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Paranos P, Pournaras S, Meletiadis J. A single-layer spot assay for easy, fast, and high-throughput quantitation of phages against multidrug-resistant Gram-negative pathogens. J Clin Microbiol 2024:e0074324. [PMID: 39072625 DOI: 10.1128/jcm.00743-24] [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: 05/17/2024] [Accepted: 07/16/2024] [Indexed: 07/30/2024] Open
Abstract
Double-layer agar (DLA) overlay plaque assay is the gold standard for phage enumeration. However, it is cumbersome and time-consuming. Given the great interest in phage therapy, we explored alternative assays for phage quantitation. A total of 16 different phages belonging to Myoviridae, Siphoviridae, and Podoviridae families were quantitated with five K. pneumoniae, eight P. aeruginosa, and three A. baumannii host isolates. Phages were quantitated with the standard DLA assay (10 mL of LB soft agar 0.7% on LB hard agar 1.5%) and the new single-layer agar (SLA) assay (10 mL of LB soft agar 0.7%) with phages spread (spread) into or spotted (spot) onto soft agar. Phage concentrations with each assay were correlated with the standard assay, and the relative and absolute differences between each assay and the standard double-layer agar spread were calculated. Phage concentrations 1 × 104-8.3 x1012 PFU/mL with the standard DLA assay were quantitated with SLA-spread, SLA-spot, and DLA-spot assays, and the median (range) relative and absolute differences were <10% and <0.98 log10PFU/mL, respectively, for all phage/bacterial species (ANOVA P = 0.1-0.43), and they were highly correlated (r > 0.77, P < 0.01). Moreover, plaques could be quantified at 37°C after 4-h incubation for K. pneumoniae phages and 6-h incubation for P. aeruginosa and A. baumannii phages, and estimated concentrations remained the same over 24 hours. Compared to DLA assay, the SLA-spot assay required less media, it was 10 times faster, and generated same-day results. The SLA-spot assay was cheaper, faster, easier to perform, and generated similar phage concentrations as the standard DLA-spread assay.
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Affiliation(s)
- Paschalis Paranos
- Clinical Microbiology Laboratory, Attikon University Hospital, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Spyros Pournaras
- Clinical Microbiology Laboratory, Attikon University Hospital, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Joseph Meletiadis
- Clinical Microbiology Laboratory, Attikon University Hospital, Medical School, National and Kapodistrian University of Athens, Athens, Greece
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2
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Ndiaye I, Debarbieux L, Diagne MM, Sow O, Cissé A, Ba BS, Fall C, Dieye Y, Dia N, Seck A, de Magny GC. Complete genome sequences of two Klebsiella pneumoniae phages from Dakar, Senegal. Microbiol Resour Announc 2024; 13:e0004724. [PMID: 38376338 PMCID: PMC11209732 DOI: 10.1128/mra.00047-24] [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: 01/18/2024] [Accepted: 02/11/2024] [Indexed: 02/21/2024] Open
Abstract
Two bacteriophages (phages) of Klebsiella pneumoniae were isolated from sewage water collected from Dakar, Senegal. Phage vKpIN17 belongs to the Przondovirus genus within the Autographiviridae family, with double-stranded DNA genomes, whereas vKpIN18 belongs to the Webervirus genus of the Drexlerviridae family.
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Affiliation(s)
- Issa Ndiaye
- Pole de Microbiologie, Institut Pasteur de Dakar, Dakar, Senegal
- Faculté de Médecine, Pharmacie et Odontostomatologie, Université Cheikh Anta Diop, Dakar, Senegal
| | - Laurent Debarbieux
- Laboratoire de Bactériophage, Bactérie, Hôte, Département de Microbiologie, Institut Pasteur Paris, Paris, France
| | | | - Ousmane Sow
- Pole de Microbiologie, Institut Pasteur de Dakar, Dakar, Senegal
| | - Abdoulaye Cissé
- Pole de Microbiologie, Institut Pasteur de Dakar, Dakar, Senegal
| | | | - Cheikh Fall
- Pole de Microbiologie, Institut Pasteur de Dakar, Dakar, Senegal
| | - Yakhya Dieye
- Pole de Microbiologie, Institut Pasteur de Dakar, Dakar, Senegal
| | - Ndongo Dia
- Département de Virologie, Institut Pasteur de Dakar, Dakar, Senegal
| | - Abdoulaye Seck
- Pole de Microbiologie, Institut Pasteur de Dakar, Dakar, Senegal
- Faculté de Médecine, Pharmacie et Odontostomatologie, Université Cheikh Anta Diop, Dakar, Senegal
| | - Guillaume Constantin de Magny
- MIVEGEC, Univ. Montpellier, CNRS, IRD, Montpellier, France
- MEEDiN, Montpellier Ecology and Evolution of Disease Network, Montpellier, France
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3
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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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Li F, Li L, Na S, Zhao J, Liu F, Liu P, Li Y, Li M, Lei M, Zhang D, Nazir A, Wang G. Isolation, characterization and genomic analysis of a novel phage IME178 with lytic activity against Escherichia coli. Microb Pathog 2023; 179:106099. [PMID: 37060965 DOI: 10.1016/j.micpath.2023.106099] [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: 02/07/2023] [Revised: 04/04/2023] [Accepted: 04/05/2023] [Indexed: 04/17/2023]
Abstract
Bacteriophages have been used in phage therapy for the treatment of bacterial infections. They are biological agents that used for management of diseases caused by resistant bacteria. As compared to antibiotics, phages can kill bacteria specifically, requiring more awareness about phage-host interactions by exploring new phages. Escherichia coli (E. coli) is a conditional pathogen and cause infections like pneumonia and diarrhea in hospitalized patients. In the current research work, a virus IME178, a novel strain, was extracted from the sewage of hospital against the clinical E. coli of multidrug resistant nature. Genomic characterization and transmission electron microscopy have exhibited relation of phage to the Tequintavirus genus, Demerecviridae family. The Phage IME178's double-stranded DNA genome was 108588 bp long, with a GC content of 39%. The phage genome transcribes 155 open reading frames, 72 are hypothetical proteins, 81 have putative functions assigned to them, and two are unknown to any database. A total number of 19 tRNA genes were found in the genome of this phage. There were no genes associated with virulence or drug resistance in the phage genome. According to a comparative genomic analysis, the genomic sequence of phage IME178 is 91% identical to E. coli phage phiLLS (NC 047822.1). The phage's host range and one-step growth curve were also estimated. As per genomic and bioinformatics analysis findings, Phage IME178, a propitious biological agent that infects E. coli and have the potential to use in phage therapies.
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Affiliation(s)
- Fei Li
- Center for Clinical Laboratory, The Affiliated Taian City Central Hospital of Qingdao University, Taian, 271000, Shandong, China.
| | - Lu Li
- Physical and Chemical Laboratory, Taian Center for Disease Control and Prevention, Taian, 271000, Shandong, China
| | - Shi Na
- Center for Clinical Laboratory, The Affiliated Taian City Central Hospital of Qingdao University, Taian, 271000, Shandong, China
| | - Jian Zhao
- Department of Orthopedics, The Affiliated Taian City Central Hospital of Qingdao University, Taian, 271000, Shandong, China
| | - Fei Liu
- Department of General Surgury, The Affiliated Taian City Central Hospital of Qingdao University, Taian, 271000, Shandong, China
| | - Pengfei Liu
- Clinical Psychology, The Affiliated Taian City Central Hospital of Qingdao University, Taian, 271000, Shandong, China
| | - Yuexiu Li
- Department of Stomatology, The Affiliated Taian City Central Hospital of Qingdao University, Taian, 271000, Shandong, China
| | - Ming Li
- Department of Gastroenterology, The Affiliated Taian City Central Hospital of Qingdao University, Taian, 271000, Shandong, China
| | - Ming Lei
- Department of Minimally Invasive Cancer, The Affiliated Taian City Central Hospital of Qingdao University, Taian, 271000, Shandong, China.
| | - Deqing Zhang
- Center for Clinical Laboratory, The Affiliated Taian City Central Hospital of Qingdao University, Taian, 271000, Shandong, China.
| | - Amina Nazir
- Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, 250000, Shandong, China.
| | - Guojun Wang
- Department of Neurosurgery, The Affiliated Taian City Central Hospital of Qingdao University, Taian, 271000, Shandong, China.
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Characterization of the novel temperate Staphylococcus haemolyticus phage IME1365_01. Arch Virol 2023; 168:41. [PMID: 36609576 DOI: 10.1007/s00705-022-05650-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2022] [Accepted: 10/03/2022] [Indexed: 01/09/2023]
Abstract
The presence of a novel functional prophage, IME1365_01, was predicted from bacterial high-throughput sequencing data and then successfully induced from Staphylococcus haemolyticus by mitomycin C treatment. Transmission electron microscopy showed that phage IME1365_01 has an icosahedral head (43 nm in diameter) and a long tail (172 nm long). This phage possesses a double-stranded DNA genome of 44,875 bp with a G+C content of 35.35%. A total of 63 putative open reading frames (ORFs) were identified in its genome. BLASTn analysis revealed that IME1365_01 is similar to Staphylococcus phage vB_SepS_E72, but with a genome homology coverage of only 26%. The phage genome does not have fixed termini. In ORF24 of phage IME1365_01, a conserved Toll-interleukin-1 receptor domain of the TIR_2 superfamily (accession no. c123749) is located at its N-terminus, and this might serve as a component of an anti-bacterial system. In conclusion, we developed a platform to obtain active temperate phage from prediction, identification, and induction from its bacterial host. After mass screening using this platform, numerous temperate phages and their innate anti-bacterial elements can provide extensive opportunities for therapy against bacterial (especially drug-resistant bacterial) infections.
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Li T, Zhao X, Wang X, Wang Z, Tian C, Shi W, Qi Y, Wei H, Song C, Xue H, Gou H. Characterization and Preliminary Application of Phage Isolated From Listeria monocytogenes. Front Vet Sci 2022; 9:946814. [PMID: 35990275 PMCID: PMC9387353 DOI: 10.3389/fvets.2022.946814] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 06/20/2022] [Indexed: 11/13/2022] Open
Abstract
Listeria monocytogenes (LM) is one of the four major foodborne bacteria that cause bacteremia and meningitis. To explore the control of listeriosis with natural phages, we used the double-layer agar plate method to isolate LM from slaughterhouse sewage and designated LP8. The result of electron microscopy indicated that the phage belonged to the family of Myoviridae. Whole-genome sequencing indicated that the genome size of LP8 is 87,038 bp and contains 120 genes. Mice were infected with LM and treated with penicillin G sodium, LP8, and the combination of these two. From the levels of lymphocyte subsets (CD4+, CD8+), the expression of cytokines (TNF-α, IL1β, IL-10, and IFN-γ), observation of pathological changes in organs (heart, liver, spleen, kidney, and brain), and the bacterial load of the spleen, we concluded the therapeutic effect of LP8 against listeriosis and demonstrate the feasibility of a combined therapy to reduce the use of antibiotics. This provides a new avenue for the treatment of listeriosis.
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Affiliation(s)
- Tianhao Li
- College of Veterinary Medical, Gansu Agricultural University, Lanzhou, China
| | - Xuehui Zhao
- College of Veterinary Medical, Gansu Agricultural University, Lanzhou, China
| | - Xuejian Wang
- Infectious Diseases Section, Xigu District Animal Disease Prevention and Control Center, Lanzhou, China
| | - Zijian Wang
- Infectious Diseases Section, Gansu Province Animal Disease Prevention and Control Center, Lanzhou, China
| | - Changqing Tian
- College of Veterinary Medical, Gansu Agricultural University, Lanzhou, China
| | - Wenjing Shi
- College of Veterinary Medical, Gansu Agricultural University, Lanzhou, China
| | - Yumei Qi
- College of Veterinary Medical, Gansu Agricultural University, Lanzhou, China
| | - Huilin Wei
- College of Veterinary Medical, Gansu Agricultural University, Lanzhou, China
| | - Chen Song
- College of Veterinary Medical, Gansu Agricultural University, Lanzhou, China
| | - Huiwen Xue
- College of Veterinary Medical, Gansu Agricultural University, Lanzhou, China
- *Correspondence: Huiwen Xue
| | - Huitian Gou
- College of Veterinary Medical, Gansu Agricultural University, Lanzhou, China
- Huitian Gou
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7
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Flagellotropic Bacteriophages: Opportunities and Challenges for Antimicrobial Applications. Int J Mol Sci 2022; 23:ijms23137084. [PMID: 35806089 PMCID: PMC9266447 DOI: 10.3390/ijms23137084] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 06/18/2022] [Accepted: 06/21/2022] [Indexed: 12/22/2022] Open
Abstract
Bacteriophages (phages) are the most abundant biological entities in the biosphere. As viruses that solely infect bacteria, phages have myriad healthcare and agricultural applications including phage therapy and antibacterial treatments in the foodservice industry. Phage therapy has been explored since the turn of the twentieth century but was no longer prioritized following the invention of antibiotics. As we approach a post-antibiotic society, phage therapy research has experienced a significant resurgence for the use of phages against antibiotic-resistant bacteria, a growing concern in modern medicine. Phages are extraordinarily diverse, as are their host receptor targets. Flagellotropic (flagellum-dependent) phages begin their infection cycle by attaching to the flagellum of their motile host, although the later stages of the infection process of most of these phages remain elusive. Flagella are helical appendages required for swimming and swarming motility and are also of great importance for virulence in many pathogenic bacteria of clinical relevance. Not only is bacterial motility itself frequently important for virulence, as it allows pathogenic bacteria to move toward their host and find nutrients more effectively, but flagella can also serve additional functions including mediating bacterial adhesion to surfaces. Flagella are also a potent antigen recognized by the human immune system. Phages utilizing the flagellum for infections are of particular interest due to the unique evolutionary tradeoff they force upon their hosts: by downregulating or abolishing motility to escape infection by a flagellotropic phage, a pathogenic bacterium would also likely attenuate its virulence. This factor may lead to flagellotropic phages becoming especially potent antibacterial agents. This review outlines past, present, and future research of flagellotropic phages, including their molecular mechanisms of infection and potential future applications.
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Computational Viromics: Applications of the Computational Biology in Viromics Studies. Virol Sin 2021; 36:1256-1260. [PMID: 34057678 PMCID: PMC8165334 DOI: 10.1007/s12250-021-00395-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 04/14/2021] [Indexed: 12/30/2022] Open
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Spilsberg B, Sekse C, Urdahl AM, Nesse LL, Johannessen GS. Persistence of a Stx-Encoding Bacteriophage in Minced Meat Investigated by Application of an Improved DNA Extraction Method and Digital Droplet PCR. Front Microbiol 2021; 11:581575. [PMID: 33552009 PMCID: PMC7855172 DOI: 10.3389/fmicb.2020.581575] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 12/01/2020] [Indexed: 12/01/2022] Open
Abstract
Shiga toxin-producing Escherichia coli (STEC) are important food-borne pathogens with Shiga toxins as the main virulence factor. Shiga toxins are encoded on Shiga toxin-encoding bacteriophages (Stx phages). Stx phages may exist as free bacteriophages in the environment or in foods or as prophages integrated into the host genome. From a food safety perspective, it is important to have knowledge on the survival and persistence of Stx phages in food products since these may integrate into the bacterial hosts through transduction if conditions are right. Here, we present the results from a study investigating the survival of a Stx phage in minced meat from beef stored at a suboptimal temperature (8°C) for food storage along with modifications and optimizations of the methods applied. Minced meat from beef was inoculated with known levels of a labeled Stx phage prior to storage. Phage filtrates were used for plaque assays and DNA extraction, followed by real-time PCR and digital droplet PCR (ddPCR). The results from the pilot study suggested that the initial DNA extraction protocol was not optimal, and several modifications were tested before a final protocol was defined. The final DNA extraction protocol comprised ultra-centrifugation of the entire phage filtrate for concentrating phages and two times phenol–chloroform extraction. The protocol was used for two spiking experiments. The DNA extraction protocol resulted in flexibility in the amount of DNA available for use in PCR analyses, ultimately increasing the sensitivity of the method used for quantification of phages in a sample. All three quantification methods employed (i.e., plaque assays, real-time PCR, and ddPCR) showed similar trends in the development of the phages during storage, where ddPCR has the benefit of giving absolute quantification of DNA copies in a simple experimental setup. The results indicate that the Stx phages persist and remain infective for at least 20 days under the storage conditions used in the present study. Stx phages in foods might represent a potential risk for humans. Although it can be speculated that transduction may take place at 8°C with subsequent forming of STEC, it can be expected to be a rare event. However, such an event may possibly take place under more optimal conditions, such as an increase in storage temperature of foods or in the gastrointestinal tract of humans.
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Affiliation(s)
- B Spilsberg
- Section for Molecular Biology, Norwegian Veterinary Institute, Oslo, Norway
| | - C Sekse
- Section for Molecular Biology, Norwegian Veterinary Institute, Oslo, Norway
| | - Anne M Urdahl
- Section for Food Safety and Animal Health Research, Norwegian Veterinary Institute, Oslo, Norway
| | - Live L Nesse
- Section for Food Safety and Animal Health Research, Norwegian Veterinary Institute, Oslo, Norway
| | - Gro S Johannessen
- Section for Food Safety and Animal Health Research, Norwegian Veterinary Institute, Oslo, Norway
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