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Reyneke B, Havenga B, Waso-Reyneke M, Khan S, Khan W. Benefits and Challenges of Applying Bacteriophage Biocontrol in the Consumer Water Cycle. Microorganisms 2024; 12:1163. [PMID: 38930545 PMCID: PMC11205630 DOI: 10.3390/microorganisms12061163] [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: 05/08/2024] [Revised: 05/31/2024] [Accepted: 06/05/2024] [Indexed: 06/28/2024] Open
Abstract
Bacteria (including disinfection- and antibiotic-resistant bacteria) are abundant in the consumer water cycle, where they may cause disease, and lead to biofouling and infrastructure damage in distributions systems, subsequently resulting in significant economic losses. Bacteriophages and their associated enzymes may then offer a biological control solution for application within the water sector. Lytic bacteriophages are of particular interest as biocontrol agents as their narrow host range can be exploited for the targeted removal of specific bacteria in a designated environment. Bacteriophages can also be used to improve processes such as wastewater treatment, while bacteriophage-derived enzymes can be applied to combat biofouling based on their effectiveness against preformed biofilms. However, the host range, environmental stability, bacteriophage resistance and biosafety risks are some of the factors that need to be considered prior to the large-scale application of these bacterial viruses. Characteristics of bacteriophages that highlight their potential as biocontrol agents are thus outlined in this review, as well as the potential application of bacteriophage biocontrol throughout the consumer water cycle. Additionally, the limitations of bacteriophage biocontrol and corresponding mitigation strategies are outlined, including the use of engineered bacteriophages for improved host ranges, environmental stability and the antimicrobial re-sensitisation of bacteria. Finally, the potential public and environmental risks associated with large-scale bacteriophage biocontrol application are considered, and alternative applications of bacteriophages to enhance the functioning of the consumer water cycle, including their use as water quality or treatment indicators and microbial source tracking markers, are discussed.
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Affiliation(s)
- Brandon Reyneke
- Department of Microbiology, Faculty of Science, Stellenbosch University, Private Bag X1, Stellenbosch 7602, South Africa
| | - Benjamin Havenga
- Department of Microbiology, Faculty of Science, Stellenbosch University, Private Bag X1, Stellenbosch 7602, South Africa
| | - Monique Waso-Reyneke
- Faculty of Health Sciences, University of Johannesburg, P.O. Box 17011, Doornfontein 2028, South Africa
| | - Sehaam Khan
- Faculty of Health Sciences, University of Johannesburg, P.O. Box 17011, Doornfontein 2028, South Africa
| | - Wesaal Khan
- Department of Microbiology, Faculty of Science, Stellenbosch University, Private Bag X1, Stellenbosch 7602, South Africa
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Ipoutcha T, Racharaks R, Huttelmaier S, Wilson CJ, Ozer EA, Hartmann EM. A synthetic biology approach to assemble and reboot clinically relevant Pseudomonas aeruginosa tailed phages. Microbiol Spectr 2024; 12:e0289723. [PMID: 38294230 PMCID: PMC10913387 DOI: 10.1128/spectrum.02897-23] [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: 08/04/2023] [Accepted: 12/17/2023] [Indexed: 02/01/2024] Open
Abstract
The rise in the frequency of antibiotic resistance has made bacterial infections, specifically Pseudomonas aeruginosa, a cause for greater concern. Phage therapy is a promising solution that uses naturally isolated phages to treat bacterial infections. Ecological limitations, which stipulate a discrete host range and the inevitable evolution of resistance, may be overcome through a better understanding of phage biology and the utilization of engineered phages. In this study, we developed a synthetic biology approach to construct tailed phages that naturally target clinically relevant strains of Pseudomonas aeruginosa. As proof of concept, we successfully cloned and assembled the JG024 and DMS3 phage genomes in yeast using transformation-associated recombination cloning and rebooted these two phage genomes in two different strains of P. aeruginosa. We identified factors that affected phage reboot efficiency like the phage species or the presence of antiviral defense systems in the bacterial strain. We have successfully extended this method to two other phage species and observed that the method enables the reboot of phages that are naturally unable to infect the strain used for reboot. This research represents a critical step toward the construction of clinically relevant, engineered P. aeruginosa phages.IMPORTANCEPseudomonas aeruginosa is a bacterium responsible for severe infections and a common major complication in cystic fibrosis. The use of antibiotics to treat bacterial infections has become increasingly difficult as antibiotic resistance has become more prevalent. Phage therapy is an alternative solution that is already being used in some European countries, but its use is limited by the narrow host range due to the phage receptor specificity, the presence of antiviral defense systems in the bacterial strain, and the possible emergence of phage resistance. In this study, we demonstrate the use of a synthetic biology approach to construct and reboot clinically relevant P. aeruginosa tailed phages. This method enables a significant expansion of possibilities through the construction of engineered phages for therapy applications.
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Affiliation(s)
- Thomas Ipoutcha
- Department of Civil and Environmental Engineering, Northwestern University, Evanston, Illinois, USA
| | - Ratanachat Racharaks
- Department of Civil and Environmental Engineering, Northwestern University, Evanston, Illinois, USA
| | - Stefanie Huttelmaier
- Department of Civil and Environmental Engineering, Northwestern University, Evanston, Illinois, USA
| | - Cole J. Wilson
- Department of Civil and Environmental Engineering, Northwestern University, Evanston, Illinois, USA
| | - Egon A. Ozer
- Division of Infectious Diseases, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
| | - Erica M. Hartmann
- Department of Civil and Environmental Engineering, Northwestern University, Evanston, Illinois, USA
- Center for Synthetic Biology, Northwestern University, Evanston, Illinois, USA
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Bae HW, Choi SY, Cho YH. An outer membrane determinant for RNA phage genome entry in Pseudomonas aeruginosa. iScience 2024; 27:108675. [PMID: 38213628 PMCID: PMC10783630 DOI: 10.1016/j.isci.2023.108675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 11/06/2023] [Accepted: 12/05/2023] [Indexed: 01/13/2024] Open
Abstract
Host range of a phage is determined at the various life cycle stages during phage infection. We reported the limited phage-receptor interaction between the RNA phage, PP7 and its host Pseudomonas aeruginosa strains: PAO1 has susceptible type IV pilus (TFP) pilin, whereas PA14 has resistant pilin. Here, we have created a PA14 derivative (PA14P) with the PAO1 pilin gene and found that other determinants than TFP pilin could limit PP7 infectivity in PA14P. Transposon mutant screens revealed that PP7 infectivity was restored in the PA14P mutants (htrB2) lacking a secondary acyltransferase in lipid A biosynthesis. The lack of this enzyme increased the RNA phage entry, which is deemed attributed to the loosened lipopolysaccharide (LPS) structure. Polymyxin B treatment also selectively increased the RNA phage entry. These results demonstrated that LPS structures could limit the entry stage of RNA phages, providing another determinant for the host range in diverse P. aeruginosa strains.
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Affiliation(s)
- Hee-Won Bae
- Department of Pharmacy, College of Pharmacy and Institute of Pharmaceutical Sciences, CHA University, Gyeonggi-do 13488, Korea
| | - Shin-Yae Choi
- Department of Pharmacy, College of Pharmacy and Institute of Pharmaceutical Sciences, CHA University, Gyeonggi-do 13488, Korea
| | - You-Hee Cho
- Department of Pharmacy, College of Pharmacy and Institute of Pharmaceutical Sciences, CHA University, Gyeonggi-do 13488, Korea
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Aljabali AAA, Aljbaly MBM, Obeid MA, Shahcheraghi SH, Tambuwala MM. The Next Generation of Drug Delivery: Harnessing the Power of Bacteriophages. Methods Mol Biol 2024; 2738:279-315. [PMID: 37966606 DOI: 10.1007/978-1-0716-3549-0_18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2023]
Abstract
The use of biomaterials, such as bacteriophages, as drug delivery vehicles (DDVs) has gained increasing interest in recent years due to their potential to address the limitations of conventional drug delivery systems. Bacteriophages offer several advantages as drug carriers, such as high specificity for targeting bacterial cells, low toxicity, and the ability to be engineered to express specific proteins or peptides for enhanced targeting and drug delivery. In addition, bacteriophages have been shown to reduce the development of antibiotic resistance, which is a major concern in the field of antimicrobial therapy. Many initiatives have been taken to take up various payloads selectively and precisely by surface functionalization of the outside or interior of self-assembling viral protein capsids. Bacteriophages have emerged as a promising platform for the targeted delivery of therapeutic agents, including drugs, genes, and imaging agents. They possess several properties that make them attractive as drug delivery vehicles, including their ability to specifically target bacterial cells, their structural diversity, their ease of genetic manipulation, and their biocompatibility. Despite the potential advantages of using bacteriophages as drug carriers, several challenges and limitations need to be addressed. One of the main challenges is the limited host range of bacteriophages, which restricts their use to specific bacterial strains. However, this can also be considered as an advantage, as it allows for precise and targeted drug delivery to the desired bacterial cells. The use of biomaterials, including bacteriophages, as drug delivery vehicles has shown promising potential to address the limitations of conventional drug delivery systems. Further research is needed to fully understand the potential of these biomaterials and address the challenges and limitations associated with their use.
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Affiliation(s)
- Alaa A A Aljabali
- Department of Pharmaceutics and Pharmaceutical Technology, Faculty of Pharmacy, Yarmouk University, Irbid, Jordan.
| | | | - Mohammad A Obeid
- Department of Pharmaceutics and Pharmaceutical Technology, Faculty of Pharmacy, Yarmouk University, Irbid, Jordan
| | - Seyed Hossein Shahcheraghi
- Department of Medical Genetics, School of Medicine, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | - Murtaza M Tambuwala
- Lincoln Medical School, Brayford Pool Campus, University of Lincoln, Lincoln, UK.
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Mondal P, Halder P, Mallick B, Bhaumik S, Koley H, Dutta S, Dutta M. Controlling the bacterial load of Salmonella Typhi in an experimental mouse model by a lytic Salmonella phage STWB21: a phage therapy approach. BMC Microbiol 2023; 23:324. [PMID: 37924001 PMCID: PMC10623789 DOI: 10.1186/s12866-023-03040-3] [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: 07/21/2023] [Accepted: 10/03/2023] [Indexed: 11/06/2023] Open
Abstract
BACKGROUND Salmonella enterica serotype Typhi is one of the major pathogens causing typhoid fever and a public health burden worldwide. Recently, the increasing number of multidrug-resistant strains of Salmonella spp. has made this utmost necessary to consider bacteriophages as a potential alternative to antibiotics for S. Typhi infection treatment. Salmonella phage STWB21, isolated from environmental water, has earlier been reported to be effective as a safe biocontrol agent by our group. In this study, we evaluated the efficacy of phage STWB21 in reducing the burden of salmonellosis in a mammalian host by inhibiting Salmonella Typhi invasion into the liver and spleen tissue. RESULTS Phage treatment significantly improved the survival percentage of infected mice. This study also demonstrated that oral administration of phage treatment could be beneficial in both preventive and therapeutic treatment of salmonellosis caused by S. Typhi. Altogether the result showed that the phage treatment could control tissue inflammation in mice before and after Salmonella infection. CONCLUSIONS To the best of our knowledge, this is the first report of phage therapy in a mouse model against a clinically isolated Salmonella Typhi strain that includes direct visualization of histopathology and ultrathin section microscopy images from the liver and spleen sections.
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Affiliation(s)
- Payel Mondal
- Division of Electron Microscopy, ICMR-National Institute of Cholera & Enteric Diseases, P-33, C.I.T. Road, Scheme XM, Beliaghata, 700010, Kolkata, West Bengal, India
| | - Prolay Halder
- Division of Bacteriology, ICMR-National Institute of Cholera & Enteric Diseases, P-33, C.I.T. Road, Scheme XM, Beliaghata, 700010, Kolkata, West Bengal, India
| | - Bani Mallick
- Division of Electron Microscopy, ICMR-National Institute of Cholera & Enteric Diseases, P-33, C.I.T. Road, Scheme XM, Beliaghata, 700010, Kolkata, West Bengal, India
| | - Subhadip Bhaumik
- University Science Instrumentation Centre, The University of Burdwan, Golapbag, Burdwan, 713104, West Bengal, India
| | - Hemanta Koley
- Division of Bacteriology, ICMR-National Institute of Cholera & Enteric Diseases, P-33, C.I.T. Road, Scheme XM, Beliaghata, 700010, Kolkata, West Bengal, India
| | - Shanta Dutta
- Division of Bacteriology, ICMR-National Institute of Cholera & Enteric Diseases, P-33, C.I.T. Road, Scheme XM, Beliaghata, 700010, Kolkata, West Bengal, India
| | - Moumita Dutta
- Division of Electron Microscopy, ICMR-National Institute of Cholera & Enteric Diseases, P-33, C.I.T. Road, Scheme XM, Beliaghata, 700010, Kolkata, West Bengal, India.
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Dlamini SB, Gigante AM, Hooton SPT, Atterbury RJ. Efficacy of Different Encapsulation Techniques on the Viability and Stability of Diverse Phage under Simulated Gastric Conditions. Microorganisms 2023; 11:2389. [PMID: 37894046 PMCID: PMC10608910 DOI: 10.3390/microorganisms11102389] [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: 08/16/2023] [Revised: 09/11/2023] [Accepted: 09/15/2023] [Indexed: 10/29/2023] Open
Abstract
Salmonella causes a range of diseases in humans and livestock of considerable public health and economic importance. Widespread antimicrobial use, particularly in intensively produced livestock (e.g., poultry and pigs) may contribute to the rise of multidrug-resistant Salmonella strains. Alternative treatments such as bacteriophages have shown promise when used to reduce the intestinal carriage of Salmonella in livestock. However, the digestive enzymes and low pH encountered in the monogastric GI tract can significantly reduce phage viability and impact therapeutic outcomes. This study deployed alginate-carrageenan microcapsules with and without CaCO3 to protect a genomically diverse set of five Salmonella bacteriophages from simulated gastrointestinal conditions. None of the unprotected phage could be recovered following exposure to pH < 3 for 10 min. Alginate-carrageenan encapsulation improved phage viability at pH 2-2.5 after exposure for 10 min, but not at pH 2 after 1 h. Including 1% (w/v) CaCO3 in the formulation further reduced phage loss to <0.5 log10 PFU/mL, even after 1 h at pH 2. In all cases, phage were efficiently released from the microcapsules following a shift to a neutral pH (7.5), simulating passage to the duodenum. In summary, alginate-carrageenan-CaCO3 encapsulation is a promising approach for targeted intestinal delivery of genomically diverse Salmonella bacteriophages.
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Affiliation(s)
- Sicelo B Dlamini
- School of Agricultural Sciences, Faculty of Agriculture and Natural Sciences, University of Mpumalanga, Nelspruit 1200, South Africa
| | - Adriano M Gigante
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington, Leicestershire LE12 5RD, UK
| | - Steven P T Hooton
- Department of Genetics and Genome Biology, University of Leicester, University Road, Leicester LE1 7RH, UK
| | - Robert J Atterbury
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington, Leicestershire LE12 5RD, UK
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Son B, Kim Y, Yu B, Kong M. Isolation and Characterization of a Weizmannia coagulans Bacteriophage Youna2 and Its Endolysin PlyYouna2. J Microbiol Biotechnol 2023; 33:1050-1056. [PMID: 37218442 PMCID: PMC10468668 DOI: 10.4014/jmb.2303.03021] [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: 04/18/2023] [Accepted: 04/27/2023] [Indexed: 05/24/2023]
Abstract
Weizmannia coagulans (formerly Bacillus coagulans) is Gram-positive, and spore-forming bacteria causing food spoilage, especially in acidic canned food products. To control W. coagulans, we isolated a bacteriophage Youna2 from a sewage sludge sample. Morphological analysis revealed that phage Youna2 belongs to the Siphoviridae family with a non-contractile and flexible tail. Youna2 has 52,903 bp double-stranded DNA containing 61 open reading frames. There are no lysogeny-related genes, suggesting that Youna2 is a virulent phage. plyYouna2, a putative endolysin gene was identified in the genome of Youna2 and predicted to be composed of a N-acetylmuramoyl-L-alanine amidase domain (PF01520) at the N-terminus and unknown function DUF5776 domain (PF19087) at the C-terminus. While phage Youna2 has a narrow host range, infecting only certain strains of W. coagulans, PlyYouna2 exhibited a broad antimicrobial spectrum beyond the Bacillus genus. Interestingly, PlyYouna2 can lyse Gram-negative bacteria such as Escherichia coli, Yersinia enterocolitica, Pseudomonas putida and Cronobacter sakazakii without other additives to destabilize bacterial outer membrane. To the best of our knowledge, Youna2 is the first W. coagulans-infecting phage and we speculate its endolysin PlyYouna2 can provide the basis for the development of a novel biocontrol agent against various foodborne pathogens.
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Affiliation(s)
- Bokyung Son
- Department of Food Biotechnology, Dong-A University, Busan 49315, Republic of Korea
| | - Youna Kim
- Department of Food Science and Technology, Seoul National University of Science and Technology, Seoul 01811, Republic of Korea
| | - Booyoung Yu
- Department of Food Science and Technology, Seoul National University of Science and Technology, Seoul 01811, Republic of Korea
| | - Minsuk Kong
- Department of Food Science and Technology, Seoul National University of Science and Technology, Seoul 01811, Republic of Korea
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Osman AH, Kotey FCN, Odoom A, Darkwah S, Yeboah RK, Dayie NTKD, Donkor ES. The Potential of Bacteriophage-Antibiotic Combination Therapy in Treating Infections with Multidrug-Resistant Bacteria. Antibiotics (Basel) 2023; 12:1329. [PMID: 37627749 PMCID: PMC10451467 DOI: 10.3390/antibiotics12081329] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 08/04/2023] [Accepted: 08/05/2023] [Indexed: 08/27/2023] Open
Abstract
The growing threat of antibiotic resistance is a significant global health challenge that has intensified in recent years. The burden of antibiotic resistance on public health is augmented due to its multifaceted nature, as well as the slow-paced and limited development of new antibiotics. The threat posed by resistance is now existential in phage therapy, which had long been touted as a promising replacement for antibiotics. Consequently, it is imperative to explore the potential of combination therapies involving antibiotics and phages as a feasible alternative for treating infections with multidrug-resistant bacteria. Although either bacteriophage or antibiotics can potentially treat bacterial infections, they are each fraught with resistance. Combination therapies, however, yielded positive outcomes in most cases; nonetheless, a few combinations did not show any benefit. Combination therapies comprising the synergistic activity of phages and antibiotics and combinations of phages with other treatments such as probiotics hold promise in the treatment of drug-resistant bacterial infections.
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Affiliation(s)
| | | | | | | | | | | | - Eric S. Donkor
- Department of Medical Microbiology, University of Ghana Medical School, Korle Bu, Accra P.O. Box KB 4236, Ghana; (A.-H.O.); (F.C.N.K.); (A.O.); (S.D.); (R.K.Y.); (N.T.K.D.D.)
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Nayak T, Kakkar A, Singh RK, Jaiswal LK, Singh AK, Temple L, Gupta A. Isolation and characterization of a novel mycobacteriophage Kashi-VT1 infecting Mycobacterium species. Front Cell Infect Microbiol 2023; 13:1173894. [PMID: 37545854 PMCID: PMC10400892 DOI: 10.3389/fcimb.2023.1173894] [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: 02/28/2023] [Accepted: 06/19/2023] [Indexed: 08/08/2023] Open
Abstract
Mycobacteriophages are viruses that infect members of genus Mycobacterium. Because of the rise in antibiotic resistance in mycobacterial diseases such as tuberculosis, mycobacteriophages have received renewed attention as alternative therapeutic agents. Mycobacteriophages are highly diverse, and, on the basis of their genome sequences, they are grouped into 30 clusters and 10 singletons. In this article, we have described the isolation and characterization of a novel mycobacteriophage Kashi-VT1 (KVT1) infecting Mycobacterium >smegmatis mc2 155 (M. smegmatis) and Mycobacterium fortuitum isolated from Varanasi, India. KVT1 is a cluster K1 temperate phage that belongs to Siphoviridae family as visualized in transmission electron microscopy. The phage genome is 61,010 base pairs with 66.5% Guanine/Cytosine (GC) content, encoding 101 putative open reading frames. The KVT1 genome encodes an immunity repressor, a tyrosine integrase, and an excise protein, which are the characteristics of temperate phages. It also contains genes encoding holin, lysin A, and lysin B involved in host cell lysis. The one-step growth curve demonstrated that KVT1 has a latency time of 90 min and an average burst size of 101 phage particles per infected cell. It can withstand a temperature of up to 45°C and has a maximum viability between pH 8 and 9. Some mycobacteriophages from cluster K are known to infect the pathogenic Mycobacterium tuberculosis (M. tuberculosis); hence, KVT1 holds potential for the phage therapy against tuberculosis, and it can also be engineered to convert into an exclusively lytic phage.
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Affiliation(s)
- Tanmayee Nayak
- Molecular Microbiology Laboratory, Department of Biochemistry, Institute of Science, Banaras Hindu University, Varanasi, India
| | - Anuja Kakkar
- Molecular Microbiology Laboratory, Department of Biochemistry, Institute of Science, Banaras Hindu University, Varanasi, India
| | - Rakesh Kumar Singh
- Molecular Microbiology Laboratory, Department of Biochemistry, Institute of Science, Banaras Hindu University, Varanasi, India
| | - Lav Kumar Jaiswal
- Molecular Microbiology Laboratory, Department of Biochemistry, Institute of Science, Banaras Hindu University, Varanasi, India
| | - Anand Kumar Singh
- Interdisciplinary School of Life Sciences, Institute of Science, Banaras Hindu University, Varanasi, India
| | - Louise Temple
- School of Integrated Sciences, James Madison University, Harrisonburg, VA, United States
| | - Ankush Gupta
- Molecular Microbiology Laboratory, Department of Biochemistry, Institute of Science, Banaras Hindu University, Varanasi, India
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Kumar M, Parkhey P, Mishra SK, Paul PK, Singh A, Singh V. Phage for drug delivery vehicles. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2023; 201:191-201. [PMID: 37770171 DOI: 10.1016/bs.pmbts.2023.04.008] [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: 10/03/2023]
Abstract
Viruses being the natural carriers of gene have been widely used as drug delivery systems. However, the commonly used eukaryotic viruses such as adenoviruses, retroviruses, and lentiviruses, besides efficiently targeting the cells, can also stimulate immunological response or disrupt tumour suppressor genes leading to cancer. Consequently, there has been an increase interest in the scientific fraternity towards exploring other alternatives, which are safer and equally efficient for drug delivery. Bacteriophages, in this context have been at the forefront as an efficient, reliable, and safer choice. Novel phage dependent technologies led the foundation of peptide libraries and provides way to recognising abilities and targeting of specific ligands. Hybridisation of phage with inorganic complexes could be an appropriate strategy for the construction of carrying bioinorganic carriers. In this chapter, we have tried to cover major advances in the phage species that can be used as drug delivery vehicles.
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Affiliation(s)
- Mohit Kumar
- Department of Biotechnology, National Institute of Technology, Raipur, Chhattisgarh, India
| | - Piyush Parkhey
- Techno-Commercial Division, Trinity International, New Delhi, India
| | - Santosh Kumar Mishra
- Department of Life Sciences, School of Basic Sciences and Research, Sharda University, Greater Noida, Uttar Pradesh, India.
| | - Prabir Kumar Paul
- Department of Biotechnology Manav Rachna International Institute of Research and Studies, Faridabad, Haryana, India
| | - Avinash Singh
- Department of Biotechnology, Meerut Institute of Engineering & Technology, Meerut, U.P., India
| | - Vijai Singh
- Department of Biosciences, School of Science, Indrashil University, Rajpur, Mehsana, Gujarat, India
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Marshall K, Marsella R. Topical Bacteriophage Therapy for Staphylococcal Superficial Pyoderma in Horses: A Double-Blind, Placebo-Controlled Pilot Study. Pathogens 2023; 12:828. [PMID: 37375518 DOI: 10.3390/pathogens12060828] [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: 05/22/2023] [Revised: 06/07/2023] [Accepted: 06/09/2023] [Indexed: 06/29/2023] Open
Abstract
Increased antimicrobial resistance highlights the need for alternatives to antibiotics. Bacteriophages, which are benign viruses that kill bacteria, are promising. We studied the efficacy of topical bacteriophages for treating equine staphylococcal superficial pyodermas. Eight Staphylococcus aureus isolates were tested against a bacteriophage bank, and a cocktail consisting of two bacteriophages was prepared. Twenty horses with clinical and cytological evidence of superficial pyoderma and confirmed S. aureus infection based on swabbed culture were enrolled in the study. Each horse received both the bacteriophage cocktail and the placebo at two different infection sites, once daily for four weeks. Clinical lesions and cytology were evaluated weekly by an investigator who was unaware of the treatment sites. All infection sites were swabbed and cultured at the end of the study. A linear mixed model showed no significant differences between the placebo and treatment sites in terms of clinical signs, cytological scores of inflammation, and bacterial counts at the end of the study. It is possible that the bacteriophage cocktail killed S. aureus, but cytology scores did not change as new populations of cocci took over. The study limitations included a small sample size and inconsistent control of the underlying causes of pyodermas.
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Affiliation(s)
- Kalie Marshall
- Department of Small Animal Clinical Sciences, College of Veterinary Medicine, University of Florida, 2015 SW 16th Avenue, Gainesville, FL 32610, USA
| | - Rosanna Marsella
- Department of Small Animal Clinical Sciences, College of Veterinary Medicine, University of Florida, 2015 SW 16th Avenue, Gainesville, FL 32610, USA
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12
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Jia PP, Yang YF, Junaid M, Jia HJ, Li WG, Pei DS. Bacteriophage-based techniques for elucidating the function of zebrafish gut microbiota. Appl Microbiol Biotechnol 2023; 107:2039-2059. [PMID: 36847856 DOI: 10.1007/s00253-023-12439-x] [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: 12/03/2022] [Revised: 02/06/2023] [Accepted: 02/08/2023] [Indexed: 03/01/2023]
Abstract
Bacteriophages (or phages) are unique viruses that can specifically infect bacteria. Since their discovery by Twort and d'Herelle, phages with bacterial specificity have played important roles in microbial regulation. The intestinal microbiota and host health are intimately linked with nutrient, metabolism, development, and immunity aspects. However, the mechanism of interactions between the composition of the microbiota and their functions in maintaining host health still needs to be further explored. To address the lack of methodology and functions of intestinal microbiota in the host, we first proposed that, with the regulations of special intestinal microbiota and applications of germ-free (GF) zebrafish model, phages would be used to infect and reduce/eliminate the defined gut bacteria in the conventionally raised (CR) zebrafish and compared with the GF zebrafish colonized with defined bacterial strains. Thus, this review highlighted the background and roles of phages and their functional characteristics, and we also summarized the phage-specific infection of target microorganisms, methods to improve the phage specificity, and their regulation within the zebrafish model and gut microbial functional study. Moreover, the primary protocol of phage therapy to control the intestinal microbiota in zebrafish models from larvae to adults was recommended including phage screening from natural sources, identification of host ranges, and experimental design in the animal. A well understanding of the interaction and mechanism between phages and gut bacteria in the host can potentially provide powerful strategies or techniques for preventing bacteria-related human diseases by precisely regulating in vitro and in vivo, which will provide novel insights for phages' application and combined research in the future. KEY POINTS: • Zebrafish models for clarifying the microbial and phages' functions were discussed • Phages infect host bacteria with exquisite specificity and efficacy • Phages can reduce/eliminate the defined gut bacteria to clarify their function.
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Affiliation(s)
- Pan-Pan Jia
- School of Public Health, Chongqing Medical University, Chongqing, 400016, China
| | - Yi-Fan Yang
- School of Public Health, Chongqing Medical University, Chongqing, 400016, China
- College of Life Science, Henan Normal University, Xinxiang, 453007, China
| | - Muhammad Junaid
- Joint Laboratory of Guangdong Province and Hong Kong Region On Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou, China
| | - Huang-Jie Jia
- School of Public Health, Chongqing Medical University, Chongqing, 400016, China
| | - Wei-Guo Li
- College of Life Science, Henan Normal University, Xinxiang, 453007, China
| | - De-Sheng Pei
- School of Public Health, Chongqing Medical University, Chongqing, 400016, China.
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13
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Mehmood Khan F, Manohar P, Singh Gondil V, Mehra N, Kayode Oyejobi G, Odiwuor N, Ahmad T, Huang G. The applications of animal models in phage therapy: An update. Hum Vaccin Immunother 2023; 19:2175519. [PMID: 36935353 PMCID: PMC10072079 DOI: 10.1080/21645515.2023.2175519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/21/2023] Open
Abstract
The rapid increase in antibiotic resistance presents a dire situation necessitating the need for alternative therapeutic agents. Among the current alternative therapies, phage therapy (PT) is promising. This review extensively summarizes preclinical PT approaches in various in-vivo models. PT has been evaluated in several recent clinical trials. However, there are still several unanswered concerns due to a lack of appropriate regulation and pharmacokinetic data regarding the application of phages in human therapeutic procedures. In this review, we also presented the current state of PT and considered how animal models can be used to adapt these therapies for humans. The development of realistic solutions to circumvent these constraints is critical for advancing this technology.
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Affiliation(s)
- Fazal Mehmood Khan
- College of Civil and Transportation Engineering, Shenzhen University, Shenzhen, China.,Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, China.,Institute for Innovative Development of Food Industry, Shenzhen University, Shenzhen, China.,Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Prasanth Manohar
- School of Biosciences and Technology, Vellore Institute of Technology, Vellore, India
| | - Vijay Singh Gondil
- Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei, China.,Department of Microbiology and Immunology, University of Rochester School of Medicine and Dentistry, Rochester, New York, USA
| | - Nancy Mehra
- Department of Pediatrics, Advanced Pediatrics Centre, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Greater Kayode Oyejobi
- Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei, China.,Department of Microbiology, Osun State University, Osogbo, Nigeria.,School of Pharmaceutical Sciences, Wuhan University, Wuhan, Hubei, China
| | - Nelson Odiwuor
- Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei, China.,International College, University of Chinese Academy of Sciences, Beijing, China.,Microbiology, Sino-Africa Joint Research Centre, Nairobi, Kenya
| | - Tauseef Ahmad
- Department of Epidemiology and Health Statistics, School of Public Health, Southeast University, Nanjing, China
| | - Guangtao Huang
- Department of Burn and Plastic Surgery, Shenzhen Institute of Translational Medicine, The First Affiliated Hospital of Shenzhen University, Shenzhen, China.,Department of Burns and Plastic Surgery, Affiliated Hospital of Zunyi Medical University, Zunyi, China.,Department of Plastic and Reconstructive Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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14
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Durr HA, Leipzig ND. Advancements in bacteriophage therapies and delivery for bacterial infection. MATERIALS ADVANCES 2023; 4:1249-1257. [PMID: 36895585 PMCID: PMC9987412 DOI: 10.1039/d2ma00980c] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 01/25/2023] [Indexed: 06/02/2023]
Abstract
Having co-evolved with bacteria over hundreds of millions of years, bacteriophage are effective killers of specific bacterial hosts. Therefore, phage therapies for infection are a promising treatment avenue, can provide a solution for antibiotic resistant bacterial infections, and have specified targeting of infectious bacteria while allowing the natural microbiome to survive which systemic antibiotics often wipe out. Many phages have well studied genomes that can be modified to change target, widen target range, or change mode of action of killing bacterial hosts. Phage delivery can also be designed to increase efficacy of treatment, including encapsulation and delivery via biopolymers. Increased research into phage potential for therapies can allow new avenues to develop to treat a larger range of infections.
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Affiliation(s)
- Hannah A Durr
- Department of Integrated Biosciences, University of Akron Ohio 44325 USA
| | - Nic D Leipzig
- Department of Chemical, Biomolecular, and Corrosion Engineering, University of Akron Ohio 44325 USA
- Department of Integrated Biosciences, University of Akron Ohio 44325 USA
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15
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Sun Q, Shen L, Zhang BL, Yu J, Wei F, Sun Y, Chen W, Wang S. Advance on Engineering of Bacteriophages by Synthetic Biology. Infect Drug Resist 2023; 16:1941-1953. [PMID: 37025193 PMCID: PMC10072152 DOI: 10.2147/idr.s402962] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 03/16/2023] [Indexed: 04/03/2023] Open
Abstract
Since bacteriophages (phages) were firstly reported at the beginning of the 20th century, the study on them experiences booming-fading-emerging with discovery and overuse of antibiotics. Although they are the hotspots for therapy of antibiotic-resistant strains nowadays, natural phage applications encounter some challenges such as limited host range and bacterial resistance to phages. Synthetic biology, one of the most dramatic directions in the recent 20-years study of microbiology, has generated numerous methods and tools and has contributed a lot to understanding phage evolution, engineering modification, and controlling phage-bacteria interactions. In order to better modify and apply phages by using synthetic biology techniques in the future, in this review, we comprehensively introduce various strategies on engineering or modification of phage genome and rebooting of recombinant phages, summarize the recent researches and potential directions of phage synthetic biology, and outline the current application of engineered phages in practice.
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Affiliation(s)
- Qingqing Sun
- Key Laboratory of Resources Biology and Biotechnology in Western China, Ministry of Education, Provincial Key Laboratory of Biotechnology of Shaanxi Province, the College of Life Sciences, Northwest University, Xi’an, 710069, People’s Republic of China
| | - Lixin Shen
- Key Laboratory of Resources Biology and Biotechnology in Western China, Ministry of Education, Provincial Key Laboratory of Biotechnology of Shaanxi Province, the College of Life Sciences, Northwest University, Xi’an, 710069, People’s Republic of China
| | - Bai-Ling Zhang
- Department of Laboratory Medicine, The Second Affiliated Hospital of Nanchang University, Nanchang, 330006, People’s Republic of China
| | - Jiaoyang Yu
- Key Laboratory of Resources Biology and Biotechnology in Western China, Ministry of Education, Provincial Key Laboratory of Biotechnology of Shaanxi Province, the College of Life Sciences, Northwest University, Xi’an, 710069, People’s Republic of China
- Clinical Research Center, the Second Hospital of Nanjing, Nanjing University of Chinese Medicine, Nanjing, 210003, People’s Republic of China
| | - Fu Wei
- Key Laboratory of Resources Biology and Biotechnology in Western China, Ministry of Education, Provincial Key Laboratory of Biotechnology of Shaanxi Province, the College of Life Sciences, Northwest University, Xi’an, 710069, People’s Republic of China
| | - Yanmei Sun
- Key Laboratory of Resources Biology and Biotechnology in Western China, Ministry of Education, Provincial Key Laboratory of Biotechnology of Shaanxi Province, the College of Life Sciences, Northwest University, Xi’an, 710069, People’s Republic of China
| | - Wei Chen
- Clinical Research Center, the Second Hospital of Nanjing, Nanjing University of Chinese Medicine, Nanjing, 210003, People’s Republic of China
- The Clinical Infectious Disease Center of Nanjing, Nanjing, 210003, People’s Republic of China
- Correspondence: Wei Chen; Shiwei Wang, Email ;
| | - Shiwei Wang
- Key Laboratory of Resources Biology and Biotechnology in Western China, Ministry of Education, Provincial Key Laboratory of Biotechnology of Shaanxi Province, the College of Life Sciences, Northwest University, Xi’an, 710069, People’s Republic of China
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16
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Liang S, Qi Y, Yu H, Sun W, Raza SHA, Alkhorayef N, Alkhalil SS, Salama EEA, Zhang L. Bacteriophage Therapy as an Application for Bacterial Infection in China. Antibiotics (Basel) 2023; 12:antibiotics12020417. [PMID: 36830327 PMCID: PMC9952293 DOI: 10.3390/antibiotics12020417] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2022] [Revised: 01/31/2023] [Accepted: 02/05/2023] [Indexed: 02/22/2023] Open
Abstract
Antibiotic resistance has emerged as a significant issue to be resolved around the world. Bacteriophage (phage), in contrast to antibiotics, can only kill the target bacteria with no adverse effect on the normal bacterial flora. In this review, we described the biological characteristics of phage, and summarized the phage application in China, including in mammals, ovipara, aquatilia, and human clinical treatment. The data showed that phage had a good therapeutic effect on drug-resistant bacteria in veterinary fields, as well as in the clinical treatment of humans. However, we need to take more consideration of the narrow lysis spectrum, the immune response, the issues of storage, and the pharmacokinetics of phages. Due to the particularity of bacteriophage as a bacterial virus, there is no unified standard or regulation for the use of bacteriophage in the world at present, which hinders the application of bacteriophage as a substitute for antibiotic biological products. We aimed to highlight the rapidly advancing field of phage therapy as well as the challenges that China faces in reducing its reliance on antibiotics.
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Affiliation(s)
- Shuang Liang
- College of Animal Science and Technology, Jilin Agricultural University, Changchun 130000, China
| | - Yanling Qi
- College of Animal Science and Technology, Jilin Agricultural University, Changchun 130000, China
| | - Huabo Yu
- College of Animal Science and Technology, Jilin Agricultural University, Changchun 130000, China
| | - Wuwen Sun
- College of Animal Science and Technology, Jilin Agricultural University, Changchun 130000, China
- Borui Technology Co., Ltd., Changchun 130000, China
| | | | - Nada Alkhorayef
- Department of Clinical Laboratory Science, College of Applied Medical Sciences, Al-Quway’iyah, Shaqra University, Riyadh 19257, Saudi Arabia
| | - Samia S. Alkhalil
- Department of Clinical Laboratory Sciences, Faculty of Applied Medical Sciences, Shaqra University, Shaqra 11961, Saudi Arabia
| | | | - Lei Zhang
- College of Animal Science and Technology, Jilin Agricultural University, Changchun 130000, China
- Borui Technology Co., Ltd., Changchun 130000, China
- Correspondence:
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17
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Shim H. Three Innovations of Next-Generation Antibiotics: Evolvability, Specificity, and Non-Immunogenicity. Antibiotics (Basel) 2023; 12:antibiotics12020204. [PMID: 36830114 PMCID: PMC9952447 DOI: 10.3390/antibiotics12020204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 01/13/2023] [Accepted: 01/16/2023] [Indexed: 01/21/2023] Open
Abstract
Antimicrobial resistance is a silent pandemic exacerbated by the uncontrolled use of antibiotics. Since the discovery of penicillin, we have been largely dependent on microbe-derived small molecules to treat bacterial infections. However, the golden era of antibiotics is coming to an end, as the emergence and spread of antimicrobial resistance against these antibacterial compounds are outpacing the discovery and development of new antibiotics. The current antibiotic market suffers from various shortcomings, including the absence of profitability and investment. The most important underlying issue of traditional antibiotics arises from the inherent properties of these small molecules being mostly broad-spectrum and non-programmable. As the scientific knowledge of microbes progresses, the scientific community is starting to explore entirely novel approaches to tackling antimicrobial resistance. One of the most prominent approaches is to develop next-generation antibiotics. In this review, we discuss three innovations of next-generation antibiotics compared to traditional antibiotics as specificity, evolvability, and non-immunogenicity. We present a number of potential antimicrobial agents, including bacteriophage-based therapy, CRISPR-Cas-based antimicrobials, and microbiome-derived antimicrobial agents. These alternative antimicrobial agents possess innovative properties that may overcome the inherent shortcomings of traditional antibiotics, and some of these next-generation antibiotics are not merely far-fetched ideas but are currently in clinical development. We further discuss some related issues and challenges such as infection diagnostics and regulatory frameworks that still need to be addressed to bring these next-generation antibiotics to the antibiotic market as viable products to combat antimicrobial resistance using a diversified set of strategies.
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Affiliation(s)
- Hyunjin Shim
- Center for Biosystems and Biotech Data Science, Ghent University Global Campus, Incheon 21985, Republic of Korea
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18
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Yuan S, Shi J, Jiang J, Ma Y. Genome-scale top-down strategy to generate viable genome-reduced phages. Nucleic Acids Res 2022; 50:13183-13197. [PMID: 36511873 PMCID: PMC9825161 DOI: 10.1093/nar/gkac1168] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 11/18/2022] [Accepted: 11/23/2022] [Indexed: 12/14/2022] Open
Abstract
Efforts have been made to reduce the genomes of living cells, but phage genome reduction remains challenging. It is of great interest to investigate whether genome reduction can make phages obtain new infectious properties. We developed a CRISPR/Cas9-based iterative phage genome reduction (CiPGr) approach and applied this to four distinct phages, thereby obtaining heterogeneous genome-reduced mutants. We isolated and sequenced 200 mutants with loss of up to 8-23% (3.3-35 kbp) of the original sequences. This allowed the identification of non-essential genes for phage propagation, although loss of these genes is mostly detrimental to phage fitness to various degrees. Notwithstanding this, mutants with higher infectious efficiency than their parental strains were characterized, indicating a trade-off between genome reduction and infectious fitness for phages. In conclusion, this study provides a foundation for future work to leverage the information generated by CiPGr in phage synthetic biology research.
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Affiliation(s)
- Shengjian Yuan
- Shenzhen Key Laboratory of Synthetic Genomics, Guangdong Provincial Key Laboratory of Synthetic Genomics, CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Juan Shi
- Shenzhen Key Laboratory of Synthetic Genomics, Guangdong Provincial Key Laboratory of Synthetic Genomics, CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Jianrong Jiang
- Shenzhen Key Laboratory of Synthetic Genomics, Guangdong Provincial Key Laboratory of Synthetic Genomics, CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Yingfei Ma
- To whom correspondence should be addressed. Tel: +86 755 8639 2674;
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19
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Bacteriophage genome engineering with CRISPR-Cas13a. Nat Microbiol 2022; 7:1956-1966. [PMID: 36316452 PMCID: PMC9722621 DOI: 10.1038/s41564-022-01243-4] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 09/02/2022] [Indexed: 12/05/2022]
Abstract
Jumbo phages such as Pseudomonas aeruginosa ФKZ have potential as antimicrobials and as a model for uncovering basic phage biology. Both pursuits are currently limited by a lack of genetic engineering tools due to a proteinaceous 'phage nucleus' structure that protects from DNA-targeting CRISPR-Cas tools. To provide reverse-genetics tools for DNA jumbo phages from this family, we combined homologous recombination with an RNA-targeting CRISPR-Cas13a enzyme and used an anti-CRISPR gene (acrVIA1) as a selectable marker. We showed that this process can insert foreign genes, delete genes and add fluorescent tags to genes in the ФKZ genome. Fluorescent tagging of endogenous gp93 revealed that it is ejected with the phage DNA while deletion of the tubulin-like protein PhuZ surprisingly had only a modest impact on phage burst size. Editing of two other phages that resist DNA-targeting CRISPR-Cas systems was also achieved. RNA-targeting Cas13a holds great promise for becoming a universal genetic editing tool for intractable phages, enabling the systematic study of phage genes of unknown function.
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20
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Integrated Omics Reveal Time-Resolved Insights into T4 Phage Infection of E. coli on Proteome and Transcriptome Levels. Viruses 2022; 14:v14112502. [PMID: 36423111 PMCID: PMC9697503 DOI: 10.3390/v14112502] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 11/07/2022] [Accepted: 11/08/2022] [Indexed: 11/16/2022] Open
Abstract
Bacteriophages are highly abundant viruses of bacteria. The major role of phages in shaping bacterial communities and their emerging medical potential as antibacterial agents has triggered a rebirth of phage research. To understand the molecular mechanisms by which phages hijack their host, omics technologies can provide novel insights into the organization of transcriptional and translational events occurring during the infection process. In this study, we apply transcriptomics and proteomics to characterize the temporal patterns of transcription and protein synthesis during the T4 phage infection of E. coli. We investigated the stability of E. coli-originated transcripts and proteins in the course of infection, identifying the degradation of E. coli transcripts and the preservation of the host proteome. Moreover, the correlation between the phage transcriptome and proteome reveals specific T4 phage mRNAs and proteins that are temporally decoupled, suggesting post-transcriptional and translational regulation mechanisms. This study provides the first comprehensive insights into the molecular takeover of E. coli by bacteriophage T4. This data set represents a valuable resource for future studies seeking to study molecular and regulatory events during infection. We created a user-friendly online tool, POTATO4, which is available to the scientific community and allows access to gene expression patterns for E. coli and T4 genes.
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21
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Magaziner SJ, Salmond GPC. A novel T4- and λ-based receptor binding protein family for bacteriophage therapy host range engineering. Front Microbiol 2022; 13:1010330. [PMID: 36386655 PMCID: PMC9659904 DOI: 10.3389/fmicb.2022.1010330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 10/10/2022] [Indexed: 11/21/2022] Open
Abstract
Widespread multidrug antimicrobial resistance in emerging pathogens has led to a renewed interest in phage therapy as an alternative or supplement to traditional small molecule drugs. The primary limiting factors of phage therapy deployment rest in the narrow host range specificity of phage as well as a poor understanding of many phages’ unintended downstream effects on host physiology and microbiota as well as on adverse pathogen evolution. Consequently, this has made assembling well-defined and safe “phage-cocktails” of solely naturally occurring phages labor- and time-intensive. To increase the speed, efficacy, and safety of therapeutic deployment, there is exceptional interest in modulating the host ranges of well-characterized lytic phages (e.g., T4 and T7) by using synthetic strategies to the swap phage tail components, the receptor binding proteins (RBPs) key for host specificity. Here we identify the RBP of the Citrobacter rodentium temperate phage ΦNP as ORF6. Through bioinformatic and phylogenetic assays, we demonstrate this RBP to be closely related to the known RBPs of T4 and λ. Further investigation reveals a novel, greater than 200 members RBP family with phages targeting several notable human pathogens, including Klebsiella pneumoniae, Escherichia coli O157:H7, Salmonella spp., and Shigella spp. With well characterized lytic members, this RBP family represents an ideal candidate for use in synthetic strategies for expanding therapeutic phage host ranges.
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22
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Nazli A, He DL, Liao D, Khan MZI, Huang C, He Y. Strategies and progresses for enhancing targeted antibiotic delivery. Adv Drug Deliv Rev 2022; 189:114502. [PMID: 35998828 DOI: 10.1016/j.addr.2022.114502] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 08/10/2022] [Accepted: 08/16/2022] [Indexed: 01/24/2023]
Abstract
Antibiotic resistance is a global health issue and a potential risk for society. Antibiotics administered through conventional formulations are devoid of targeting effect and often spread to various undesired body sites, leading to sub-lethal concentrations at the site of action and thus resulting in emergence of resistance, as well as side effects. Moreover, we have a very slim antibiotic pipeline. Drug-delivery systems have been designed to control the rate, time, and site of drug release, and innovative approaches for antibiotic delivery provide a glint of hope for addressing these issues. This review elaborates different delivery strategies and approaches employed to overcome the limitations of conventional antibiotic therapy. These include antibiotic conjugates, prodrugs, and nanocarriers for local and targeted antibiotic release. In addition, a wide range of stimuli-responsive nanocarriers and biological carriers for targeted antibiotic delivery are discussed. The potential advantages and limitations of targeted antibiotic delivery strategies are described along with possible solutions to avoid these limitations. A number of antibiotics successfully delivered through these approaches with attained outcomes and potentials are reviewed.
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Affiliation(s)
- Adila Nazli
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, PR China
| | - David L He
- College of Chemistry, University of California, Berkeley, CA 94720, United States
| | - Dandan Liao
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, PR China
| | | | - Chao Huang
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, PR China.
| | - Yun He
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, PR China.
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23
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Abdulhussein AA, O. Abdulsattar B. Isolation and characterization of two novel phages as a possible therapeutic alternative against multi-drug resistant E. coli. GENE REPORTS 2022. [DOI: 10.1016/j.genrep.2022.101644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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24
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Cell-free production of personalized therapeutic phages targeting multidrug-resistant bacteria. Cell Chem Biol 2022; 29:1434-1445.e7. [PMID: 35820417 DOI: 10.1016/j.chembiol.2022.06.003] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 03/11/2022] [Accepted: 06/16/2022] [Indexed: 12/26/2022]
Abstract
Bacteriophages are potent therapeutics against biohazardous bacteria, which rapidly develop multidrug resistance. However, routine administration of phage therapy is hampered by a lack of rapid production, safe bioengineering, and detailed characterization of phages. Thus, we demonstrate a comprehensive cell-free platform for personalized production, transient engineering, and proteomic characterization of a broad spectrum of phages. Using mass spectrometry, we validated hypothetical and non-structural proteins and could also monitor the protein expression during phage assembly. Notably, a few microliters of a one-pot reaction produced effective doses of phages against enteroaggregative Escherichia coli (EAEC), Yersinia pestis, and Klebsiella pneumoniae. By co-expressing suitable host factors, we could extend the range of cell-free production to phages targeting gram-positive bacteria. We further introduce a non-genomic phage engineering method, which adds functionalities for only one replication cycle. In summary, we expect this cell-free methodology to foster reverse and forward phage engineering and customized production of clinical-grade bacteriophages.
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25
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The resurgence of phage-based therapy in the era of increasing antibiotic resistance: from research progress to challenges and prospects. Microbiol Res 2022; 264:127155. [DOI: 10.1016/j.micres.2022.127155] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Revised: 07/29/2022] [Accepted: 07/29/2022] [Indexed: 12/23/2022]
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26
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Korzeniowski P, Śliwka P, Kuczkowski M, Mišić D, Milcarz A, Kuźmińska-Bajor M. Bacteriophage Cocktail Can Effectively Control Salmonella Biofilm in Poultry Housing. Front Microbiol 2022; 13:901770. [PMID: 35847069 PMCID: PMC9277115 DOI: 10.3389/fmicb.2022.901770] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 06/02/2022] [Indexed: 11/13/2022] Open
Abstract
Salmonella enterica serovar Enteritidis (S. Enteritidis) is the major contaminant of poultry products, and its ability to form biofilms on produced food and poultry farm processing surfaces contributes to Salmonella transmission to humans. Bacteriophages have come under increasing interest for anti-Salmonella biofilm control. In this study, we used the three previously sequenced and described phages UPWr_S1, UPWr_S3, and UPWr_S4 and a phage cocktail, UPWr_S134, containing these three phages to degrade biofilms formed by two S. Enteritidis strains, 327 lux and ATCC 13076, in vitro. It was found that treatment with bacteriophages significantly reduced biofilm on a 96-well microplate (32–69%) and a stainless steel surface (52–98%) formed by S. Enteritidis 327 lux. The reduction of biofilm formed by S. Enteritidis ATCC 13076 in the 96-well microplate and on a stainless steel surface for bacteriophage treatment was in the range of 73–87% and 60–97%, respectively. Under laboratory conditions, an experimental model utilizing poultry drinkers artificially contaminated with S. Enteritidis 327 lux and treated with UPWr_S134 phage cocktail was applied. In in vitro trials, the phage cocktail significantly decreased the number of Salmonella on the surface of poultry drinkers. Moreover, the phage cocktail completely eradicated Salmonella from the abundant bacterial load on poultry drinkers in an experimentally infected chickens. Therefore, the UPWr_S134 phage cocktail is a promising candidate for Salmonella biocontrol at the farm level.
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Affiliation(s)
- Paweł Korzeniowski
- Department of Biotechnology and Food Microbiology, Faculty of Biotechnology and Food Sciences, Wrocław University of Environmental and Life Sciences, Wrocław, Poland
| | - Paulina Śliwka
- Department of Biotechnology and Food Microbiology, Faculty of Biotechnology and Food Sciences, Wrocław University of Environmental and Life Sciences, Wrocław, Poland
| | - Maciej Kuczkowski
- Department of Epizootiology and Clinic of Birds and Exotic Animals, Faculty of Veterinary Medicine, Wrocław University of Environmental and Life Sciences, Wrocław, Poland
| | - Dušan Mišić
- Department of Functional Food Products Development, Faculty of Biotechnology and Food Sciences, Wrocław University of Environmental and Life Sciences, Wrocław, Poland
| | - Agata Milcarz
- Department of Biotechnology and Food Microbiology, Faculty of Biotechnology and Food Sciences, Wrocław University of Environmental and Life Sciences, Wrocław, Poland
| | - Marta Kuźmińska-Bajor
- Department of Biotechnology and Food Microbiology, Faculty of Biotechnology and Food Sciences, Wrocław University of Environmental and Life Sciences, Wrocław, Poland
- *Correspondence: Marta Kuźmińska-Bajor
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27
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Isolation of Three Coliphages and the Evaluation of Their Phage Cocktail for Biocontrol of Shiga Toxin-Producing Escherichia coli O157 in Milk. Curr Microbiol 2022; 79:216. [PMID: 35678865 DOI: 10.1007/s00284-022-02908-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Accepted: 05/16/2022] [Indexed: 11/03/2022]
Abstract
Shiga toxin-producing Escherichia coli (STEC) O157 is a well-known foodborne pathogen and a leading cause of many intestinal diseases. In this study, we explore the use of a phage cocktail to help control STEC O157 in broth and milk. We isolated three virulent phages from sanitary sewages using a STEC O157 as the indicator bacterium. Phenotypical characterizations revealed that these three phages belong to the Myoviridae family and were stable at different temperatures and pH. They displayed a short latent period between 10 and 20 min, and a burst size (32-65 per infected cell). No virulence factors and drug resistance genes were found in their genomes. Bacterial lysis assays showed that a phage cocktail comprising these three phages was more effective (at least 4.32 log reduction) against STEC O157 at 25 °C with multiplicity of infection (MOI) = 1000 in broth medium. At 4 °C, a 3.8 log reduction in the number of viable STEC O157 after 168-h treatment with phage cocktail at MOI = 1000 was observed in milk, compared to phage-free bacterial control group. Characterizations of phages suggest they could be developed into novel therapeutic agents to control STEC O157 in milk production.
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Understanding the Mechanisms That Drive Phage Resistance in Staphylococci to Prevent Phage Therapy Failure. Viruses 2022; 14:v14051061. [PMID: 35632803 PMCID: PMC9146914 DOI: 10.3390/v14051061] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 05/11/2022] [Accepted: 05/13/2022] [Indexed: 02/07/2023] Open
Abstract
Despite occurring at the microscopic scale, the armed race between phages and their bacterial hosts involves multiple mechanisms, some of which are just starting to be understood. On the one hand, bacteria have evolved strategies that can stop the viral infection at different stages (adsorption, DNA injection and replication, biosynthesis and assembly of the viral progeny and/or release of the newly formed virions); on the other, phages have gradually evolved counterattack strategies that allow them to continue infecting their prey. This co-evolutionary process has played a major role in the development of microbial populations in both natural and man-made environments. Notably, understanding the parameters of this microscopic war will be paramount to fully benefit from the application of phage therapy against dangerous, antibiotic-resistant human pathogens. This review gathers the current knowledge regarding the mechanisms of phage resistance in the Staphylococcus genus, which includes Staphylococcus aureus, one of the most concerning microorganisms in terms of antibiotic resistance acquisition. Some of these strategies involve permanent changes to the bacterial cell via mutations, while others are transient, adaptive changes whose expression depends on certain environmental cues or the growth phase. Finally, we discuss the most plausible strategies to limit the impact of phage resistance on therapy, with a special emphasis on the importance of a rational design of phage cocktails in order to thwart therapeutic failure.
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Samir S, El-Far A, Okasha H, Mahdy R, Samir F, Nasr S. Isolation and characterization of lytic bacteriophages from sewage at an egyptian tertiary care hospital against methicillin-resistant Staphylococcus aureus clinical isolates. Saudi J Biol Sci 2022; 29:3097-3106. [PMID: 35360502 PMCID: PMC8961222 DOI: 10.1016/j.sjbs.2022.03.019] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 01/25/2022] [Accepted: 03/15/2022] [Indexed: 12/03/2022] Open
Abstract
Background Methicillin resistant Staphylococcus aureus (MRSA) is a pathogen to humans causing life-threatening infections. MRSA have the capability to grow resistance to many antibiotics, and phage therapy is one treatment option for this infection. Objectives The aim of the present study was to isolate and characterize the lytic bacteriophages specific to MRSA from domestic sewage water at a tertiary care hospital in Egypt. Methods Thirty MRSA strains were isolated from different clinical samples admitted to the microbiology lab at Theodor Bilharz Research institute (TBRI) hospital, Giza, Egypt. They were confirmed to be MRSA through phenotypic detection and conventional PCR for mecA gene. They were used for the isolation of phages from sewage water of TBRI hospital. Plaque assay was applied to purify and quantify the titer of the isolated phages. The host range of the isolated phages was detected using the spot test assay. The morphology of phages was confirmed using transmission electron microscope (TEM). Digestion of DNA extracted from phages with endonuclease enzymes including EcoRI and SmaI was performed. SDS-PAGE was performed to analyze MRSA specific phage proteins. As a positive control prophages were isolated from a mitomycin C (MitC) treated culture of S. aureus strain ATCC25923. Further characterization using conventional polymerase chain reaction (PCR) was used to select three known Staphylophages by detecting the endolysin gene of phage K, the polymerase gene of phage 44AHJD, and the minor tail gene of phage P68. Results Isolated phages in this research displayed a wide host range against MRSA using the spot test, out of thirty tested MRSA isolates 24 were sensitive and got lysed (80%). The titer of the phages was estimated to be 1.04 × 106 pfu/ml using plaque test. Identification of head and tail morphology of the phages was achieved using TEM and they were designated to tailed phages of order Caudovirales, they composed an icosahedral capsid. Prophages were isolated through MitC induction. DNA of phages was digested by endonuclease enzymes. Conventional PCR yielded 341 bp of phage K endolysin gene and phage P68 minor tail protein gene 501 bp. Protein analysis using SDS-PAGE showed 4 proteins of sizes between 42 kDa and 140 kDa. Conclusion Phages isolated here are alike to others mentioned in previous studies. The high broad host range of the isolated phages is promising to control MRSA and can be in the future commercially suitable for treatment as lysate preparations. Animal models of phage-bacterial interaction will be our next step that may help in resolving the multidrug resistant crisis of MRSA in Egypt.
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Affiliation(s)
- Safia Samir
- Biochemistry and Molecular Biology Department, Theodor Bilharz Research Institute (TBRI), Giza, Egypt
| | - Amira El-Far
- Microbiology Department, Theodor Bilharz Research Institute (TBRI), Giza, Egypt
| | - Hend Okasha
- Biochemistry and Molecular Biology Department, Theodor Bilharz Research Institute (TBRI), Giza, Egypt
| | - Rania Mahdy
- Microbiology Department, Theodor Bilharz Research Institute (TBRI), Giza, Egypt
| | - Fatima Samir
- Biochemistry and Molecular Biology Department, Theodor Bilharz Research Institute (TBRI), Giza, Egypt
| | - Sami Nasr
- Biochemistry and Molecular Biology Department, Theodor Bilharz Research Institute (TBRI), Giza, Egypt
- Corresponding author at: Theodor Bilharz Research Institute, Cornish El-Nile Street, Warrak El-Hadar, Giza, 12411, Egypt
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Chen X, Tang Q, Li X, Zheng X, Li P, Li M, Wu F, Xu Z, Lu R, Zhang W. Isolation, characterization, and genome analysis of bacteriophage P929 that could specifically lyase the KL19 capsular type of Klebsiella pneumoniae. Virus Res 2022; 314:198750. [DOI: 10.1016/j.virusres.2022.198750] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 03/15/2022] [Accepted: 03/16/2022] [Indexed: 01/09/2023]
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Wang J, Childers WS. The Future Potential of Biosensors to Investigate the Gut-Brain Axis. Front Bioeng Biotechnol 2022; 9:826479. [PMID: 35096802 PMCID: PMC8795891 DOI: 10.3389/fbioe.2021.826479] [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: 11/30/2021] [Accepted: 12/28/2021] [Indexed: 11/13/2022] Open
Abstract
The multifaceted and heterogeneous nature of depression presents challenges in pinpointing treatments. Among these contributions are the interconnections between the gut microbiome and neurological function termed the gut-brain axis. A diverse range of microbiome-produced metabolites interact with host signaling and metabolic pathways through this gut-brain axis relationship. Therefore, biosensor detection of gut metabolites offers the potential to quantify the microbiome's contributions to depression. Herein we review synthetic biology strategies to detect signals that indicate gut-brain axis dysregulation that may contribute to depression. We also highlight future challenges in developing living diagnostics of microbiome conditions influencing depression.
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Affiliation(s)
| | - W. Seth Childers
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, United States
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Application of novel lytic bacteriophages to control Vibrio parahaemolyticus load in seafood. J Verbrauch Lebensm 2022. [DOI: 10.1007/s00003-021-01356-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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Sørensen PE, Ng DYK, Duchateau L, Ingmer H, Garmyn A, Butaye P. Classification of In Vitro Phage-Host Population Growth Dynamics. Microorganisms 2021; 9:2470. [PMID: 34946072 PMCID: PMC8708399 DOI: 10.3390/microorganisms9122470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 11/23/2021] [Accepted: 11/25/2021] [Indexed: 11/23/2022] Open
Abstract
The therapeutic use of bacteriophages (phage therapy) represents a promising alternative to antibiotics to control bacterial pathogens. However, the understanding of the phage-bacterium interactions and population dynamics seems essential for successful phage therapy implementation. Here, we investigated the effect of three factors: phage species (18 lytic E. coli-infecting phages); bacterial strain (10 APEC strains); and multiplicity of infection (MOI) (MOI 10, 1, and 0.1) on the bacterial growth dynamics. All factors had a significant effect, but the phage appeared to be the most important. The results showed seven distinct growth patterns. The first pattern corresponded to the normal bacterial growth pattern in the absence of a phage. The second pattern was complete bacterial killing. The remaining patterns were in-between, characterised by delayed growth and/or variable killing of the bacterial cells. In conclusion, this study demonstrates that the phage-host dynamics is an important factor in the capacity of a phage to eliminate bacteria. The classified patterns show that this is an essential factor to consider when developing a phage therapy. This methodology can be used to rapidly screen for novel phage candidates for phage therapy. Accordingly, the most promising candidates were phages found in Group 2, characterised by growth dynamics with high bacterial killing.
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Affiliation(s)
- Patricia E. Sørensen
- Department of Pathobiology, Pharmacology and Zoological Medicine, Ghent University, 9820 Merelbeke, Belgium; (A.G.); (P.B.)
- Department of Biomedical Sciences, Ross University School of Veterinary Medicine, Basseterre 42123, Saint Kitts and Nevis
| | - Duncan Y. K. Ng
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, 2300 Copenhagen, Denmark;
| | - Luc Duchateau
- Biometrics Research Center, Ghent University, 9820 Merelbeke, Belgium;
| | - Hanne Ingmer
- Department of Veterinary and Animal Sciences, University of Copenhagen, 1870 Frederiksberg, Denmark;
| | - An Garmyn
- Department of Pathobiology, Pharmacology and Zoological Medicine, Ghent University, 9820 Merelbeke, Belgium; (A.G.); (P.B.)
| | - Patrick Butaye
- Department of Pathobiology, Pharmacology and Zoological Medicine, Ghent University, 9820 Merelbeke, Belgium; (A.G.); (P.B.)
- Department of Biomedical Sciences, Ross University School of Veterinary Medicine, Basseterre 42123, Saint Kitts and Nevis
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Kamiya R, Uchiyama J, Matsuzaki S, Murata K, Iwasaki K, Miyazaki N. Acid-stable capsid structure of Helicobacter pylori bacteriophage KHP30 by single-particle cryoelectron microscopy. Structure 2021; 30:300-312.e3. [PMID: 34597601 DOI: 10.1016/j.str.2021.09.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2021] [Revised: 07/04/2021] [Accepted: 09/09/2021] [Indexed: 10/20/2022]
Abstract
The acid-stable capsid structures of Helicobacter pylori phages KHP30 and KHP40 are solved at 2.7 and 3.0 Å resolutions by cryoelectron microscopy, respectively. The capsids have icosahedral T = 9 symmetry and consist of each 540 copies of 2 structural proteins, a major capsid protein, and a cement protein. The major capsid proteins form 12 pentagonal capsomeres occupying icosahedral vertexes and 80 hexagonal capsomeres located at icosahedral faces and edges. The major capsid protein has a unique protruding loop extending to the neighboring subunit that stabilizes hexagonal capsomeres. Furthermore, the capsid is decorated with trimeric cement proteins with a jelly roll motif. The cement protein trimer sits on the quasi-three-fold axis formed by three major capsid protein capsomeres, thereby enhancing the particle stability by connecting these capsomeres. Sequence and structure comparisons between the related Helicobacter pylori phages suggest a possible mechanism of phage adaptation to the human gastric environment.
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Affiliation(s)
- Ryosuke Kamiya
- Life Science Center for Survival Dynamics, Tsukuba Advanced Research Alliance, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8777, Japan
| | - Jumpei Uchiyama
- Laboratory of Veterinary Microbiology I, School of Veterinary Medicine, Azabu University, Kanagawa 252-5201, Japan; Department of Bacteriology, Graduate School of Medicine Dentistry and Pharmaceutical Sciences, Okayama University, Okayama 700-8558, Japan
| | - Shigenobu Matsuzaki
- Department of Clinical Laboratory Science, Faculty of Health Sciences, Kochi Gakuen University, Kochi 780-0955, Japan
| | - Kazuyoshi Murata
- National Institute for Physiological Sciences, Okazaki, Aichi 444-8585, Japan
| | - Kenji Iwasaki
- Life Science Center for Survival Dynamics, Tsukuba Advanced Research Alliance, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8777, Japan
| | - Naoyuki Miyazaki
- Life Science Center for Survival Dynamics, Tsukuba Advanced Research Alliance, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8777, Japan.
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Kim K, Islam MM, Kim D, Yun SH, Kim J, Lee JC, Shin M. Characterization of a Novel Phage ΦAb1656-2 and Its Endolysin with Higher Antimicrobial Activity against Multidrug-Resistant Acinetobacter baumannii. Viruses 2021; 13:v13091848. [PMID: 34578429 PMCID: PMC8473069 DOI: 10.3390/v13091848] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 09/08/2021] [Accepted: 09/13/2021] [Indexed: 12/18/2022] Open
Abstract
Acinetobacter baumannii is a nosocomial pathogen, which is a problem worldwide due to the emergence of a difficult-to-treat multidrug-resistant A. baumannii (MDRAB). Endolysins are hydrolytic enzymes produced by a bacteriophage that can be used as a potential therapeutic agent for multidrug-resistant bacterial infection in replacing antibiotics. Here, we isolated a novel bacteriophage through prophage induction using mitomycin C from clinical A. baumannii 1656-2. Morphologically, ΦAb1656-2 was identified as a Siphoviridae family bacteriophage, which can infect MDRAB. The whole genome of ΦAb1656-2 was sequenced, and it showed that it is 50.9 kb with a G + C content of 38.6% and 68 putative open reading frames (ORFs). A novel endolysin named AbEndolysin with an N-acetylmuramidase-containing catalytic domain was identified, expressed, and purified from ΦAb1656-2. Recombinant AbEndolysin showed significant antibacterial activity against MDRAB clinical strains without any outer membrane permeabilizer. These results suggest that AbEndolysin could represent a potential antimicrobial agent for treating MDRAB clinical isolates.
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Affiliation(s)
- Kyeongmin Kim
- Department of Microbiology, School of Medicine, Kyungpook National University, 680 Gukchaebosang-ro, Jung-gu, Daegu 41944, Korea; (K.K.); (M.M.I.); (D.K.); (J.K.); (J.C.L.)
| | - Md Maidul Islam
- Department of Microbiology, School of Medicine, Kyungpook National University, 680 Gukchaebosang-ro, Jung-gu, Daegu 41944, Korea; (K.K.); (M.M.I.); (D.K.); (J.K.); (J.C.L.)
| | - Dooyoung Kim
- Department of Microbiology, School of Medicine, Kyungpook National University, 680 Gukchaebosang-ro, Jung-gu, Daegu 41944, Korea; (K.K.); (M.M.I.); (D.K.); (J.K.); (J.C.L.)
| | - Sung Ho Yun
- Bio-Chemical Analysis Team, Korea Basic Science Institute,162 Yeongudanji-ro, Ochang-eup, Cheongwon-gu, Cheongju-si 28119, Korea;
| | - Jungmin Kim
- Department of Microbiology, School of Medicine, Kyungpook National University, 680 Gukchaebosang-ro, Jung-gu, Daegu 41944, Korea; (K.K.); (M.M.I.); (D.K.); (J.K.); (J.C.L.)
| | - Je Chul Lee
- Department of Microbiology, School of Medicine, Kyungpook National University, 680 Gukchaebosang-ro, Jung-gu, Daegu 41944, Korea; (K.K.); (M.M.I.); (D.K.); (J.K.); (J.C.L.)
| | - Minsang Shin
- Department of Microbiology, School of Medicine, Kyungpook National University, 680 Gukchaebosang-ro, Jung-gu, Daegu 41944, Korea; (K.K.); (M.M.I.); (D.K.); (J.K.); (J.C.L.)
- Correspondence: ; Tel.: +82-53-420-4841
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Prophylactic Administration of a Bacteriophage Cocktail Is Safe and Effective in Reducing Salmonella enterica Serovar Typhimurium Burden in Vivo. Microbiol Spectr 2021; 9:e0049721. [PMID: 34431719 PMCID: PMC8552648 DOI: 10.1128/spectrum.00497-21] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Nontyphoidal Salmonella bacteria are the causative agent of salmonellosis, which accounts for the majority of foodborne illness of bacterial etiology in humans. Here, we demonstrate the safety and efficacy of the prophylactic administration of a bacteriophage preparation termed FOP (foodborne outbreak pill), which contains lytic phages targeting Salmonella (SalmoFresh phage cocktail), Shiga toxin-producing Escherichia coli (STEC), and Listeria monocytogenes, for lowering Salmonella burdens in OMM12 gnotobiotic mice. Prophylactic administration of FOP significantly reduced the levels of Salmonella in feces and in intestinal sections compared to the levels in controls. Moreover, the overall symptoms of the disease were also considerably lessened. Dose-dependent administration of FOP showed that phage amplification reached similarly high levels in less than 48 h independent of dose. In addition, 16S rRNA gene analysis showed that FOP did not alter the intestinal microbiota of healthy OMM12 mice and reduced microbiota perturbations induced by Salmonella. FOP maintained its full potency against Salmonella in comparison to that of SalmoFresh, its Salmonella-targeting component phages alone. Altogether, the data support that preventive administration of FOP may offer a safe and effective approach for reducing the risk of foodborne infections caused by Salmonella and, potentially, other foodborne bacteria (namely, STEC and L. monocytogenes) targeted by the FOP preparation. IMPORTANCE Foodborne bacterial infections cause worldwide economic loss. During an epidemic, the use of antibiotics to slow down the spread of the disease is not recommended because of their side effects on the resident microbiota and the selection of antibiotic-resistant bacteria. Here, we investigated the potential for the prophylactic administration of bacteriophages (viruses infecting bacteria) to reduce the burden of Salmonella in vivo using mice colonized by a synthetic microbiota. We found that the repeated administration of bacteriophages was safe and efficient in lowering the Salmonella burden. Perturbations of the microbiota by the Salmonella infection were also reduced when mice received bacteriophages. Altogether, these data support the use of bacteriophages as a prophylactic intervention to lower the spread of foodborne epidemics.
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Crespo-Piazuelo D, Lawlor PG. Livestock-associated methicillin-resistant Staphylococcus aureus (LA-MRSA) prevalence in humans in close contact with animals and measures to reduce on-farm colonisation. Ir Vet J 2021; 74:21. [PMID: 34362463 PMCID: PMC8348836 DOI: 10.1186/s13620-021-00200-7] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 07/13/2021] [Indexed: 12/14/2022] Open
Abstract
Since the 1940s, Staphylococcus aureus has adapted to the use of different antimicrobials to treat infections. Although S. aureus can act as a commensal bacterium, some strains are facultative pathogens and acquiring them can be fatal. In particular, treating infections caused by S. aureus with acquired antimicrobial resistance is problematic, as their treatment is more difficult. Some of these S. aureus variants are methicillin-resistant S. aureus (MRSA) with prevalence across the globe in health-care facilities, community settings and on livestock farms. Apart from humans, MRSA can colonise other animal species, and because of this, resistance to new antimicrobials can appear and jump between species. Livestock and companion animals are particularly important in this regard considering the relatively high usage of antimicrobials in these species. There is a risk to humans who come into direct contact with animals acquiring MRSA but there is also the risk of animals acquiring MRSA from colonised humans. In this review, we summarise studies conducted worldwide to characterise the prevalence of MRSA in veterinarians, farmers and other personnel who come into close contact with animals. Finally, alternative treatment, preventive measures and on-farm strategies to reduce MRSA introduction to a farm and carriage within a herd are discussed.
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Affiliation(s)
- Daniel Crespo-Piazuelo
- Teagasc, Pig Development Department, Animal & Grassland Research & Innovation Centre, Moorepark, Fermoy, Co. Cork, P61 C996, Ireland
| | - Peadar G Lawlor
- Teagasc, Pig Development Department, Animal & Grassland Research & Innovation Centre, Moorepark, Fermoy, Co. Cork, P61 C996, Ireland.
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Sarhan WA, Salem HG, Khalil MAF, El-Sherbiny IM, Azzazy HME. Fabrication of gelatin/silk fibroin/phage nanofiber scaffold effective against multidrug resistant Pseudomonas aeruginosa. Drug Dev Ind Pharm 2021; 47:947-953. [PMID: 34278896 DOI: 10.1080/03639045.2021.1957915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
OBJECTIVE The alarming rise of multi-drug resistant (MDR) Pseudomonas aeruginosa has prompted the World Health Organization to consider it a serious threat to human health. Although phage (Phg), an effective antibacterial treatment option, can maintain long-term infectivity via lyophilized storage, freeze-drying can be expensive and time-consuming. Thus, we propose electrospun gelatin/fibroin (G/F) nanofibrous formulation for dehydrating and storing phage against MDR P. aeruginosa. SIGNIFICANCE The formulation of phage within the nanofibrous structure of the electrospun G/F scaffold would result in antimicrobial activity against MDR P. aeruginosa leading to enhanced wound healing. METHODS Phg effective against MDR P. aeruginosa was isolated, characterized and loaded within G/F nanofibers by electrospinning. Morphology, crystallinity and thermal stability as well as the antimicrobial activity and the biocompatibility of the developed G/F/Phg nanofibers were determined. RESULTS Phg-loaded G/F nanofibers revealed an amorphous structure with good thermal stability at temperatures below 300 °C and exhibited effective antibacterial activity against MDR P. aeruginosa with ∼2 log reduction in the bacterial count which increased to ∼4 log reduction in bacterial count after 16 h as compared to both the G/F nanofibers and the negative control. Lack of cytotoxic effects on cultured fibroblasts supported the biocompatibility of G/F/Phg nanofibers. CONCLUSION The developed G/F/Phg nanofibers are able to maintain the viability of phage and represent a promising antimicrobial dressing for wounds infected with MDR P. aeruginosa.
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Affiliation(s)
- W A Sarhan
- Department of Chemistry, School of Sciences & Engineering, The American University in Cairo, New Cairo, Egypt.,Center for Materials Science, Zewail City of Science and Technology, Giza, Egypt
| | - H G Salem
- Department of Mechanical Engineering, School of Sciences and Engineering, The American University in Cairo, New Cairo, Egypt
| | - M A F Khalil
- Department of Microbiology and Immunology, Faculty of Pharmacy, Fayoum University, Fayoum, Egypt
| | - I M El-Sherbiny
- Center for Materials Science, Zewail City of Science and Technology, Giza, Egypt
| | - H M E Azzazy
- Department of Chemistry, School of Sciences & Engineering, The American University in Cairo, New Cairo, Egypt
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Levy E, Stintzi A, Cohen A, Desjardins Y, Marette A, Spahis S. Critical appraisal of the mechanisms of gastrointestinal and hepatobiliary infection by COVID-19. Am J Physiol Gastrointest Liver Physiol 2021; 321:G99-G112. [PMID: 34009033 PMCID: PMC8289353 DOI: 10.1152/ajpgi.00106.2021] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
COVID-19 represents a novel infectious disease induced by SARS-CoV-2. It has to date affected 24,240,000 individuals and killed 2,735,805 people worldwide. The highly infectious virus attacks mainly the lung, causing fever, cough, and fatigue in symptomatic patients, but also pneumonia in severe cases. However, growing evidence highlights SARS-CoV-2-mediated extrarespiratory manifestations, namely, gastrointestinal (GI) and hepatic complications. The detection of 1) the virus in the GI system (duodenum, colon, rectum, anal region, and feces); 2) the high expression of additional candidate coreceptors/auxiliary proteins to facilitate the virus entry; 3) the abundant viral angiotensin-converting enzyme 2 receptor; 4) the substantial expression of host transmembrane serine protease 2, necessary to induce virus-cell fusion; 5) the viral replication in the intestinal epithelial cells; and 6) the primarily GI disorders in the absence of respiratory symptoms lead to increased awareness of the risk of disease transmission via the fecal-oral route. The objectives of this review are to provide a brief update of COVID-19 pathogenesis and prevalence, present a critical overview of its GI and liver complications that affect clinical COVID-19 outcomes, clarify associated mechanisms (notably microbiota-related), define whether gut/liver disorders occur more frequently among critically ill patients with COVID-19, determine the impact of COVID-19 on preexisting gut/liver complications and vice versa, and discuss the available strategies for prevention and treatment to improve prognosis of the patients. The novel SARS-CoV-2 can cause gastrointestinal and hepatobiliary manifestations. Metagenomics studies of virobiota in response to SARS-CoV-2 infection are necessary to highlight the contribution of bacterial microflora to COVID-19 phenotype, which is crucial for developing biomarkers and therapeutics.
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Affiliation(s)
- Emile Levy
- 1Research Centre, Sainte-Justine University Health Center, Université de Montréal, Quebec, Canada,2Department of Nutrition, Université de Montréal, Quebec, Canada,3Department of Pediatrics, Gastroenterology and Hepatology Unit, Université de Montréal, Quebec, Canada,4Institute of Nutrition and Functional Foods, Laval University, Quebec, Canada
| | - Alain Stintzi
- 5Department of Biochemistry, Microbiology and Immunology, Ottawa Institute of Systems Biology, University of Ottawa, Ontario, Canada
| | - Albert Cohen
- 6Division of Gastroenterology, Jewish General Hospital, Quebec, Canada
| | - Yves Desjardins
- 4Institute of Nutrition and Functional Foods, Laval University, Quebec, Canada
| | - André Marette
- 4Institute of Nutrition and Functional Foods, Laval University, Quebec, Canada
| | - Schohraya Spahis
- 1Research Centre, Sainte-Justine University Health Center, Université de Montréal, Quebec, Canada,2Department of Nutrition, Université de Montréal, Quebec, Canada,4Institute of Nutrition and Functional Foods, Laval University, Quebec, Canada
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Vlassov VV, Tikunova NV, Morozova VV. Bacteriophages as Therapeutic Preparations: What Restricts Their Application in Medicine. BIOCHEMISTRY (MOSCOW) 2021; 85:1350-1361. [PMID: 33280578 DOI: 10.1134/s0006297920110061] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The increasing prevalence of bacterial pathogens with multiple antibiotic resistance requires development of new approaches to control infections. Phage therapy is one of the most promising approaches. In recent years, research organizations and a number of pharmaceutical companies have intensified investigations aimed at developing bacteriophage-based therapeutics. In the United States and European countries, special centers have been established that experimentally apply phage therapy to treat patients who do not respond to antibiotic therapy. This review describes the features of bacteriophages as therapeutic tools, critically discusses the results of clinical trials of bacteriophage preparations, and assesses the prospects for using phage therapy to treat certain types of infectious diseases.
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Affiliation(s)
- V V Vlassov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia.
| | - N V Tikunova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia
| | - V V Morozova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia
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Mkwata HM, Omoregie AI, Nissom PM. Lytic bacteriophages isolated from limestone caves for biocontrol of Pseudomonas aeruginosa. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2021. [DOI: 10.1016/j.bcab.2021.102011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Chung IY, Kim BO, Han JH, Park J, Kang HK, Park Y, Cho YH. A phage protein-derived antipathogenic peptide that targets type IV pilus assembly. Virulence 2021; 12:1377-1387. [PMID: 34008466 PMCID: PMC8143254 DOI: 10.1080/21505594.2021.1926411] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/29/2022] Open
Abstract
Phage-inspired antibacterial discovery is a new approach that recruits phages in search for antibacterials with new molecular targets, in that phages are the biological entities well adapted to hijack host bacterial physiology in favor of their own thrive. We previously observed that phage-mediated twitching motility inhibition was effective to control the acute infections caused by Pseudomonas aeruginosa and that the motility inhibition was attributed to the delocalization of PilB, the type IV pilus (TFP) assembly ATPase by binding of the 136-amino acid (aa) phage protein, Tip. Here, we created a series of truncated and point-mutant Tip proteins to identify the critical residues in the Tip bioactivity: N-terminal 80-aa residues were dispensable for the Tip activity; we identified that Asp82, Leu84, and Arg85 are crucial in the Tip function. Furthermore, a synthetic 15-aa peptide (P1) that corresponds to Leu73 to Ala87 is shown to suffice for PilB delocalization, twitching inhibition, and virulence attenuation upon exogenous administration. The transgenic flies expressing the 15-aa peptide were resistant to P. aeruginosa infections as well. Taken together, this proof-of-concept study reveals a new antipathogenic peptide hit targeting bacterial motility and provides an insight into antibacterial discovery targeting TFP assembly.
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Affiliation(s)
- In-Young Chung
- Department of Pharmacy, College of Pharmacy and Institute of Pharmaceutical Sciences, CHA University, Seongnam-si, Korea
| | - Bi-O Kim
- Department of Pharmacy, College of Pharmacy and Institute of Pharmaceutical Sciences, CHA University, Seongnam-si, Korea
| | - Ju-Hyun Han
- Department of Pharmacy, College of Pharmacy and Institute of Pharmaceutical Sciences, CHA University, Seongnam-si, Korea
| | - Jonggwan Park
- Department of Biomedical Science, Chosun University, Gwangju, Korea
| | - Hee Kyoung Kang
- Department of Biomedical Science, Chosun University, Gwangju, Korea
| | - Yoonkyung Park
- Department of Biomedical Science, Chosun University, Gwangju, Korea
| | - You-Hee Cho
- Department of Pharmacy, College of Pharmacy and Institute of Pharmaceutical Sciences, CHA University, Seongnam-si, Korea
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Łobocka M, Dąbrowska K, Górski A. Engineered Bacteriophage Therapeutics: Rationale, Challenges and Future. BioDrugs 2021; 35:255-280. [PMID: 33881767 PMCID: PMC8084836 DOI: 10.1007/s40259-021-00480-z] [Citation(s) in RCA: 62] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/29/2021] [Indexed: 12/20/2022]
Abstract
The current problems with increasing bacterial resistance to antibacterial therapies, resulting in a growing frequency of incurable bacterial infections, necessitates the acceleration of studies on antibacterials of a new generation that could offer an alternative to antibiotics or support their action. Bacteriophages (phages) can kill antibiotic-sensitive as well as antibiotic-resistant bacteria, and thus are a major subject of such studies. Their efficacy in curing bacterial infections has been demonstrated in in vivo experiments and in the clinic. Unlike antibiotics, phages have a narrow range of specificity, which makes them safe for commensal microbiota. However, targeting even only the most clinically relevant strains of pathogenic bacteria requires large collections of well characterized phages, whose specificity would cover all such strains. The environment is a rich source of diverse phages, but due to their complex relationships with bacteria and safety concerns, only some naturally occurring phages can be considered for therapeutic applications. Still, their number and diversity make a detailed characterization of all potentially promising phages virtually impossible. Moreover, no single phage combines all the features required of an ideal therapeutic agent. Additionally, the rapid acquisition of phage resistance by bacteria may make phages already approved for therapy ineffective and turn the search for environmental phages of better efficacy and new specificity into an endless race. An alternative strategy for acquiring phages with desired properties in a short time with minimal cost regarding their acquisition, characterization, and approval for therapy could be based on targeted genome modifications of phage isolates with known properties. The first example demonstrating the potential of this strategy in curing bacterial diseases resistant to traditional therapy is the recent successful treatment of a progressing disseminated Mycobacterium abscessus infection in a teenage patient with the use of an engineered phage. In this review, we briefly present current methods of phage genetic engineering, highlighting their advantages and disadvantages, and provide examples of genetically engineered phages with a modified host range, improved safety or antibacterial activity, and proven therapeutic efficacy. We also summarize novel uses of engineered phages not only for killing pathogenic bacteria, but also for in situ modification of human microbiota to attenuate symptoms of certain bacterial diseases and metabolic, immune, or mental disorders.
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Affiliation(s)
- Małgorzata Łobocka
- Institute of Biochemistry and Biophysics of the Polish Academy of Sciences, Warsaw, Poland
| | - Krystyna Dąbrowska
- Institute of Immunology and Experimental Therapy of the Polish Academy of Sciences, Wrocław, Poland
| | - Andrzej Górski
- Institute of Immunology and Experimental Therapy of the Polish Academy of Sciences, Wrocław, Poland
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Isolation and Characterization of Two Virulent Phages to Combat Staphylococcus aureus and Enterococcus faecalis causing Dental Caries. JOURNAL OF PURE AND APPLIED MICROBIOLOGY 2021. [DOI: 10.22207/jpam.15.1.25] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
This study aimed to isolate and characterize bacteriophages, as a biocontrol agent, against certain antibiotic-resistant bacteria causing dental caries. Here, two dental caries-causing bacteria S. aureus and E. faecalis were isolated and characterized biochemically using the automated VITEK® 2 system. Antibiotic sensitivity pattern of the isolated dental caries bacteria was assessed against selection of antibiotics. The two isolates showed resistance against most of the tested antibiotics. To overcome this problem, two lytic phages vB_SauM-EG-AE3 and vB_EfaP-EF01 were isolated, identified, and applied to control the growth of S. aureus and E. faecalis, respectively. Phages were identified morphologically using TEM and showed that vB_SauM-EG-AE3 phage is related to Myoviridae and vB_EfaP-EF01 phage belongs to Podoviridae. The two phages exhibited high lytic activity, high stability, and a narrow host range. The one-step growth curve of phages showed burst sizes of 78.87 and 113.55 PFU/cell with latent periods of 25 and 30 minutes for S. aureus phage and E. faecalis phage respectively. In addition, the two phages showed different structural protein profiles and exhibited different patterns using different restriction enzymes. The genome sizes were estimated to be 13.30 Kb and 15.60 Kb for phages vB_SauM-EGAE3, vB_EfaP-EGAE1, respectively. Complete inhibition of bacterial growth was achieved using phages with MOIs of 103, 102 and 10 after 1, 3, 5, and 24 h of incubation at 37°C. Hence, this study indicates that the isolated bacteriophages are promising biocontrol agents that could challenge antibiotic-resistant dental caries bacteria to announce new successful alternatives to antibiotics.
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Pereira C, Costa P, Pinheiro L, Balcão VM, Almeida A. Kiwifruit bacterial canker: an integrative view focused on biocontrol strategies. PLANTA 2021; 253:49. [PMID: 33502587 DOI: 10.1007/s00425-020-03549-1] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 12/22/2020] [Indexed: 06/12/2023]
Abstract
Phage-based biocontrol strategies can be an effective alternative to control Psa-induced bacterial canker of kiwifruit. The global production of kiwifruit has been seriously affected by Pseudomonas syringae pv. actinidiae (Psa) over the last decade. Psa damages both Actinidia chinensis var. deliciosa (green kiwifruit) but specially the susceptible Actinidia chinensis var. chinensis (gold kiwifruit), resulting in severe economic losses. Treatments for Psa infections currently available are scarce, involving frequent spraying of the kiwifruit plant orchards with copper products. However, copper products should be avoided since they are highly toxic and lead to the development of bacterial resistance to this metal. Antibiotics are also used in some countries, but bacterial resistance to antibiotics is a serious worldwide problem. Therefore, it is essential to develop new approaches for sustainable agriculture production, avoiding the emergence of resistant Psa bacterial strains. Attempts to develop and establish highly accurate approaches to combat and prevent the occurrence of bacterial canker in kiwifruit plants are currently under study, using specific viruses of bacteria (bacteriophages, or phages) to eliminate the Psa. This review discusses the characteristics of Psa-induced kiwifruit canker, Psa transmission pathways, prevention and control, phage-based biocontrol strategies as a new approach to control Psa in kiwifruit orchards and its advantages over other therapies, together with potential ways to bypass phage inactivation by abiotic factors.
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Affiliation(s)
- Carla Pereira
- Department of Biology and CESAM, University of Aveiro, Campus de Santiago, 3810-193, Aveiro, Portugal
| | - Pedro Costa
- Department of Biology and CESAM, University of Aveiro, Campus de Santiago, 3810-193, Aveiro, Portugal
| | - Larindja Pinheiro
- Department of Biology and CESAM, University of Aveiro, Campus de Santiago, 3810-193, Aveiro, Portugal
| | - Victor M Balcão
- Department of Biology and CESAM, University of Aveiro, Campus de Santiago, 3810-193, Aveiro, Portugal.
- PhageLab - Laboratory of Biofilms and Bacteriophages, University of Sorocaba, Sorocaba, SP, CEP 18023-000, Brazil.
| | - Adelaide Almeida
- Department of Biology and CESAM, University of Aveiro, Campus de Santiago, 3810-193, Aveiro, Portugal.
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Pires DP, Monteiro R, Mil-Homens D, Fialho A, Lu TK, Azeredo J. Designing P. aeruginosa synthetic phages with reduced genomes. Sci Rep 2021; 11:2164. [PMID: 33495501 PMCID: PMC7835345 DOI: 10.1038/s41598-021-81580-2] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Accepted: 12/29/2020] [Indexed: 12/18/2022] Open
Abstract
In the era where antibiotic resistance is considered one of the major worldwide concerns, bacteriophages have emerged as a promising therapeutic approach to deal with this problem. Genetically engineered bacteriophages can enable enhanced anti-bacterial functionalities, but require cloning additional genes into the phage genomes, which might be challenging due to the DNA encapsulation capacity of a phage. To tackle this issue, we designed and assembled for the first time synthetic phages with smaller genomes by knocking out up to 48% of the genes encoding hypothetical proteins from the genome of the newly isolated Pseudomonas aeruginosa phage vB_PaeP_PE3. The antibacterial efficacy of the wild-type and the synthetic phages was assessed in vitro as well as in vivo using a Galleria mellonella infection model. Overall, both in vitro and in vivo studies revealed that the knock-outs made in phage genome do not impair the antibacterial properties of the synthetic phages, indicating that this could be a good strategy to clear space from phage genomes in order to enable the introduction of other genes of interest that can potentiate the future treatment of P. aeruginosa infections.
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Affiliation(s)
- Diana P Pires
- CEB - Centre of Biological Engineering, Universidade Do Minho, Campus de Gualtar, Braga, Portugal.
| | - Rodrigo Monteiro
- CEB - Centre of Biological Engineering, Universidade Do Minho, Campus de Gualtar, Braga, Portugal
| | - Dalila Mil-Homens
- Institute for Bioengineering and Biosciences (iBB), Instituto Superior Técnico, Lisboa, Portugal
| | - Arsénio Fialho
- Institute for Bioengineering and Biosciences (iBB), Instituto Superior Técnico, Lisboa, Portugal
- Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Lisboa, Portugal
| | - Timothy K Lu
- Department of Electrical Engineering and Computer Science and Department of Biological Engineering, Synthetic Biology Center, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA
| | - Joana Azeredo
- CEB - Centre of Biological Engineering, Universidade Do Minho, Campus de Gualtar, Braga, Portugal.
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Comparison of single and multi-host enrichment approach for harnessing lytic phages against antimicrobial-resistant E. coli: Repurposing the enrichment step. Biologia (Bratisl) 2021. [DOI: 10.2478/s11756-020-00652-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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48
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Wu MY, Li WW, Christie G, Setlow P, Li YQ. Characterization of Heterogeneity and Dynamics of Lysis of Single Bacillus subtilis Cells upon Prophage Induction During Spore Germination, Outgrowth, and Vegetative Growth Using Raman Tweezers and Live-Cell Phase-Contrast Microscopy. Anal Chem 2020; 93:1443-1450. [PMID: 33369381 DOI: 10.1021/acs.analchem.0c03341] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
A prophage comprises a bacteriophage genome that has integrated into a host bacterium's DNA, which generally permits the cell to grow and divide normally. However, the prophage can be induced by various stresses, or induction can occur spontaneously. After prophage induction, viral replication and production of endolysins begin until the cell lyses and phage particles are released. However, the heterogeneity of prophage induction and lysis of individual cells in a population and the dynamics of a cell undergoing lysis by prophage induction have not been fully characterized. Here, we used Raman tweezers and live-cell phase-contrast microscopy to characterize the Raman spectral and cell length changes that occur during the lysis of individual Bacillus subtilis cells from spores that carry PBSX prophage during spores' germination, outgrowth, and then vegetative growth. Major findings of this work are as follows: (i) After addition of xylose to trigger prophage induction, the intensities of Raman spectral bands associated with nucleic acids of single cells in induced cultures gradually fell to zero, in contrast to the much smaller changes in protein band intensities and no changes in nucleic acid bands in uninduced cultures; (ii) the nucleic acid band intensities from an individual induced cell exhibited a rapid decrease, following a long lag period; (iii) after the addition of nutrient-rich medium with xylose, single spores underwent a long period (228 ± 41.4 min) for germination, outgrowth, and vegetative growth, followed by a short period of cell burst in 1.5 ± 0.8 min at a cell length of 8.2 ± 5.5 μm; (iv) the latent time (Tlatent) between the addition of xylose and the start of cell burst was heterogeneous in cell populations; however, the period (ΔTburst) from the latent time to the completion of cell lysis was quite small; (v) in a poor medium with l-alanine alone, addition of xylose caused prophage induction following spore germination but with longer Tlatent and ΔTburst times and without cell elongation; (vi) spontaneous prophage induction and lysis of individual cells from spores in a minimal nutrient medium were observed without xylose addition, and cell length prior to cell lysis was ∼4.1 μm, but spontaneous prophage induction was not observed in a rich medium; (vii) in a rich medium, addition of xylose at a time well after spore germination and outgrowth significantly shortened the average Tlatent time. The results of this study provide new insights into the heterogeneity and dynamics of lysis of individual B. subtilis cells derived from spores upon prophage induction.
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Affiliation(s)
- Mei-Yan Wu
- Department of Physics, East Carolina University, Greenville, North Carolina 27858-4353, United States
| | | | - Graham Christie
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge CB3 0AS, U.K
| | - Peter Setlow
- Department of Molecular Biology and Biophysics, UCONN Health, Farmington, Connecticut 06030-3305, United States
| | - Yong-Qing Li
- Department of Physics, East Carolina University, Greenville, North Carolina 27858-4353, United States.,School of Electronic Engineering, Dongguan University of Technology, Dongguan, Guangdong 523808, P. R. China
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λ Recombineering Used to Engineer the Genome of Phage T7. Antibiotics (Basel) 2020; 9:antibiotics9110805. [PMID: 33202746 PMCID: PMC7697293 DOI: 10.3390/antibiotics9110805] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 11/10/2020] [Accepted: 11/12/2020] [Indexed: 01/21/2023] Open
Abstract
Bacteriophage T7 and T7-like bacteriophages are valuable genetic models for lytic phage biology that have heretofore been intractable with in vivo genetic engineering methods. This manuscript describes that the presence of λ Red recombination proteins makes in vivo recombineering of T7 possible, so that single base changes and whole gene replacements on the T7 genome can be made. Red recombination functions also increase the efficiency of T7 genome DNA transfection of cells by ~100-fold. Likewise, Red function enables two other T7-like bacteriophages that do not normally propagate in E. coli to be recovered following genome transfection. These results constitute major technical advances in the speed and efficiency of bacteriophage T7 engineering and will aid in the rapid development of new phage variants for a variety of applications.
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50
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Oral delivery of bacteria: Basic principles and biomedical applications. J Control Release 2020; 327:801-833. [DOI: 10.1016/j.jconrel.2020.09.011] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Accepted: 09/05/2020] [Indexed: 12/18/2022]
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