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Vu NT, Kim H, Lee S, Hwang IS, Kwon CT, Oh CS. Bacteriophage cocktail for biocontrol of soft rot disease caused by Pectobacterium species in Chinese cabbage. Appl Microbiol Biotechnol 2024; 108:11. [PMID: 38159122 DOI: 10.1007/s00253-023-12881-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2023] [Revised: 09/26/2023] [Accepted: 10/05/2023] [Indexed: 01/03/2024]
Abstract
Pectobacterium spp. are necrotrophic plant pathogens that cause the soft rot disease in Chinese cabbage, resulting in severe yield loss. The use of conventional antimicrobial agents, copper-based bactericides, and antibiotics has encountered several limitations, such as bioaccumulation on plants and microbial resistance. Bacteriophages (phages) are considered promising alternative antimicrobial agents against diverse phytopathogens. In this study, we isolated and characterized two virulent phages (phiPccP-2 and phiPccP-3) to develop a phage cocktail. Morphological and genomic analyses revealed that two phages belonged to the Tevenvirinae and Mccorquodalevirinae subfamilies, respectively. The phiPccP-2 and phiPccP-3 phages, which have a broad host range, were stable at various environmental conditions, such as various pHs and temperatures and exposure to ultraviolet light. The phage cocktail developed using these two lytic phages inhibited the emergence of phage-resistant bacteria compared to single-phage treatments in in vitro challenge assays. The phage cocktail treatment effectively prevented the development of soft rot symptom in matured Chinese cabbage leaves. Additionally, the phage cocktail comprising three phages (phiPccP-1, phiPccP-2, and phiPccP-3) showed superior biocontrol efficacy against the mixture of Pectobacterium strains in Chinese cabbage seedlings. These results suggest that developing phage cocktails is an effective approach for biocontrol of soft rot disease caused by Pectobacterium strains in crops compared to single-phage treatments. KEY POINTS: •Two newly isolated Pectobacterium phages, phiPccP-2 and phiPccP-3, infected diverse Pectobacterium species and effectively inhibited the emergence of phage-resistant bacteria. •Genomic and physiological analyses suggested that both phiPccP-2 and phiPccP-3 are lytic phages and that their lytic activities are stable in the environmental conditions under which Chinese cabbage grows. •Treatment using a phage cocktail comprising phiPccP-2 and phiPccP-3 efficiently suppressed soft rot disease in detached mature leaves and seedlings of Chinese cabbage, indicating the applicability of the phage cocktail as an alternative antimicrobial agent.
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Affiliation(s)
- Nguyen Trung Vu
- Department of Green-Bio Science, Kyung Hee University, Yongin, 17104, Republic of Korea
| | - Hyeongsoon Kim
- Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea
| | - Soohong Lee
- Department of Green-Bio Science, Kyung Hee University, Yongin, 17104, Republic of Korea
| | - In Sun Hwang
- Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea
| | - Choon-Tak Kwon
- Department of Green-Bio Science, Kyung Hee University, Yongin, 17104, Republic of Korea
| | - Chang-Sik Oh
- Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea.
- Department of Agricultural Biotechnology, College of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea.
- Plant Genomics and Breeding Institute, Seoul National University, Seoul, 08826, Republic of Korea.
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2
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Sun X, Xue F, Cong C, Murtaza B, Wang L, Li X, Li S, Xu Y. Characterization of two virulent Salmonella phages and transient application in egg, meat and lettuce safety. Food Res Int 2024; 190:114607. [PMID: 38945617 DOI: 10.1016/j.foodres.2024.114607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Revised: 05/13/2024] [Accepted: 06/04/2024] [Indexed: 07/02/2024]
Abstract
Salmonella, a prominent foodborne pathogen, has posed enduring challenges to the advancement of food safety and global public health. The escalating concern over antibiotic misuse, resulting in the excessive presence of drug residues in animal-derived food products, necessitates urgent exploration of alternative strategies for Salmonella control. Bacteriophages emerge as promising green biocontrol agents against pathogenic bacteria. This study delineates the identification of two novel virulent Salmonella phages, namely phage vB_SalS_ABTNLsp11241 (referred to as sp11241) and phage 8-19 (referred to as 8-19). Both phages exhibited efficient infectivity against Salmonella enterica serotype Enteritidis (SE). Furthermore, this study evaluated the effectiveness of two phages to control SE in three different foods (whole chicken eggs, raw chicken meat, and lettuce) at different MOIs (1, 100, and 10000) at 4°C. It's worth noting that sp11241 and 8-19 achieved complete elimination of SE on eggs after 3 h and 6 h at MOI = 100, and after 2 h and 5 h at MOI = 10000, respectively. After 12 h of treatment with sp11241, a maximum reduction of 3.17 log10 CFU/mL in SE was achieved on raw chicken meat, and a maximum reduction of 3.00 log10 CFU/mL was achieved on lettuce. Phage 8-19 has the same effect on lettuce as sp11241, but is slightly less effective than sp11241 on chicken meat (a maximum 2.69 log10 CFU/mL reduction). In conclusion, sp11241 and 8-19 exhibit considerable potential for controlling Salmonella contamination in food at a low temperature and represent viable candidates as green antibacterial agents for food applications.
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Affiliation(s)
- XiaoWen Sun
- MOE Key Laboratory of Bio-Intelligent Manufacturing, School of Bioengineering, Dalian University of Technology, Dalian 116024, China
| | - Fan Xue
- MOE Key Laboratory of Bio-Intelligent Manufacturing, School of Bioengineering, Dalian University of Technology, Dalian 116024, China
| | - Cong Cong
- College of Fisheries and Life Science, Dalian Ocean University, Dalian 116023, China
| | - Bilal Murtaza
- MOE Key Laboratory of Bio-Intelligent Manufacturing, School of Bioengineering, Dalian University of Technology, Dalian 116024, China; Dalian SEM Bio-Engineering Technology Co. Ltd., Dalian 116620, China
| | - LiLi Wang
- MOE Key Laboratory of Bio-Intelligent Manufacturing, School of Bioengineering, Dalian University of Technology, Dalian 116024, China; Center for Food Safety of Animal Origin, Ministry of Education, Dalian University of Technology, Dalian 116600, China
| | - XiaoYu Li
- MOE Key Laboratory of Bio-Intelligent Manufacturing, School of Bioengineering, Dalian University of Technology, Dalian 116024, China; Center for Food Safety of Animal Origin, Ministry of Education, Dalian University of Technology, Dalian 116600, China
| | - ShuYing Li
- Dalian SEM Bio-Engineering Technology Co. Ltd., Dalian 116620, China
| | - YongPing Xu
- MOE Key Laboratory of Bio-Intelligent Manufacturing, School of Bioengineering, Dalian University of Technology, Dalian 116024, China; Dalian SEM Bio-Engineering Technology Co. Ltd., Dalian 116620, China; Center for Food Safety of Animal Origin, Ministry of Education, Dalian University of Technology, Dalian 116600, China.
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Bayat F, Hilal A, Thirugnanasampanthar M, Tremblay D, Filipe CDM, Moineau S, Didar TF, Hosseinidoust Z. High throughput platform technology for rapid target identification in personalized phage therapy. Nat Commun 2024; 15:5626. [PMID: 38992046 PMCID: PMC11239838 DOI: 10.1038/s41467-024-49710-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Accepted: 06/13/2024] [Indexed: 07/13/2024] Open
Abstract
As bacteriophages continue to gain regulatory approval for personalized human therapy against antibiotic-resistant infections, there is a need for transformative technologies for rapid target identification through multiple, large, decentralized therapeutic phages biobanks. Here, we design a high throughput phage screening platform comprised of a portable library of individual shelf-stable, ready-to-use phages, in all-inclusive solid tablets. Each tablet encapsulates one phage along with luciferin and luciferase enzyme stabilized in a sugar matrix comprised of pullulan and trehalose capable of directly detecting phage-mediated adenosine triphosphate (ATP) release through ATP bioluminescence reaction upon bacterial cell burst. The tablet composition also enhances desiccation tolerance of all components, which should allow easier and cheaper international transportation of phages and as a result, increased accessibility to therapeutic phages. We demonstrate high throughput screening by identifying target phages for select multidrug-resistant clinical isolates of Pseudomonas aeruginosa, Salmonella enterica, Escherichia coli, and Staphylococcus aureus with targets identified within 30-120 min.
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Affiliation(s)
- Fereshteh Bayat
- School of Biomedical Engineering, McMaster University, Hamilton, Ontario, Canada
| | - Arwa Hilal
- School of Biomedical Engineering, McMaster University, Hamilton, Ontario, Canada
| | | | - Denise Tremblay
- Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, Québec City, QC, Canada
- Groupe de recherche en écologie buccale, Faculté de médecine dentaire, Université Laval, Québec City, QC, Canada
- Félix d'Hérelle Reference Center for Bacterial Viruses, Université Laval, Québec City, QC, Canada
| | - Carlos D M Filipe
- Department of Chemical Engineering, McMaster University, Hamilton, Ontario, Canada
| | - Sylvain Moineau
- Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, Québec City, QC, Canada
- Groupe de recherche en écologie buccale, Faculté de médecine dentaire, Université Laval, Québec City, QC, Canada
- Félix d'Hérelle Reference Center for Bacterial Viruses, Université Laval, Québec City, QC, Canada
| | - Tohid F Didar
- School of Biomedical Engineering, McMaster University, Hamilton, Ontario, Canada.
- Department of Mechanical Engineering, McMaster University, Hamilton, Ontario, Canada.
- Michael DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada.
| | - Zeinab Hosseinidoust
- School of Biomedical Engineering, McMaster University, Hamilton, Ontario, Canada.
- Department of Chemical Engineering, McMaster University, Hamilton, Ontario, Canada.
- Michael DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada.
- Farncombe Family Digestive Health Research Institute, McMaster University, Hamilton, Ontario, Canada.
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Chakraborty S, Rohit A, Prasanthi SJ, Chauhan A. A New Casjensviridae Bacteriophage Isolated from Hospital Sewage for Inactivation of Biofilms of Carbapenem Resistant Klebsiella pneumoniae Clinical Isolates. Pharmaceutics 2024; 16:904. [PMID: 39065601 DOI: 10.3390/pharmaceutics16070904] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2024] [Revised: 06/19/2024] [Accepted: 06/21/2024] [Indexed: 07/28/2024] Open
Abstract
Klebsiella pneumoniae, a member of the ESKAPE pathogen group, is a prominent cause of hospital-acquired infections. The WHO has recognized carbapenem-resistant K. pneumoniae as a critical-one priority pathogen. These resilient superbugs have the ability to form biofilms and present a significant global threat. In the present study, we isolated and characterized a bacteriophage SAKp02, from hospital sewage, infectious to carbapenem-resistant K. pneumoniae patient isolates. SAKp02 could infect 43 of 72 clinical isolates, indicating a broad host spectrum. Whole genome analysis classified SAKp02 within the family Casjensviridae, with a 59,343 bp genome encoding 82 ORFs. Comparative genomic analysis revealed significant differences between SAKp02 and its closest viruses, indicating a distinct genetic makeup positioning it as a novel phage strain within the lineage. The SAKp02 genome comprises bacteriolytic enzymes, including holin, endolysin, and phage depolymerase, crucial for bacterial lysis and biofilm disruption. It reduced biofilm biomass by over threefold compared to the control and eradicated 99% of viable cells within a 4 h treatment period. Scanning electron microscopy corroborated the ability of the phage to dismantle biofilm matrices and lyse bacterial cells. Safe and effective treatments are warranted, and hence, the fully characterized lytic phages with therapeutic potential against drug-resistant clinical isolates of bacteria are needed. Our study is the first to report the antibacterial and antibiofilm activity of Casjensviridae phages, and our discovery of a novel K. pneumoniae phage broadens the arsenal against the bacteria.
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Affiliation(s)
- Sambuddha Chakraborty
- Department of Microbiology, Tripura University, Suryamaninagar 799022, India
- Department of Microbiology, University of Delhi South Campus, Benito Jaurez Marg, New Delhi 110021, India
| | - Anusha Rohit
- Madras Medical Mission Hospital, Chennai 600037, India
| | | | - Ashwini Chauhan
- Department of Microbiology, Tripura University, Suryamaninagar 799022, India
- Department of Microbiology, University of Delhi South Campus, Benito Jaurez Marg, New Delhi 110021, India
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Azari R, Yousefi MH, Fallah AA, Alimohammadi A, Nikjoo N, Wagemans J, Berizi E, Hosseinzadeh S, Ghasemi M, Mousavi Khaneghah A. Controlling of foodborne pathogen biofilms on stainless steel by bacteriophages: A systematic review and meta-analysis. Biofilm 2024; 7:100170. [PMID: 38234712 PMCID: PMC10793095 DOI: 10.1016/j.bioflm.2023.100170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 11/27/2023] [Accepted: 12/10/2023] [Indexed: 01/19/2024] Open
Abstract
This study investigates the potential of using bacteriophages to control foodborne pathogen biofilms on stainless steel surfaces in the food industry. Biofilm-forming bacteria can attach to stainless steel surfaces, rendering them difficult to eradicate even after a thorough cleaning and sanitizing procedures. Bacteriophages have been proposed as a possible solution, as they can penetrate biofilms and destroy bacterial cells within, reducing the number of viable bacteria and preventing the growth and spread of biofilms. This systematic review and meta-analysis evaluates the potential of bacteriophages against different biofilm-forming foodborne bacteria, including Cronobacter sakazakii, Escherichia coli, Staphylococcus aureus, Pseudomonas fluorescens, Pseudomonas aeruginosa and Listeria monocytogenes. Bacteriophage treatment generally causes a significant average reduction of 38 % in biofilm formation of foodborne pathogens on stainless steel. Subgroup analyses revealed that phages are more efficient in long-duration treatment. Also, applying a cocktail of phages is 1.26-fold more effective than applying individual phages. Phages at concentrations exceeding 107 PFU/ml are significantly more efficacious in eradicating bacteria within a biofilm. The antibacterial phage activity decreases substantially by 3.54-fold when applied at 4 °C compared to temperatures above 25 °C. This analysis suggests that bacteriophages can be a promising solution for controlling biofilms in the food industry.
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Affiliation(s)
- Rahim Azari
- Department of Food Hygiene and Quality Control, School of Nutrition and Food Sciences, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mohammad Hashem Yousefi
- Department of Food Hygiene and Public Health, School of Veterinary Medicine, Shiraz University, Shiraz, 71946-84471, Iran
| | - Aziz A. Fallah
- Department of Food Hygiene and Quality Control, School of Veterinary Medicine, Shahrekord University, Shahrekord, 34141, Iran
| | - Arezoo Alimohammadi
- Department of Food Hygiene and Quality Control, School of Nutrition and Food Sciences, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Nastaran Nikjoo
- Department of Food Hygiene and Quality Control, School of Nutrition and Food Sciences, Shiraz University of Medical Sciences, Shiraz, Iran
| | | | - Enayat Berizi
- 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, 71946-84471, Iran
| | - Mohammad Ghasemi
- Department of Pharmacology, School of Veterinary Medicine, Shahrekord University, P. O. Box 115, Shahrekord, Iran
| | - Amin Mousavi Khaneghah
- Food Health Research Center, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
- Department of Fruit and Vegetable Product Technology, Prof. Wacław Dąbrowski Institute of Agricultural and Food Biotechnology—State Research Institute, 36 Rakowiecka St., 02-532, Warsaw, Poland
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6
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Duan S, Zhang Z, Wang X, Sun Y, Dong Y, Ren L, Geng L, Xiu Z. Co-production of 1,3-propanediol and phage phiKpS2 from the glycerol fermentation by Klebsiella pneumoniae. BIORESOUR BIOPROCESS 2024; 11:44. [PMID: 38722416 PMCID: PMC11082122 DOI: 10.1186/s40643-024-00760-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Accepted: 04/18/2024] [Indexed: 05/12/2024] Open
Abstract
As an alternative to antibiotics in response to antimicrobial-resistant infections, bacteriophages (phages) are garnering renewed interest in recent years. However, the massive preparation of phage is restricted using traditional pathogens as host cells, which incurs additional costs and contamination. In this study, an opportunistic pathogen, Klebsiella pneumoniae used to convert glycerol to 1,3-propanediol (1,3-PDO), was reused to prepare phage after fermentation. The phage infection showed that the fed-batch fermentation broth containing 71.6 g/L 1,3-PDO can be directly used for preparation of phage with a titer of 1 × 108 pfu/mL. Then, the two-step salting-out extraction was adopted to remove most impurities, e.g. acetic acid (93.5%), ethanol (91.5%) and cells (99.4%) at the first step, and obtain 1,3-PDO (56.6%) in the top phase as well as phage (97.4%) in the middle phase at the second step. This integrated process provides a cheap and environment-friendly manner for coproduction of 1,3-PDO and phage.
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Affiliation(s)
- Suyang Duan
- School of Bioengineering, Dalian University of Technology, Linggong Road 2, Dalian, 116024, P. R. China
| | - Zhirong Zhang
- School of Bioengineering, Dalian University of Technology, Linggong Road 2, Dalian, 116024, P. R. China
| | - Xiaoli Wang
- School of Bioengineering, Dalian University of Technology, Linggong Road 2, Dalian, 116024, P. R. China
| | - Yaqin Sun
- School of Bioengineering, Dalian University of Technology, Linggong Road 2, Dalian, 116024, P. R. China
| | - Yuesheng Dong
- School of Bioengineering, Dalian University of Technology, Linggong Road 2, Dalian, 116024, P. R. China
| | - Lina Ren
- Department of Respiratory, Affiliated Dalian Municipal Central Hospital of Dalian University of Technology, Dalian, 116033, Liaoning, P. R. China
| | - Lili Geng
- Department of Respiratory, Affiliated Dalian Municipal Central Hospital of Dalian University of Technology, Dalian, 116033, Liaoning, P. R. China
| | - Zhilong Xiu
- School of Bioengineering, Dalian University of Technology, Linggong Road 2, Dalian, 116024, P. R. China.
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7
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Tadeu AD, Duarte J, Trindade D, Costa P, Venâncio C, Lopes I, Oliveira V, Gomes NCM, Almeida A, Pereira C. Bacteriophages to control Vibrio alginolyticus in live feeds prior to their administration in larviculture. J Appl Microbiol 2024; 135:lxae115. [PMID: 38710582 DOI: 10.1093/jambio/lxae115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Revised: 04/16/2024] [Accepted: 05/04/2024] [Indexed: 05/08/2024]
Abstract
AIMS This study aimed to evaluate the efficiency of two phages [VB_VaC_TDDLMA (phage TDD) and VB_VaC_SRILMA (phage SRI)] alone and in a cocktail to control Vibrio alginolyticus in brine shrimp before their administration in larviculture. METHODS AND RESULTS Phages were isolated from seawater samples and characterized by host spectrum, growth parameters, adsorption rate, genomic analysis, and inactivation efficiency. Both phages belong to the Caudoviricetes class and lack known virulence or antibiotic-resistance genes. They exhibit specificity, infecting only their host, V. alginolyticus CECT 521. Preliminary experiments in a culture medium showed that phage TDD (reduction of 5.8 log CFU ml-1 after 10 h) outperformed phage SRI (reduction of 4.6 log CFU ml-1 after 6 h) and the cocktail TDD/SRI (reduction of 5.2 log CFU ml-1 after 8 h). In artificial marine water experiments with Artemia franciscana, both single phage suspensions and the phage cocktail, effectively inactivated V. alginolyticus in culture water (reduction of 4.3, 2.1, and 1.9 log CFU ml-1 for phages TDD, SRI, and the phage cocktail, respectively, after 12 h) and in A. franciscana (reduction of 51.6%, 87.3%, and 85.3% for phages TDD, SRI, and the phage cocktail, respectively, after 24 h). The two phages and the phage cocktail did not affect A. franciscana natural microbiota or other Vibrio species in the brine shrimp. CONCLUSIONS The results suggest that phages can safely and effectively control V. alginolyticus in A. franciscana prior to its administration in larviculture.
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Affiliation(s)
- Amanda Dias Tadeu
- Department of Biology and CESAM, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
| | - João Duarte
- Department of Biology and CESAM, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
| | - David Trindade
- Department of Biology and CESAM, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
| | - Pedro Costa
- Department of Biology and CESAM, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
| | - Cátia Venâncio
- Department of Biology and CESAM, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
| | - Isabel Lopes
- Department of Biology and CESAM, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
| | - Vanessa Oliveira
- Department of Biology and CESAM, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
| | - Newton C M Gomes
- Department of Biology and CESAM, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
| | - Adelaide Almeida
- Department of Biology and CESAM, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
| | - Carla Pereira
- Department of Biology and CESAM, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
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Bailey ZM, Igler C, Wendling CC. Prophage maintenance is determined by environment-dependent selective sweeps rather than mutational availability. Curr Biol 2024; 34:1739-1749.e7. [PMID: 38599209 DOI: 10.1016/j.cub.2024.03.025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 01/19/2024] [Accepted: 03/14/2024] [Indexed: 04/12/2024]
Abstract
Prophages, viral sequences integrated into bacterial genomes, can be beneficial and costly. Despite the risk of prophage activation and subsequent bacterial death, active prophages are present in most bacterial genomes. However, our understanding of the selective forces that maintain prophages in bacterial populations is limited. Combining experimental evolution with stochastic modeling, we show that prophage maintenance and loss are primarily determined by environmental conditions that alter the net fitness effect of a prophage on its bacterial host. When prophages are too costly, they are rapidly lost through environment-specific sequences of selective sweeps. Conflicting selection pressures that select against the prophage but for a prophage-encoded accessory gene can maintain prophages. The dynamics of prophage maintenance additionally depend on the sociality of this accessory gene. Prophage-encoded genes that exclusively benefit the lysogen maintain prophages at higher frequencies compared with genes that benefit the entire population. That is because the latter can protect phage-free "cheaters," reducing the benefit of maintaining the prophage. Our simulations suggest that environmental variation plays a larger role than mutation rates in determining prophage maintenance. These findings highlight the complexity of selection pressures that act on mobile genetic elements and challenge our understanding of the role of environmental factors relative to random chance events in shaping the evolutionary trajectory of bacterial populations. By shedding light on the key factors that shape microbial populations in the face of environmental changes, our study significantly advances our understanding of the complex dynamics of microbial evolution and diversification.
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Affiliation(s)
- Zachary M Bailey
- Institute of Integrative Biology, ETH Zürich, 8092 Zürich, Switzerland.
| | - Claudia Igler
- Institute of Integrative Biology, ETH Zürich, 8092 Zürich, Switzerland; Division of Evolution, Infection and Genomics, School of Biological Sciences, University of Manchester, Manchester M13 9PL, UK
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9
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Liu Y, Lin Y, Zhu W. Systemic Effects of a Phage Cocktail on Healthy Weaned Piglets. BIOLOGY 2024; 13:271. [PMID: 38666883 PMCID: PMC11048100 DOI: 10.3390/biology13040271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2024] [Revised: 04/12/2024] [Accepted: 04/14/2024] [Indexed: 04/28/2024]
Abstract
Numerous studies have demonstrated that bacteriophages (phages) can effectively treat intestinal bacterial infections. However, research on the impact of phages on overall body health once they enter the intestine is limited. This study utilized weaned piglets as subjects to evaluate the systemic effects of an orally administered phage cocktail on their health. Twelve 21-day-old weaned piglets were divided into control (CON) and phage gavage (Phages) groups. The phage cocktail consisted of five lytic phages, targeting Salmonella enterica serovar Choleraesuis (S. choleraesuis), Enteropathogenic Escherichia coli (EPEC), and Shiga tox-in-producing Escherichia coli (STEC). The phages group received 10 mL of phage cocktail orally for 20 consecutive days. The results show that the phage gavage did not affect the piglets' growth performance, serum biochemical indices, or most organ indices, except for the pancreas. However, the impact on the intestine was complex. Firstly, although the pancreatic index decreased, it did not affect the secretion of digestive enzymes in the intestine. Secondly, phages increased the pH of jejunum chyme and relative weight of the ileum, and enhanced intestinal barrier function without affecting the morphology of the intestine. Thirdly, phages did not proliferate in the intestine, but altered the intestinal microbiota structure and increased concentrations of microbial metabolites isobutyric acid and isovaleric acid in the colonic chyme. In addition, phages impacted the immune status, significantly increasing serum IgA, IgG, and IgM, as well as serum and intestinal mucosal IFN-γ, IL-1β, IL-17, and TGF-β, and decreasing IL-4 and IL-10. They also activated toll-like receptors TLR-4 and TLR-9. Apart from an increase in basophil numbers, the counts of other immune cells in the blood did not change. This study indicates that the impact of phages on body health is complex, especially regarding immune status, warranting further attention. Short-term phage gavage did not have significant negative effects on health but could enhance intestinal barrier function.
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Affiliation(s)
- Yankun Liu
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; (Y.L.); (W.Z.)
- National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing 210095, China
| | - Yan Lin
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; (Y.L.); (W.Z.)
- National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing 210095, China
- National Experimental Teaching Demonstration Center of Animal Science, Nanjing Agricultural University, Nanjing 210095, China
| | - Weiyun Zhu
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; (Y.L.); (W.Z.)
- National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing 210095, China
- National Experimental Teaching Demonstration Center of Animal Science, Nanjing Agricultural University, Nanjing 210095, China
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10
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Young J, Lee SW, Shariyate MJ, Cronin A, Wixted JJ, Nazarian A, Rowley CF, Rodriguez EK. Bacteriophage therapy and current delivery strategies for orthopedic infections: A SCOPING review. J Infect 2024; 88:106125. [PMID: 38373574 DOI: 10.1016/j.jinf.2024.106125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 02/09/2024] [Accepted: 02/14/2024] [Indexed: 02/21/2024]
Abstract
OBJECTIVES Interest in phages as adjunctive therapy to treat difficult infections has grown in the last decade. However, phage dosing and delivery for orthopedic infections have not been systematically summarized. METHODS Following PRISMA-ScR guidelines, we conducted a SCOPING review through September 1st, 2023, of MEDLINE, Embase, Web of Science Core Collection, and Cochrane Central. RESULTS In total, 77 studies were included, of which 19 (24.7%) were in vitro studies, 17 (22.1%) were animal studies, and 41 (53.2%) were studies in humans. A total of 137 contemporary patients receiving phage therapy are described. CONCLUSIONS Direct phage delivery remains the most studied form of phage therapy, notably in prosthetic joint infections, osteomyelitis, and diabetic foot ulcers. Available evidence describing phage therapy in humans suggests favorable outcomes for orthopedic infections, though this evidence is composed largely of low-level descriptive studies. Several phage delivery devices have been described, though a lack of comparative and in-human evidence limits their therapeutic application. Limitations to the use of phage therapy for orthopedic infections that need to be overcome include a lack of understanding related to optimal dosing and phage pharmacokinetics, bacterial heterogeneity in an infection episode, and phage therapy toxicity.
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Affiliation(s)
- Jason Young
- Harvard Combined Orthopedic Residency Program, Boston, MA, USA; Harvard Medical School, Boston, MA, USA.
| | | | - Mohammad J Shariyate
- Musculoskeletal Translational Innovation Initiative, Carl J. Shapiro Department of Orthopedic Surgery, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | | | - John J Wixted
- Harvard Medical School, Boston, MA, USA; Carl J. Shapiro Department of Orthopedic Surgery, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Ara Nazarian
- Musculoskeletal Translational Innovation Initiative, Carl J. Shapiro Department of Orthopedic Surgery, Beth Israel Deaconess Medical Center, Boston, MA, USA; Carl J. Shapiro Department of Orthopedic Surgery, Beth Israel Deaconess Medical Center, Boston, MA, USA; Department of Orthopedic Surgery, Yerevan State Medical University, Yerevan, Armenia
| | - Christopher F Rowley
- Division of Infectious Diseases, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA; Harvard School of Public Health, Boston, MA, USA
| | - Edward K Rodriguez
- Harvard Medical School, Boston, MA, USA; Carl J. Shapiro Department of Orthopedic Surgery, Beth Israel Deaconess Medical Center, Boston, MA, USA
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11
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Tuck OT, Adler BA, Armbruster EG, Lahiri A, Hu JJ, Zhou J, Pogliano J, Doudna JA. Hachiman is a genome integrity sensor. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.29.582594. [PMID: 38464307 PMCID: PMC10925250 DOI: 10.1101/2024.02.29.582594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Hachiman is a broad-spectrum antiphage defense system of unknown function. We show here that Hachiman comprises a heterodimeric nuclease-helicase complex, HamAB. HamA, previously a protein of unknown function, is the effector nuclease. HamB is the sensor helicase. HamB constrains HamA activity during surveillance of intact dsDNA. When the HamAB complex detects DNA damage, HamB helicase activity liberates HamA, unleashing nuclease activity. Hachiman activation degrades all DNA in the cell, creating 'phantom' cells devoid of both phage and host DNA. We demonstrate Hachiman activation in the absence of phage by treatment with DNA-damaging agents, suggesting that Hachiman responds to aberrant DNA states. Phylogenetic similarities between the Hachiman helicase and eukaryotic enzymes suggest this bacterial immune system has been repurposed for diverse functions across all domains of life.
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Affiliation(s)
- Owen T. Tuck
- Department of Chemistry, University of California, Berkeley, Berkeley, CA USA
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA USA
| | - Benjamin A. Adler
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA USA
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, Berkeley, CA USA
| | - Emily G. Armbruster
- School of Biological Sciences, University of California San Diego, La Jolla, CA USA
| | - Arushi Lahiri
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California USA
| | - Jason J. Hu
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California USA
| | - Julia Zhou
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California USA
| | - Joe Pogliano
- School of Biological Sciences, University of California San Diego, La Jolla, CA USA
| | - Jennifer A. Doudna
- Department of Chemistry, University of California, Berkeley, Berkeley, CA USA
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA USA
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, Berkeley, CA USA
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California USA
- Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA USA
- MBIB Division, Lawrence Berkeley National Laboratory, Berkeley, CA USA
- Gladstone Institutes, University of California, San Francisco, San Francisco, CA USA
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA USA
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12
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Costa AR, van den Berg DF, Esser JQ, Muralidharan A, van den Bossche H, Bonilla BE, van der Steen BA, Haagsma AC, Fluit AC, Nobrega FL, Haas PJ, Brouns SJJ. Accumulation of defense systems in phage-resistant strains of Pseudomonas aeruginosa. SCIENCE ADVANCES 2024; 10:eadj0341. [PMID: 38394193 PMCID: PMC10889362 DOI: 10.1126/sciadv.adj0341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 01/22/2024] [Indexed: 02/25/2024]
Abstract
Prokaryotes encode multiple distinct anti-phage defense systems in their genomes. However, the impact of carrying a multitude of defense systems on phage resistance remains unclear, especially in a clinical context. Using a collection of antibiotic-resistant clinical strains of Pseudomonas aeruginosa and a broad panel of phages, we demonstrate that defense systems contribute substantially to defining phage host range and that overall phage resistance scales with the number of defense systems in the bacterial genome. We show that many individual defense systems target specific phage genera and that defense systems with complementary phage specificities co-occur in P. aeruginosa genomes likely to provide benefits in phage-diverse environments. Overall, we show that phage-resistant phenotypes of P. aeruginosa with at least 19 phage defense systems exist in the populations of clinical, antibiotic-resistant P. aeruginosa strains.
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Affiliation(s)
- Ana Rita Costa
- Department of Bionanoscience, Delft University of Technology, 2629 HZ Delft, Netherlands
- Kavli Institute of Nanoscience, Delft University of Technology, 2629 HZ Delft, Netherlands
| | - Daan F. van den Berg
- Department of Bionanoscience, Delft University of Technology, 2629 HZ Delft, Netherlands
- Kavli Institute of Nanoscience, Delft University of Technology, 2629 HZ Delft, Netherlands
| | - Jelger Q. Esser
- Department of Bionanoscience, Delft University of Technology, 2629 HZ Delft, Netherlands
- Kavli Institute of Nanoscience, Delft University of Technology, 2629 HZ Delft, Netherlands
| | - Aswin Muralidharan
- Department of Bionanoscience, Delft University of Technology, 2629 HZ Delft, Netherlands
- Kavli Institute of Nanoscience, Delft University of Technology, 2629 HZ Delft, Netherlands
| | - Halewijn van den Bossche
- Department of Bionanoscience, Delft University of Technology, 2629 HZ Delft, Netherlands
- Kavli Institute of Nanoscience, Delft University of Technology, 2629 HZ Delft, Netherlands
| | - Boris Estrada Bonilla
- Department of Bionanoscience, Delft University of Technology, 2629 HZ Delft, Netherlands
- Kavli Institute of Nanoscience, Delft University of Technology, 2629 HZ Delft, Netherlands
| | - Baltus A. van der Steen
- Department of Bionanoscience, Delft University of Technology, 2629 HZ Delft, Netherlands
- Kavli Institute of Nanoscience, Delft University of Technology, 2629 HZ Delft, Netherlands
| | - Anna C. Haagsma
- Department of Bionanoscience, Delft University of Technology, 2629 HZ Delft, Netherlands
- Kavli Institute of Nanoscience, Delft University of Technology, 2629 HZ Delft, Netherlands
| | - Ad C. Fluit
- Medical Microbiology, University Medical Center Utrecht, Utrecht University, 3584 CX Utrecht, Netherlands
| | - Franklin L. Nobrega
- School of Biological Sciences, University of Southampton, SO17 1BJ Southampton, UK
| | - Pieter-Jan Haas
- Medical Microbiology, University Medical Center Utrecht, Utrecht University, 3584 CX Utrecht, Netherlands
| | - Stan J. J. Brouns
- Department of Bionanoscience, Delft University of Technology, 2629 HZ Delft, Netherlands
- Kavli Institute of Nanoscience, Delft University of Technology, 2629 HZ Delft, Netherlands
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13
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Dufour N, Delattre R, Debarbieux L. High-Throughput Bacteriophage Testing with Potency Determination: Validation of an Automated Pipetting and Phage Drop-Off Method. Biomedicines 2024; 12:466. [PMID: 38398068 PMCID: PMC10886619 DOI: 10.3390/biomedicines12020466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Revised: 02/15/2024] [Accepted: 02/16/2024] [Indexed: 02/25/2024] Open
Abstract
The development of bacteriophages (phages) as active pharmaceutical ingredients for the treatment of patients is on its way and regulatory agencies are calling for reliable methods to assess phage potency. As the number of phage banks is increasing, so is the number of phages that need to be tested to identify therapeutic candidates. Currently, assessment of phage potency on a semi-solid medium to observe plaque-forming units is unavoidable and proves to be labor intensive when considering dozens of phage candidates. Here, we present a method based on automated pipetting and phage drop-off performed by a liquid-handling robot, allowing high-throughput testing and phage potency determination (based on phage titer and efficiency of plaquing). Ten phages were tested, individually and assembled into one cocktail, against 126 Escherichia coli strains. This automated method was compared to the reference one (manual assay) and validated in terms of reproducibility and concordance (ratio of results according to the Bland and Altman method: 0.99; Lin's concordance correlation coefficient: 0.86). We found that coefficients of variation were lower with automated pipetting (mean CV: 13.3% vs. 24.5%). Beyond speeding up the process of phage screening, this method could be used to standardize phage potency evaluation.
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Affiliation(s)
- Nicolas Dufour
- Réanimation Médico-Chirurgicale, Hôpital NOVO—Site de Pontoise, 95300 Pontoise, France
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Bacteriophage Bacterium Host, 75015 Paris, France (L.D.)
- IAME, Université de Paris, INSERM U1137, Université Sorbonne Paris Nord, 75018 Paris, France
| | - Raphaëlle Delattre
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Bacteriophage Bacterium Host, 75015 Paris, France (L.D.)
- IAME, Université de Paris, INSERM U1137, Université Sorbonne Paris Nord, 75018 Paris, France
- Réanimation, Centre Hospitalier de Digne-les-Bains, 04000 Digne-les-Bains, France
| | - Laurent Debarbieux
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Bacteriophage Bacterium Host, 75015 Paris, France (L.D.)
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14
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Ismael NM, Azzam M, Abdelmoteleb M, El-Shibiny A. Phage vB_Ec_ZCEC14 to treat antibiotic-resistant Escherichia coli isolated from urinary tract infections. Virol J 2024; 21:44. [PMID: 38365702 PMCID: PMC10873995 DOI: 10.1186/s12985-024-02306-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2023] [Accepted: 01/29/2024] [Indexed: 02/18/2024] Open
Abstract
Escherichia coli is a commensal bacterial species in the human gastrointestinal tract; however, it could be pathogenic and cause severe infections in intra and extra-intestinal sites. Uropathogenic E. coli accounts for 80-90% of urinary tract infections that can result in urosepsis and septic shock. Consequently, multidrug-resistant uropathogenic E. coli poses a considerable risk to the healthcare system worldwide. Phage therapy is demonstrated as an optimistic solution to over-the-counter antibiotics that contribute to the global issue of multidrug-resistant bacteria. This study aims to isolate a novel phage that could be implemented to cure urinary tract infections mediated by multidrug-resistant E. coli. Twenty-seven E. coli isolates were collected from patients with urinary tract infections to assess the antibacterial efficacy of phage vB_Ec_ZCEC14. Phage kinetics were encountered against the E. coli strain (EC/4), in addition to evaluating phage stability under various temperatures, pH values, and UV exposure periods. Full genome sequencing and morphological analysis were conducted for further phage characterization, which revealed that phage vB_Ec_ZCEC14 belongs to the family Straboviridae. Phage vB_Ec_ZCEC14 showed thermal tolerance at 80 ℃, pH stability between pH 3 and pH 12, and endurance to UV exposure for 45 min. The phage-host interaction results revealed that phage vB_Ec_ZCEC14 has strong and steady antibacterial action at lower concentrations (MOI 0.1). The study findings strongly indicate that phage vB_Ec_ZCEC14 holds significant promise as a potential therapeutic alternative for treatment of antibiotic-resistant uropathogenic E. coli.
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Affiliation(s)
- Nedaa M Ismael
- Center for Microbiology and Phage Therapy, Zewail City of Science and Technology, 12578, Giza, Egypt
| | - Mohamed Azzam
- Center for Microbiology and Phage Therapy, Zewail City of Science and Technology, 12578, Giza, Egypt
| | - Mohamed Abdelmoteleb
- Department of Botany, Faculty of Science, Mansoura University, 35516, Mansoura, Egypt
| | - Ayman El-Shibiny
- Center for Microbiology and Phage Therapy, Zewail City of Science and Technology, 12578, Giza, Egypt.
- Faculty of Environmental Agricultural Sciences, Arish University, 45511, Arish, Egypt.
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15
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Liao YT, Ho KJ, Zhang Y, Salvador A, Wu VCH. A new Rogue-like Escherichia phage UDF157lw to control Escherichia coli O157:H7. Front Microbiol 2024; 14:1302032. [PMID: 38318127 PMCID: PMC10838988 DOI: 10.3389/fmicb.2023.1302032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 12/28/2023] [Indexed: 02/07/2024] Open
Abstract
Introduction Shiga toxin-producing Escherichia coli (STEC) O157:H7 is one of the notorious foodborne pathogens causing high mortality through the consumption of contaminated food items. The food safety risk from STEC pathogens could escalate when a group of bacterial cells aggregates to form a biofilm. Bacterial biofilm can diminish the effects of various antimicrobial interventions and enhance the pathogenicity of the pathogens. Therefore, there is an urgent need to have effective control measurements. Bacteriophages can kill the target bacterial cells through lytic infection, and some enzymes produced during the infection have the capability to penetrate the biofilm for mitigation compared to traditional interventions. This study aimed to characterize a new Escherichia phage vB_EcoS-UDF157lw (or UDF157lw) and determine its antimicrobial efficacy against E. coli O157:H7. Methods Phage characterization included biological approaches, including phage morphology, one-step growth curve, stability tests (pH and temperature), and genomic approaches (whole-genome sequencing). Later, antimicrobial activity tests, including productive infection against susceptible bacterial strains, in vitro antimicrobial activity, and anti-biofilm, were conducted. Results UDF157lw is a new member of the phages belonging to the Rogunavirus genus, comprising a long and non-contractile tail, isolated from bovine feces and shares close genomic evolutionary similarities with Escherichia phages vB_EcoS-BECP10 and bV_EcoS_AKS96. When used against E. coli O157:H7 (ATCC35150), phage UDF157lw exhibited a latent period of 14 min and a burst size of 110 PFU per infected cell. The phage remained viable in a wide range of pH values (pH 4-11) and temperatures (4-60°C). No virulence genes, such as stx, lysogenic genes, and antibiotic resistance genes, were found. Phage UDF157lw demonstrated high infection efficiencies against different E. coli O157:H7 and generic E. coli strains. In addition, UDF157lw encoded a unique major tail protein (ORF_26) with prominent depolymerase enzyme activity against various E. coli O157:H7 strains, causing large plaque sizes. In contrast to the phage without encoding depolymerase gene, UDF157lw was able to reduce the 24-h and 48-h E. coli O157:H7 biofilm after 1-h phage treatment. Discussion The findings of this study provide insights into a new member of the Rogunavirus phages and demonstrate its antimicrobial potential against E. coli O157:H7 in vitro.
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Affiliation(s)
| | | | | | | | - Vivian C. H. Wu
- Produce Safety and Microbiology Research Unit, U.S. Department of Agriculture, Agricultural Research Service, Western Regional Research Center, Albany, CA, United States
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16
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Brenner T, Schultze DM, Mahoney D, Wang S. Reduction of Nontyphoidal Salmonella enterica in Broth and on Raw Chicken Breast by a Broad-spectrum Bacteriophage Cocktail. J Food Prot 2024; 87:100207. [PMID: 38142823 DOI: 10.1016/j.jfp.2023.100207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 12/15/2023] [Accepted: 12/18/2023] [Indexed: 12/26/2023]
Abstract
Globally, nontyphoidal Salmonella (NTS) causes approximately 150 million foodborne illnesses annually; many of which are linked to poultry products. Thus, improving food safety interventions in the poultry sector can reduce foodborne illness associated with prevalent NTS serotypes. Bacteriophages (phages) have shown promise as food-safe alternatives to current antimicrobial practices. However, challenges such as limited host range, bactericidal effectiveness in practical production settings, and the risk of developing host resistance remain as barriers for the widespread use of phages in commercial poultry operations. A broad-spectrum three-phage cocktail was evaluated against S. enterica subsp. enterica serotypes Enteritidis, Typhimurium, and Kentucky. The impact of multiplicity of infection (MOI) on NTS growth was assessed in broth at 22°C for 18 hours (h). Then, phage cocktail efficacy was evaluated on raw chicken breast samples inoculated with the NTS cocktail and stored at 10°C or 22°C for 0, 1, and 5 days or 0, 4, 8, and 16 h, respectively. Most probable number (MPN) calculations were performed for NTS counts on chicken after phage treatment and storage at 10°C to account for samples with NTS counts below the detection limit. In general, a higher MOI corresponded to reduced NTS growth; however, residual nutrition in growth media and initial NTS contamination level affected samples treated with the phage cocktail at identical MOIs. On chicken, phage cocktail treatment significantly reduced NTS counts at 10°C and 22°C. After storage at 10°C for 5 days, NTS counts were reduced by >3.2 log compared to the control. After storage at 22°C for 16 h, NTS counts were reduced by >1.7 log compared to the control. Overall, the phage cocktail was effective at reducing a diverse set of prominent NTS strains in broth and on raw chicken breast, highlighting its potential for commercialization and use alongside other hurdles in poultry production.
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Affiliation(s)
- Thomas Brenner
- Food, Nutrition and Health, Faculty of Land and Food Systems, The University of British Columbia, Vancouver, BC, Canada
| | - Danielle Morgan Schultze
- Food, Nutrition and Health, Faculty of Land and Food Systems, The University of British Columbia, Vancouver, BC, Canada
| | - David Mahoney
- Food, Nutrition and Health, Faculty of Land and Food Systems, The University of British Columbia, Vancouver, BC, Canada
| | - Siyun Wang
- Food, Nutrition and Health, Faculty of Land and Food Systems, The University of British Columbia, Vancouver, BC, Canada.
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17
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Merabishvili M, Pirnay JP, De Vos D. Guidelines to Compose an Ideal Bacteriophage Cocktail. Methods Mol Biol 2024; 2734:49-66. [PMID: 38066362 DOI: 10.1007/978-1-0716-3523-0_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2023]
Abstract
Properly designed bacteriophage therapeutics are the cornerstone for a successful outcome of bacteriophage therapy. Here we present an overview of the different strategies and steps that can be taken to develop a bacteriophage cocktail that complies with relevant quality and safety requirements. It is based on empirical bacteriophage therapy knowledge from over a century of experience, more recently performed studies, and emerging technologies. We emphasize the selection of adequate bacteriophages and describe a modified Appelmans' method to improve the overall performance of therapeutic bacteriophages individually and collectively in the cocktail. We present two versions of the method, which differ from each other by the employed techniques to evaluate phage activity and synergy: photometric assessment of bacterial growth versus measurement of bacterial respiration via the Omnilog® system.
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Affiliation(s)
- Maia Merabishvili
- Laboratory for Molecular and Cellular Technology, Queen Astrid Military Hospital, Brussels, Belgium.
| | - Jean-Paul Pirnay
- Laboratory for Molecular and Cellular Technology, Queen Astrid Military Hospital, Brussels, Belgium
| | - Daniel De Vos
- Laboratory for Molecular and Cellular Technology, Queen Astrid Military Hospital, Brussels, Belgium
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18
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Hill CM, Hatoum-Aslan A. Genetic Engineering of Therapeutic Phages Using Type III CRISPR-Cas Systems. Methods Mol Biol 2024; 2734:279-299. [PMID: 38066376 DOI: 10.1007/978-1-0716-3523-0_18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2023]
Abstract
The functional characterization of "hypothetical" phage genes is a major bottleneck in basic and applied phage research. To compound this issue, the most suitable phages for therapeutic applications-the strictly lytic variety-are largely recalcitrant to classical genetic techniques due to low recombination rates and lack of selectable markers. Here we describe methods for fast and effective phage engineering that rely upon a Type III-A CRISPR-Cas system. In these methods, the CRISPR-Cas system is used as a powerful counterselection tool to isolate rare phage recombinants.
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Affiliation(s)
- Courtney M Hill
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Asma Hatoum-Aslan
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
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19
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Imklin N, Patikae P, Poomirut P, Arunvipas P, Nasanit R, Sajapitak S. Isolation of bacteriophages specific to bovine mastitis-causing bacteria and characterization of their lytic activity in pasteurized milk. Vet World 2024; 17:207-215. [PMID: 38406365 PMCID: PMC10884585 DOI: 10.14202/vetworld.2024.207-215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 12/28/2023] [Indexed: 02/27/2024] Open
Abstract
Background and Aim Bovine mastitis is one of the most serious issues in dairy production. It is caused by contagious and coliform pathogens such as Staphylococcus spp., Escherichia coli, and Klebsiella pneumoniae. In addition, the emergence of drug-resistant bacteria raises urgent concerns in the field of drug treatment, thus requiring the exploration of alternative treatments. Bacteriophage therapy has been shown to be a promising alternative approach for the control of antibiotic-resistant pathogens. In this study, we aimed to isolate phages specific to contagious mastitis and coliform mastitis, characterize the isolated phages, and examine their ability to lyse bacteria in pasteurized milk samples. Materials and Methods The Staphylococcus phage vB_Sau-RP15 isolated from raw milk in our previous study was used in this study. Other three phages, vB_Eco-RN12i1, vB_Kpn-RN14i1, and vB_Ssc-RN20i3, were isolated from wastewater using E. coli 5823, K. pneumoniae 194, and Staphylococcus sciuri MM01 as hosts, respectively. The host range and efficiency of plating (EOP) were determined following phage isolation. Moreover, the lysis activities of these phages against their hosts were investigated in pasteurized milk using a multiplicity of infections (MOIs) of 10 and 100 at 37°C. Phages were applied using individual and combination phages. Results According to the EOP results, all phages showed high specificity to their respective hosts. They are tailed phages with distinct morphologies. Individual phage treatments in spiked pasteurized milk with their respective bacterial hosts significantly reduced the bacterial counts in both MOI conditions during the first 2 h of the treatment (approximately 1-8 log reduction compared to the control). Although these phages specifically infected only their hosts, the phage cocktail resulted in a better result compared to the use of individual phage. However, bacterial regrowth was observed in all experiments, which may be related to the development of phage-insensitive mutants. Conclusion Our findings suggest that the application of phages could be used to treat bovine mastitis. Phage cocktail is suitable to promote the efficacy of phage treatment in pasteurized milk. However, when considering the use of phages in dairy cows, certain phage properties in raw milk and in vivo and ex vivo should be highlighted to ensure their effectiveness as biocontrol agents for bovine mastitis treatment.
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Affiliation(s)
- Napakhwan Imklin
- Department of Biotechnology, Faculty of Engineering and Industrial Technology, Silpakorn University, Nakhon Pathom, Thailand
| | - Patinya Patikae
- Veterinary Clinical Study Program, Faculty of Veterinary Medicine, Kasetsart University, Nakhon Pathom, Thailand
- Faculty of Veterinary Sciences, Mahasarakham University, Maha Sarakham, Thailand
| | - Peekarn Poomirut
- Veterinary Clinical Study Program, Faculty of Veterinary Medicine, Kasetsart University, Nakhon Pathom, Thailand
| | - Pipat Arunvipas
- Department of Large Animal and Wildlife Clinical Sciences, Faculty of Veterinary Medicine, Kasetsart University, Nakhon Pathom, Thailand
| | - Rujikan Nasanit
- Department of Biotechnology, Faculty of Engineering and Industrial Technology, Silpakorn University, Nakhon Pathom, Thailand
| | - Somchai Sajapitak
- Department of Large Animal and Wildlife Clinical Sciences, Faculty of Veterinary Medicine, Kasetsart University, Nakhon Pathom, Thailand
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20
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Gil J, Paulson J, Zahn H, Brown M, Nguyen MM, Erickson S. Development of a Replication-Deficient Bacteriophage Reporter Lacking an Essential Baseplate Wedge Subunit. Viruses 2023; 16:8. [PMID: 38275943 PMCID: PMC10821221 DOI: 10.3390/v16010008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 12/15/2023] [Accepted: 12/18/2023] [Indexed: 01/27/2024] Open
Abstract
Engineered bacteriophages (phages) can be effective diagnostic reporters for detecting a variety of bacterial pathogens. Although a promising biotechnology, the large-scale use of these reporters may result in the unintentional release of genetically modified viruses. In order to limit the potential environmental impact, the ability of these phages to propagate outside the laboratory was targeted. The phage SEA1 has been previously engineered to facilitate food safety as an accurate and sensitive reporter for Salmonella contamination. In this study, homologous recombination was used to replace the expression of an essential baseplate wedge subunit (gp141) in SEA1 with a luciferase, NanoLuc®. This reporter, referred to as SEA1Δgp141.NL, demonstrated a loss of plaque formation and a failure to increase in titer following infection of Salmonella. SEA1Δgp141.NL was thus incapable of producing infectious progeny in the absence of gp141. In contrast, production of high titer stocks was possible when gp141 was artificially supplied in trans during infection. As a reporter, SEA1Δgp141.NL facilitated rapid, sensitive, and robust detection of Salmonella despite an inability to replicate. These results suggest that replication-deficient reporter phages are an effective method to obtain improved containment without sacrificing significant performance or the ease of production associated with many phage-based diagnostic methods.
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Affiliation(s)
- Jose Gil
- Laboratory Corporation of America Holdings, Los Angeles, CA 90062, USA;
| | - John Paulson
- Laboratory Corporation of America Holdings, New Brighton, MN 55112, USA; (J.P.); (H.Z.); (M.M.N.)
| | - Henriett Zahn
- Laboratory Corporation of America Holdings, New Brighton, MN 55112, USA; (J.P.); (H.Z.); (M.M.N.)
| | - Matthew Brown
- Laboratory Corporation of America Holdings, Burlington, NC 27215, USA;
| | - Minh M. Nguyen
- Laboratory Corporation of America Holdings, New Brighton, MN 55112, USA; (J.P.); (H.Z.); (M.M.N.)
| | - Stephen Erickson
- Laboratory Corporation of America Holdings, New Brighton, MN 55112, USA; (J.P.); (H.Z.); (M.M.N.)
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21
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Chen Y, Li L, Wei X, Hu M, Zhao X, Zhang Q, Luo Y, Zhao M, Liu Z, Cai Y, Liu Y. Phage Tail Fiber Protein as a Specific Probe for Recognition of Shiga Toxin-Producing Escherichia coli O91, O103, and O111. Anal Chem 2023; 95:18407-18414. [PMID: 38053255 DOI: 10.1021/acs.analchem.3c03370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/07/2023]
Abstract
The ability to quickly identify specific serotypes of Shiga toxin-producing Escherichia coli (STEC) could facilitate the monitoring and control of STEC pathogens. In this study, we identified the receptors and receptor-binding proteins (RBPs) of three novel phages (pO91, pO103, and pO111) isolated from hospital wastewater. Recombinant versions of these RBPs (pO91-ORF43, pO103-ORF42, and pO111-ORF8) fused to a fluorescent reporter protein were then constructed. Both fluorescence microscopy and transmission electron microscopy showed that all three recombinant RBPs were bound to the bacterial surface. Indirect enzyme-linked immunosorbent assay was used to verify that each recombinant RBP bound specifically to E. coli O91, O103, or O111, but not to any of the 83 strains of E. coli with different O-antigens, nor to 10 other bacterial species that were tested. The recombinant RBPs adsorbed to their respective host bacteria within 10 min of incubation. The minimum concentration of bacteria required for detection by the recombinant RBPs was 33 colony-forming units (CFU)/mL (range: 3.3 × 10 to 3.3 × 108 CFU/mL). Furthermore, each recombinant RBP was also able to detect bacteria in lettuce, chicken breast meat, and infected mice, indicating that their usage will facilitate the detection of STEC and may help to reduce the spread of STEC-related infections and diseases.
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Affiliation(s)
- Yibao Chen
- Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan 250100, China
| | - Lulu Li
- Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan 250100, China
| | - Xiaotian Wei
- Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan 250100, China
| | - Ming Hu
- Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan 250100, China
| | - Xiaonan Zhao
- Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan 250100, China
| | - Qing Zhang
- Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan 250100, China
| | - Yanbo Luo
- Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan 250100, China
| | - Min Zhao
- Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan 250100, China
| | - Zhengjie Liu
- Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan 250100, China
| | - Yumei Cai
- College of Veterinary Medicine, Shandong Agricultural University, Taian 271018, China
| | - Yuqing Liu
- Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan 250100, China
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22
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Mohammed HT, Mageeney C, Korenberg J, Graham L, Ware VC. Characterization of novel recombinant mycobacteriophages derived from homologous recombination between two temperate phages. G3 (BETHESDA, MD.) 2023; 13:jkad210. [PMID: 37713616 PMCID: PMC10700106 DOI: 10.1093/g3journal/jkad210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 08/15/2023] [Accepted: 08/31/2023] [Indexed: 09/17/2023]
Abstract
Comparative analyses of mycobacteriophage genomes reveals extensive genetic diversity in genome organization and gene content, contributing to widespread mosaicism. We previously reported that the prophage of mycobacteriophage Butters (cluster N) provides defense against infection by Island3 (subcluster I1). To explore the anti-Island3 defense mechanism, we attempted to isolate Island3 defense escape mutants on a Butters lysogen, but only uncovered phages with recombinant genomes comprised of regions of Butters and Island3 arranged from left arm to right arm as Butters-Island3-Butters (BIBs). Recombination occurs within two distinct homologous regions that encompass lysin A, lysin B, and holin genes in one segment, and RecE and RecT genes in the other. Structural genes of mosaic BIB genomes are contributed by Butters while the immunity cassette is derived from Island3. Consequently, BIBs are morphologically identical to Butters (as shown by transmission electron microscopy) but are homoimmune with Island3. Recombinant phages overcome antiphage defense and silencing of the lytic cycle. We leverage this observation to propose a stratagem to generate novel phages for potential therapeutic use.
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Affiliation(s)
- Hamidu T Mohammed
- Department of Biological Sciences, Lehigh University, Bethlehem, PA 18015, USA
- Memsel, Inc., 3500 Camp Bowie Blvd., Fort Worth, TX 76107, USA
| | - Catherine Mageeney
- Department of Biological Sciences, Lehigh University, Bethlehem, PA 18015, USA
- Biotechnology and Bioengineering Department, Sandia National Laboratories, Livermore, CA 94551, USA
| | - Jamie Korenberg
- Department of Biological Sciences, Lehigh University, Bethlehem, PA 18015, USA
- New York Institute of Technology College of Osteopathic Medicine, 101 Northern Blvd., Glen Head, NY 11545, USA
| | - Lee Graham
- Department of Biological Sciences, Lehigh University, Bethlehem, PA 18015, USA
| | - Vassie C Ware
- Department of Biological Sciences, Lehigh University, Bethlehem, PA 18015, USA
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23
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Silva EC, Rodrigues LMR, Vila MMDC, Balcão VM. Newly isolated phages preying on Pseudomonas syringae pv. garcae: In vitro and ex vivo inactivation studies in coffee plant leafs. Enzyme Microb Technol 2023; 171:110325. [PMID: 37716050 DOI: 10.1016/j.enzmictec.2023.110325] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 08/18/2023] [Accepted: 09/10/2023] [Indexed: 09/18/2023]
Abstract
Coffee canker, or bacterial halo blight (BHB) of coffee, is a disease caused by the phytopathogenic bacterium Pseudomonas syringae pv. garcae (Psg), having been found for the first time in 1955, in the Garça region (State of São Paulo), and which has stood out in the Brazilian coffee plantations in recent years, leading to severe economic losses that seriously affect coffee trade. The treatments available are still scarce, involving frequent spraying of coffee plantations with either copper derivatives or the antibiotic kasugamycin. However, these compounds should be avoided due to environmental toxicity and the development of bacterial resistances. Herein we report the isolation and physical/biological characterisation of two novel lytic phages and their efficacy in the control of Psg. Phages ph002F and ph004F were isolated from coffee plant leaves in Brazil (Sorocaba/SP and Itu/SP cities), using Psg IBSBF-158 as the host. According to the transmission electron microscopy analyses, both phages belong to the class Caudoviricetes and present myovirus-like morphotypes. Phages ph002F and ph004F showed eclipse times of 5 min and 20 min, respectively, and a burst size of 123 PFU/host cell and 12 PFU/host cell, respectively, allowing to conclude they replicate well in Psg IBSBF-158 with latency periods of 50 min. Phage ph002F (reduction of 4.59 log CFU/mL, compared to uninfected culture) was more effective in inactivating Psg than phage ph004F (reduction of 3.85 log CFU/mL) after 10 h of incubation at a MOI of 10. As a cocktail, the two phages were highly effective in reducing the bacterial load (reduction of 5.26 log CFU/mL at a MOI of 0.1 or reduction of 5.03 log CFU/mL at a MOI of 10, relative to untreated culture), after 12 h of treatment. This study provides evidence that the isolated phages are promising candidates against the causative agent of BHB in coffee plants.
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Affiliation(s)
- Erica C Silva
- VBlab - Laboratory of Bacterial Viruses, University of Sorocaba, 18023-000 Sorocaba, SP, Brazil
| | - Lucas M R Rodrigues
- VBlab - Laboratory of Bacterial Viruses, University of Sorocaba, 18023-000 Sorocaba, SP, Brazil; Agronomic Institute of Campinas (IAC), Centro de café Alcides Carvalho, Campinas, SP, Brazil
| | - Marta M D C Vila
- VBlab - Laboratory of Bacterial Viruses, University of Sorocaba, 18023-000 Sorocaba, SP, Brazil
| | - Victor M Balcão
- VBlab - Laboratory of Bacterial Viruses, University of Sorocaba, 18023-000 Sorocaba, SP, Brazil; Department of Biology and CESAM, University of Aveiro, Campus Universitário de Santiago, P-3810-193 Aveiro, Portugal.
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24
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El-Nour SAA, Hammad AA, Fathy R, Eid AS. Application of coliphage as biocontrol agent in combination with gamma irradiation to eliminate multi-drug-resistant E. coli in minimally processed vegetables. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:123907-123924. [PMID: 37995029 PMCID: PMC10746767 DOI: 10.1007/s11356-023-31071-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 11/12/2023] [Indexed: 11/24/2023]
Abstract
Biofilm formation is a rising concern in the food industry. Escherichia coli (E. coli) is one of the most important food-borne pathogens that can survive in food and food-related environments and eventually produce biofilms. This study suggested that both coliphages used were successful in preventing the creation of new biofilms as well as removing existing ones. Confocal laser scanning microscopy verified these findings. According to the findings, neither coliphage survived at 37 °C, but both remained stable at 4 °C and - 20 °C for extended periods of time. The study revealed that both coliphages demonstrated a greater degree of gamma irradiation resistance when compared to E. coli. The study's results indicate that the implementation of a dual method, which incorporates gamma irradiation (1.5 kGy) and coliphage treatment, on various kinds of vegetables that were infected with E. coli, resulted in a significant reduction in bacterial count (surpassing 99.99%) following a 24-h incubation period. Combining gamma irradiation and the coliphage approach was significantly effective at lowering polysaccharide concentrations and proteins in the biofilm matrix. The results revealed that the pairing of gamma irradiation and coliphages acted in conjunction to cause disruptions in the matrix of biofilm, thereby promoting cell removal compared with either of the individual treatments. Ca+ ions strengthen the weak virion interaction with the relevant bacterial host cell receptors during the adsorption process. In conclusion, use of coliphage in combination with gamma irradiation treatment can be applied to improve fresh produce's microbial safety and enhance its storability in supermarkets.
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Affiliation(s)
- Salwa A Abou El-Nour
- Radiation Microbiology Department, National Center for Radiation Research and Technology (NCRRT), Egyptian Atomic Energy Authority (EAEA), Cairo, Egypt
| | - Ali A Hammad
- Radiation Microbiology Department, National Center for Radiation Research and Technology (NCRRT), Egyptian Atomic Energy Authority (EAEA), Cairo, Egypt
| | - Reham Fathy
- Radiation Microbiology Department, National Center for Radiation Research and Technology (NCRRT), Egyptian Atomic Energy Authority (EAEA), Cairo, Egypt.
| | - Amal S Eid
- Radiation Microbiology Department, National Center for Radiation Research and Technology (NCRRT), Egyptian Atomic Energy Authority (EAEA), Cairo, Egypt
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25
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Plumet L, Morsli M, Ahmad-Mansour N, Clavijo-Coppens F, Berry L, Sotto A, Lavigne JP, Costechareyre D, Molle V. Isolation and Characterization of New Bacteriophages against Staphylococcal Clinical Isolates from Diabetic Foot Ulcers. Viruses 2023; 15:2287. [PMID: 38140529 PMCID: PMC10747802 DOI: 10.3390/v15122287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 11/09/2023] [Accepted: 11/19/2023] [Indexed: 12/24/2023] Open
Abstract
Staphylococcus sp. is the most common bacterial genus in infections related to diabetic foot ulcers (DFUs). The emergence of multidrug-resistant bacteria places a serious burden on public health systems. Phage therapy is an alternative treatment to antibiotics, overcoming the issue of antibiotic resistance. In this study, six phages (SAVM01 to SAVM06) were isolated from effluents and were used against a panel of staphylococcal clinical samples isolated from DFUs. A genomic analysis revealed that the phages belonged to the Herelleviridae family, with sequences similar to those of the Kayvirus genus. No lysogeny-associated genes, known virulence or drug resistance genes were identified in the phage genomes. The phages displayed a strong lytic and antibiofilm activity against DFU clinical isolates, as well as against opportunistic pathogenic coagulase-negative staphylococci. The results presented here suggest that these phages could be effective biocontrol agents against staphylococcal clinical isolates from DFUs.
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Affiliation(s)
- Lucile Plumet
- VBIC, INSERM U1047, University of Montpellier, 34095 Montpellier, France; (L.P.); (N.A.-M.)
| | - Madjid Morsli
- VBIC, INSERM U1047, Department of Microbiology and Hospital Hygiene, University of Montpellier, CHU Nîmes, 30908 Nîmes, France; (M.M.); (J.-P.L.)
| | - Nour Ahmad-Mansour
- VBIC, INSERM U1047, University of Montpellier, 34095 Montpellier, France; (L.P.); (N.A.-M.)
| | | | - Laurence Berry
- Laboratory of Pathogen and Host Immunity, CNRS UMR5294, University of Montpellier, 34095 Montpellier, France;
| | - Albert Sotto
- VBIC, INSERM U1047, Department of Infectious Diseases, University of de Montpellier, CHU Nîmes, 30908 Nîmes, France;
| | - Jean-Philippe Lavigne
- VBIC, INSERM U1047, Department of Microbiology and Hospital Hygiene, University of Montpellier, CHU Nîmes, 30908 Nîmes, France; (M.M.); (J.-P.L.)
| | | | - Virginie Molle
- VBIC, INSERM U1047, University of Montpellier, 34095 Montpellier, France; (L.P.); (N.A.-M.)
- VBIC, INSERM U1047, Department of Microbiology and Hospital Hygiene, University of Montpellier, CHU Nîmes, 30908 Nîmes, France; (M.M.); (J.-P.L.)
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26
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Barrero-Canosa J, Wang L, Oyugi A, Klaes S, Fischer P, Adrian L, Szewzyk U, Cooper M. Characterization of phage vB_EcoS-EE09 infecting E. coli DSM613 Isolated from Wastewater Treatment Plant Effluent and Comparative Proteomics of the Infected and Non-Infected Host. Microorganisms 2023; 11:2688. [PMID: 38004701 PMCID: PMC10673088 DOI: 10.3390/microorganisms11112688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 10/28/2023] [Accepted: 10/30/2023] [Indexed: 11/26/2023] Open
Abstract
Phages influence microbial communities, can be applied in phage therapy, or may serve as bioindicators, e.g., in (waste)water management. We here characterized the Escherichia phage vB_EcoS-EE09 isolated from an urban wastewater treatment plant effluent. Phage vB_EcoS-EE09 belongs to the genus Dhillonvirus, class Caudoviricetes. It has an icosahedral capsid with a long non-contractile tail and a dsDNA genome with an approximate size of 44 kb and a 54.6% GC content. Phage vB_EcoS-EE09 infected 12 out of the 17 E. coli strains tested. We identified 16 structural phage proteins, including the major capsid protein, in cell-free lysates by protein mass spectrometry. Comparative proteomics of protein extracts of infected E. coli cells revealed that proteins involved in amino acid and protein metabolism were more abundant in infected compared to non-infected cells. Among the proteins involved in the stress response, 74% were less abundant in the infected cultures compared to the non-infected controls, with six proteins showing significant less abundance. Repressing the expression of these proteins may be a phage strategy to evade host defense mechanisms. Our results contribute to diversifying phage collections, identifying structural proteins to enable better reliability in annotating taxonomically related phage genomes, and understanding phage-host interactions at the protein level.
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Affiliation(s)
- Jimena Barrero-Canosa
- Institute of Environmental Technology, Chair of Environmental Microbiology, Technische Universität Berlin, Straße des 17. Juni 135, 10623 Berlin, Germany; (L.W.); (A.O.); (P.F.); (U.S.); (M.C.)
| | - Luyao Wang
- Institute of Environmental Technology, Chair of Environmental Microbiology, Technische Universität Berlin, Straße des 17. Juni 135, 10623 Berlin, Germany; (L.W.); (A.O.); (P.F.); (U.S.); (M.C.)
| | - Angelah Oyugi
- Institute of Environmental Technology, Chair of Environmental Microbiology, Technische Universität Berlin, Straße des 17. Juni 135, 10623 Berlin, Germany; (L.W.); (A.O.); (P.F.); (U.S.); (M.C.)
| | - Simon Klaes
- Institute of Biotechnology, Chair of Geobiotechnology, Technische Universität Berlin, Ackerstraße 76, 13355 Berlin, Germany; (S.K.)
- Helmholtz Centre for Environmental Research GmbH—UFZ, Department of Environmental Biotechnology, Permoserstraße 15, 04318 Leipzig, Germany
| | - Pascal Fischer
- Institute of Environmental Technology, Chair of Environmental Microbiology, Technische Universität Berlin, Straße des 17. Juni 135, 10623 Berlin, Germany; (L.W.); (A.O.); (P.F.); (U.S.); (M.C.)
| | - Lorenz Adrian
- Institute of Biotechnology, Chair of Geobiotechnology, Technische Universität Berlin, Ackerstraße 76, 13355 Berlin, Germany; (S.K.)
- Helmholtz Centre for Environmental Research GmbH—UFZ, Department of Environmental Biotechnology, Permoserstraße 15, 04318 Leipzig, Germany
| | - Ulrich Szewzyk
- Institute of Environmental Technology, Chair of Environmental Microbiology, Technische Universität Berlin, Straße des 17. Juni 135, 10623 Berlin, Germany; (L.W.); (A.O.); (P.F.); (U.S.); (M.C.)
| | - Myriel Cooper
- Institute of Environmental Technology, Chair of Environmental Microbiology, Technische Universität Berlin, Straße des 17. Juni 135, 10623 Berlin, Germany; (L.W.); (A.O.); (P.F.); (U.S.); (M.C.)
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27
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Yousefi MH, Wagemans J, Shekarforoush SS, Vallino M, Pozhydaieva N, Höfer K, Lavigne R, Hosseinzadeh S. Isolation and molecular characterization of the Salmonella Typhimurium orphan phage Arash. BMC Microbiol 2023; 23:297. [PMID: 37858092 PMCID: PMC10585845 DOI: 10.1186/s12866-023-03056-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 10/11/2023] [Indexed: 10/21/2023] Open
Abstract
The current threat of multidrug resistant strains necessitates development of alternatives to antibiotics such as bacteriophages. This study describes the isolation and characterization of a novel Salmonella Typhimurium phage 'Arash' from hospital wastewater in Leuven, Belgium. Arash has a myovirus morphology with a 95 nm capsid and a 140 nm tail. The host range of Arash is restricted to its isolation host. Approximately 86% of the phage particles are adsorbed to a host cell within 10 min. Arash has latent period of 65 min and burst size of 425 PFU/cell. Arash has a dsDNA genome of 180,819 bp with GC content of 53.02% with no similarities to any characterized phages, suggesting Arash as a novel species in the novel 'Arashvirus' genus. Arash carries no apparent lysogeny-, antibiotic resistance- nor virulence-related genes. Proteome analysis revealed 116 proteins as part of the mature phage particles of which 27 could be assigned a function. Therefore, the present findings shed light on the morphological, microbiological and genomic characteristics of Arash and suggest its potential application as therapeutic and/or biocontrol agent.
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Affiliation(s)
- Mohammad Hashem Yousefi
- Department of Food Hygiene and Public Health, School of Veterinary Medicine, Shiraz University, Shiraz, 71946- 84471, Iran
| | | | - Seyed Shahram Shekarforoush
- Department of Food Hygiene and Public Health, School of Veterinary Medicine, Shiraz University, Shiraz, 71946- 84471, Iran
| | - Marta Vallino
- Institute of Sustainable Plant Protection, National Research Council of Italy, Turin, 10135, Italy
| | - Nadiia Pozhydaieva
- Max Planck Institute for Terrestrial Microbiology, SYNMIKRO, Karl-von-Frisch-Strasse 16, Marburg, 35043, Germany
| | - Katharina Höfer
- Max Planck Institute for Terrestrial Microbiology, SYNMIKRO, Karl-von-Frisch-Strasse 16, Marburg, 35043, Germany
| | - Rob Lavigne
- Department of Biosystems, KU Leuven, Leuven, 3001, Belgium
| | - Saeid Hosseinzadeh
- Department of Food Hygiene and Public Health, School of Veterinary Medicine, Shiraz University, Shiraz, 71946- 84471, Iran.
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28
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Zhao J, Lin Y, Wang C, Zayda M, Maung AT, Mohammadi TN, Duc HM, Yu P, Ma M, Gong D, Sato J, Masuda Y, Honjoh KI, Miyamoto T, Zeng Z. Biocontrol of Salmonella Typhimurium in milk, lettuce, raw pork meat and ready-to-eat steamed-chicken breast by using a novel bacteriophage with broad host range. Int J Food Microbiol 2023; 402:110295. [PMID: 37352774 DOI: 10.1016/j.ijfoodmicro.2023.110295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 06/07/2023] [Accepted: 06/10/2023] [Indexed: 06/25/2023]
Abstract
Salmonella spp., one of the most frequently reported bacteria, causes foodborne illness and economic losses. Due to the threat of increasing antibiotic resistant foodborne pathogens, application of bacteriophages as novel antibacterial agents in food matrices has become an emerging strategy. In this study, a novel Salmonella phage PS3-1 with high lytic activity against Salmonella Typhimurium was identified from previously isolated phages. PS3-1 belonged to the class Caudoviricetes with a broad host range, and had relatively short latent period (15 min), large burst size (92 PFU/cell), high pH stability (pH 3.0-11.0) and thermal tolerance (4-60 °C). Genome sequencing analysis showed that PS3-1 genome consisted of 107,110 bp DNA, without antibiotic resistance and virulence related genes. The results of growth curve and time-kill assay showed that PS3-1 not only inhibited the growth of S. Typhimurium, but also effectively decreased the viable cell counts (0.30-4.72 log) after 24-h incubation at 7, 25 and 37 °C (P < 0.05). Moreover, >1.28 log of established biofilm cells were effectively removed after 24-h treatment with PS3-1. Besides, PS3-1 significantly reduced the viability of S. Typhimurium in milk, lettuce, raw pork meat and ready-to-eat steamed-chicken breast at different temperatures (P < 0.05). These results demonstrated that PS3-1 may be an excellent antibacterial agent for controlling S. Typhimurium in food industry.
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Affiliation(s)
- Junxin Zhao
- State Key Laboratory of Food Science and Resources, Nanchang University, Nanchang 330047, China; Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Yunzhi Lin
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Chen Wang
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Mahmoud Zayda
- Department of Food Hygiene and Control, Faculty of Veterinary Medicine, University of Sadat City, 32897 Sadat City, Egypt
| | - Aye Thida Maung
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Tahir Noor Mohammadi
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Hoang Minh Duc
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Ping Yu
- State Key Laboratory of Food Science and Resources, Nanchang University, Nanchang 330047, China
| | - Maomao Ma
- State Key Laboratory of Food Science and Resources, Nanchang University, Nanchang 330047, China
| | - Deming Gong
- State Key Laboratory of Food Science and Resources, Nanchang University, Nanchang 330047, China
| | - Jun Sato
- Safety Science Research, R&D, Kao Corporation, 2606 Akabane, Ichikai-Machi, Haga-Gun, Tochigi 321-3497, Japan
| | - Yoshimitsu Masuda
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Ken-Ichi Honjoh
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Takahisa Miyamoto
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan.
| | - Zheling Zeng
- State Key Laboratory of Food Science and Resources, Nanchang University, Nanchang 330047, China.
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29
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Kim SH, Lee H, Park MK. Isolation, characterization, and application of a novel, lytic phage vB_SalA_KFSST3 with depolymerase for the control of Salmonella and its biofilm on cantaloupe under cold temperature. Food Res Int 2023; 172:113062. [PMID: 37689855 DOI: 10.1016/j.foodres.2023.113062] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Revised: 05/25/2023] [Accepted: 05/26/2023] [Indexed: 09/11/2023]
Abstract
This study investigated the efficacy of a novel Salmonella phage with depolymerase activity to control S. Typhimurium (ST) and its biofilm on cantaloupes, for the first time, under simulated cold temperature. vB_SalA_KFSST3 forming a halo zone was isolated and purified from a slaughterhouse with a final concentration of 12.1 ± 0.1 log PFU/mL. Based on the morphological and bioinformatics analyses, vB_SalA_KFSST3 was identified as a novel phage belonging to the family Ackermannviridae. Before employing the phage on cantaloupe, its genetic characteristics, specificity, stability, and bactericidal effect were investigated. Genetic analyses confirmed its safety and identified endolysin and two depolymerase domains possessing antibiofilm potential. In addition, the phage exhibited a broad specificity with great efficiencies toward five Salmonella strains at 4 °C, 22 °C, and 37 °C, as well as stable lytic activity over a wide range of pHs (3 to 11) and temperatures (-20 °C to 60 °C). The optimal multiplicity of infection (MOI) and exposure time of phage were determined to be 100 and 2 h, respectively, based on the highest bacterial reduction of ∼2.7 log CFU/mL. Following the formation of ST biofilm on cantaloupe at 4 °C and 22 °C, the cantaloupe was treated with phage at an MOI of 100 for 2 h. The antibiofilm efficacy of phage was evaluated via the plate count method, confocal laser scanning microscopy, and scanning electron microscopy (SEM). The initial biofilm population at 22 °C was significantly greater and more condensed than that at 4 °C. After phage treatment, biofilm population and the percentage of viable ST in biofilm were reduced by ∼4.6 log CFU/cm2 and ∼90% within 2 h, respectively, which were significantly greater than those at 22 °C (∼2.0 log CFU/cm2 and ∼45%) (P < 0.05). SEM images also confirmed more drastic destruction of the cohesive biofilm architecture at 4 °C than at 22 °C. As a result of its cold temperature-robust lytic activity and the contribution of endolysin and two depolymerases, vB_SalA_KFSST3 demonstrated excellent antibiofilm efficacy at cold temperature, highlighting its potential as a promising practical biocontrol agent for the control of ST and its biofilm.
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Affiliation(s)
- Su-Hyeon Kim
- School of Food Science and Biotechnology, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Heejeong Lee
- School of Food Science and Biotechnology, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Mi-Kyung Park
- School of Food Science and Biotechnology, Kyungpook National University, Daegu 41566, Republic of Korea; Food and Bio-Industry Institute, Kyungpook National University, Daegu 41566, Republic of Korea.
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30
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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: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [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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31
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Olsen NS, Nielsen TK, Cui L, Dedon P, Neve H, Hansen L, Kot W. A novel Queuovirinae lineage of Pseudomonas aeruginosa phages encode dPreQ0 DNA modifications with a single GA motif that provide restriction and CRISPR Cas9 protection in vitro. Nucleic Acids Res 2023; 51:8663-8676. [PMID: 37503841 PMCID: PMC10484667 DOI: 10.1093/nar/gkad622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 06/02/2023] [Accepted: 07/14/2023] [Indexed: 07/29/2023] Open
Abstract
Deazaguanine DNA modifications are widespread in phages, particularly in those with pathogenic hosts. Pseudomonas phage iggy substitutes ∼16.5% of its genomic 2'-deoxyguanosine (G) with dPreQ0, and the iggy deazaguanine transglycosylase (DpdA) is unique in having a strict GA target motif, not observed previously. The iggy PreQ0 modification is shown to provide protection against both restriction endonucleases and Cas9 (when present in PAM), thus expanding our understanding of the deazaguanine modification system, its potential, and diversity. Phage iggy represents a new genus of Pseudomonas phages within the Queuovirinae subfamily; which have very little in common with other published phage genomes in terms of nucleotide similarity (<10%) and common proteins (<2%). Interestingly, shared similarity is concentrated in dpdA and preQ0 biosynthesis genes. TEM imaging confirmed a siphovirus morphology with a prolate icosahedral head and a non-contractile flexible tail with one long central tail spike. The observed protective effect of the deazaguanine modification on the iggy DNA may contribute to its broad within-species host range. Phage iggy was isolated on Pseudomonas aeruginosa PAO1, but also infects PDO300, PAK, PA14, as well as 10 of 27 tested environmental isolates and 13 of 20 tested clinical isolates of P. aeruginosa from patients with cystic fibrosis.
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Affiliation(s)
- Nikoline S Olsen
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg C, Denmark
| | - Tue K Nielsen
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg C, Denmark
| | - Liang Cui
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Singapore
| | - Peter Dedon
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Singapore
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, US
| | - Horst Neve
- Department of Microbiology and Biotechnology, Max Rubner-Institut, Kiel, Germany
| | - Lars H Hansen
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg C, Denmark
| | - Witold Kot
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg C, Denmark
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32
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Krishnappa G, Mandal M, Ganesan S, Babu S, Padavattan S, Haradara Bahubali VK, Padmanabhan B. Structural and biochemical insights into the bacteriophage PlyGRCS endolysin targeting methicillin-resistant Staphylococcus aureus (MRSA) and serendipitous discovery of its interaction with a cold shock protein C (CspC). Protein Sci 2023; 32:e4737. [PMID: 37497650 PMCID: PMC10443338 DOI: 10.1002/pro.4737] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 07/21/2023] [Accepted: 07/24/2023] [Indexed: 07/28/2023]
Abstract
Methicillin-resistant Staphylococcus aureus (MRSA) causes life-threatening human infections. Bacteriophage-encoded endolysins degrade the cell walls of Gram-positive bacteria by selectively hydrolyzing the peptidoglycan layer and thus are promising candidates to combat bacterial infections. PlyGRCS, the S. aureus-specific bacteriophage endolysin, contains a catalytic CHAP domain and a cell-wall binding SH3_5 domain connected by a linker. Here, we show the crystal structure of full-length PlyGRCS refined to 2.1 Å resolution. In addition, a serendipitous finding revealed that PlyGRCS binds to cold-shock protein C (CspC) by interacting with its CHAP and SH3_5 domains. CspC is an RNA chaperone that plays regulatory roles by conferring bacterial adaptability to various stress conditions. PlyGRCS has substantial lytic activity against S. aureus and showed only minimal change in its lytic activity in the presence of CspC. Whereas the PlyGRCS-CspC complex greatly reduced CspC-nucleic acid binding, the aforesaid complex may downregulate the CspC function during bacterial infection. Overall, the crystal structure and biochemical results of PlyGRCS provide a molecular basis for the bacteriolytic activity of PlyGRCS against S. aureus.
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Affiliation(s)
- Gopinatha Krishnappa
- Department of BiophysicsNational Institute of Mental Health and Neuro Sciences (NIMHANS)BengaluruIndia
| | - Mitali Mandal
- Department of BiophysicsNational Institute of Mental Health and Neuro Sciences (NIMHANS)BengaluruIndia
| | - Saranya Ganesan
- Department of BiophysicsNational Institute of Mental Health and Neuro Sciences (NIMHANS)BengaluruIndia
| | - Sudhagar Babu
- Department of BiophysicsNational Institute of Mental Health and Neuro Sciences (NIMHANS)BengaluruIndia
| | - Sivaraman Padavattan
- Department of BiophysicsNational Institute of Mental Health and Neuro Sciences (NIMHANS)BengaluruIndia
| | | | - Balasundaram Padmanabhan
- Department of BiophysicsNational Institute of Mental Health and Neuro Sciences (NIMHANS)BengaluruIndia
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33
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Woudstra C, Brøndsted L. Producing Tailocins from Phages Using Osmotic Shock and Benzalkonium Chloride. PHAGE (NEW ROCHELLE, N.Y.) 2023; 4:136-140. [PMID: 37841391 PMCID: PMC10574523 DOI: 10.1089/phage.2023.0014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/17/2023]
Abstract
In the light of the worldwide antimicrobial resistance crisis, new substitutes to antibiotics are urgently needed. Tailocins or phage tail-like bacteriocin particles, produced by bacteria for environmental competition, are a potential antimicrobial alternative to antibiotic treatment. Yet, the availability of characterized Tailocins is limited. We explored the possibility to produce new Tailocins from phage particles, using osmotic shock or chemical treatment by the ammonium quaternary compound benzalkonium chloride on Ackermannviridae phage S117 and using Straboviridae phage T4 as control. We report that phage S117 was resistant to such treatment, while successful production of Tailocins by osmotic shock was achieved for phage T4. Finally, chemical treatment with benzalkonium chloride was inefficient on phage S117 but successfully inactivated phage T4 without production of Tailocins. Further studies are needed to implement such treatments of phages for producing Tailocins with killing activity.
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Affiliation(s)
- Cedric Woudstra
- Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg C, Denmark
| | - Lone Brøndsted
- Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg C, Denmark
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34
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Britton AP, Visser KA, Ongenae VMA, Zhang P, Wassink H, Doerksen TA, Welke CA, Lynch KH, van Belkum MJ, Dennis JJ, Yang X, Claessen D, Briegel A, Martin-Visscher LA. Characterization of Bacteriophage cd2, a Siphophage Infecting Carnobacterium divergens and a Representative Species of a New Genus of Phage. Microbiol Spectr 2023; 11:e0097323. [PMID: 37458599 PMCID: PMC10434151 DOI: 10.1128/spectrum.00973-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Accepted: 06/24/2023] [Indexed: 08/19/2023] Open
Abstract
Carnobacterium divergens is frequently isolated from natural environments and is a predominant species found in refrigerated foods, particularly meat, seafood, and dairy. While there is substantial interest in using C. divergens as biopreservatives and/or probiotics, some strains are known to be fish pathogens, and the uncontrolled growth of C. divergens has been associated with food spoilage. Bacteriophages offer a selective approach to identify and control the growth of bacteria; however, to date, few phages targeting C. divergens have been reported. In this study, we characterize bacteriophage cd2, which we recently isolated from minced beef. A detailed host range study reveals that phage cd2 infects certain phylogenetic groups of C. divergens. This phage has a latent period of 60 min and a burst size of ~28 PFU/infected cell. The phage was found to be acid and heat sensitive, with a complete loss of phage activity when stored at pH 2 or heated to 60°C. Electron microscopy shows that phage cd2 is a siphophage, and while it shares the B3 morphotype with a unique cluster of Listeria and Enterococcus phages, a comparison of genomes reveals that phage cd2 comprises a new genus of phage, which we have termed as Carnodivirus. IMPORTANCE Currently, very little is known about phages that infect carnobacteria, an important genus of lactic acid bacteria with both beneficial and detrimental effects in the food and aquaculture industries. This report provides a detailed characterization of phage cd2, a novel siphophage that targets Carnobacterium divergens, and sets the groundwork for understanding the biology of these phages and their potential use in the detection and biocontrol of C. divergens isolates.
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Affiliation(s)
- Angelle P. Britton
- Department of Chemistry, The King’s University, Edmonton, Alberta, Canada
| | - Kaitlyn A. Visser
- Department of Chemistry, The King’s University, Edmonton, Alberta, Canada
| | - Véronique M. A. Ongenae
- Molecular Biotechnology, Institute of Biology, Leiden University, Leiden, the Netherlands
- Centre for Microbial Cell Biology, Leiden University, Leiden, the Netherlands
| | - Peipei Zhang
- Agriculture and Agri-Food Canada, Lacombe, Alberta, Canada
| | - Heather Wassink
- Department of Chemistry, The King’s University, Edmonton, Alberta, Canada
| | - Thomas A. Doerksen
- Department of Chemistry, The King’s University, Edmonton, Alberta, Canada
| | - Catherine A. Welke
- Department of Chemistry, The King’s University, Edmonton, Alberta, Canada
| | - Karlene H. Lynch
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | | | - Jonathan J. Dennis
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Xianqin Yang
- Agriculture and Agri-Food Canada, Lacombe, Alberta, Canada
| | - Dennis Claessen
- Molecular Biotechnology, Institute of Biology, Leiden University, Leiden, the Netherlands
- Centre for Microbial Cell Biology, Leiden University, Leiden, the Netherlands
| | - Ariane Briegel
- Molecular Biotechnology, Institute of Biology, Leiden University, Leiden, the Netherlands
- Centre for Microbial Cell Biology, Leiden University, Leiden, the Netherlands
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35
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Ribeiro JM, Pereira GN, Durli Junior I, Teixeira GM, Bertozzi MM, Verri WA, Kobayashi RKT, Nakazato G. Comparative analysis of effectiveness for phage cocktail development against multiple Salmonella serovars and its biofilm control activity. Sci Rep 2023; 13:13054. [PMID: 37567926 PMCID: PMC10421930 DOI: 10.1038/s41598-023-40228-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 08/07/2023] [Indexed: 08/13/2023] Open
Abstract
Foodborne diseases are a major challenge in the global food industry, especially those caused by multidrug-resistant (MDR) bacteria. Bacteria capable of biofilm formation, in addition to MDR strains, reduce the treatment efficacy, posing a significant threat to bacterial control. Bacteriophages, which are viruses that infect and kill bacteria, are considered a promising alternative in combating MDR bacteria, both in human medicine and animal production. Phage cocktails, comprising multiple phages, are commonly employed to broaden the host range and prevent or delay the development of phage resistance. There are numerous techniques and protocols available to evaluate the lytic activity of bacteriophages, with the most commonly used methods being Spot Test Assays, Efficiency of Plating (EOP), and infection assays in liquid culture. However, there is currently no standardization for which analyses should be employed and the possible differences among them in order to precisely determine the host range of phages and the composition of a cocktail. A preliminary selection using the Spot Test Assay resulted in four phages for subsequent evaluation against a panel of 36 Salmonella isolates of numerous serovars. Comparing EOP and infection assays in liquid culture revealed that EOP could underestimate the lytic activity of phages, directly influencing phage cocktail development. Moreover, the phage cocktail containing the four selected phages was able to control or remove biofilms formed by 66% (23/35) of the isolates, including those exhibiting low susceptibility to phages, according to EOP. Phages were characterized genomically, revealing the absence of genes associated with antibiotic resistance, virulence factors, or integrases. According to confocal laser scanning microscopy analysis, the biofilm maturation of one Salmonella isolate, which exhibited high susceptibility to phages in liquid culture and 96-well plates biofilm viability assays but had low values for EOP, was found to be inhibited and controlled by the phage cocktail. These observations indicate that phages could control and remove Salmonella biofilms throughout their growth and maturation process, despite their low EOP values. Moreover, using infection assays in liquid culture enables a more precise study of phage interactions for cocktail design timelessly and effortlessly. Hence, integrating strategies and techniques to comprehensively assess the host range and lytic activity of bacteriophages under different conditions can demonstrate more accurately the antibacterial potential of phage cocktails.
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Affiliation(s)
- Jhonatan Macedo Ribeiro
- Laboratory of Basic and Applied Bacteriology, State University of Londrina, Londrina, PR, Brazil
| | - Giovana Nicolete Pereira
- Laboratory of Basic and Applied Bacteriology, State University of Londrina, Londrina, PR, Brazil
| | - Itamar Durli Junior
- Laboratory of Bioinformatics, Federal University of Santa Catarina, Florianópolis, SC, Brazil
| | | | - Mariana Marques Bertozzi
- Laboratory of Pain, Inflammation, Neuropathy, and Cancer, State University of Londrina, Londrina, PR, Brazil
| | - Waldiceu A Verri
- Laboratory of Pain, Inflammation, Neuropathy, and Cancer, State University of Londrina, Londrina, PR, Brazil
| | | | - Gerson Nakazato
- Laboratory of Basic and Applied Bacteriology, State University of Londrina, Londrina, PR, Brazil.
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36
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Riber L, Carstens AB, Dougherty PE, Roy C, Willenbücher K, Hille F, Franz CMAP, Hansen LH. Pheno- and Genotyping of Three Novel Bacteriophage Genera That Target a Wheat Phyllosphere Sphingomonas Genus. Microorganisms 2023; 11:1831. [PMID: 37513003 PMCID: PMC10385605 DOI: 10.3390/microorganisms11071831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2023] [Revised: 07/14/2023] [Accepted: 07/16/2023] [Indexed: 07/30/2023] Open
Abstract
Bacteriophages are viral agents that infect and replicate within bacterial cells. Despite the increasing importance of phage ecology, environmental phages-particularly those targeting phyllosphere-associated bacteria-remain underexplored, and current genomic databases lack high-quality phage genome sequences linked to specific environmentally important bacteria, such as the ubiquitous sphingomonads. Here, we isolated three novel phages from a Danish wastewater treatment facility. Notably, these phages are among the first discovered to target and regulate a Sphingomonas genus within the wheat phyllosphere microbiome. Two of the phages displayed a non-prolate Siphovirus morphotype and demonstrated a narrow host range when tested against additional Sphingomonas strains. Intergenomic studies revealed limited nucleotide sequence similarity within the isolated phage genomes and to publicly available metagenome data of their closest relatives. Particularly intriguing was the limited homology observed between the DNA polymerase encoding genes of the isolated phages and their closest relatives. Based on these findings, we propose three newly identified genera of viruses: Longusvirus carli, Vexovirus birtae, and Molestusvirus kimi, following the latest ICTV binomial nomenclature for virus species. These results contribute to our current understanding of phage genetic diversity in natural environments and hold promising implications for phage applications in phyllosphere microbiome manipulation strategies.
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Affiliation(s)
- Leise Riber
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg, Denmark
| | - Alexander Byth Carstens
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg, Denmark
| | - Peter Erdmann Dougherty
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg, Denmark
| | - Chayan Roy
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg, Denmark
| | - Katharina Willenbücher
- Department of Microbiology and Biotechnology, Max Rubner-Institut, Hermann-Weigmann-Strasse 1, 24103 Kiel, Germany
| | - Frank Hille
- Department of Microbiology and Biotechnology, Max Rubner-Institut, Hermann-Weigmann-Strasse 1, 24103 Kiel, Germany
| | - Charles M A P Franz
- Department of Microbiology and Biotechnology, Max Rubner-Institut, Hermann-Weigmann-Strasse 1, 24103 Kiel, Germany
| | - Lars Hestbjerg Hansen
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg, Denmark
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37
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Yesil M, Kasler DR, Huang E, Yousef AE. Lytic Escherichia phage OSYSP acts additively and synergistically with gaseous ozone against Escherichia coli O157:H7 on spinach leaves. Sci Rep 2023; 13:10706. [PMID: 37400589 DOI: 10.1038/s41598-023-36815-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 06/10/2023] [Indexed: 07/05/2023] Open
Abstract
Bacteriophage and gaseous ozone are evolving as meritorious alternatives to conventional sanitizers in food postharvest applications. Here, we investigated the efficacy of sequential treatments of a lytic bacteriophage and gaseous ozone, during vacuum cooling of fresh produce, against Escherichia coli O157:H7. Spinach leaves were spot-inoculated with 105-107 CFU g-1 E. coli O157:H7 B6-914 and treated with Escherichia phage OSYSP spray (109 PFU g-1), gaseous ozone, or their combination. Vacuum cooling, which preceded or followed phage application but ran concomitantly with ozone treatment, was performed in a custom-made vessel at the following process sequence: vacuum to 28.5 in. Hg, vessel pressurization to 10 psig with gas containing 1.5 g ozone/kg gas-mix, holding for 30 min, and vessel depressurization to ambient pressure. Bacteriophage or gaseous ozone inactivated E. coli O157:H7, applied at different initial populations on spinach leaves, by 1.7-2.0 or 1.8-3.5 log CFU g-1, respectively. At the high inoculum levels tested (7.1 log CFU g-1), sequential treatments of phage and ozone reduced E. coli O157:H7 population by 4.0 log CFU g-1, but when treatment order was reversed (i.e., ozone followed by bacteriophage), the combination synergistically decreased pathogen's population on spinach leaves by 5.2 log CFU g-1. Regardless the antibacterial application order, E. coli O157:H7 populations, applied initially at ~ 105 CFU g-1, were reduced below the enumeration method's detection level (i.e., < 101 CFU g-1). The study proved that bacteriophage-ozone combination, applied in conjunction with vacuum cooling, is a potent pathogen intervention strategy in fresh produce post-harvest applications.
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Affiliation(s)
- Mustafa Yesil
- Department of Food Science and Technology, The Ohio State University, 2015 Fyffe Road, Columbus, OH, 43210, USA
| | - David R Kasler
- Department of Food Science and Technology, The Ohio State University, 2015 Fyffe Road, Columbus, OH, 43210, USA
| | - En Huang
- Department of Food Science and Technology, The Ohio State University, 2015 Fyffe Road, Columbus, OH, 43210, USA
- Department of Environmental Health Sciences, University of Arkansas for Medical Sciences, Little Rock, AR, 72205, USA
| | - Ahmed E Yousef
- Department of Food Science and Technology, The Ohio State University, 2015 Fyffe Road, Columbus, OH, 43210, USA.
- Department of Microbiology, The Ohio State University, 105 Biological Sciences Building, 484 W. 12th Ave, Columbus, OH, 43210, USA.
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38
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Suladze T, Jaiani E, Darsavelidze M, Elizbarashvili M, Gorge O, Kusradze I, Kokashvili T, Lashkhi N, Tsertsvadze G, Janelidze N, Chubinidze S, Grdzelidze M, Tsanava S, Valade E, Tediashvili M. New Bacteriophages with Podoviridal Morphotypes Active against Yersinia pestis: Characterization and Application Potential. Viruses 2023; 15:1484. [PMID: 37515171 PMCID: PMC10385128 DOI: 10.3390/v15071484] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 06/22/2023] [Accepted: 06/26/2023] [Indexed: 07/30/2023] Open
Abstract
Phages of highly pathogenic bacteria represent an area of growing interest for bacterial detection and identification and subspecies typing, as well as for phage therapy and environmental decontamination. Eight new phages-YpEc56, YpEc56D, YpEc57, YpEe58, YpEc1, YpEc2, YpEc11, and YpYeO9-expressing lytic activity towards Yersinia pestis revealed a virion morphology consistent with the Podoviridae morphotype. These phages lyse all 68 strains from 2 different sets of Y. pestis isolates, thus limiting their potential application for subtyping of Y. pestis strains but making them rather promising in terms of infection control. Two phages-YpYeO9 and YpEc11-were selected for detailed studies based on their source of isolation and lytic cross activity towards other Enterobacteriaceae. The full genome sequencing demonstrated the virulent nature of new phages. Phage YpYeO9 was identified as a member of the Teseptimavirus genus and YpEc11 was identified as a member of the Helsettvirus genus, thereby representing new species. A bacterial challenge assay in liquid microcosm with a YpYeO9/YpEc11 phage mixture showed elimination of Y. pestis EV76 during 4 h at a P/B ratio of 1000:1. These results, in combination with high lysis stability results of phages in liquid culture, the low frequency of formation of phage resistant mutants, and their viability under different physical-chemical factors indicate their potential for their practical use as an antibacterial mean.
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Affiliation(s)
- Tamar Suladze
- George Eliava Institute of Bacteriophages, Microbiology and Virology (Eliava IBMV), 3, Gotua Str., 0160 Tbilisi, Georgia
| | - Ekaterine Jaiani
- George Eliava Institute of Bacteriophages, Microbiology and Virology (Eliava IBMV), 3, Gotua Str., 0160 Tbilisi, Georgia
| | - Marina Darsavelidze
- George Eliava Institute of Bacteriophages, Microbiology and Virology (Eliava IBMV), 3, Gotua Str., 0160 Tbilisi, Georgia
| | - Maia Elizbarashvili
- George Eliava Institute of Bacteriophages, Microbiology and Virology (Eliava IBMV), 3, Gotua Str., 0160 Tbilisi, Georgia
| | - Olivier Gorge
- French Armed Forces Biomedical Research Institute (IRBA), 1, Place du Général Valérie André-BP 73, 91223 Bretigny-sur-Orge, France
| | - Ia Kusradze
- George Eliava Institute of Bacteriophages, Microbiology and Virology (Eliava IBMV), 3, Gotua Str., 0160 Tbilisi, Georgia
| | - Tamar Kokashvili
- George Eliava Institute of Bacteriophages, Microbiology and Virology (Eliava IBMV), 3, Gotua Str., 0160 Tbilisi, Georgia
- School of Science and Technology, University of Georgia, 77a, Kostava Str., 0171 Tbilisi, Georgia
| | - Nino Lashkhi
- George Eliava Institute of Bacteriophages, Microbiology and Virology (Eliava IBMV), 3, Gotua Str., 0160 Tbilisi, Georgia
| | - George Tsertsvadze
- George Eliava Institute of Bacteriophages, Microbiology and Virology (Eliava IBMV), 3, Gotua Str., 0160 Tbilisi, Georgia
| | - Nino Janelidze
- George Eliava Institute of Bacteriophages, Microbiology and Virology (Eliava IBMV), 3, Gotua Str., 0160 Tbilisi, Georgia
- School of Science and Technology, University of Georgia, 77a, Kostava Str., 0171 Tbilisi, Georgia
| | - Svetlana Chubinidze
- National Center for Disease Control and Pubic Health (NCDC), 99, Kakheti Highway, 0109 Tbilisi, Georgia
| | - Marina Grdzelidze
- National Center for Disease Control and Pubic Health (NCDC), 99, Kakheti Highway, 0109 Tbilisi, Georgia
| | - Shota Tsanava
- National Center for Disease Control and Pubic Health (NCDC), 99, Kakheti Highway, 0109 Tbilisi, Georgia
| | - Eric Valade
- French Armed Forces Biomedical Research Institute (IRBA), 1, Place du Général Valérie André-BP 73, 91223 Bretigny-sur-Orge, France
| | - Marina Tediashvili
- George Eliava Institute of Bacteriophages, Microbiology and Virology (Eliava IBMV), 3, Gotua Str., 0160 Tbilisi, Georgia
- School of Science and Technology, University of Georgia, 77a, Kostava Str., 0171 Tbilisi, Georgia
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39
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Kornienko M, Bespiatykh D, Gorodnichev R, Abdraimova N, Shitikov E. Transcriptional Landscapes of Herelleviridae Bacteriophages and Staphylococcus aureus during Phage Infection: An Overview. Viruses 2023; 15:1427. [PMID: 37515114 PMCID: PMC10383478 DOI: 10.3390/v15071427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 06/16/2023] [Accepted: 06/22/2023] [Indexed: 07/30/2023] Open
Abstract
The issue of antibiotic resistance in healthcare worldwide has led to a pressing need to explore and develop alternative approaches to combat infectious diseases. Among these methods, phage therapy has emerged as a potential solution to tackle this growing challenge. Virulent phages of the Herelleviridae family, known for their ability to cause lysis of Staphylococcus aureus, a clinically significant pathogen frequently associated with multidrug resistance, have proven to be one of the most effective viruses utilized in phage therapy. In order to utilize phages for therapeutic purposes effectively, a thorough investigation into their physiology and mechanisms of action on infected cells is essential. The use of omics technologies, particularly total RNA sequencing, is a promising approach for analyzing the interaction between phages and their hosts, allowing for the assessment of both the behavior of the phage during infection and the cell's response. This review aims to provide a comprehensive overview of the physiology of the Herelleviridae family, utilizing existing analyses of their total phage transcriptomes. Additionally, it sheds light on the changes that occur in the metabolism of S. aureus when infected with virulent bacteriophages, contributing to a deeper understanding of the phage-host interaction.
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Affiliation(s)
- Maria Kornienko
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency Medicine, Moscow 119435, Russia
| | - Dmitry Bespiatykh
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency Medicine, Moscow 119435, Russia
| | - Roman Gorodnichev
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency Medicine, Moscow 119435, Russia
| | - Narina Abdraimova
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency Medicine, Moscow 119435, Russia
| | - Egor Shitikov
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency Medicine, Moscow 119435, Russia
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40
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Stojowska-Swędrzyńska K, Kuczyńska-Wiśnik D, Laskowska E. New Strategies to Kill Metabolically-Dormant Cells Directly Bypassing the Need for Active Cellular Processes. Antibiotics (Basel) 2023; 12:1044. [PMID: 37370363 DOI: 10.3390/antibiotics12061044] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2023] [Revised: 06/09/2023] [Accepted: 06/11/2023] [Indexed: 06/29/2023] Open
Abstract
Antibiotic therapy failure is often caused by the presence of persister cells, which are metabolically-dormant bacteria capable of surviving exposure to antimicrobials. Under favorable conditions, persisters can resume growth leading to recurrent infections. Moreover, several studies have indicated that persisters may promote the evolution of antimicrobial resistance and facilitate the selection of specific resistant mutants; therefore, in light of the increasing numbers of multidrug-resistant infections worldwide, developing efficient strategies against dormant cells is of paramount importance. In this review, we present and discuss the efficacy of various agents whose antimicrobial activity is independent of the metabolic status of the bacteria as they target cell envelope structures. Since the biofilm-environment is favorable for the formation of dormant subpopulations, anti-persister strategies should also include agents that destroy the biofilm matrix or inhibit biofilm development. This article reviews examples of selected cell wall hydrolases, polysaccharide depolymerases and antimicrobial peptides. Their combination with standard antibiotics seems to be the most promising approach in combating persistent infections.
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Affiliation(s)
- Karolina Stojowska-Swędrzyńska
- Department of General and Medical Biochemistry, Faculty of Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland
| | - Dorota Kuczyńska-Wiśnik
- Department of General and Medical Biochemistry, Faculty of Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland
| | - Ewa Laskowska
- Department of General and Medical Biochemistry, Faculty of Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland
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41
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Pereira AO, Barros NMA, Guerrero BR, Emencheta SC, Baldo DÂ, Oliveira JM, Vila MMDC, Balcão VM. An Edible Biopolymeric Microcapsular Wrapping Integrating Lytic Bacteriophage Particles for Salmonella enterica: Potential for Integration into Poultry Feed. Antibiotics (Basel) 2023; 12:988. [PMID: 37370307 DOI: 10.3390/antibiotics12060988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 05/28/2023] [Accepted: 05/29/2023] [Indexed: 06/29/2023] Open
Abstract
This research work aimed at developing an edible biopolymeric microcapsular wrapping (EBMW) integrating lytic bacteriophage particles for Salmonella enterica, with potential application in poultry feed for biocontrol of that pathogen. This pathogen is known as one of the main microorganisms responsible for contamination in the food industry and in foodstuff. The current techniques for decontamination and pathogen control in the food industry can be very expensive, not very selective, and even outdated, such as the use of broad-spectrum antibiotics that end up selecting resistant bacteria. Hence, there is a need for new technologies for pathogen biocontrol. In this context, bacteriophage-based biocontrol appears as a potential alternative. As a cocktail, both phages were able to significantly reduce the bacterial load after 12 h of treatment, at either multiplicity of infection (MOI) 1 and 10, by 84.3% and 87.6%, respectively. Entrapment of the phage virions within the EBMW matrix did not exert any deleterious effect upon their lytic activity. The results obtained showed high promise for integration in poultry feed aiming at controlling Salmonella enterica, since the edible biopolymeric microcapsular wrapping integrating lytic bacteriophage particles developed was successful in maintaining lytic phage viability while fully stabilizing the phage particles.
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Affiliation(s)
- Arthur O Pereira
- PhageLab-Laboratory of Biofilms and Bacteriophages, University of Sorocaba, Sorocaba 18023-000, SP, Brazil
| | - Nicole M A Barros
- PhageLab-Laboratory of Biofilms and Bacteriophages, University of Sorocaba, Sorocaba 18023-000, SP, Brazil
| | - Bruna R Guerrero
- PhageLab-Laboratory of Biofilms and Bacteriophages, University of Sorocaba, Sorocaba 18023-000, SP, Brazil
| | - Stephen C Emencheta
- PhageLab-Laboratory of Biofilms and Bacteriophages, University of Sorocaba, Sorocaba 18023-000, SP, Brazil
- Department of Pharmaceutical Microbiology and Biotechnology, University of Nigeria, Nsukka 410001, Enugu, Nigeria
| | - Denicezar  Baldo
- LaFiNAU-Laboratory of Applied Nuclear Physics, University of Sorocaba, Sorocaba 18023-000, SP, Brazil
| | - José M Oliveira
- LaFiNAU-Laboratory of Applied Nuclear Physics, University of Sorocaba, Sorocaba 18023-000, SP, Brazil
| | - Marta M D C Vila
- PhageLab-Laboratory of Biofilms and Bacteriophages, University of Sorocaba, Sorocaba 18023-000, SP, Brazil
| | - Victor M Balcão
- PhageLab-Laboratory of Biofilms and Bacteriophages, University of Sorocaba, Sorocaba 18023-000, SP, Brazil
- Department of Biology and CESAM, University of Aveiro, Campus Universitário de Santiago, P-3810-193 Aveiro, Portugal
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42
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Zaki BM, Mohamed AA, Dawoud A, Essam K, Hammouda ZK, Abdelsattar AS, El-Shibiny A. Isolation, screening and characterization of phage. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2023; 200:13-60. [PMID: 37739553 DOI: 10.1016/bs.pmbts.2023.03.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/24/2023]
Abstract
Bacterial resistance threatens public health due to a lack of novel antibacterial classes since the 21st century. Bacteriophages, the most ubiquitous microorganism on Earth and natural predators of bacteria, have the potential to save the world from the post-antibiotic era. Therefore, phage isolation and characterization are in high demand to find suitable phages for therapeutic and bacterial control applications. The chapter presents brief guidance supported by recommendations on the isolation of phages, and initial screening of phage antimicrobial efficacy, in addition to, conducting comprehensive characterization addressing morphological, biological, genomic, and taxonomic features.
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Affiliation(s)
- Bishoy Maher Zaki
- Center for Microbiology and Phage Therapy, Zewail City of Science and Technology, Giza, Egypt; Microbiology and Immunology Department, Faculty of Pharmacy, October University for Modern Sciences and Arts (MSA), Giza, Egypt
| | - Amira A Mohamed
- Center for Microbiology and Phage Therapy, Zewail City of Science and Technology, Giza, Egypt
| | - Alyaa Dawoud
- Center for Microbiology and Phage Therapy, Zewail City of Science and Technology, Giza, Egypt; Biochemistry Department, Faculty of Pharmacy and Biotechnology, German University in Cairo, Cairo, Egypt
| | - Kareem Essam
- Center for Microbiology and Phage Therapy, Zewail City of Science and Technology, Giza, Egypt
| | - Zainab K Hammouda
- Microbiology and Immunology Department, Faculty of Pharmacy, October University for Modern Sciences and Arts (MSA), Giza, Egypt
| | - Abdallah S Abdelsattar
- Center for Microbiology and Phage Therapy, Zewail City of Science and Technology, Giza, Egypt
| | - Ayman El-Shibiny
- Center for Microbiology and Phage Therapy, Zewail City of Science and Technology, Giza, Egypt; Faculty of Environmental Agricultural Sciences, Arish University, Arish, Egypt
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43
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Azari R, Yousefi MH, Taghipour Z, Wagemans J, Lavigne R, Hosseinzadeh S, Mazloomi SM, Vallino M, Khalatbari-Limaki S, Berizi E. Application of the lytic bacteriophage Rostam to control Salmonella enteritidis in eggs. Int J Food Microbiol 2023; 389:110097. [PMID: 36731200 DOI: 10.1016/j.ijfoodmicro.2023.110097] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 01/09/2023] [Accepted: 01/10/2023] [Indexed: 01/16/2023]
Abstract
Foodborne Salmonella enteritidis infections place human health at risk, driven by regular outbreaks and individual cases by different contaminated food materials. This study was conducted to characterize and employ a single bacteriophage as a potential biocontrol agent. Phage Rostam was isolated, characterized and then applied as biocontrol agent against S. enteritidis in liquid whole eggs and eggshell. Rostam is a novel myovirus belonging to the Rosemountvirus genus and active against Escherichia coli and Salmonella spp. Rostam is stable in a pH range from 4 to 10, a salt concentration of 1-9 %, whereas UV radiation gradually reduces phage stability, and its 53 kb genome sequence indicates this phage does not contain known toxins or lysogeny-associated genes. Its latent period is short with a burst size of 151 PFU/cell, under standard growth conditions. Killing curves indicate that at higher multiplicities of infection (MOI), the reduction in S. enteritidis count is more pronounced. Phage Rostam (MOI 10,000) reduces S. enteritidis growth to below the detection limit at 4 °C in both liquid whole eggs and on the eggshell within 24 h. Due to its high lytic activity and stability in relevant conditions, Rostam has the potential to be an efficient biopreservative for egg and egg products.
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Affiliation(s)
- Rahim Azari
- Department of Food Hygiene and Quality Control, School of Nutrition and Food Sciences, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mohammad Hashem Yousefi
- Department of Food Hygiene and Public Health, School of Veterinary Medicine, Shiraz University, Shiraz, Iran
| | - Zohreh Taghipour
- Department of Food Hygiene and Quality Control, School of Nutrition and Food Sciences, Shiraz University of Medical Sciences, Shiraz, Iran
| | | | - Rob Lavigne
- Department of Biosystems, KU Leuven, 3001 Leuven, Belgium
| | - Saeid Hosseinzadeh
- Department of Food Hygiene and Public Health, School of Veterinary Medicine, Shiraz University, Shiraz, Iran
| | - Seyed Mohammad Mazloomi
- Department of Food Hygiene and Quality Control, School of Nutrition and Food Sciences, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Marta Vallino
- Institute of Sustainable Plant Protection, National Research Council of Italy, 10135 Turin, Italy
| | - Sepideh Khalatbari-Limaki
- Department of Food Hygiene and Public Health, School of Veterinary Medicine, Shiraz University, Shiraz, Iran
| | - Enayat Berizi
- Department of Food Hygiene and Quality Control, School of Nutrition and Food Sciences, Shiraz University of Medical Sciences, Shiraz, Iran.
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44
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Development and Evaluation of Bacteriophage Cocktail to Eradicate Biofilms Formed by an Extensively Drug-Resistant (XDR) Pseudomonas aeruginosa. Viruses 2023; 15:v15020427. [PMID: 36851640 PMCID: PMC9965693 DOI: 10.3390/v15020427] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 01/22/2023] [Accepted: 01/31/2023] [Indexed: 02/05/2023] Open
Abstract
Extensive and multiple drug resistance in P. aeruginosa combined with the formation of biofilms is responsible for its high persistence in nosocomial infections. A sequential method to devise a suitable phage cocktail with a broad host range and high lytic efficiency against a biofilm forming XDR P. aeruginosa strain is presented here. Out of a total thirteen phages isolated against P. aeruginosa, five were selected on the basis of their high lytic spectra assessed using spot assay and productivity by efficiency of plating assay. Phages, after selection, were tested individually and in combinations of two-, three-, four-, and five-phage cocktails using liquid infection model. Out of total 22 combinations tested, the cocktail comprising four phages viz. φPA170, φPA172, φPA177, and φPA180 significantly inhibited the bacterial growth in liquid infection model (p < 0.0001). The minimal inhibitory dose of each phage in a cocktail was effectively reduced to >10 times than the individual dose in the inhibition of XDR P. aeruginosa host. Field emission-scanning electron microscopy was used to visualize phage cocktail mediated eradication of 4-day-old multi-layers of XDR P. aeruginosa biofilms from urinary catheters and glass cover slips, and was confirmed by absence of any viable cells. Differential bacterial inhibition was observed with different phage combinations where multiple phages were found to enhance the cocktail's lytic range, but the addition of too many phages reduced the overall inhibition. This study elaborates an effective and sequential method for the preparation of a phage cocktail and evaluates its antimicrobial potential against biofilm forming XDR strains of P. aeruginosa.
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45
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Ding Y, Nan Y, Qiu Y, Niu D, Stanford K, Holley R, McAllister T, Narváez‐Bravo C. Use of a phage cocktail to reduce the numbers of seven
Escherichia coli
strains belonging to different
STEC
serogroups applied to fresh produce and seeds. J Food Saf 2023. [DOI: 10.1111/jfs.13044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- Yiran Ding
- Food and Human Nutritional Sciences University of Manitoba Winnipeg Manitoba Canada
| | - Yuchen Nan
- Food and Human Nutritional Sciences University of Manitoba Winnipeg Manitoba Canada
| | - Yang Qiu
- Food and Human Nutritional Sciences University of Manitoba Winnipeg Manitoba Canada
| | - Dongyan Niu
- Ecosystem & Public Health University of Calgary Calgary Alberta Canada
| | - Kim Stanford
- Department of Biological Sciences University of Lethbridge Lethbridge Canada
| | - Rick Holley
- Food and Human Nutritional Sciences University of Manitoba Winnipeg Manitoba Canada
| | - Tim McAllister
- Food and Human Nutritional Sciences University of Manitoba Winnipeg Manitoba Canada
- Ecosystem & Public Health University of Calgary Calgary Alberta Canada
- Department of Biological Sciences University of Lethbridge Lethbridge Canada
- Agriculture and Agri‐Food Canada Lethbridge Research and Development Centre Lethbridge Alberta Canada
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46
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Gewtaisong J, Chukeatirote E, Ahn J. Characterization of Bacillus subtilis bacteriophage BasuTN3 isolated from Thua Nao, a thai fermented soybean food product. Food Sci Biotechnol 2023; 32:203-208. [PMID: 36647518 PMCID: PMC9839916 DOI: 10.1007/s10068-022-01188-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 09/22/2022] [Accepted: 10/11/2022] [Indexed: 01/19/2023] Open
Abstract
The infection of bacteriophage is of great concern in food industry as this can result in complete fermentation failure. In this study, a virulent bacteriophage, named BasuTN3, was isolated from Thua Nao, a Thai fermented soybean. The stability of BasuTN3 was evaluated under various ranges of temperature, pH, chloroform, UV, and disinfectants. The results showed that the isolated BasuTN3 appeared to be specific to its bacterial host, which was identified as Bacillus subtilis strain TN3 based on the 16 S rRNA gene sequence analysis. Under TEM, the BasuTN3 belonged to the family Myoviridae. The isolated BasuTN3 could withstand wide temperature ranges (4-45 °C) and pH conditions (5-11). The BasuTN3 was susceptible to chloroform, UV, and commonly used disinfectants. The results obtained expand the knowledge of the Bacillus bacteriophage diversity in the fermented soybean products and provide useful information for the bacteriophage and its bacterial starter cultures.
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Affiliation(s)
| | | | - Juhee Ahn
- Department of Biomedical Science, Institute of Bioscience and Biotechnology, Kangwon National University, Chuncheon, Gangwon 24341 Republic of Korea
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47
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Egido JE, Toner-Bartelds C, Costa AR, Brouns SJJ, Rooijakkers SHM, Bardoel BW, Haas PJ. Monitoring phage-induced lysis of gram-negatives in real time using a fluorescent DNA dye. Sci Rep 2023; 13:856. [PMID: 36646746 PMCID: PMC9842612 DOI: 10.1038/s41598-023-27734-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Accepted: 01/06/2023] [Indexed: 01/18/2023] Open
Abstract
Bacteriophages (phages) are viruses that specifically attack bacteria. Their use as therapeutics, which constitutes a promising alternative to antibiotics, heavily relies on selecting effective lytic phages against the pathogen of interest. Current selection techniques are laborious and do not allow for direct visualization of phage infection dynamics. Here, we present a method that circumvents these limitations. It can be scaled for high-throughput and permits monitoring of the phage infection in real time via a fluorescence signal readout. This is achieved through the use of a membrane-impermeant nucleic acid dye that stains the DNA of damaged or lysed bacteria and new phage progeny. We have tested the method on Pseudomonas aeruginosa and Klebsiella pneumoniae and show that an increase in fluorescence reflects phage-mediated killing. This is confirmed by other techniques including spot tests, colony plating, flow cytometry and metabolic activity measurements. Furthermore, we illustrate how our method may be used to compare the activity of different phages and to screen the susceptibility of clinical isolates to phage. Altogether, we present a fast, reliable way of selecting phages against Gram-negative bacteria, which may be valuable in optimizing the process of selecting phages for therapeutic use.
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Affiliation(s)
- Julia E Egido
- Medical Microbiology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Catherine Toner-Bartelds
- Medical Microbiology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Ana Rita Costa
- Department of Bionanoscience, Delft University of Technology, Delft, The Netherlands.,Kavli Institute of Nanoscience, Delft, The Netherlands.,Fagenbank, Delft, The Netherlands
| | - Stan J J Brouns
- Department of Bionanoscience, Delft University of Technology, Delft, The Netherlands.,Kavli Institute of Nanoscience, Delft, The Netherlands.,Fagenbank, Delft, The Netherlands
| | - Suzan H M Rooijakkers
- Medical Microbiology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Bart W Bardoel
- Medical Microbiology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Pieter-Jan Haas
- Medical Microbiology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands.
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48
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Leprince A, Mahillon J. Phage Adsorption to Gram-Positive Bacteria. Viruses 2023; 15:196. [PMID: 36680236 PMCID: PMC9863714 DOI: 10.3390/v15010196] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Revised: 01/03/2023] [Accepted: 01/06/2023] [Indexed: 01/12/2023] Open
Abstract
The phage life cycle is a multi-stage process initiated by the recognition and attachment of the virus to its bacterial host. This adsorption step depends on the specific interaction between bacterial structures acting as receptors and viral proteins called Receptor Binding Proteins (RBP). The adsorption process is essential as it is the first determinant of phage host range and a sine qua non condition for the subsequent conduct of the life cycle. In phages belonging to the Caudoviricetes class, the capsid is attached to a tail, which is the central player in the adsorption as it comprises the RBP and accessory proteins facilitating phage binding and cell wall penetration prior to genome injection. The nature of the viral proteins involved in host adhesion not only depends on the phage morphology (i.e., myovirus, siphovirus, or podovirus) but also the targeted host. Here, we give an overview of the adsorption process and compile the available information on the type of receptors that can be recognized and the viral proteins taking part in the process, with the primary focus on phages infecting Gram-positive bacteria.
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49
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Ávila M, Sánchez C, Calzada J, Mayer MJ, Berruga MI, López-Díaz TM, Narbad A, Garde S. Isolation and characterization of new bacteriophages active against Clostridium tyrobutyricum and their role in preventing the late blowing defect of cheese. Food Res Int 2023; 163:112222. [PMID: 36596151 DOI: 10.1016/j.foodres.2022.112222] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 11/17/2022] [Accepted: 11/20/2022] [Indexed: 11/25/2022]
Abstract
Lytic bacteriophages (phages) offer a great potential as biocontrol agents for spoilage Clostridium tyrobutyricum, responsible for butyric acid fermentation in semi-hard and hard ripened cheeses, resulting in late gas blowing defect. With this aim, we have isolated, identified and characterized new lytic phages of C. tyrobutyricum, and have evaluated their efficacy to control cheese late blowing by adding them to manufacture milk. Silage, soil, milk and cheese from dairy farms were screened for anti-clostridial phages, obtaining 96 isolates active against C. tyrobutyricum. According to host range, source and plaque morphology, we obtained 20 phage profiles, 8 of them (represented by phages FA3, FA21, FA29, FA52, FA58, FA67, FA70 and FA88) showing a wider host range and high quality lysis, which were further characterized. Selected isolates showed a non-contractile tail, belonging to the Siphoviridae family, and were grouped into 3 restriction profiles. Viable phages were detected after storage in sodium-magnesium buffer (SM buffer), skim milk and acidified skim milk (pH 5) for 7 d at 4 °C, 12 °C and 37 °C, although a decline in infectivity was observed in some cases. Good phage survival was also detected during semi-hard cheese manufacture and ripening (60 d), and cheese lactococci counts, pH, dry matter values, and volatile compounds were not affected by phage addition. In semi-hard cheese, phage FA67 impaired the early germination of C. tyrobutyricum spores and caused a significant decrease in clostridial vegetative cells counts at 14 d of ripening, delaying by 2 weeks the consumption of lactic acid, formation of butyric acid and appearance of late blowing symptoms, compared to the spoilt control cheese without the phage. This is the first report on the application of phage to control C. tyrobutyricum in cheese.
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Affiliation(s)
- 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.
| | - 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.
| | - 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.
| | - Melinda J Mayer
- Gut Microbes and Health Institute Strategic Programme, Quadram Institute Bioscience, Colney, Norwich NR4 7UA, UK.
| | - M Isabel Berruga
- Food Quality Research Group, Institute for Regional Development (IDR), Universidad de Castilla-La Mancha, 02071 Albacete, Spain.
| | - Teresa M López-Díaz
- Department of Food Hygiene and Food Technology, Veterinary Faculty, Universidad de León, Campus de Vegazana s/n, 24071, León, Spain.
| | - Arjan Narbad
- Gut Microbes and Health Institute Strategic Programme, Quadram Institute Bioscience, Colney, Norwich NR4 7UA, UK.
| | - 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.
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Zhong KX, Wirth JF, Chan AM, Suttle CA. Mortality by ribosomal sequencing (MoRS) provides a window into taxon-specific cell lysis. THE ISME JOURNAL 2023; 17:105-116. [PMID: 36209336 PMCID: PMC9751121 DOI: 10.1038/s41396-022-01327-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 09/15/2022] [Accepted: 09/20/2022] [Indexed: 11/05/2022]
Abstract
Microbes are by far the dominant biomass in the world's oceans and drive biogeochemical cycles that are critical to life on Earth. The composition of marine microbial communities is highly dynamic, spatially and temporally, with consequent effects on their functional roles. In part, these changes in composition result from viral lysis, which is taxon-specific and estimated to account for about half of marine microbial mortality. Here, we show that extracellular ribosomal RNA (rRNAext) is produced by viral lysis, and that specific lysed populations can be identified by sequencing rRNAext recovered from seawater samples. In ten seawater samples collected at five depths between the surface and 265 m during and following a phytoplankton bloom, lysis was detected in about 15% of 16,946 prokaryotic taxa, identified from amplicon sequence variants (ASVs), with lysis occurring in up to 34% of taxa within a water sample. The ratio of rRNAext to cellular rRNA (rRNAcell) was used as an index of taxon-specific lysis, and revealed that higher relative lysis was most commonly associated with copiotrophic bacteria that were in relatively low abundance, such as those in the genera Escherichia and Shigella spp., as well as members of the Bacteriodetes; whereas, relatively low lysis was more common in taxa that are often relatively abundant, such as members of the Pelagibacterales (i.e., SAR11 clade), cyanobacteria in the genus Synechococcus, and members of the phylum Thaumarchaeota (synonym, Nitrososphaerota) that comprised about 13-15% of the 16 S rRNA gene sequences below 30 m. These results provide an explanation for the long-standing conundrum of why highly productive bacteria that are readily isolated from seawater are often in very low abundance. The ability to estimate taxon-specific cell lysis will help explore the distribution and abundance of microbial populations in nature.
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Affiliation(s)
- Kevin Xu Zhong
- Department of Earth, Ocean, and Atmospheric Sciences, University of British Columbia, Vancouver, BC, Canada.
| | - Jennifer F Wirth
- Department of Earth, Ocean, and Atmospheric Sciences, University of British Columbia, Vancouver, BC, Canada
- Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, MT, USA
| | - Amy M Chan
- Department of Earth, Ocean, and Atmospheric Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Curtis A Suttle
- Department of Earth, Ocean, and Atmospheric Sciences, University of British Columbia, Vancouver, BC, Canada.
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada.
- Department of Botany, University of British Columbia, Vancouver, BC, Canada.
- Institute for the Oceans and Fisheries, University of British Columbia, Vancouver, BC, Canada.
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