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Ssekatawa K, Ntulume I, Byarugaba DK, Michniewski S, Jameson E, Wampande EM, Nakavuma J. Isolation and Characterization of Novel Lytic Bacteriophages Infecting Carbapenem-Resistant Pathogenic Diarrheagenic and Uropathogenic Escherichia Coli. Infect Drug Resist 2024; 17:3367-3384. [PMID: 39135747 PMCID: PMC11317518 DOI: 10.2147/idr.s466101] [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: 02/27/2024] [Accepted: 07/31/2024] [Indexed: 08/15/2024] Open
Abstract
Background The evolution of antimicrobial resistance has dramatically reduced the efficacy of the first-choice and last-resort antibiotics used to treat E. coli infections. Thus, searching for novel therapeutics to treat and control the emergence of antibiotic resistance is urgent. Therefore, this study aimed to illustrate the lytic effect of phages against carbapenem-resistant pathogenic E. coli. Methods Phages were isolated from hospital effluents by the enrichment assay. This was followed by the evaluation of the host range of the phages by the spot assay. The time taken by phages to bind to the host bacterial cells was determined by the adsorption assay. The phage latent period and burst size were determined using a one-step growth experiment. Phage morphology was determined by the Transmission Electron Microscopy. Molecular characterization of phages was done by whole genome sequencing. Results Two phages named UGKSEcP1 and UGKSEcP2 were isolated from hospital effluents. The phages were professionally lytic with a broad host range. The two phages recorded an average adsorption time of 11.25 minutes, an adsorption rate of 99.3%, a latency period of 20 minutes, and a burst size of approximately 528 phages/infected cell. Phages UGKSEcP1 and UGKSEcP2 had genome lengths of 167433bp, and 167221bp with 277 and 276 predicted genes, respectively, and no undesirable genes were detected. Phylogenetic analysis revealed the two phages belonged genus Tequatrovirus. TEM micrograph showed that the two phages had a similar morphotype with icosahedral heads and contractile tails; thus, classified as members of the Myoviridae phage family. Conclusion The findings demonstrate that the study isolated two novel professionally lytic phages with a broad host range and thus, are candidates for phage-mediated biocontrol.
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Affiliation(s)
- Kenneth Ssekatawa
- Department of Science Technical and Vocational Education, Makerere University, Kampala, Uganda
- Africa Center of Excellence in Materials, Product Development and Nanotechnology (MAPRONANO ACE), Makerere University, Kampala, Uganda
| | - Ibrahim Ntulume
- Department of Biotechnical and Diagnostic Sciences, Makerere University, Kampala, Uganda
| | | | | | - Eleanor Jameson
- School of Environmental and Natural Sciences, Bangor University, Gwynedd, UK
| | - Eddie M Wampande
- Department of Veterinary Pharmacy, Clinical and Comparative Medicine, Makerere University, Kampala, Uganda
| | - Jesca Nakavuma
- Department of Biotechnical and Diagnostic Sciences, Makerere University, Kampala, Uganda
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2
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Zalewska-Piątek B. Phage Therapy-Challenges, Opportunities and Future Prospects. Pharmaceuticals (Basel) 2023; 16:1638. [PMID: 38139765 PMCID: PMC10747886 DOI: 10.3390/ph16121638] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 11/14/2023] [Accepted: 11/20/2023] [Indexed: 12/24/2023] Open
Abstract
The increasing drug resistance of bacteria to commonly used antibiotics creates the need to search for and develop alternative forms of treatment. Phage therapy fits this trend perfectly. Phages that selectively infect and kill bacteria are often the only life-saving therapeutic option. Full legalization of this treatment method could help solve the problem of multidrug-resistant infectious diseases on a global scale. The aim of this review is to present the prospects for the development of phage therapy, the ethical and legal aspects of this form of treatment given the current situation of such therapy, and the benefits of using phage products in persons for whom available therapeutic options have been exhausted or do not exist at all. In addition, the challenges faced by this form of therapy in the fight against bacterial infections are also described. More clinical studies are needed to expand knowledge about phages, their dosage, and a standardized delivery system. These activities are necessary to ensure that phage-based therapy does not take the form of an experiment but is a standard medical treatment. Bacterial viruses will probably not become a miracle cure-a panacea for infections-but they have a chance to find an important place in medicine.
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Affiliation(s)
- Beata Zalewska-Piątek
- Department of Molecular Biotechnology and Microbiology, Chemical Faculty, Gdańsk University of Technology, Narutowicza 11/12, 80-233 Gdańsk, Poland
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3
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Sagar SS, Rani S, Pushpa Sadanandan S. Combined Effect of Isolated Bacteriophage and Neem Extract on Isolated Multiple Drug-Resistant Pathogenic Escherichia coli E1 From Well Water. ENVIRONMENTAL HEALTH INSIGHTS 2023; 17:11786302231166818. [PMID: 37223331 PMCID: PMC10201146 DOI: 10.1177/11786302231166818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Accepted: 03/13/2023] [Indexed: 05/25/2023]
Abstract
Multiple drug-resistant Escherichia coli (E. coli) is a serious cause of concern, and they can be observed in hospital settings, natural environment, and animals. Dissemination of multiple drug-resistant (MDR) E. coli can pose a high risk to public health. Moreover, they are hard to control with commercial antibiotics, since they have acquired resistance against most of them. Therefore, to control multiple drug-resistant bacteria, alternative strategies have been adopted such as phage therapy, herbal remedies, nanoparticles etc. In the current study, the combined application of neem leaf extract and bacteriophage is used to control an isolated multiple drug-resistant E. coli E1. We have applied 0.1 mg/ml concentration of neem extract in combination with an isolated phage vB_EcoM_C2 of 1011 titer and found that the combinatorial treatment approach significantly controls the growth of E. coli E1 as compared to a single non-combinatorial treatment. In this study, every E. coli cell is targeted by 2 antimicrobials (phage and neem extract) at the same time, which is more effective as compared to the sole treatment. Implementation of the neem extract with phage opens a new alternative approach to the chemotherapeutics for the control of multiple drug-resistant bacterial pathogens. This approach may be effective, economical, and eco-friendly to combat MDR.
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Affiliation(s)
- Sadhana Singh Sagar
- Sadhana Singh Sagar, Ecology and
Environment Research Group, Center for Water Resources Development and
management, Kunnamangalam, Kozhikode 673571, Kerala.
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4
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Crum E, Merchant Z, Ene A, Miller-Ensminger T, Johnson G, Wolfe AJ, Putonti C. Coliphages of the human urinary microbiota. PLoS One 2023; 18:e0283930. [PMID: 37053131 PMCID: PMC10101464 DOI: 10.1371/journal.pone.0283930] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 03/20/2023] [Indexed: 04/14/2023] Open
Abstract
Due to its frequent association with urinary tract infections (UTIs), Escherichia coli is the best characterized constituent of the urinary microbiota (urobiome). However, uropathogenic E. coli is just one member of the urobiome. In addition to bacterial constituents, the urobiome of both healthy and symptomatic individuals is home to a diverse population of bacterial viruses (bacteriophages). A prior investigation found that most bacterial species in the urobiome are lysogens, harboring one or more phages integrated into their genome (prophages). Many of these prophages are temperate phages, capable of entering the lytic cycle and thus lysing their bacterial host. This transition from the lysogenic to lytic life cycle can impact the bacterial diversity of the urobiome. While many phages that infect E. coli (coliphages) have been studied for decades in the laboratory setting, the coliphages within the urobiome have yet to be cataloged. Here, we investigated the diversity of urinary coliphages by first identifying prophages in all publicly available urinary E. coli genomes. We detected 3,038 intact prophage sequences, representative of 1,542 unique phages. These phages include both novel species as well as species also found within the gut microbiota. Ten temperate phages were isolated from urinary E. coli strains included in our analysis, and we assessed their ability to infect and lyse urinary E. coli strains. We also included in these host range assays other urinary coliphages and laboratory coliphages. The temperate phages and other urinary coliphages were successful in lysing urinary E. coli strains. We also observed that coliphages from non-urinary sources were most efficient in killing urinary E. coli strains. The two phages, T2 and N4, were capable of lysing 83.5% (n = 86) of strains isolated from females with UTI symptoms. In conclusion, our study finds a diverse community of coliphages in the urobiome, many of which are predicted to be temperate phages, ten of which were confirmed here. Their ability to infect and lyse urinary E. coli strains suggests that urinary coliphages may play a role in modulating the E. coli strain diversity of the urobiome.
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Affiliation(s)
- Elias Crum
- Bioinformatics Program, Loyola University Chicago, Chicago, Illinois, United States of America
- Department of Biology, Loyola University Chicago, Chicago, Illinois, United States of America
| | - Zubia Merchant
- Department of Biology, Loyola University Chicago, Chicago, Illinois, United States of America
| | - Adriana Ene
- Bioinformatics Program, Loyola University Chicago, Chicago, Illinois, United States of America
- Department of Biology, Loyola University Chicago, Chicago, Illinois, United States of America
| | - Taylor Miller-Ensminger
- Bioinformatics Program, Loyola University Chicago, Chicago, Illinois, United States of America
| | - Genevieve Johnson
- Bioinformatics Program, Loyola University Chicago, Chicago, Illinois, United States of America
| | - Alan J. Wolfe
- Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, Illinois, United States of America
| | - Catherine Putonti
- Bioinformatics Program, Loyola University Chicago, Chicago, Illinois, United States of America
- Department of Biology, Loyola University Chicago, Chicago, Illinois, United States of America
- Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, Illinois, United States of America
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5
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Yuanyuan N, Xiaobo Y, Shang W, Yutong Y, Hongrui Z, Chenyu L, Bin X, Xi Z, Chen Z, Zhiqiang S, Jingfeng W, Yun L, Pingfeng Y, Zhigang Q. Isolation and characterization of two homolog phages infecting Pseudomonas aeruginosa. Front Microbiol 2022; 13:946251. [PMID: 35935197 PMCID: PMC9348578 DOI: 10.3389/fmicb.2022.946251] [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: 05/17/2022] [Accepted: 06/24/2022] [Indexed: 12/02/2022] Open
Abstract
Bacteriophages (phages) are capable of infecting specific bacteria, and therefore can be used as a biological control agent to control bacteria-induced animal, plant, and human diseases. In this study, two homolog phages (named PPAY and PPAT) that infect Pseudomonas aeruginosa PAO1 were isolated and characterized. The results of the phage plaque assay showed that PPAT plaques were transparent dots, while the PPAY plaques were translucent dots with a halo. Transmission electron microscopy results showed that PPAT (65 nm) and PPAY (60 nm) strains are similar in size and have an icosahedral head and a short tail. Therefore, these belong to the short-tailed phage family Podoviridae. One-step growth curves revealed the latent period of 20 min and burst time of 30 min for PPAT and PPAY. The burst size of PPAT (953 PFUs/infected cell) was higher than that of PPAY (457 PFUs/infected cell). Also, the adsorption rate constant of PPAT (5.97 × 10−7 ml/min) was higher than that of PPAY (1.32 × 10−7 ml/min) at 5 min. Whole-genome sequencing of phages was carried out using the Illumina HiSeq platform. The genomes of PPAT and PPAY have 54,888 and 50,154 bp, respectively. Only 17 of the 352 predicted ORFs of PPAT could be matched to homologous genes of known function. Likewise, among the 351 predicted ORFs of PPAY, only 18 ORFs could be matched to genes of established functions. Homology and evolutionary analysis indicated that PPAT and PPAY are closely related to PA11. The presence of tail fiber proteins in PPAY but not in PPAT may have contributed to the halo effect of its plaque spots. In all, PPAT and PPAY, newly discovered P. aeruginosa phages, showed growth inhibitory effects on bacteria and can be used for research and clinical purposes.
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Affiliation(s)
- Niu Yuanyuan
- College of Marine Ecology and Environment, Shanghai Ocean University, Shanghai, China
- Key Laboratory of Risk Assessment and Control for Environment and Food Safety, TianJin Institute of Environmental and Operational Medicine, Tianjin, China
| | - Yang Xiaobo
- Key Laboratory of Risk Assessment and Control for Environment and Food Safety, TianJin Institute of Environmental and Operational Medicine, Tianjin, China
| | - Wang Shang
- Key Laboratory of Risk Assessment and Control for Environment and Food Safety, TianJin Institute of Environmental and Operational Medicine, Tianjin, China
| | - Yang Yutong
- Key Laboratory of Risk Assessment and Control for Environment and Food Safety, TianJin Institute of Environmental and Operational Medicine, Tianjin, China
| | - Zhou Hongrui
- Key Laboratory of Risk Assessment and Control for Environment and Food Safety, TianJin Institute of Environmental and Operational Medicine, Tianjin, China
| | - Li Chenyu
- Key Laboratory of Risk Assessment and Control for Environment and Food Safety, TianJin Institute of Environmental and Operational Medicine, Tianjin, China
| | - Xue Bin
- Key Laboratory of Risk Assessment and Control for Environment and Food Safety, TianJin Institute of Environmental and Operational Medicine, Tianjin, China
| | - Zhang Xi
- Key Laboratory of Risk Assessment and Control for Environment and Food Safety, TianJin Institute of Environmental and Operational Medicine, Tianjin, China
| | - Zhao Chen
- Key Laboratory of Risk Assessment and Control for Environment and Food Safety, TianJin Institute of Environmental and Operational Medicine, Tianjin, China
| | - Shen Zhiqiang
- Key Laboratory of Risk Assessment and Control for Environment and Food Safety, TianJin Institute of Environmental and Operational Medicine, Tianjin, China
| | - Wang Jingfeng
- Key Laboratory of Risk Assessment and Control for Environment and Food Safety, TianJin Institute of Environmental and Operational Medicine, Tianjin, China
| | - Ling Yun
- College of Marine Ecology and Environment, Shanghai Ocean University, Shanghai, China
- *Correspondence: Ling Yun,
| | - Yu Pingfeng
- College of Environment and Resource Sciences, Zhejiang University, Hangzhou, China
| | - Qiu Zhigang
- College of Marine Ecology and Environment, Shanghai Ocean University, Shanghai, China
- Key Laboratory of Risk Assessment and Control for Environment and Food Safety, TianJin Institute of Environmental and Operational Medicine, Tianjin, China
- Qiu Zhigang,
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6
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Ezzeroug Ezzraimi A, Hannachi N, Mariotti A, Rolland C, Levasseur A, Baron SA, Rolain JM, Camoin-Jau L. The Antibacterial Effect of Platelets on Escherichia coli Strains. Biomedicines 2022; 10:biomedicines10071533. [PMID: 35884840 PMCID: PMC9313237 DOI: 10.3390/biomedicines10071533] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 06/23/2022] [Accepted: 06/24/2022] [Indexed: 01/02/2023] Open
Abstract
Platelets play an important role in defense against pathogens; however, the interaction between Escherichia coli and platelets has not been well described and detailed. Our goal was to study the interaction between platelets and selected strains of E. coli in order to evaluate the antibacterial effect of platelets and to assess bacterial effects on platelet activation. Washed platelets and supernatants of pre-activated platelets were incubated with five clinical colistin-resistant and five laboratory colistin-sensitive strains of E. coli in order to study bacterial growth. Platelet activation was measured with flow cytometry by evaluating CD62P expression. To identify the difference in strain behavior toward platelets, a pangenome analysis using Roary and O-antigen serotyping was carried out. Both whole platelets and the supernatant of activated platelets inhibited growth of three laboratory colistin-sensitive strains. In contrast, platelets promoted growth of the other strains. There was a negative correlation between platelet activation and bacterial growth. The Roary results showed no logical clustering to explain the mechanism of platelet resistance. The diversity of the responses might be due to strains of different types of O-antigen. Our results show a bidirectional interaction between platelets and E. coli whose expression is dependent on the bacterial strain involved.
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Affiliation(s)
- Amina Ezzeroug Ezzraimi
- Aix Marseille University, IRD, APHM, MEPHI, IHU Méditerranée Infection, 13385 Marseille, France; (A.E.E.); (N.H.); (A.M.); (S.A.B.); (J.-M.R.)
- IHU Méditerranée Infection, Boulevard Jean Moulin, 13385 Marseille, France; (C.R.); (A.L.)
| | - Nadji Hannachi
- Aix Marseille University, IRD, APHM, MEPHI, IHU Méditerranée Infection, 13385 Marseille, France; (A.E.E.); (N.H.); (A.M.); (S.A.B.); (J.-M.R.)
- Département de Pharmacie, Faculté de Médecine, Université Ferhat Abbas Sétif I, Sétif 19000, Algeria
| | - Antoine Mariotti
- Aix Marseille University, IRD, APHM, MEPHI, IHU Méditerranée Infection, 13385 Marseille, France; (A.E.E.); (N.H.); (A.M.); (S.A.B.); (J.-M.R.)
- IHU Méditerranée Infection, Boulevard Jean Moulin, 13385 Marseille, France; (C.R.); (A.L.)
- Laboratoire d’Hématologie, Hôpital de la Timone, APHM, Boulevard Jean-Moulin, 13385 Marseille, France
| | - Clara Rolland
- IHU Méditerranée Infection, Boulevard Jean Moulin, 13385 Marseille, France; (C.R.); (A.L.)
- Aix Marseille University, IRD, SSA, APHM, VITROME, IHU Méditerranée Infection, 13385 Marseille, France
| | - Anthony Levasseur
- IHU Méditerranée Infection, Boulevard Jean Moulin, 13385 Marseille, France; (C.R.); (A.L.)
- Aix Marseille University, IRD, SSA, APHM, VITROME, IHU Méditerranée Infection, 13385 Marseille, France
| | - Sophie Alexandra Baron
- Aix Marseille University, IRD, APHM, MEPHI, IHU Méditerranée Infection, 13385 Marseille, France; (A.E.E.); (N.H.); (A.M.); (S.A.B.); (J.-M.R.)
- IHU Méditerranée Infection, Boulevard Jean Moulin, 13385 Marseille, France; (C.R.); (A.L.)
| | - Jean-Marc Rolain
- Aix Marseille University, IRD, APHM, MEPHI, IHU Méditerranée Infection, 13385 Marseille, France; (A.E.E.); (N.H.); (A.M.); (S.A.B.); (J.-M.R.)
- IHU Méditerranée Infection, Boulevard Jean Moulin, 13385 Marseille, France; (C.R.); (A.L.)
| | - Laurence Camoin-Jau
- Aix Marseille University, IRD, APHM, MEPHI, IHU Méditerranée Infection, 13385 Marseille, France; (A.E.E.); (N.H.); (A.M.); (S.A.B.); (J.-M.R.)
- IHU Méditerranée Infection, Boulevard Jean Moulin, 13385 Marseille, France; (C.R.); (A.L.)
- Laboratoire d’Hématologie, Hôpital de la Timone, APHM, Boulevard Jean-Moulin, 13385 Marseille, France
- Correspondence: ; Tel.: +33-4-13-73-24-01; Fax: +33-4-13-73-24-02
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7
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Maffei E, Shaidullina A, Burkolter M, Heyer Y, Estermann F, Druelle V, Sauer P, Willi L, Michaelis S, Hilbi H, Thaler DS, Harms A. Systematic exploration of Escherichia coli phage-host interactions with the BASEL phage collection. PLoS Biol 2021; 19:e3001424. [PMID: 34784345 PMCID: PMC8594841 DOI: 10.1371/journal.pbio.3001424] [Citation(s) in RCA: 77] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Accepted: 09/27/2021] [Indexed: 01/08/2023] Open
Abstract
Bacteriophages, the viruses infecting bacteria, hold great potential for the treatment of multidrug-resistant bacterial infections and other applications due to their unparalleled diversity and recent breakthroughs in their genetic engineering. However, fundamental knowledge of the molecular mechanisms underlying phage-host interactions is mostly confined to a few traditional model systems and did not keep pace with the recent massive expansion of the field. The true potential of molecular biology encoded by these viruses has therefore remained largely untapped, and phages for therapy or other applications are often still selected empirically. We therefore sought to promote a systematic exploration of phage-host interactions by composing a well-assorted library of 68 newly isolated phages infecting the model organism Escherichia coli that we share with the community as the BASEL (BActeriophage SElection for your Laboratory) collection. This collection is largely representative of natural E. coli phage diversity and was intensively characterized phenotypically and genomically alongside 10 well-studied traditional model phages. We experimentally determined essential host receptors of all phages, quantified their sensitivity to 11 defense systems across different layers of bacterial immunity, and matched these results to the phages' host range across a panel of pathogenic enterobacterial strains. Clear patterns in the distribution of phage phenotypes and genomic features highlighted systematic differences in the potency of different immunity systems and suggested the molecular basis of receptor specificity in several phage groups. Our results also indicate strong trade-offs between fitness traits like broad host recognition and resistance to bacterial immunity that might drive the divergent adaptation of different phage groups to specific ecological niches. We envision that the BASEL collection will inspire future work exploring the biology of bacteriophages and their hosts by facilitating the discovery of underlying molecular mechanisms as the basis for an effective translation into biotechnology or therapeutic applications.
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Affiliation(s)
- Enea Maffei
- Biozentrum, University of Basel, Basel, Switzerland
| | | | | | - Yannik Heyer
- Biozentrum, University of Basel, Basel, Switzerland
| | | | | | | | - Luc Willi
- Biozentrum, University of Basel, Basel, Switzerland
| | - Sarah Michaelis
- Institute of Medical Microbiology, University of Zürich, Zürich, Switzerland
| | - Hubert Hilbi
- Institute of Medical Microbiology, University of Zürich, Zürich, Switzerland
| | - David S. Thaler
- Biozentrum, University of Basel, Basel, Switzerland
- Program for the Human Environment, Rockefeller University, New York City, New York, United States of America
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8
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Genome sequence analysis of Cronobacter phage PF-CE2 and proposal of a new species in the genus Pseudotevenvirus. Arch Virol 2021; 166:3467-3472. [PMID: 34601635 DOI: 10.1007/s00705-021-05255-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Accepted: 08/16/2021] [Indexed: 10/20/2022]
Abstract
The genome of a Cronobacter sakazakii M1 phage named PF-CE2 was characterized in this work, and a new species named "Cronobacter virus PF-CE2", in the genus Pseudotevenvirus of the subfamily Tevenvirinae of the family Myoviridae is proposed. The Gp190 gene of phage PF-CE2 is predicted to encode a bacteriophage-borne glycanase that is capable of degrading fucose-containing exopolysaccharides produced by C. sakazakii M1. Furthermore, we propose changing the taxonomic status of eight additional phages based on nucleotide sequence comparisons. This work provides a theoretical basis for subsequent heterologous expression of the phage PF-CE2 glycanase and provides an important reference for the preservation and sharing of these phages.
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9
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Khan MSI, Gao X, Liang K, Mei S, Zhan J. Virulent Drexlervirial Bacteriophage MSK, Morphological and Genome Resemblance With Rtp Bacteriophage Inhibits the Multidrug-Resistant Bacteria. Front Microbiol 2021; 12:706700. [PMID: 34504479 PMCID: PMC8421802 DOI: 10.3389/fmicb.2021.706700] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 06/14/2021] [Indexed: 11/13/2022] Open
Abstract
Phage-host interactions are likely to have the most critical aspect of phage biology. Phages are the most abundant and ubiquitous infectious acellular entities in the biosphere, where their presence remains elusive. Here, the novel Escherichia coli lytic bacteriophage, named MSK, was isolated from the lysed culture of E. coli C (phix174 host). The genome of phage MSK was sequenced, comprising 45,053 bp with 44.8% G + C composition. In total, 73 open reading frames (ORFs) were predicted, out of which 24 showed a close homology with known functional proteins, including one tRNA-arg; however, the other 49 proteins with no proven function in the genome database were called hypothetical. Electron Microscopy and genome characterization have revealed that MSK phage has a rosette-like tail tip. There were, in total, 46 ORFs which were homologous to the Rtp genome. Among these ORFs, the tail fiber protein with a locus tag of MSK_000019 was homologous to Rtp 43 protein, which determines the host specificity. The other protein, MSK_000046, encodes lipoprotein (cor gene); that protein resembles Rtp 45, responsible for preventing adsorption during cell lysis. Thirteen MSK structural proteins were identified by SDS-PAGE analysis. Out of these, 12 were vital structural proteins, and one was a hypothetical protein. Among these, the protein terminase large (MSK_000072) subunit, which may be involved in DNA packaging and proposed packaging strategy of MSK bacteriophage genome, takes place through headful packaging using the pac-sites. Biosafety assessment of highly stable phage MSK genome analysis has revealed that the phage did not possess virulence genes, which indicates proper phage therapy. MSK phage potentially could be used to inhibit the multidrug-resistant bacteria, including AMP, TCN, and Colistin. Further, a comparative genome and lifestyle study of MSK phage confirmed the highest similarity level (87.18% ANI). These findings suggest it to be a new lytic isolated phage species. Finally, Blast and phylogenetic analysis of the large terminase subunit and tail fiber protein put it in Rtp viruses' genus of family Drexlerviridae.
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Affiliation(s)
- Muhammad Saleem Iqbal Khan
- Department of Biochemistry, Cancer Institute of the Second Affiliated Hospital (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education), School of Medicine, Zhejiang University, Hangzhou, China
| | - Xiangzheng Gao
- Department of Biochemistry, Cancer Institute of the Second Affiliated Hospital (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education), School of Medicine, Zhejiang University, Hangzhou, China
| | - Keying Liang
- Department of Biochemistry, Cancer Institute of the Second Affiliated Hospital (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education), School of Medicine, Zhejiang University, Hangzhou, China
| | - Shengsheng Mei
- Department of Biochemistry, Cancer Institute of the Second Affiliated Hospital (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education), School of Medicine, Zhejiang University, Hangzhou, China
| | - Jinbiao Zhan
- Department of Biochemistry, Cancer Institute of the Second Affiliated Hospital (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education), School of Medicine, Zhejiang University, Hangzhou, China
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10
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Structural, functional, resistome and pathogenicity profiling of the Cooum river. Microb Pathog 2021; 158:105048. [PMID: 34139279 DOI: 10.1016/j.micpath.2021.105048] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 05/12/2021] [Accepted: 06/06/2021] [Indexed: 01/26/2023]
Abstract
The microbial community's structure and functions determine the health, quality, and anthropogenic conditions of the river ecosystems. The presence of Bacteria such as Arcobacter spp, Escherichia spp, and Campylobacters spp, have been shown to reflect the poor water quality of rivers. Apprehension of the microbial community in polluted water bodies is significant because it affects human health and the environment. Culture-independent metagenomic and metatranscriptomic approaches employed in the current study of the Cooum river unraveled the taxonomic classification of diverse microbes, including archaea, bacteria, viruses, and phages. The presence of abundant Macellibacteroides fermentans, Arcobacter bivolvorium, Arcobacter butzleri, Methanothrix soenhngeii, and Bacteroides graminisolvens were noted. Viruses and phages like Caudovirales, Human mastadenovirus C, Siphoviridae, Escherichia phage, Erwinia phage, Synechoccus phage, and Vibrio phage were relatively predominant. Various metabolic pathways like methane, sulfur, and nitrogen metabolism adopted by the microbiome confer dangerous gases. Mechanisms such as secretory systems, signal transduction, Chemotaxis, quorum sensing, transportation of chemicals and ions were significantly enriched. The microbes expressed antimicrobial resistance mechanisms as identified from the genes encoding beta-lactamase enzymes and aminoglycoside phosphotransferase enzymes. Metal resistance mechanisms against copper, tellurium, chromium, and cadmium were plentiful. Presence of human pathogens interactions with Yersinia pestis, Campylobacter jejuni, Escherichia coli, Helicobacter pylori, and Francisella tularensis subsp. tularensis suggested the possibilities of transmission of pathogenesis to humans. The current study is the first to apprehend the detailed microbiome composition of one of the highly polluted rivers in South India. The study elaborated the microbiome's structure, functions, and metabolic potential at a specific site of the polluted river.
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11
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Abdelrhim AS, Ahmad AA, Omar MOA, Hammad AMM, Huang Q. A new Streptomyces scabies-infecting bacteriophage from Egypt with promising biocontrol traits. Arch Microbiol 2021; 203:4233-4242. [PMID: 34091692 DOI: 10.1007/s00203-021-02415-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Revised: 05/19/2021] [Accepted: 05/28/2021] [Indexed: 11/26/2022]
Abstract
Potato common scab caused by Streptomyces scabies is one of the most economically important diseases infecting potato. It reduces the quality of potato tubers, which subsequently decreases the tuber prices and causes significant economic losses for potato growers. Biological control using bacteriophages is a promising strategy for controlling this disease. In this study, a novel bacteriophage with high lytic efficacy against S. scabies was isolated from a potato field at El-Minya, Egypt, and was designated SscP1EGY. The phage has an icosahedral head of 55 nm and a short tail of 7.5 nm, typical of a podovirus. Its infection cycle was 90 min, including 50 min of latent time and 40 min of rise period with a burst size of approximately 200 PFU per infected cell. The genome of SscP1EGY consists 51,751 nucleotides with 76 predicted genes. SscP1EGY infected and completely lysed seven tested S. scabies strains but showed no lytic activity against three beneficial Streptomyces species, other beneficial bacterial species, and non-target plant pathogenic bacteria. In greenhouse experiments, treatment of S. scabies-inoculated potato tubers with phage SscP1EGY resulted in reductions of (1) the severity of scab, (2) the number of lesions, and (3) the percentage of lesion surface, as compared to the inoculated tubers without phage treatment. Also, scab lesions appeared superficial in phage-treated tubers but pitted in non-phage-treated tubers. Our results suggest that SscP1EGY has a potential as a biological control agent for S. scabies. Based on our knowledge, SscP1EGY is the first sequenced S. scabies-infecting phage in Egypt.
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Affiliation(s)
- Abdelrazek S Abdelrhim
- Department of Plant Pathology, Faculty of Agriculture, Minia University, El-Minia, 61519, Egypt
| | - Abdelmonim Ali Ahmad
- Department of Plant Pathology, Faculty of Agriculture, Minia University, El-Minia, 61519, Egypt
| | - Maha O A Omar
- Department of Microbiology, Faculty of Agriculture, Minia University, El-Minia, 61519, Egypt
| | - Adel M M Hammad
- Department of Microbiology, Faculty of Agriculture, Minia University, El-Minia, 61519, Egypt
| | - Qi Huang
- Floral and Nursery Plants Research Unit, United States Department of Agriculture, Agricultural Research Service, United States National Arboretum, Beltsville, MD, USA.
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12
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Abstract
Bacteriophages-viruses that infect bacteria-are abundant within our bodies, but their significance to human health is only beginning to be explored. Here, we synthesize what is currently known about our phageome and its interactions with the immune system. We first review how phages indirectly affect immunity via bacterial expression of phage-encoded proteins. We next review how phages directly influence innate immunity and bacterial clearance. Finally, we discuss adaptive immunity against phages and its implications for phage/bacterial interactions. In light of these data, we propose that our microbiome can be understood as an interconnected network of bacteria, bacteriophages, and human cells and that the stability of these tri-kingdom interactions may be important for maintaining our immunologic and metabolic health. Conversely, the disruption of this balance, through exposure to exogenous phages, microbial dysbiosis, or immune dysregulation, may contribute to disease. Expected final online publication date for the Annual Review of Virology, Volume 8 is September 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Medeea Popescu
- Division of Infectious Diseases, School of Medicine, Stanford University, Stanford, California 94305, USA; .,Immunology Program, School of Medicine, Stanford University, Stanford, California 94305, USA.,These authors contributed equally to this article
| | - Jonas D Van Belleghem
- Division of Infectious Diseases, School of Medicine, Stanford University, Stanford, California 94305, USA; .,These authors contributed equally to this article
| | - Arya Khosravi
- Division of Infectious Diseases, School of Medicine, Stanford University, Stanford, California 94305, USA;
| | - Paul L Bollyky
- Division of Infectious Diseases, School of Medicine, Stanford University, Stanford, California 94305, USA;
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13
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Hedžet S, Rupnik M, Accetto T. Novel Siphoviridae Bacteriophages Infecting Bacteroides uniformis Contain Diversity Generating Retroelement. Microorganisms 2021; 9:microorganisms9050892. [PMID: 33919474 PMCID: PMC8143477 DOI: 10.3390/microorganisms9050892] [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] [Received: 03/26/2021] [Revised: 04/19/2021] [Accepted: 04/19/2021] [Indexed: 11/25/2022] Open
Abstract
Intestinal phages are abundant and important components of gut microbiota, yet the isolated and characterized representatives that infect abundant gut bacteria are sparse. Here we describe the isolation of human intestinal phages infecting Bacteroidesuniformis. Bacteroides is one of the most common bacterial groups in the global human gut microbiota; however, to date not many Bacteroides specific phages are known. Phages isolated in this study belong to a novel viral genus, Bacuni, within the Siphoviridae family. Their genomes encode diversity-generating retroelements (DGR), which were shown in other bacteriophages to promote phage adaptation to rapidly changing environmental conditions and to broaden their host range. Three isolated phages showed 99.83% genome identity but one of them infected a distinct B. uniformis strain. The tropism of Bacuni phages appeared to be dependent on the interplay of DGR mediated sequence variations of gene encoding putative phage fimbrial tip proteins and mutations in host genes coding for outer-membrane proteins. We found prophages with up to 85% amino acid similarity over two-thirds of the Bacuni phage genome in the B. acidifaciens and Prevotella sp. genomes. Despite the abundance of Bacteroides within the human microbiome, we found Bacuni phages only in a limited subset of published gut metagenomes.
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Affiliation(s)
- Stina Hedžet
- Centre for Medical Microbiology, Department for Microbiological Research, National Laboratory for Health, Environment and Food (NLZOH), 2000 Maribor, Slovenia; (S.H.); (M.R.)
| | - Maja Rupnik
- Centre for Medical Microbiology, Department for Microbiological Research, National Laboratory for Health, Environment and Food (NLZOH), 2000 Maribor, Slovenia; (S.H.); (M.R.)
- Faculty of Medicine, University of Maribor, 2000 Maribor, Slovenia
| | - Tomaž Accetto
- Animal Science Department, Biotechnical Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia
- Correspondence:
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Żaczek M, Weber-Dąbrowska B, Międzybrodzki R, Górski A. Phage Prevalence in the Human Urinary Tract-Current Knowledge and Therapeutic Implications. Microorganisms 2020; 8:microorganisms8111802. [PMID: 33212807 PMCID: PMC7696197 DOI: 10.3390/microorganisms8111802] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 11/05/2020] [Accepted: 11/06/2020] [Indexed: 12/20/2022] Open
Abstract
Recent metagenomic analyses imply an immense abundance of phages in the human body. Samples collected from different sites (lungs, skin, oral cavity, intestines, ascitic fluid, and urine) reveal a generally greater number of phage particles than that of eukaryotic viruses. The presence of phages in those tissues and fluids reflects the paths they must overcome in the human body, but may also relate to the health statuses of individuals. Besides shaping bacterial metabolism and community structure, the role of phages circulating in body fluids has not been fully understood yet. The lack of relevant reports is especially visible with regard to the human urobiome. Certainly, phage presence and the role they have to fulfill in the human urinary tract raises questions on potential therapeutic connotations. Urinary tract infections (UTIs) are among the most common bacterial infections in humans and their treatment poses a difficult therapeutic dilemma. Despite effective antibiotic therapy, these infections tend to recur. In this review, we summarized the recent data on phage presence in the human urinary tract and its possible implications for health and disease.
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Affiliation(s)
- Maciej Żaczek
- Bacteriophage Laboratory, Ludwik Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, 53-114 Wrocław, Poland; (M.Ż.); (B.W.-D.); (R.M.)
| | - Beata Weber-Dąbrowska
- Bacteriophage Laboratory, Ludwik Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, 53-114 Wrocław, Poland; (M.Ż.); (B.W.-D.); (R.M.)
- Phage Therapy Unit, Ludwik Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, 53-114 Wrocław, Poland
| | - Ryszard Międzybrodzki
- Bacteriophage Laboratory, Ludwik Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, 53-114 Wrocław, Poland; (M.Ż.); (B.W.-D.); (R.M.)
- Phage Therapy Unit, Ludwik Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, 53-114 Wrocław, Poland
- Department of Clinical Immunology, Transplantation Institute, Medical University of Warsaw, 02-006 Warsaw, Poland
| | - Andrzej Górski
- Bacteriophage Laboratory, Ludwik Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, 53-114 Wrocław, Poland; (M.Ż.); (B.W.-D.); (R.M.)
- Phage Therapy Unit, Ludwik Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, 53-114 Wrocław, Poland
- Infant Jesus Hospital, Medical University of Warsaw, 02-005 Warsaw, Poland
- Correspondence:
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Koonjan S, Seijsing F, Cooper CJ, Nilsson AS. Infection Kinetics and Phylogenetic Analysis of vB_EcoD_SU57, a Virulent T1-Like Drexlerviridae Coliphage. Front Microbiol 2020; 11:565556. [PMID: 33329423 PMCID: PMC7718038 DOI: 10.3389/fmicb.2020.565556] [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: 05/28/2020] [Accepted: 09/11/2020] [Indexed: 12/13/2022] Open
Abstract
The morphology, infection kinetics, genome sequence and phylogenetic characterization of the previously isolated bacteriophage vB_EcoD_SU57 are presented. The phage vB_EcoD_SU57 was isolated on Escherichia coli strain ECOR57 from the E. coli reference collection and was shown to produce four mm clear plaques with halos. Infection kinetics, as assessed by one-step growth analyses, suggest that vB_EcoD_SU57 is a virulent phage with an adsorption rate of 8.5 × 10-10 mL × min-1, a latency period of 14 min, and a burst size of 13 PFU per bacterium. Transmission electron microscopy confirmed vB_EcoD_SU57 to be a phage that used to be classified as a Siphoviridae phage. Bioinformatics analyses showed that the genome was 46,150 base pairs long, contained 29 genes with predicted protein functions, and 51 open reading frames encoding proteins with unknown function, many of which were gathered in clusters. A putative tRNA gene was also identified. Phylogenetic analyses showed that vB_EcoD_SU57 is a Braunvirinae phage of the newly formed Drexlerviridae family and closely related to T1-like E. coli phages vB_EcoS_ACG-M12 (Guelphvirus) and Rtp (Rtpvirus) as well as the unclassified phages vB_EcoS_CEB_EC3a and ECH1.
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Affiliation(s)
- Shazeeda Koonjan
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Fredrik Seijsing
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Callum J. Cooper
- School of Pharmacy, Pharmaceutical and Cosmetic Sciences, Faculty of Health Sciences and Wellbeing, University of Sunderland, Sunderland, United Kingdom
| | - Anders S. Nilsson
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
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Żaczek M, Górski A, Skaradzińska A, Łusiak-Szelachowska M, Weber-Dąbrowska B. Phage penetration of eukaryotic cells: practical implications. Future Virol 2019. [DOI: 10.2217/fvl-2019-0110] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The inability to infect eukaryotic cells has been considered as the most undeniable feature of all bacterial viruses. Such specificity, limited only for bacterial hosts, raises questions about the paths and challenges phages should overcome when circulating through the human body. Recently, it has been shown that phages are able to continually penetrate human organs and tissues. Latest reports revealed that phages can cross eukaryotic cell barriers both para- and transcellularly and even reach the nucleus. Further, phages are capable of internalizing within cells through different endocytic mechanisms. Such phenomenon indicates that phages could shape human microbiome composition and affect all aspects of human health. Thus, herein, we summarize the current state of knowledge and describe this phenomenon with a particular emphasis on endocytic pathways.
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Affiliation(s)
- Maciej Żaczek
- Bacteriophage Laboratory, Hirszfeld Institute of Immunology & Experimental Therapy, Polish Academy of Sciences (HIIET PAS), R. Weigla 12, 53-114 Wrocław, Poland
| | - Andrzej Górski
- Bacteriophage Laboratory, Hirszfeld Institute of Immunology & Experimental Therapy, Polish Academy of Sciences (HIIET PAS), R. Weigla 12, 53-114 Wrocław, Poland
- Phage Therapy Unit, Hirszfeld Institute of Immunology & Experimental Therapy, Polish Academy of Sciences (HIIET PAS), R. Weigla 12, 53-114 Wrocław, Poland
| | - Aneta Skaradzińska
- Department of Biotechnology & Food Microbiology, Faculty of Biotechnology & Food Science, Wrocław University of Environmental & Life Sciences, Chełmońskiego 37, 51-630 Wrocław, Poland
| | - Marzanna Łusiak-Szelachowska
- Bacteriophage Laboratory, Hirszfeld Institute of Immunology & Experimental Therapy, Polish Academy of Sciences (HIIET PAS), R. Weigla 12, 53-114 Wrocław, Poland
| | - Beata Weber-Dąbrowska
- Bacteriophage Laboratory, Hirszfeld Institute of Immunology & Experimental Therapy, Polish Academy of Sciences (HIIET PAS), R. Weigla 12, 53-114 Wrocław, Poland
- Phage Therapy Unit, Hirszfeld Institute of Immunology & Experimental Therapy, Polish Academy of Sciences (HIIET PAS), R. Weigla 12, 53-114 Wrocław, Poland
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