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Mota LC, Silva EC, Quinde CA, Cieza B, Basu A, Rodrigues LMR, Vila MMDC, Balcão VM. Potential of a newly isolated lytic bacteriophage to control Pseudomonas coronafaciens pv. garcae in coffee plants: Molecular characterization with in vitro and ex vivo experiments. Enzyme Microb Technol 2025; 184:110573. [PMID: 39700746 DOI: 10.1016/j.enzmictec.2024.110573] [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: 08/18/2024] [Revised: 12/03/2024] [Accepted: 12/13/2024] [Indexed: 12/21/2024]
Abstract
Traditionally, control of coffee plant bacterial halo blight (BHB) caused by the phytopathogen Pseudomonas coronafaciens pv. garcae (Pcg) involves frequent spraying of coffee plantations with non-environmentally friendly and potentially bacterial resistance-promoting copper products or with kasugamycin hydrochloride. In this study we report a leap forward in the quest for a new ecofriendly approach, characterizing (both physicochemically and biologically) and testing both in vitro and ex vivo a new lytic phage for Pcg. An in-depth molecular (genomic and DNA structural features) characterization of the phage was also undertaken. Phage PcgS01F belongs to the class Caudoviricetes, Drexlerviridae family and genus Guelphvirus, and presents a siphovirus-like morphotype. Phage PcgS01F showed a latency period of 40 min and a burst size of 46 PFU/host cell, allowing to conclude that it replicates well in Pcg IBSBF-158. At Multiplicity Of Infection (MOI, or the ratio of phage to bacteria) 1000, the performance of phage PcgS01F was much better than at MOI 10, promoting increasing bacterial reductions until the end of the in vitro inactivation assays, stabilizing at a significant 82 % bacterial load reduction. Phage PcgS01F infected and killed Pcg cells ex vivo in coffee plant leaves artificially contaminated, with a maximum of Pcg inactivation of 7.66 log CFU/mL at MOI 1000 after 36 h of incubation. This study provides evidence that the isolated phage is a promising candidate against the causative agent of BHB in coffee plants.
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Affiliation(s)
- Luan C Mota
- VBlab - Laboratory of Bacterial Viruses, University of Sorocaba, Sorocaba, SP 18023-000, Brazil.
| | - Erica C Silva
- VBlab - Laboratory of Bacterial Viruses, University of Sorocaba, Sorocaba, SP 18023-000, Brazil.
| | - Carlos A Quinde
- Department of Biological Sciences, University of South Carolina, Columbia, SC, USA.
| | - Basilio Cieza
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University, Baltimore, MD, USA.
| | - Aakash Basu
- Department of Biosciences, Durham University, Durham, United Kingdom.
| | - Lucas M R Rodrigues
- VBlab - Laboratory of Bacterial Viruses, University of Sorocaba, Sorocaba, SP 18023-000, Brazil; Agronomic Institute of Campinas (IAC), Centro de Café Alcides Carvalho, Campinas, SP 13075-630, Brazil.
| | - Marta M D C Vila
- VBlab - Laboratory of Bacterial Viruses, University of Sorocaba, Sorocaba, SP 18023-000, Brazil.
| | - Victor M Balcão
- VBlab - Laboratory of Bacterial Viruses, University of Sorocaba, Sorocaba, SP 18023-000, Brazil; Department of Biology and CESAM, University of Aveiro, Campus Universitário de Santiago, Aveiro P-3810-193, Portugal.
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Zanaty AA, Dishisha T, El-Sayed-Ahmed MAEG, Abdel-Fattah MM, Ahmed KA, Abdelkader K. Characterization, genomic analysis and preclinical evaluation of the lytic Staphylococcus bacteriophage PSK against methicillin-resistant Staphylococcus aureus wound isolate. Ann Clin Microbiol Antimicrob 2025; 24:17. [PMID: 40022070 PMCID: PMC11871620 DOI: 10.1186/s12941-025-00783-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2024] [Accepted: 02/05/2025] [Indexed: 03/03/2025] Open
Abstract
BACKGROUND The dissemination of multi-drug-resistant bacteria, particularly Methicillin-resistant Staphylococcus aureus (MRSA), necessitates exploring new alternatives for their control. Bacteriophages are promising antibiotic alternatives with unique features. Here, we have performed a comprehensive characterization of a newly isolated bacteriophage (PSK) and compared its therapeutic potential with vancomycin in vivo. METHODS Sewage samples were processed and enriched with the MRSA S. aureus SK1 strain in a search for isolation of a lytic bacteriophage. The isolated bacteriophage was assessed in vitro in terms of thermal and pH stability and kinetic parameters using absorption and one step growth curve assays. Moreover, its potential antibacterial activity was evaluated against S. aureus SK1 lone and in combination of standard of care antibiotics used for treatment of wound infections. We further analyzed its genome to exclude the presence of any potential toxin or antibiotic resistance genes. Finally, its antibacterial potential and capability to alleviate wound infection were assessed using a murine wound-infection model. RESULTS The lytic bacteriophage (PSK) was isolated as a new species of the genus Rosenblumvirus with a genome size of 17,571 bp that is free from potential resistance or virulence genes. PSK displays infectivity against 4/10 S. aureus strains including two vancomycin-resistant strains. Moreover, it demonstrates favorable infection kinetics of fast adsorption with latent period and burst size of 20 min and 123 PFU/infected cell, respectively. Stability analysis revealed thermal stability up to 60 °C with wide pH range stability (4-11). In vitro, PSK kills S. aureus SK1 with multiplicity of infection (MOI) as low as 10- 4 with an overall mutation frequency of 2.47 × 10- 6 CFU/mL that is further improved when combined with 0.25× MIC of oxacillin, fusidic acid or vancomycin. In vivo, a single dose of PSK in murine wound infection model exhibited a comparable performance to four doses of vancomycin, when treatment started 2 h post-infection. However, when applied 2 days post-infection, PSK demonstrates superior antibacterial activity (up to 4.58 log unit count reduction) and enhances wound closure and tissue healing. CONCLUSION These findings represent PSK as a potential vancomycin alternative effective in treating S. aureus- induced wound infections.
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Affiliation(s)
- Abanoub A Zanaty
- Department of Microbiology and Immunology, Faculty of Pharmacy, Beni-Suef University, Beni-Suef, 62511, Egypt
- Department of Microbiology and Immunology, Faculty of Pharmacy, Misr University for Science and Technology (MUST), Cairo, Egypt
| | - Tarek Dishisha
- Department of Microbiology and Immunology, Faculty of Pharmacy, Beni-Suef University, Beni-Suef, 62511, Egypt
| | | | - Maha M Abdel-Fattah
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, Beni-Suef University, Beni-Suef, 62511, Egypt
| | - Kawkab A Ahmed
- Department of Pathology, Faculty of Veterinary Medicine, Cairo University, Giza, 12211, Egypt
| | - Karim Abdelkader
- Department of Microbiology and Immunology, Faculty of Pharmacy, Beni-Suef University, Beni-Suef, 62511, Egypt.
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53
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Mirza KA, Tchatchiashvili T, Marquet M, Nietzsche S, Pletz MW, Makarewicz O. Characterization and genome analysis of novel Klebsiella pneumoniae phage vbKpUKJ_2 isolated from hospital sewage water. BMC Microbiol 2025; 25:96. [PMID: 40011819 PMCID: PMC11863478 DOI: 10.1186/s12866-025-03813-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2024] [Accepted: 02/07/2025] [Indexed: 02/28/2025] Open
Abstract
INTRODUCTION Multidrug-resistant (MDR) Klebsiella pneumoniae is a critical healthcare challenge due to its extensive resistance to antibiotics and role in causing severe infections. Bacteriophages offer a promising alternative for targeting MDR pathogens. This study characterizes a novel phage, vbKpUKJ_2, isolated from hospital sewage water, against clinical K. pneumoniae isolates. METHODS Phage vbKpUKJ_2 was isolated and purified using the double agar overlay method. Host range and sensitivity were tested against 40 clinical K. pneumoniae isolates using growth inhibition assays. Morphological characterization was performed using transmission electron microscopy (TEM). Genomic analysis was conducted to evaluate the absence of antibiotic resistance genes and determine phylogenetic relationships. Stability assays assessed the phage's thermal and pH tolerance. RESULTS Phage vbKpUKJ_2 demonstrated broad range activity against clinical K. pneumoniae isolates. TEM revealed it belongs to the Drexlerviridae family. Genomic analysis confirmed the absence of antibiotic resistance genes and identified conserved functional regions shared with related phages. vbKpUKJ_2 exhibited broad pH stability (pH 4-10) and thermal stability between 30 °C and 60 °C. The one-step growth curve indicated rapid lytic activity, with a burst size of 323 phage particles per cell. CONCLUSION vbKpUKJ_2 shows promising therapeutic potential against MDR K. pneumoniae. Its stability, absence of resistance genes, and rapid lytic cycle highlight its suitability for inclusion in phage therapy protocols, particularly as part of combination therapies targeting MDR infections.
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Affiliation(s)
- Kamran Ahmad Mirza
- Institute of Infectious Diseases and Infection Control, Jena University Hospital, Friedrich-Schiller-University Jena, Am Klinikum 1, 07747, Jena, Germany.
- Leibniz Center for Photonics in Infection Research, 07747, Jena, Germany.
| | - Tinatini Tchatchiashvili
- Institute of Infectious Diseases and Infection Control, Jena University Hospital, Friedrich-Schiller-University Jena, Am Klinikum 1, 07747, Jena, Germany
- Leibniz Center for Photonics in Infection Research, 07747, Jena, Germany
| | - Mike Marquet
- Institute of Infectious Diseases and Infection Control, Jena University Hospital, Friedrich-Schiller-University Jena, Am Klinikum 1, 07747, Jena, Germany
| | - Sandor Nietzsche
- Center for Electron Microscopy, Jena University Hospital, Friedrich-Schiller-University Jena, 07743, Jena, Germany
| | - Mathias W Pletz
- Institute of Infectious Diseases and Infection Control, Jena University Hospital, Friedrich-Schiller-University Jena, Am Klinikum 1, 07747, Jena, Germany
- Leibniz Center for Photonics in Infection Research, 07747, Jena, Germany
| | - Oliwia Makarewicz
- Institute of Infectious Diseases and Infection Control, Jena University Hospital, Friedrich-Schiller-University Jena, Am Klinikum 1, 07747, Jena, Germany
- Leibniz Center for Photonics in Infection Research, 07747, Jena, Germany
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Nour El-Din HT, Kettal M, Granados Maciel JC, Beaudoin G, Oktay U, Hrapovic S, Sad S, Dennis JJ, Peters DL, Chen W. Isolation, Characterization, and Genomic Analysis of Bacteriophages Against Pseudomonas aeruginosa Clinical Isolates from Early and Chronic Cystic Fibrosis Patients for Potential Phage Therapy. Microorganisms 2025; 13:511. [PMID: 40142404 PMCID: PMC11945000 DOI: 10.3390/microorganisms13030511] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2025] [Revised: 02/20/2025] [Accepted: 02/21/2025] [Indexed: 03/28/2025] Open
Abstract
Pseudomonas aeruginosa is associated with both community and hospital-acquired infections. It colonizes the lungs of cystic fibrosis (CF) patients, establishing an ecological niche where it adapts and evolves from early to chronic stages, resulting in deteriorating lung function and frequent exacerbations. With antibiotics resistance on the rise, there is a pressing need for alternative personalized treatments (such as bacteriophage therapy) to combat P. aeruginosa infections. In this study, we aimed to isolate and characterize phages targeting both early and chronic P. aeruginosa isolates and evaluate their potential for phage therapy. Four highly virulent phages belonging to myoviral, podviral, and siphoviral morphotypes were isolated from sewage samples. These phages have a broad host range and effectively target 62.5% of the P. aeruginosa isolates with a positive correlation to the early isolates. All the phages have a virulence index of ≥0.90 (0.90-0.98), and one has a large burst size of 331 PFU/cell and a latency period of 30 min. All phages are stable under a wide range of temperature and pH conditions. Genomic analysis suggests the four phages are strictly lytic and devoid of identifiable temperate phage repressors and genes associated with antibiotic resistance and virulence. More significantly, two of the phages significantly delayed the onset of larval death when evaluated in a lethal Galleria mellonella infection model, suggesting their promise as phage therapy candidates for P. aeruginosa infections.
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Affiliation(s)
- Hanzada T. Nour El-Din
- Department of Immunobiology, Human Health Therapeutics Research Center, National Research Council Canada, Ottawa, ON K1N 5A2, Canada; (M.K.); (J.C.G.M.); (G.B.); (D.L.P.); (W.C.)
| | - Maryam Kettal
- Department of Immunobiology, Human Health Therapeutics Research Center, National Research Council Canada, Ottawa, ON K1N 5A2, Canada; (M.K.); (J.C.G.M.); (G.B.); (D.L.P.); (W.C.)
| | - José C. Granados Maciel
- Department of Immunobiology, Human Health Therapeutics Research Center, National Research Council Canada, Ottawa, ON K1N 5A2, Canada; (M.K.); (J.C.G.M.); (G.B.); (D.L.P.); (W.C.)
| | - Greg Beaudoin
- Department of Immunobiology, Human Health Therapeutics Research Center, National Research Council Canada, Ottawa, ON K1N 5A2, Canada; (M.K.); (J.C.G.M.); (G.B.); (D.L.P.); (W.C.)
| | - Umut Oktay
- Faculty of Science, Biological Sciences, University of Alberta, Edmonton, AB T6G 2R3, Canada; (U.O.); (J.J.D.)
| | - Sabahudin Hrapovic
- Aquatic and Crop Resource Development (ACRD) Research Center, National Research Council Canada, Montreal, QC H4P 2R2, Canada;
| | - Subash Sad
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON K1N 6N5, Canada;
| | - Jonathan J. Dennis
- Faculty of Science, Biological Sciences, University of Alberta, Edmonton, AB T6G 2R3, Canada; (U.O.); (J.J.D.)
| | - Danielle L. Peters
- Department of Immunobiology, Human Health Therapeutics Research Center, National Research Council Canada, Ottawa, ON K1N 5A2, Canada; (M.K.); (J.C.G.M.); (G.B.); (D.L.P.); (W.C.)
| | - Wangxue Chen
- Department of Immunobiology, Human Health Therapeutics Research Center, National Research Council Canada, Ottawa, ON K1N 5A2, Canada; (M.K.); (J.C.G.M.); (G.B.); (D.L.P.); (W.C.)
- Department of Biology, Brock University, St. Catharines, ON L2S 3A1, Canada
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Cao L, Mi J, He Y, Xuan G, Wang J, Li M, Tong Y. Quorum sensing inhibits phage infection by regulating biofilm formation of P. aeruginosa PAO1. J Virol 2025; 99:e0187224. [PMID: 39745428 PMCID: PMC11853092 DOI: 10.1128/jvi.01872-24] [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: 10/24/2024] [Accepted: 12/13/2024] [Indexed: 02/26/2025] Open
Abstract
Quorum sensing (QS) can regulate diverse critical phenotypic responses in Pseudomonas. aeruginosa (P. aeruginosa), enabling bacterial adaptation to external environmental fluctuations and optimizing population advantages. While there is emerging evidence of QS's involvement in influencing phage infections, our current understanding remains limited, necessitating further investigation. In this study, we isolated and characterized a novel phage designated as BUCT640 that infected P. aeruginosa PAO1. This phage belonged to class Caudoviricetes, genus Bruynoghevirus, with a podovirus morphology, and its adsorption was dependent on Psl polysaccharides, a repeating pentamer used to support biofilm structure. Leveraging phage BUCT640 as a model, we analyzed the role of both rhl QS and las QS in bacteria-phage interactions. Based on its distinctive plaque formation performances on different QS-related mutants, we investigated the variations of phage sensitivity to these strains and ultimately elucidated the mechanism underlying how QS inhibited phage infection to PAO1. Specifically, we unveiled that the las QS could inhibit phage adsorption, which is related to the thickness change caused by biofilm differentiation. Our findings suggest that the inhibition of QS may enhance phage infectivity, potentially facilitating advanced phage therapy combined with QS interference. IMPORTANCE Phage therapy is a powerful solution to combat drug-resistant pathogenic bacterial infections and has earned remarkable success in clinical treatment. However, recent insights underscore the potential impact of bacterial QS on phage infection dynamics. Here, we reported a unique phenomenon wherein QS, particularly in the las QS pathway, showed distinctive plaque formation behaviors by enlarging halos around plaques in mutant strains. In addition to this, we first elucidated the correlation between biofilm formation and phage infection. Notably, the las QS could inhibit phage adsorption, an effect closely related to biofilm thickness. Such research could be the evidence to steer bacterial QS toward favorable therapeutical outcomes. Therefore, our work can extend the comprehension of the interactions between bacteria and phages influenced by QS, thereby providing new perspectives on leveraging QS interference to enhance the efficacy of phage therapy for clinical applications.
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Affiliation(s)
- Lei Cao
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, Beijing, China
| | - Jinhui Mi
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, Beijing, China
| | - Yile He
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, Beijing, China
| | - Guanhua Xuan
- Food Safety Laboratory, College of Food Science and Engineering, Ocean University of China, Qingdao, Shandong, China
| | - Jingxue Wang
- Food Safety Laboratory, College of Food Science and Engineering, Ocean University of China, Qingdao, Shandong, China
| | - Mengzhe Li
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, Beijing, China
- Qinhuangdao Bohai Biological Research Institute, Beijing University of Chemical Technology, Qinhuangdao, Hebei, China
| | - Yigang Tong
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, Beijing, China
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56
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Gittrich MR, Sanderson CM, Wainaina JM, Noel CM, Leopold JE, Babusci E, Selbes SC, Farinas OR, Caine J, Davis II J, Mutalik VK, Hyman P, Sullivan MB. Isolation and characterization of 24 phages infecting the plant growth-promoting rhizobacterium Klebsiella sp. M5al. PLoS One 2025; 20:e0313947. [PMID: 39982899 PMCID: PMC11845039 DOI: 10.1371/journal.pone.0313947] [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: 06/18/2024] [Accepted: 11/03/2024] [Indexed: 02/23/2025] Open
Abstract
Bacteriophages largely impact bacterial communities via lysis, gene transfer, and metabolic reprogramming and thus are increasingly thought to alter nutrient and energy cycling across many of Earth's ecosystems. However, there are few model systems to mechanistically and quantitatively study phage-bacteria interactions, especially in soil systems. Here, we isolated, sequenced, and genomically characterized 24 novel phages infecting Klebsiella sp. M5al, a plant growth-promoting, nonencapsulated rhizosphere-associated bacterium, and compared many of their features against all 565 sequenced, dsDNA Klebsiella phage genomes. Taxonomic analyses revealed that these Klebsiella phages belong to three known phage families (Autographiviridae, Drexlerviridae, and Straboviridae) and two newly proposed phage families (Candidatus Mavericviridae and Ca. Rivulusviridae). At the phage family level, we found that core genes were often phage-centric proteins, such as structural proteins for the phage head and tail and DNA packaging proteins. In contrast, genes involved in transcription, translation, or hypothetical proteins were commonly not shared or flexible genes. Ecologically, we assessed the phages' ubiquity in recent large-scale metagenomic datasets, which revealed they were not widespread, as well as a possible direct role in reprogramming specific metabolisms during infection by screening their genomes for phage-encoded auxiliary metabolic genes (AMGs). Even though AMGs are common in the environmental literature, only one of our phage families, Straboviridae, contained AMGs, and the types of AMGs were correlated at the genus level. Host range phenotyping revealed the phages had a wide range of infectivity, infecting between 1-14 of our 22 bacterial strain panel that included pathogenic Klebsiella and Raoultella strains. This indicates that not all capsule-independent Klebsiella phages have broad host ranges. Together, these isolates, with corresponding genome, AMG, and host range analyses, help build the Klebsiella model system for studying phage-host interactions of rhizosphere-associated bacteria.
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Affiliation(s)
- Marissa R. Gittrich
- Department of Microbiology, The Ohio State University, Columbus, Ohio, United States of America
- Center of Microbiome Science, The Ohio State University, Columbus, Ohio, United States of America
| | - Courtney M. Sanderson
- Department of Microbiology, The Ohio State University, Columbus, Ohio, United States of America
- Center of Microbiome Science, The Ohio State University, Columbus, Ohio, United States of America
| | - James M. Wainaina
- Department of Microbiology, The Ohio State University, Columbus, Ohio, United States of America
- Center of Microbiome Science, The Ohio State University, Columbus, Ohio, United States of America
- Department of Biology, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts, United States of America
| | - Cara M. Noel
- Department of Microbiology, The Ohio State University, Columbus, Ohio, United States of America
| | - Jonathan E. Leopold
- Department of Microbiology, The Ohio State University, Columbus, Ohio, United States of America
| | - Erica Babusci
- School of the Environment and Natural Resources, The Ohio State University, Columbus, Ohio, United States of America
| | - Sumeyra C. Selbes
- Department of Psychology, The Ohio State University, Columbus, Ohio, United States of America
| | - Olivia R. Farinas
- College of Public Health, Division of Environmental Health Sciences, The Ohio State University, Columbus, Ohio, United States of America
| | - Jack Caine
- Department of Biology, Kenyon College, Gambier, Ohio, United States of America
| | - Joshua Davis II
- Department of Microbiology, The Ohio State University, Columbus, Ohio, United States of America
| | - Vivek K. Mutalik
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Paul Hyman
- Department of Biology/Toxicology, Ashland University, Ashland, Ohio, United States of America
| | - Matthew B. Sullivan
- Department of Microbiology, The Ohio State University, Columbus, Ohio, United States of America
- Center of Microbiome Science, The Ohio State University, Columbus, Ohio, United States of America
- Department of Civil, Environmental, and Geodetic Engineering, The Ohio State University, Columbus, Ohio, United States of America
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57
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Ali Z, Abdelkader K, Abdel-Fattah MM, Azmy AF, El-Gendy AO, Dishisha T. Therapeutic potential of a newly isolated bacteriophage against multi-drug resistant Enterococcus faecalis infections: in vitro and in vivo characterization. BMC Microbiol 2025; 25:80. [PMID: 39979834 PMCID: PMC11841226 DOI: 10.1186/s12866-025-03785-z] [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: 10/27/2024] [Accepted: 01/26/2025] [Indexed: 02/22/2025] Open
Abstract
BACKGROUND In nosocomial settings, vancomycin-resistant Enterococcus faecalis is a major health threat leading to increased morbidities, mortalities, and treatment costs. Nowadays, several approaches are under investigation to enhance the activity of or replace the traditional antibiotics. Bacteriophage therapy was sought as a potential approach for combating E. faecalis infections. The present study focuses on isolating and characterizing bacteriophage against clinical multi-drug resistant (MDR) E. faecalis strain Lb-1492. The phage stability, lytic activity, host-range, latent period, burst size, the ability to detach the pre-formed biofilm and destroy entrapped cells were investigated. The phage genome was purified, sequenced, and subjected to bioinformatics analysis for identifying and characterizing its features, as well as, the suitability for clinical application. Finally, the ability of the phage to rescue mice from deadly, experimentally induced E. faecalis bacteremia was evaluated. RESULTS A virulent phage was isolated from sewage water against a clinical MDR E. faecalis isolate. Morphological and genomic studies indicated that the phage belongs to the Efquatrovirus genus, with a long tail, icosahedral head and a linear double-stranded DNA genome of approximately 42.9 kbp. The phage was named vB_Efa_ZAT1 (shortly ZAT1). It demonstrated a shorter latent period and larger burst size than regular-tailed phages, and a characteristic stability over a wide range of pH and temperatures, with the optimum activity at pH 7.4 and 37 °C, respectively. Phage ZAT1 showed a narrow spectrum of activity and a characteristic biofilm disruption ability. The phage managed successfully to control E. faecalis-induced bacteremia in mice models, which was lethal within 48 h in the control group. An intraperitoneal injection of 3 × 108 PFU of the phage solution given 1 h after the bacterial challenge was sufficient to save all the animals, completely reversing the trend of 100% mortality caused by this bacterium. CONCLUSIONS Phage therapy can be a promising alternative to traditional antibiotics in the post-antibiotic era with a significant antimicrobial and antibiofilm activities against MDR E. faecalis.
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Affiliation(s)
- Zienab Ali
- Department of Pharmaceutical Microbiology and Immunology, Faculty of Pharmacy, Beni-Suef University, Beni-Suef, 62511, Egypt
| | - Karim Abdelkader
- Department of Pharmaceutical Microbiology and Immunology, Faculty of Pharmacy, Beni-Suef University, Beni-Suef, 62511, Egypt
| | - Maha M Abdel-Fattah
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, Beni-Suef University, Beni-Suef, 62511, Egypt
| | - Ahmed Farag Azmy
- Department of Pharmaceutical Microbiology and Immunology, Faculty of Pharmacy, Beni-Suef University, Beni-Suef, 62511, Egypt
| | - Ahmed O El-Gendy
- Department of Pharmaceutical Microbiology and Immunology, Faculty of Pharmacy, Beni-Suef University, Beni-Suef, 62511, Egypt
| | - Tarek Dishisha
- Department of Pharmaceutical Microbiology and Immunology, Faculty of Pharmacy, Beni-Suef University, Beni-Suef, 62511, Egypt.
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Singh PSS, Toh WK, Lim BH, Wong HL, Loh PC. Complete genome sequence analysis of the novel bacteriophage PA-1 infecting phytopathogenic Pantoea ananatis in Malaysia. Arch Virol 2025; 170:60. [PMID: 39961917 DOI: 10.1007/s00705-025-06239-z] [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: 03/20/2024] [Accepted: 01/03/2025] [Indexed: 03/08/2025]
Abstract
A novel bacteriophage, PA-1, was isolated using Pantoea ananatis, a bacterium that is responsible for rice leaf blight worldwide, as the host. PA-1 has a linear genome of 46,332 bp with a GC content of 50.55%. It contains 83 protein-encoding genes, and no tRNA-encoding genes were detected. The genome is densely organized, with an average CDS size of 516 bp, and 92.38% of the genome consists of protein-coding regions. Whole-genome sequencing and phylogenetic and morphological analysis showed that PA-1 is a novel phage that is phylogenetically distinct, suggesting that it may represent a new genus within the class Caudoviricetes..
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Affiliation(s)
| | - Wai Keat Toh
- Faculty of Science, Universiti Tunku Abdul Rahman, Jalan Universiti, Kampar, Perak, 31900, Malaysia
| | - Boon Hoe Lim
- Faculty of Science, Universiti Tunku Abdul Rahman, Jalan Universiti, Kampar, Perak, 31900, Malaysia
| | - Hann Ling Wong
- Faculty of Science, Universiti Tunku Abdul Rahman, Jalan Universiti, Kampar, Perak, 31900, Malaysia.
| | - Pek Chin Loh
- Faculty of Science, Universiti Tunku Abdul Rahman, Jalan Universiti, Kampar, Perak, 31900, Malaysia.
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59
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Liu S, Lei T, Tan Y, Huang X, Zhao W, Zou H, Su J, Zeng J, Zeng H. Discovery, structural characteristics and evolutionary analyses of functional domains in Acinetobacter baumannii phage tail fiber/spike proteins. BMC Microbiol 2025; 25:73. [PMID: 39939914 PMCID: PMC11823257 DOI: 10.1186/s12866-025-03790-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2024] [Accepted: 01/28/2025] [Indexed: 02/14/2025] Open
Abstract
BACKGROUND The global rise in multidrug-resistant Acinetobacter baumannii infections poses a significant healthcare challenge. Bacteriophage offer a promising alternative to antibiotics for treating A. baumannii infections. Phage tail fiber and spike proteins are essential for host recognition, with some exhibiting depolymerase activity that aids in degrading the bacterial cell wall, facilitating infection. Detailed studies of the functional domains responsible for depolymerase activity and receptor-binding in phage tail fiber/spike proteins are a crucial step toward developing effective phage treatments. RESULTS A total of 32 functional domains were identified across 313 tail fiber and spike proteins from 204 publicly available Acinetobacter baumannii phages using InterPro and AlphaFold3. Domains associated with depolymerase function were Pectin lyase-like domain (PLD), phage_tailspike_middle domain (PTMD), Transglycosidases domain (TGD), and SGNH hydrolase domain (SHD). These domains were primarily found in phages from the Autographiviridae family, specifically within the Friunavirus genus. The predominant PLD domain displayed high variability, with its sequence conserved only in a 25-amino-acid region among two closely related fiber/spike protein lineages. All enzymatic domains exhibit high sequence diversity yet retain structural stability, which is essential for enzymatic function. As for receptor-binding domains, four types of pyocin_knob domains (PKD) were initially identified, characterized by unique β-sheet and α-helix configurations. Each type of PKD exhibited distinct potential receptor-binding sites, primarily located within the α-helix region, and was closely associated with the Obolenskvirus genus, as well as the Autographiviridae and Straboviridae families. The G3DSA:2.60.40.3940 domain, exhibiting minor structural variations, was predominantly found in phages of the Obolenskvirus genus. Additionally, a novel Obo-β-sandwich structure, identified as a potential receptor-binding domain, was discovered within Obolenskvirus genus cluster. The structural diversity of these receptor-binding domains accounts for their interactions with various receptors. CONCLUSIONS This research deepens the understanding of the relationship between A. baumannii phage genera and the functional domains within their tail fiber/spike proteins, emphasizing the compatibility between structural characteristics and functional roles. The data obtained could serve as a reference for the targeted modification of phages or their tail fiber/spike proteins, enhancing their therapeutic applications.
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Affiliation(s)
- Shenshen Liu
- School of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, Guangzhou, 510006, China
| | - Tao Lei
- School of Public Health, Xiangnan University, Chenzhou, China
| | - Yujing Tan
- School of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, Guangzhou, 510006, China
| | - Xiaoyi Huang
- School of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, Guangzhou, 510006, China
| | - Wenxin Zhao
- School of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, Guangzhou, 510006, China
| | - Huanhuan Zou
- School of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, Guangzhou, 510006, China
| | - Jianhui Su
- School of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, Guangzhou, 510006, China
| | - Ji Zeng
- School of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, Guangzhou, 510006, China
| | - Haiyan Zeng
- School of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, Guangzhou, 510006, China.
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Savich V, Akhremchuk A, Herasimovich A, Leanovich S, Valentovich L, Sidarenka A. Isolation, characterization, and whole-genome analysis of the novel temperate bacteriophage Ph-p5 infecting Glutamicibacter halophytocola. Arch Virol 2025; 170:46. [PMID: 39907824 DOI: 10.1007/s00705-025-06225-5] [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: 07/04/2024] [Accepted: 11/19/2024] [Indexed: 02/06/2025]
Abstract
Bacteria of the genus Glutamicibacter, due to their ubiquity, nutritional versatility, and ability to adapt to environmental stresses, play an important role in natural ecosystems and have been extensively studied. Nevertheless, there remains a significant gap in our knowledge regarding Glutamicibacter phages, particularly in comparison to those of the related actinobacteria. To date, only two virulent phages infecting G. arilaitensis have been described. To our knowledge, this is the first report on the isolation, characterization, and genome analysis of a temperate phage targeting G. halophytocola, an endophytic bacterium known for its plant-growth-promoting effect. The phage Ph-p5, with siphovirus structure, was isolated from soil. It exhibited a long latent period (120 min), a moderate burst size (87 ± 3 PFU/infected cell), and stability over a wide range of pH and temperature. The circularly permuted linear double-stranded DNA genome of phage Ph-p5, comprising 43,694 bp with a G + C content of 57.1%, contains 65 putative protein-coding sequences and one sequence encoding tRNA. Of the identified open reading frames, 33 were of unknown function, while the remaining ones were grouped into functional modules, including structural proteins, DNA replication and regulation, lysogeny, and lysis. The presence of intact lysogeny-related genes, together with the capacity for lysogenisation of the host strain G. halophytocola BIM B-1594, provides evidence that Ph-p5 is a temperate phage. Phylogenetic analysis demonstrated that phage Ph-p5 belongs to the class Caudoviricetes but exhibits significant divergence from known phages and may be assigned to a new genus, for which we propose the name "Petuglutavirus".
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Affiliation(s)
- Viktoryia Savich
- The Institute of Microbiology of the National Academy of Sciences of Belarus, 220084, Minsk, Belarus.
| | - Artur Akhremchuk
- The Institute of Microbiology of the National Academy of Sciences of Belarus, 220084, Minsk, Belarus
| | - Aliaksandra Herasimovich
- The Institute of Microbiology of the National Academy of Sciences of Belarus, 220084, Minsk, Belarus
| | - Sviatlana Leanovich
- The Institute of Microbiology of the National Academy of Sciences of Belarus, 220084, Minsk, Belarus
| | - Leonid Valentovich
- The Institute of Microbiology of the National Academy of Sciences of Belarus, 220084, Minsk, Belarus
| | - Anastasiya Sidarenka
- The Institute of Microbiology of the National Academy of Sciences of Belarus, 220084, Minsk, Belarus.
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61
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Rajab AAH, Khafagy ES, Lila ASA, Yousef N, Askoura M. Combating enteropathogenic and multidrug resistant Escherichia coli using the lytic bacteriophage vB_EcoM_ECO78, which disrupts bacterial biofilm formation and exhibits a remarkable environmental stability. J Appl Microbiol 2025; 136:lxaf028. [PMID: 39919762 DOI: 10.1093/jambio/lxaf028] [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: 11/05/2024] [Revised: 01/31/2025] [Accepted: 02/06/2025] [Indexed: 02/09/2025]
Abstract
AIM The current study aimed to establish a phenotypic and genotypic characterization record of a novel lytic bacteriophage (phage) against multidrug-resistant (MDR) Escherichia coli (E. coli) infections. METHODS AND RESULTS Phenotypic characterization of the isolated phage included the assessment of phage morphology, host range, stability, and antibiofilm activity. The isolated phage vB_EcoM_ECO78 demonstrated a high lytic activity against MDR E. coli and E. coli serotypes O78: K80: H12 and O26: H11. Additionally, it showed a marked antibiofilm activity and high physical stability at a wide range of temperatures and pH. Genotypic investigations identified a double-stranded DNA genome of 165 912 base pairs (bp) spanning 258 open reading frames (ORFs), out of which 149 ORFs were identified and annotated. In vivo analysis further confirmed the therapeutic potential of vB_EcoM_ECO78 which effectively increased the survival of mice infected with MDR E. coli. CONCLUSION The isolated phage vB_EcoM_ECO78 exhibits considerable stability and antibiofilm activity against MDR E. coli isolates, supported by notable environmental fitness and in vivo antibacterial capability.
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Affiliation(s)
- Azza A H Rajab
- Department of Microbiology and Immunology, Faculty of Pharmacy, Zagazig University, Zagazig 44519, Egypt
| | - El-Sayed Khafagy
- Department of Pharmaceutics, College of Pharmacy, Prince Sattam bin Abdulaziz University, Al-Kharj 11942, Saudi Arabia
- Department of Pharmaceutics and Industrial Pharmacy, Faculty of Pharmacy, Suez Canal University, Ismailia 41522, Egypt
| | - Amr S Abu Lila
- Department of Pharmaceutics, College of Pharmacy, University of Hail, Hail 81442, Saudi Arabia
| | - Nehal Yousef
- Department of Microbiology and Immunology, Faculty of Pharmacy, Zagazig University, Zagazig 44519, Egypt
| | - Momen Askoura
- Department of Microbiology and Immunology, Faculty of Pharmacy, Zagazig University, Zagazig 44519, Egypt
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Uskudar-Guclu A, Yalcin S. A novel Enterococcus faecalis bacteriophage Ef212: biological and genomic features. Int Microbiol 2025; 28:365-375. [PMID: 38935199 DOI: 10.1007/s10123-024-00547-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Revised: 05/30/2024] [Accepted: 06/14/2024] [Indexed: 06/28/2024]
Abstract
This study aimed to isolate and characterize biological and genomic features of a phage infecting Enterococcus faecalis. The phage was isolated from environmental water and temperature and pH stability, one-step growth curve, and multiplicity of infection (MOI) were determined. Whole genome sequencing (WGS) and structural and functional annotations were performed. Its antibiofilm activity was also evaluated. The optimal MOI was 0.01, the latency period was 5 min, and the burst size was 202 plaque forming unit (PFU). High phage survival rates were observed at between pH 4-10 and temperatures between 4-50 °C. WGS and Transmission electron microscopy (TEM) showed that it was an Efquatrovirus representing siphovirus morphotype respectively. It was named as Enterococcus phage Ef212 and has a linear 40,690 bp double-stranded DNA with 45.3% G + C content (GenBank accession number: OR052631). BACPHLIP tool demonstrated that Enterococcus phage Ef212 is a lytic phage (88%). A total of 80 open reading frames (ORFs) were found and there were no antibiotic resistance genes, pathogenicity, virulence genes, or tRNAs in the phage genome. It was diverged from the most similar phages (identity, 88.35%; coverage, 89%) by phylogenetic analysis. Phage Ef212 shared a large part of its genome (60/80) with several other phages, yet some unique parts were found in their genomes. Host range analysis showed that phage Ef212 showed lytic activity against vancomycin-resistant and vancomycin-susceptible E. faecalis clinical isolates. This novel phage Ef212 showed the ability to inhibit and reduce the biofilm formation by around 42% and 38%, respectively. The biological and genomic features indicate that having an effective antibacterial activity, phage Ef212 seemed a promising therapeutic and biocontrol agent.
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Affiliation(s)
- Aylin Uskudar-Guclu
- Faculty of Medicine, Department of Medical Microbiology, Baskent University, Ankara, Türkiye.
| | - Suleyman Yalcin
- Microbiology References Laboratory, Ministry of Health General Directorate of Public Health, Ankara, Türkiye
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Weinheimer AR, Ha AD, Aylward FO. Towards a unifying phylogenomic framework for tailed phages. PLoS Genet 2025; 21:e1011595. [PMID: 39908317 PMCID: PMC11835377 DOI: 10.1371/journal.pgen.1011595] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2024] [Revised: 02/18/2025] [Accepted: 01/28/2025] [Indexed: 02/07/2025] Open
Abstract
Classifying viruses systematically has remained a key challenge of virology due to the absence of universal genes and vast genetic diversity of viruses. In particular, the most dominant and diverse group of viruses, the tailed double-stranded DNA viruses of prokaryotes belonging to the class Caudoviricetes, lack sufficient similarity in the genetic machinery that unifies them to reconstruct an inclusive, stable phylogeny of these genes. While previous approaches to organize tailed phage diversity have managed to distinguish various taxonomic levels, these methods are limited in scalability, reproducibility, and the inclusion of modes of evolution, like gene gains and losses, remain key challenges. Here, we present a novel, comprehensive, and reproducible framework for examining evolutionary relationships of tailed phages. In this framework, we compare phage genomes based on the presence and absence of a fixed set of gene families which are used as binary trait data that is input into maximum likelihood models. Our resulting phylogeny stably recovers known taxonomic families of tailed phages, with and without the inclusion of metagenome-derived phages. We also quantify the mosaicism of replication and structural genes among known families, and our results suggest that these exchanges likely underpin the emergence of new families. Additionally, we apply this framework to large phages (>100 kilobases) to map emergences of traits associated with genome expansion. Taken together, this evolutionary framework for charting and organizing tailed phage diversity improves the systemization of phage taxonomy, which can unify phage studies and advance our understanding of their evolution.
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Affiliation(s)
- Alaina R. Weinheimer
- Department of Biological Sciences, Virginia Tech; Blacksburg, Virginia, United States of America
- Bigelow Laboratory for Ocean Sciences, East Boothbay, Maine, United States of America
| | - Anh D. Ha
- Department of Biological Sciences, Virginia Tech; Blacksburg, Virginia, United States of America
| | - Frank O. Aylward
- Department of Biological Sciences, Virginia Tech; Blacksburg, Virginia, United States of America
- Center for Emerging, Zoonotic, and Arthropod-Borne Infectious Disease, Virginia Tech; Blacksburg, Virginia, United States of America
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Jintasakul V, Pattano J, Preeprem S, Mittraparp-Arthorn P. Characterization and genome analysis of lytic Vibrio phage VPK8 with potential in lysing Vibrio parahaemolyticus isolates from clinical and seafood sources. Virol J 2025; 22:21. [PMID: 39885536 PMCID: PMC11783711 DOI: 10.1186/s12985-025-02637-6] [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: 12/07/2024] [Accepted: 01/20/2025] [Indexed: 02/01/2025] Open
Abstract
BACKGROUND Vibrio parahaemolyticus is a marine bacterium causing seafood-associated gastrointestinal illness in humans and acute hepatopancreatic necrosis disease (AHPND) in shrimp. Bacteriophages have emerged as promising biocontrol agents against V. parahaemolyticus. This study characterizes Vibrio phage VPK8, focusing on host specificity, efficiency of plating (EOP) variability across V. parahaemolyticus isolates from diverse sources and other Vibrio species, morphology, genomic features, and bacteriolytic potential. METHODS Vibrio phage VPK8 was isolated from blood cockles in Thailand using a mixed-host approach and purified via the double-layer agar method. Host specificity was evaluated using spot assays and EOP measurements against 120 Vibrio strains, including AHPND-associated, clinical, and seafood isolates. Phage morphology was characterized by transmission electron microscopy (TEM), while genomic features were analyzed using next-generation sequencing. Lytic characteristics, including latent period and burst size, were determined through one-step growth curves, and bacterial growth reduction was evaluated over a 24-h. RESULTS Vibrio phage VPK8 is a lytic phage with a 42,866 bp linear double-stranded genome, G + C content of 49.4%, and 48 coding sequences. Phylogenetic analysis grouped it within the Autographiviridae family, showing 95.96% similarity to Vibrio phage vB_VpaP_MGD1. Viral proteomic analysis placed VPK8 within the Pseudomonadota host group. Spot assays indicated broad lytic activity, but EOP analysis revealed high infectivity in clinical and seafood V. parahaemolyticus isolates, as well as some V. cholerae and V. mimicus strains. TEM revealed an icosahedral head (~ 60 nm) and a short tail. At a multiplicity of infection of 0.01, VPK8 exhibited a latent period of 25 min, a burst size of 115, and effectively inhibited the reference host V. parahaemolyticus PSU5124 within 6 h, maintaining its lytic activity and stability for over 24 h. CONCLUSIONS This study provides a detailed characterization of Vibrio phage VPK8 which exhibits targeted infectivity with high EOP in clinical and seafood V. parahaemolyticus isolates, as well as selected Vibrio species. Its stable lytic performance, rapid replication, and genomic safety suggest its potential for phage-based applications. Further studies should explore its in vivo efficacy and the genetic features contributing to phage resistance mechanisms, enhancing its potential applicability in managing Vibrio-related diseases.
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Affiliation(s)
- Valalak Jintasakul
- Division of Biological Science, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla, 90110, Thailand
- Center of Research and Innovation Development of Microbiology for Sustainability (RIMS), Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla, 90110, Thailand
| | - Jiranan Pattano
- Division of Biological Science, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla, 90110, Thailand
- Center of Research and Innovation Development of Microbiology for Sustainability (RIMS), Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla, 90110, Thailand
| | - Sutima Preeprem
- Medical and Industrial Microbiology Program, Faculty of Science Technology and Agriculture, Yala Rajabhat University, Yala, 95000, Thailand
| | - Pimonsri Mittraparp-Arthorn
- Division of Biological Science, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla, 90110, Thailand.
- Center of Research and Innovation Development of Microbiology for Sustainability (RIMS), Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla, 90110, Thailand.
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Bandoo RA, Kraberger S, Ozturk C, Lund MC, Zhu Q, Cook C, Smith B, Varsani A. Identification of Diverse Bacteriophages Associated with Bees and Hoverflies. Viruses 2025; 17:201. [PMID: 40006956 PMCID: PMC11860568 DOI: 10.3390/v17020201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2024] [Revised: 01/24/2025] [Accepted: 01/27/2025] [Indexed: 02/27/2025] Open
Abstract
Bacteriophages are the most numerous, ubiquitous, and diverse biological entities on the planet. Prior studies have identified bacteriophages associated with pathogenic and commensal microbiota of honeybees. In this study we expand on what is known about bacteriophages from the lineages Caudoviricetes, Inoviridae, and Microviridae, which are associated with honeybees (Apidae, Apis mellifera), solitary bees of the genus Nomia (Halictidae, Nomia), and hoverflies (Syrphidae). The complete genomes of seven caudoviruses, seven inoviruses, and 288 microviruses were assembled from honeybees (n = 286) and hoverflies in Arizona (n = 2). We used bacterial host predictive software and sequence read mapping programs to infer the commensal and transient bacterial hosts of pollinating insects. Lastly, this study explores the phylogenetic relationships of microviruses sampled from bees, opportunistically sampled pollinating insects such as hoverflies, and blackflies.
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Affiliation(s)
- Rohan A. Bandoo
- School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA; (R.A.B.); (C.O.); (Q.Z.); (B.S.)
| | - Simona Kraberger
- The Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, AZ 85287, USA;
| | - Cahit Ozturk
- School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA; (R.A.B.); (C.O.); (Q.Z.); (B.S.)
| | - Michael C. Lund
- The Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, AZ 85287, USA;
| | - Qiyun Zhu
- School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA; (R.A.B.); (C.O.); (Q.Z.); (B.S.)
- The Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, AZ 85287, USA;
| | - Chelsea Cook
- Department of Biological Sciences, Marquette University, Milwaukee, WI 53233, USA;
| | - Brian Smith
- School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA; (R.A.B.); (C.O.); (Q.Z.); (B.S.)
| | - Arvind Varsani
- School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA; (R.A.B.); (C.O.); (Q.Z.); (B.S.)
- The Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, AZ 85287, USA;
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ 85287, USA
- Structural Biology Research Unit, Department of Integrative Biomedical Sciences, University of Cape Town, Rondebosch, Cape Town 7700, South Africa
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Mathur Y, Boyd CM, Farnham JE, Monir MM, Islam MT, Sultana M, Ahmed T, Alam M, Seed KD. Capturing dynamic phage-pathogen coevolution by clinical surveillance. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.01.29.635557. [PMID: 39975409 PMCID: PMC11838301 DOI: 10.1101/2025.01.29.635557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 02/21/2025]
Abstract
Bacteria harness diverse defense systems that protect against phage predation1, many of which are encoded on horizontally transmitted mobile genetic elements (MGEs)2. In turn, phages evolve counter-defenses3, driving a dynamic arms race that remains underexplored in human disease contexts. For the diarrheal pathogen Vibrio cholerae, a higher burden of its lytic phage, ICP1, in patient stool correlates with reduced disease severity4. However, direct molecular evidence of phage-driven selection of epidemic V. cholerae has not been demonstrated. Here, through clinical surveillance in cholera-endemic Bangladesh, we capture the acquisition of a parasitic anti-phage MGE, PLE11, that initiated a selective sweep coinciding with the largest cholera outbreak in recent records. PLE11 exhibited potent anti-phage activity against co-circulating ICP1, explaining its rapid and dominating emergence. We identify PLE11-encoded Rta as the novel defense responsible and provide evidence that Rta restricts phage tail assembly. Using experimental evolution, we predict phage counteradaptations against PLE11 and document the eventual emergence and selection of ICP1 that achieves a convergent evolutionary outcome. By probing how PLEs hijack phage structural proteins to drive their horizontal transmission while simultaneously restricting phage tail assembly, we discover that PLEs manipulate tail assembly to construct chimeric tails comprised of MGE and phage-encoded proteins. Collectively, our findings reveal the molecular basis of the natural selection of a globally significant pathogen and its virus in a clinically relevant context.
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Affiliation(s)
- Yamini Mathur
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Caroline M. Boyd
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Jeannette E. Farnham
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Md Mamun Monir
- icddr,b, International Centre for Diarrhoeal Disease Research, Bangladesh, Dhaka, Bangladesh
| | - Mohammad Tarequl Islam
- icddr,b, International Centre for Diarrhoeal Disease Research, Bangladesh, Dhaka, Bangladesh
| | - Marzia Sultana
- icddr,b, International Centre for Diarrhoeal Disease Research, Bangladesh, Dhaka, Bangladesh
| | - Tahmeed Ahmed
- icddr,b, International Centre for Diarrhoeal Disease Research, Bangladesh, Dhaka, Bangladesh
| | - Munirul Alam
- icddr,b, International Centre for Diarrhoeal Disease Research, Bangladesh, Dhaka, Bangladesh
| | - Kimberley D. Seed
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, USA
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Liu X, Tang Y, Chen H, Liu JX, Sun HZ. Rumen DNA virome and its relationship with feed efficiency in dairy cows. MICROBIOME 2025; 13:14. [PMID: 39819730 PMCID: PMC11740651 DOI: 10.1186/s40168-024-02019-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Accepted: 12/19/2024] [Indexed: 01/19/2025]
Abstract
BACKGROUND The rumen harbors a diverse virome that interacts with other microorganisms, playing pivotal roles in modulating metabolic processes within the rumen environment. However, the characterization of rumen viruses remains incomplete, and their association with production traits, such as feed efficiency (FE), has not been documented. In this study, rumen fluid from 30 Chinese Holstein dairy cows was analyzed using next-generation sequencing (NGS) and High-Fidelity (HiFi) sequencing to elucidate the rumen DNA virome profile and uncover potential viral mechanisms influencing FE. RESULTS Integrated NGS and HiFi sequencing enhanced the length, completeness, and resolution of viral operational taxonomic units (vOTUs) compared to NGS. A total of 6,922 vOTUs were identified, including 4,716 lytic and 1,961 temperate vOTUs. At the family level, lytic viruses were predominantly from Siphoviridae (30.35%) and Schitoviridae (23.93%), while temperate viruses were primarily Siphoviridae (67.21%). The study annotated 2,382 auxiliary metabolic genes (AMGs), comprising 1,752 lytic virus-associated AMGs across 51 functional categories and 589 temperate virus-associated AMGs across 29 categories. Additionally, 2,232 vOTU-host metagenome-assembled genome (hMAG) linkages were predicted, with Firmicutes_A (33.60%) and Bacteroidota (33.24%) being the most prevalent host phyla. Significant differences in viral populations were observed between high and low FE groups across multiple taxonomic levels (P < 0.05). Two pathways were proposed to explain how rumen viruses might modulate FE: (1) Lytic viruses could lyse beneficial host bacteria linked to favorable cattle phenotypes, such as vOTU1836 targeting Ruminococcaceae, resulting in diminished organic acid production and consequently lower FE; (2) AMG-mediated host metabolism modulation, exemplified by GT2 carried by vOTU0897, which may enhance Lachnospiraceae fermentation capacity, increasing organic acid production and thereby improving FE. CONCLUSIONS This study constructed a comprehensive rumen DNA virome profile for Holstein dairy cows, elucidating the structural and functional complexity of rumen viruses, the roles of AMGs, and vOTU-hMAG linkages. The integration of these data offers novel insights into the mechanisms by which rumen viruses may regulate nutrient utilization, potentially influencing FE in dairy cows. Video Abstract.
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Affiliation(s)
- Xiaohan Liu
- Institute of Dairy Science, MoE Key Laboratory of Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University, Hangzhou, China
| | - Yifan Tang
- Institute of Dairy Science, MoE Key Laboratory of Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University, Hangzhou, China
| | - Hongyi Chen
- Institute of Dairy Science, MoE Key Laboratory of Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University, Hangzhou, China
| | - Jian-Xin Liu
- Institute of Dairy Science, MoE Key Laboratory of Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University, Hangzhou, China
| | - Hui-Zeng Sun
- Institute of Dairy Science, MoE Key Laboratory of Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University, Hangzhou, China.
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Negrete-Méndez H, Valencia-Toxqui G, Martínez-Peñafiel E, Medina-Contreras O, Fernández-Ramírez F, Morales-Ríos E, Navarro-González LJ, Torres-Flores JM, Kameyama L. A Lambda-evo (λ evo) phage platform for Zika virus E DIII protein display. Appl Microbiol Biotechnol 2025; 109:8. [PMID: 39820667 PMCID: PMC11739229 DOI: 10.1007/s00253-024-13380-3] [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: 09/18/2024] [Revised: 12/04/2024] [Accepted: 12/06/2024] [Indexed: 01/19/2025]
Abstract
One of the most significant bacteriophage technologies is phage display, in which heterologous peptides are exhibited on the virion surface. This work describes the display of λ decorative protein Dλ linked to the E protein domain III of Zika virus (Dλ-ZEDIII), to the GFP protein (Dλ-GFP), or to different domain III epitopes of the EZIKV protein (Dλ-TD), exhibited on the surface of an in vitro evolved lambda phage (λevo). This phage harbors a gene D deletion and was subjected to directed evolution using Escherichia coli W3110/pDλ-ZEDIII as background. After 20 days (20 cycles of dilution), the λevo phage developed a ~ 22% genome deletion affecting the non-essential λ b region, rendering a more stable phage that exhibited fusion proteins Dλ-ZEDIII or Dλ-GFP but not Dλ-TD. Despite the λevo system was able to decorate itself with the Dλ-ZEDIII protein, the production of viral particles was ~ 1000-fold lower than the λ wild-type, due to the unexpected Dλ-ZEDIII protein aggregation into bacterial inclusion bodies. Decorated phages (106 PFU (plaque forming units)/100 µl) were inoculated into BALB/c mice, and subsequent dot blot and Western blot immunoassays proved the production of murine antibodies against ZIKV (Zika virus). This multipurpose λevo phage display platform may be used interchangeably with other more soluble peptides, providing better yields. KEY POINTS: • λevo platform for displaying recombinant peptides. • Directed evolution to generate λevo with more efficient decoration. • Antigenic reaction in BALB/c mice by inoculating λevo with recombinant peptides.
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Affiliation(s)
- Honorio Negrete-Méndez
- Departamento de Genética y Biología Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Av. Instituto Politécnico Nacional No, 2508, C.P. 07360, Mexico City, Mexico
| | | | - Eva Martínez-Peñafiel
- Departamento de Genética y Biología Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Av. Instituto Politécnico Nacional No, 2508, C.P. 07360, Mexico City, Mexico
| | - Oscar Medina-Contreras
- Unidad de Investigación Epidemiológica en Endocrinología y Nutrición, Hospital Infantil de México Federico Gómez, Dr. Márquez No. 162, Mexico City, Mexico
| | | | - Edgar Morales-Ríos
- Departamento de Bioquímica, Centro de Investigación y de Estudios Avanzados del IPN, Instituto Politécnico Nacional No, 2508, C.P. 07360, Mexico City, Av, Mexico
| | - Luis Janiel Navarro-González
- Departamento de Bioquímica, Centro de Investigación y de Estudios Avanzados del IPN, Instituto Politécnico Nacional No, 2508, C.P. 07360, Mexico City, Av, Mexico
| | - Jesús M Torres-Flores
- Laboratorio Nacional de Vacunología y Virus Tropicales, Escuela Nacional de Ciencias Biológicas del IPN, Mexico City, Mexico
| | - Luis Kameyama
- Departamento de Genética y Biología Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Av. Instituto Politécnico Nacional No, 2508, C.P. 07360, Mexico City, Mexico.
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Leshkasheli L, Kusradze I, Bolkvadze D, Askilashvili L, Chichashvili M, Tsertsvadze G, Zaldastanishvili E. Klebsiella pneumoniae Phage M198 and Its Therapeutic Potential. Viruses 2025; 17:115. [PMID: 39861904 PMCID: PMC11768853 DOI: 10.3390/v17010115] [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: 12/30/2024] [Revised: 01/13/2025] [Accepted: 01/15/2025] [Indexed: 01/27/2025] Open
Abstract
The rapid worldwide spread of antibiotic resistance is quickly becoming an increasingly concerning problem for human healthcare. Non-antibiotic antibacterial agents are in high demand for many Gram-negative bacterial pathogens, including Klebsiella pneumoniae. Klebsiella-targeting phages are among the most promising alternative therapy options. They have already been successfully applied in a number of cases, and it is expected that the need for anti-Klebsiella phages will only increase in the future. This prospect highlights the need for well-characterized therapeutic phages. In this work, we describe a K. pneumoniae phage, which also infects strains of Klebsiella oxytoca. Here, we characterize phage M198 in terms of its biological and genetic properties. Since in some phage therapy cases, phages are administered in combination with antibiotics, here, we also screen for possible synergistic effects of combining phage M198 with six different antibiotics. We found that phage M198 has good lytic activity against clinical isolates; it does not have any indications of a temperate lifestyle, and it has synergistic potential when combined with some therapeutically relevant antibiotics.
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Affiliation(s)
- Lika Leshkasheli
- Laboratory of Molecular Biology, G. Eliava Institute of Bacteriophages, Microbiology and Virology, 0160 Tbilisi, Georgia; (L.L.); (D.B.); (L.A.)
| | - Ia Kusradze
- Laboratory of General Microbiology, G. Eliava Institute of Bacteriophages, Microbiology and Virology, 0160 Tbilisi, Georgia; (I.K.); (M.C.)
- Faculty of Medicine, European University, 0141 Tbilisi, Georgia
| | - Darejan Bolkvadze
- Laboratory of Molecular Biology, G. Eliava Institute of Bacteriophages, Microbiology and Virology, 0160 Tbilisi, Georgia; (L.L.); (D.B.); (L.A.)
- Program of Ecology, Faculty of Natural Sciences and Medicine, Ilia State University, 0162 Tbilisi, Georgia
| | - Lia Askilashvili
- Laboratory of Molecular Biology, G. Eliava Institute of Bacteriophages, Microbiology and Virology, 0160 Tbilisi, Georgia; (L.L.); (D.B.); (L.A.)
| | - Maria Chichashvili
- Laboratory of General Microbiology, G. Eliava Institute of Bacteriophages, Microbiology and Virology, 0160 Tbilisi, Georgia; (I.K.); (M.C.)
- Department of Immunology and Microbiology, Faculty of Exact and Natural Sciences, Ivane Javakhishvili Tbilisi State University, 0179 Tbilisi, Georgia
| | - Giorgi Tsertsvadze
- Electron Microscopy Unit, G. Eliava Institute of Bacteriophages, Microbiology and Virology, 0160 Tbilisi, Georgia
| | - Elisabed Zaldastanishvili
- Laboratory of Molecular Biology, G. Eliava Institute of Bacteriophages, Microbiology and Virology, 0160 Tbilisi, Georgia; (L.L.); (D.B.); (L.A.)
- School of Science and Technology, University of Georgia, 0171 Tbilisi, Georgia
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70
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Kyrkou I, Bartell J, Lechuga A, Lood C, Marvig RL, Lavigne R, Molin S, Krogh Johansen H. Pseudomonas aeruginosa maintains an inducible array of novel and diverse prophages over lengthy persistence in cystic fibrosis lungs. FEMS Microbiol Lett 2025; 372:fnaf017. [PMID: 39890605 PMCID: PMC11846083 DOI: 10.1093/femsle/fnaf017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Revised: 11/24/2024] [Accepted: 01/30/2025] [Indexed: 02/03/2025] Open
Abstract
Pseudomonas aeruginosa has increasing clinical relevance and commonly occupies the cystic fibrosis (CF) airways. Its ability to colonize and persist in diverse niches is attributed to its large accessory genome, where prophages represent a common feature and may contribute to its fitness and persistence. We focused on the CF airways niche and used 197 longitudinal isolates from 12 patients persistently infected by P. aeruginosa. We computationally predicted intact prophages for each longitudinal group and scored their long-term persistence. We then confirmed prophage inducibility and mapped their location in the host chromosome with lysate sequencing. Using comparative genomics, we evaluated prophage genomic diversity, long-term persistence, and level of genomic maintenance. Our findings support previous findings that most P. aeruginosa genomes harbour prophages some of which can self-induce, and that a common CF-treating antibiotic, ciprofloxacin, can induce prophages. Induced prophage genomes displayed high diversity and even genomic novelty. Finally, all induced prophages persisted long-term with their genomes avoiding gene loss and degradation over 4 years of host replication in the stressful CF airways niche. This and our detection of phage genes, which contribute to host competitiveness and adaptation, lends support to our hypothesis that the vast majority of prophages detected as intact and inducible in this study facilitated their host fitness and persistence.
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Affiliation(s)
- Ifigeneia Kyrkou
- Department of Veterinary and Animal Sciences, Food Safety and Zoonosis, University of Copenhagen, 1870 Frederiksberg, Denmark
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Jennifer Bartell
- Department of Clinical Microbiology, Rigshospitalet, 2100 Copenhagen, Denmark
| | - Ana Lechuga
- Laboratory of Gene Technology, Department of Biosystems, KU Leuven, 3001 Heverlee, Belgium
| | - Cédric Lood
- Laboratory of Gene Technology, Department of Biosystems, KU Leuven, 3001 Heverlee, Belgium
- Laboratory of Computational Systems Biology, Department of Microbial and Molecular Systems, KU Leuven, 3001 Heverlee, Belgium
| | - Rasmus L Marvig
- Center for Genomic Medicine, Rigshospitalet, 2100 Copenhagen, Denmark
| | - Rob Lavigne
- Laboratory of Gene Technology, Department of Biosystems, KU Leuven, 3001 Heverlee, Belgium
| | - Søren Molin
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Helle Krogh Johansen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
- Department of Clinical Microbiology, Rigshospitalet, 2100 Copenhagen, Denmark
- Department of Clinical Medicine, University of Copenhagen, 2100 Copenhagen, Denmark
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71
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Yakubovskij VI, Morozova VV, Kozlova YN, Tikunov AY, Fedorets VA, Zhirakovskaya EV, Babkin IV, Bardasheva AV, Tikunova NV. Phage vB_KlebPS_265 Active Against Resistant/MDR and Hypermucoid K2 Strains of Klebsiella pneumoniae. Viruses 2025; 17:83. [PMID: 39861872 PMCID: PMC11769527 DOI: 10.3390/v17010083] [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: 12/16/2024] [Revised: 12/30/2024] [Accepted: 01/01/2025] [Indexed: 01/27/2025] Open
Abstract
Klebsiella pneumoniae is an important opportunistic pathogen often resistant to antibiotics. Specific phages can be useful in eliminating infection caused by K. pneumoniae. Klebsiella phage vB_KlebPS_265 (KlebP_265) and its host strain were isolated from the sputum of a patient with Klebsiella infection. KlebP_265 was specific mainly to K. pneumoniae-type K2 strains including hypermucoid strains. Most of the hypermucoid KlebP_265-susceptible strains were antibiotic-resistant. This siphophage demonstrated good lytic activity and stability. The KlebP_265 genome was 46,962 bp and contained 88 putative genes; functions were predicted for 37 of them. No genes encoding integrases, toxins, or antibiotic resistance were found in the genome. So, KlebP_265 could potentially be a therapeutic phage. Comparative analysis indicated that KlebP_265 with the most relative Klebsiella phage DP01 formed the putative Dipiunovirus genus. Genome analysis revealed a large monophyletic group of phages related to KlebP_265 and DP01. This group is divided into two monophyletic clusters of phages forming new putative subfamilies Skatevirinae and Roufvirinae. Phylogenetic analysis showed extensive gene exchange between phages from the putative subfamilies. Horizontal transfer even involved conservative genes and led to clear genomic mosaicism, indicating multiple recombination events in the ancestral phages during evolution.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Nina V. Tikunova
- Laboratory of Molecular Microbiology, Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia; (V.V.M.); (I.V.B.)
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72
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Xu T, Ni Y, Li H, Wu S, Yan S, Chen L, Yu Y, Wang Y. Discovery and characterization of complete genomes of 38 head-tailed proviruses in four predominant phyla of archaea. Microbiol Spectr 2025; 13:e0049224. [PMID: 39545734 PMCID: PMC11705971 DOI: 10.1128/spectrum.00492-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Accepted: 09/23/2024] [Indexed: 11/17/2024] Open
Abstract
Archaea play a significant role in natural ecosystems and the human body. Archaeal viruses exert a considerable influence on the structure and composition of archaeal communities and their associated ecological environments. The present study revealed the complete genomes of 38 archaeal head-tailed proviruses through comprehensive data mining. The hosts of these proviruses were identified as belonging to the following four dominant phyla: Halobacteriota, Thermoplasmatota, Thermoproteota, and Nanoarchaeota. In addition to the 14 proviruses of halophilic archaea related to the Graaviviridae family, the remaining proviruses exhibited limited genetic similarities to known (pro)viruses, suggesting the existence of 14 potential novel families. Of the 38 archaeal proviruses, 30 have the potential to lyse host cells. Eleven proviruses contain genes linked to antiviral defense mechanisms, including those involved in restriction modification (RM), clustered regularly interspaced short palindromic repeat (CRISPR)-associated (CRISPR-Cas) nucleases, defense island system associated with restriction-modification (DISARM), and DNA degradation (Dnd). Moreover, auxiliary metabolic genes were identified in the proviruses of Bathyarchaeia and Halobacteriota archaea, including those involved in carbohydrate and amino acid metabolism. Our findings indicate the diversity of archaeal viruses, their interactions with archaeal hosts, and their roles in the adaptation of the host.IMPORTANCEThe field of archaeal virology has seen a rapid expansion through the use of metagenomics, yet the diversity of these viruses remains largely uncharted. In this study, the complete genomes of 38 novel archaeal proviruses were identified for the following four dominant phyla: Halobacteriota, Thermoplasmatota, Thermoproteota, and Nanoarchaeota. Two families and six genera of Archaea were the first to be identified as hosts for viruses. The proviruses were found to contain diverse genes that were involved in distinct adaptation strategies of viruses to hosts. Our findings contribute to the expansion of the lineages of archaeal viruses and highlight their intricate interactions and essential roles in enabling host survival and adaptation to diverse environmental conditions.
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Affiliation(s)
- Tianqi Xu
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, China
| | - Yimin Ni
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, China
| | - Hailing Li
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, China
| | - Shuang Wu
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, China
| | - Shuling Yan
- Entwicklungsgenetik und Zellbiologie der Tiere, Philipps-Universität Marburg, Marburg, Germany
| | - Lanming Chen
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, China
| | - Yongxin Yu
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, China
| | - Yongjie Wang
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, China
- Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao, China
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73
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Park EJ, Lee S, Na JB, Kim YB, Lee KM, Park SY, Kim JH. Characterization of Broad Spectrum Bacteriophage vB ESM-pEJ01 and Its Antimicrobial Efficacy Against Shiga Toxin-Producing Escherichia coli in Green Juice. Microorganisms 2025; 13:103. [PMID: 39858871 PMCID: PMC11767321 DOI: 10.3390/microorganisms13010103] [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: 11/11/2024] [Revised: 12/28/2024] [Accepted: 12/30/2024] [Indexed: 01/27/2025] Open
Abstract
Shiga toxin-producing Escherichia coli (STEC) infections have increased in humans, animals, and the food industry, with ready-to-eat (RTE) food products being particularly susceptible to contamination. The prevalence of multidrug-resistant strains has rendered the current control strategies insufficient to effectively control STEC infections. Herein, we characterized the newly isolated STEC phage vB_ESM-pEJ01, a polyvalent phage capable of infecting Escherichia and Salmonella species, and assessed its efficacy in reducing STEC in vitro and food matrices. The phage, belonging to the Tevenvirinae, exhibits effective bacteriolytic activity, a short latent period, large burst size, and stability under a broad pH range and moderate temperatures. Moreover, the phage demonstrated strong anti-biofilm efficacy even at low concentrations. Genomic analysis revealed that the phage was similar to the well-characterized RB49 phage (T4-like phage) but possesses distinct host-specificity-related genes that potentially contribute to its extensive host range. The efficacy of phage vB_ESM-pEJ01 was evaluated in artificially STEC-inoculated green juice samples, where it significantly reduced STEC and the abundance of Shiga toxin-producing genes at 4 and 25 °C. Therefore, these results suggest that the polyvalent phage vB_ESM-pEJ01 is a promising biocontrol agent for foodborne pathogens in RTE foods such as fresh juices.
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Affiliation(s)
- Eun Jeong Park
- Department of Food Science and Biotechnology, College of Bionano Technology, Gachon University, Seongnam 13120, Republic of Korea; (E.J.P.); (J.B.N.); (Y.B.K.); (K.M.L.)
| | - Seungki Lee
- Biological and Genetic Resources Assessment Division, National Institute of Biological Resources, Incheon 22689, Republic of Korea;
| | - Jong Beom Na
- Department of Food Science and Biotechnology, College of Bionano Technology, Gachon University, Seongnam 13120, Republic of Korea; (E.J.P.); (J.B.N.); (Y.B.K.); (K.M.L.)
| | - Ye Bin Kim
- Department of Food Science and Biotechnology, College of Bionano Technology, Gachon University, Seongnam 13120, Republic of Korea; (E.J.P.); (J.B.N.); (Y.B.K.); (K.M.L.)
| | - Kee Man Lee
- Department of Food Science and Biotechnology, College of Bionano Technology, Gachon University, Seongnam 13120, Republic of Korea; (E.J.P.); (J.B.N.); (Y.B.K.); (K.M.L.)
| | - Seon Young Park
- Laboratory of Aquatic Biomedicine, College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul 08826, Republic of Korea
| | - Ji Hyung Kim
- Department of Food Science and Biotechnology, College of Bionano Technology, Gachon University, Seongnam 13120, Republic of Korea; (E.J.P.); (J.B.N.); (Y.B.K.); (K.M.L.)
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74
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Osei EK, O'Hea R, Cambillau C, Athalye A, Hille F, Franz CMAP, O'Doherty Á, Wilson M, Murray GGR, Weinert LA, Manzanilla EG, Mahony J, Kenny JG. Isolation of phages infecting the zoonotic pathogen Streptococcus suis reveals novel structural and genomic characteristics. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.01.07.631744. [PMID: 39829746 PMCID: PMC11741397 DOI: 10.1101/2025.01.07.631744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 01/22/2025]
Abstract
Bacteriophage research has experienced a renaissance in recent years, owing to their therapeutic potential and versatility in biotechnology, particularly in combating antibiotic resistant-bacteria along the farm-to-fork continuum. However, certain pathogens remain underexplored as targets for phage therapy, including the zoonotic pathogen Streptococcus suis which causes infections in pigs and humans. Despite global efforts, the genome of only one infective S. suis phage has been described. Here, we report the isolation of two phages that infect S. suis: Bonnie and Clyde. The phages infect 58% of 100 S. suis strains tested, including representatives of seven different serotypes and thirteen known sequence types from diverse geographical origins. Clyde suppressed bacterial growth in vitro within two multi-strain mixes designed to simulate a polyclonal S. suis infection. Both phages demonstrated stability across various temperatures and pH levels, highlighting their potential to withstand storage conditions and maintain viability in delivery formulations. Genome comparisons revealed that neither phage shares significant nucleotide identity with any cultivated phages in the NCBI database and thereby represent novel species belonging to two distinct novel genera. This study is the first to investigate the adhesion devices of S. suis infecting phages. Structure prediction and analysis of adhesion devices with AlphaFold2 revealed two distinct lineages of S. suis phages: Streptococcus thermophilus-like (Bonnie) and S. suis-like (Clyde). The structural similarities between the adhesion devices of Bonnie and S. thermophilus phages, despite the lack of nucleotide similarity and differing ecological niches, suggest a common ancestor or convergent evolution, highlighting evolutionary links between pathogenic and non-pathogenic streptococcal species. These findings provide valuable insights into the genetic and phenotypic characteristics of phages that can infect S. suis, providing new data for the therapeutic application of phages in a One Health context.
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Affiliation(s)
- Emmanuel Kuffour Osei
- School of Microbiology, University College Cork, Co. Cork, T12 K8AF, Ireland
- APC Microbiome Ireland, University College Cork, Co. Cork, T12 YT20, Ireland
- Food Bioscience, Teagasc Food Research Centre, Moorepark, Co. Cork, P61 C996, Ireland
| | - Reuben O'Hea
- School of Microbiology, University College Cork, Co. Cork, T12 K8AF, Ireland
| | - Christian Cambillau
- School of Microbiology, University College Cork, Co. Cork, T12 K8AF, Ireland
- APC Microbiome Ireland, University College Cork, Co. Cork, T12 YT20, Ireland
- Laboratoire d'Ingénierie des Systèmes Macromoléculaires (LISM), Institut de Microbiologie, Bioénergies et Biotechnologie (IMM), Aix-Marseille Université - CNRS, UMR 7255 Marseille, France
| | - Ankita Athalye
- School of Microbiology, University College Cork, Co. Cork, T12 K8AF, Ireland
| | - Frank Hille
- Department of Microbiology and Biotechnology, Max Rubner-Institute, Hermann-Weigmann-Str. 1, 24103 Kiel, Germany
| | - Charles M A P Franz
- Department of Microbiology and Biotechnology, Max Rubner-Institute, Hermann-Weigmann-Str. 1, 24103 Kiel, Germany
| | - Áine O'Doherty
- Central Veterinary Research Laboratory, Backweston, Co. Kildare, Ireland
| | - Margaret Wilson
- Central Veterinary Research Laboratory, Backweston, Co. Kildare, Ireland
| | - Gemma G R Murray
- Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge, CB3 0ES, UK
- Department of Genetics, Evolution and Environment, University College London, Gower Street, London, WC1E 6BT, UK
| | - Lucy A Weinert
- Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge, CB3 0ES, UK
| | - Edgar Garcia Manzanilla
- Pig and Poultry Research and Knowledge Transfer Department, Teagasc Animal and Grassland Research and Innovation Centre, Moorepark, Fermoy, Cork, P61 C996, Ireland
- School of Veterinary Medicine, University College Dublin, Co. Dublin, D04 V1W8 Ireland
| | - Jennifer Mahony
- School of Microbiology, University College Cork, Co. Cork, T12 K8AF, Ireland
- APC Microbiome Ireland, University College Cork, Co. Cork, T12 YT20, Ireland
| | - John G Kenny
- APC Microbiome Ireland, University College Cork, Co. Cork, T12 YT20, Ireland
- Food Bioscience, Teagasc Food Research Centre, Moorepark, Co. Cork, P61 C996, Ireland
- VistaMilk SFI Research Centre, Fermoy, Co. Cork, P61 C996, Ireland
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Yu C, Yu M, Ma R, Wei S, Jin M, Jiao N, Zheng Q, Zhang R, Feng X. A novel Alteromonas phage with tail fiber containing six potential iron-binding domains. Microbiol Spectr 2025; 13:e0093424. [PMID: 39565130 PMCID: PMC11705849 DOI: 10.1128/spectrum.00934-24] [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: 04/14/2024] [Accepted: 09/20/2024] [Indexed: 11/21/2024] Open
Abstract
Viruses play a vital role in regulating microbial communities, contributing to biogeochemical cycles of carbon, nitrogen, and essential metals. Alteromonas is widespread and plays an essential role in marine microbial ecology. However, there is limited knowledge about the interactions of Alteromonas and its viruses (alterophages). This study isolated a novel podovirus, vB_AmeP-R22Y (R22Y), which infects Alteromonas marina SW-47 (T). Phylogenetic analysis suggested that R22Y represented a novel viral genus within the Schitoviridae family. R22Y exhibited a broad host range and a relatively large burst size, exerting an important impact on the adaptability and dynamics of host populations. Two auxiliary metabolic genes, encoding Acyl carrier protein and AAA domain-containing protein, were predicted in R22Y, which may potentially assist in host fatty acid metabolism and VB12 biosynthesis, respectively. Remarkably, the prediction of the R22Y tail fiber structure revealed six conserved histidine residues (HxH motifs) that could potentially bind iron ions, suggesting that alterophages may function as organic iron-binding ligands in the marine environment. Our isolation and characterization of R22Y complements the Trojan Horse hypothesis, proposes the possible role of alterophages for marine iron biogeochemical cycling, and provides new insights into phage-host interactions in the iron-limited ocean.IMPORTANCEIron (Fe), as an essential micronutrient, is often a limiting factor for microbial growth in marine ecosystems. The Trojan Horse hypothesis suggests that iron in the phage tail fibers is recognized by the host's siderophore-bound iron receptor, enabling the phage to attach and initiate infection. The potential role of phages as iron-binding ligands has significant implications for oceanic trace metal biogeochemistry. In this study, we isolated a new phage R22Y with the potential to bind iron ions, using Alteromonas, a major siderophore producer, as the host. The tail fiber structure of R22Y exhibits six conserved HxH motifs, suggesting that each phage could potentially bind up to 36 iron ions. R22Y may contribute to colloidal organically complexed dissolved iron in the marine environment. This finding provides further insights into the Trojan Horse hypothesis, suggesting that alterophages may act as natural iron-binding ligands in the marine environment.
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Affiliation(s)
- Chen Yu
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
- Archaeal Biology Center, Synthetic Biology Research Center, Shenzhen Key Laboratory of Marine Microbiome Engineering, Key Laboratory of Marine Microbiome Engineering of Guangdong Higher Education Institutes, Institute for Advanced Study, Shenzhen University, Shenzhen, China
| | - Meishun Yu
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
- State Key Laboratory Breeding Base of Marine Genetic Resource, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China
| | - Ruijie Ma
- Archaeal Biology Center, Synthetic Biology Research Center, Shenzhen Key Laboratory of Marine Microbiome Engineering, Key Laboratory of Marine Microbiome Engineering of Guangdong Higher Education Institutes, Institute for Advanced Study, Shenzhen University, Shenzhen, China
| | - Shuzhen Wei
- School of Ocean and Earth Science, Tongji University, Shanghai, China
| | - Min Jin
- State Key Laboratory Breeding Base of Marine Genetic Resource, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China
| | - Nianzhi Jiao
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Qiang Zheng
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Rui Zhang
- Archaeal Biology Center, Synthetic Biology Research Center, Shenzhen Key Laboratory of Marine Microbiome Engineering, Key Laboratory of Marine Microbiome Engineering of Guangdong Higher Education Institutes, Institute for Advanced Study, Shenzhen University, Shenzhen, China
| | - Xuejin Feng
- State Key Laboratory Breeding Base of Marine Genetic Resource, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China
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Rolland C, Wittmann J, Reimer LC, Sardà Carbasse J, Schober I, Dudek CA, Ebeling C, Koblitz J, Bunk B, Overmann J. PhageDive: the comprehensive strain database of prokaryotic viral diversity. Nucleic Acids Res 2025; 53:D819-D825. [PMID: 39373542 PMCID: PMC11701545 DOI: 10.1093/nar/gkae878] [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: 08/14/2024] [Revised: 09/18/2024] [Accepted: 09/25/2024] [Indexed: 10/08/2024] Open
Abstract
Prokaryotic viruses represent the most diverse and abundant biological entities on Earth. So far, data on bacteriophages are not standardized, not readily available for comparative analyses and cannot be linked to the rapidly growing (meta)genomic data. We developed PhageDive (https://phagedive.dsmz.de), a comprehensive database for prokaryotic viruses gathering all existing data dispersed across multiple sources, like scientific publications, specialized databases or internal files of culture collections. PhageDive allows to link own research data to the existing information through an easy and central access, providing fields for various experimental data (host range, genomic data, etc.) and available metadata (e.g. geographical origin, isolation source). An important feature is the link between experimental data, the culture collection number and the repository of the corresponding physical bioresource. To date, PhageDive covers 1167 phages from three different world-renowned public collections (DSMZ, Félix d'Hérelle Reference Center for Bacterial Viruses and NCTC) and features an advanced search function using all data fields from the sections like taxonomy or morphology by controlled vocabulary and ontologies. PhageDive is fully interoperable with other resources including NCBI, the Viral Host Range database (VHRdb) of Institute Pasteur or the BacDive and MediaDive databases of DSMZ.
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Affiliation(s)
- Clara Rolland
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures GmbH, 38124 Braunschweig, Germany
| | - Johannes Wittmann
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures GmbH, 38124 Braunschweig, Germany
| | - Lorenz C Reimer
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures GmbH, 38124 Braunschweig, Germany
| | - Joaquim Sardà Carbasse
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures GmbH, 38124 Braunschweig, Germany
| | - Isabel Schober
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures GmbH, 38124 Braunschweig, Germany
| | - Christian-Alexander Dudek
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures GmbH, 38124 Braunschweig, Germany
| | - Christian Ebeling
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures GmbH, 38124 Braunschweig, Germany
| | - Julia Koblitz
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures GmbH, 38124 Braunschweig, Germany
| | - Boyke Bunk
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures GmbH, 38124 Braunschweig, Germany
| | - Jörg Overmann
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures GmbH, 38124 Braunschweig, Germany
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Patel KM, Seed KD. A Class 1 OLD family nuclease encoded by Vibrio cholerae is countered by a vibriophage-encoded direct inhibitor. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.01.06.631583. [PMID: 39829814 PMCID: PMC11741312 DOI: 10.1101/2025.01.06.631583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 01/22/2025]
Abstract
Bacteria are constantly threatened by their viral predators (phages), which has resulted in the development of defense systems for bacterial survival. One family of defense systems found widely across bacteria are OLD (for overcoming lysogeny defect) family nucleases. Despite recent discoveries regarding Class 2 and 4 OLD family nucleases and how phages overcome them, Class 1 OLD family nucleases warrant further study as there has only been one anti-phage Class 1 OLD family nuclease described to date. Here, we identify the Vibrio cholerae-encoded Class 1 OLD family nuclease Vc OLD and describe its disruption of genome replication of the lytic vibriophage ICP1. Furthermore, we examine its in vitro activity, identifying Vc OLD as a DNA nickase. Finally, we identify the first direct inhibitor of a Class 1 OLD family nuclease, the ICP1-encoded Oad1. Our research further illuminates Class 1 OLD family nucleases' role in phage defense and explores the dynamic arms race between V. cholerae and its predatory phage ICP1.
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Affiliation(s)
- Kishen M. Patel
- Infectious Diseases and Immunity Graduate Group, School of Public Health, University of California, Berkeley, Berkeley, CA, USA
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, California, USA
| | - Kimberley D. Seed
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, California, USA
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78
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Li A, Chen C, Li Y, Wang Y, Li X, Zhu Q, Zhang Y, Tian S, Xia Q. Characterisation of a new virulent phage isolated from Hainan Island with potential against multidrug-resistant Pseudomonas aeruginosa infections. Res Microbiol 2025; 176:104250. [PMID: 39477080 DOI: 10.1016/j.resmic.2024.104250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2024] [Revised: 10/26/2024] [Accepted: 10/27/2024] [Indexed: 11/04/2024]
Abstract
Multidrug-resistant (MDR) Pseudomonas aeruginosa is a serious life-threatening pathogen. The rise in P. aeruginosa resistance rates has renewed interest in phages as an alternative therapeutic approach for treating bacterial infections. In this study, we investigated the characteristics of the first Pseudomonas phage, vB_PaP_HN01, isolated from Hainan, the only tropical island in China. The lytic rate of this phage against P. aeruginosa reached 64.3 % (27/42). Under the optimal multiplicity of infection (MOI) of 0.1, more than 90 % of phage particles absorb onto the host cell within 10 min, with an eclipse period of around 15 min, and a high titer phage production (1011 PFU/ml) within 90 min was demonstrated. vB_PaP_HN01 maintains a robust titer after 1 h exposure to pH values and temperatures (up to 50 °C). Genome annotation revealed that vB_PaP_HN01 did not contain drug-resistance or lysogeny-associated genes. It can effectively inhibit the formation of biofilms of MDR P. aeruginosa and eliminated aggressive biofilms (removal rate about 70 %). In the in vivo infection models, it was demonstrated that the survival rate and lifespan of Galleria mellonella larvae were increased alongside the injection of vB_PaP_HN01. These data revealed the potential of vB_PaP_HN01 against P. aeruginosa in clinic.
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Affiliation(s)
- Anyang Li
- NHC Key Laboratory of Tropical Disease Control, School of Tropical Medicine and the Second Affiliated Hospital, Hainan Medical University, Haikou, Hainan, China
| | - Chen Chen
- Medical Laboratory Department, Traditional Chinese Medicine Hospital of Yaan, Sichuan, China
| | - Yanmei Li
- NHC Key Laboratory of Tropical Disease Control, School of Tropical Medicine and the Second Affiliated Hospital, Hainan Medical University, Haikou, Hainan, China
| | - Yanshuang Wang
- Department of Clinical Laboratory, The Second Affiliated Hospital, Hainan Medical University, Haikou, China
| | - Xuemiao Li
- NHC Key Laboratory of Tropical Disease Control, School of Tropical Medicine and the Second Affiliated Hospital, Hainan Medical University, Haikou, Hainan, China
| | - Qiao Zhu
- NHC Key Laboratory of Tropical Disease Control, School of Tropical Medicine and the Second Affiliated Hospital, Hainan Medical University, Haikou, Hainan, China
| | - Yue Zhang
- NHC Key Laboratory of Tropical Disease Control, School of Tropical Medicine and the Second Affiliated Hospital, Hainan Medical University, Haikou, Hainan, China
| | - Shen Tian
- NHC Key Laboratory of Tropical Disease Control, School of Tropical Medicine and the Second Affiliated Hospital, Hainan Medical University, Haikou, Hainan, China.
| | - Qianfeng Xia
- NHC Key Laboratory of Tropical Disease Control, School of Tropical Medicine and the Second Affiliated Hospital, Hainan Medical University, Haikou, Hainan, China.
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79
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Vidigal PMP, Hungaro HM. Genome sequencing of Escherichia coli phage UFJF_EcSW4 reveals a novel lytic Kayfunavirus species. 3 Biotech 2025; 15:10. [PMID: 39691801 PMCID: PMC11646959 DOI: 10.1007/s13205-024-04172-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2024] [Accepted: 11/24/2024] [Indexed: 12/19/2024] Open
Abstract
The Escherichia coli phage UFJF_EcSW4 was isolated from polluted stream water and showed clear lysis plaques on the host, measuring 0.67 ± 0.43 mm, with a titer of 9.57 ± 0.23 log PFU/ml. It demonstrated a very narrow host range, infecting only its host. Additionally, it has a short latent period of 9 min, a burst size of 49 PFU/infected cell, and stability over a wide range of pH, temperature, and free residual chlorine. The phage has a double-stranded DNA genome spanning 40,299 bp, with a GC content of 49.87% and short-direct terminal repeats (DTR) sequences of 286 bp. The UFJF_EcSW4 genome contains 55 genes, organized into functional modules with a unidirectional arrangement, regulated by 22 promoters (three from the phage and 19 from the host) and three Rho-independent terminators. Comparative analysis revealed that the UFJF_EcSW4 genome shares an average genomic similarity of 77.82% with the genome sequences of phages from the Kayfunavirus genus but does not surpass the 95% threshold necessary for species classification. Therefore, the UFJF_EcSW4 is a novel Kayfunavirus UFJF_EcSW4 species belonging to the Studiervirinae subfamily. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-024-04172-7.
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Affiliation(s)
- Pedro Marcus Pereira Vidigal
- Núcleo de Análise de Biomoléculas (NuBioMol), Campus da UFV, Universidade Federal de Viçosa (UFV), Viçosa, MG 36570-900 Brazil
| | - Humberto Moreira Hungaro
- Departamento de Ciências Farmacêuticas, Faculdade de Farmácia, Universidade Federal de Juiz de Fora (UFJF), Juiz de Fora, MG 36036-900 Brazil
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80
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Prabhu A, Zaugg J, Chan CX, McIlroy SJ, Rinke C. Insights Into Phylogeny, Diversity and Functional Potential of Poseidoniales Viruses. Environ Microbiol 2025; 27:e70017. [PMID: 39777783 PMCID: PMC11706807 DOI: 10.1111/1462-2920.70017] [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: 07/14/2024] [Revised: 11/07/2024] [Accepted: 11/26/2024] [Indexed: 01/11/2025]
Abstract
Viruses infecting archaea play significant ecological roles in marine ecosystems through host infection and lysis, yet they have remained an underexplored component of the virosphere. In this study, we recovered 451 archaeal viruses from a subtropical estuary, identifying 63 that are associated with the dominant marine order Poseidoniales (Marine Group II Archaea). Phylogenetic analyses of a subset of complete and nearly-complete viral genomes assigned these viruses to the order Magrovirales, a lineage of Poseidoniales viruses, and identified a novel group of viruses distinct from Magrovirales. Utilising demarcation criteria established for the classification of archaeal tailed viruses, we propose two families within the order Magrovirales: Apasviridae (magrovirus group A), comprising the genera Agnivirus and Savitrvirus, and Krittikaviridae (magrovirus group E) encompassing the genus Velanvirus. Additionally, we propose a new order, distinct from Magrovirales, named Adrikavirales, which includes the genus Vyasavirus. Our detailed genomic characterisation of the new viral lineages revealed genes involved in viral assembly and egress, such as those responsible for creating holin rafts to lyse host cell membranes, a feature predominantly known from bacteriophages. Furthermore, we identified a broad spectrum of auxiliary metabolic genes, suggesting that these viruses can modulate host metabolism. Collectively, our findings substantially enhance the current understanding of the diversity and functional potential of Poseidoniales viruses.
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Affiliation(s)
- Apoorva Prabhu
- School of Chemistry and Molecular Biosciences, Australian Centre for EcogenomicsThe University of QueenslandBrisbaneQueenslandAustralia
| | - Julian Zaugg
- School of Chemistry and Molecular Biosciences, Australian Centre for EcogenomicsThe University of QueenslandBrisbaneQueenslandAustralia
| | - Cheong Xin Chan
- School of Chemistry and Molecular Biosciences, Australian Centre for EcogenomicsThe University of QueenslandBrisbaneQueenslandAustralia
| | - Simon J. McIlroy
- Centre for Microbiome Research, School of Biomedical Sciences, Translational Research InstituteQueensland University of TechnologyBrisbaneQueenslandAustralia
| | - Chris Rinke
- School of Chemistry and Molecular Biosciences, Australian Centre for EcogenomicsThe University of QueenslandBrisbaneQueenslandAustralia
- Department of MicrobiologyUniversity of InnsbruckInnsbruckAustria
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81
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Pascual-Benito M, Méndez J, Ramos-Barbero MD, Jorba-Plassa A, Martín-Díaz J, Blanch AR. Efficient quantification of somatic coliphages in water: Development and validation of the Enumera® Rapid kit. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 957:177500. [PMID: 39551208 DOI: 10.1016/j.scitotenv.2024.177500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2024] [Revised: 11/06/2024] [Accepted: 11/08/2024] [Indexed: 11/19/2024]
Abstract
The integration of somatic coliphage analysis into water quality regulations has driven the development of more streamlined, easier, and faster detection methods. These include the Bluephage method, initially designed for the qualitative assessment of coliphages in 100 mL water samples. In the present study this technique was adapted for quantitative analysis using the most probable number method, enabling quantification of somatic coliphages in 100 mL water samples within 6.5 h of incubation. Early readings were optimised using an algorithm developed from an extensive dataset of over 400 environmental samples. This new quantitative method has been refined and commercialised as the Enumera® Rapid kit (BPF-SE, Bluephage S.L.), which includes a new reference somatic coliphage, strain GR8. After sequencing and further characterisation, it was confirmed that the new strain belongs to the same species as the reference somatic coliphage of the ISO 10705-2 method. The Enumera® Rapid kit was then validated by assessing its efficacy across 151 samples from various water matrices. The method provided a mean recovery rate of 103 %, ranging from 95 % for drinking water to 116 % for wastewater, at concentrations from 0 to 300 PFU/100 mL. In comparison, ISO 10705-2 applied after membrane filtration yielded a mean recovery rate of 63.8 %, with the highest rate observed for wastewater (88.9 %). The results obtained with the Enumera® Rapid kit did not differ significantly compared to the reference method after adjusting for potential losses during the concentration stage outlined in ISO 10705-3. The new method also demonstrated a robust accuracy of 0.16 logs, good linearity, and achieved a limit of detection and quantification of 1 MPN/100 mL. The Enumera® Rapid kit enables rapid and straightforward quantification of somatic coliphages in 100 mL water samples within a single working day. Its streamlined workflow serves as a useful tool for microbial water quality monitoring.
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Affiliation(s)
- Miriam Pascual-Benito
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona, Diagonal 643, 08028 Barcelona, Spain; Bluephage S.L. Gavà 4, 08820, El Prat de Llobregat, Barcelona, Spain.
| | - Javier Méndez
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona, Diagonal 643, 08028 Barcelona, Spain
| | - María Dolores Ramos-Barbero
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona, Diagonal 643, 08028 Barcelona, Spain
| | | | - Julia Martín-Díaz
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona, Diagonal 643, 08028 Barcelona, Spain; Bluephage S.L. Gavà 4, 08820, El Prat de Llobregat, Barcelona, Spain
| | - Anicet R Blanch
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona, Diagonal 643, 08028 Barcelona, Spain
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82
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Oluwarinde BO, Ajose DJ, Abolarinwa TO, Montso PK, Njom HA, Ateba CN. Molecular characterization and safety properties of multi drug-resistant Escherichia coli O157:H7 bacteriophages. BMC Microbiol 2024; 24:528. [PMID: 39695941 DOI: 10.1186/s12866-024-03691-w] [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: 04/08/2024] [Accepted: 12/06/2024] [Indexed: 12/20/2024] Open
Abstract
The increase in multi drug resistance (MDR) amongst food-borne pathogens such as Escherichia coli O157:H7, coupled with the upsurge of food-borne infections caused by these pathogens is a major public health concern. Lytic phages have been employed as an alternative to antibiotics for use against food-borne pathogens. However, for effective application, phages should be selectively toxic. Therefore, the objective of this study was to characterise lytic E. coli O157:H7 phages isolated from wastewater as possible biocontrol agents and access their genomes for the absence of genes that denotes virulence, resistance, toxins, and lysogeny using whole genome sequencing. E. coli O157:H7 bacteriophages showed clear plaques ranging in size from 1.0 mm to 2.0 mm. Spot test and Efficiency of plating (EOP) analysis demonstrated that isolated phages could infect various environmental E. coli strains. Four phages; vB_EcoM_EP32a, vB_EcoP_EP32b, vB_EcoM_EP57, and vB_EcoM_EP69 demonstrated broad lytic spectra against E. coli O157:H7 strains. Transmission Electron Microscopy (TEM) showed that all phages have tails and were classified as Caudoviricetes. Growth parameters showed an average latent period of 15 ± 3.8 min, with a maximum burst size of 392 PFU/cell. The phages were stable at three distinct temperatures (4 °C, 28 °C, and 37 °C) and at pH values of 3.5, 5.0, 7.0, 9.0, and 11.0. Based on their morphological distinctiveness, three phages were included in the Whole Genome Sequencing (WGS) analysis. WGS results revealed that E. coli O157:H7 phages (vB_EcoM_EP32a, vB_EcoP_EP32b, and vB_EcoM_EP57) were composed of linear double-stranded DNA (dsDNA) with genome sizes 163,906, 156,698, and 130,723 bp and GC contents of 37.61, 37, and 39% respectively. Phages vB_EcoM_EP32a and vB_EcoP_EP32b genomes were classified under the class Caudoviricetes, Straboviridae family, and the new genus "Phapecoctavirus", while vB_EcoM_EP57 was classified under the class Caudoviricetes, Autographiviridae family. Genome analysis revealed no lysogenic (integrase), virulence, or antimicrobial resistance sequences in all three Escherichia phage genomes. The overall results provided evidence that lytic E. coli O157:H7 bacteriophages in this study, are relatively stable, can infect diverse E. coli strains, and does not contain genes responsible for virulence, resistance, toxins, and lysogeny. Thus, they can be considered as biocontrol candidates against MDR pathogenic E. coli O157:H7 strains in the food industry.
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Affiliation(s)
- Bukola Opeyemi Oluwarinde
- Antimicrobial Resistance and Phage Biocontrol Research Group (AREPHABREG), Department of Microbiology, School of Biological Sciences, Faculty of Natural and Agricultural Sciences, North‒West University, Private Mail Bag X2046, Mmabatho, 2735, South Africa
- Food Security and Safety Focus Area, Faculty of Natural and Agricultural Sciences, North‒West University, Private Mail Bag X2046, Mmabatho, 2735, South Africa
| | - Daniel Jesuwenu Ajose
- Antimicrobial Resistance and Phage Biocontrol Research Group (AREPHABREG), Department of Microbiology, School of Biological Sciences, Faculty of Natural and Agricultural Sciences, North‒West University, Private Mail Bag X2046, Mmabatho, 2735, South Africa
- Food Security and Safety Focus Area, Faculty of Natural and Agricultural Sciences, North‒West University, Private Mail Bag X2046, Mmabatho, 2735, South Africa
| | - Tesleem Olatunde Abolarinwa
- Antimicrobial Resistance and Phage Biocontrol Research Group (AREPHABREG), Department of Microbiology, School of Biological Sciences, Faculty of Natural and Agricultural Sciences, North‒West University, Private Mail Bag X2046, Mmabatho, 2735, South Africa
- Food Security and Safety Focus Area, Faculty of Natural and Agricultural Sciences, North‒West University, Private Mail Bag X2046, Mmabatho, 2735, South Africa
| | - Peter Kotsoana Montso
- Antimicrobial Resistance and Phage Biocontrol Research Group (AREPHABREG), Department of Microbiology, School of Biological Sciences, Faculty of Natural and Agricultural Sciences, North‒West University, Private Mail Bag X2046, Mmabatho, 2735, South Africa
- Food Security and Safety Focus Area, Faculty of Natural and Agricultural Sciences, North‒West University, Private Mail Bag X2046, Mmabatho, 2735, South Africa
| | - Henry Akum Njom
- Agricultural Research Council, Private Mail Bag X2046, Potchefstroom, 2531, South Africa
| | - Collins Njie Ateba
- Antimicrobial Resistance and Phage Biocontrol Research Group (AREPHABREG), Department of Microbiology, School of Biological Sciences, Faculty of Natural and Agricultural Sciences, North‒West University, Private Mail Bag X2046, Mmabatho, 2735, South Africa.
- Food Security and Safety Focus Area, Faculty of Natural and Agricultural Sciences, North‒West University, Private Mail Bag X2046, Mmabatho, 2735, South Africa.
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83
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Wang W, Wang H, Zou X, Liu Y, Zheng K, Chen X, Wang X, Sun S, Yang Y, Wang M, Shao H, Liang Y. A novel virus potentially evolved from the N4-like viruses represents a unique viral family: Poorviridae. Appl Environ Microbiol 2024; 90:e0155924. [PMID: 39570022 DOI: 10.1128/aem.01559-24] [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: 08/06/2024] [Accepted: 09/27/2024] [Indexed: 11/22/2024] Open
Abstract
Pseudoalteromonas are widely distributed in marine extreme habitats and exhibit diverse extracellular protease activity, which is essential for marine biogeochemical cycles. However, our understanding of viruses that infect Pseudoalteromonas remains limited. This study isolated a virus infecting Pseudoalteromonas nigrifaciens from Xiaogang in Qingdao, China. vB_PunP_Y3 comprises a linear, double-strand DNA genome with a length of 48,854 bp, encoding 52 putative open reading frames. Transmission electron microscopy demonstrates the short-tailed morphology of vB_PunP_Y3. Phylogenetic and genome-content-based analysis indicate that vB_PunP_Y3 represents a novel virus family named as Poorviridae, along with three high-quality uncultivated viral genomes. Biogeographical analyses show that Poorviridae is distributed across five viral ecological zones, and is predominantly detected in the Antarctic, Arctic, and bathypelagic zones. Comparative genomics analyses identified three of the seven hallmark proteins of N4-like viruses (DNA polymerase, major capsid protein, and virion-encapsulated RNA polymerase) from vB_PunP_Y3, combing with the protein tertiary structures of the major capsid protein, suggesting that vB_PunP_Y3 might evolve from the N4-like viruses. IMPORTANCE vB_PunP_Y3 is a unique strain containing three of the seven hallmark proteins of N4-like viruses, but is grouped into a novel family-level viral cluster with three uncultured viruses from metagenomics, named Poorviridae. This study enhanced the understanding about the genetic diversity, evolution, and distribution of Pseudoalteromonas viruses and provided insights into the novel evolution mechanism of marine viruses.
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Affiliation(s)
- Wei Wang
- College of Marine Life Sciences, MoE Key Laboratory of Evolution & Marine Biodiversity, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China
| | - Hongmin Wang
- College of Marine Life Sciences, MoE Key Laboratory of Evolution & Marine Biodiversity, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China
| | - Xiao Zou
- Xiangdong Hospital, Hunan Normal University, Liling, China
| | - Yundan Liu
- College of Marine Life Sciences, MoE Key Laboratory of Evolution & Marine Biodiversity, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China
| | - Kaiyang Zheng
- College of Marine Life Sciences, MoE Key Laboratory of Evolution & Marine Biodiversity, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China
| | - Xin Chen
- College of Marine Life Sciences, MoE Key Laboratory of Evolution & Marine Biodiversity, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China
| | - Xinyi Wang
- College of Marine Life Sciences, MoE Key Laboratory of Evolution & Marine Biodiversity, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China
| | - Shujuan Sun
- College of Marine Life Sciences, MoE Key Laboratory of Evolution & Marine Biodiversity, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China
| | - Yang Yang
- College of Marine Life Sciences, MoE Key Laboratory of Evolution & Marine Biodiversity, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China
| | - Min Wang
- College of Marine Life Sciences, MoE Key Laboratory of Evolution & Marine Biodiversity, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China
- UMT-OUC Joint Centre for Marine Studies, Qingdao, China
- Haide College, Ocean University of China, Qingdao, China
- The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Hongbing Shao
- College of Marine Life Sciences, MoE Key Laboratory of Evolution & Marine Biodiversity, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China
- UMT-OUC Joint Centre for Marine Studies, Qingdao, China
| | - Yantao Liang
- College of Marine Life Sciences, MoE Key Laboratory of Evolution & Marine Biodiversity, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China
- UMT-OUC Joint Centre for Marine Studies, Qingdao, China
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84
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Tellez-Carrasquilla S, Salazar-Ospina L, Jiménez JN. High activity and specificity of bacteriophage cocktails against carbapenem-resistant Klebsiella pneumoniae belonging to the high-risk clones CG258 and ST307. Front Microbiol 2024; 15:1502593. [PMID: 39717270 PMCID: PMC11663894 DOI: 10.3389/fmicb.2024.1502593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2024] [Accepted: 11/25/2024] [Indexed: 12/25/2024] Open
Abstract
Introduction The widespread clinical and environmental dissemination of successful clones of carbapenem-resistant Klebsiella pneumoniae (CRKP) represents a serious global public health threat. In this context, lytic bacteriophages have emerged as a promising alternative for controlling these pathogens. This study describes the biological, structural, and genomic characteristics of lytic bacteriophages against the high-risk CRKP clones CG258 and ST307 and describes their performance in combination. Methods An experimental study was carried out. Bacteriophages were isolated from hospital wastewater and from wastewater treatment plants (WWTP). Bacteriophages were isolated using the double layer agar technique and their characterization included host range (individual and cocktail), plating efficiency (EOP), infection or bacterial killing curve, one-step curve, bacteriophage stability at pH and temperature conditions, transmission electron microscopy (TEM) and whole genome sequencing. Results After purification, five active bacteriophages against CRKP were obtained, three bacteriophages (FKP3, FKP4 and FKP14) had targeted activities against CG258 CRKP and two (FKP10 and FKP12) against ST307 isolates. Seven cocktails were prepared, of which Cocktail 2, made up of the bacteriophages FKP3, FKP10, and FKP14, showed the best activity against 85.7% (n = 36/42) of CRKP isolates belonging to both clones, CG258 (80.8%; n = 21/26) and ST307 (93.8%, n = 15/16). The efficiency of the plating (EOP), infection curve, and one-step growth curve showed that the cocktail phages efficiently infected other CRKP isolates (EOP ≥ 0.5), controlled bacterial growth up to 73.5%, and had short latency periods, respectively, (5-10 min). In addition, they were stable at temperatures between 4°C and 50°C and pH between 4 and 10. All bacteriophages belonged to the Caudoviricetes class, and no genes associated with virulence factors or antibiotic resistance were detected. Conclusion These findings showed bacteriophages and phage cocktails with high specificity against CRKP belonging to the successful clones CG258 and ST307 with promising characteristics, making them an alternative for controlling these clones in different environmental or health settings, biocontrol agents, or disinfectants in industry and in the field of diagnosis.
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Affiliation(s)
| | | | - J. Natalia Jiménez
- Grupo de Investigación en Microbiología Básica y Aplicada (MICROBA), Escuela de Microbiología, Universidad de Antioquia, Medellín, Colombia
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85
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Zhang J, Shang J, Liu B, Zhu D, Li Q, Yin L, Ohore OE, Wen S, Ding C, Zhang Y, Yue Z, Zou Y. Hot spots of resistance: Transit centers as breeding grounds for airborne ARG-carrying bacteriophages. JOURNAL OF HAZARDOUS MATERIALS 2024; 480:136165. [PMID: 39418908 DOI: 10.1016/j.jhazmat.2024.136165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2024] [Revised: 09/15/2024] [Accepted: 10/12/2024] [Indexed: 10/19/2024]
Abstract
The presence of pathogenic bacteria and antibiotic resistance genes (ARGs) in urban air poses a significant threat to public health. While prevailing research predominantly focuses on the airborne transmission of ARGs by bacteria, the potential influence of other vectors, such as bacteriophages, is often overlooked. This study aims to investigate the characteristics of phages and ARGs in aerosols originating from hospitals, public transit centers, wastewater treatment plants, and landfill sites. The average abundance of ARGs carried by phages in the public transit centers was 8.81 ppm, which was 2 to 3 times higher than that at the other three sites. Additionally, the abundance of ARGs across different risk levels at this site was also significantly higher than at the other three sites. The assembled phage communities bearing ARGs in public transit centers are chiefly governed by homogeneous selection processes, likely influenced by human movement. Furthermore, observations at public transit sites revealed that the average abundance ratio of virulent phages to their hosts was 1.01, and the correlation coefficient between their auxiliary metabolic genes and hosts' metabolic genes was 0.59, which were 20 times and 3 times higher, respectively, than those of temperate phages. This suggests that virulent phages may enhance their survival by altering host metabolism, thereby aiding the dispersion of ARGs and bacterial resistance. These revelations furnish fresh insights into phage-mediated ARG transmission, offering scientific substantiation for strategies aimed at preventing and controlling resistance within aerosols.
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Affiliation(s)
- Jing Zhang
- NHC Key Laboratory of Tropical Disease Control, School of Tropical Medicine, Hainan Medical University, Haikou, Hainan 571199, China.
| | - Jiayu Shang
- Department of Information Engineering, The Chinese University of Hong Kong, Hong Kong (SAR), China
| | - Beibei Liu
- Hainan Key Laboratory of Tropical Eco-Circular Agriculture, Environmental and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; Key Laboratory of Low-carbon Green Agriculture in Tropical Region of China, Ministry of Agriculture and Rural Affairs, Environmental and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; Hainan Danzhou Tropical Agro-ecosystem National Observation and Research Station, Chinese Academy of Tropical Agricultural Sciences, Danzhou 571737, China
| | - Dong Zhu
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Qinfen Li
- Hainan Key Laboratory of Tropical Eco-Circular Agriculture, Environmental and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; Key Laboratory of Low-carbon Green Agriculture in Tropical Region of China, Ministry of Agriculture and Rural Affairs, Environmental and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; Hainan Danzhou Tropical Agro-ecosystem National Observation and Research Station, Chinese Academy of Tropical Agricultural Sciences, Danzhou 571737, China
| | - Li Yin
- NHC Key Laboratory of Tropical Disease Control, School of Tropical Medicine, Hainan Medical University, Haikou, Hainan 571199, China
| | - Okugbe Ebiotubo Ohore
- NHC Key Laboratory of Tropical Disease Control, School of Tropical Medicine, Hainan Medical University, Haikou, Hainan 571199, China
| | - Shaobai Wen
- NHC Key Laboratory of Tropical Disease Control, School of Tropical Medicine, Hainan Medical University, Haikou, Hainan 571199, China
| | - Changfeng Ding
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Yican Zhang
- College of Life Sciences, Jilin Agricultural University, Changchun 130118, China
| | - Zhengfu Yue
- Hainan Key Laboratory of Tropical Eco-Circular Agriculture, Environmental and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; Key Laboratory of Low-carbon Green Agriculture in Tropical Region of China, Ministry of Agriculture and Rural Affairs, Environmental and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; Hainan Danzhou Tropical Agro-ecosystem National Observation and Research Station, Chinese Academy of Tropical Agricultural Sciences, Danzhou 571737, China.
| | - Yukun Zou
- Hainan Key Laboratory of Tropical Eco-Circular Agriculture, Environmental and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; Key Laboratory of Low-carbon Green Agriculture in Tropical Region of China, Ministry of Agriculture and Rural Affairs, Environmental and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; Hainan Danzhou Tropical Agro-ecosystem National Observation and Research Station, Chinese Academy of Tropical Agricultural Sciences, Danzhou 571737, China
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86
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Li Y, Zhang Y, Li A, Zhang T, Yi J, Zhang N, Kang X, Liu W, Tian S, Xia Q. Characterization of a novel lytic phage against methicillin resistance Staphylococcus aureus in Hainan island. Virology 2024; 600:110264. [PMID: 39471608 DOI: 10.1016/j.virol.2024.110264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2024] [Revised: 09/19/2024] [Accepted: 10/16/2024] [Indexed: 11/01/2024]
Abstract
Methicillin resistance Staphylococcus aureus (MRSA) is currently threatening global public health, and a similar issue was encountered in Hainan. For establishing a promising alternative therapeutic option, a phage with the capacity of lysing 18 out of 35 MRSA clinical isolates was recovered from domestic natural sources, which was termed as vB_SauP_L1 due to its morphology and genomic similarity with Rountreeviridae. Satisfactory proliferation rate and environmental tolerance were demonstrated by subsequent infectious properties tests and stability assessments. Sequencing revealed that its genome consisted of a linear double-stranded DNA of 17,114 bp, in which neither virulent nor resistant gene was detected, indicating its potential in MRSA prevention and treatment.
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Affiliation(s)
- Yanmei Li
- School of Tropical Medicine, Hainan Medical University, Haikou, 571199, China
| | - Yue Zhang
- School of Tropical Medicine, Hainan Medical University, Haikou, 571199, China
| | - Anyang Li
- School of Tropical Medicine, Hainan Medical University, Haikou, 571199, China
| | - Ting Zhang
- School of Tropical Medicine, Hainan Medical University, Haikou, 571199, China
| | - Jiling Yi
- Key Laboratory of Tropical Medicinal Resource Chemistry of Ministry of Education, College of Chemistry and Chemical Engineering, Hainan Normal University, Haikou, 571158, China; Key Laboratory of Tropical Medicinal Plant Chemistry of Hainan Province, College of Chemistry and Chemical Engineering, Hainan Normal University, Haikou, 571158, China
| | - Nan Zhang
- School of Tropical Medicine, Hainan Medical University, Haikou, 571199, China
| | - Xun Kang
- School of Tropical Medicine, Hainan Medical University, Haikou, 571199, China
| | - Wei Liu
- School of Tropical Medicine, Hainan Medical University, Haikou, 571199, China
| | - Shen Tian
- School of Tropical Medicine, Hainan Medical University, Haikou, 571199, China.
| | - Qianfeng Xia
- School of Tropical Medicine, Hainan Medical University, Haikou, 571199, China.
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87
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Wójcicki M, Shymialevich D, Średnicka P, Emanowicz P, Ostrowska A, Cieślak H, Sokołowska B. Phenotypic Characterization and Genome Analysis of New Broad-Spectrum Virulent Salmophage, Salmonella Phage KKP_3822, for Biocontrol of Multidrug-Resistant Salmonella enterica Strains. Int J Mol Sci 2024; 25:12930. [PMID: 39684641 DOI: 10.3390/ijms252312930] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2024] [Revised: 11/30/2024] [Accepted: 11/30/2024] [Indexed: 12/18/2024] Open
Abstract
Salmonella is one of the main foodborne pathogens. Irrational antibiotic management has led to an increase in the incidence of multidrug-resistant strains. Bacteriophages may be an alternative method of food biopreservation and contribute to reducing the number of food poisonings requiring pharmacotherapy. This study aimed to isolate a bacteriophage (phage) targeting indigenous multidrug-resistant (MDR) Salmonella strains, followed by their biological, morphological, and genomic characterization. In this study we isolated Salmonella phage KKP_3822, targeting MDR Salmonella Manchester strain KKP 1213. Salmonella phage KKP_3822 retained high activity in the temperature range from -20 °C to 40 °C and active acidity from pH 3 to 11. Temperatures of 70 °C and 80 °C and extreme pH values (2 and 12) significantly reduced the phage titer. Its activity decreased proportionally to the time of UV exposure. Genome analysis (linear dsDNA with a length of 114,843 bp) revealed the presence of 27 tRNA genes. Proteins encoded by the vB_Sen-IAFB3822 phage were divided into functional modules related to (i) phage structure/assembly, (ii) DNA replication/modification/regulation, (iii) phage lysis, and (iv) DNA packaging into the capsid. No genes associated with antibiotic resistance or integration into the host genome, markers of temperate bacteriophages, were annotated in the Salmonella phage KKP_3822 genome. Based on morphological features and whole-genome sequence analysis, the newly isolated Salmonella phage KKP_3822 shows the greatest similarity to representatives of tailed phages from the Caudoviricetes class, Demerecviridae family, and Epseptimavirus genus. Genome analysis confirmed the virulent nature of the Salmonella phage KKP_3822, making it a potential candidate for food biocontrol.
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Affiliation(s)
- Michał Wójcicki
- Department of Microbiology, Prof. Wacław Dąbrowski Institute of Agricultural and Food Biotechnology-State Research Institute, Rakowiecka 36 Str., 02-532 Warsaw, Poland
| | - Dziyana Shymialevich
- Department of Microbiology, Prof. Wacław Dąbrowski Institute of Agricultural and Food Biotechnology-State Research Institute, Rakowiecka 36 Str., 02-532 Warsaw, Poland
| | - Paulina Średnicka
- Department of Microbiology, Prof. Wacław Dąbrowski Institute of Agricultural and Food Biotechnology-State Research Institute, Rakowiecka 36 Str., 02-532 Warsaw, Poland
| | - Paulina Emanowicz
- Department of Microbiology, Prof. Wacław Dąbrowski Institute of Agricultural and Food Biotechnology-State Research Institute, Rakowiecka 36 Str., 02-532 Warsaw, Poland
| | - Agnieszka Ostrowska
- Department of Nanobiotechnology, Institute of Biology, Warsaw University of Life Sciences (WULS-SGGW), Ciszewskiego 8 Str., 02-786 Warsaw, Poland
| | - Hanna Cieślak
- Department of Microbiology, Prof. Wacław Dąbrowski Institute of Agricultural and Food Biotechnology-State Research Institute, Rakowiecka 36 Str., 02-532 Warsaw, Poland
| | - Barbara Sokołowska
- Department of Microbiology, Prof. Wacław Dąbrowski Institute of Agricultural and Food Biotechnology-State Research Institute, Rakowiecka 36 Str., 02-532 Warsaw, Poland
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88
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Rastegar S, Skurnik M, Niaz H, Tadjrobehkar O, Samareh A, Hosseini-Nave H, Sabouri S. Isolation, characterization, and potential application of Acinetobacter baumannii phages against extensively drug-resistant strains. Virus Genes 2024; 60:725-736. [PMID: 39256307 DOI: 10.1007/s11262-024-02103-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2024] [Accepted: 08/15/2024] [Indexed: 09/12/2024]
Abstract
One of the significant issues in treating bacterial infections is the increasing prevalence of extensively drug-resistant (XDR) strains of Acinetobacter baumannii. In the face of limited or no viable treatment options for extensively drug-resistant (XDR) bacteria, there is a renewed interest in utilizing bacteriophages as a treatment option. Three Acinetobacter phages (vB_AbaS_Ftm, vB_AbaS_Eva, and vB_AbaS_Gln) were identified from hospital sewage and analyzed for their morphology, host ranges, and their genome sequences were determined and annotated. These phages and vB_AbaS_SA1 were combined to form a phage cocktail. The antibacterial effects of this cocktail and its combinations with selected antimicrobial agents were evaluated against the XDR A. baumannii strains. The phages exhibited siphovirus morphology. Out of a total of 30 XDR A. baumannii isolates, 33% were sensitive to vB_AbaS_Ftm, 30% to vB_AbaS_Gln, and 16.66% to vB_AbaS_Eva. When these phages were combined with antibiotics, they demonstrated a synergistic effect. The genome sizes of vB_AbaS_Ftm, vB_AbaS_Eva, and vB_AbaS_Gln were 48487, 50174, and 50043 base pairs (bp), respectively, and showed high similarity. Phage cocktail, when combined with antibiotics, showed synergistic effects on extensively drug-resistant (XDR) strains of A. baumannii. However, the need for further study to fully understand the mechanisms of action and potential limitations of using these phages is highlighted.
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Affiliation(s)
- Sanaz Rastegar
- Medical Mycology and Bacteriology Research Center, Kerman University of Medical Sciences, Kerman, Iran
- Department of Medical Microbiology (Bacteriology and Virology), Afzalipour School of Medicine, Kerman, Iran
| | - Mikael Skurnik
- Department of Bacteriology and Immunology, Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Hira Niaz
- Department of Bacteriology and Immunology, Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Omid Tadjrobehkar
- Medical Mycology and Bacteriology Research Center, Kerman University of Medical Sciences, Kerman, Iran
- Department of Medical Microbiology (Bacteriology and Virology), Afzalipour School of Medicine, Kerman, Iran
| | - Ali Samareh
- Department of Biochemistry, School of Medicine, Kerman University of Medical Sciences, Kerman, Iran
| | - Hossein Hosseini-Nave
- Medical Mycology and Bacteriology Research Center, Kerman University of Medical Sciences, Kerman, Iran.
- Department of Medical Microbiology (Bacteriology and Virology), Afzalipour School of Medicine, Kerman, Iran.
- Department of Microbiology and Virology, School of Medicine, Kerman University of Medical Sciences, Kerman, 7616913439, Iran.
| | - Salehe Sabouri
- Extremophile and Productive Microorganisms Research Center, Kerman University of Medical Sciences, Kerman, Iran.
- Department of Pharmaceutical Biotechnology, Faculty of Pharmacy, Kerman University of Medical Sciences, Kerman, Iran.
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89
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Moon K, Song SH, Oh DJ, Park JG, Lee AH, Kwon M. Genome sequence data of Caudoviricetes bacteriophage MK21 infecting Xanthomonas citri, the causative agent of citrus canker. Data Brief 2024; 57:110897. [PMID: 39314900 PMCID: PMC11418155 DOI: 10.1016/j.dib.2024.110897] [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: 07/01/2024] [Revised: 08/26/2024] [Accepted: 08/27/2024] [Indexed: 09/25/2024] Open
Abstract
This dataset reports the isolation and genomic characterization of the Caudoviricetes bacteriophage MK21, a novel bacteriophage infecting Xanthomonas citri subsp. citri (XCC), collected from soil samples on Jeju Island, South Korea. The phage was isolated and enriched using double agar layer plaque assays on nutrient media. Genomic analysis revealed that the phage MK21 is a double-stranded circular DNA genome of 43,495 bp, comprising 61 genes with high coding density. The dataset includes detailed genomic information, highlighting genes related to structural components, lysis mechanisms, and DNA/RNA metabolism. Phylogenetic analysis shows a close relationship with Xanthomonas phage CP1, supporting its potential use in comparative genomic studies and the development of antibacterial agents against citrus canker. This dataset offers valuable insights for the advancement of phage therapy and sustainable agricultural practices.
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Affiliation(s)
- Kira Moon
- Division of Environmental Materials, Honam National Institute of Biological Resources (HNIBR), Mokpo 58762, Republic of Korea
| | - Seung Hui Song
- Division of Environmental Materials, Honam National Institute of Biological Resources (HNIBR), Mokpo 58762, Republic of Korea
| | - Dae-Ju Oh
- Biodiversity Research Institute, Jeju Technopark (JTP), Jeju 63608, Republic of Korea
| | - Ji-Gweon Park
- Biodiversity Research Institute, Jeju Technopark (JTP), Jeju 63608, Republic of Korea
| | - Aslan Hwanwhi Lee
- Division of Environmental Materials, Honam National Institute of Biological Resources (HNIBR), Mokpo 58762, Republic of Korea
| | - Miye Kwon
- Biodiversity Research Institute, Jeju Technopark (JTP), Jeju 63608, Republic of Korea
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90
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Wu Z, Liu S, Ni J. Metagenomic characterization of viruses and mobile genetic elements associated with the DPANN archaeal superphylum. Nat Microbiol 2024; 9:3362-3375. [PMID: 39448846 DOI: 10.1038/s41564-024-01839-y] [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: 11/24/2023] [Accepted: 09/25/2024] [Indexed: 10/26/2024]
Abstract
The archaeal superphylum DPANN (an acronym formed from the initials of the first five phyla discovered: Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanohaloarchaeota and Nanoarchaeota) is a group of ultrasmall symbionts able to survive in extreme ecosystems. The diversity and dynamics between DPANN archaea and their virome remain largely unknown. Here we use a metagenomic clustered regularly interspaced short palindromic repeats (CRISPR) screening approach to identify 97 globally distributed, non-redundant viruses and unclassified mobile genetic elements predicted to infect hosts across 8 DPANN phyla, including 7 viral groups not previously characterized. Genomic analysis suggests a diversity of viral morphologies including head-tailed, tailless icosahedral and spindle-shaped viruses with the potential to establish lytic, chronic or lysogenic infections. We also find evidence of a virally encoded Cas12f1 protein (probably originating from uncultured DPANN archaea) and a mini-CRISPR array, which could play a role in modulating host metabolism. Many metagenomes have virus-to-host ratios >10, indicating that DPANN viruses play an important role in controlling host populations. Overall, our study illuminates the underexplored diversity, functional repertoires and host interactions of the DPANN virome.
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Affiliation(s)
- Zongzhi Wu
- College of Environmental Sciences and Engineering, Peking University, Key Laboratory of Water and Sediment Sciences, Ministry of Education, Beijing, People's Republic of China
- Eco-environment and Resource Efficiency Research Laboratory, School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen, People's Republic of China
| | - Shufeng Liu
- College of Resources and Environmental Sciences, China Agricultural University, Beijing, People's Republic of China
| | - Jinren Ni
- College of Environmental Sciences and Engineering, Peking University, Key Laboratory of Water and Sediment Sciences, Ministry of Education, Beijing, People's Republic of China.
- Eco-environment and Resource Efficiency Research Laboratory, School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen, People's Republic of China.
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91
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Deng A, Wang J, Li L, Shi R, Li X, Wen T. Synoptic Variation Drives Genetic Diversity and Transmission Mode of Airborne DNA Viruses in Urban Space. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2404512. [PMID: 39435753 PMCID: PMC11633480 DOI: 10.1002/advs.202404512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2024] [Revised: 09/30/2024] [Indexed: 10/23/2024]
Abstract
Airborne viruses are ubiquitous and play critical roles in maintaining ecosystem balance, however, they remain unexplored. Here, it is aimed to demonstrate that highly diverse airborne viromes carry out specific metabolic functions and use different transmission modes under different air quality conditions. A total of 263.5-Gb data are collected from 13 air samples for viral metagenomic analysis. After assembly and curation, a total of 12 484 viral contigs (1.5-184.2 kb) are assigned to 221 genus-level clades belonging to 47 families, 19 orders, and 15 classes. The composition of viral communities is influenced by weather conditions, with the main biomarker being Caudoviricetes. The most dominant viruses in these air samples belong to the dsDNA Caudoviricetes (54.0%) and ssDNA Repensiviricetes (31.2%) classes. Twelve novel candidate viruses are identified at the order/family/genus levels by alignment of complete genomes and core genes. Notably, Caudoviricetes are highly prevalent in cloudy and smoggy air, whereas Repensiviricetes are highly dominant in sunny and rainy air. Diverse auxiliary metabolic genes of airborne viruses are mainly involved in deoxynucleotide synthesis, implying their unique roles in atmosphere ecosystem. These findings deepen the understanding of the meteorological impacts on viral composition, transmission mode, and ecological roles in the air that we breathe.
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Affiliation(s)
- Aihua Deng
- State Key Laboratory of Animal Nutrition and Feeding, Ministry of Agriculture and Rural Affairs Feed Industry CentreChina Agricultural UniversityBeijing100193P. R. China
- State Key Laboratory of Microbial ResourcesInstitute of MicrobiologyChinese Academy of SciencesBeijing100101P. R. China
- Beijing Bio‐Feed Additives Key LaboratoryBeijing100193P. R. China
| | - Junyue Wang
- State Key Laboratory of Microbial ResourcesInstitute of MicrobiologyChinese Academy of SciencesBeijing100101P. R. China
| | - Lai Li
- State Key Laboratory of Microbial ResourcesInstitute of MicrobiologyChinese Academy of SciencesBeijing100101P. R. China
| | - Ruilin Shi
- State Key Laboratory of Microbial ResourcesInstitute of MicrobiologyChinese Academy of SciencesBeijing100101P. R. China
| | - Xuemin Li
- Department of OphthalmologyPeking University Third HospitalBeijing100191P. R. China
| | - Tingyi Wen
- State Key Laboratory of Microbial ResourcesInstitute of MicrobiologyChinese Academy of SciencesBeijing100101P. R. China
- Savaid Medical SchoolUniversity of Chinese Academy of SciencesBeijing100049P. R. China
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92
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Mayne R, Aiewsakun P, Turner D, Adriaenssens E, Simmonds P. GRAViTy-V2: a grounded viral taxonomy application. NAR Genom Bioinform 2024; 6:lqae183. [PMID: 39703433 PMCID: PMC11655284 DOI: 10.1093/nargab/lqae183] [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: 08/06/2024] [Revised: 11/30/2024] [Accepted: 12/03/2024] [Indexed: 12/21/2024] Open
Abstract
Taxonomic classification of viruses is essential for understanding their evolution. Genomic classification of viruses at higher taxonomic ranks, such as order or phylum, is typically based on alignment and comparison of amino acid sequence motifs in conserved genes. Classification at lower taxonomic ranks, such as genus or species, is usually based on nucleotide sequence identities between genomic sequences. Building on our whole-genome analytical classification framework, we here describe Genome Relationships Applied to Viral Taxonomy Version 2 (GRAViTy-V2), which encompasses a greatly expanded range of features and numerous optimisations, packaged as an application that may be used as a general-purpose virus classification tool. Using 28 datasets derived from the ICTV 2022 taxonomy proposals, GRAViTy-V2 output was compared against human expert-curated classifications used for assignments in the 2023 round of ICTV taxonomy changes. GRAViTy-V2 produced taxonomies equivalent to manually-curated versions down to the family level and in almost all cases, to genus and species levels. The majority of discrepant results arose from errors in coding sequence annotations in INDSC records, or from inclusion of incomplete genome sequences in the analysis. Analysis times ranged from 1-506 min (median 3.59) on datasets with 17-1004 genomes and mean genome length of 3000-1 000 000 bases.
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Affiliation(s)
- Richard Mayne
- Peter Medawar Building for Pathogen Research, Nuffield Department of Medicine, University of Oxford, 3 South Parks Road, OX1 3SY Oxfordshire, UK
| | - Pakorn Aiewsakun
- Department of Microbiology, Faculty of Science, Mahidol University, 272 Rama VI Road, Thung Phaya Thai, Ratchathewi, Bangkok 10400, Thailand
| | - Dann Turner
- School of Applied Sciences, University of the West of England, Frenchay Campus, BS16 1QY Bristol, UK
| | | | - Peter Simmonds
- Peter Medawar Building for Pathogen Research, Nuffield Department of Medicine, University of Oxford, 3 South Parks Road, OX1 3SY Oxfordshire, UK
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93
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Parra B, Sandoval M, Arriagada V, Amsteins L, Aguayo C, Opazo-Capurro A, Dechesne A, González-Rocha G. Isolation and Characterization of Lytic Bacteriophages Capable of Infecting Diverse Multidrug-Resistant Strains of Pseudomonas aeruginosa: PaCCP1 and PaCCP2. Pharmaceuticals (Basel) 2024; 17:1616. [PMID: 39770458 PMCID: PMC11728774 DOI: 10.3390/ph17121616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2024] [Revised: 11/26/2024] [Accepted: 11/27/2024] [Indexed: 01/16/2025] Open
Abstract
BACKGROUND/OBJECTIVES Antimicrobial resistance (AMR) is a major public health threat, which is exacerbated by the lack of new antibiotics and the emergence of multidrug-resistant (MDR) superbugs. Comprehensive efforts and alternative strategies to combat AMR are urgently needed to prevent social, medical, and economic consequences. Pseudomonas aeruginosa is a pathogen responsible for a wide range of infections, from soft tissue infections to life-threatening conditions such as bacteremia and pneumonia. Bacteriophages have been considered as a potential therapeutic option to treat bacterial infections. Our aim was to isolate phages able to infect MDR P. aeruginosa strains. METHODS We isolated two lytic phages, using the conventional double layer agar technique (DLA), from samples obtained from the influent of a wastewater treatment plant in Concepción, Chile. The phages, designated as PaCCP1 and PaCCP2, were observed by electron microscopy and their host range was determined against multiple P. aeruginosa strains using DLA. Moreover, their genomes were sequenced and analyzed. RESULTS Phage PaCCP1 is a member of the Septimatrevirus genus and phage PaCCP2 is a member of the Pbunavirus genus. Both phages are tailed and contain dsDNA. The genome of PaCCP1 is 43,176 bp in length with a GC content of 54.4%, encoding 59 ORFs, one of them being a tRNA gene. The genome of PaCCP2 is 66,333 bp in length with a GC content of 55.6%, encoding 102 non-tRNA ORFs. PaCCP1 is capable of infecting five strains of P. aeruginosa, whereas phage PaCCP2 is capable of infecting three strains of P. aeruginosa. Both phages do not contain bacterial virulence or AMR genes and contain three and six putative Anti-CRISPR proteins. CONCLUSIONS Phages PaCCP1 and PaCCP2 show promise as effective treatments for MDR P. aeruginosa strains, offering a potential strategy for controlling this clinically important pathogen through phage therapy.
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Affiliation(s)
- Boris Parra
- Laboratorio de Investigación en Agentes Antibacterianos (LIAA), Departamento de Microbiología, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción 4070409, Chile
- Grupo de Estudio en Resistencia Antimicrobiana (GRAM), Universidad de Concepción, Concepción 4070409, Chile
- Facultad de Medicina Veterinaria y Agronomía, Instituto de Ciencias Naturales, Universidad de las Américas, Av. Jorge Alessandri 1160, Campus El Boldal, Concepción 4070409, Chile
| | - Maximiliano Sandoval
- Laboratorio de Investigación en Agentes Antibacterianos (LIAA), Departamento de Microbiología, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción 4070409, Chile
- Grupo de Estudio en Resistencia Antimicrobiana (GRAM), Universidad de Concepción, Concepción 4070409, Chile
| | - Vicente Arriagada
- Laboratorio de Investigación en Agentes Antibacterianos (LIAA), Departamento de Microbiología, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción 4070409, Chile
- Grupo de Estudio en Resistencia Antimicrobiana (GRAM), Universidad de Concepción, Concepción 4070409, Chile
| | - Luis Amsteins
- Laboratorio de Investigación en Agentes Antibacterianos (LIAA), Departamento de Microbiología, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción 4070409, Chile
- Grupo de Estudio en Resistencia Antimicrobiana (GRAM), Universidad de Concepción, Concepción 4070409, Chile
| | - Cristobal Aguayo
- Laboratorio de Investigación en Agentes Antibacterianos (LIAA), Departamento de Microbiología, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción 4070409, Chile
- Grupo de Estudio en Resistencia Antimicrobiana (GRAM), Universidad de Concepción, Concepción 4070409, Chile
| | - Andrés Opazo-Capurro
- Laboratorio de Investigación en Agentes Antibacterianos (LIAA), Departamento de Microbiología, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción 4070409, Chile
- Grupo de Estudio en Resistencia Antimicrobiana (GRAM), Universidad de Concepción, Concepción 4070409, Chile
| | - Arnaud Dechesne
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofs Plads, Building 221, 2800 Kongens Lyngby, Denmark
| | - Gerardo González-Rocha
- Laboratorio de Investigación en Agentes Antibacterianos (LIAA), Departamento de Microbiología, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción 4070409, Chile
- Grupo de Estudio en Resistencia Antimicrobiana (GRAM), Universidad de Concepción, Concepción 4070409, Chile
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Cortes-Ortega E, Hansen EG, Iskender I, Farmer ML, Martinez-Villalobos JM, Vitt JD, Bowden SD. Isolation and characterization of Salmonella enterica- and Escherichia coli-specific bacteriophages of the genus Epseptimavirus from wastewater in Minnesota. Arch Virol 2024; 169:255. [PMID: 39601978 DOI: 10.1007/s00705-024-06190-5] [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: 09/10/2024] [Accepted: 11/12/2024] [Indexed: 11/29/2024]
Abstract
Five lytic bacteriophages specific for Salmonella enterica and Escherichia coli were isolated from wastewater in Minnesota. These phages, designated vB_Sal_EH1, vB_Sal_EH2, vB_Sal_EH3, vB_Sal_EH4, and vB_Sal_EH7, were characterized, and their genomes were sequenced. Phylogenetic analysis showed that they grouped within the genus Epseptimavirus, with genome sizes ranging from 108,554 to 115,218 bp. All five phages exhibited lytic activity against both S. enterica and Shiga-toxin-producing E. coli O157:H7. Transposon mutagenesis of the host genome identified the outer membrane protein BtuB as essential for phage infection, suggesting that it is a putative receptor. Genome sequence comparisons revealed genetic loci that are variable among the isolated phages and potentially influence their host specificity and virulence.
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Affiliation(s)
- Estephany Cortes-Ortega
- Department of Food Science and Nutrition, University of Minnesota-Twin Cities, Saint Paul, MN, 55108, USA
| | - Eleanore G Hansen
- Department of Food Science and Nutrition, University of Minnesota-Twin Cities, Saint Paul, MN, 55108, USA
- Division of Environmental Health Science, School of Public Health, University of Minnesota-Twin Cities, Minneapolis, MN, 55455, USA
| | - Irem Iskender
- Department of Food Science and Nutrition, University of Minnesota-Twin Cities, Saint Paul, MN, 55108, USA
| | - Meredith L Farmer
- Department of Food Science and Nutrition, University of Minnesota-Twin Cities, Saint Paul, MN, 55108, USA
| | - Juan M Martinez-Villalobos
- Institute of Biotechnology, Autonomous University of Nuevo León, 66451, San Nicolás de los Garza, NL, Mexico
| | - Jacob D Vitt
- Department of Food Science and Nutrition, University of Minnesota-Twin Cities, Saint Paul, MN, 55108, USA
| | - Steven D Bowden
- Department of Food Science and Nutrition, University of Minnesota-Twin Cities, Saint Paul, MN, 55108, USA.
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95
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Steiner LX, Schmittmann L, Rahn T, Lachnit T, Jahn MT, Hentschel U. Phage-induced disturbance of a marine sponge microbiome. ENVIRONMENTAL MICROBIOME 2024; 19:97. [PMID: 39593141 PMCID: PMC11590407 DOI: 10.1186/s40793-024-00637-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2024] [Accepted: 11/07/2024] [Indexed: 11/28/2024]
Abstract
BACKGROUND Bacteriophages are known modulators of community composition and activity in environmental and host-associated microbiomes. However, the impact single phages have on bacterial community dynamics under viral predation, the extent and duration of their effect, are not completely understood. In this study, we combine morphological and genomic characterization of a novel marine phage, isolated from the Baltic sponge Halichondria panicea, and report on first attempts of controlled phage-manipulation of natural sponge-associated microbiomes. RESULTS We used culture-based and culture-independent (16S rRNA gene amplicon sequencing) methods to investigate bacterial community composition and dynamics in sponge microbiomes with and without the addition of phages. Upon application of a novel Maribacter specialist phage Panino under controlled conditions, we were able to detect community-wide shifts in the microbiome composition and load after 72 h. While bacterial community composition became more dissimilar over time in the presence of phages, species evenness and richness were maintained. Upon phage exposure, we observed the loss of several low-abundance constituent taxa of the resident microbiota, while other originally underrepresented taxa increased. Virulent phages likely induce community-wide disturbances, evident in changes in the total sponge microbial profile by specific elimination of constituent taxa, which leads to an increase in bacterial abundance of opportunistic taxa, such as the genera Vibrio, Pseudoalteromonas, and Photobacterium. CONCLUSIONS Our findings suggest that sponge microbiome diversity and, by extension, its resilience depend on the maintenance of resident bacterial community members, irrespective of their abundance. Phage-induced disturbances can significantly alter community structure by promoting the growth of opportunistic bacteria like Vibrio and shifting the microbiome to a dysbiotic state. These insights highlight the role of bacteriophages in shaping microbiome dynamics and underscore the potential for phage application in managing bacterial community composition in marine host-associated environments.
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Affiliation(s)
- Leon X Steiner
- GEOMAR Helmholtz Centre for Ocean Research Kiel, RD3 Marine Ecology, RU Marine Symbioses, Kiel, Germany.
| | - Lara Schmittmann
- GEOMAR Helmholtz Centre for Ocean Research Kiel, RD1 Ocean Circulation and Climate Dynamics, RU Ocean Dynamics, Kiel, Germany
| | - Tanja Rahn
- GEOMAR Helmholtz Centre for Ocean Research Kiel, RD3 Marine Ecology, RU Marine Symbioses, Kiel, Germany
| | - Tim Lachnit
- Zoological Institute, Christian-Albrechts Universität Kiel, Kiel, Germany
| | - Martin T Jahn
- Department of Biology, University of Oxford, Oxford, UK
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Ute Hentschel
- GEOMAR Helmholtz Centre for Ocean Research Kiel, RD3 Marine Ecology, RU Marine Symbioses, Kiel, Germany.
- Christian-Albrechts-Universität Kiel, Kiel, Germany.
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96
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Kornienko M, Bespiatykh D, Abdraimova N, Gorodnichev R, Gostev V, Boldyreva D, Selezneva O, Veselovsky V, Pobeguts O, Smirnov I, Arapidi G, Klimina K, Shitikov E. Multiomics analysis of Staphylococcus aureus ST239 strains resistant to virulent Herelleviridae phages. Sci Rep 2024; 14:29375. [PMID: 39592862 PMCID: PMC11599779 DOI: 10.1038/s41598-024-80909-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Accepted: 11/22/2024] [Indexed: 11/28/2024] Open
Abstract
In the context of the antimicrobial therapy crisis, the significance of studying and implementing alternative treatment methods, particularly phage therapy, is increasingly evident. This study aimed to investigate the resistance of clinical Staphylococcus aureus ST239 strains to Herelleviridae phages through comparative genomics, transcriptomics, and proteomics. Analysis of resistant and sensitive S. aureus strains showed that resistant strains form a separate cluster on the phylogenetic tree, suggesting unique genetic traits underlying their phage resistance. Further in-depth analysis of the resistant SA191 strain infected with Herelleviridae phage, compared to an uninfected control, unveiled significant changes in the transcription of 462 genes (271↑ 191↓) at 5 min and 504 genes (276↑ 228↓) at 30 min post-infection. Proteomic analysis identified 184 differentially abundant proteins (41↑ 143↓) at 30 min. Functional analysis highlighted changes in the glycolysis, the tricarboxylic acid cycle, and transport systems; notable, changes were also observed in the transcription of prophage genes. Despite the observed metabolic shifts, classical resistance mechanisms related to teichoic acid synthesis, restriction-modification, and toxin-antitoxin systems were not identified, suggesting the existence of other mechanism. Our study contributes to the elucidation of S. aureus resistance mechanisms against Herelleviridae phages, highlighting the intricate nature of bacterial defense mechanisms.
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Affiliation(s)
- M Kornienko
- Department of Biomedicine and Genomics, Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia.
| | - D Bespiatykh
- Department of Biomedicine and Genomics, Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
| | - N Abdraimova
- Department of Biomedicine and Genomics, Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
| | - R Gorodnichev
- Department of Biomedicine and Genomics, Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
| | - V Gostev
- Pediatric Research and Clinical Center for Infectious Diseases, Saint Petersburg, Russia
- North-Western State Medical University Named After I. I. Mechnikov, Saint Petersburg, Russia
| | - D Boldyreva
- Department of Biomedicine and Genomics, Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
| | - O Selezneva
- Department of Biomedicine and Genomics, Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
| | - V Veselovsky
- Department of Biomedicine and Genomics, Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
| | - O Pobeguts
- Department of Post-Genomic Technologies, Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
| | - I Smirnov
- Department of Post-Genomic Technologies, Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
| | - G Arapidi
- Department of Post-Genomic Technologies, Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russia
| | - K Klimina
- Department of Biomedicine and Genomics, Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
| | - E Shitikov
- Department of Biomedicine and Genomics, Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
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97
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Chen H, Liu H, Gong Y, Dunstan RA, Ma Z, Zhou C, Zhao D, Tang M, Lithgow T, Zhou T. A Klebsiella-phage cocktail to broaden the host range and delay bacteriophage resistance both in vitro and in vivo. NPJ Biofilms Microbiomes 2024; 10:127. [PMID: 39543151 PMCID: PMC11564825 DOI: 10.1038/s41522-024-00603-8] [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: 06/11/2024] [Accepted: 11/05/2024] [Indexed: 11/17/2024] Open
Abstract
Bacteriophages (phages), viruses capable of infecting and lysing bacteria, are a promising alternative for treating infections from hypervirulent, antibiotic-resistant pathogens like Klebsiella pneumoniae, though narrow host range and phage resistance remain challenges. In this study, the hypervirulent K. pneumoniae NTUH-K2044 was used to purify phage ΦK2044, while two ΦK2044-resistant strains were used to purify two further phages: ΦKR1, and ΦKR8 from hospital sewage. A detailed characterization showed that ΦK2044 specifically killed KL1 capsule-type K. pneumoniae, while ΦKR1 and ΦKR8 targeted 13 different capsular serotypes. The phage cocktail (ΦK2044 + ΦKR1 + ΦKR8) effectively killed K. pneumoniae in biofilms, pre-treatment biofilm formation, and delayed phage-resistance. The phage cocktail improved 7-day survival in Galleria mellonella and mouse models and showed therapeutic potential in a catheter biofilm model. In summary, this proof-of-principle phage cocktail has a broad host range, including hypervirulent and highly drug-resistant K. pneumoniae, and serves as a promising starting point for optimizing phage therapy.
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Affiliation(s)
- Huanchang Chen
- Department of Clinical Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Key Laboratory of Clinical Laboratory Diagnosis and Translational Research of Zhejiang Province, Wenzhou, Zhejiang, China
- Centre to Impact AMR, Monash University, Melbourne, VIC, 3800, Australia
| | - Haifeng Liu
- Department of Clinical Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Key Laboratory of Clinical Laboratory Diagnosis and Translational Research of Zhejiang Province, Wenzhou, Zhejiang, China
| | - Yanchun Gong
- Department of Clinical Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Key Laboratory of Clinical Laboratory Diagnosis and Translational Research of Zhejiang Province, Wenzhou, Zhejiang, China
| | - Rhys A Dunstan
- Centre to Impact AMR, Monash University, Melbourne, VIC, 3800, Australia
- Infection Program and Department of Microbiology, Biomedicine Discovery Institute, Monash University, Melbourne, VIC, 3800, Australia
| | - Zhexiao Ma
- School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Cui Zhou
- Department of Clinical Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Key Laboratory of Clinical Laboratory Diagnosis and Translational Research of Zhejiang Province, Wenzhou, Zhejiang, China
| | - Deyi Zhao
- School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Miran Tang
- Department of Clinical Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Key Laboratory of Clinical Laboratory Diagnosis and Translational Research of Zhejiang Province, Wenzhou, Zhejiang, China
| | - Trevor Lithgow
- Centre to Impact AMR, Monash University, Melbourne, VIC, 3800, Australia.
- Infection Program and Department of Microbiology, Biomedicine Discovery Institute, Monash University, Melbourne, VIC, 3800, Australia.
| | - Tieli Zhou
- Department of Clinical Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Key Laboratory of Clinical Laboratory Diagnosis and Translational Research of Zhejiang Province, Wenzhou, Zhejiang, China.
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98
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Lin W, Li D, Pan L, Li M, Tong Y. Cyanobacteria-cyanophage interactions between freshwater and marine ecosystems based on large-scale cyanophage genomic analysis. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 950:175201. [PMID: 39102952 DOI: 10.1016/j.scitotenv.2024.175201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Revised: 07/30/2024] [Accepted: 07/30/2024] [Indexed: 08/07/2024]
Abstract
The disparities in harmful algal blooms dynamics are largely attributed to variations in cyanobacteria populations within aquatic ecosystems. However, cyanobacteria-cyanophage interactions and their role in shaping cyanobacterial populations has been previously underappreciated. To address this knowledge gap, we isolated and sequenced 42 cyanophages from diverse water sources in China, with the majority (n = 35) originating from freshwater sources. We designated these sequences as the "Novel Cyanophage Genome sequence Collection" (NCGC). NCGC displayed notable genetic variations, with 95 % (40/42) of the sequences representing previously unidentified taxonomic ranks. By integrating NCGC with public data of cyanophages and cyanobacteria, we found evidence for more frequent historical cyanobacteria-cyanophage interactions in freshwater ecosystems. This was evidenced by a higher prevalence of prophage integrase-related genes in freshwater cyanophages (37.97 %) than marine cyanophages (7.42 %). In addition, freshwater cyanophages could infect a broader range of cyanobacteria orders (n = 4) than marine ones (n = 0). Correspondingly, freshwater cyanobacteria harbored more defense systems per million base pairs in their genomes, indicating more frequent phage infections. Evolutionary and cyanophage epidemiological studies suggest that interactions between cyanobacteria and cyanophages in freshwater and marine ecosystems are interconnected, and that brackish water can act as a transitional zone for freshwater and marine cyanophages. In conclusion, our research significantly expands the genetic information database of cyanophage, offering a wider selection of cyanophages to control harmful cyanobacterial blooms. Additionally, we represent a pioneering large-scale and comprehensive analysis of cyanobacteria and cyanophage sequencing data, and it provides theoretical guidance for the application of cyanophages in different environments.
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Affiliation(s)
- Wei Lin
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Dengfeng Li
- Key Laboratory of Marine Biotechnology of Zhejiang Province, School of Marine Sciences, Ningbo University, Ningbo 315211, China
| | - Lingting Pan
- Key Laboratory of Marine Biotechnology of Zhejiang Province, School of Marine Sciences, Ningbo University, Ningbo 315211, China
| | - Mengzhe Li
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China.
| | - Yigang Tong
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China; Beijing Advanced Innovation Center for Soft Matter Science and Engineering (BAIC-SM), Beijing University of Chemical Technology, Beijing 100029, China.
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99
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Biswas S, Tewari DN, Chakrabarti AK, Dutta S. Biological Characterization and Evaluation of the Therapeutic Value of Vibrio Phages 4141 and MJW Isolated from Clinical and Sewage Water Samples of Kolkata. Viruses 2024; 16:1741. [PMID: 39599855 PMCID: PMC11598976 DOI: 10.3390/v16111741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2024] [Revised: 10/28/2024] [Accepted: 10/30/2024] [Indexed: 11/29/2024] Open
Abstract
The growing prevalence of antimicrobial resistance (AMR) necessitates the development of new treatment methods to combat diseases like cholera. Lytic bacteriophages are viruses that specifically target and lyse bacteria upon infection, making them a possible treatment option for multi-drug-resistant pathogens. The current study investigated the potential role of bacteriophages isolated from clinical stool and sewage water samples in treating multi-drug-resistant Vibrio cholerae infection, finding that over 95% of the strains were susceptible. Whole-genome sequencing (WGS) analysis revealed that both Vibrio phage 4141 (4141) and Vibrio phage MJW (MJW) contain double-stranded DNA genomes consisting of 38,498 bp (43% GC) and 49,880 bp (42.5% GC) with 46 and 64 open reading frames (ORFs), respectively. Transmission electron microscope (TEM) and WGS analysis of Vibrio phage 4141 and Vibrio phage MJW validated that they are classified under the family Autographiviridae and Zobellviridae, respectively. Furthermore, both the phages showed highly significant biofilm degradation properties. The characterization of the phages and their strict host range, high spectrum of lytic ability, high efficiency of biofilm degradation, and close genetic similarity to the therapeutic phages indicates that these phages may be useful for therapeutic purposes for treating MDR V. cholerae infection in the future.
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Affiliation(s)
| | | | - Alok Kumar Chakrabarti
- ICMR-National Institute for Research in Bacterial Infections (Formerly “ICMR-National Institute of Cholera and Enteric Diseases”), P33, CIT Road, Scheme XM Beliaghata, Kolkata 700010, India; (S.B.); (D.N.T.); (S.D.)
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100
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Li X, Cheng R, Zhang C, Shao Z. Genomic diversity of phages infecting the globally widespread genus Sulfurimonas. Commun Biol 2024; 7:1428. [PMID: 39488617 PMCID: PMC11531552 DOI: 10.1038/s42003-024-07079-4] [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: 06/10/2024] [Accepted: 10/15/2024] [Indexed: 11/04/2024] Open
Abstract
The widespread bacterial genus Sulfurimonas is metabolically versatile and occupies a key ecological niche in different habitats, but its interaction with bacteriophages remains unexplored. Here we systematically investigated the genetic diversity, taxonomy and interaction patterns of Sulfurimonas-associated phages based on sequenced microbial genomes and metagenomes. High-confidence phage contigs related to Sulfurimonas were retrieved from various ecosystems, clustered into 61 viral operational taxonomic units across three viral realms, including Duplodnaviria, Monodnaviria and Varidnaviria. Head-tail phages of Caudoviricetes were assigned to 19 genus-level viral clusters, the majority of which were distantly related to known viruses. Notably, diverse double jelly-roll viruses and inoviruses were also linked to Sulfurimonas, representing two commonly overlooked phage groups. Historical and current phage infections were revealed, implying viral impact on the evolution of host adaptive immunity. Additionally, phages carrying auxiliary metabolic genes might benefit hosts by compensating or augmenting sulfur metabolism. This study highlights the diversity and novelty of Sulfurimonas-associated phages with divergent tailless lineages, providing basis for further investigation of phage-host interactions within this genus.
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Affiliation(s)
- Xiaofeng Li
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products; Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, China
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources; State Key Laboratory Breeding Base of Marine Genetic Resource, Fujian Key Laboratory of Marine Genetic Resources, Xiamen, China
| | - Ruolin Cheng
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources; State Key Laboratory Breeding Base of Marine Genetic Resource, Fujian Key Laboratory of Marine Genetic Resources, Xiamen, China.
| | - Chuanxi Zhang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products; Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, China
| | - Zongze Shao
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources; State Key Laboratory Breeding Base of Marine Genetic Resource, Fujian Key Laboratory of Marine Genetic Resources, Xiamen, China
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