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Wan X, Mahillon J, Yuan Z, Zhang G, Geng P, Hu X. Characterization of vB_SalS_PSa2, a T5-like Demerecviridae bacteriophage, and its potential use in food matrices. Virology 2024; 596:110101. [PMID: 38754335 DOI: 10.1016/j.virol.2024.110101] [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: 01/22/2024] [Revised: 04/17/2024] [Accepted: 05/02/2024] [Indexed: 05/18/2024]
Abstract
This study characterizes a newly isolated Demerecviridae phage, named vB_SalS_PSa2, belonging to the phage T5 group. The main variations between vB_SalS_PSa2 and T5 concern structural proteins related to morphology and host recognition. vB_SalS_PSa2 is infective to 19 out of the 25 tested Salmonella enterica (including the rare "Sendai" and "Equine" serotypes) and Escherichia coli isolates, most of them being multidrug resistant. vB_SalS_PSa2 displayed good thermal stability (4-60 °C) and broad pH stability (4.0-12.0). It also exhibited antibacterial activity against S. enterica sv. Paratyphi A Enb50 at 4 °C in milk during the whole tested period (5 d), and for 3-6 h at both 25 and 37 °C. Furthermore, vB_SalS_PSa2 was able to inhibit biofilm formation and to show degradation activity on mature biofilms of E. coli K12 and S. enterica sv. Paratyphi Enb50 in both LB and milk. Altogether, these results indicate that phage vB_SalS_PSa2 is a valuable candidate for controlling foodborne S. enterica and E. coli pathogens.
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Affiliation(s)
- Xiaofu Wan
- College of Life Sciences, South-Central Minzu University, Wuhan, 430074, China
| | - Jacques Mahillon
- Laboratory of Food and Environmental Microbiology, Earth and Life Institute, UCLouvain, Louvain-la-Neuve, B-1348, Belgium
| | - Zhiming Yuan
- Key Laboratory of Special Pathogens and Biosafety, Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430070, China
| | - Gan Zhang
- College of Life Sciences, South-Central Minzu University, Wuhan, 430074, China
| | - Peiling Geng
- College of Life Sciences, South-Central Minzu University, Wuhan, 430074, China
| | - Xiaomin Hu
- College of Life Sciences, South-Central Minzu University, Wuhan, 430074, China.
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2
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Arista-Regalado AD, Viera-Segura O, de Oca SAM, Hernández-Hernández L, González-Aguilar DG, León JB. Characterization and efficacy of Salmonella phage cocktail PHA46 in the control of Salmonella Newport and Typhimurium internalized into cherry tomatoes. Int J Food Microbiol 2024; 419:110745. [PMID: 38795636 DOI: 10.1016/j.ijfoodmicro.2024.110745] [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: 01/29/2024] [Revised: 05/08/2024] [Accepted: 05/11/2024] [Indexed: 05/28/2024]
Abstract
Non-typhoid Salmonella enterica causes salmonellosis illness, and this bacterium can contaminate food throughout the production chain, including those that are consumed as raw products. Salmonella enterica can adhere to and internalize into fresh produce such as cherry tomatoes. It has been reported that lytic bacteriophages (phages) can be used as a biocontrol agent in the agricultural field, being an alternative for the control of Salmonella in red meat, fish, lettuce, and cabbage. The aim of this study was to characterize the two phages present in the PHA46 cocktail to determine their morphology, genome, host range, and resistance to different temperatures and pHs values; and later evaluate their lytic activity to reduce the adherence to and internalization of Salmonella enterica serovars Newport and Typhimurium into cherry tomatoes. In addition, in this work, we also explored the effect of the PHA46 cocktail on the virulence of S. Newport-45 and S. Typhimurium SL1344, recovered from the interior of cherry tomatoes, on the lifespan of the animal model Caenorhabditis elegans. The nematode C. elegans, recently has been used to test the virulence of Salmonella and it is easy to maintain and work with in the laboratory. The results revealed that the morphology obtained by Transmission Electron Microscopy of two phages from the PHA46 cocktail correspond to a myovirus, the analyses of their genomes sequences did not report virulence or antimicrobial resistance genes. The PHA46 sample is specific for 33 different serovars from different Salmonella strains and shows stability at 7 °C and pH 6. Also, the PHA46 cocktail was effective in reducing the adherence of S. Newport-45 and S. Typhimurium SL1344 to cherry tomatoes, at an average of 0.9 log10, respectively. Regarding internalized bacteria, the reduction was at an average of 1.2 log10, of the serovars mentioned above. The lifespan experiments in C. elegans showed by itself, that the PHA46 cocktail was harmless to the nematode, and the virulence from both Salmonella strains grown in vitro is diminished in the presence of the PHA46 cocktail. In conclusion, these results showed that the PHA46 cocktail could be a good candidate to be used as a biocontrol agent against Salmonella enterica.
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Affiliation(s)
- Aurora Dolores Arista-Regalado
- Departamento de Microbiología y Patología, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Sierra Mojada No.950, Col. Independencia, CP. 44340, Guadalajara, Jalisco, Mexico
| | - Oliver Viera-Segura
- Instituto de Investigación en Ciencias Biomédicas, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Sierra Mojada No.950, Col. Independencia, CP. 44340, Guadalajara, Jalisco, Mexico
| | - Saúl Aguilar-Montes de Oca
- Area de Proyectos de Investigación, Universidad Autónoma del Estado de México, Instituto Literario No.100, Col. Centro, CP: 50000, Toluca de Lerdo, Estado de Mexico, Mexico
| | - Leonardo Hernández-Hernández
- Departamento de Fisiología, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Sierra Mojada No.950, Col. Independencia, CP. 44340, Guadalajara, Jalisco, Mexico
| | - Delia Guillermina González-Aguilar
- Departamento de Salud Pública, Centro de ciencias Biológico Agropecuarias, Universidad de Guadalajara, Camino Ramón Padilla Sánchez No. 2100, Col. Las agujas, C.P., 45200, Zapopan, Jalisco, Mexico
| | - Jeannette Barba León
- Departamento de Salud Pública, Centro de ciencias Biológico Agropecuarias, Universidad de Guadalajara, Camino Ramón Padilla Sánchez No. 2100, Col. Las agujas, C.P., 45200, Zapopan, Jalisco, Mexico.
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González-Gómez JP, Rodríguez-Arellano SN, Gomez-Gil B, Vergara-Jiménez MDJ, Chaidez C. Genomic and biological characterization of bacteriophages against Enterobacter cloacae, a high-priority pathogen. Virology 2024; 595:110100. [PMID: 38714025 DOI: 10.1016/j.virol.2024.110100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 04/20/2024] [Accepted: 05/02/2024] [Indexed: 05/09/2024]
Abstract
Enterobacter cloacae is a clinically significant pathogen due to its multi-resistance to antibiotics, presenting a challenge in the treatment of infections. As concerns over antibiotic resistance escalate, novel therapeutic approaches have been explored. Bacteriophages, characterized by their remarkable specificity and ability to self-replicate within target bacteria, are emerging as a promising alternative therapy. In this study, we isolated and partially characterized nine lytic bacteriophages targeting E. cloacae, with two selected for comprehensive genomic analysis based on their host range and bacteriolytic activity. All identified phages exhibited a narrow host range, demonstrated stability within a temperature range of 30-60 °C, displayed pH tolerance from 3 to 10, and showed an excellent bacteriolytic capacity for up to 18 h. Notably, the fully characterized phage genomes revealed an absence of lysogenic, virulence, or antibiotic-resistance genes, positioning them as promising candidates for therapeutic intervention against E. cloacae-related diseases. Nonetheless, translating this knowledge into practical therapeutic applications mandates a deeper understanding of bacteriophage interactions within complex biological environments.
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Affiliation(s)
- Jean Pierre González-Gómez
- Laboratorio Nacional para la Investigación en Inocuidad Alimentaria (LANIIA), Centro de Investigación en Alimentación y Desarrollo, A.C. (CIAD), Carretera a Eldorado km 5.5, Campo El Diez, 80110, Culiacan, Sinaloa, Mexico
| | | | - Bruno Gomez-Gil
- Centro de Investigación en Alimentación y Desarrollo, A.C. (CIAD), Unidad Mazatlán en Acuicultura y Manejo Ambiental, AP 711, Mazatlan, Sinaloa, Mexico
| | | | - Cristobal Chaidez
- Laboratorio Nacional para la Investigación en Inocuidad Alimentaria (LANIIA), Centro de Investigación en Alimentación y Desarrollo, A.C. (CIAD), Carretera a Eldorado km 5.5, Campo El Diez, 80110, Culiacan, Sinaloa, Mexico.
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Guzel M, Yucefaydali A, Yetiskin S, Deniz A, Yaşar Tel O, Akçelik M, Soyer Y. Genomic analysis of Salmonella bacteriophages revealed multiple endolysin ORFs and importance of ligand-binding site of receptor-binding protein. FEMS Microbiol Ecol 2024; 100:fiae079. [PMID: 38816206 PMCID: PMC11180984 DOI: 10.1093/femsec/fiae079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 05/02/2024] [Accepted: 05/29/2024] [Indexed: 06/01/2024] Open
Abstract
Salmonella is a prevalent foodborne pathogen causing millions of global cases annually. Antimicrobial resistance is a growing public health concern, leading to search for alternatives like bacteriophages. A total of 97 bacteriophages, isolated from cattle farms (n = 48), poultry farms (n = 37), and wastewater (n = 5) samples in Türkiye, were subjected to host-range analysis using 36 Salmonella isolates with 18 different serotypes. The broadest host range belonged to an Infantis phage (MET P1-091), lysing 28 hosts. A total of 10 phages with the widest host range underwent further analysis, revealing seven unique genomes (32-243 kb), including a jumbophage (>200 kb). Except for one with lysogenic properties, none of them harbored virulence or antibiotic resistance genes, making them potential Salmonella reducers in different environments. Examining open reading frames (ORFs) of endolysin enzymes revealed surprising findings: five of seven unique genomes contained multiple endolysin ORFs. Despite sharing same endolysin sequences, phages exhibited significant differences in host range. Detailed analysis unveiled diverse receptor-binding protein sequences, with similar structures but distinct ligand-binding sites. These findings emphasize the importance of ligand-binding sites of receptor-binding proteins. Additionally, bacterial reduction curve and virulence index revealed that Enteritidis phages inhibit bacterial growth even at low concentrations, unlike Infantis and Kentucky phages.
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Affiliation(s)
- Mustafa Guzel
- Department of Biotechnology, Middle East Technical University, Ankara 06800, Türkiye
- Department of Food Engineering, Hitit University, Corum 19030, Türkiye
| | - Aysenur Yucefaydali
- Department of Food Engineering, Faculty of Engineering, Middle East Technical University, Ankara 06800, Türkiye
| | - Segah Yetiskin
- Department of Food Engineering, Faculty of Engineering, Middle East Technical University, Ankara 06800, Türkiye
| | - Aysu Deniz
- Department of Food Engineering, Faculty of Engineering, Middle East Technical University, Ankara 06800, Türkiye
| | - Osman Yaşar Tel
- Faculty of Veterinary Medicine, Harran University, Şanlıurfa 63300, Türkiye
| | - Mustafa Akçelik
- Department of Biology, Ankara University, Ankara 06100, Türkiye
| | - Yeşim Soyer
- Department of Biotechnology, Middle East Technical University, Ankara 06800, Türkiye
- Department of Food Engineering, Faculty of Engineering, Middle East Technical University, Ankara 06800, Türkiye
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Remesh AT, Viswanathan R. CrAss-Like Phages: From Discovery in Human Fecal Metagenome to Application as a Microbial Source Tracking Marker. FOOD AND ENVIRONMENTAL VIROLOGY 2024; 16:121-135. [PMID: 38413544 DOI: 10.1007/s12560-024-09584-5] [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: 06/08/2023] [Accepted: 01/24/2024] [Indexed: 02/29/2024]
Abstract
CrAss-like phages are a diverse group of bacteriophages genetically similar to the prototypical crAssphage (p-crAssphage), which was discovered in the human gut microbiome through a metagenomics approach. It was identified as a ubiquitous and highly abundant bacteriophage group in the gut microbiome. Initial co-occurrence analysis postulated Bacteroides spp. as the prospective bacterial host. Subsequent studies have confirmed multiple host species under Phylum Bacteroidetes and some Firmicutes. Detection of crAss-like phages in sewage-contaminated environmental water and robust correlation with enteric viruses and bacteria has culminated in their adoption as a microbial source tracking (MST) marker. Polymerase chain reaction (PCR) and real-time PCR assays have been developed utilizing the conserved genes in the p-crAssphage genome to detect human fecal contamination of different water sources, with high specificity. Numerous investigations have examined the implications of crAss-like phages in diverse disease conditions, including ulcerative colitis, obesity and metabolic syndrome, autism spectrum disorders, rheumatoid arthritis, atopic eczema, and other autoimmune disorders. These studies have unveiled associations between certain diseases and diminished abundance and diversity of crAss-like phages. This review offers insights into the diverse aspects of research on crAss-like phages, including their discovery, genomic characteristics, structure, taxonomy, isolation, molecular detection, application as an MST marker, and role as a gut microbiome modulator with consequential health implications.
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Zhu X, Tang L, Wang Z, Xie F, Zhang W, Li Y. A comparative analysis of phage classification methods in light of the recent ICTV taxonomic revisions. Virology 2024; 594:110016. [PMID: 38461619 DOI: 10.1016/j.virol.2024.110016] [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: 01/13/2024] [Revised: 02/02/2024] [Accepted: 02/09/2024] [Indexed: 03/12/2024]
Abstract
Recent ICTV taxonomy updates significantly changed phage taxonomy, yet a thorough phage classification workflow doesn't exist. This study compares six categorization tools and establishes a novel multi-method approach, combining genome similarity and specialized protein analysis. Applying the method to APEC phage P151 showed consistent categorization across platforms. A possible workflow for phage classification is proposed; offering a versatile tool for phage research and development.
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Affiliation(s)
- Xihui Zhu
- Sanya Institute of Nanjing Agricultural University, Sanya, Hainan, 572000, China; College of Animal Medicine, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
| | - Luqi Tang
- Sanya Institute of Nanjing Agricultural University, Sanya, Hainan, 572000, China; College of Animal Medicine, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
| | - Zhiwei Wang
- College of Agronomy and Agricultural Engineering, Liaocheng University, Liaocheng, Shandong, 252059, China
| | - Feng Xie
- Sanya Institute of Nanjing Agricultural University, Sanya, Hainan, 572000, China; College of Animal Medicine, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
| | - Wei Zhang
- Sanya Institute of Nanjing Agricultural University, Sanya, Hainan, 572000, China; College of Animal Medicine, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China.
| | - Yubao Li
- College of Agronomy and Agricultural Engineering, Liaocheng University, Liaocheng, Shandong, 252059, China.
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Sabri M, El Handi K, Cara O, De Stradis A, Valentini F, Elbeaino T. Xylella phage MATE 2: a novel bacteriophage with potent lytic activity against Xylella fastidiosa subsp. pauca. Front Microbiol 2024; 15:1412650. [PMID: 38863752 PMCID: PMC11165191 DOI: 10.3389/fmicb.2024.1412650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2024] [Accepted: 05/14/2024] [Indexed: 06/13/2024] Open
Abstract
Xylella fastidiosa (Xf) is a major phytosanitary threat to global agricultural production. The complexity and difficulty of controlling Xf underscore the pressing need for novel antibacterial agents, i.e., bacteriophages, which are natural predators of bacteria. In this study, a novel lytic bacteriophage of Xf subsp. pauca, namely Xylella phage MATE 2 (MATE 2), was isolated from sewage water in southern Italy. Biological characterization showed that MATE 2 possessed a broad-spectrum of antibacterial activity against various phytobacteria within the family Xanthomonadaceae, a rapid adsorption time (10 min), and high resistance to a broad range of pH (4-10) and temperatures (4-60°C). Most importantly, MATE 2 was able to suppress the growth of Xf subsp. pauca cells in liquid culture for 7 days, demonstrating its potential as an effective antibacterial agent against Xf. The genomic and electron microscopy analyses revealed that MATE 2 is a new species tentatively belonging to the genus Carpasinavirus within the class Caudoviricetes, with an isometric capsid head of 60 ± 5 nm along with a contractile tail of 120 ± 7.5 nm. Furthermore, the high-throughput sequencing and de novo assembly generated a single contig of 63,695 nucleotides in length; representing a complete genome composed of 95 Open Reading Frames. Bioinformatics analysis performed on MATE 2 genome revealed the absence of lysogenic mediated genes, and genes encoding virulence factors, antibiotic resistance, and toxins. This study adds a new phage to the very short list of Xf-infecting lytic phages, whose in-vitro antibacterial activity has been ascertained, while its efficacy on Xf-infected olive trees in the field has yet to be determined.
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Affiliation(s)
- Miloud Sabri
- International Centre for Advanced Mediterranean Agronomic Studies (CIHEAM of Bari), Valenzano, Italy
| | - Kaoutar El Handi
- International Centre for Advanced Mediterranean Agronomic Studies (CIHEAM of Bari), Valenzano, Italy
| | - Orges Cara
- International Centre for Advanced Mediterranean Agronomic Studies (CIHEAM of Bari), Valenzano, Italy
- Department of Soil, Plant and Food Science, University of Bari, Bari, Italy
| | - Angelo De Stradis
- Institute for Sustainable Plant Protection (IPSP), National Research Council of Italy (CNR), University of Bari, Bari, Italy
| | - Franco Valentini
- International Centre for Advanced Mediterranean Agronomic Studies (CIHEAM of Bari), Valenzano, Italy
| | - Toufic Elbeaino
- International Centre for Advanced Mediterranean Agronomic Studies (CIHEAM of Bari), Valenzano, Italy
- Institute for Sustainable Plant Protection (IPSP), National Research Council of Italy (CNR), Portici, Italy
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Mets T, Kurata T, Ernits K, Johansson MJO, Craig SZ, Evora GM, Buttress JA, Odai R, Wallant KC, Nakamoto JA, Shyrokova L, Egorov AA, Doering CR, Brodiazhenko T, Laub MT, Tenson T, Strahl H, Martens C, Harms A, Garcia-Pino A, Atkinson GC, Hauryliuk V. Mechanism of phage sensing and restriction by toxin-antitoxin-chaperone systems. Cell Host Microbe 2024:S1931-3128(24)00174-4. [PMID: 38821063 DOI: 10.1016/j.chom.2024.05.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Revised: 04/10/2024] [Accepted: 05/07/2024] [Indexed: 06/02/2024]
Abstract
Toxin-antitoxins (TAs) are prokaryotic two-gene systems composed of a toxin neutralized by an antitoxin. Toxin-antitoxin-chaperone (TAC) systems additionally include a SecB-like chaperone that stabilizes the antitoxin by recognizing its chaperone addiction (ChAD) element. TACs mediate antiphage defense, but the mechanisms of viral sensing and restriction are unexplored. We identify two Escherichia coli antiphage TAC systems containing host inhibition of growth (HigBA) and CmdTA TA modules, HigBAC and CmdTAC. HigBAC is triggered through recognition of the gpV major tail protein of phage λ. Chaperone HigC recognizes gpV and ChAD via analogous aromatic molecular patterns, with gpV outcompeting ChAD to trigger toxicity. For CmdTAC, the CmdT ADP-ribosyltransferase toxin modifies mRNA to halt protein synthesis and limit phage propagation. Finally, we establish the modularity of TACs by creating a hybrid broad-spectrum antiphage system combining the CmdTA TA warhead with a HigC chaperone phage sensor. Collectively, these findings reveal the potential of TAC systems in broad-spectrum antiphage defense.
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Affiliation(s)
- Toomas Mets
- Department of Experimental Medical Science, Lund University, 221 00 Lund, Sweden; University of Tartu, Institute of Technology, 50411 Tartu, Estonia
| | - Tatsuaki Kurata
- Department of Experimental Medical Science, Lund University, 221 00 Lund, Sweden
| | - Karin Ernits
- Department of Experimental Medical Science, Lund University, 221 00 Lund, Sweden
| | - Marcus J O Johansson
- Department of Experimental Medical Science, Lund University, 221 00 Lund, Sweden
| | - Sophie Z Craig
- Cellular and Molecular Microbiology (CM2), Faculté des Sciences, Université Libre de Bruxelles (ULB), Campus La Plaine, Building BC, Room 1C4203, Boulevard du Triomphe, 1050 Brussels, Belgium
| | - Gabriel Medina Evora
- Department of Experimental Medical Science, Lund University, 221 00 Lund, Sweden; Cellular and Molecular Microbiology (CM2), Faculté des Sciences, Université Libre de Bruxelles (ULB), Campus La Plaine, Building BC, Room 1C4203, Boulevard du Triomphe, 1050 Brussels, Belgium
| | - Jessica A Buttress
- Centre for Bacterial Cell Biology, Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4AX, UK
| | - Roni Odai
- Department of Experimental Medical Science, Lund University, 221 00 Lund, Sweden
| | - Kyo Coppieters't Wallant
- Centre for Structural Biology and Bioinformatics, Université Libre de Bruxelles (ULB), Boulevard du Triomphe, Building BC, 1050 Bruxelles, Belgium
| | - Jose A Nakamoto
- Department of Experimental Medical Science, Lund University, 221 00 Lund, Sweden
| | - Lena Shyrokova
- Department of Experimental Medical Science, Lund University, 221 00 Lund, Sweden
| | - Artyom A Egorov
- Department of Experimental Medical Science, Lund University, 221 00 Lund, Sweden
| | | | | | - Michael T Laub
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA; Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Tanel Tenson
- University of Tartu, Institute of Technology, 50411 Tartu, Estonia
| | - Henrik Strahl
- Centre for Bacterial Cell Biology, Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4AX, UK
| | - Chloe Martens
- Centre for Structural Biology and Bioinformatics, Université Libre de Bruxelles (ULB), Boulevard du Triomphe, Building BC, 1050 Bruxelles, Belgium
| | - Alexander Harms
- ETH Zurich, Institute of Food, Nutrition and Health, 8092 Zürich, Switzerland
| | - Abel Garcia-Pino
- Cellular and Molecular Microbiology (CM2), Faculté des Sciences, Université Libre de Bruxelles (ULB), Campus La Plaine, Building BC, Room 1C4203, Boulevard du Triomphe, 1050 Brussels, Belgium.
| | - Gemma C Atkinson
- Department of Experimental Medical Science, Lund University, 221 00 Lund, Sweden; Virus Centre, Lund University, Lund, Sweden.
| | - Vasili Hauryliuk
- Department of Experimental Medical Science, Lund University, 221 00 Lund, Sweden; University of Tartu, Institute of Technology, 50411 Tartu, Estonia; Virus Centre, Lund University, Lund, Sweden; Science for Life Laboratory, Lund, Sweden.
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9
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Yi C, Chen J, She X. The emerging role of the gut virome in necrotizing enterocolitis. Heliyon 2024; 10:e30496. [PMID: 38711648 PMCID: PMC11070903 DOI: 10.1016/j.heliyon.2024.e30496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Revised: 04/09/2024] [Accepted: 04/29/2024] [Indexed: 05/08/2024] Open
Abstract
Necrotizing enterocolitis (NEC) is the most common gastrointestinal emergency in neonates, particularly preterm infants. Many factors can lead to NEC, but microbial dysbiosis is one of the most important risk factors that can induce this disease. Given the major role of the gut virome in shaping bacterial homeostasis, virome research is a fledgling but rapidly evolving area in the field of microbiome that is increasingly connected to human diseases, including NEC. This review provides an overview of the development of the gut virome in newborns, discusses its emerging role in NEC, and explores promising therapeutic applications, including phage therapy and fecal virome transplantation.
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Affiliation(s)
- Cong Yi
- Department of Pediatrics, Mianyang Central Hospital, School of Medicine, University of Electronic Science and Technology of China, Mianyang, 621000, China
| | - Jia Chen
- Department of Pediatrics, Mianyang Central Hospital, School of Medicine, University of Electronic Science and Technology of China, Mianyang, 621000, China
| | - Xiang She
- Department of Pediatrics, Mianyang Central Hospital, School of Medicine, University of Electronic Science and Technology of China, Mianyang, 621000, China
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10
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Guo J, Zhong Y, Wang Y, Liu P, Jin H, Wang Y, Shi L, Wang P, Li W. Phylogenetic Relationships and Evolution of the Genus Eganvirus (186-Type) Yersinia pestis Bacteriophages. Viruses 2024; 16:748. [PMID: 38793629 PMCID: PMC11126057 DOI: 10.3390/v16050748] [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: 03/18/2024] [Revised: 05/02/2024] [Accepted: 05/06/2024] [Indexed: 05/26/2024] Open
Abstract
Plague is an endemic infectious disease caused by Yersinia pestis. In this study, we isolated fourteen phages with similar sequence arrangements to phage 186; these phages exhibited different lytic abilities in Enterobacteriaceae strains. To illustrate the phylogenetic relationships and evolutionary relationships between previously designated 186-type phages, we analysed the complete sequences and important genes of the phages, including whole-genome average nucleotide identity (ANI) and collinearity comparison, evolutionary analysis of four conserved structural genes (V, T, R, and Q genes), and analysis of the regulatory genes (cI, apl, and cII) and integrase gene (int). Phylogenetic analysis revealed that thirteen of the newly isolated phages belong to the genus Eganvirus and one belongs to the genus Felsduovirus in the family Peduoviridae, and these Eganvirus phages can be roughly clustered into three subgroups. The topological relationships exhibited by the whole-genome and structural genes seemed similar and stable, while the regulatory genes presented different topological relationships with the structural genes, and these results indicated that there was some homologous recombination in the regulatory genes. These newly isolated 186-type phages were mostly isolated from dogs, suggesting that the resistance of Canidae to Y. pestis infection may be related to the wide distribution of phages with lytic capability.
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Affiliation(s)
- Jin Guo
- National Institute for Communicable Disease Control and Prevention, China CDC, Changping, Beijing 102206, China; (J.G.); (Y.W.); (H.J.); (Y.W.)
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, Beijing 102206, China
| | - Youhong Zhong
- Yunnan Institute for Endemic Disease Control and Prevention, Dali 671000, China; (Y.Z.); (P.L.); (L.S.)
- Yunnan Provincial Key Laboratory for Zoonosis Control and Prevention, Dali 671000, China
| | - Yiting Wang
- National Institute for Communicable Disease Control and Prevention, China CDC, Changping, Beijing 102206, China; (J.G.); (Y.W.); (H.J.); (Y.W.)
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, Beijing 102206, China
| | - Pan Liu
- Yunnan Institute for Endemic Disease Control and Prevention, Dali 671000, China; (Y.Z.); (P.L.); (L.S.)
- Yunnan Provincial Key Laboratory for Zoonosis Control and Prevention, Dali 671000, China
| | - Haixiao Jin
- National Institute for Communicable Disease Control and Prevention, China CDC, Changping, Beijing 102206, China; (J.G.); (Y.W.); (H.J.); (Y.W.)
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, Beijing 102206, China
| | - Yumeng Wang
- National Institute for Communicable Disease Control and Prevention, China CDC, Changping, Beijing 102206, China; (J.G.); (Y.W.); (H.J.); (Y.W.)
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, Beijing 102206, China
| | - Liyuan Shi
- Yunnan Institute for Endemic Disease Control and Prevention, Dali 671000, China; (Y.Z.); (P.L.); (L.S.)
- Yunnan Provincial Key Laboratory for Zoonosis Control and Prevention, Dali 671000, China
| | - Peng Wang
- Yunnan Institute for Endemic Disease Control and Prevention, Dali 671000, China; (Y.Z.); (P.L.); (L.S.)
- Yunnan Provincial Key Laboratory for Zoonosis Control and Prevention, Dali 671000, China
| | - Wei Li
- National Institute for Communicable Disease Control and Prevention, China CDC, Changping, Beijing 102206, China; (J.G.); (Y.W.); (H.J.); (Y.W.)
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, Beijing 102206, China
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11
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Gapińska M, Zajko W, Skowronek K, Figiel M, Krawczyk P, Egorov A, Dziembowski A, Johansson MO, Nowotny M. Structure-functional characterization of Lactococcus AbiA phage defense system. Nucleic Acids Res 2024; 52:4723-4738. [PMID: 38587192 PMCID: PMC11077055 DOI: 10.1093/nar/gkae230] [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: 05/28/2023] [Revised: 02/01/2024] [Accepted: 03/20/2024] [Indexed: 04/09/2024] Open
Abstract
Bacterial reverse transcriptases (RTs) are a large and diverse enzyme family. AbiA, AbiK and Abi-P2 are abortive infection system (Abi) RTs that mediate defense against bacteriophages. What sets Abi RTs apart from other RT enzymes is their ability to synthesize long DNA products of random sequences in a template- and primer-independent manner. Structures of AbiK and Abi-P2 representatives have recently been determined, but there are no structural data available for AbiA. Here, we report the crystal structure of Lactococcus AbiA polymerase in complex with a single-stranded polymerization product. AbiA comprises three domains: an RT-like domain, a helical domain that is typical for Abi polymerases, and a higher eukaryotes and prokaryotes nucleotide-binding (HEPN) domain that is common for many antiviral proteins. AbiA forms a dimer that distinguishes it from AbiK and Abi-P2, which form trimers/hexamers. We show the DNA polymerase activity of AbiA in an in vitro assay and demonstrate that it requires the presence of the HEPN domain which is enzymatically inactive. We validate our biochemical and structural results in vivo through bacteriophage infection assays. Finally, our in vivo results suggest that AbiA-mediated phage defense may not rely on AbiA-mediated cell death.
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Affiliation(s)
- Marta Gapińska
- Laboratory of Protein Structure, International Institute of Molecular and Cell Biology, Warsaw, Poland
| | - Weronika Zajko
- Laboratory of Protein Structure, International Institute of Molecular and Cell Biology, Warsaw, Poland
| | - Krzysztof Skowronek
- Biophysics Core Facility, International Institute of Molecular and Cell Biology, Warsaw, Poland
| | - Małgorzata Figiel
- Laboratory of Protein Structure, International Institute of Molecular and Cell Biology, Warsaw, Poland
| | - Paweł S Krawczyk
- Laboratory of RNA Biology, International Institute of Molecular and Cell Biology, Warsaw, Poland
| | - Artyom A Egorov
- Department of Experimental Medical Science, Lund University, 221 00 Lund, Sweden
| | - Andrzej Dziembowski
- Laboratory of RNA Biology, International Institute of Molecular and Cell Biology, Warsaw, Poland
| | - Marcus J O Johansson
- Department of Experimental Medical Science, Lund University, 221 00 Lund, Sweden
| | - Marcin Nowotny
- Laboratory of Protein Structure, International Institute of Molecular and Cell Biology, Warsaw, Poland
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12
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Khong E, Oh JJ, Jimenez JM, Liu R, Dunham S, Monsibais A, Rhoads A, Ghatbale P, Garcia A, Cobián Güemes AG, Blanc AN, Chiu M, Kuo P, Proost M, Kline A, Aslam S, Schooley RT, Whiteson K, Fraley SI, Pride DT. A simple solid media assay for detection of synergy between bacteriophages and antibiotics. Microbiol Spectr 2024; 12:e0322123. [PMID: 38526142 PMCID: PMC11064537 DOI: 10.1128/spectrum.03221-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Accepted: 02/24/2024] [Indexed: 03/26/2024] Open
Abstract
The emergence of antibiotic-resistant bacteria (ARB) has necessitated the development of alternative therapies to deal with this global threat. Bacteriophages (viruses that target bacteria) that kill ARB are one such alternative. Although phages have been used clinically for decades with inconsistent results, a number of recent advances in phage selection, propagation, and purification have enabled a reevaluation of their utility in contemporary clinical medicine. In most phage therapy cases, phages are administered in combination with antibiotics to ensure that patients receive the standard-of-care treatment. Some phages may work cooperatively with antibiotics to eradicate ARB, as often determined using non-standardized broth assays. We sought to develop a solid media-based assay to assess cooperativity between antibiotics and phages to offer a standardized platform for such testing. We modeled the interactions that occur between antibiotics and phages on solid medium to measure additive, antagonistic, and synergistic interactions. We then tested the method using different bacterial isolates and identified a number of isolates where synergistic interactions were identified. These interactions were not dependent on the specific organism, phage family, or antibiotic used. A priori susceptibility to the antibiotic or the specific phage were not requirements to observe synergistic interactions. Our data also confirm the potential for the restoration of vancomycin to treat vancomycin-resistant Enterococcus (VRE) when used in combination with phages. Solid media assays for the detection of cooperative interactions between antibiotics and phages can be an accessible technique adopted by clinical laboratories to evaluate antibiotic and phage choices in phage therapy.IMPORTANCEBacteriophages have become an important alternative treatment for individuals with life-threatening antibiotic-resistant bacteria (ARB) infections. Because antibiotics represent the standard-of-care for treatment of ARB, antibiotics and phages often are delivered together without evidence that they work cooperatively. Testing for cooperativity can be difficult due to the equipment necessary and a lack of standardized means for performing the testing in liquid medium. We developed an assay using solid medium to identify interactions between antibiotics and phages for gram-positive and gram-negative bacteria. We modeled the interactions between antibiotics and phages on solid medium, and then tested multiple replicates of vancomycin-resistant Enterococcus (VRE) and Stenotrophomonas in the assay. For each organism, we identified synergy between different phage and antibiotic combinations. The development of this solid media assay for assessing synergy between phages and antibiotics will better inform the use of these combinations in the treatment of ARB infections.
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Affiliation(s)
- Ethan Khong
- Department of Pathology, University of California San Diego, La Jolla, California, USA
| | - Joseph J. Oh
- Department of Pathology, University of California San Diego, La Jolla, California, USA
| | - Julian M. Jimenez
- Department of Bioengineering, University of California San Diego, La Jolla, California, USA
| | - Roland Liu
- Department of Pathology, University of California San Diego, La Jolla, California, USA
| | - Sage Dunham
- Department of Molecular Biology and Biochemistry, University of California Irvine, Irvine, California, USA
| | - Alisha Monsibais
- Department of Molecular Biology and Biochemistry, University of California Irvine, Irvine, California, USA
| | - Alison Rhoads
- Department of Pathology, University of California San Diego, La Jolla, California, USA
| | - Pooja Ghatbale
- Department of Pathology, University of California San Diego, La Jolla, California, USA
| | - Andrew Garcia
- Department of Pathology, University of California San Diego, La Jolla, California, USA
| | | | - Alisha N. Blanc
- Department of Pathology, University of California San Diego, La Jolla, California, USA
| | - Megan Chiu
- Department of Pathology, University of California San Diego, La Jolla, California, USA
| | - Peiting Kuo
- Department of Pathology, University of California San Diego, La Jolla, California, USA
| | - Marissa Proost
- Department of Pathology, University of California San Diego, La Jolla, California, USA
| | - Ahnika Kline
- Department of Pathology, University of California San Diego, La Jolla, California, USA
| | - Saima Aslam
- Department of Medicine, University of California San Diego, La Jolla, California, USA
| | - Robert T. Schooley
- Department of Medicine, University of California San Diego, La Jolla, California, USA
| | - Katrine Whiteson
- Department of Molecular Biology and Biochemistry, University of California Irvine, Irvine, California, USA
| | - Stephanie I. Fraley
- Department of Bioengineering, University of California San Diego, La Jolla, California, USA
| | - David T. Pride
- Department of Pathology, University of California San Diego, La Jolla, California, USA
- Department of Medicine, University of California San Diego, La Jolla, California, USA
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13
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Cook R, Crisci MA, Pye HV, Telatin A, Adriaenssens EM, Santini JM. Decoding huge phage diversity: a taxonomic classification of Lak megaphages. J Gen Virol 2024; 105:001997. [PMID: 38814706 PMCID: PMC11165621 DOI: 10.1099/jgv.0.001997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Accepted: 05/21/2024] [Indexed: 05/31/2024] Open
Abstract
High-throughput sequencing for uncultivated viruses has accelerated the understanding of global viral diversity and uncovered viral genomes substantially larger than any that have so far been cultured. Notably, the Lak phages are an enigmatic group of viruses that present some of the largest known phage genomes identified in human and animal microbiomes, and are dissimilar to any cultivated viruses. Despite the wealth of viral diversity that exists within sequencing datasets, uncultivated viruses have rarely been used for taxonomic classification. We investigated the evolutionary relationships of 23 Lak phages and propose a taxonomy for their classification. Predicted protein analysis revealed the Lak phages formed a deeply branching monophyletic clade within the class Caudoviricetes which contained no other phage genomes. One of the interesting features of this clade is that all current members are characterised by an alternative genetic code. We propose the Lak phages belong to a new order, the 'Grandevirales'. Protein and nucleotide-based analyses support the creation of two families, three sub-families, and four genera within the order 'Grandevirales'. We anticipate that the proposed taxonomy of Lak megaphages will simplify the future classification of related viral genomes as they are uncovered. Continued efforts to classify divergent viruses are crucial to aid common analyses of viral genomes and metagenomes.
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Affiliation(s)
- Ryan Cook
- Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
| | - Marco A. Crisci
- Department of Structural and Molecular Biology, Division of Biosciences, UCL, London, UK
| | - Hannah V. Pye
- Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
| | - Andrea Telatin
- Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
| | | | - Joanne M. Santini
- Department of Structural and Molecular Biology, Division of Biosciences, UCL, London, UK
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14
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Ma J, Qian C, Hu Q, Zhang J, Gu G, Liang X, Zhang L. The bacteriome-coupled phage communities continuously contract and shift to orchestrate the traditional rice vinegar fermentation. Food Res Int 2024; 184:114244. [PMID: 38609223 DOI: 10.1016/j.foodres.2024.114244] [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: 10/17/2023] [Revised: 03/12/2024] [Accepted: 03/14/2024] [Indexed: 04/14/2024]
Abstract
Amounts of microbiome studies have uncovered the microbial communities of traditional food fermentations, while in which the phageome development with time is poorly understood. Here, we conducted a study to decipher both phageome and bacteriome of the traditional rice vinegar fermentation. The vinegar phageomes showed significant differences in the alpha diversity, network density and clustering coefficient over time. Peduoviridae had the highest relative abundance. Moreover, the phageome negatively correlated to the cognate bacteriome in alpha diversity, and undergone constantly contracting and shifting across the temporal scale. Nevertheless, 257 core virial clusters (VCs) persistently occurred with time whatever the significant impacts imposed by the varied physiochemical properties. Glycoside hydrolase (GH) and glycosyltransferase (GT) families genes displayed the higher abundances across all samples. Intriguingly, diversely structuring of toxin-antitoxin systems (TAs) and CRISPR-Cas arrays were frequently harbored by phage genomes. Their divergent organization and encoding attributes underlie the multiple biological roles in modulation of network and/or contest of phage community as well as bacterial host community. This phageome-wide mapping will fuel the current insights of phage community ecology in other traditional fermented ecosystems that are challenging to decipher.
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Affiliation(s)
- Jiawen Ma
- School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, Zhejiang Province 310018, China
| | - Chenggong Qian
- School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, Zhejiang Province 310018, China
| | - Qijie Hu
- Huzhou Institute of Food and Drug Control, Huzhou, Zhejiang Province 313002, China
| | - Jianping Zhang
- Haining Yufeng Brewing Co., Ltd, Haining, Zhejiang Province 314408, China
| | - Guizhang Gu
- Huzhou Institute of Food and Drug Control, Huzhou, Zhejiang Province 313002, China
| | - Xinle Liang
- School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, Zhejiang Province 310018, China.
| | - Lei Zhang
- School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, Zhejiang Province 310018, China.
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15
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Fernandez-Cassi X, Kohn T. Comparison of Three Viral Nucleic Acid Preamplification Pipelines for Sewage Viral Metagenomics. FOOD AND ENVIRONMENTAL VIROLOGY 2024:10.1007/s12560-024-09594-3. [PMID: 38647859 DOI: 10.1007/s12560-024-09594-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Accepted: 03/01/2024] [Indexed: 04/25/2024]
Abstract
Viral metagenomics is a useful tool for detecting multiple human viruses in urban sewage. However, more refined protocols are required for its effective use in disease surveillance. In this study, we investigated the performance of three different preamplification pipelines (specific to RNA viruses, DNA viruses or both) for viral genome sequencing using spiked-in Phosphate Buffered Saline and sewage samples containing known concentrations of viruses. We found that compared to the pipeline targeting all genome types, the RNA pipeline performed better in detecting RNA viruses in both spiked and unspiked sewage samples, allowing the detection of various mammalian viruses including members from the Reoviridae, Picornaviridae, Astroviridae and Caliciviridae. However, the DNA-specific pipeline did not improve the detection of mammalian DNA viruses. We also measured viral recovery by quantitative reverse transcription polymerase chain reaction and assessed the impact of genetic background (non-viral genetic material) on viral coverage. Our results indicate that viral recoveries were generally lower in sewage (average of 11.0%) and higher in Phosphate Buffered Saline (average of 23.4%) for most viruses. Additionally, spiked-in viruses showed lower genome coverage in sewage, demonstrating the negative effect of genetic background on sequencing. Finally, correlation analysis revealed a relationship between virus concentration and genome normalized reads per million, indicating that viral metagenomic sequencing can be semiquantitative.
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Affiliation(s)
- Xavier Fernandez-Cassi
- Laboratory of Environmental Chemistry, School of Architecture, Civil and Environmental Engineering, École Polytechnique Fédérale de Lausanne (EPFL), Vaud, Lausanne, Switzerland.
- Departament of Biology, Healthcare and Environment, Faculty of Pharmacy and Food Sciences, University of Barcelona (UB), Barcelona, Catalunya, Spain.
| | - Tamar Kohn
- Laboratory of Environmental Chemistry, School of Architecture, Civil and Environmental Engineering, École Polytechnique Fédérale de Lausanne (EPFL), Vaud, Lausanne, Switzerland
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16
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Lerdsittikul V, Apiratwarrasakul S, Atithep T, Withatanung P, Indrawattana N, Pumirat P, Chaiwattanarungruengpaisan S, Thongdee M. Isolation and characterisation of a novel Silviavirus bacteriophage promising antimicrobial agent against methicillin-resistant Staphylococcus aureus infections. Sci Rep 2024; 14:9251. [PMID: 38649443 PMCID: PMC11035597 DOI: 10.1038/s41598-024-59903-w] [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: 11/02/2023] [Accepted: 04/16/2024] [Indexed: 04/25/2024] Open
Abstract
The increasing prevalence of methicillin-resistant Staphylococcus aureus (MRSA) emphasises the urgent need for novel antimicrobial agents as alternatives to antibiotics. Bacteriophage therapy is one of the most promising antimicrobial strategies. Here, we isolated and comprehensively characterized a novel Staphylococcus phage, vB_SauM_VL10 (VL10), from urban sewage. The VL10 genome displays 141,746 bp of linear double-stranded DNA, containing 193 open reading frames and lacking tRNA, virulence, or antibiotic resistance genes. Phylogenetic analysis categorizes VL10 as a novel species within the Silviavirus genus, Twortvirinae subfamily. VL10 exhibits lytic behaviour characterized by efficient adsorption, a short latent period, and substantial burst size, with environmental stability. It demonstrates lytic activity against 79.06% of tested S. aureus strains, highlighting its species specificity. Additionally, VL10 effectively targets MRSA biofilms, reducing biomass and viable cells. In MRSA-infected G. mellonella larvae, VL10 enhances survival rates, supporting its potential for phage therapy applications. Moreover, the emergence of VL10-resistant S. aureus strains associated with fitness trade-offs, including reduced growth, biofilm formation, and virulence. Altogether, these findings emphasize VL10 as a promising candidate for developing therapeutic agents against MRSA infections, providing insights into phage biology and resistance dynamics.
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Affiliation(s)
- Varintip Lerdsittikul
- Veterinary Diagnostic Center, Faculty of Veterinary Science, Mahidol University, Nakhon Pathom, Thailand.
| | - Sukanya Apiratwarrasakul
- Veterinary Diagnostic Center, Faculty of Veterinary Science, Mahidol University, Nakhon Pathom, Thailand
| | - Thassanant Atithep
- Frontier Research Center, Vidyasirimedhi Institute of Science and Technology, Rayong, Thailand
| | - Patoo Withatanung
- Department of Immunology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Nitaya Indrawattana
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- Siriraj Center of Research and Excellence in Allergy and Immunology (SiALL), Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Pornpan Pumirat
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Somjit Chaiwattanarungruengpaisan
- The Monitoring Surveillance Center for Zoonotic Diseases in Wildlife and Exotic Animals, Faculty of Veterinary Science, Mahidol University, Nakhon Pathom, Thailand
| | - Metawee Thongdee
- The Monitoring Surveillance Center for Zoonotic Diseases in Wildlife and Exotic Animals, Faculty of Veterinary Science, Mahidol University, Nakhon Pathom, Thailand
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17
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Alsaadi SE, Lu H, Zhang M, Dykes GF, Allison HE, Horsburgh MJ. Bacteriophages from human skin infecting coagulase-negative Staphylococcus: diversity, novelty and host resistance. Sci Rep 2024; 14:8245. [PMID: 38589670 PMCID: PMC11001980 DOI: 10.1038/s41598-024-59065-9] [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: 11/24/2023] [Accepted: 04/06/2024] [Indexed: 04/10/2024] Open
Abstract
The human skin microbiome comprises diverse populations that differ temporally between body sites and individuals. The virome is a less studied component of the skin microbiome and the study of bacteriophages is required to increase knowledge of the modulation and stability of bacterial communities. Staphylococcus species are among the most abundant colonisers of skin and are associated with both health and disease yet the bacteriophages infecting the most abundant species on skin are less well studied. Here, we report the isolation and genome sequencing of 40 bacteriophages from human skin swabs that infect coagulase-negative Staphylococcus (CoNS) species, which extends our knowledge of phage diversity. Six genetic clusters of phages were identified with two clusters representing novel phages, one of which we characterise and name Alsa phage. We identified that Alsa phages have a greater ability to infect the species S. hominis that was otherwise infected less than other CoNS species by the isolated phages, indicating an undescribed barrier to phage infection that could be in part due to numerous restriction-modification systems. The extended diversity of Staphylococcus phages here enables further research to define their contribution to skin microbiome research and the mechanisms that limit phage infection.
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Affiliation(s)
- Samah E Alsaadi
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Hanshuo Lu
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Minxing Zhang
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Gregory F Dykes
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Heather E Allison
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Malcolm J Horsburgh
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK.
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18
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Tang Y, Zhou M, Yang C, Liu R, Du H, Ma M. Advances in isolated phages that affect Ralstonia solanacearum and their application in the biocontrol of bacterial wilt in plants. Lett Appl Microbiol 2024; 77:ovae037. [PMID: 38573829 DOI: 10.1093/lambio/ovae037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Revised: 03/25/2024] [Accepted: 04/03/2024] [Indexed: 04/06/2024]
Abstract
Bacterial wilt is a widespread and devastating disease that impacts the production of numerous crucial crops worldwide. The main causative agent of the disease is Ralstonia solanacearum. Due to the pathogen's broad host range and prolonged survival in the soil, it is challenging to control the disease with conventional strategies. Therefore, it is of great importance to develop effective alternative disease control strategies. In recent years, phage therapy has emerged as an environmentally friendly and sustainable biocontrol alternative, demonstrating significant potential in controlling this severe disease. This paper summarized basic information about isolated phages that infect R. solanacearum, and presented some examples of their application in the biocontrol of bacterial wilt. The risks of phage application and future prospect in this area were also discussed. Overall, R. solanacearum phages have been isolated from various regions and environments worldwide. These phages belong mainly to the Inoviridae, Autographiviridae, Peduoviridae, and Cystoviridae families, with some being unclassified. Studies on the application of these phages have demonstrated their ability to reduce pathogenicity of R. solanacearum through direct lysis or indirect alteration of the pathogen's physiological properties. These findings suggested bacteriophage is a promising tool for biocontrol of bacterial wilt in plants.
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Affiliation(s)
- You Tang
- Chongqing Key Laboratory of Scientific Utilization of Tobacco Resources, China Tobacco Chongqing Industrial Co Ltd, Nan'an, Chongqing 400060, China
| | - Moxi Zhou
- Chongqing Key Laboratory of Scientific Utilization of Tobacco Resources, China Tobacco Chongqing Industrial Co Ltd, Nan'an, Chongqing 400060, China
| | - Chuyun Yang
- Chongqing Key Laboratory of Scientific Utilization of Tobacco Resources, China Tobacco Chongqing Industrial Co Ltd, Nan'an, Chongqing 400060, China
| | - Rong Liu
- Chongqing Key Laboratory of Scientific Utilization of Tobacco Resources, China Tobacco Chongqing Industrial Co Ltd, Nan'an, Chongqing 400060, China
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
| | - Hongyi Du
- Chongqing Key Laboratory of Scientific Utilization of Tobacco Resources, China Tobacco Chongqing Industrial Co Ltd, Nan'an, Chongqing 400060, China
| | - Ming Ma
- Chongqing Key Laboratory of Scientific Utilization of Tobacco Resources, China Tobacco Chongqing Industrial Co Ltd, Nan'an, Chongqing 400060, China
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19
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Flores VS, Amgarten DE, Iha BKV, Ryon KA, Danko D, Tierney BT, Mason C, da Silva AM, Setubal JC. Discovery and description of novel phage genomes from urban microbiomes sampled by the MetaSUB consortium. Sci Rep 2024; 14:7913. [PMID: 38575625 PMCID: PMC10994904 DOI: 10.1038/s41598-024-58226-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 03/26/2024] [Indexed: 04/06/2024] Open
Abstract
Bacteriophages are recognized as the most abundant members of microbiomes and have therefore a profound impact on microbial communities through the interactions with their bacterial hosts. The International Metagenomics and Metadesign of Subways and Urban Biomes Consortium (MetaSUB) has sampled mass-transit systems in 60 cities over 3 years using metagenomics, throwing light into these hitherto largely unexplored urban environments. MetaSUB focused primarily on the bacterial community. In this work, we explored MetaSUB metagenomic data in order to recover and analyze bacteriophage genomes. We recovered and analyzed 1714 phage genomes with size at least 40 kbp, from the class Caudoviricetes, the vast majority of which (80%) are novel. The recovered genomes were predicted to belong to temperate (69%) and lytic (31%) phages. Thirty-three of these genomes have more than 200 kbp, and one of them reaches 572 kbp, placing it among the largest phage genomes ever found. In general, the phages tended to be site-specific or nearly so, but 194 genomes could be identified in every city from which phage genomes were retrieved. We predicted hosts for 48% of the phages and observed general agreement between phage abundance and the respective bacterial host abundance, which include the most common nosocomial multidrug-resistant pathogens. A small fraction of the phage genomes are carriers of antibiotic resistance genes, and such genomes tended to be particularly abundant in the sites where they were found. We also detected CRISPR-Cas systems in five phage genomes. This study expands the previously reported MetaSUB results and is a contribution to the knowledge about phage diversity, global distribution, and phage genome content.
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Affiliation(s)
- Vinicius S Flores
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, 05508-000, Brazil
| | - Deyvid E Amgarten
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, 05508-000, Brazil
- Hospital Israelita Albert Einstein, São Paulo, Brazil
| | - Bruno Koshin Vázquez Iha
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, 05508-000, Brazil
| | | | | | - Braden T Tierney
- Weill Cornell Medicine, New York, NY, USA
- Harvard Medical School, Cambridge, MA, USA
| | | | - Aline Maria da Silva
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, 05508-000, Brazil.
| | - João Carlos Setubal
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, 05508-000, Brazil.
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20
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Zamora PF, Reidy TG, Armbruster CR, Sun M, Van Tyne D, Turner PE, Koff JL, Bomberger JM. Lytic bacteriophages induce the secretion of antiviral and proinflammatory cytokines from human respiratory epithelial cells. PLoS Biol 2024; 22:e3002566. [PMID: 38652717 PMCID: PMC11037538 DOI: 10.1371/journal.pbio.3002566] [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: 09/29/2023] [Accepted: 02/27/2024] [Indexed: 04/25/2024] Open
Abstract
Phage therapy is a therapeutic approach to treat multidrug-resistant (MDR) infections that employs lytic bacteriophages (phages) to eliminate bacteria. Despite the abundant evidence for its success as an antimicrobial in Eastern Europe, there is scarce data regarding its effects on the human host. Here, we aimed to understand how lytic phages interact with cells of the airway epithelium, the tissue site that is colonized by bacterial biofilms in numerous chronic respiratory disorders. Using a panel of Pseudomonas aeruginosa phages and human airway epithelial cells (AECs) derived from a person with cystic fibrosis (CF), we determined that interactions between phages and epithelial cells depend on specific phage properties as well as physiochemical features of the microenvironment. Although poor at internalizing phages, the airway epithelium responds to phage exposure by changing its transcriptional profile and secreting antiviral and proinflammatory cytokines that correlate with specific phage families. Overall, our findings indicate that mammalian responses to phages are heterogenous and could potentially alter the way that respiratory local defenses aid in bacterial clearance during phage therapy. Thus, besides phage receptor specificity in a particular bacterial isolate, the criteria to select lytic phages for therapy should be expanded to include mammalian cell responses.
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Affiliation(s)
- Paula F. Zamora
- Department of Microbiology and Immunology, Dartmouth Geisel School of Medicine, Hanover, New Hampshire, United States of America
| | - Thomas G. Reidy
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Catherine R. Armbruster
- Department of Microbiology and Immunology, Dartmouth Geisel School of Medicine, Hanover, New Hampshire, United States of America
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | - Ming Sun
- Center for Biological Imaging, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Daria Van Tyne
- Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
| | - Paul E. Turner
- Center for Phage Biology and Therapy, Yale University, New Haven, Connecticut, United States of America
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, United States of America
- Program in Microbiology, Yale School of Medicine, New Haven, Connecticut, United States of America
- Quantitative Biology Institute, Yale University, New Haven, Connecticut, United States of America
| | - Jonathan L. Koff
- Center for Phage Biology and Therapy, Yale University, New Haven, Connecticut, United States of America
- Department of Medicine, Yale University, New Haven, Connecticut, United States of America
| | - Jennifer M. Bomberger
- Department of Microbiology and Immunology, Dartmouth Geisel School of Medicine, Hanover, New Hampshire, United States of America
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21
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Usman SS, Christina E. Characterization and genome-informatic analysis of a novel lytic mendocina phage vB_PmeS_STP12 suitable for phage therapy pseudomonas or biocontrol. Mol Biol Rep 2024; 51:419. [PMID: 38483683 DOI: 10.1007/s11033-024-09362-3] [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: 11/25/2023] [Accepted: 02/16/2024] [Indexed: 03/19/2024]
Abstract
BACKGROUND A novel lytic bacteriophage (phage) was isolated with Pseudomonas mendocina strain STP12 (P. mendocina) from the untreated site of Sewage Treatment Plant of Lovely Professional University, India. P. mendocina is a Gram-negative, rod-shaped, aerobic bacterium belonging to the family Pseudomonadaceae and has been reported in fifteen (15) cases of economically important diseases worldwide. METHODS AND RESULTS Here, a novel phage specifically infecting and killing P. mendocina strain STP12 was isolated from sewage sample using enrichment, spot test and double agar overlay (DAOL) method and was designated as vB_PmeS_STP12. The phage vB-PmeS-STP12 was viable at wide range of pH and temperature ranging from 4 to10 and - 20 to 70 °C respectively. Host range and efficiency of plating (EOP) analysis indicated that phage vB-PmeS-STP12 was capable of infecting and killing P. mendocina strain STP6 with EOP of 0.34. Phage vB_PmeS_STP12 was found to have a significant bacterial reduction (p < 0.005) at all the doses administered, particularly at optimal MOI of 1 PFU/CFU, compared to the control. Morphological analysis using high resolution transmission electron microscopy (HR-TEM) revealed an icosahedral capsid of ~ 55 nm in diameter on average with a short, non-contractile tail. The genome of vB_PmeS_STP12 is a linear, dsDNA containing 36,212 bp in size with a GC content of 58.87% harbouring 46 open reading frames (ORFs). The 46 predicted ORFs encode proteins with functional information categorized as lysis, replication, packaging, regulation, assembly, infection, immune, and hypothetical. However, the genome of vB_PmeS_STP12 appeared to be devoid of tRNAs, integrase gene, toxins genes, virulence factors, antimicrobial resistance genes (ARGs) and CRISPR arrays. The blast analysis with phylogeny revealed that vB_PmeS_STP12 is genetically similar to Pseudomonas phage PMBT14, Pseudomonas phage Almagne and Serratia phage Serbin with a highest identity of 74.00%, 74.93% and 59.48% respectively. CONCLUSIONS Taken together, characterization, morphological analysis and genome-informatics indicated that vB_PmeS_STP12 is podovirus morphotype belonging to the class Caudoviticetes, family Zobellviridae which appeared to be devoid of integrase gene, ARGs, CRISPR arrays, virulence factors and toxins genes, exhibiting stability and infectivity at wide range of pH (4 to10) and temperature (-20 to 70 °C), thereby making vB_PmeS_STP12 suitable for phage therapy or biocontrol. Based on the bibliometric analysis and data availability with respect to sequences deposited in GenBank, this is the first report of a phage infecting Pseudomonas mendocina.
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Affiliation(s)
- Sani Sharif Usman
- Department of Molecular Biology and Genetic Engineering, School of Bioengineering and Biosciences, Lovely Professional University, Jalandhar-Delhi G.T. Road, Phagwara, Punjab, 144401, India
- Department of Biological Sciences, Faculty of Science, Federal University of Kashere, P.M.B. 0182, Gombe, Nigeria
| | - Evangeline Christina
- Department of Molecular Biology and Genetic Engineering, School of Bioengineering and Biosciences, Lovely Professional University, Jalandhar-Delhi G.T. Road, Phagwara, Punjab, 144401, India.
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22
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Skowron PM, Łubkowska B, Sobolewski I, Zylicz-Stachula A, Šimoliūnienė M, Šimoliūnas E. Bacteriophages of Thermophilic ' Bacillus Group' Bacteria-A Systematic Review, 2023 Update. Int J Mol Sci 2024; 25:3125. [PMID: 38542099 PMCID: PMC10969951 DOI: 10.3390/ijms25063125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Revised: 02/27/2024] [Accepted: 02/28/2024] [Indexed: 04/05/2024] Open
Abstract
Bacteriophages associated with thermophiles are gaining increased attention due to their pivotal roles in various biogeochemical and ecological processes, as well as their applications in biotechnology and bionanotechnology. Although thermophages are not suitable for controlling bacterial infections in humans or animals, their individual components, such as enzymes and capsid proteins, can be employed in molecular biology and significantly contribute to the enhancement of human and animal health. Despite their significance, thermophages still remain underrepresented in the known prokaryotic virosphere, primarily due to limited in-depth investigations. However, due to their unique properties, thermophages are currently attracting increasing interest, as evidenced by several newly discovered phages belonging to this group. This review offers an updated compilation of thermophages characterized to date, focusing on species infecting the thermophilic bacilli. Moreover, it presents experimental findings, including novel proteomic data (39 proteins) concerning the model TP-84 bacteriophage, along with the first announcement of 6 recently discovered thermophages infecting Geobacillus thermodenitrificans: PK5.2, PK2.1, NIIg10.1, NIIg2.1, NIIg2.2, and NIIg2.3. This review serves as an update to our previous publication in 2021.
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Affiliation(s)
- Piotr M. Skowron
- Department of Molecular Biotechnology, Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland; (I.S.); (A.Z.-S.)
| | - Beata Łubkowska
- Faculty of Health and Life Sciences, Gdansk University of Physical Education and Sport, K. Gorskiego 1, 80-336 Gdansk, Poland;
- Department of Life and Environmental Sciences, University of Cagliari, 09124 Cagliari, Italy
| | - Ireneusz Sobolewski
- Department of Molecular Biotechnology, Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland; (I.S.); (A.Z.-S.)
| | - Agnieszka Zylicz-Stachula
- Department of Molecular Biotechnology, Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland; (I.S.); (A.Z.-S.)
| | - Monika Šimoliūnienė
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Center, Vilnius University, Sauletekio Av. 7, LT-10257 Vilnius, Lithuania; (M.Š.); (E.Š.)
| | - Eugenijus Šimoliūnas
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Center, Vilnius University, Sauletekio Av. 7, LT-10257 Vilnius, Lithuania; (M.Š.); (E.Š.)
- Department of Microbiology and Biotechnology, Institute of Bioscience, Life Sciences Center, Vilnius University, Sauletekio Av. 7, LT-10257 Vilnius, Lithuania
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23
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Biosca EG, Delgado Santander R, Morán F, Figàs-Segura À, Vázquez R, Català-Senent JF, Álvarez B. First European Erwinia amylovora Lytic Bacteriophage Cocktails Effective in the Host: Characterization and Prospects for Fire Blight Biocontrol. BIOLOGY 2024; 13:176. [PMID: 38534446 DOI: 10.3390/biology13030176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2024] [Revised: 03/01/2024] [Accepted: 03/05/2024] [Indexed: 03/28/2024]
Abstract
Fire blight, caused by the plant-pathogenic bacterium Erwinia amylovora, is a highly contagious and difficult-to-control disease due to its efficient dissemination and survival and the scarcity of effective control methods. Copper and antibiotics are the most used treatments but pose environmental and human health risks. Bacteriophages (phages) constitute an ecological, safe, and sustainable fire blight control alternative. The goal of this study was to search for specific E. amylovora phages from plant material, soil, and water samples in Mediterranean environments. A collection of phages able to specifically infect and lyse E. amylovora strains was generated from former fire blight-affected orchards in Eastern Spain. Following in vitro characterization, assays in immature fruit revealed that preventively applying some of the phages or their combinations delayed the onset of fire blight symptoms and reduced the disease's severity, suggesting their biocontrol potential in Spain and other countries. The morphological and molecular characterization of the selected E. amylovora phages classified them as members of the class Caudoviricetes (former Myoviridae family) and genus Kolesnikvirus. This study reveals Mediterranean settings as plausible sources of E. amylovora-specific bacteriophages and provides the first effective European phage cocktails in plant material for the development of sustainable fire blight management measures.
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Affiliation(s)
- Elena G Biosca
- Departamento de Microbiología y Ecología, Universitat de València (UV), 46100 Valencia, Spain
| | - Ricardo Delgado Santander
- Departamento de Microbiología y Ecología, Universitat de València (UV), 46100 Valencia, Spain
- Irrigated Agriculture Research and Extension Center, Department of Plant Pathology, Washington State University, Prosser, WA 99350, USA
| | - Félix Morán
- Departamento de Microbiología y Ecología, Universitat de València (UV), 46100 Valencia, Spain
| | - Àngela Figàs-Segura
- Departamento de Microbiología y Ecología, Universitat de València (UV), 46100 Valencia, Spain
| | - Rosa Vázquez
- Departamento de Microbiología y Ecología, Universitat de València (UV), 46100 Valencia, Spain
| | | | - Belén Álvarez
- Departamento de Microbiología y Ecología, Universitat de València (UV), 46100 Valencia, Spain
- Departamento de Investigación Aplicada y Extensión Agraria, Instituto Madrileño de Investigación y Desarrollo Rural, Agrario y Alimentario (IMIDRA), 28805 Madrid, Spain
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24
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Klose SM, Legione AR, Bushell RN, Browning GF, Vaz PK. Unveiling genome plasticity and a novel phage in Mycoplasma felis: Genomic investigations of four feline isolates. Microb Genom 2024; 10:001227. [PMID: 38546735 PMCID: PMC11004492 DOI: 10.1099/mgen.0.001227] [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: 01/09/2024] [Accepted: 03/18/2024] [Indexed: 04/12/2024] Open
Abstract
Mycoplasma felis has been isolated from diseased cats and horses, but to date only a single fully assembled genome of this species, of an isolate from a horse, has been characterized. This study aimed to characterize and compare the completely assembled genomes of four clinical isolates of M. felis from three domestic cats, assembled with the aid of short- and long-read sequencing methods. The completed genomes encoded a median of 759 ORFs (range 743-777) and had a median average nucleotide identity of 98.2 % with the genome of the available equid origin reference strain. Comparative genomic analysis revealed the occurrence of multiple horizontal gene transfer events and significant genome reassortment. This had resulted in the acquisition or loss of numerous genes within the Australian felid isolate genomes, encoding putative proteins involved in DNA transfer, metabolism, DNA replication, host cell interaction and restriction modification systems. Additionally, a novel mycoplasma phage was detected in one Australian felid M. felis isolate by genomic analysis and visualized using cryo-transmission electron microscopy. This study has highlighted the complex genomic dynamics in different host environments. Furthermore, the sequences obtained in this work will enable the development of new diagnostic tools, and identification of future infection control and treatment options for the respiratory disease complex in cats.
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Affiliation(s)
- Sara M. Klose
- Asia-Pacific Centre for Animal Health, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, VIC, Australia
- Institute of Molecular Medicine and Experimental Immunology, Faculty of Medicine, University of Bonn, NRW, Germany
| | - Alistair R. Legione
- Asia-Pacific Centre for Animal Health, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, VIC, Australia
| | - Rhys N. Bushell
- Department of Veterinary Clinical Sciences, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, VIC, Australia
| | - Glenn F. Browning
- Asia-Pacific Centre for Animal Health, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, VIC, Australia
| | - Paola K. Vaz
- Asia-Pacific Centre for Animal Health, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, VIC, Australia
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25
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Zhang C, Li X, Li S, Yin H, Zhao Z. Characterization and genomic analysis of a broad-spectrum lytic phage PG288: A potential natural therapy candidate for Vibrio infections. Virus Res 2024; 341:199320. [PMID: 38224841 PMCID: PMC10835289 DOI: 10.1016/j.virusres.2024.199320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Revised: 01/03/2024] [Accepted: 01/12/2024] [Indexed: 01/17/2024]
Abstract
Vibrio parahaemolyticus, an important zoonotic pathogen, can cause severe diseases and even death in aquatic animals and humans. As the widespread use of antibiotics gradually diminishes their effectiveness, phages, which can selectively lyse bacteria, are garnering increased attention as a valuable alternative antibacterial strategy. This study characterized PG288, a lytic phage utilizing V. parahaemolyticus strain G855 as its host. Morphologically, the phage features a polyhedral head and a long, non-retractable tail. Bactericidal assays revealed that phage PG288 exhibited a strong lytic ability against V. parahaemolyticus strain G855 and demonstrated a broad host range, as evidenced by the ability to infect several distinct Vibrio species. The one-step growth curve indicated a latent period of approximately 50 min for phage PG288, with a burst size of roughly 92 PFU per cell. Additionally, phage PG288 exhibited remarkable stability within a temperature range of 20-50°C and a pH range of 4-10. Genomic analysis unveiled 105 ORFs within phage PG288, notably devoid of genes associated with antibiotic resistance, virulence, and lysogenic activity. Phylogenetic analysis conclusively identified it as a new member of the genus Mardecavirus within the class Caudoviricetes. In summary, this study contributes valuable insights to the phage database, presenting phage PG288 as a promising candidate for phage therapies against Vibrio infections.
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Affiliation(s)
- Chen Zhang
- Jiangsu Province Engineering Research Center for Marine Bio-resources Sustainable Utilization, Hohai University, Nanjing 210098, China; Department of Marine Biology, College of Oceanography, Hohai University, Nanjing 210098, China
| | - Xixi Li
- Jiangsu Province Engineering Research Center for Marine Bio-resources Sustainable Utilization, Hohai University, Nanjing 210098, China; Department of Marine Biology, College of Oceanography, Hohai University, Nanjing 210098, China
| | - Shen'ao Li
- Jiangsu Province Engineering Research Center for Marine Bio-resources Sustainable Utilization, Hohai University, Nanjing 210098, China; Department of Marine Biology, College of Oceanography, Hohai University, Nanjing 210098, China
| | - Han Yin
- Jiangsu Province Engineering Research Center for Marine Bio-resources Sustainable Utilization, Hohai University, Nanjing 210098, China; Department of Marine Biology, College of Oceanography, Hohai University, Nanjing 210098, China
| | - Zhe Zhao
- Jiangsu Province Engineering Research Center for Marine Bio-resources Sustainable Utilization, Hohai University, Nanjing 210098, China; Department of Marine Biology, College of Oceanography, Hohai University, Nanjing 210098, China.
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26
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Putzeys L, Wicke L, Boon M, van Noort V, Vogel J, Lavigne R. Refining the transcriptional landscapes for distinct clades of virulent phages infecting Pseudomonas aeruginosa. MICROLIFE 2024; 5:uqae002. [PMID: 38444699 PMCID: PMC10914365 DOI: 10.1093/femsml/uqae002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 01/24/2024] [Accepted: 02/27/2024] [Indexed: 03/07/2024]
Abstract
The introduction of high-throughput sequencing has resulted in a surge of available bacteriophage genomes, unveiling their tremendous genomic diversity. However, our current understanding of the complex transcriptional mechanisms that dictate their gene expression during infection is limited to a handful of model phages. Here, we applied ONT-cappable-seq to reveal the transcriptional architecture of six different clades of virulent phages infecting Pseudomonas aeruginosa. This long-read microbial transcriptomics approach is tailored to globally map transcription start and termination sites, transcription units, and putative RNA-based regulators on dense phage genomes. Specifically, the full-length transcriptomes of LUZ19, LUZ24, 14-1, YuA, PAK_P3, and giant phage phiKZ during early, middle, and late infection were collectively charted. Beyond pinpointing traditional promoter and terminator elements and transcription units, these transcriptional profiles provide insights in transcriptional attenuation and splicing events and allow straightforward validation of Group I intron activity. In addition, ONT-cappable-seq data can guide genome-wide discovery of novel regulatory element candidates, including noncoding RNAs and riboswitches. This work substantially expands the number of annotated phage-encoded transcriptional elements identified to date, shedding light on the intricate and diverse gene expression regulation mechanisms in Pseudomonas phages, which can ultimately be sourced as tools for biotechnological applications in phage and bacterial engineering.
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Affiliation(s)
- Leena Putzeys
- Department of Biosystems, Laboratory of Gene Technology, KU Leuven, Kasteelpark Arenberg 21, 3001 Leuven, Belgium
| | - Laura Wicke
- Department of Biosystems, Laboratory of Gene Technology, KU Leuven, Kasteelpark Arenberg 21, 3001 Leuven, Belgium
- Institute for Molecular Infection Biology (IMIB), Medical Faculty, University of Würzburg, Josef-Schneider-Straße 2, 97080 Würzburg, Germany
| | - Maarten Boon
- Department of Biosystems, Laboratory of Gene Technology, KU Leuven, Kasteelpark Arenberg 21, 3001 Leuven, Belgium
| | - Vera van Noort
- Centre of Microbial and Plant Genetics, KU Leuven, Kasteelpark Arenberg 20, 3001 Leuven, Belgium
- Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE Leiden, the Netherlands
| | - Jörg Vogel
- Institute for Molecular Infection Biology (IMIB), Medical Faculty, University of Würzburg, Josef-Schneider-Straße 2, 97080 Würzburg, Germany
- Helmholtz Institute for RNA-Based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Josef-Schneider-Straße 2, 97080 Würzburg, Germany
| | - Rob Lavigne
- Department of Biosystems, Laboratory of Gene Technology, KU Leuven, Kasteelpark Arenberg 21, 3001 Leuven, Belgium
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27
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Pyzik E, Urban-Chmiel R, Kurek Ł, Herman K, Stachura R, Marek A. Bacteriophages for Controlling Staphylococcus spp. Pathogens on Dairy Cattle Farms: In Vitro Assessment. Animals (Basel) 2024; 14:683. [PMID: 38473068 DOI: 10.3390/ani14050683] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 02/16/2024] [Accepted: 02/20/2024] [Indexed: 03/14/2024] Open
Abstract
Pathogenic Staphylococcus spp. strains are significant agents involved in mastitis and in skin and limb infections in dairy cattle. The aim of this study was to assess the antibacterial effectiveness of bacteriophages isolated from dairy cattle housing as potential tools for maintaining environmental homeostasis. The research will contribute to the use of phages as alternatives to antibiotics. The material was 56 samples obtained from dairy cows with signs of limb and hoof injuries. Staphylococcus species were identified by phenotypic, MALDI-TOF MS and PCR methods. Antibiotic resistance was determined by the disc diffusion method. Phages were isolated from cattle housing systems. Phage activity (plaque forming units, PFU/mL) was determined on double-layer agar plates. Morphology was examined using TEM microscopy, and molecular characteristics were determined with PCR. Among 52 strains of Staphylococcus spp., 16 were used as hosts for bacteriophages. Nearly all isolates (94%, 15/16) showed resistance to neomycin, and 87% were resistant to spectinomycin. Cefuroxime and vancomycin were the most effective antibiotics. On the basis of their morphology, bacteriophages were identified as class Caudoviricetes, formerly Caudovirales, families Myoviridae-like (6), and Siphoviridae-like (9). Three bacteriophages of the family Myoviridae-like, with the broadest spectrum of activity, were used for further analysis. This study showed a wide spectrum of activity against the Staphylococcus spp. strains tested. The positive results indicate that bacteriophages can be used to improve the welfare of cattle.
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Affiliation(s)
- Ewelina Pyzik
- Department of Veterinary Prevention and Avian Diseases, Faculty of Veterinary Medicine, University of Life Sciences in Lublin, 20-033 Lublin, Poland
| | - Renata Urban-Chmiel
- Department of Veterinary Prevention and Avian Diseases, Faculty of Veterinary Medicine, University of Life Sciences in Lublin, 20-033 Lublin, Poland
| | - Łukasz Kurek
- Department and Clinic of Animal Internal Diseases, Sub-Department of Internal Diseases of Farm Animals and Horses, Faculty of Veterinary Medicine, University of Life Sciences in Lublin, 20-033 Lublin, Poland
| | - Klaudia Herman
- Department of Veterinary Prevention and Avian Diseases, Faculty of Veterinary Medicine, University of Life Sciences in Lublin, 20-033 Lublin, Poland
| | - Rafał Stachura
- Agromarina Company, Kulczyn-Kolonia 48, 22-235 Hańsk Pierwszy, Poland
| | - Agnieszka Marek
- Department of Veterinary Prevention and Avian Diseases, Faculty of Veterinary Medicine, University of Life Sciences in Lublin, 20-033 Lublin, Poland
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28
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Banar M, Rokaya D, Azizian R, Khurshid Z, Banakar M. Oral bacteriophages: metagenomic clues to interpret microbiomes. PeerJ 2024; 12:e16947. [PMID: 38406289 PMCID: PMC10885796 DOI: 10.7717/peerj.16947] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 01/24/2024] [Indexed: 02/27/2024] Open
Abstract
Bacteriophages are bacterial viruses that are distributed throughout the environment. Lytic phages and prophages in saliva, oral mucosa, and dental plaque interact with the oral microbiota and can change biofilm formation. The interactions between phages and bacteria can be considered a portion of oral metagenomics. The metagenomic profile of the oral microbiome indicates various bacteria. Indeed, there are various phages against these bacteria in the oral cavity. However, some other phages, like phages against Absconditabacteria, Chlamydiae, or Chloroflexi, have not been identified in the oral cavity. This review gives an overview of oral bacteriophage and used for metagenomics. Metagenomics of these phages deals with multi-drug-resistant bacterial plaques (biofilms) in oral cavities and oral infection. Hence, dentists and pharmacologists should know this metagenomic profile to cope with predental and dental infectious diseases.
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Affiliation(s)
- Maryam Banar
- Department of Pathobiology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Dinesh Rokaya
- Department of Basic Medical and Dental Sciences, Faculty of Dentistry, Zarqa University, Zarqa, Jordan
| | - Reza Azizian
- Biomedical Innovation and Start-up student association (Biomino), Tehran University of Medical Sciences, Tehran, Iran
- Pediatric Infectious Diseases Research Center (PIDRC), Tehran University of Medical Sciences, Tehran, Iran
| | - Zohaib Khurshid
- Department of Prosthodontics and Implantology, College of Dentistry, King Faisal University, Al-Hofuf, Al Ahsa, Saudi Arabia
- Center of Excellence for Regenerative Dentistry, Department of Anatomy, Faculty of Dentistry, Chulalongkorn University, Bangkok, Thailand
| | - Morteza Banakar
- Dental Research Center, Dentistry Research Institute, Tehran University of Medical Sciences, Tehran, Iran
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29
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Li E, Saleem F, Edge TA, Schellhorn HE. Assessment of crAssphage as a human fecal source tracking marker in the lower Great Lakes. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 912:168840. [PMID: 38036144 DOI: 10.1016/j.scitotenv.2023.168840] [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: 08/14/2023] [Revised: 10/27/2023] [Accepted: 11/22/2023] [Indexed: 12/02/2023]
Abstract
CrAssphage or crAss-like phage ranks as the most abundant phage in the human gut and is present in human feces-contaminated environments. Due to its high human specificity and sensitivity, crAssphage is a potentially robust source tracking indicator that can distinguish human fecal contamination from agricultural or wildlife sources. Its suitability in the Great Lakes area, one of the world's most important water systems, has not been well tested. In this study, we tested a qPCR-based quantification method using two crAssphage marker genes (ORF18-mod and CPQ_064) at Toronto recreational beaches along with their adjacent river mouths. Our results showed a 71.4 % (CPQ_064) and 100 % (ORF18-mod) human sensitivity for CPQ_064 and ORF18-mod, and a 100 % human specificity for both marker genes. CrAssphage was present in 57.7 % or 71.2 % of environmental water samples, with concentrations ranging from 1.45 to 5.14 log10 gene copies per 100 mL water. Though concentrations of the two marker genes were strongly correlated, ORF18-mod features a higher human sensitivity and higher positive detection rates in environmental samples. Quantifiable crAssphage was mostly present in samples collected in June and July 2021 associated with higher rainfall. In addition, rivers had more frequent crAssphage presence and higher concentrations than their associated beaches, indicating more frequent and greater human fecal contamination in the rivers. However, crAssphage was more correlated with E. coli and Enterococcus at the beaches than in the rivers, suggesting human fecal sources may be more predominant in driving the increases in E. coli and Enterococcus at the beaches when impacted by river plumes.
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Affiliation(s)
- Enze Li
- Department of Biology, McMaster University, Ontario L8S 4L8, Canada
| | - Faizan Saleem
- Department of Biology, McMaster University, Ontario L8S 4L8, Canada
| | - Thomas A Edge
- Department of Biology, McMaster University, Ontario L8S 4L8, Canada
| | - Herb E Schellhorn
- Department of Biology, McMaster University, Ontario L8S 4L8, Canada.
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30
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Mukherjee A, Kizziah JL, Hawkins NC, Nasef MO, Parker LK, Dokland T. Structure of the Portal Complex from Staphylococcus aureus Pathogenicity Island 1 Transducing Particles In Situ and In Isolation. J Mol Biol 2024; 436:168415. [PMID: 38135177 PMCID: PMC10923094 DOI: 10.1016/j.jmb.2023.168415] [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: 10/24/2023] [Revised: 12/15/2023] [Accepted: 12/18/2023] [Indexed: 12/24/2023]
Abstract
Staphylococcus aureus is an important human pathogen, and the prevalence of antibiotic resistance is a major public health concern. The evolution of pathogenicity and resistance in S. aureus often involves acquisition of mobile genetic elements (MGEs). Bacteriophages play an especially important role, since transduction represents the main mechanism for horizontal gene transfer. S. aureus pathogenicity islands (SaPIs), including SaPI1, are MGEs that carry genes encoding virulence factors, and are mobilized at high frequency through interactions with specific "helper" bacteriophages, such as 80α, leading to packaging of the SaPI genomes into virions made from structural proteins supplied by the helper. Among these structural proteins is the portal protein, which forms a ring-like portal at a fivefold vertex of the capsid, through which the DNA is packaged during virion assembly and ejected upon infection of the host. We have used high-resolution cryo-electron microscopy to determine structures of the S. aureus bacteriophage 80α portal itself, produced by overexpression, and in situ in the empty and full SaPI1 virions, and show how the portal interacts with the capsid. These structures provide a basis for understanding portal and capsid assembly and the conformational changes that occur upon DNA packaging and ejection.
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Affiliation(s)
- Amarshi Mukherjee
- Department of Microbiology, The University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - James L Kizziah
- Department of Microbiology, The University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - N'Toia C Hawkins
- Department of Microbiology, The University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Mohamed O Nasef
- Department of Microbiology, The University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Laura K Parker
- Department of Microbiology, The University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Terje Dokland
- Department of Microbiology, The University of Alabama at Birmingham, Birmingham, AL 35294, USA.
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31
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Kifelew LG, Warner MS, Morales S, Gordon DL, Thomas N, Mitchell JG, Speck PG. Lytic activity of phages against bacterial pathogens infecting diabetic foot ulcers. Sci Rep 2024; 14:3515. [PMID: 38347019 PMCID: PMC10861545 DOI: 10.1038/s41598-024-53317-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 01/30/2024] [Indexed: 02/15/2024] Open
Abstract
Complications of diabetes, such as diabetic foot ulcers (DFUs), are common, multifactorial in origin, and costly to treat. DFUs are the cause of nearly 90% of limb amputations among persons with diabetes. In most chronic infections such as DFU, biofilms are involved. Bacteria in biofilms are 100-1000 times more resistant to antibiotics than their planktonic counterparts. Multidrug-resistant (MDR) Staphylococcus aureus and Pseudomonas aeruginosa infections in DFUs may require alternative therapeutic agents such as bacteriophages ("phages"). This study describes the lytic activity of phage cocktails AB-SA01 (3-phage cocktail) and AB-PA01 (4-phage cocktail), which target S. aureus and P. aeruginosa, respectively. The host range and lytic effect of AB-SA01 and AB-PA01 on a planktonic culture, single-species biofilm, and mixed-species biofilm were evaluated. In vitro testing showed that 88.7% of S. aureus and 92.7% of P. aeruginosa isolates were susceptible to AB-SA01 and AB-PA01, respectively, in the planktonic state. The component phages of AB-SA01 and AB-PA01 infected 66% to 94.3% of the bacterial isolates tested. Furthermore, AB-SA01 and AB-PA01 treatment significantly (p < 0.05) reduced the biofilm biomass of their hosts, regardless of the antibiotic-resistant characteristics of the isolates and the presence of a non-susceptible host. In conclusion, the strong lytic activity, broad host range, and significant biofilm biomass reduction of AB-SA01 and AB-PA01 suggest the considerable potential of phages in treating antibiotic-resistant S. aureus and P. aeruginosa infections alone or as coinfections in DFUs.
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Affiliation(s)
- Legesse Garedew Kifelew
- College of Science and Engineering, Flinders University, Bedford Park, SA, 5042, Australia.
- St Paul's Hospital Millennium Medical College, 1271, Addis Ababa, Ethiopia.
| | - Morgyn S Warner
- Infectious Diseases Unit, Queen Elizabeth Hospital, Woodville, SA, 5011, Australia
- Discipline of Medicine, University of Adelaide, Adelaide, SA, 5005, Australia
| | - Sandra Morales
- AmpliPhi Australia Pty Ltd., Brookvale, NSW, 2100, Australia
- Phage Consulting, Sydney, NSW, 2100, Australia
| | - David L Gordon
- Department of Microbiology and Infectious Diseases, College of Medicine and Public Health, Flinders University, Bedford Park, SA, 5042, Australia
| | - Nicky Thomas
- Basil Hetzel Institute for Translational Health Research, Woodville South, SA, 5011, Australia
- Centre for Pharmaceutical Innovation, University of South Australia, North Terrace, Adelaide, SA, 5000, Australia
| | - James G Mitchell
- College of Science and Engineering, Flinders University, Bedford Park, SA, 5042, Australia
| | - Peter G Speck
- College of Science and Engineering, Flinders University, Bedford Park, SA, 5042, Australia.
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32
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Kamiński B, Paczesny J. Bacteriophage Challenges in Industrial Processes: A Historical Unveiling and Future Outlook. Pathogens 2024; 13:152. [PMID: 38392890 PMCID: PMC10893365 DOI: 10.3390/pathogens13020152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Revised: 02/01/2024] [Accepted: 02/02/2024] [Indexed: 02/25/2024] Open
Abstract
Humans have used fermentation processes since the Neolithic period, mainly to produce beverages. The turning point occurred in the 1850s, when Louis Pasteur discovered that fermentation resulted from the metabolism of living microorganisms. This discovery led to the fast development of fermented food production. The importance of industrial processes based on fermentation significantly increased. Many branches of industry rely on the metabolisms of bacteria, for example, the dairy industry (cheese, milk, yogurts), pharmaceutical processes (insulin, vaccines, antibiotics), or the production of chemicals (acetone, butanol, acetic acid). These are the mass production processes involving a large financial outlay. That is why it is essential to minimize threats to production. One major threat affecting bacteria-based processes is bacteriophage infections, causing substantial economic losses. The first reported phage infections appeared in the 1930s, and companies still struggle to fight against phages. This review shows the cases of phage infections in industry and the most common methods used to prevent phage infections.
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Affiliation(s)
| | - Jan Paczesny
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland;
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33
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Zamora PF, Reidy TG, Armbruster CR, Sun M, Van Tyne D, Turner PE, Koff JL, Bomberger JM. Lytic bacteriophages interact with respiratory epithelial cells and induce the secretion of antiviral and proinflammatory cytokines. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.06.579115. [PMID: 38370761 PMCID: PMC10871231 DOI: 10.1101/2024.02.06.579115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
Phage therapy is a therapeutic approach to treat multidrug resistant infections that employs lytic bacteriophages (phages) to eliminate bacteria. Despite the abundant evidence for its success as an antimicrobial in Eastern Europe, there is scarce data regarding its effects on the human host. Here, we aimed to understand how lytic phages interact with cells of the airway epithelium, the tissue site that is colonized by bacterial biofilms in numerous chronic respiratory disorders. We determined that interactions between phages and epithelial cells depend on specific phage properties as well as physiochemical features of the microenvironment. Although poor at internalizing phages, the airway epithelium responds to phage exposure by changing its transcriptional profile and secreting antiviral and proinflammatory cytokines that correlate with specific phage families. Overall, our findings indicate that mammalian responses to phages are heterogenous and could potentially alter the way that respiratory local defenses aid in bacterial clearance during phage therapy. Thus, besides phage receptor specificity in a particular bacterial isolate, the criteria to select lytic phages for therapy should be expanded to include mammalian cell responses.
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Affiliation(s)
- Paula F. Zamora
- Department of Microbiology and Immunology, Dartmouth Geisel School of Medicine, Hanover, NH
| | - Thomas G. Reidy
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA
| | - Catherine R. Armbruster
- Department of Microbiology and Immunology, Dartmouth Geisel School of Medicine, Hanover, NH
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA
| | - Ming Sun
- Center for Biological Imaging, University of Pittsburgh, Pittsburgh, PA
| | - Daria Van Tyne
- Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA
| | - Paul E. Turner
- Center for Phage Biology and Therapy, Yale University, New Haven, CT
| | - Jonathan L. Koff
- Center for Phage Biology and Therapy, Yale University, New Haven, CT
| | - Jennifer M. Bomberger
- Department of Microbiology and Immunology, Dartmouth Geisel School of Medicine, Hanover, NH
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34
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Ouyang R, Ongenae V, Muok A, Claessen D, Briegel A. Phage fibers and spikes: a nanoscale Swiss army knife for host infection. Curr Opin Microbiol 2024; 77:102429. [PMID: 38277900 DOI: 10.1016/j.mib.2024.102429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 12/19/2023] [Accepted: 01/08/2024] [Indexed: 01/28/2024]
Abstract
Bacteriophages are being rediscovered as potent agents for medical and industrial applications. However, finding a suitable phage relies on numerous factors, including host specificity, burst size, and infection cycle. The host range of a phage is, besides phage defense systems, initially determined by the recognition and attachment of receptor-binding proteins (RBPs) to the target receptors of susceptible bacteria. RBPs include tail (or occasionally head) fibers and tailspikes. Owing to the potential flexibility and heterogeneity of these structures, they are often overlooked during structural studies. Recent advances in cryo-electron microscopy studies and computational approaches have begun to unravel their structural and fundamental mechanisms during phage infection. In this review, we discuss the current state of research on different phage tail and head fibers, spike models, and molecular mechanisms. These details may facilitate the manipulation of phage-host specificity, which in turn will have important implications for science and society.
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Affiliation(s)
- Ruochen Ouyang
- Department of Microbial Sciences, Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE Leiden, the Netherlands; MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xianning West Road 28, Xi'an 710049, China
| | - Véronique Ongenae
- Department of Microbial Sciences, Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE Leiden, the Netherlands; Centre for Microbial Cell Biology, Leiden University, Leiden, the Netherlands
| | - Alise Muok
- Department of Microbial Sciences, Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE Leiden, the Netherlands
| | - Dennis Claessen
- Department of Microbial Sciences, Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE Leiden, the Netherlands; Centre for Microbial Cell Biology, Leiden University, Leiden, the Netherlands
| | - Ariane Briegel
- Department of Microbial Sciences, Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE Leiden, the Netherlands; Centre for Microbial Cell Biology, Leiden University, Leiden, the Netherlands.
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35
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Liu K, Wang C, Zhou X, Guo X, Yang Y, Liu W, Zhao R, Song H. Bacteriophage therapy for drug-resistant Staphylococcus aureus infections. Front Cell Infect Microbiol 2024; 14:1336821. [PMID: 38357445 PMCID: PMC10864608 DOI: 10.3389/fcimb.2024.1336821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2023] [Accepted: 01/09/2024] [Indexed: 02/16/2024] Open
Abstract
Drug-resistant Staphylococcus aureus stands as a prominent pathogen in nosocomial and community-acquired infections, capable of inciting various infections at different sites in patients. This includes Staphylococcus aureus bacteremia (SaB), which exhibits a severe infection frequently associated with significant mortality rate of approximately 25%. In the absence of better alternative therapies, antibiotics is still the main approach for treating infections. However, excessive use of antibiotics has, in turn, led to an increase in antimicrobial resistance. Hence, it is imperative that new strategies are developed to control drug-resistant S. aureus infections. Bacteriophages are viruses with the ability to infect bacteria. Bacteriophages, were used to treat bacterial infections before the advent of antibiotics, but were subsequently replaced by antibiotics due to limited theoretical understanding and inefficient preparation processes at the time. Recently, phages have attracted the attention of many researchers again because of the serious problem of antibiotic resistance. This article provides a comprehensive overview of phage biology, animal models, diverse clinical case treatments, and clinical trials in the context of drug-resistant S. aureus phage therapy. It also assesses the strengths and limitations of phage therapy and outlines the future prospects and research directions. This review is expected to offer valuable insights for researchers engaged in phage-based treatments for drug-resistant S. aureus infections.
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Affiliation(s)
- Kaixin Liu
- College of Public Health, Zhengzhou University, Zhengzhou, China
- Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - Chao Wang
- Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - Xudong Zhou
- Chinese PLA Center for Disease Control and Prevention, Beijing, China
- College of Public Health, China Medical University, Shenyang, China
| | - Xudong Guo
- Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - Yi Yang
- Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - Wanying Liu
- Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - Rongtao Zhao
- Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - Hongbin Song
- College of Public Health, Zhengzhou University, Zhengzhou, China
- Chinese PLA Center for Disease Control and Prevention, Beijing, China
- College of Public Health, China Medical University, Shenyang, China
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36
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Gordon M, Ramirez P. Efficacy and Experience of Bacteriophages in Biofilm-Related Infections. Antibiotics (Basel) 2024; 13:125. [PMID: 38391511 PMCID: PMC10886175 DOI: 10.3390/antibiotics13020125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Revised: 01/16/2024] [Accepted: 01/19/2024] [Indexed: 02/24/2024] Open
Abstract
Bacterial infection has always accompanied human beings, causing suffering and death while also contributing to the advancement of medical science. However, the treatment of infections has become more complex in recent times. The increasing resistance of bacterial strains to antibiotics has diminished the effectiveness of the therapeutic arsenal, making it less likely to find the appropriate empiric antibiotic option. Additionally, the development and persistence of bacterial biofilms have become more prevalent, attributed to the greater use of invasive devices that facilitate biofilm formation and the enhanced survival of chronic infection models where biofilm plays a crucial role. Bacteria within biofilms are less susceptible to antibiotics due to physical, chemical, and genetic factors. Bacteriophages, as biological weapons, can overcome both antimicrobial resistance and biofilm protection. In this review, we will analyze the scientific progress achieved in vitro to justify their clinical application. In the absence of scientific evidence, we will compile publications of clinical cases where phages have been used to treat infections related to biofilm. The scientific basis obtained in vitro and the success rate and safety observed in clinical practice should motivate the medical community to conduct clinical trials establishing a protocol for the proper use of bacteriophages.
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Affiliation(s)
- Monica Gordon
- Critical Care Department, Hospital Universitario y Politécnico la Fe, Av. Vicente Abril Martorell 106, 46026 Valencia, Spain
| | - Paula Ramirez
- Critical Care Department, Hospital Universitario y Politécnico la Fe, Av. Vicente Abril Martorell 106, 46026 Valencia, Spain
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37
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Ishola OA, Kublik S, Durai Raj AC, Ohnmacht C, Schulz S, Foesel BU, Schloter M. Comparative Metagenomic Analysis of Bacteriophages and Prophages in Gnotobiotic Mouse Models. Microorganisms 2024; 12:255. [PMID: 38399658 PMCID: PMC10892684 DOI: 10.3390/microorganisms12020255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 01/19/2024] [Accepted: 01/23/2024] [Indexed: 02/25/2024] Open
Abstract
Gnotobiotic murine models are important to understand microbiota-host interactions. Despite the role of bacteriophages as drivers for microbiome structure and function, there is no information about the structure and function of the gut virome in gnotobiotic models and the link between bacterial and bacteriophage/prophage diversity. We studied the virome of gnotobiotic murine Oligo-MM12 (12 bacterial species) and reduced Altered Schaedler Flora (ASF, three bacterial species). As reference, the virome of Specific Pathogen-Free (SPF) mice was investigated. A metagenomic approach was used to assess prophages and bacteriophages in the guts of 6-week-old female mice. We identified a positive correlation between bacteria diversity, and bacteriophages and prophages. Caudoviricetes (82.4%) were the most prominent class of phages in all samples with differing relative abundance. However, the host specificity of bacteriophages belonging to class Caudoviricetes differed depending on model bacterial diversity. We further studied the role of bacteriophages in horizontal gene transfer and microbial adaptation to the host's environment. Analysis of mobile genetic elements showed the contribution of bacteriophages to the adaptation of bacterial amino acid metabolism. Overall, our results implicate virome "dark matter" and interactions with the host system as factors for microbial community structure and function which determine host health. Taking the importance of the virome in the microbiome diversity and horizontal gene transfer, reductions in the virome might be an important factor driving losses of microbial biodiversity and the subsequent dysbiosis of the gut microbiome.
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Affiliation(s)
- Oluwaseun A. Ishola
- Research Unit for Comparative Microbiome Analysis, Helmholtz Zentrum München—German Research Center for Environmental Health, 85764 Neuherberg, Germany; (O.A.I.)
| | - Susanne Kublik
- Research Unit for Comparative Microbiome Analysis, Helmholtz Zentrum München—German Research Center for Environmental Health, 85764 Neuherberg, Germany; (O.A.I.)
| | - Abilash Chakravarthy Durai Raj
- Research Unit for Comparative Microbiome Analysis, Helmholtz Zentrum München—German Research Center for Environmental Health, 85764 Neuherberg, Germany; (O.A.I.)
| | - Caspar Ohnmacht
- Mucosal Immunology Group, Center of Allery and Environment (ZAUM), Technical University of Munich, Helmholtz Zentrum München, 85764 München, Germany
| | - Stefanie Schulz
- Research Unit for Comparative Microbiome Analysis, Helmholtz Zentrum München—German Research Center for Environmental Health, 85764 Neuherberg, Germany; (O.A.I.)
| | - Bärbel U. Foesel
- Research Unit for Comparative Microbiome Analysis, Helmholtz Zentrum München—German Research Center for Environmental Health, 85764 Neuherberg, Germany; (O.A.I.)
| | - Michael Schloter
- Research Unit for Comparative Microbiome Analysis, Helmholtz Zentrum München—German Research Center for Environmental Health, 85764 Neuherberg, Germany; (O.A.I.)
- Chair for Environmental Microbiology, TUM School of Life Science, Technical University of Munich, 85354 Freising, Germany
- Central Institute for Nutrition and Health, Technical University of Munich, 85354 Freising, Germany
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38
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Silva EC, Quinde CA, Cieza B, Basu A, Vila MMDC, Balcão VM. Molecular Characterization and Genome Mechanical Features of Two Newly Isolated Polyvalent Bacteriophages Infecting Pseudomonas syringae pv. garcae. Genes (Basel) 2024; 15:113. [PMID: 38255005 PMCID: PMC10815195 DOI: 10.3390/genes15010113] [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: 12/09/2023] [Revised: 01/06/2024] [Accepted: 01/16/2024] [Indexed: 01/24/2024] Open
Abstract
Coffee plants have been targeted by a devastating bacterial disease, a condition known as bacterial blight, caused by the phytopathogen Pseudomonas syringae pv. garcae (Psg). Conventional treatments of coffee plantations affected by the disease involve frequent spraying with copper- and kasugamycin-derived compounds, but they are both highly toxic to the environment and stimulate the appearance of bacterial resistance. Herein, we report the molecular characterization and mechanical features of the genome of two newly isolated (putative polyvalent) lytic phages for Psg. The isolated phages belong to class Caudoviricetes and present a myovirus-like morphotype belonging to the genuses Tequatrovirus (PsgM02F) and Phapecoctavirus (PsgM04F) of the subfamilies Straboviridae (PsgM02F) and Stephanstirmvirinae (PsgM04F), according to recent bacterial viruses' taxonomy, based on their complete genome sequences. The 165,282 bp (PsgM02F) and 151,205 bp (PsgM04F) genomes do not feature any lysogenic-related (integrase) genes and, hence, can safely be assumed to follow a lytic lifestyle. While phage PsgM02F produced a morphogenesis yield of 124 virions per host cell, phage PsgM04F produced only 12 virions per host cell, indicating that they replicate well in Psg with a 50 min latency period. Genome mechanical analyses established a relationship between genome bendability and virion morphogenesis yield within infected host cells.
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Affiliation(s)
- Erica C. Silva
- VBlab—Laboratory of Bacterial Viruses, University of Sorocaba, Sorocaba 18023-000, SP, Brazil; (E.C.S.); (M.M.D.C.V.)
| | - Carlos A. Quinde
- Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA;
| | - Basilio Cieza
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University, Baltimore, MD 21218, USA;
| | - Aakash Basu
- Department of Biosciences, Durham University, Durham DH1 3LE, UK;
| | - Marta M. D. C. Vila
- VBlab—Laboratory of Bacterial Viruses, University of Sorocaba, Sorocaba 18023-000, SP, Brazil; (E.C.S.); (M.M.D.C.V.)
| | - Victor M. Balcão
- VBlab—Laboratory of Bacterial Viruses, University of Sorocaba, Sorocaba 18023-000, SP, Brazil; (E.C.S.); (M.M.D.C.V.)
- Department of Biology and CESAM, University of Aveiro, Campus Universitário de Santiago, P-3810-193 Aveiro, Portugal
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Veldsman WP, Yang C, Zhang Z, Huang Y, Chowdhury D, Zhang L. Structural and Functional Disparities within the Human Gut Virome in Terms of Genome Topology and Representative Genome Selection. Viruses 2024; 16:134. [PMID: 38257834 PMCID: PMC10820185 DOI: 10.3390/v16010134] [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: 12/18/2023] [Revised: 01/12/2024] [Accepted: 01/16/2024] [Indexed: 01/24/2024] Open
Abstract
Circularity confers protection to viral genomes where linearity falls short, thereby fulfilling the form follows function aphorism. However, a shift away from morphology-based classification toward the molecular and ecological classification of viruses is currently underway within the field of virology. Recent years have seen drastic changes in the International Committee on Taxonomy of Viruses' operational definitions of viruses, particularly for the tailed phages that inhabit the human gut. After the abolition of the order Caudovirales, these tailed phages are best defined as members of the class Caudoviricetes. To determine the epistemological value of genome topology in the context of the human gut virome, we designed a set of seven experiments to assay the impact of genome topology and representative viral selection on biological interpretation. Using Oxford Nanopore long reads for viral genome assembly coupled with Illumina short-read polishing, we showed that circular and linear virus genomes differ remarkably in terms of genome quality, GC skew, transfer RNA gene frequency, structural variant frequency, cross-reference functional annotation (COG, KEGG, Pfam, and TIGRfam), state-of-the-art marker-based classification, and phage-host interaction. Furthermore, the disparity profile changes during dereplication. In particular, our phage-host interaction results demonstrated that proportional abundances cannot be meaningfully compared without due regard for genome topology and dereplication threshold, which necessitates the need for standardized reporting. As a best practice guideline, we recommend that comparative studies of the human gut virome always report the ratio of circular to linear viral genomes along with the dereplication threshold so that structural and functional metrics can be placed into context when assessing biologically relevant metagenomic properties such as proportional abundance.
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Affiliation(s)
- Werner P. Veldsman
- Department of Computer Science, Hong Kong Baptist University, Kowloon, Hong Kong SAR, China; (W.P.V.); (C.Y.); (Z.Z.)
| | - Chao Yang
- Department of Computer Science, Hong Kong Baptist University, Kowloon, Hong Kong SAR, China; (W.P.V.); (C.Y.); (Z.Z.)
| | - Zhenmiao Zhang
- Department of Computer Science, Hong Kong Baptist University, Kowloon, Hong Kong SAR, China; (W.P.V.); (C.Y.); (Z.Z.)
| | | | - Debajyoti Chowdhury
- School of Chinese Medicine, Hong Kong Baptist University, Hong Kong SAR, China;
- Computational Medicine Laboratory, Hong Kong Baptist University, Hong Kong SAR, China
| | - Lu Zhang
- Department of Computer Science, Hong Kong Baptist University, Kowloon, Hong Kong SAR, China; (W.P.V.); (C.Y.); (Z.Z.)
- Institute for Research and Continuing Education, Hong Kong Baptist University, Shenzhen 518057, China
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40
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Oh M, Cevallos-Urena A, Kim BS. Bacteriophages PECP14, PECP20, and their endolysins as effective biocontrol agents for Escherichia coli O157:H7 and other foodborne pathogens. Int J Food Microbiol 2024; 409:110460. [PMID: 37925886 DOI: 10.1016/j.ijfoodmicro.2023.110460] [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: 08/22/2023] [Revised: 10/17/2023] [Accepted: 10/19/2023] [Indexed: 11/07/2023]
Abstract
Escherichia coli O157:H7 is a notorious foodborne pathogen known to cause severe illnesses such as hemolytic colitis and hemolytic uremic syndrome, with fresh produce consumption being implicated in recent outbreaks. The inappropriate use of antimicrobials to combat pathogens has led to the emergence and rapid dissemination of antimicrobial-resistant microorganisms including pathogenic E. coli, presenting a significant risk to humans. Here, we isolated two E. coli O157:H7 infecting bacteriophages, PECP14 and PECP20, from irrigation water and city sewage, respectively, as alternatives to antimicrobials. Both phages were stable for at least 16 h in a broad range of pH (pH 3-11) and temperature (4-40 °C) conditions and have a double-stranded DNA chromosome. PECP14 and PECP20, classified under the Epseptimavirus and Mosigvirus genera, respectively, exhibit specificity in targeting different host receptors, BtuB protein and lipopolysaccharide. Interestingly, these phages demonstrate the ability to infect not only E. coli O157:H7 but also other foodborne enteric pathogens like Shigella sonnei and S. flexneri. Upon mixing phages with their respective host bacteria, rapid adsorption (at least 68 % adsorption within 10 min) and substantial bacterial lysis were observed. The efficacy of phage treatment was further validated through the reduction of E. coli O157:H7 on radish sprouts. Moreover, purified endolysins, LysPECP14 and LysPECP20, derived from each phage exhibited remarkable bacteriolytic activity against E. coli O157:H7 cells pretreated with EDTA. In particular, the activity of LysPECP20 was also noticeable against Listeria monocytogenes and Bacillus cereus, suggesting its potential for broader antimicrobial applications in food industry. The combined results showed that the phages PECP14, PECP20, and their endolysins could be used for biological control of E. coli O157:H7 in various circumstances, from production, harvesting, and storage stages to processing and distribution steps of agricultural products.
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Affiliation(s)
- Minjin Oh
- Department of Food Science and Biotechnology, ELTEC College of Engineering, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Ana Cevallos-Urena
- Department of Food Science and Biotechnology, ELTEC College of Engineering, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Byoung Sik Kim
- Department of Food Science and Biotechnology, ELTEC College of Engineering, Ewha Womans University, Seoul 03760, Republic of Korea.
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41
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Parra B, Cockx B, Lutz VT, Brøndsted L, Smets BF, Dechesne A. Isolation and characterization of novel plasmid-dependent phages infecting bacteria carrying diverse conjugative plasmids. Microbiol Spectr 2024; 12:e0253723. [PMID: 38063386 PMCID: PMC10782986 DOI: 10.1128/spectrum.02537-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Accepted: 11/12/2023] [Indexed: 12/23/2023] Open
Abstract
IMPORTANCE This work was undertaken because plasmid-dependent phages can reduce the prevalence of conjugative plasmids and can be leveraged to prevent the acquisition and dissemination of ARGs by bacteria. The two novel phages described in this study, Lu221 and Hi226, can infect Escherichia coli, Salmonella enterica, Kluyvera sp. and Enterobacter sp. carrying conjugative plasmids. This was verified with plasmids carrying resistance determinants and belonging to the most common plasmid families among Gram-negative pathogens. Therefore, the newly isolated phages could have the potential to help control the spread of ARGs and thus help combat the antimicrobial resistance crisis.
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Affiliation(s)
- Boris Parra
- Department of Environmental Engineering and Resource Engineering, Technical University of Denmark, Kongens Lyngby, Denmark
- Laboratorio de Investigación de Agentes Antibacterianos, Departamento de Microbiología, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile
- Instituto de Ciencias Naturales, Facultad de Medicina Veterinaria y Agronomía, Universidad de las Américas, Concepción, Chile
| | - Bastiaan Cockx
- Department of Environmental Engineering and Resource Engineering, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Veronika T. Lutz
- Department of Veterinary and Animal Sciences, University of Copenhagen, København, Denmark
| | - Lone Brøndsted
- Department of Veterinary and Animal Sciences, University of Copenhagen, København, Denmark
| | - Barth F. Smets
- Department of Environmental Engineering and Resource Engineering, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Arnaud Dechesne
- Department of Environmental Engineering and Resource Engineering, Technical University of Denmark, Kongens Lyngby, Denmark
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42
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Koonin EV, Kuhn JH, Dolja VV, Krupovic M. Megataxonomy and global ecology of the virosphere. THE ISME JOURNAL 2024; 18:wrad042. [PMID: 38365236 PMCID: PMC10848233 DOI: 10.1093/ismejo/wrad042] [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: 11/22/2023] [Revised: 12/22/2023] [Accepted: 12/28/2023] [Indexed: 02/18/2024]
Abstract
Nearly all organisms are hosts to multiple viruses that collectively appear to be the most abundant biological entities in the biosphere. With recent advances in metagenomics and metatranscriptomics, the known diversity of viruses substantially expanded. Comparative analysis of these viruses using advanced computational methods culminated in the reconstruction of the evolution of major groups of viruses and enabled the construction of a virus megataxonomy, which has been formally adopted by the International Committee on Taxonomy of Viruses. This comprehensive taxonomy consists of six virus realms, which are aspired to be monophyletic and assembled based on the conservation of hallmark proteins involved in capsid structure formation or genome replication. The viruses in different major taxa substantially differ in host range and accordingly in ecological niches. In this review article, we outline the latest developments in virus megataxonomy and the recent discoveries that will likely lead to reassessment of some major taxa, in particular, split of three of the current six realms into two or more independent realms. We then discuss the correspondence between virus taxonomy and the distribution of viruses among hosts and ecological niches, as well as the abundance of viruses versus cells in different habitats. The distribution of viruses across environments appears to be primarily determined by the host ranges, i.e. the virome is shaped by the composition of the biome in a given habitat, which itself is affected by abiotic factors.
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Affiliation(s)
- Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, United States
| | - Jens H Kuhn
- Integrated Research Facility at Fort Detrick, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD 21702, United States
| | - Valerian V Dolja
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, United States
| | - Mart Krupovic
- Institut Pasteur, Université Paris Cité, Archaeal Virology Unit, 75015 Paris, France
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43
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Łubkowska B, Sobolewski I, Adamowicz K, Zylicz-Stachula A, Skowron PM. Recombinant TP-84 Bacteriophage Glycosylase-Depolymerase Confers Activity against Thermostable Geobacillus stearothermophilus via Capsule Degradation. Int J Mol Sci 2024; 25:722. [PMID: 38255796 PMCID: PMC10815759 DOI: 10.3390/ijms25020722] [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: 12/09/2023] [Revised: 01/02/2024] [Accepted: 01/04/2024] [Indexed: 01/24/2024] Open
Abstract
The TP-84 bacteriophage, which infects Geobacillus stearothermophilus strain 10 (G. stearothermophilus), has a genome size of 47.7 kilobase pairs (kbps) and contains 81 predicted protein-coding ORFs. One of these, TP84_26 encodes a putative tail fiber protein possessing capsule depolymerase activity. In this study, we cloned the TP84_26 gene into a high-expression Escherichia coli (E. coli) system, modified its N-terminus with His-tag, expressed both the wild type gene and His-tagged variant, purified the recombinant depolymerase variants, and further evaluated their properties. We developed a direct enzymatic assay for the depolymerase activity toward G. stearothermophilus capsules. The recombinant TP84_26 protein variants effectively degraded the existing bacterial capsules and inhibited the formation of new ones. Our results provide insights into the novel TP84_26 depolymerase with specific activity against thermostable G. stearothermophilus and its role in the TP-84 life cycle. The identification and characterization of novel depolymerases, such as TP84_26, hold promise for innovative strategies to combat bacterial infections and improve various industrial processes.
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Affiliation(s)
- Beata Łubkowska
- Faculty of Health and Life Sciences, Gdansk University of Physical Education and Sport, K. Gorskiego 1, 80-336 Gdansk, Poland
| | - Ireneusz Sobolewski
- Faculty of Chemistry, Department of Molecular Biotechnology, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland; (I.S.); (K.A.); (A.Z.-S.); (P.M.S.)
| | - Katarzyna Adamowicz
- Faculty of Chemistry, Department of Molecular Biotechnology, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland; (I.S.); (K.A.); (A.Z.-S.); (P.M.S.)
| | - Agnieszka Zylicz-Stachula
- Faculty of Chemistry, Department of Molecular Biotechnology, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland; (I.S.); (K.A.); (A.Z.-S.); (P.M.S.)
| | - Piotr M. Skowron
- Faculty of Chemistry, Department of Molecular Biotechnology, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland; (I.S.); (K.A.); (A.Z.-S.); (P.M.S.)
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44
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Kuiper BP, Schöntag AMC, Oksanen HM, Daum B, Quax TEF. Archaeal virus entry and egress. MICROLIFE 2024; 5:uqad048. [PMID: 38234448 PMCID: PMC10791045 DOI: 10.1093/femsml/uqad048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 11/08/2023] [Accepted: 01/02/2024] [Indexed: 01/19/2024]
Abstract
Archaeal viruses display a high degree of structural and genomic diversity. Few details are known about the mechanisms by which these viruses enter and exit their host cells. Research on archaeal viruses has lately made significant progress due to advances in genetic tools and imaging techniques, such as cryo-electron tomography (cryo-ET). In recent years, a steady output of newly identified archaeal viral receptors and egress mechanisms has offered the first insight into how archaeal viruses interact with the archaeal cell envelope. As more details about archaeal viral entry and egress are unravelled, patterns are starting to emerge. This helps to better understand the interactions between viruses and the archaeal cell envelope and how these compare to infection strategies of viruses in other domains of life. Here, we provide an overview of recent developments in the field of archaeal viral entry and egress, shedding light onto the most elusive part of the virosphere.
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Affiliation(s)
- Bastiaan P Kuiper
- Biology of Archaea and Viruses, Department of Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, Faculty for Science and Engineering, University of Groningen, 7th floor, Nijenborgh 7, 9747 AG Groningen, the Netherlands
| | - Anna M C Schöntag
- Biology of Archaea and Viruses, Department of Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, Faculty for Science and Engineering, University of Groningen, 7th floor, Nijenborgh 7, 9747 AG Groningen, the Netherlands
| | - Hanna M Oksanen
- Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Viikinkaari 9, FI-00014 Helsinki, Finland
| | - Bertram Daum
- Living Systems Institute, Faculty of Health and Life Sciences, University of Exeter, Exeter EX4 4QD, United Kingdom
| | - Tessa E F Quax
- Biology of Archaea and Viruses, Department of Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, Faculty for Science and Engineering, University of Groningen, 7th floor, Nijenborgh 7, 9747 AG Groningen, the Netherlands
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45
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Vu TN, Clark JR, Jang E, D'Souza R, Nguyen LP, Pinto NA, Yoo S, Abadie R, Maresso AW, Yong D. Appelmans protocol - A directed in vitro evolution enables induction and recombination of prophages with expanded host range. Virus Res 2024; 339:199272. [PMID: 37981215 PMCID: PMC10730860 DOI: 10.1016/j.virusres.2023.199272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 10/26/2023] [Accepted: 11/16/2023] [Indexed: 11/21/2023]
Abstract
Infections caused by carbapenem-resistant Acinetobacter baumannii (CRAB) present significant healthcare challenges due to limited treatment options. Bacteriophage (phage) therapy offers potential as an alternative treatment. However, the high host specificity of phages poses challenges for their therapeutic application. To broaden the phage spectrum, laboratory-based phage training using the Appelmans protocol was employed in this study. As a result, the protocol successfully expanded the host range of a phage cocktail targeting CRAB. Further analysis revealed that the expanded host range phages isolated from the output cocktail were identified as recombinant derivatives originating from prophages induced from encountered bacterial strains. These findings provide valuable genetic insights into the protocol's mechanism when applied to phages infecting A. baumannii strains that have never been investigated before. However, it is noteworthy that the expanded host range phages obtained from this protocol exhibited limited stability, raising concerns about their suitability for therapeutic purposes.
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Affiliation(s)
- Thao Nguyen Vu
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul, South Korea
| | - Justin Ryan Clark
- Tailored Antibacterials and Innovative Laboratories for Phage Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, US
| | - Eris Jang
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Seoul, South Korea; University of Georgia Terry College of Business, Athens, GA, US
| | - Roshan D'Souza
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Seoul, South Korea
| | - Le Phuong Nguyen
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Seoul, South Korea; Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA, US
| | - Naina Adren Pinto
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Seoul, South Korea
| | - Seongjun Yoo
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul, South Korea
| | - Ricardo Abadie
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul, South Korea
| | - Anthony William Maresso
- Tailored Antibacterials and Innovative Laboratories for Phage Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, US
| | - Dongeun Yong
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Seoul, South Korea.
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46
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Heinrichs ME, Piedade GJ, Popa O, Sommers P, Trubl G, Weissenbach J, Rahlff J. Breaking the Ice: A Review of Phages in Polar Ecosystems. Methods Mol Biol 2024; 2738:31-71. [PMID: 37966591 DOI: 10.1007/978-1-0716-3549-0_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] [Indexed: 11/16/2023]
Abstract
Bacteriophages, or phages, are viruses that infect and replicate within bacterial hosts, playing a significant role in regulating microbial populations and ecosystem dynamics. However, phages from extreme environments such as polar regions remain relatively understudied due to challenges such as restricted ecosystem access and low biomass. Understanding the diversity, structure, and functions of polar phages is crucial for advancing our knowledge of the microbial ecology and biogeochemistry of these environments. In this review, we will explore the current state of knowledge on phages from the Arctic and Antarctic, focusing on insights gained from -omic studies, phage isolation, and virus-like particle abundance data. Metagenomic studies of polar environments have revealed a high diversity of phages with unique genetic characteristics, providing insights into their evolutionary and ecological roles. Phage isolation studies have identified novel phage-host interactions and contributed to the discovery of new phage species. Virus-like particle abundance and lysis rate data, on the other hand, have highlighted the importance of phages in regulating bacterial populations and nutrient cycling in polar environments. Overall, this review aims to provide a comprehensive overview of the current state of knowledge about polar phages, and by synthesizing these different sources of information, we can better understand the diversity, dynamics, and functions of polar phages in the context of ongoing climate change, which will help to predict how polar ecosystems and residing phages may respond to future environmental perturbations.
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Affiliation(s)
- Mara Elena Heinrichs
- Institute for Chemistry and Biology of the Marine Environment, Carl von Ossietzky University, Oldenburg, Germany
| | - Gonçalo J Piedade
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, 't Horntje, The Netherlands
- Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, Amsterdam, The Netherlands
| | - Ovidiu Popa
- Institute of Quantitative and Theoretical Biology Heinrich-Heine University Duesseldorf, Duesseldorf, Germany
| | | | - Gareth Trubl
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Julia Weissenbach
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Department of Biology and Environmental Science, Linnaeus University, Kalmar, Sweden
| | - Janina Rahlff
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Department of Biology and Environmental Science, Linnaeus University, Kalmar, Sweden.
- Aero-Aquatic Virus Research Group, Friedrich Schiller University Jena, Jena, Germany.
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47
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Rossi FPN, Flores VS, Uceda-Campos G, Amgarten DE, Setubal JC, da Silva AM. Comparative Analyses of Bacteriophage Genomes. Methods Mol Biol 2024; 2802:427-453. [PMID: 38819567 DOI: 10.1007/978-1-0716-3838-5_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2024]
Abstract
Bacterial viruses (bacteriophages or phages) are the most abundant and diverse biological entities on Earth. There is a renewed worldwide interest in phage-centered research motivated by their enormous potential as antimicrobials to cope with multidrug-resistant pathogens. An ever-growing number of complete phage genomes are becoming available, derived either from newly isolated phages (cultivated phages) or recovered from metagenomic sequencing data (uncultivated phages). Robust comparative analysis is crucial for a comprehensive understanding of genotypic variations of phages and their related evolutionary processes, and to investigate the interaction mechanisms between phages and their hosts. In this chapter, we present a protocol for phage comparative genomics employing tools selected out of the many currently available, focusing on complete genomes of phages classified in the class Caudoviricetes. This protocol provides accurate identification of similarities, differences, and patterns among new and previously known complete phage genomes as well as phage clustering and taxonomic classification.
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Affiliation(s)
| | - Vinicius Sousa Flores
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Sao Paulo, SP, Brazil
| | - Guillermo Uceda-Campos
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Sao Paulo, SP, Brazil
| | | | - João Carlos Setubal
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Sao Paulo, SP, Brazil
| | - Aline Maria da Silva
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Sao Paulo, SP, Brazil.
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48
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Le HT, Lubian AF, Bowring B, van der Poorten D, Iredell J, George J, Venturini C, Ahlenstiel G, Read S. Using a human colonoid-derived monolayer to study bacteriophage translocation. Gut Microbes 2024; 16:2331520. [PMID: 38517357 PMCID: PMC10962583 DOI: 10.1080/19490976.2024.2331520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/21/2024] [Accepted: 03/13/2024] [Indexed: 03/23/2024] Open
Abstract
Bacteriophages (phages) are estimated to be the most abundant microorganisms on Earth. Their presence in human blood suggests that they can translocate from non-sterile sites such as the gastrointestinal tract where they are concentrated. To examine phage translocation ex vivo, we adapted a primary colonoid monolayer model possessing cell diversity and architecture, and a thick layer of mucus akin to the colonic environment in vivo. We show that the colonoid monolayer is superior to the Caco-2 cell-line model, possessing intact and organized tight junctions and generating a physiologically relevant mucus layer. We showed, using two different phages, that translocation across the colonoid monolayer was largely absent in differentiated monolayers that express mucus, unlike Caco-2 cultures that expressed little to no mucus. By stimulating mucus production or removing mucus, we further demonstrated the importance of colonic mucus in preventing phage translocation. Finally, we used etiological drivers of gut permeability (alcohol, fat, and inflammatory cytokines) to measure their effects on phage translocation, demonstrating that all three stimuli have the capacity to amplify phage translocation. These findings suggest that phage translocation does occur in vivo but may be largely dependent on colonic mucus, an important insight to consider in future phage applications.
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Affiliation(s)
- Huu Thanh Le
- Blacktown Clinical School, Western Sydney University, Sydney, Australia
- Storr Liver Centre, Westmead Institute for Medical Research, Sydney, Australia
| | - Alicia Fajardo Lubian
- Centre for Infectious Diseases and Microbiology (CIDM), Westmead Institute for Medical Research, Sydney, Australia
- Sydney Infectious Diseases Institute, Faculty of Medicine and Health, University of Sydney, Sydney, Australia
| | - Bethany Bowring
- Centre for Infectious Diseases and Microbiology (CIDM), Westmead Institute for Medical Research, Sydney, Australia
| | - David van der Poorten
- Department of Hepatology and Gastroenterology, Westmead Hospital, Westmead, Australia
| | - Jonathan Iredell
- Centre for Infectious Diseases and Microbiology (CIDM), Westmead Institute for Medical Research, Sydney, Australia
- Sydney Infectious Diseases Institute, Faculty of Medicine and Health, University of Sydney, Sydney, Australia
| | - Jacob George
- Storr Liver Centre, Westmead Institute for Medical Research, Sydney, Australia
- Department of Hepatology and Gastroenterology, Westmead Hospital, Westmead, Australia
- School of Medicine, The University of Sydney, Sydney, Australia
| | - Carola Venturini
- Centre for Infectious Diseases and Microbiology (CIDM), Westmead Institute for Medical Research, Sydney, Australia
- Sydney School of Veterinary Science, The University of Sydney, Sydney, Australia
| | - Golo Ahlenstiel
- Blacktown Clinical School, Western Sydney University, Sydney, Australia
- Storr Liver Centre, Westmead Institute for Medical Research, Sydney, Australia
- Blacktown Mt Druitt Hospital, Sydney, Australia
| | - Scott Read
- Blacktown Clinical School, Western Sydney University, Sydney, Australia
- Storr Liver Centre, Westmead Institute for Medical Research, Sydney, Australia
- Blacktown Mt Druitt Hospital, Sydney, Australia
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49
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Cortés-Martín A, Denise R, Guerin E, Stockdale SR, Draper LA, Ross RP, Shkoporov AN, Hill C. Isolation and characterization of a novel lytic Parabacteroides distasonis bacteriophage φPDS1 from the human gut. Gut Microbes 2024; 16:2298254. [PMID: 38178369 PMCID: PMC10773633 DOI: 10.1080/19490976.2023.2298254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 12/19/2023] [Indexed: 01/06/2024] Open
Abstract
The human gut microbiome plays a significant role in health and disease. The viral component (virome) is predominantly composed of bacteriophages (phages) and has received significantly less attention in comparison to the bacteriome. This knowledge gap is largely due to challenges associated with the isolation and characterization of novel gut phages, and bioinformatic hurdles such as the lack of a universal phage marker gene and the absence of sufficient numbers of homologs in viral databases. Here, we describe the isolation from human feces of a novel lytic phage with siphovirus morphology, φPDS1, infecting Parabacteroides distasonis APCS2/PD, and classified within a newly proposed Sagittacolavirus genus. In silico and biological characterization of this phage is presented in this study. Key to the isolation of φPDS1 was the antibiotic-driven selective enrichment of the bacterial host in a fecal fermenter. Despite producing plaques and lacking genes associated with lysogeny, φPDS1 demonstrates the ability to coexist in liquid culture for multiple days without affecting the abundance of its host. Multiple studies have shown that changes in Parabacteroides distasonis abundance can be linked to various disease states, rendering this novel phage-host pair and their interactions of particular interest.
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Affiliation(s)
- Adrián Cortés-Martín
- APC Microbiome Ireland & School of Microbiology, University College Cork, Cork, Ireland
| | - Rémi Denise
- APC Microbiome Ireland & School of Microbiology, University College Cork, Cork, Ireland
| | - Emma Guerin
- APC Microbiome Ireland & School of Microbiology, University College Cork, Cork, Ireland
| | - Stephen R. Stockdale
- APC Microbiome Ireland & School of Microbiology, University College Cork, Cork, Ireland
| | - Lorraine A. Draper
- APC Microbiome Ireland & School of Microbiology, University College Cork, Cork, Ireland
| | - R. Paul Ross
- APC Microbiome Ireland & School of Microbiology, University College Cork, Cork, Ireland
| | - Andrey N. Shkoporov
- APC Microbiome Ireland & School of Microbiology, University College Cork, Cork, Ireland
| | - Colin Hill
- APC Microbiome Ireland & School of Microbiology, University College Cork, Cork, Ireland
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50
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Xiong L, Li Y, Zeng K, Wei Y, Li H, Ji X. Revealing viral diversity in the Napahai plateau wetland based on metagenomics. Antonie Van Leeuwenhoek 2023; 117:3. [PMID: 38153618 DOI: 10.1007/s10482-023-01912-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Accepted: 11/22/2023] [Indexed: 12/29/2023]
Abstract
We focused on exploring the diversity of viruses in the Napahai plateau wetland, a unique ecosystem located in Yunnan, China. While viruses in marine environments have been extensively studied for their influence on microbial metabolism and biogeochemical cycles, little is known about their composition and function in plateau wetlands. Metagenomic analysis was employed to investigate the viral diversity and biogeochemical impacts in the Napahai wetland. It revealed that the Caudoviricetes and Malgrandaviricetes class level was the most abundant viral category based on phylogenetic analysis. Additionally, a gene-sharing network highlighted the presence of numerous unexplored viruses and demonstrated their unique characteristics and significant variation within the viral community of the Napahai wetland. Furthermore, the study identified the auxiliary metabolic genes (AMGs). AMGs provide phages with additional functions, such as protection against host degradation and involvement in metabolic pathways, such as the pentose phosphate pathway and DNA biosynthesis. The viruses in the Napahai wetland were found to influence carbon, nitrogen, sulfur, and amino acid metabolism, indirectly contributing to biogeochemical cycling through these AMGs. Overall, the research sheds light on the diverse and unique viral communities in the Napahai plateau wetland and emphasizes the significant roles of viruses in microbial ecology. The findings contribute to a deeper understanding of the characteristics and ecological functions of viral communities in plateau wetland ecosystems.
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Affiliation(s)
- Lingling Xiong
- Faculty of Science and Technology, Kunming University of Science and Technology, Kunming, 650500, China
| | - Yanmei Li
- Faculty of Science and Technology, Kunming University of Science and Technology, Kunming, 650500, China
| | - Kun Zeng
- Faculty of Science and Technology, Kunming University of Science and Technology, Kunming, 650500, China
| | - Yunlin Wei
- Faculty of Science and Technology, Kunming University of Science and Technology, Kunming, 650500, China
| | - Haiyan Li
- Medical School, Kunming University of Science and Technology, Kunming, 650500, China.
| | - Xiuling Ji
- Faculty of Science and Technology, Kunming University of Science and Technology, Kunming, 650500, China.
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