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Panhwar S, Çelikkan H, Evran E, Ekiz E, Ozkan Hukum K, Çetin D, Suludere Z, Hakki Boyaci I, Tamer U. Phage probe on RAFT polymer surface for rapid enumeration of E. coli K12. Bioelectrochemistry 2024; 160:108785. [PMID: 39094446 DOI: 10.1016/j.bioelechem.2024.108785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2024] [Revised: 07/24/2024] [Accepted: 07/26/2024] [Indexed: 08/04/2024]
Abstract
This study presents a simple, fast, and sensitive label-free sensing assay for the precise enumeration of modeled pathogenic Escherichia coli K12 (E. coli K12) bacteria for the first time. The method employs the covalent binding bacteriophage technique on the surface of a reversible addition-fragmentation chain transfer (RAFT) polymer film. The Nyquist plots obtained from electrochemical impedance spectroscopy (EIS) identified the charge transfer resistance Rct was calculated from a suitable electrochemical circuit model through an evaluation of the relevant parameter after the immobilization of the bacteriophage and the binding of specific E. coli K12. The impedimetric biosensor reveals specific and reproducible detection with sensitivity in the linear working range of 104.2-107.0 CFU/mL, a limit of detection (LOD) of 101.3 CFU/mL, and a short response time of 15 min. The SERS response validates the surface roughness and interaction of the SERS-tag with E. coli K12-modified electrodes. Furthermore, the covalently immobilized active phage selectivity was proved against various non-targeting bacterial strains in the presence of targeted E.coli K12 with a result of 94 % specificity and 98 % sensitivity. Therefore, the developed phage-based electrode surface can be used as a disposable, label-free impedimetric biosensor for rapid and real-time monitoring of serum samples.
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Affiliation(s)
- Sallahuddin Panhwar
- Department of Analytical Chemistry, Faculty of Pharmacy, Gazi University, 06330 Ankara, Türkiye; Department of Civil Engineering, National University of Sciences and Technology, Quetta 24090, Balochistan, Pakistan
| | - Hüseyin Çelikkan
- Gazi University, Faculty of Science, Department of Chemistry, Ankara, Türkiye
| | - Eylul Evran
- Department of Food Engineering, Faculty of Engineering, Hacettepe University, Beytepe 06800 Ankara, Türkiye
| | - Esra Ekiz
- Department of Food Engineering, Faculty of Engineering, Hacettepe University, Beytepe 06800 Ankara, Türkiye
| | - Kubra Ozkan Hukum
- Gazi University, Faculty of Science, Department of Chemistry, Ankara, Türkiye
| | - Demet Çetin
- Department of Mathematics and Science Education, Gazi Faculty of Education, Gazi University, Besevler, Ankara 06500, Türkiye
| | - Zekiye Suludere
- Faculty of Science, Department of Biology, Gazi University, 06500 Ankara, Türkiye
| | - Ismail Hakki Boyaci
- Department of Food Engineering, Faculty of Engineering, Hacettepe University, Beytepe 06800 Ankara, Türkiye
| | - Uğur Tamer
- Department of Analytical Chemistry, Faculty of Pharmacy, Gazi University, 06330 Ankara, Türkiye; METU MEMS Research and Application Center, Ankara, Türkiye.
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Lin W, Li D, Pan L, Li M, Tong Y. Cyanobacteria-cyanophage interactions between freshwater and marine ecosystems based on large-scale cyanophage genomic analysis. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 950:175201. [PMID: 39102952 DOI: 10.1016/j.scitotenv.2024.175201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Revised: 07/30/2024] [Accepted: 07/30/2024] [Indexed: 08/07/2024]
Abstract
The disparities in harmful algal blooms dynamics are largely attributed to variations in cyanobacteria populations within aquatic ecosystems. However, cyanobacteria-cyanophage interactions and their role in shaping cyanobacterial populations has been previously underappreciated. To address this knowledge gap, we isolated and sequenced 42 cyanophages from diverse water sources in China, with the majority (n = 35) originating from freshwater sources. We designated these sequences as the "Novel Cyanophage Genome sequence Collection" (NCGC). NCGC displayed notable genetic variations, with 95 % (40/42) of the sequences representing previously unidentified taxonomic ranks. By integrating NCGC with public data of cyanophages and cyanobacteria, we found evidence for more frequent historical cyanobacteria-cyanophage interactions in freshwater ecosystems. This was evidenced by a higher prevalence of prophage integrase-related genes in freshwater cyanophages (37.97 %) than marine cyanophages (7.42 %). In addition, freshwater cyanophages could infect a broader range of cyanobacteria orders (n = 4) than marine ones (n = 0). Correspondingly, freshwater cyanobacteria harbored more defense systems per million base pairs in their genomes, indicating more frequent phage infections. Evolutionary and cyanophage epidemiological studies suggest that interactions between cyanobacteria and cyanophages in freshwater and marine ecosystems are interconnected, and that brackish water can act as a transitional zone for freshwater and marine cyanophages. In conclusion, our research significantly expands the genetic information database of cyanophage, offering a wider selection of cyanophages to control harmful cyanobacterial blooms. Additionally, we represent a pioneering large-scale and comprehensive analysis of cyanobacteria and cyanophage sequencing data, and it provides theoretical guidance for the application of cyanophages in different environments.
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Affiliation(s)
- Wei Lin
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Dengfeng Li
- Key Laboratory of Marine Biotechnology of Zhejiang Province, School of Marine Sciences, Ningbo University, Ningbo 315211, China
| | - Lingting Pan
- Key Laboratory of Marine Biotechnology of Zhejiang Province, School of Marine Sciences, Ningbo University, Ningbo 315211, China
| | - Mengzhe Li
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China.
| | - Yigang Tong
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China; Beijing Advanced Innovation Center for Soft Matter Science and Engineering (BAIC-SM), Beijing University of Chemical Technology, Beijing 100029, China.
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3
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Monsibais AN, Tea O, Ghatbale P, Phan J, Lam K, Paulson M, Tran N, Suder DS, Blanc AN, Samillano C, Suh J, Dunham S, Gonen S, Pride D, Whiteson K. Enhanced Suppression of Stenotrophomonas maltophilia by a Three-Phage Cocktail: Genomic Insights and Kinetic Profiling. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.14.607921. [PMID: 39185190 PMCID: PMC11343209 DOI: 10.1101/2024.08.14.607921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/27/2024]
Abstract
In our era of rising antibiotic resistance, Stenotrophomonas maltophilia (STM) is an understudied, gram-negative, aerobic bacterium widespread in the environment and increasingly causing opportunistic infections. Treating STM infections remains difficult, leading to an increase in disease severity and higher hospitalization rates in people with Cystic Fibrosis (pwCF), cancer, and other immunocompromised health conditions. The lack of effective antibiotics has led to renewed interest in phage therapy; however, there is a need for well-characterized phages. In response to an oncology patient with a respiratory infection, we collected 18 phages from Southern California wastewater influent that exhibit different plaque morphology against STM host strain B28B, cultivated from a blood sample. Here, we characterize the genomes and life cycle kinetics of our STM phage collection. We hypothesize that genetically distinct phages give rise to unique lytic life cycles that can enhance bacterial killing when combined into a phage cocktail compared to the individual phages alone. We identified three genetically distinct clusters of phages, and a representative from each group was screened for potential therapeutic use and investigated for infection kinetics. The results demonstrated that the three-phage cocktail significantly suppressed bacterial growth compared to individual phages when observed for 48 hours. We also assessed the lytic impacts of our three-phage cocktail against a collection of 46 STM strains to determine if a multi-phage cocktail can expand the host range of individual phages. Our phages remained strain-specific and infect >50% of tested strains. The multi-phage cocktail maintains bacterial growth suppression and prevents the emergence of phage-resistant strains throughout our 40-hour assay. These findings suggest specialized phage cocktails may be an effective avenue of treatment for recalcitrant STM infections resistant to current antibiotics. IMPORTANCE Phage therapy could provide a vital strategy in the fight against antimicrobial resistance (AMR) bacterial infections; however, significant knowledge gaps remain. This study investigates phage cocktail development for the opportunistic pathogen Stenotrophomonas maltophilia (STM). Our findings contribute novel phages, their lytic characteristics, and limitations when exposed to an array of clinically relevant STM strains. Eighteen bacteriophages were isolated from wastewater influent from Escondido, California, and subjected to genomic analysis. We investigated genetically distinct phages to establish their infection kinetics and developed them into a phage cocktail. Our findings suggest that a genetically distinct STM phage cocktail provides an effective strategy for bacterial suppression of host strain B28B and five other clinically relevant STM strains. Phage therapy against STM remains poorly understood, as only 39 phages have been previously isolated. Future research into the underlying mechanism of how phage cocktails overwhelm the host bacteria will provide essential information that could aid in optimizing phage applications and impact alternative treatment options.
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Li X, Zhang B, Tong X, Zhou T, Li M, Barkema HW, Nobrega DB, Kastelic JP, Xu C, Han B, Gao J. Biological and genomic characterization of 4 novel bacteriophages isolated from sewage or the environment using non-aureus Staphylococci strains. Vet Microbiol 2024; 294:110133. [PMID: 38820726 DOI: 10.1016/j.vetmic.2024.110133] [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: 02/27/2024] [Revised: 05/14/2024] [Accepted: 05/27/2024] [Indexed: 06/02/2024]
Abstract
Non-aureus staphylococci (NAS) are an essential group of bacteria causing antimicrobial resistant intramammary infections in livestock, particularly dairy cows. Therefore, bacteriophages emerge as a potent bactericidal agent for NAS mastitis. This study aimed to obtain NAS-specific bacteriophages using bacterial strains isolated from cows with mastitis, subsequently evaluating their morphological, genomic, and lytic characteristics. Four distinct NAS bacteriophages were recovered from sewage or the environment of Chinese dairy farms; PT1-1, PT94, and PT1-9 were isolated using Staphylococcus chromogenes and PT1-4 using Staphylococcus gallinarum. Both PT1-1 (24/54, 44 %) and PT94 (28/54, 52 %) had broader lysis than PT1-4 (3/54, 6 %) and PT1-9 (10/54, 19 %), but PT1-4 and PT1-9 achieved cross-species lysis. All bacteriophages had a short latency period and good environmental tolerance, including surviving at pH=4-10 and at 30-60℃. Except for PT1-9, all bacteriophages had excellent bactericidal efficacy within 5 h of co-culture with host bacteria in vitro at various multiplicity of infection (MOIs). Based on whole genome sequencing, average nucleotide identity (ANI) analysis of PT1-1 and PT94 can be classified as the same species, consistent with whole-genome synteny analysis. Although motifs shared by the 4 bacteriophages differed little from those of other bacteriophages, a phylogenetic tree based on functional proteins indicated their novelty. Moreover, based on whole genome comparisons, we inferred that cross-species lysis of bacteriophage may be related to the presence of "phage tail fiber." In conclusion 4 novel NAS bacteriophages were isolated; they had good biological properties and unique genomes, with potential for NAS mastitis therapy.
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Affiliation(s)
- Xiaoping Li
- Department of Clinical Veterinary Medicine, College of Veterinary Medicine, China Agricultural University, Yuanmingyuan West Road, Beijing 100193, China
| | - Baoling Zhang
- Department of Clinical Veterinary Medicine, College of Veterinary Medicine, China Agricultural University, Yuanmingyuan West Road, Beijing 100193, China
| | - Xiaofang Tong
- Department of Clinical Veterinary Medicine, College of Veterinary Medicine, China Agricultural University, Yuanmingyuan West Road, Beijing 100193, China
| | - Tao Zhou
- Department of Clinical Veterinary Medicine, College of Veterinary Medicine, Sichuan Agricultural University, Huimin Road, Chengdu 611130, China
| | - Moli Li
- Department of Clinical Veterinary Medicine, College of Veterinary Medicine, China Agricultural University, Yuanmingyuan West Road, Beijing 100193, China
| | - Herman W Barkema
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Diego B Nobrega
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - John P Kastelic
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Chuang Xu
- Department of Clinical Veterinary Medicine, College of Veterinary Medicine, China Agricultural University, Yuanmingyuan West Road, Beijing 100193, China
| | - Bo Han
- Department of Clinical Veterinary Medicine, College of Veterinary Medicine, China Agricultural University, Yuanmingyuan West Road, Beijing 100193, China
| | - Jian Gao
- Department of Clinical Veterinary Medicine, College of Veterinary Medicine, China Agricultural University, Yuanmingyuan West Road, Beijing 100193, China.
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Li S, Xu M, Yang D, Yang M, Wu H, Li X, Yang C, Fang Z, Wu Q, Tan L, Xiao W, Weng Q. Characterization and genomic analysis of a lytic Stenotrophomonas maltophilia short-tailed phage A1432 revealed a new genus of the family Mesyanzhinovviridae. Front Microbiol 2024; 15:1400700. [PMID: 38993489 PMCID: PMC11236537 DOI: 10.3389/fmicb.2024.1400700] [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: 03/14/2024] [Accepted: 06/14/2024] [Indexed: 07/13/2024] Open
Abstract
Stenotrophomonas maltophilia (S. maltophilia) is an emerging opportunistic pathogen that exhibits resistant to a majority of commonly used antibiotics. Phages have the potential to serve as an alternative treatment for S. maltophilia infections. In this study, a lytic phage, A1432, infecting S. maltophilia YCR3A-1, was isolated and characterized from a karst cave. Transmission electron microscopy revealed that phage A1432 possesses an icosahedral head and a shorter tail. Phage A1432 demonstrated a narrow host range, with an optimal multiplicity of infection of 0.1. The one-step growth curve indicated a latent time of 10 min, a lysis period of 90 min, a burst size of 43.2 plaque-forming units per cell. In vitro bacteriolytic activity test showed that phage A1432 was capable to inhibit the growth of S. maltophilia YCR3A-1 in an MOI-dependent manner after 2 h of co-culture. BLASTn analysis showed that phage A1432 genome shares the highest similarity (81.46%) with Xanthomonas phage Xoo-sp2 in the NCBI database, while the query coverage was only 37%. The phage contains double-stranded DNA with a genome length of 61,660 bp and a GC content of 61.92%. It is predicted to have 79 open reading frames and one tRNA, with no virulence or antibiotic resistance genes. Phylogenetic analysis using terminase large subunit and DNA polymerase indicated that phage A1432 clustered with members of the Bradleyvirinae subfamily but diverged into a distinct branch. Further phylogenetic comparison analysis using Average Nucleotide Identity, proteomic phylogenetic analysis, genomic network analysis confirmed that phage A1432 belongs to a novel genus within the Bradleyvirinae subfamily, Mesyanzhinovviridae family. Additionally, phylogenetic analysis of the so far isolated S. maltophilia phages revealed significant genetic diversity among these phages. The results of this research will contribute valuable information for further studies on their morphological and genetic diversity, will aid in elucidating the evolutionary mechanisms that give rise to them.
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Affiliation(s)
- Shixia Li
- School of Life Sciences, Guizhou Normal University, Guiyang, China
| | - Man Xu
- School of Life Sciences, Guizhou Normal University, Guiyang, China
| | - Deying Yang
- School of Life Sciences, Guizhou Normal University, Guiyang, China
| | - Mei Yang
- School of Life Sciences, Guizhou Normal University, Guiyang, China
| | - Hejing Wu
- School of Life Sciences, Guizhou Normal University, Guiyang, China
| | - Xuelian Li
- School of Life Sciences, Guizhou Normal University, Guiyang, China
| | - Changzhou Yang
- School of Life Sciences, Guizhou Normal University, Guiyang, China
| | - Zheng Fang
- School of Life Sciences, Guizhou Normal University, Guiyang, China
| | - Qingshan Wu
- School of Life Sciences, Guizhou Normal University, Guiyang, China
| | - Leitao Tan
- School of Life Sciences, Guizhou Normal University, Guiyang, China
| | - Wei Xiao
- Yunnan Institute of Microbiology, Yunnan International Joint Laboratory of Virology and Immunology, Yunnan University, Kunming, China
| | - Qingbei Weng
- School of Life Sciences, Guizhou Normal University, Guiyang, China
- Qiannan Normal University for Nationalities, Duyun, China
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6
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Wang M, Zhao J, Liu Y, Huang S, Zhao C, Jiang Z, Gu Y, Xiao J, Wu Y, Ying R, Zhang J, Tian W. Deciphering soil resistance and virulence gene risks in conventional and organic farming systems. JOURNAL OF HAZARDOUS MATERIALS 2024; 468:133788. [PMID: 38367443 DOI: 10.1016/j.jhazmat.2024.133788] [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: 10/21/2023] [Revised: 01/22/2024] [Accepted: 02/12/2024] [Indexed: 02/19/2024]
Abstract
Organic farming is a sustainable agricultural practice emphasizing natural inputs and ecological balance, and has garnered significant attention for its potential health and environmental benefits. However, a comprehensive evaluation of the emergent contaminants, particularly resistance and virulence genes within organic farming system, remains elusive. Here, a total of 36 soil samples from paired conventional and organic vegetable farms were collected from Jiangsu province, China. A systematic metagenomic approach was employed to investigate the prevalence, dispersal capability, pathogenic potential, and drivers of resistance and virulence genes across both organic and conventional systems. Our findings revealed a higher abundance of antibiotic resistance genes (ARGs), biocide resistance genes (BRGs), and virulence factor genes (VFGs) in organic farming system, with ARGs exhibiting a particularly notable increase of 10.76% compared to the conventional one. Pathogens such as Pseudomonas aeruginosa, Escherichia coli, and Mycobacterium tuberculosis were hosts carrying all four gene categories, highlighting their potential health implications. The neutral community model captured 77.1% and 71.9% of the variance in community dynamics within the conventional and organic farming systems, respectively, indicating that stochastic process was the predominant factor shaping gene communities. The relative smaller m value calculated in organic farming system (0.021 vs 0.023) indicated diminished gene exchange with external sources. Moreover, farming practices were observed to influence the resistance and virulence gene landscape by modifying soil properties, managing heavy metal stress, and steering mobile genetic elements (MGEs) dynamics. The study offers insights that can guide agricultural strategies to address potential health and ecological concerns.
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Affiliation(s)
- Mengmeng Wang
- Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment (MEE), Nanjing 210042, Jiangsu, China
| | - Jiayin Zhao
- Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment (MEE), Nanjing 210042, Jiangsu, China
| | - Yu Liu
- Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment (MEE), Nanjing 210042, Jiangsu, China
| | - Sijie Huang
- Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment (MEE), Nanjing 210042, Jiangsu, China
| | - Caiyi Zhao
- Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment (MEE), Nanjing 210042, Jiangsu, China
| | - Zhongkun Jiang
- Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment (MEE), Nanjing 210042, Jiangsu, China; College of Agricultural Science and Engineering, Hohai University, Nanjing 210098, Jiangsu, China
| | - Yongjing Gu
- Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment (MEE), Nanjing 210042, Jiangsu, China; College of Agricultural Science and Engineering, Hohai University, Nanjing 210098, Jiangsu, China
| | - Jian Xiao
- Key Laboratory of Agrometeorology of Jiangsu Province, School of Ecology and Applied Meteorology, Nanjing University of Information Science & Technology, Nanjing 210044, China
| | - Yuncheng Wu
- Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment (MEE), Nanjing 210042, Jiangsu, China.
| | - Rongrong Ying
- Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment (MEE), Nanjing 210042, Jiangsu, China.
| | - Jibing Zhang
- Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment (MEE), Nanjing 210042, Jiangsu, China
| | - Wei Tian
- Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment (MEE), Nanjing 210042, Jiangsu, China
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Morozova VV, Yakubovskij VI, Baykov IK, Kozlova YN, Tikunov AY, Babkin IV, Bardasheva AV, Zhirakovskaya EV, Tikunova NV. StenM_174: A Novel Podophage That Infects a Wide Range of Stenotrophomonas spp. and Suggests a New Subfamily in the Family Autographiviridae. Viruses 2023; 16:18. [PMID: 38275953 PMCID: PMC10820202 DOI: 10.3390/v16010018] [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: 11/11/2023] [Revised: 12/13/2023] [Accepted: 12/20/2023] [Indexed: 01/27/2024] Open
Abstract
Stenotrophomonas maltophilia was discovered as a soil bacterium associated with the rhizosphere. Later, S. maltophilia was found to be a multidrug-resistant hospital-associated pathogen. Lytic bacteriophages are prospective antimicrobials; therefore, there is a need for the isolation and characterization of new Stenotrophomonas phages. The phage StenM_174 was isolated from litter at a poultry farm using a clinical strain of S. maltophilia as the host. StenM_174 reproduced in a wide range of clinical and environmental strains of Stenotrophomonas, mainly S. maltophilia, and it had a podovirus morphotype. The length of the genomic sequence of StenM_174 was 42,956 bp, and it contained 52 putative genes. All genes were unidirectional, and 31 of them encoded proteins with predicted functions, while the remaining 21 were identified as hypothetical ones. Two tail spike proteins of StenM_174 were predicted using AlphaFold2 structural modeling. A comparative analysis of the genome shows that the Stenotrophomonas phage StenM_174, along with the phages Ponderosa, Pepon, Ptah, and TS-10, can be members of the new putative genus Ponderosavirus in the Autographiviridae family. In addition, the analyzed data suggest a new subfamily within this family.
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Affiliation(s)
- Vera V. Morozova
- Laboratory of Molecular Microbiology, Institute of Chemical Biology and Fundamental Medicine Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia; (V.I.Y.); (A.Y.T.); (I.V.B.)
| | - Vyacheslav I. Yakubovskij
- Laboratory of Molecular Microbiology, Institute of Chemical Biology and Fundamental Medicine Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia; (V.I.Y.); (A.Y.T.); (I.V.B.)
- Faculty of Natural Sciences, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Ivan K. Baykov
- Laboratory of Molecular Microbiology, Institute of Chemical Biology and Fundamental Medicine Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia; (V.I.Y.); (A.Y.T.); (I.V.B.)
- Shared Research Facility “Siberian Circular Photon Source” (SRF “SKIF”) of Boreskov Institute of Catalysis SB RAS, Novosibirsk 630090, Russia
| | - Yuliya N. Kozlova
- Laboratory of Molecular Microbiology, Institute of Chemical Biology and Fundamental Medicine Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia; (V.I.Y.); (A.Y.T.); (I.V.B.)
| | - Artem Yu. Tikunov
- Laboratory of Molecular Microbiology, Institute of Chemical Biology and Fundamental Medicine Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia; (V.I.Y.); (A.Y.T.); (I.V.B.)
| | - Igor V. Babkin
- Laboratory of Molecular Microbiology, Institute of Chemical Biology and Fundamental Medicine Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia; (V.I.Y.); (A.Y.T.); (I.V.B.)
| | - Alevtina V. Bardasheva
- Laboratory of Molecular Microbiology, Institute of Chemical Biology and Fundamental Medicine Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia; (V.I.Y.); (A.Y.T.); (I.V.B.)
| | - Elena V. Zhirakovskaya
- Laboratory of Molecular Microbiology, Institute of Chemical Biology and Fundamental Medicine Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia; (V.I.Y.); (A.Y.T.); (I.V.B.)
| | - Nina V. Tikunova
- Laboratory of Molecular Microbiology, Institute of Chemical Biology and Fundamental Medicine Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia; (V.I.Y.); (A.Y.T.); (I.V.B.)
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8
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Koshy CM, Sugumar S. Isolation, characterization, and genome analysis of novel bacteriophage - Stenotrophomonas phageCM1. Microb Pathog 2023; 185:106403. [PMID: 37879452 DOI: 10.1016/j.micpath.2023.106403] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Revised: 10/13/2023] [Accepted: 10/17/2023] [Indexed: 10/27/2023]
Abstract
A common environmental bacteria called Stenotrophomonas maltophilia has become an organism responsible for significant nosocomial infection, mortality in immunocompromised patients, and significantly increasing morbidity and is challenging to treat due to the antibiotic resistance activity of the organism. and bacteriophage therapy is one of the promising treatments against the organism. In this research, we isolated, identified, and characterized Stenotrophomonas phage CM1 against S. maltophilia. Stenotrophomonas phage CM1 head was measured to have a diameter of around 224.25 nm and a tail length of about 159 nm. The phage was found to have noticeable elongated tail spikes around 125 nm in length, the Myoviridae family of viruses, which is categorized under the order Caudovirales. The ideal pH for growth was around 7, demonstrated good thermal stability when incubated at 37-60 °C for 30 min or 60 min, and phage infectivity decreased marginally after 30 min of incubation at 1-5% chloroform concentration. Phage was 3,19,518 base pairs long and had an averaged G + C composition of 43.9 %; 559 open-reading frames (ORFs) were found in the bacteriophage genome, in which 508 of them are hypothetical proteins, 22 of them are other known proteins, 29 of them are tRNAs, and one of them is restriction enzyme. A phylogenetic tree was reconstructed, demonstrating that CM1 shares a close evolutionary relationship with other Stenotrophomonas phages.
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Affiliation(s)
- Calmly M Koshy
- Department of Genetic Engineering, Faculty of Engineering and Technology, School of Bioengineering, SRM Institute of Science and Technology, SRM Nagar, Kattankulathur, Kanchipuram, Chennai, Tamil Nadu, 603203, India.
| | - Shobana Sugumar
- Department of Genetic Engineering, Faculty of Engineering and Technology, School of Bioengineering, SRM Institute of Science and Technology, SRM Nagar, Kattankulathur, Kanchipuram, Chennai, Tamil Nadu, 603203, India.
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9
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Dong Y, Huang Y, Fan H, Song L, An X, Xu S, Li M, Tong Y. Characterization, complete genome sequencing, and CRISPR/Cas9 system-based decontamination of a novel Escherichia coli phage TR1 from fermentation substrates. Front Microbiol 2023; 14:1230775. [PMID: 37637117 PMCID: PMC10450929 DOI: 10.3389/fmicb.2023.1230775] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Accepted: 07/25/2023] [Indexed: 08/29/2023] Open
Abstract
Phage contamination has become a major concern for industrial bacteria, such as Escherichia coli BL21(DE3), used in fermentation processes. Herein, we report a CRISPR/Cas9 defense system-based strategy to precisely prey and degrade phage DNA to decontaminate target phages. First, we isolated a novel phage from fermentation substrates with BL21(DE3) as the host, named TR1. It showed a typical podovirus morphology with a head diameter of 51.46 ± 2.04 nm and a tail length of 9.31 ± 2.77 nm. The burst size of phage TR1 was 151 PFU/cell, suggesting its strong fecundity in the fermentation system. Additionally, whole-genome sequencing revealed that phage TR1 has a DNA genome of 44,099 bp in length with a 43.8% GC content, encoding a total of 68 open reading frames. Comparative genomics and phylogenetic analysis designated this phage to be a new species of the genus Christensenvirus. To counteract phage TR1, we employed the CRISPR/Cas9 system-based strategy and constructed two phage-resistant E. coli strains, BL21-C and BL21-T, based on conserved genes. Both EOP assays and growth curves indicated strong phage resistance of the recombinant strains, without affecting cell growth. Therefore, this study aimed to provide a resilient strategy to respond to ever-changing phages and ongoing phage-host arm race in industrial fermentation environments by the personalized design of spacers in the recombinant CRISPR/Cas system-containing plasmid. More importantly, our research sparks the use of phage defense mechanism to prevent phage contamination in extensive biotechnological applications.
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Affiliation(s)
- Yuqi Dong
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Yunfei Huang
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Huahao Fan
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Lihua Song
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Xiaoping An
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Shan Xu
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Mengzhe Li
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
- Qinhuangdao Bohai Biological Research Institute, Beijing University of Chemical Technology, Qinhuangdao, Hebei, China
| | - Yigang Tong
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, Beijing, China
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Song F, Sheng J, Tan J, Xie H, Wang X, Guo W. Characterization of an Enterococcus faecalis bacteriophage SFQ1 as a potential therapeutic agent. Front Microbiol 2023; 14:1210319. [PMID: 37426023 PMCID: PMC10324664 DOI: 10.3389/fmicb.2023.1210319] [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: 04/22/2023] [Accepted: 06/07/2023] [Indexed: 07/11/2023] Open
Abstract
Enterococcus faecalis is a well-established resident of the human gastrointestinal tract and is also a major cause of human infections. Unfortunately, therapeutic options for E. faecalis infections remain limited, particularly with the emergence of vancomycin-resistant strains in hospital settings. Consequently, there has been a renewed interest in phage therapy as an alternative to antibiotics. In this study, we have isolated a bacteriophage, vB_EfaS-SFQ1, from hospital sewage, which effectively infects E. faecalis strain EFS01. Phage SFQ1 is a siphovirus and exhibits a relatively broad host range. Furthermore, it has a short latent period of approximately 10 min and a large burst size of about 110 PFU/cell at a multiplicity of infection (MOI) of 0.01, and it could effectively disrupt the biofilms formed by E. faecalis. Thus, this study provides a detailed characterization of E. faecalis phage SFQ1, which has great potential for treating E. faecalis infections.
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Affiliation(s)
- Fuqiang Song
- Department of Medical Laboratory, The General Hospital of Western Theater Command, Chengdu, China
| | - Jun Sheng
- Department of Orthopaedics, The General Hospital of Western Theater Command, Chengdu, China
| | - Jishan Tan
- Department of Medical Laboratory, The General Hospital of Western Theater Command, Chengdu, China
| | - Huajie Xie
- Department of Medical Laboratory, The General Hospital of Western Theater Command, Chengdu, China
| | - Xiaoyu Wang
- Department of Clinical Pharmacy, The General Hospital of Western Theater Command, Chengdu, China
| | - Wenqiong Guo
- School of Nursing, Chengdu Medical College, Chengdu, China
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