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Chakraborty S, Rohit A, Prasanthi SJ, Chauhan A. A New Casjensviridae Bacteriophage Isolated from Hospital Sewage for Inactivation of Biofilms of Carbapenem Resistant Klebsiella pneumoniae Clinical Isolates. Pharmaceutics 2024; 16:904. [PMID: 39065601 PMCID: PMC11280391 DOI: 10.3390/pharmaceutics16070904] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2024] [Revised: 06/19/2024] [Accepted: 06/21/2024] [Indexed: 07/28/2024] Open
Abstract
Klebsiella pneumoniae, a member of the ESKAPE pathogen group, is a prominent cause of hospital-acquired infections. The WHO has recognized carbapenem-resistant K. pneumoniae as a critical-one priority pathogen. These resilient superbugs have the ability to form biofilms and present a significant global threat. In the present study, we isolated and characterized a bacteriophage SAKp02, from hospital sewage, infectious to carbapenem-resistant K. pneumoniae patient isolates. SAKp02 could infect 43 of 72 clinical isolates, indicating a broad host spectrum. Whole genome analysis classified SAKp02 within the family Casjensviridae, with a 59,343 bp genome encoding 82 ORFs. Comparative genomic analysis revealed significant differences between SAKp02 and its closest viruses, indicating a distinct genetic makeup positioning it as a novel phage strain within the lineage. The SAKp02 genome comprises bacteriolytic enzymes, including holin, endolysin, and phage depolymerase, crucial for bacterial lysis and biofilm disruption. It reduced biofilm biomass by over threefold compared to the control and eradicated 99% of viable cells within a 4 h treatment period. Scanning electron microscopy corroborated the ability of the phage to dismantle biofilm matrices and lyse bacterial cells. Safe and effective treatments are warranted, and hence, the fully characterized lytic phages with therapeutic potential against drug-resistant clinical isolates of bacteria are needed. Our study is the first to report the antibacterial and antibiofilm activity of Casjensviridae phages, and our discovery of a novel K. pneumoniae phage broadens the arsenal against the bacteria.
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Affiliation(s)
- Sambuddha Chakraborty
- Department of Microbiology, Tripura University, Suryamaninagar 799022, India
- Department of Microbiology, University of Delhi South Campus, Benito Jaurez Marg, New Delhi 110021, India
| | - Anusha Rohit
- Madras Medical Mission Hospital, Chennai 600037, India
| | | | - Ashwini Chauhan
- Department of Microbiology, Tripura University, Suryamaninagar 799022, India
- Department of Microbiology, University of Delhi South Campus, Benito Jaurez Marg, New Delhi 110021, India
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2
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Maffei E, Woischnig AK, Burkolter MR, Heyer Y, Humolli D, Thürkauf N, Bock T, Schmidt A, Manfredi P, Egli A, Khanna N, Jenal U, Harms A. Phage Paride can kill dormant, antibiotic-tolerant cells of Pseudomonas aeruginosa by direct lytic replication. Nat Commun 2024; 15:175. [PMID: 38168031 PMCID: PMC10761892 DOI: 10.1038/s41467-023-44157-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Accepted: 12/01/2023] [Indexed: 01/05/2024] Open
Abstract
Bacteriophages are ubiquitous viral predators that have primarily been studied using fast-growing laboratory cultures of their bacterial hosts. However, microbial life in nature is mostly in a slow- or non-growing, dormant state. Here, we show that diverse phages can infect deep-dormant bacteria and suspend their replication until the host resuscitates ("hibernation"). However, a newly isolated Pseudomonas aeruginosa phage, named Paride, can directly replicate and induce the lysis of deep-dormant hosts. While non-growing bacteria are notoriously tolerant to antibiotic drugs, the combination with Paride enables the carbapenem meropenem to eradicate deep-dormant cultures in vitro and to reduce a resilient bacterial infection of a tissue cage implant in mice. Our work might inspire new treatments for persistent bacterial infections and, more broadly, highlights two viral strategies to infect dormant bacteria (hibernation and direct replication) that will guide future studies on phage-host interactions.
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Affiliation(s)
- Enea Maffei
- Biozentrum, University of Basel, Basel, Switzerland
- Institute of Food, Nutrition and Health, D-HEST, ETH Zurich, Zurich, Switzerland
| | - Anne-Kathrin Woischnig
- Laboratory of Infection Biology, Department of Biomedicine, University and University Hospital Basel, Basel, Switzerland
| | - Marco R Burkolter
- Biozentrum, University of Basel, Basel, Switzerland
- Institute of Food, Nutrition and Health, D-HEST, ETH Zurich, Zurich, Switzerland
| | - Yannik Heyer
- Biozentrum, University of Basel, Basel, Switzerland
| | - Dorentina Humolli
- Institute of Food, Nutrition and Health, D-HEST, ETH Zurich, Zurich, Switzerland
| | | | - Thomas Bock
- Biozentrum, University of Basel, Basel, Switzerland
| | | | | | - Adrian Egli
- Division of Clinical Bacteriology and Mycology, University Hospital Basel, Basel, Switzerland
- Applied Microbiology Research, Department of Biomedicine, University of Basel, Basel, Switzerland
- Division of Infectious Diseases and Hospital Epidemiology, University and University Hospital of Basel, Basel, Switzerland
| | - Nina Khanna
- Institute of Food, Nutrition and Health, D-HEST, ETH Zurich, Zurich, Switzerland
- Laboratory of Infection Biology, Department of Biomedicine, University and University Hospital Basel, Basel, Switzerland
| | - Urs Jenal
- Biozentrum, University of Basel, Basel, Switzerland
| | - Alexander Harms
- Biozentrum, University of Basel, Basel, Switzerland.
- Institute of Food, Nutrition and Health, D-HEST, ETH Zurich, Zurich, Switzerland.
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3
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Oliveira H, Santos S, Pires DP, Boeckaerts D, Pinto G, Domingues R, Otero J, Briers Y, Lavigne R, Schmelcher M, Dötsch A, Azeredo J. CkP1 bacteriophage, a S16-like myovirus that recognizes Citrobacter koseri lipopolysaccharide through its long tail fibers. Appl Microbiol Biotechnol 2023; 107:3621-3636. [PMID: 37133800 PMCID: PMC10175313 DOI: 10.1007/s00253-023-12547-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 04/11/2023] [Accepted: 04/17/2023] [Indexed: 05/04/2023]
Abstract
Citrobacter koseri is an emerging Gram-negative bacterial pathogen, which causes urinary tract infections. We isolated and characterized a novel S16-like myovirus CKP1 (vB_CkoM_CkP1), infecting C. koseri. CkP1 has a host range covering the whole C. koseri species, i.e., all strains that were tested, but does not infect other species. Its linear 168,463-bp genome contains 291 coding sequences, sharing sequence similarity with the Salmonella phage S16. Based on surface plasmon resonance and recombinant green florescence protein fusions, the tail fiber (gp267) was shown to decorate C. koseri cells, binding with a nanomolar affinity, without the need of accessory proteins. Both phage and the tail fiber specifically bind to bacterial cells by the lipopolysaccharide polymer. We further demonstrate that CkP1 is highly stable towards different environmental conditions of pH and temperatures and is able to control C. koseri cells in urine samples. Altogether, CkP1 features optimal in vitro characteristics to be used both as a control and detection agent towards drug-resistant C. koseri infections. KEY POINTS: • CkP1 infects all C. koseri strains tested • CkP1 recognizes C. koseri lipopolysaccharide through its long tail fiber • Both phage CkP1 and its tail fiber can be used to treat or detect C. koseri pathogens.
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Affiliation(s)
- Hugo Oliveira
- Centre of Biological Engineering, University of Minho, Braga, Portugal.
- LABBELS -Associate Laboratory, Braga, Guimarães, Portugal.
| | - Sílvio Santos
- Centre of Biological Engineering, University of Minho, Braga, Portugal
- LABBELS -Associate Laboratory, Braga, Guimarães, Portugal
| | - Diana P Pires
- Centre of Biological Engineering, University of Minho, Braga, Portugal
- LABBELS -Associate Laboratory, Braga, Guimarães, Portugal
| | | | - Graça Pinto
- Centre of Biological Engineering, University of Minho, Braga, Portugal
- LABBELS -Associate Laboratory, Braga, Guimarães, Portugal
| | - Rita Domingues
- Centre of Biological Engineering, University of Minho, Braga, Portugal
- LABBELS -Associate Laboratory, Braga, Guimarães, Portugal
| | - Jennifer Otero
- Centre of Biological Engineering, University of Minho, Braga, Portugal
- Departament de Genètica I de Microbiologia, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Yves Briers
- Department of Biotechnology, Ghent University, Ghent, Belgium
| | - Rob Lavigne
- Department of Biosystems, KU Leuven, Louvain, Belgium
| | - Mathias Schmelcher
- Institute of Food, Nutrition and Health, ETH Zurich, Zurich, Switzerland
| | - Andreas Dötsch
- Max Rubner-Institute, Department of Physiology and Biochemistry of Nutrition, Karlsruhe, Germany
| | - Joana Azeredo
- Centre of Biological Engineering, University of Minho, Braga, Portugal.
- LABBELS -Associate Laboratory, Braga, Guimarães, Portugal.
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Chen GY, Thorup NR, Miller AJ, Li YC, Ayres JS. Cooperation between physiological defenses and immune resistance produces asymptomatic carriage of a lethal bacterial pathogen. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.22.525099. [PMID: 36711884 PMCID: PMC9882269 DOI: 10.1101/2023.01.22.525099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Animals have evolved two defense strategies to survive infections. Antagonistic strategies include mechanisms of immune resistance that operate to sense and kill invading pathogens. Cooperative or physiological defenses mediate host adaptation to the infected state, limiting physiological damage and disease, without killing the pathogen, and have been shown to cause asymptomatic carriage and transmission of lethal pathogens. Here we demonstrate that physiological defenses cooperate with the adaptive immune response to generate long-term asymptomatic carriage of the lethal enteric murine pathogen, Citrobacter rodentium. Asymptomatic carriage of genetically virulent C. rodentium provided immune resistance against subsequent infections. Host immune protection was dependent on systemic antibody responses and pathogen virulence behavior, rather than the recognition of specific virulent factor antigens. Finally, we demonstrate that an avirulent strain of C. rodentium in the field has background mutations in two genes that are important for LPS structure. Our work reveals novel insight into how asymptomatic infections can arise mechanistically with immune resistance, mediating exclusion of phenotypically virulent enteric pathogen to promote asymptomatic carriage.
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Affiliation(s)
- Grischa Y Chen
- Molecular and Systems Physiology Lab, The Salk Institute for Biological Studies, La Jolla, CA 92037
- Gene Expression Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037
- NOMIS Center for Immunobiology and Microbial Pathogenesis, The Salk Institute for Biological Studies, La Jolla, CA 92037
| | - Natalia R Thorup
- Molecular and Systems Physiology Lab, The Salk Institute for Biological Studies, La Jolla, CA 92037
- Gene Expression Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037
- NOMIS Center for Immunobiology and Microbial Pathogenesis, The Salk Institute for Biological Studies, La Jolla, CA 92037
| | - Abigail J Miller
- Molecular and Systems Physiology Lab, The Salk Institute for Biological Studies, La Jolla, CA 92037
- Gene Expression Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037
- NOMIS Center for Immunobiology and Microbial Pathogenesis, The Salk Institute for Biological Studies, La Jolla, CA 92037
| | - Yao-Cheng Li
- Gene Expression Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037
| | - Janelle S Ayres
- Molecular and Systems Physiology Lab, The Salk Institute for Biological Studies, La Jolla, CA 92037
- Gene Expression Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037
- NOMIS Center for Immunobiology and Microbial Pathogenesis, The Salk Institute for Biological Studies, La Jolla, CA 92037
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5
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Aldaihani R, Heath LS. Connecting genomic islands across prokaryotic and phage genomes via protein families. Sci Rep 2023; 13:344. [PMID: 36611105 PMCID: PMC9825383 DOI: 10.1038/s41598-023-27584-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 01/04/2023] [Indexed: 01/09/2023] Open
Abstract
Prokaryotic genomes evolve via horizontal gene transfer (HGT), mutations, and rearrangements. A noteworthy part of the HGT process is facilitated by genomic islands (GIs). While previous computational biology research has focused on developing tools to detect GIs in prokaryotic genomes, there has been little research investigating GI patterns and biological connections across species. We have pursued the novel idea of connecting GIs across prokaryotic and phage genomes via patterns of protein families. Such patterns are sequences of protein families frequently present in the genomes of multiple species. We combined the large data set from the IslandViewer4 database with protein families from Pfam while implementing a comprehensive strategy to identify patterns making use of HMMER, BLAST, and MUSCLE. we also implemented Python programs that link the analysis into a single pipeline. Research results demonstrated that related GIs often exist in species that are evolutionarily unrelated and in multiple bacterial phyla. Analysis of the discovered patterns led to the identification of biological connections among prokaryotes and phages. These connections suggest broad HGT connections across the bacterial kingdom and its associated phages. The discovered patterns and connections could provide the basis for additional analysis on HGT breadth and the patterns in pathogenic GIs.
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Affiliation(s)
- Reem Aldaihani
- Department of Computer Science, Kuwait University, Kuwait City, State of Kuwait. .,Department of Computer Science, Virginia Tech, Blacksburg, VA, USA.
| | - Lenwood S. Heath
- grid.438526.e0000 0001 0694 4940Department of Computer Science, Virginia Tech, Blacksburg, VA USA
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6
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Schumann AR, Sue AD, Roach DR. Hypoxia Increases the Tempo of Phage Resistance and Mutational Bottlenecking of Pseudomonas aeruginosa. Front Microbiol 2022; 13:905343. [PMID: 35979493 PMCID: PMC9376454 DOI: 10.3389/fmicb.2022.905343] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Accepted: 06/16/2022] [Indexed: 11/23/2022] Open
Abstract
Viruses that infect bacteria (i.e., phages) are abundant and widespread in the human body, and new anti-infective approaches such as phage therapy are essential for the future of effective medicine. Our understanding of microenvironmental factors such as tissue oxygen availability at the site of phage-bacteria interaction remains limited, and it is unknown whether evolved resistance is sculpted differentially under normoxia vs. hypoxia. We, therefore, analyzed the phage-bacteria interaction landscape via adsorption, one-step, time-kill dynamics, and genetic evolution under both normoxia and hypoxia. This revealed that adsorption of phages to Pseudomonas aeruginosa decreased under 14% environmental oxygen (i.e., hypoxia), but phage time-kill and one-step growth kinetics were not further influenced. Tracking the adaptation of P. aeruginosa to phages uncovered a higher frequency of phage resistance and constrained types of spontaneous mutation under hypoxia. Given the interest in developing phage therapies, developing our understanding of the phage-pathogen interaction under microenvironmental conditions resembling those in the body offers insight into possible strategies to overcome multidrug-resistant (MDR) bacteria.
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Affiliation(s)
- Ashley R. Schumann
- Department of Biology, San Diego State University, San Diego, CA, United States
| | - Andrew D. Sue
- Department of Biology, San Diego State University, San Diego, CA, United States
| | - Dwayne R. Roach
- Department of Biology, San Diego State University, San Diego, CA, United States
- Viral Information Institute, San Diego State University, San Diego, CA, United States
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7
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Kabwe M, Dashper S, Tucci J. The Microbiome in Pancreatic Cancer-Implications for Diagnosis and Precision Bacteriophage Therapy for This Low Survival Disease. Front Cell Infect Microbiol 2022; 12:871293. [PMID: 35663462 PMCID: PMC9160434 DOI: 10.3389/fcimb.2022.871293] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 04/19/2022] [Indexed: 11/13/2022] Open
Abstract
While the mortality rates for many cancers have decreased due to improved detection and treatments, that of pancreatic cancer remains stubbornly high. The microbiome is an important factor in the progression of many cancers. Greater understanding of the microbiome in pancreatic cancer patients, as well as its manipulation, may assist in diagnosis and treatment of this disease. In this report we reviewed studies that compared microbiome changes in pancreatic cancer patients and non-cancer patients. We then identified which bacterial genera were most increased in relative abundance across the oral, pancreatic, duodenal, and faecal tissue microbiomes. In light of these findings, we discuss the potential for utilising these bacteria as diagnostic biomarkers, as well as their potential control using precision targeting with bacteriophages, in instances where a causal oncogenic link is made.
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Affiliation(s)
- Mwila Kabwe
- Department of Rural Clinical Sciences, La Trobe Rural Health School, La Trobe University, Bendigo, VIC, Australia
- La Trobe Institute for Molecular Science, La Trobe University, Bendigo, VIC, Australia
| | - Stuart Dashper
- Melbourne Dental School, University of Melbourne, Melbourne, VIC, Australia
| | - Joseph Tucci
- Department of Rural Clinical Sciences, La Trobe Rural Health School, La Trobe University, Bendigo, VIC, Australia
- La Trobe Institute for Molecular Science, La Trobe University, Bendigo, VIC, Australia
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8
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Finney AG, Perry JM, Evans DR, Westbrook KJ, McElheny CL, Iovleva A, Doi Y, Shields RK, Van Tyne D. Isolation and Characterization of Lytic Bacteriophages Targeting Diverse Enterobacter spp. Clinical Isolates. PHAGE (NEW ROCHELLE, N.Y.) 2022; 3:50-58. [PMID: 36147219 PMCID: PMC9041515 DOI: 10.1089/phage.2021.0011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Background: Enterobacter spp. are opportunistic pathogens that cause nosocomial infections. Bacteriophages could be used to treat antibiotic-resistant Enterobacter infections. Materials and Methods: We used 10 genetically diverse clinical Enterobacter spp. isolates to identify lytic bacteriophages in hospital and municipal wastewater. Comparative genomics was performed on host bacterial isolates and isolated phages. Activity of each phage against all 10 host isolates was determined. We also tested phage activity against paired isolates from two patients who developed ceftazidime-avibactam resistance. Results: Bacteria belonged to three Enterobacter species and Klebsiella aerogenes. We isolated 12 bacteriophages, most of which belonged to the Myoviridae and Autographiviridae families. Most phages were able to lyse multiple bacterial isolates, and many lysed isolates of different species. Ceftazidime-avibactam-resistant isolates were still phage susceptible, and one isolate showed increased susceptibility compared with the parent isolate. Conclusion: The phages we isolated expand the diversity of Enterobacter-targeting phages, and could be useful for treating antibiotic-resistant Enterobacter infections.
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Affiliation(s)
- Amanda G. Finney
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Jalyne M. Perry
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Daniel R. Evans
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Kevin J. Westbrook
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Christi L. McElheny
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Alina Iovleva
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Yohei Doi
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Ryan K. Shields
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Daria Van Tyne
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
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Li J, Zhao F, Zhan W, Li Z, Zou L, Zhao Q. Challenges for the application of bacteriophages as effective antibacterial agents in the food industry. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2022; 102:461-471. [PMID: 34487550 DOI: 10.1002/jsfa.11505] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 07/12/2021] [Accepted: 09/06/2021] [Indexed: 06/13/2023]
Abstract
Food contamination caused by foodborne pathogens is one of the most important concerns in public health worldwide, and accounts for a significant portion of food loss every year. The emergence of antimicrobial resistant bacteria has turned the attention of researchers back to the potential of bacteriophages as antibacterial agents, and their use has been attempted in various pre-and post-harvest food production settings. The application of phage-based antibacterial products has achieved considerable success but a number of technical, environmental and administrative challenges remain unaddressed. In this review, we summarize the current status of bacteriophage application in the food industry. We discuss the obstacles facing the further development of phage-based antibacterial products from the aspects of technology, environmental safety, and administrative policy. We also advance some possible solutions to these challenges. © 2021 Society of Chemical Industry.
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Affiliation(s)
- Jian Li
- Institute of Cancer Biology and Drug Discovery, Chengdu University, Chengdu, China
- School of Basic Medical Sciences, Chengdu University, Chengdu, China
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Chengdu University, Chengdu, China
| | - Feng Zhao
- School of Food and Biological Engineering, Chengdu University, Chengdu, China
| | - Wenyao Zhan
- School of Food and Biological Engineering, Chengdu University, Chengdu, China
| | - Zhiqi Li
- School of Food and Biological Engineering, Chengdu University, Chengdu, China
| | - Liang Zou
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Chengdu University, Chengdu, China
- School of Food and Biological Engineering, Chengdu University, Chengdu, China
| | - Qi Zhao
- School of Food and Biological Engineering, Chengdu University, Chengdu, China
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10
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Fathima B, Archer AC. Bacteriophage therapy: Recent developments and applications of a renaissant weapon. Res Microbiol 2021; 172:103863. [PMID: 34293451 DOI: 10.1016/j.resmic.2021.103863] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 07/08/2021] [Accepted: 07/08/2021] [Indexed: 10/20/2022]
Abstract
Antimicrobial resistance is a global health problem and one of the leading concerns in healthcare sector. Bacteriophages are antibacterial agents ubiquitous in nature. With increase in antibiotic resistance, use of bacteriophages as therapeutics has become resurgent in recent times. This review focuses on the recent developments in phage therapy and its applications with respect to human infections, animal, food and environment. Moreover, use of phage proteins, bioengineered bacteriophages, and phage derived vaccines is also highlighted. Additionally, the limitations and challenges with regard to implementation of phage therapy, host safety and immune responses are also reviewed in this article.
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Affiliation(s)
- Bibi Fathima
- Department of Microbiology, Faculty of Life Sciences, JSS Academy of Higher Education & Research, Sri Shivarathreeshwara Nagara, Mysuru, Karnataka, 570015, India
| | - Ann Catherine Archer
- Department of Microbiology, Faculty of Life Sciences, JSS Academy of Higher Education & Research, Sri Shivarathreeshwara Nagara, Mysuru, Karnataka, 570015, India.
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11
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Huss P, Meger A, Leander M, Nishikawa K, Raman S. Mapping the functional landscape of the receptor binding domain of T7 bacteriophage by deep mutational scanning. eLife 2021; 10:e63775. [PMID: 33687327 PMCID: PMC8043750 DOI: 10.7554/elife.63775] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Accepted: 03/04/2021] [Indexed: 12/13/2022] Open
Abstract
The interaction between a bacteriophage and its host is mediated by the phage's receptor binding protein (RBP). Despite its fundamental role in governing phage activity and host range, molecular rules of RBP function remain a mystery. Here, we systematically dissect the functional role of every residue in the tip domain of T7 phage RBP (1660 variants) by developing a high-throughput, locus-specific, phage engineering method. This rich dataset allowed us to cross compare functional profiles across hosts to precisely identify regions of functional importance, many of which were previously unknown. Substitution patterns showed host-specific differences in position and physicochemical properties of mutations, revealing molecular adaptation to individual hosts. We discovered gain-of-function variants against resistant hosts and host-constricting variants that eliminated certain hosts. To demonstrate therapeutic utility, we engineered highly active T7 variants against a urinary tract pathogen. Our approach presents a generalized framework for characterizing sequence-function relationships in many phage-bacterial systems.
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Affiliation(s)
- Phil Huss
- Department of Biochemistry, University of Wisconsin-MadisonMadisonUnited States
- Department of Bacteriology, University of Wisconsin-MadisonMadisonUnited States
| | - Anthony Meger
- Department of Biochemistry, University of Wisconsin-MadisonMadisonUnited States
| | - Megan Leander
- Department of Biochemistry, University of Wisconsin-MadisonMadisonUnited States
| | - Kyle Nishikawa
- Department of Biochemistry, University of Wisconsin-MadisonMadisonUnited States
| | - Srivatsan Raman
- Department of Biochemistry, University of Wisconsin-MadisonMadisonUnited States
- Department of Bacteriology, University of Wisconsin-MadisonMadisonUnited States
- Department of Chemical and Biological Engineering, University of Wisconsin-MadisonMadisonUnited States
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12
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Hodges FE, Sicheritz-Pontén T, Clokie MR. The Effect of Oxygen Availability on Bacteriophage Infection: A Review. PHAGE (NEW ROCHELLE, N.Y.) 2021; 2:16-25. [PMID: 36148442 PMCID: PMC9041485 DOI: 10.1089/phage.2020.0041] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Bacteriophages offer a viable solution to addressing the global issue of bacterial resistance to antimicrobials. Although knowledge of bacteriophages has increased greatly since their discovery in 1915, a significant amount of what is currently known is based on studies conducted in model conditions and aerobic environments. There are a variety of environments in which bacteriophages could be applied to successfully replace or supplement antimicrobials in agriculture, food production, and human medicine where the amount of oxygen is limited. There is a need to use phages in oxygen-limited environments, but few studies have examined the impact oxygen-limited environments have on the ability of phages to kill their hosts. The work that has been done is, however, insightful and will likely stimulate this area that is growing in importance as our need to use phages grows. This review summarizes the studies to date that have reported the characteristics of phages in both oxygen-rich and oxygen-limited environments. We also discuss the importance of considering the ultimate environment a phage will be applied to when designing experiments to isolate and characterize phages for use in phage-based antimicrobial products.
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Affiliation(s)
- Francesca E. Hodges
- Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
| | - Thomas Sicheritz-Pontén
- Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
- Centre of Excellence for Omics-Driven Computational Biodiscovery (COMBio), Faculty of Applied Sciences, AIMST University, Kedah, Malaysia
| | - Martha R.J. Clokie
- Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
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Kumar P, Meghvansi MK, Kamboj DV. Phenotypic Characterization and Whole-Genome Analysis of a Novel Bacteriophage HCF1 Infecting Citrobacter amalonaticus and C. freundii. Front Microbiol 2021; 12:644013. [PMID: 33569047 PMCID: PMC7868345 DOI: 10.3389/fmicb.2021.644013] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Accepted: 01/04/2021] [Indexed: 12/26/2022] Open
Abstract
Citrobacter species often occur in sewage, food, soil, wastewater, and in the intestinal tract of animals and humans. Citrobacter spp. cause urinary tract infections (UTIs) and infantile meningitis in humans. Due to the presence of plasmid-encoded resistance genes, Citrobacter spp. are often resistant to many antibiotics. In this study, Citrobacter virus HCF1, a novel virulent bacteriophage capable of killing Citrobacter amalonaticus and Citrobacter freundii, was isolated from the sewage water. The isolated bacteriophage was characterized with respect to transmission electron microscopy, one-step growth curve, host range, in vitro efficacy, storage stability, and environmental stress tolerance. The one-step growth curve analysis revealed that the latent period of HCF1 was 30 min and the estimated burst size was 121 plaque-forming units (PFU) per bacterial cell. Host range testing indicated that the HCF1 was specific to the Citrobacter genus. In vitro efficacy assay in the effluent of an anaerobic biodigester showed that the HCF1 completely eliminated the host within 4 and 5 h at MOI:100 and MOI:10, respectively, thereby indicating its potential for combating C. amalonaticus infections. The isolated bacteriophage is considerably stable and tolerant to environmental stress. Furthermore, the complete genome of HCF1 was sequenced using Oxford Nanopore sequencing and the data were subjected to detailed bioinformatic analyses. NCBI-BLASTn analysis revealed that the HCF1 genome had a query coverage of 15-21% and a maximum similarity of 77.27-78.49% with 11 bacteriophages of the Drexlerviridae family. Detailed bioinformatic analysis of the genome profile suggests that HCF1 is a novel T1svirus belonging to the Tempevirinae subfamily of the Drexlerviridae family.
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Affiliation(s)
| | | | - Dev V. Kamboj
- Biotechnology Division, Defence Research and Development Establishment, Gwalior, India
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Does over a century of aerobic phage work provide a solid framework for the study of phages in the gut? Anaerobe 2021; 68:102319. [PMID: 33465423 DOI: 10.1016/j.anaerobe.2021.102319] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 01/09/2021] [Accepted: 01/11/2021] [Indexed: 12/13/2022]
Abstract
Bacterial viruses (bacteriophages, phages) of the gut have increasingly become a focus in microbiome studies, with an understanding that they are likely key players in health and disease. However, characterization of the virome remains largely based on bioinformatic approaches, with the impact of these viromes inferred based on a century of knowledge from aerobic phage work. Studying the phages infecting anaerobes is difficult, as they are often technically demanding to isolate and propagate. In this review, we primarily discuss the phages infecting three well-studied anaerobes in the gut: Bifidobacterium, Clostridia and Bacteroides, with a particular focus on the challenges in isolating and characterizing these phages. We contrast the lessons learned from these to other anaerobic work on phages infecting facultative anaerobes of the gut: Enterococcus and Lactobacillus. Phages from the gut do appear to adhere to the lessons learned from aerobic work, but the additional challenges of working on them has required ingenious new approaches to enable their study. This, in turn, has uncovered remarkable biology likely underpinning phage-host relationships in many stable environments.
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