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Characterization and genome analysis of Escherichia phage fBC-Eco01, isolated from wastewater in Tunisia. Arch Virol 2023; 168:44. [PMID: 36609878 PMCID: PMC9825357 DOI: 10.1007/s00705-022-05680-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 11/01/2022] [Indexed: 01/09/2023]
Abstract
The rise of antibiotic resistance in bacterial strains has led to vigorous exploration for alternative treatments. To this end, phage therapy has been revisited, and it is gaining increasing attention, as it may represent an efficient alternative for treating multiresistant pathogenic bacteria. Phage therapy is considered safe, and phages do not infect eukaryotic cells. There have been many studies investigating phage-host bacteria interactions and the ability of phages to target specific hosts. Escherichia coli is the causative agent of a multitude of infections, ranging from urinary tract infections to sepsis, with growing antibiotic resistance. In this study, we characterized the Escherichia phage fBC-Eco01, which was isolated from a water sample collected at Oued, Tunis. Electron microscopy showed that fBC-Eco01 phage particles have siphovirus morphology, with an icosahedral head of 61 ± 3 nm in diameter and a non-contractile tail of 94 ± 2 nm in length and 12 ± 0.9 nm in width. The genome of fBC-Eco01 is a linear double-stranded DNA of 43.466 bp with a GC content of 50.4%. Comparison to databases allowed annotation of the functions to 39 of the 78 predicted gene products. A single-step growth curve revealed that fBC-Eco01 has a latent period of 30 minutes and a burst size of 175 plaque-forming units (PFU) per infected cell. Genomic analysis indicated that fBC-Eco01 is a member of the subfamily Guernseyvirinae. It is most closely related to a group of phages of the genus Kagunavirus that infect Enterobacter, Raoultella, and Escherichia strains.
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Smith-Zaitlik T, Shibu P, McCartney AL, Foster G, Hoyles L, Negus D. Extended genomic analyses of the broad-host-range phages vB_KmiM-2Di and vB_KmiM-4Dii reveal slopekviruses have highly conserved genomes. MICROBIOLOGY (READING, ENGLAND) 2022; 168. [PMID: 36156193 DOI: 10.1099/mic.0.001247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
High levels of antimicrobial resistance among members of the Klebsiella oxytoca complex (KoC) have led to renewed interest in the use of bacteriophage (phage) therapy to tackle infections caused by these bacteria. In this study we characterized two lytic phages, vB_KmiM-2Di and vB_KmiM-4Dii, that were isolated from sewage water against two GES-5-positive Klebsiella michiganensis strains (PS_Koxy2 and PS_Koxy4, respectively). ViPTree analysis showed both phages belonged to the genus Slopekvirus. rpoB gene-based sequence analysis of 108 presumptive K. oxytoca isolates (n=59 clinical, n=49 veterinary) found K. michiganensis to be more prevalent (46 % clinical and 43 % veterinary, respectively) than K. oxytoca (40 % clinical and 6 % veterinary, respectively). Host range analysis against these 108 isolates found both vB_KmiM-2Di and vB_KmiM-4Dii showed broad lytic activity against KoC species. Several hypothetical homing endonuclease genes were encoded within the genomes of both phages, which may contribute to their broad host range. Differences in the tail fibre protein may explain the non-identical host range of the two phages. Pangenome analysis of 24 slopekviruses found that genomes within this genus are highly conserved, with more than 50 % of all predicted coding sequences representing core genes at ≥95 % identity and ≥70 % coverage. Given their broad host ranges, our results suggest vB_KmiM-2Di and vB_KmiM-4Dii represent attractive potential therapeutics. In addition, current recommendations for phage-based pangenome analyses may require revision.
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Affiliation(s)
| | - Preetha Shibu
- Life Sciences, University of Westminster, London, UK.,Present address: Berkshire and Surrey Pathology Services, Frimley Health NHS Trust, Wexham Park Hospital, Slough, UK
| | - Anne L McCartney
- Department of Food and Nutritional Sciences, University of Reading, Reading, UK
| | | | - Lesley Hoyles
- Department of Biosciences, Nottingham Trent University, Nottingham NG1 4FQ, UK
| | - David Negus
- Department of Biosciences, Nottingham Trent University, Nottingham NG1 4FQ, UK
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Rodea M GE, González-Villalobos E, Medina-Contreras O, Castelán-Sánchez HG, Aguilar-Rodea P, Velázquez-Guadarrama N, Hernández-Chiñas U, Eslava-Campos CA, Balcázar JL, Molina-López J. Genomic characterization of two bacteriophages (vB_EcoS-phiEc3 and vB_EcoS-phiEc4) belonging to the genus Kagunavirus with lytic activity against uropathogenic Escherichia coli. Microb Pathog 2022; 165:105494. [DOI: 10.1016/j.micpath.2022.105494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 03/16/2022] [Accepted: 03/17/2022] [Indexed: 11/29/2022]
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Fu P, Zhao Q, Shi L, Xiong Q, Ren Z, Xu H, Chai S, Xu Q, Sun X, Sang M. Identification and characterization of two bacteriophages with lytic activity against multidrug-resistant Escherichia coli. Virus Res 2020; 291:198196. [PMID: 33098914 DOI: 10.1016/j.virusres.2020.198196] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 10/02/2020] [Accepted: 10/10/2020] [Indexed: 01/21/2023]
Abstract
Escherichia coli is an opportunistic bacterial pathogen that causes a wide range of nosocomial infections. The emergence of multidrug resistance in E. coli poses a severe threat to global health. Phage therapies are an alternative method to control multidrug-resistant pathogens, which have been attracting increasing attention. Owing to their ability to lyse bacteria specifically and efficiently, bacteriophages are considered novel antimicrobial agents. In this study, we used multidrug-resistant E. coli as an indicator and isolated, characterized, and compared two new phages of the Siphoviridae family referred to as vB_EcoS_XF and vB_EcoS_XY2. These phages were able to infect several pathogenic multidrug-resistant E. coli strains. A short latent period and large burst size ensured their rapidly reproduction in host cells. Their tolerance of high temperatures and high pH levels meant that remained stable when used to control pathogenic E. coli strains. No obvious cytotoxicity was observed when either HEK293 T or A549 cells were incubated with these two phages. Mass spectrometry analysis allowed us to identify several phage-encoded proteins. Genomic analysis revealed that no toxic proteins or antibiotic proteins were encoded. Genome comparison and phylogenetic analysis indicated that the phages identified show high similarity with E. coli phages of the genus Kagunavirus. The desirable characteristics of the novel phages identified make them good potential therapeutic candidates, and components of phage cocktails to treat multidrug-resistant E. coli in the future.
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Affiliation(s)
- Pan Fu
- Center for Translational Medicine, Hubei Clinical Research Center of Parkinson's disease, Hubei Key Laboratory of Wudang Local Chinese Medicine Research, Xiangyang No.1 People's Hospital, Hubei University of Medicine, Xiangyang, 441000, China.
| | - Qiang Zhao
- Center for Translational Medicine, Hubei Clinical Research Center of Parkinson's disease, Hubei Key Laboratory of Wudang Local Chinese Medicine Research, Xiangyang No.1 People's Hospital, Hubei University of Medicine, Xiangyang, 441000, China.
| | - Li Shi
- Department of Clinical Laboratory, Xiangyang No. 1 People's Hospital, Hubei University of Medicine, Xiangyang, 441000, China.
| | - Qin Xiong
- Department of Clinical Laboratory, Xiangyang No. 1 People's Hospital, Hubei University of Medicine, Xiangyang, 441000, China.
| | - Zijing Ren
- Center for Translational Medicine, Hubei Clinical Research Center of Parkinson's disease, Hubei Key Laboratory of Wudang Local Chinese Medicine Research, Xiangyang No.1 People's Hospital, Hubei University of Medicine, Xiangyang, 441000, China.
| | - Hongxia Xu
- Center for Translational Medicine, Hubei Clinical Research Center of Parkinson's disease, Hubei Key Laboratory of Wudang Local Chinese Medicine Research, Xiangyang No.1 People's Hospital, Hubei University of Medicine, Xiangyang, 441000, China.
| | - Senmao Chai
- Center for Translational Medicine, Hubei Clinical Research Center of Parkinson's disease, Hubei Key Laboratory of Wudang Local Chinese Medicine Research, Xiangyang No.1 People's Hospital, Hubei University of Medicine, Xiangyang, 441000, China.
| | - Qianqian Xu
- Center for Translational Medicine, Hubei Clinical Research Center of Parkinson's disease, Hubei Key Laboratory of Wudang Local Chinese Medicine Research, Xiangyang No.1 People's Hospital, Hubei University of Medicine, Xiangyang, 441000, China.
| | - Xiaodong Sun
- Center for Translational Medicine, Hubei Clinical Research Center of Parkinson's disease, Hubei Key Laboratory of Wudang Local Chinese Medicine Research, Xiangyang No.1 People's Hospital, Hubei University of Medicine, Xiangyang, 441000, China.
| | - Ming Sang
- Center for Translational Medicine, Hubei Clinical Research Center of Parkinson's disease, Hubei Key Laboratory of Wudang Local Chinese Medicine Research, Xiangyang No.1 People's Hospital, Hubei University of Medicine, Xiangyang, 441000, China.
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