation effect to CHG-tolerant P. aeruginosa and reduced the emergence of strains resistant to CHG and phage. This study demonstrated the potential of bacteriophage as adjuvants to traditional disinfectants. The use of bacteriophage in combination with commercial disinfectants might be a promising method for controlling the spread of bacteria in hospitals.
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Affiliation(s)
- Yan Liu
- Department of Clinical Laboratory, Key Laboratory of Clinical Laboratory Diagnosis and Translational Research of Zhejiang Province, the First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325000, China
| | - Yining Zhao
- Department of Clinical Laboratory, Key Laboratory of Clinical Laboratory Diagnosis and Translational Research of Zhejiang Province, the First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325000, China
| | - Changrui Qian
- School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, 325000, Zhejiang Province, China
| | - Zeyu Huang
- Department of Clinical Laboratory, Key Laboratory of Clinical Laboratory Diagnosis and Translational Research of Zhejiang Province, the First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325000, China
| | - Luozhu Feng
- Department of Medical Lab Science, School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, Zhejiang Province, China
| | - Lijiang Chen
- Department of Clinical Laboratory, Key Laboratory of Clinical Laboratory Diagnosis and Translational Research of Zhejiang Province, the First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325000, China
| | - Zhuocheng Yao
- Department of Medical Lab Science, School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, Zhejiang Province, China
| | - Chunquan Xu
- Department of Clinical Laboratory, Key Laboratory of Clinical Laboratory Diagnosis and Translational Research of Zhejiang Province, the First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325000, China
| | - Jianzhong Ye
- Department of Clinical Laboratory, Key Laboratory of Clinical Laboratory Diagnosis and Translational Research of Zhejiang Province, the First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325000, China.
| | - Tieli Zhou
- Department of Clinical Laboratory, Key Laboratory of Clinical Laboratory Diagnosis and Translational Research of Zhejiang Province, the First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325000, China.
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