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Damar Celik D, Karaynir A, Salih Dogan H, Bozdogan B, Ozbek Celik B. Characterization and genomic analysis of PA-56 Pseudomonas phage from Istanbul, Turkey: Antibacterial and antibiofilm efficacy alone and with antibiotics. Heliyon 2024; 10:e36243. [PMID: 39263065 PMCID: PMC11387251 DOI: 10.1016/j.heliyon.2024.e36243] [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: 03/26/2024] [Revised: 08/08/2024] [Accepted: 08/13/2024] [Indexed: 09/13/2024] Open
Abstract
Phages are ubiquitous in freshwater, seawater, soil, the human body, and sewage water. They are potent biopharmaceuticals against antimicrobial-resistant bacteria and offer a promising alternative for treating infectious diseases. Also, combining phages with antibiotics enhances the antibiotics' efficacy. This study focused on two Pseudomonas aeruginosa phages isolated from lake and sewage water samples and one of them selected for further investigation. Isolated phages PA-56 and PA-18 infected 92 % and 86 % of the tested 25 clinical Pseudomonas aeruginosa strains, respectively. PA-56 with strong activity was chosen for detailed characterization, antimicrobial studies, and genome analysis. Combining PA-56 with ciprofloxacin or meropenem demonstrated phage-antibiotic synergism and increased antibiofilm efficacy. Genome analysis revealed a GC ratio of 54 % and a genome size of 42.761 bp, with no virulence or antibiotic resistance genes. Notably, PA-56 harboured the toxin-antitoxin protein, MazG. Overall, this study suggests that PA-56 holds promise for future applications in industry or medicine.
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Affiliation(s)
- Damla Damar Celik
- Istanbul University Institute of Graduate Studies in Health Sciences Department of Pharmaceutical Microbiology, 34116, Beyazıt, Istanbul, Turkey
| | - Abdulkerim Karaynir
- Recombinant DNA and Recombinant Protein Research Center (REDPROM), Aydın Adnan Menderes University, Aydın, Turkey
| | - Hanife Salih Dogan
- Recombinant DNA and Recombinant Protein Research Center (REDPROM), Aydın Adnan Menderes University, Aydın, Turkey
| | - Bulent Bozdogan
- Recombinant DNA and Recombinant Protein Research Center (REDPROM), Aydın Adnan Menderes University, Aydın, Turkey
- Medical Faculty, Department of Medical Microbiology, Aydın Adnan Menderes University, Aydın, Turkey
| | - Berna Ozbek Celik
- Department of Pharmaceutical Microbiology, Faculty of Pharmacy, Istanbul University, 34116, Beyazit, Istanbul, Turkey
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2
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Li S, Wei B, Xu L, Cong C, Murtaza B, Wang L, Li X, Li J, Xu M, Yin J, Xu Y. A novel Saclayvirus Acinetobacter baumannii phage genomic analysis and effectiveness in preventing pneumonia. Appl Microbiol Biotechnol 2024; 108:428. [PMID: 39066795 PMCID: PMC11283397 DOI: 10.1007/s00253-024-13208-0] [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: 10/25/2023] [Revised: 03/12/2024] [Accepted: 05/27/2024] [Indexed: 07/30/2024]
Abstract
Acinetobacter baumannii, which is resistant to multiple drugs, is an opportunistic pathogen responsible for severe nosocomial infections. With no antibiotics available, phages have obtained clinical attention. However, since immunocompromised patients are often susceptible to infection, the appropriate timing of administration is particularly important. During this research, we obtained a lytic phage vB_AbaM_P1 that specifically targets A. baumannii. We then assessed its potential as a prophylactic treatment for lung infections caused by clinical strains. The virus experiences a period of inactivity lasting 30 min and produces approximately 788 particles during an outbreak. Transmission electron microscopy shows that vB_AbaM_P1 was similar to the Saclayvirus. Based on the analysis of high-throughput sequencing and bioinformatics, vB_AbaM_P1 consists of 107537 bases with a G + C content of 37.68%. It contains a total of 177 open reading frames and 14 tRNAs. No antibiotic genes were detected. In vivo experiments, using a cyclophosphamide-induced neutrophil deficiency model, tested the protective effect of phage on neutrophil-deficient rats by prophylactic application of phage. The use of phages resulted in a decrease in rat mortality caused by A. baumannii and a reduction in the bacterial burden in the lungs. Histologic examination of lung tissue revealed a decrease in the presence of immune cells. The presence of phage vB_AbaM_P1 had a notable impact on preventing A. baumannii infection, as evidenced by the decrease in oxidative stress in lung tissue and cytokine levels in serum. Our research offers more robust evidence for the early utilization of bacteriophages to mitigate A. baumannii infection. KEY POINTS: •A novel Saclayvirus phage infecting A. baumannii was isolated from sewage. •The whole genome was determined, analyzed, and compared to other phages. •Assaying the effect of phage in preventing infection in neutrophil-deficient models.
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Affiliation(s)
- Shibin Li
- School of Bioengineering, Dalian University of Technology, Dalian, 116024, China
| | - Bingdong Wei
- Institute of Animal Nutrition and Feed Science, Jilin Academy of Agricultural Sciences, Gongzhuling, 136100, China
| | - Le Xu
- School of Bioengineering, Dalian University of Technology, Dalian, 116024, China
| | - Cong Cong
- School of Bioengineering, Dalian University of Technology, Dalian, 116024, China
| | - Bilal Murtaza
- School of Bioengineering, Dalian University of Technology, Dalian, 116024, China
| | - Lili Wang
- School of Bioengineering, Dalian University of Technology, Dalian, 116024, China
| | - Xiaoyu Li
- School of Bioengineering, Dalian University of Technology, Dalian, 116024, China
| | - Jibin Li
- Liaoning Innovation Center for Phage Application Professional Technology, Dalian, 116620, Liaoning, China
| | - Mu Xu
- Dalian SEM Bio-Engineering Technology Co. Ltd., Dalian, 116620, China
| | - Jiajun Yin
- Department of General Surgery, Affiliated Zhongshan Hospital of Dalian University, Dalian, 116300, China.
| | - Yongping Xu
- School of Bioengineering, Dalian University of Technology, Dalian, 116024, China.
- Department of General Surgery, Affiliated Zhongshan Hospital of Dalian University, Dalian, 116300, China.
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Evseev PV, Sukhova AS, Tkachenko NA, Skryabin YP, Popova AV. Lytic Capsule-Specific Acinetobacter Bacteriophages Encoding Polysaccharide-Degrading Enzymes. Viruses 2024; 16:771. [PMID: 38793652 PMCID: PMC11126041 DOI: 10.3390/v16050771] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Revised: 05/09/2024] [Accepted: 05/10/2024] [Indexed: 05/26/2024] Open
Abstract
The genus Acinetobacter comprises both environmental and clinically relevant species associated with hospital-acquired infections. Among them, Acinetobacter baumannii is a critical priority bacterial pathogen, for which the research and development of new strategies for antimicrobial treatment are urgently needed. Acinetobacter spp. produce a variety of structurally diverse capsular polysaccharides (CPSs), which surround the bacterial cells with a thick protective layer. These surface structures are primary receptors for capsule-specific bacteriophages, that is, phages carrying tailspikes with CPS-depolymerizing/modifying activities. Phage tailspike proteins (TSPs) exhibit hydrolase, lyase, or esterase activities toward the corresponding CPSs of a certain structure. In this study, the data on all lytic capsule-specific phages infecting Acinetobacter spp. with genomes deposited in the NCBI GenBank database by January 2024 were summarized. Among the 149 identified TSPs encoded in the genomes of 143 phages, the capsular specificity (K specificity) of 46 proteins has been experimentally determined or predicted previously. The specificity of 63 TSPs toward CPSs, produced by various Acinetobacter K types, was predicted in this study using a bioinformatic analysis. A comprehensive phylogenetic analysis confirmed the prediction and revealed the possibility of the genetic exchange of gene regions corresponding to the CPS-recognizing/degrading parts of different TSPs between morphologically and taxonomically distant groups of capsule-specific Acinetobacter phages.
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Affiliation(s)
- Peter V. Evseev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia;
- State Research Center for Applied Microbiology and Biotechnology, City District Serpukhov, Moscow Region, 142279 Obolensk, Russia; (A.S.S.); (Y.P.S.)
- Pirogov Russian National Research Medical University, 117997 Moscow, Russia
| | - Anastasia S. Sukhova
- State Research Center for Applied Microbiology and Biotechnology, City District Serpukhov, Moscow Region, 142279 Obolensk, Russia; (A.S.S.); (Y.P.S.)
| | - Nikolay A. Tkachenko
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia;
| | - Yuriy P. Skryabin
- State Research Center for Applied Microbiology and Biotechnology, City District Serpukhov, Moscow Region, 142279 Obolensk, Russia; (A.S.S.); (Y.P.S.)
| | - Anastasia V. Popova
- State Research Center for Applied Microbiology and Biotechnology, City District Serpukhov, Moscow Region, 142279 Obolensk, Russia; (A.S.S.); (Y.P.S.)
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Peters DL, Gaudreault F, Chen W. Functional domains of Acinetobacter bacteriophage tail fibers. Front Microbiol 2024; 15:1230997. [PMID: 38690360 PMCID: PMC11058221 DOI: 10.3389/fmicb.2024.1230997] [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: 05/30/2023] [Accepted: 03/08/2024] [Indexed: 05/02/2024] Open
Abstract
A rapid increase in antimicrobial resistant bacterial infections around the world is causing a global health crisis. The Gram-negative bacterium Acinetobacter baumannii is categorized as a Priority 1 pathogen for research and development of new antimicrobials by the World Health Organization due to its numerous intrinsic antibiotic resistance mechanisms and ability to quickly acquire new resistance determinants. Specialized phage enzymes, called depolymerases, degrade the bacterial capsule polysaccharide layer and show therapeutic potential by sensitizing the bacterium to phages, select antibiotics, and serum killing. The functional domains responsible for the capsule degradation activity are often found in the tail fibers of select A. baumannii phages. To further explore the functional domains associated with depolymerase activity, tail-associated proteins of 71 sequenced and fully characterized phages were identified from published literature and analyzed for functional domains using InterProScan. Multisequence alignments and phylogenetic analyses were conducted on the domain groups and assessed in the context of noted halo formation or depolymerase characterization. Proteins derived from phages noted to have halo formation or a functional depolymerase, but no functional domain hits, were modeled with AlphaFold2 Multimer, and compared to other protein models using the DALI server. The domains associated with depolymerase function were pectin lyase-like (SSF51126), tailspike binding (cd20481), (Trans)glycosidases (SSF51445), and potentially SGNH hydrolases. These findings expand our knowledge on phage depolymerases, enabling researchers to better exploit these enzymes for therapeutic use in combating the antimicrobial resistance crisis.
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Affiliation(s)
- Danielle L. Peters
- Human Health Therapeutics (HHT) Research Center, National Research Council Canada, Ottawa, ON, Canada
| | | | - Wangxue Chen
- Human Health Therapeutics (HHT) Research Center, National Research Council Canada, Ottawa, ON, Canada
- Department of Biology, Brock University, St. Catharines, ON, Canada
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Raees F, Harun A, Ahmed A, Deris ZZ. Potential Usefulness of Bacteriophages for the Treatment of Multidrug-Resistant Acinetobacter Infection. Malays J Med Sci 2023; 30:7-22. [PMID: 37928784 PMCID: PMC10624448 DOI: 10.21315/mjms2023.30.5.2] [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: 01/28/2022] [Accepted: 03/11/2022] [Indexed: 11/07/2023] Open
Abstract
Bacteriophages were discovered in early 20th century. However, the interest in bacteriophage research was reduced with the discovery of antibiotics. With the increasing number of infections due to multidrug-resistant (MDR) organisms, the potential usefulness of bacteriophages as therapeutic agents has been re-evaluated. In this review, we found that more than 30 lytic bacteriophages that infect Acinetobacter species have been characterised. These are mainly members of Caudovirales, with genome sizes ranging from 31 kb to 234 kb and G+C contents ranging from 33.5% to 45.5%. The host range can be as low as < 10% of all tested Acinetobacter strains. Fourteen published murine trials indicated positive outcomes in bacteriophage-treated groups. Only two case reports were pertaining to the use of bacteriophages in the treatment of Acinetobacter infections in humans; in both cases, the infections were resolved with bacteriophage therapy. The use of bacteriophages has been associated with reduced Acinetobacter burden in the environment, as shown in two studies. The major limitation of bacteriophage therapy is its highly selective host strain. In conclusion, the potential usefulness of bacteriophage therapy for the treatment of MDR Acinetobacter species has been documented only in limited studies and more research is needed prior to its extensive use in clinical practice.
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Affiliation(s)
- Fahad Raees
- Department of Medical Microbiology and Parasitology, School of Medical Sciences, Universiti Sains Malaysia, Kelantan, Malaysia
- Department of Microbiology, College of Medicine, Umm al-Qura University, Makkah, Kingdom of Saudi Arabia
| | - Azian Harun
- Department of Medical Microbiology and Parasitology, School of Medical Sciences, Universiti Sains Malaysia, Kelantan, Malaysia
- Hospital Universiti Sains Malaysia, Kelantan, Malaysia
| | - Abdalla Ahmed
- Department of Microbiology, College of Medicine, Umm al-Qura University, Makkah, Kingdom of Saudi Arabia
| | - Zakuan Zainy Deris
- Department of Medical Microbiology and Parasitology, School of Medical Sciences, Universiti Sains Malaysia, Kelantan, Malaysia
- Hospital Universiti Sains Malaysia, Kelantan, Malaysia
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Gihawi A, Cooper CS, Brewer DS. Caution regarding the specificities of pan-cancer microbial structure. Microb Genom 2023; 9:mgen001088. [PMID: 37555750 PMCID: PMC10483429 DOI: 10.1099/mgen.0.001088] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 07/25/2023] [Indexed: 08/10/2023] Open
Abstract
Results published in an article by Poore et al. (Nature. 2020;579:567-574) suggested that machine learning models can almost perfectly distinguish between tumour types based on their microbial composition using machine learning models. Whilst we believe that there is the potential for microbial composition to be used in this manner, we have concerns with the paper that make us question the certainty of the conclusions drawn. We believe there are issues in the areas of the contribution of contamination, handling of batch effects, false positive classifications and limitations in the machine learning approaches used. This makes it difficult to identify whether the authors have identified true biological signal and how robust these models would be in use as clinical biomarkers. We commend Poore et al. on their approach to open data and reproducibility that has enabled this analysis. We hope that this discourse assists the future development of machine learning models and hypothesis generation in microbiome research.
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Affiliation(s)
- Abraham Gihawi
- Bob Champion Research & Education Building, Norwich Medical School, University of East Anglia, Norwich NR4 7UQ, UK
| | - Colin S. Cooper
- Bob Champion Research & Education Building, Norwich Medical School, University of East Anglia, Norwich NR4 7UQ, UK
| | - Daniel S. Brewer
- Bob Champion Research & Education Building, Norwich Medical School, University of East Anglia, Norwich NR4 7UQ, UK
- Earlham Institute, Norwich Research Park, Colney Lane, Norwich NR4 7UG, UK
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Kaur R, Mandal D, Kumar A. Phage therapy for Acinetobacter baumannii infection. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2023; 200:303-324. [PMID: 37739559 DOI: 10.1016/bs.pmbts.2023.04.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/24/2023]
Abstract
Acinetobacter is a gram-negative nosocomial pathogenic bacteria. The contributing factor for the pathogenicity of Acinetobacter is severe due to its property of antibacterial drug resistance. Often antibiotic treatment is used to treat bacterial infection, however due to the resistance of a broad range of antibiotics by Acinetobacter the treatment viability of this bacterial species seems to be reduced. To combat this diverse treatment options are being incorporated with phage therapy being an effective choice due to its intrinsic property to infect bacteria. In this chapter the various phage therapy used in recent times has been elaborated on. The phage therapy is considered to be in response to Carbapenem resistance. The various mode of phage propagation has been mentioned in this chapter along with the type of resistance conferred to the administered therapy. The chapter deals with the advances observed due to therapy of Acibel004, Acibel007, vB-GEC_Ab-M-G7, ZZ1 and Bacteriophage p54 containing Endolysin LysAB54 bacteriophages have been elucidated.
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Affiliation(s)
- Ramneet Kaur
- Department of Basic and Applied Sciences, RIMT University, Punjab, India
| | - Dibita Mandal
- Department of Biosciences, SBST, Vellore Institute of Technology, Vellore, India
| | - Ajay Kumar
- Department of Biotechnology, Faculty of Engineering and Technology, Rama University, Kanpur, Uttar Pradesh, India.
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8
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Li Y, Xiao S, Huang G. Acinetobacter baumannii Bacteriophage: Progress in Isolation, Genome Sequencing, Preclinical Research, and Clinical Application. Curr Microbiol 2023; 80:199. [PMID: 37120784 PMCID: PMC10149043 DOI: 10.1007/s00284-023-03295-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 04/02/2023] [Indexed: 05/01/2023]
Abstract
Acinetobacter baumannii (A. baumannii) is a common nosocomial pathogen associated with serious clinical challenges owing to its rapidly increasing resistance to antibiotics. Due to their high host specificity and easy access to the natural environment, bacteriophages (phages) may serve as good antibacterial agents. Phage therapy has been successfully used to treat antibiotic-resistant A. baumannii infections. As a fundamental step before phage therapy, the characterization and sequencing of A. baumannii phages have been well studied. Until October 2022, 132 A. baumannii phages have been sequenced and studied, with their genomes ranging from 4 to 234 kb, and we summarize the characterized and sequenced A. baumannii phages. This review is a current and short overview that does not go into detail on the A. baumannii phages. In addition, preclinical studies and clinical applications of A. baumannii phages are also included.
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Affiliation(s)
- Yanqi Li
- Department of Burns and Plastic Surgery, Affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - Shune Xiao
- Department of Burns and Plastic Surgery, Affiliated Hospital of Zunyi Medical University, Zunyi, China.
| | - Guangtao Huang
- Department of Burns and Plastic Surgery, Affiliated Hospital of Zunyi Medical University, Zunyi, China.
- Department of Burn and Plastic Surgery, Shenzhen Institute of Translational Medicine, The First Affiliated Hospital of Shenzhen University, Shenzhen Second People's Hospital, Shenzhen, 518035, China.
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Navez M, Antoine C, Laforêt F, Goya-Jorge E, Douny C, Scippo ML, Vermeersch M, Duprez JN, Daube G, Mainil J, Taminiau B, Delcenserie V, Thiry D. In Vitro Effect on Piglet Gut Microbiota and In Vivo Assessment of Newly Isolated Bacteriophages against F18 Enterotoxigenic Escherichia coli (ETEC). Viruses 2023; 15:v15051053. [PMID: 37243139 DOI: 10.3390/v15051053] [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: 03/02/2023] [Revised: 04/19/2023] [Accepted: 04/24/2023] [Indexed: 05/28/2023] Open
Abstract
Enterotoxigenic Escherichia coli (ETEC) causing post-weaning diarrhea (PWD) in piglets have a detrimental impact on animal health and economy in pig production. ETEC strains can adhere to the host's small intestinal epithelial cells using fimbriae such as F4 and F18. Phage therapy could represent an interesting alternative to antimicrobial resistance against ETEC infections. In this study, four bacteriophages, named vB_EcoS_ULIM2, vB_EcoM_ULIM3, vB_EcoM_ULIM8 and vB_EcoM_ULIM9, were isolated against an O8:F18 E. coli strain (A-I-210) and selected based on their host range. These phages were characterized in vitro, showing a lytic activity over a pH (4-10) and temperature (25-45 °C) range. According to genomic analysis, these bacteriophages belong to the Caudoviricetes class. No gene related to lysogeny was identified. The in vivo Galleria mellonella larvae model suggested the therapeutic potential of one selected phage, vB_EcoS_ULIM2, with a statistically significant increase in survival compared to non-treated larvae. To assess the effect of this phage on the piglet gut microbiota, vB_EcoS_ULIM2 was inoculated in a static model simulating the piglet intestinal microbial ecosystem for 72 h. This study shows that this phage replicates efficiently both in vitro and in vivo in a Galleria mellonella model and reveals the safety of the phage-based treatment on the piglet microbiota.
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Affiliation(s)
- Margaux Navez
- Laboratory of Bacteriology, Department of Infectious and Parasitic Diseases, FARAH and Faculty of Veterinary Medicine, University of Liege, 4000 Liege, Belgium
- Unit of Cardiovascular Sciences, Groupe Interdisciplinaire de Génoprotéomique Appliquée (GIGA), University of Liege, 4000 Liege, Belgium
| | - Céline Antoine
- Laboratory of Bacteriology, Department of Infectious and Parasitic Diseases, FARAH and Faculty of Veterinary Medicine, University of Liege, 4000 Liege, Belgium
- Laboratory of Food Quality Management, Food Science Department, FARAH and Faculty of Veterinary Medicine, University of Liège, 4000 Liege, Belgium
| | - Fanny Laforêt
- Laboratory of Bacteriology, Department of Infectious and Parasitic Diseases, FARAH and Faculty of Veterinary Medicine, University of Liege, 4000 Liege, Belgium
- Laboratory of Food Quality Management, Food Science Department, FARAH and Faculty of Veterinary Medicine, University of Liège, 4000 Liege, Belgium
| | - Elizabeth Goya-Jorge
- Laboratory of Food Quality Management, Food Science Department, FARAH and Faculty of Veterinary Medicine, University of Liège, 4000 Liege, Belgium
| | - Caroline Douny
- Laboratory of Food Analysis, Department of Food Sciences, FARAH and Faculty of Veterinary Medicine, University of Liège, 4000 Liege, Belgium
| | - Marie-Louise Scippo
- Laboratory of Food Analysis, Department of Food Sciences, FARAH and Faculty of Veterinary Medicine, University of Liège, 4000 Liege, Belgium
| | - Marjorie Vermeersch
- Center for Microscopy and Molecular Imaging, Electron Microscopy Laboratory, ULB, 6041 Gosselies, Belgium
| | - Jean-Noël Duprez
- Laboratory of Bacteriology, Department of Infectious and Parasitic Diseases, FARAH and Faculty of Veterinary Medicine, University of Liege, 4000 Liege, Belgium
| | - Georges Daube
- Laboratory of Food Microbiology, Fundamental and Applied Research for Animals & Health (FARAH), Department of Food Sciences, Faculty of Veterinary Medicine, University of Liege, 4000 Liege, Belgium
| | - Jacques Mainil
- Laboratory of Bacteriology, Department of Infectious and Parasitic Diseases, FARAH and Faculty of Veterinary Medicine, University of Liege, 4000 Liege, Belgium
| | - Bernard Taminiau
- Laboratory of Food Microbiology, Fundamental and Applied Research for Animals & Health (FARAH), Department of Food Sciences, Faculty of Veterinary Medicine, University of Liege, 4000 Liege, Belgium
| | - Véronique Delcenserie
- Laboratory of Food Quality Management, Food Science Department, FARAH and Faculty of Veterinary Medicine, University of Liège, 4000 Liege, Belgium
| | - Damien Thiry
- Laboratory of Bacteriology, Department of Infectious and Parasitic Diseases, FARAH and Faculty of Veterinary Medicine, University of Liege, 4000 Liege, Belgium
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10
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Tu Q, Pu M, Li Y, Wang Y, Li M, Song L, Li M, An X, Fan H, Tong Y. Acinetobacter Baumannii Phages: Past, Present and Future. Viruses 2023; 15:v15030673. [PMID: 36992382 PMCID: PMC10057898 DOI: 10.3390/v15030673] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 02/23/2023] [Accepted: 02/28/2023] [Indexed: 03/06/2023] Open
Abstract
Acinetobacter baumannii (A. baumannii) is one of the most common clinical pathogens and a typical multi-drug resistant (MDR) bacterium. With the increase of drug-resistant A. baumannii infections, it is urgent to find some new treatment strategies, such as phage therapy. In this paper, we described the different drug resistances of A. baumannii and some basic properties of A. baumannii phages, analyzed the interaction between phages and their hosts, and focused on A. baumannii phage therapies. Finally, we discussed the chance and challenge of phage therapy. This paper aims to provide a more comprehensive understanding of A. baumannii phages and theoretical support for the clinical application of A. baumannii phages.
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Affiliation(s)
- Qihang Tu
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Mingfang Pu
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Yahao Li
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering (BAIC-SM), Beijing University of Chemical Technology, Beijing 100029, China
| | - Yuer Wang
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Maochen Li
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Lihua Song
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Mengzhe Li
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Xiaoping An
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Huahao Fan
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
- Correspondence: (H.F.); (Y.T.)
| | - 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
- Correspondence: (H.F.); (Y.T.)
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11
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Sun L, You J, Li D, Zhang Z, Qin X, Pang W, Li P, Han Q, Li Y, Huang Z, Zhang X, Gong M, Yang H. Variants of a putative baseplate wedge protein extend the host range of Pseudomonas phage K8. MICROBIOME 2023; 11:18. [PMID: 36721246 PMCID: PMC9887876 DOI: 10.1186/s40168-022-01459-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Accepted: 12/31/2022] [Indexed: 05/28/2023]
Abstract
BACKGROUND Narrow host range is a major limitation for phage applications, but phages can evolve expanded host range through adaptations in the receptor-binding proteins. RESULTS Here, we report that Pseudomonas phage K8 can evolve broader host range and higher killing efficiency at the cost of virion stability. Phage K8 host range mutant K8-T239A carries a mutant version of the putative baseplate wedge protein GP075, termed GP075m. While phage K8 adsorbs to hosts via the O-specific antigen of bacterial LPS, phage K8-T239A uses GP075m to also bind the bacterial core oligosaccharide, enabling infection of bacterial strains resistant to K8 infection due to modified O-specific antigens. This mutation in GP075 also alters inter-protein interactions among phage proteins, and reduces the stability of phage particles to environmental stressors like heat, acidity, and alkalinity. We find that a variety of mutations in gp075 are widespread in K8 populations, and that the gp075-like genes are widely distributed among the domains of life. CONCLUSION Our data show that a typical life history tradeoff occurs between the stability and the host range in the evolution of phage K8. Reservoirs of viral gene variants may be widely present in phage communities, allowing phages to rapidly adapt to any emerging environmental stressors. Video Abstract.
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Affiliation(s)
- Li Sun
- Key Laboratory of Industrial Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, China
| | - Jiajia You
- Key Laboratory of Industrial Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, China
| | - Donghang Li
- Key Laboratory of Industrial Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, China
| | - Zhiqiang Zhang
- Key Laboratory of Industrial Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, China
| | - Xuying Qin
- Key Laboratory of Industrial Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, China
| | - Wenjing Pang
- Key Laboratory of Industrial Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, China
| | - Peize Li
- Key Laboratory of Industrial Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, China
| | - Qingzhu Han
- Key Laboratory of Industrial Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, China
| | - Yueying Li
- Key Laboratory of Industrial Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, China
| | - Zhiwei Huang
- Key Laboratory of Industrial Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, China
| | - Xixi Zhang
- Key Laboratory of Industrial Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, China
| | | | - Hongjiang Yang
- Key Laboratory of Industrial Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, China.
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12
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Akremi I, Merabishvili M, Jlidi M, Haj Brahim A, Ben Ali M, Karoui A, Lavigne R, Wagemans J, Pirnay JP, Ben Ali M. Isolation and Characterization of Lytic Pseudomonas aeruginosa Bacteriophages Isolated from Sewage Samples from Tunisia. Viruses 2022; 14:v14112339. [PMID: 36366441 PMCID: PMC9698164 DOI: 10.3390/v14112339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 10/21/2022] [Accepted: 10/21/2022] [Indexed: 02/01/2023] Open
Abstract
Bacteriophages could be a useful adjunct to antibiotics for the treatment of multidrug-resistant Pseudomonas aeruginosa infections. In this study, lytic P. aeruginosa myoviruses PsCh, PsIn, Ps25, and Ps12on-D were isolated from Tunisian sewage samples. Phage Ps12on-D displayed an adsorption time of ~10 min, a short latency period (~10 min), and a large burst size (~115 PFU per infected cell) under standard growth conditions. All phages were active at broad temperature (4 °C to 50 °C) and pH (3.0 to 11.0) ranges and were able to lyse a wide variety of P. aeruginosa strains isolated from clinical and environmental samples worldwide. Illumina sequencing revealed double-stranded DNA genomes ranging from 87,887 and 92,710 bp with high sequence identity to Pseudomonas phage PAK_P1. All four phages based on sequence analysis were assigned to the Pakpunavirus genus. The presented characterization and preclinical assessment are part of an effort to establish phage therapy treatment as an alternative strategy for the management of multidrug-resistant P. aeruginosa infections in Tunisia.
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Affiliation(s)
- Ismahen Akremi
- Laboratory of Microbial Biotechnology, Enzymatics and Biomolecules (LBMEB), Center of Biotechnology of Sfax (CBS), University of Sfax, Road of Sidi Mansour km 6, P.O. Box 1177, Sfax 3018, Tunisia
- Correspondence: (I.A.); (J.-P.P.); (M.B.A.)
| | - Maya Merabishvili
- Laboratory for Molecular and Cellular Technology, Queen Astrid Military Hospital, Bruynstraat 1, B-1120 Brussels, Belgium
| | - Mouna Jlidi
- Laboratory of Microbial Biotechnology, Enzymatics and Biomolecules (LBMEB), Center of Biotechnology of Sfax (CBS), University of Sfax, Road of Sidi Mansour km 6, P.O. Box 1177, Sfax 3018, Tunisia
| | - Adel Haj Brahim
- Laboratory of Microbial Biotechnology, Enzymatics and Biomolecules (LBMEB), Center of Biotechnology of Sfax (CBS), University of Sfax, Road of Sidi Mansour km 6, P.O. Box 1177, Sfax 3018, Tunisia
| | - Manel Ben Ali
- Laboratory of Microbial Biotechnology, Enzymatics and Biomolecules (LBMEB), Center of Biotechnology of Sfax (CBS), University of Sfax, Road of Sidi Mansour km 6, P.O. Box 1177, Sfax 3018, Tunisia
- Astrum Biotech, Business Incubator, Center of Biotechnology of Sfax (CBS), University of Sfax, Road of Sidi Mansour km 6, P.O. Box 1177, Sfax 3018, Tunisia
| | - Anis Karoui
- Agrovet, Street of Tunis km 1, Soliman 8020, Tunisia
| | - Rob Lavigne
- Laboratory of Gene Technology, Department of Biosystems, KU Leuven, Kasteelpark Arenberg 21-Box 2462, B-3001 Leuven, Belgium
| | - Jeroen Wagemans
- Laboratory of Gene Technology, Department of Biosystems, KU Leuven, Kasteelpark Arenberg 21-Box 2462, B-3001 Leuven, Belgium
| | - Jean-Paul Pirnay
- Laboratory for Molecular and Cellular Technology, Queen Astrid Military Hospital, Bruynstraat 1, B-1120 Brussels, Belgium
- Correspondence: (I.A.); (J.-P.P.); (M.B.A.)
| | - Mamdouh Ben Ali
- Laboratory of Microbial Biotechnology, Enzymatics and Biomolecules (LBMEB), Center of Biotechnology of Sfax (CBS), University of Sfax, Road of Sidi Mansour km 6, P.O. Box 1177, Sfax 3018, Tunisia
- Astrum Biotech, Business Incubator, Center of Biotechnology of Sfax (CBS), University of Sfax, Road of Sidi Mansour km 6, P.O. Box 1177, Sfax 3018, Tunisia
- Correspondence: (I.A.); (J.-P.P.); (M.B.A.)
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13
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Ghaznavi-Rad E, Komijani M, Moradabadi A, Rezaei M, Shaykh-Baygloo N. Isolation of a lytic bacteriophage against extensively drug-resistant Acinetobacter baumannii infections and its dramatic effect in rat model of burn infection. J Clin Lab Anal 2022; 36:e24497. [PMID: 35708005 PMCID: PMC9279972 DOI: 10.1002/jcla.24497] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 04/30/2022] [Accepted: 05/03/2022] [Indexed: 12/25/2022] Open
Abstract
Objectives Acinetobacter Baumannii is an opportunistic nosocomial pathogen belonging to the Moraxellaceae family. The emergence of multidrug resistant strains of this pathogen caused many problems for hospitals and patients. The aim of the current study was to isolate, identify, and morphologically, physiologically, and in vivo analyze a new lytic bacteriophage targeting extensively drug‐resistant (XDR) A. baumannii. Materials and Methods Different wastewater samples were tested for isolation of lytic bacteriophage against 19 A. baumannii isolates obtained from patients hospitalized in a hospital in Arak, Iran, from January 2019 to March 2019. The phenotypic and genotypic characteristics of A. baumannii strains (resistance genes including: adeA, adeB, adeC, adeR, adeS, ISAba1, blaOXA‐23, blaOXA‐24) were analyzed. The isolated phage characteristics including adsorption time, pH and thermal stability, host range, one‐step growth rate, electron microscopy examination, and therapeutic efficacy of the phage were also investigated. Therapeutic efficacy of the phage was evaluated in a rat model with burn infection of XDR A. baumannii. The lesion image was taken on different days after burning and infection induction and was compared with phage untreated lesions. Results The results showed unique characteristics of the isolated phage (vB‐AbauM‐Arak1) including high specificity for Acinetobacter baumannii, stability at a relatively wide range of temperatures and pH values, short adsorption time, short latent period, and large burst size. In relation to the therapeutic efficacy of the phage, the lesion area decreased in phage‐treated groups over 14 days than in those untreated, significantly (p < 0.05). Conclusion Our findings demonstrated that isolated lytic phage was able to eliminate burn infections caused by XDR A. baumannii in a rat model. So, it may be recommended as alternative options toward to developing a treatment for extensively drug resistant Acinetobacter infections.
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Affiliation(s)
- Ehsanollah Ghaznavi-Rad
- Department of Medical Laboratory Science, Faculty of Paramedicine, Arak University of Medical Sciences, Arak, Iran.,Molecular Research Center, Faculty of Medicine, Arak University of medical sciences, Arak, Iran
| | - Majid Komijani
- Department of Biology, Faculty of Science, Arak University, Arak, Iran
| | - Alireza Moradabadi
- Molecular and medicine research center, Khomein University of Medical Sciences, Khomein, Iran
| | - Marzieh Rezaei
- Department of Cell, Molecular Biology and Microbiology, Faculty of Biological Sciences and Biotechnology, University of Isfahan, Isfahan, Iran
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14
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Characterization and complete genome analysis of a novel Escherichia phage, vB_EcoM-RPN242. Arch Virol 2022; 167:1675-1679. [DOI: 10.1007/s00705-022-05479-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Accepted: 04/04/2022] [Indexed: 01/10/2023]
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15
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Havenga B, Reyneke B, Waso-Reyneke M, Ndlovu T, Khan S, Khan W. Biological Control of Acinetobacter baumannii: In Vitro and In Vivo Activity, Limitations, and Combination Therapies. Microorganisms 2022; 10:microorganisms10051052. [PMID: 35630494 PMCID: PMC9147981 DOI: 10.3390/microorganisms10051052] [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: 04/20/2022] [Revised: 05/16/2022] [Accepted: 05/17/2022] [Indexed: 02/01/2023] Open
Abstract
The survival, proliferation, and epidemic spread of Acinetobacter baumannii (A. baumannii) in hospital settings is associated with several characteristics, including resistance to many commercially available antibiotics as well as the expression of multiple virulence mechanisms. This severely limits therapeutic options, with increased mortality and morbidity rates recorded worldwide. The World Health Organisation, thus, recognises A. baumannii as one of the critical pathogens that need to be prioritised for the development of new antibiotics or treatment. The current review will thus provide a brief overview of the antibiotic resistance and virulence mechanisms associated with A. baumannii’s “persist and resist strategy”. Thereafter, the potential of biological control agents including secondary metabolites such as biosurfactants [lipopeptides (surfactin and serrawettin) and glycolipids (rhamnolipid)] as well as predatory bacteria (Bdellovibrio bacteriovorus) and bacteriophages to directly target A. baumannii, will be discussed in terms of their in vitro and in vivo activity. In addition, limitations and corresponding mitigations strategies will be outlined, including curtailing resistance development using combination therapies, product stabilisation, and large-scale (up-scaling) production.
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Affiliation(s)
- Benjamin Havenga
- Department of Microbiology, Faculty of Science, Stellenbosch University, Private Bag X1, Stellenbosch 7602, South Africa; (B.H.); (B.R.)
| | - Brandon Reyneke
- Department of Microbiology, Faculty of Science, Stellenbosch University, Private Bag X1, Stellenbosch 7602, South Africa; (B.H.); (B.R.)
| | - Monique Waso-Reyneke
- Faculty of Health Sciences, University of Johannesburg, Doornfontein 2028, South Africa; (M.W.-R.); (S.K.)
| | - Thando Ndlovu
- Department of Biological Sciences, Faculty of Science, University of Botswana, Private Bag UB, Gaborone 0022, Botswana;
| | - Sehaam Khan
- Faculty of Health Sciences, University of Johannesburg, Doornfontein 2028, South Africa; (M.W.-R.); (S.K.)
| | - Wesaal Khan
- Department of Microbiology, Faculty of Science, Stellenbosch University, Private Bag X1, Stellenbosch 7602, South Africa; (B.H.); (B.R.)
- Correspondence: ; Tel.: +27-21-808-5804
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16
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Bujak K, Decewicz P, Kitowicz M, Radlinska M. Characterization of Three Novel Virulent Aeromonas Phages Provides Insights into the Diversity of the Autographiviridae Family. Viruses 2022; 14:1016. [PMID: 35632757 PMCID: PMC9145550 DOI: 10.3390/v14051016] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 04/29/2022] [Accepted: 05/05/2022] [Indexed: 11/17/2022] Open
Abstract
In this study, we isolated and characterized three novel virulent Autographiviridae bacteriophages, vB_AspA_Bolek, vB_AspA_Lolek, and vB_AspA_Tola, which infect different Aeromonas strains. These three host-pathogen pairs were derived from the same sampling location-the arsenic-containing microbial mats of the Zloty Stok gold mine. Functional analysis showed they are psychrotolerant (4-25 °C), albeit with a much wider temperature range of propagation for the hosts (≤37 °C). Comparative genomic analyses revealed a high nucleotide and amino acid sequence similarity of vB_AspA_Bolek and vB_AspA_Lolek, with significant differences exclusively in the C-terminal region of their tail fibers, which might explain their host range discrimination. The protein-based phage network, together with a phylogenetic analysis of the marker proteins, allowed us to assign vB_AspA_Bolek and vB_AspA_Lolek to the Beijerinckvirinae and vB_AspA_Tola to the Colwellvirinae subfamilies, but as three novel species, due to their low nucleotide sequence coverage and identity with other known phage genomes. Global comparative analysis showed that the studied phages are also markedly different from most of the 24 Aeromonas autographiviruses known so far. Finally, this study provides in-depth insight into the diversity of the Autographiviridae phages and reveals genomic similarities between selected groups of this family as well as between autographiviruses and their relatives of other Caudoviricetes families.
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Affiliation(s)
| | | | | | - Monika Radlinska
- Department of Environmental Microbiology and Biotechnology, Faculty of Biology, Institute of Microbiology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland; (K.B.); (P.D.); (M.K.)
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17
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Soontarach R, Srimanote P, Enright MC, Blundell-Hunter G, Dorman MJ, Thomson NR, Taylor PW, Voravuthikunchai SP. Isolation and Characterisation of Bacteriophage Selective for Key Acinetobacter baumannii Capsule Chemotypes. Pharmaceuticals (Basel) 2022; 15:443. [PMID: 35455440 PMCID: PMC9027227 DOI: 10.3390/ph15040443] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 03/25/2022] [Accepted: 03/29/2022] [Indexed: 11/17/2022] Open
Abstract
Nineteen bacteriophages against five main capsular types of multidrug-resistant Acinetobacter baumannii were isolated from tertiary care hospital sewage. Eight representative phages from each capsular type were characterized and tested for their biological properties. The biological features revealed that phages T1245, T444, and T515 had a large burst size of more than 420 pfu/mL, together with a short latent period lasting less than 6 min, and were readily adsorbed to a bacterial host within 10 min. Moreover, these phages demonstrated host specificity and stability over a broad range of temperatures (-20 to 60 °C) and pH (5.0-9.0). A whole-genome analysis of six lytic and two temperate phages revealed high genomic similarity with double-stranded DNA between 40 and 50 kb and G + C content of 38-39%. The protein compositions disclosed the absence of toxin-coding genes. The phylogenic results, together with morphological micrographs, confirmed that three selected phages (T1245, T444, and T515) belong to the Podoviridae family within the order Caudovirales. The biological data and bioinformatics analysis indicated that these novel A. baumannii phages possess important enzymes, including depolymerase and endolysin, which could be further developed as promising alternative antibacterial agents to control A. baumannii infections.
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Affiliation(s)
- Rosesathorn Soontarach
- Division of Biological Science, Faculty of Science and Natural Product Research Center of Excellence, Prince of Songkla University, Songkhla 90110, Thailand;
- Center of Antimicrobial Biomaterial Innovation-Southeast Asia, Prince of Songkla University, Songkhla 90110, Thailand
| | - Potjanee Srimanote
- Graduate Program, Faculty of Allied Health Sciences, Thammasat University, Pathum Thani 12121, Thailand;
| | - Mark C. Enright
- Department of Life Sciences, Manchester Metropolitan University, Chester Street, Manchester M1 5GD, UK;
| | | | - Matthew J. Dorman
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK; (M.J.D.); (N.R.T.)
| | - Nicholas R. Thomson
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK; (M.J.D.); (N.R.T.)
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK
| | - Peter W. Taylor
- School of Pharmacy, University College London, London WC1N 1AX, UK; (G.B.-H.); (P.W.T.)
| | - Supayang P. Voravuthikunchai
- Division of Biological Science, Faculty of Science and Natural Product Research Center of Excellence, Prince of Songkla University, Songkhla 90110, Thailand;
- Center of Antimicrobial Biomaterial Innovation-Southeast Asia, Prince of Songkla University, Songkhla 90110, Thailand
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18
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Pan L, Li D, Sun Z, Lin W, Hong B, Qin W, Xu L, Liu W, Zhou Q, Wang F, Cai R, Qian M, Tong Y. First Characterization of a Hafnia Phage Reveals Extraordinarily Large Burst Size and Unusual Plaque Polymorphism. Front Microbiol 2022; 12:754331. [PMID: 35211099 PMCID: PMC8861465 DOI: 10.3389/fmicb.2021.754331] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 12/20/2021] [Indexed: 01/25/2023] Open
Abstract
A unique lytic phage infecting Hafnia paralvei was isolated and identified. Hafnia phage Ca belongs to the family Autographiviridae, possessing an icosahedral head with a diameter of 55 nm and a short non-contractile tail. Unusually, the burst size of Hafnia phage Ca of 10,292 ± 1,097 plaque-forming units (PFUs)/cell is much larger than other dsDNA phages reported before. Compared to the genome of the related phage, Hafnia phage Ca genome contains extra genes including DNA mimic ocr, dGTP triphosphohydrolase inhibitor, endonuclease, endonuclease VII, and HNH homing endonuclease gene. Extraordinarily, the phage developed different sizes of plaques when a single plaque was picked out and inoculated on a double-layer Luria broth agar plate with its host. Furthermore, varied packaging tightness for the tails of Hafnia phage Ca was observed (tail length: 4.35–45.92 nm). Most of the tails appeared to be like a cone with appendages, some were dot-like, bun-like, table tennis racket handle-like, and ponytail-like. Although the complete genome of Hafnia phage Ca is 40,286 bp, an incomplete genome with a deletion of a 397-bp fragment, containing one ORF predicted as HNH homing endonuclease gene (HEG), was also found by high throughput sequencing. Most of the genome of the virus particles in large plaques is complete (>98%), while most of the genome of the virus particles in small plaques is incomplete (>98%), and the abundance of both of them in medium-sized plaques is similar (complete, 40%; incomplete, 60%). In an experiment to see if the phage could be protective to brocade carps intramuscularly injected with H. paralvei LY-23 and phage Ca, the protection rate of Hafnia phage Ca to brocade carp (Cyprinus aka Koi) against H. paralvei was 33.38% (0.01 < p < 0.05). This study highlights some new insights into the peculiar biological and genomic characteristics of phage.
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Affiliation(s)
- Lingting Pan
- Key Laboratory of Marine Biotechnology, School of Marine Sciences, Ningbo University, Ningbo, China.,College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Dengfeng Li
- Key Laboratory of Marine Biotechnology, School of Marine Sciences, Ningbo University, Ningbo, China
| | - Zhitong Sun
- Key Laboratory of Marine Biotechnology, School of Marine Sciences, Ningbo University, Ningbo, China
| | - Wei Lin
- Key Laboratory of Marine Biotechnology, School of Marine Sciences, Ningbo University, Ningbo, China.,College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Binxin Hong
- Key Laboratory of Marine Biotechnology, School of Marine Sciences, Ningbo University, Ningbo, China
| | - Weinan Qin
- Key Laboratory of Marine Biotechnology, School of Marine Sciences, Ningbo University, Ningbo, China
| | - Lihua Xu
- Key Laboratory of Marine Biotechnology, School of Marine Sciences, Ningbo University, Ningbo, China
| | - Wencai Liu
- Key Laboratory of Marine Biotechnology, School of Marine Sciences, Ningbo University, Ningbo, China
| | - Qin Zhou
- Key Laboratory of Marine Biotechnology, School of Marine Sciences, Ningbo University, Ningbo, China
| | - Fei Wang
- Key Laboratory of Marine Biotechnology, School of Marine Sciences, Ningbo University, Ningbo, China
| | - Ruqian Cai
- Key Laboratory of Marine Biotechnology, School of Marine Sciences, Ningbo University, Ningbo, China
| | - Minhua Qian
- Key Laboratory of Marine Biotechnology, School of Marine Sciences, Ningbo University, Ningbo, China
| | - Yigang Tong
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
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19
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Phenotypic and Genetic Characterization of Aeromonas hydrophila Phage AhMtk13a and Evaluation of Its Therapeutic Potential on Simulated Aeromonas Infection in Danio rerio. Viruses 2022; 14:v14020412. [PMID: 35216005 PMCID: PMC8876716 DOI: 10.3390/v14020412] [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: 12/29/2021] [Revised: 01/31/2022] [Accepted: 02/10/2022] [Indexed: 01/27/2023] Open
Abstract
Phage therapy can be an effective alternative to standard antimicrobial chemotherapy for control of Aeromonas hydrophila infections in aquaculture. Aeromonas hydrophila-specific phages AhMtk13a and AhMtk13b were studied for basic biological properties and genome characteristics. Phage AhMtk13a (Myovirus, 163,879 bp genome, 41.21% CG content) was selected based on broad lytic spectrum and physiologic parameters indicating its lytic nature. The therapeutic potential of phage AhMtk13a was evaluated in experimental studies in zebrafish challenged with A. hydrophila GW3-10 via intraperitoneal injection and passive immersion in aquaria water. In experimental series 1 with single introduction of AhMtk13a phage to aquaria water at phage–bacteria ratio 10:1, cumulative mortality 44% and 62% was registered in fish exposed to phage immediately and in 4 h after bacterial challenge, correspondingly, compared to 78% mortality in the group with no added phage. In experimental series 2 with triple application of AhMtk13a phage at ratio 100:1, the mortality comprised 15% in phage-treated group compared to the 55% in the control group. Aeromonas hydrophila GW3-10 was not detectable in aquaria water from day 9 but still present in fish at low concentration. AhMtk13a phage was maintained in fish and water throughout the experiment at the higher concentration in infected fish.
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20
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Oliveira H, Domingues R, Evans B, Sutton JM, Adriaenssens EM, Turner D. Genomic Diversity of Bacteriophages Infecting the Genus Acinetobacter. Viruses 2022; 14:181. [PMID: 35215775 PMCID: PMC8878043 DOI: 10.3390/v14020181] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 01/07/2022] [Accepted: 01/10/2022] [Indexed: 01/21/2023] Open
Abstract
The number of sequenced Acinetobacter phage genomes in the International Nucleotide Sequence Database Collaboration has increased significantly in recent years, from 37 in 2017 to a total of 139 as of January 2021 with genome sizes ranging from 31 to 378 kb. Here, we explored the genetic diversity of the Acinetobacter phages using comparative genomics approaches that included assessment of nucleotide similarity, shared gene content, single gene phylogeny, and the network-based classification tool vConTACT2. Phages infecting Acinetobacter sp. are genetically diverse and can be grouped into 8 clusters (subfamilies) and 46 sub-clusters (genera), of which 8 represent genomic singletons (additional genera). We propose the creation of five new subfamilies and suggest a reorganisation of the genus Obolenskvirus. These results provide an updated view of the viruses infecting Acinetobacter species, providing insights into their diversity.
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Affiliation(s)
- Hugo Oliveira
- Centre of Biological Engineering, University of Minho, Campus de Gualtar Braga, 4710-057 Braga, Portugal; (H.O.); (R.D.)
| | - Rita Domingues
- Centre of Biological Engineering, University of Minho, Campus de Gualtar Braga, 4710-057 Braga, Portugal; (H.O.); (R.D.)
| | - Benjamin Evans
- Norwich Medical School, University of East Anglia, Norwich NR4 7TJ, UK;
| | - J. Mark Sutton
- United Kingdom Health Security Agency, Research and Evaluation, Porton Down, Salisbury SP4 OJG, UK;
| | | | - Dann Turner
- Department of Applied Sciences, Faculty of Health and Applied Sciences, University of the West of England, Bristol BS16 1QY, UK
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21
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«Development of an anti- Acinetobacter baumannii biofilm phage cocktail: Genomic Adaptation to the Host». Antimicrob Agents Chemother 2022; 66:e0192321. [PMID: 35041503 DOI: 10.1128/aac.01923-21] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The need for alternatives to antibiotic therapy due to the emergence of multidrug resistant bacteria (MDR), such as the nosocomial pathogen Acinetobacter baumannii, has led to the recovery of phage therapy. In addition, phages can be combined in cocktails to increase the host range. In this study, the evolutionary mechanism of adaptation was utilized in order to develop a phage adapted to A. baumannii, named phage Ab105-2phiΔCI404ad, from a mutant lytic phage, Ab105-2phiΔCI, previously developed by our group. The whole genome sequence of phage Ab105-2phiΔCI404ad was determined, showing that four genomic rearrangements events occurred in the tail morphogenesis module affecting the ORFs encoding the host receptor binding sites. As a consequence of the genomic rearrangements, 10 ORFs were lost and four new ORFs were obtained, all encoding tail proteins; two inverted regions were also derived from these events. The adaptation process increased the host range of the adapted phage by almost three folds. In addition, a depolymerase-expressing phenotype, indicated by formation of a halo, which was not observed in the ancestral phage, was obtained in 81% of the infected strains. A phage cocktail was formed by combining this phage with the A. baumannii phage vB_AbaP_B3, known to express a depolymerase. Both the individual phages and the phage cocktail showed strong antimicrobial activity against 5 clinical strains and 1 reference strain of A. baumannii tested. However, in all cases resistance to the bacterial strains was also observed. The antibiofilm activity of the individual phages and the cocktail was assayed. The phage cocktail displayed strong antibiofilm activity.
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22
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Sisakhtpour B, Mirzaei A, Karbasizadeh V, Hosseini N, Shabani M, Moghim S. The characteristic and potential therapeutic effect of isolated multidrug-resistant Acinetobacter baumannii lytic phage. Ann Clin Microbiol Antimicrob 2022; 21:1. [PMID: 34996464 PMCID: PMC8742398 DOI: 10.1186/s12941-022-00492-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2020] [Accepted: 01/03/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Widespread misuse of antibiotics caused bacterial resistance increasingly become a serious threat. Bacteriophage therapy promises alternative treatment strategies for combatting drug-resistant bacterial infections. In this study, we isolated and characterized a novel, potent lytic bacteriophage against multi-drug resistant (MDR) Acinetobacter baumannii and described the lytic capability and endolysin activity of the phage to evaluate the potential in phage therapy. METHODS A novel phage, pIsf-AB02, was isolated from hospital sewage. The morphological analysis, its host range, growth characteristics, stability under various conditions, genomic restriction pattern were systematically investigated. The protein pattern of the phage was analyzed, and the endolysin activity of the phage was determined under the non-denaturing condition on SDS-PAGE. The optimal lytic titer of phage was assessed by co-culture of the phage with clinical MDR A. baumannii isolates. Finally, HeLa cells were used to examine the safety of the phage. RESULTS The morphological analysis revealed that the pIsf-AB02 phage displays morphology resembling the Myoviridae family. It can quickly destroy 56.3% (27/48) of clinical MDR A. baumannii isolates. This virulent phage could decrease the bacterial host cells (from 108 CFU/ml to 103 CFU/ml) in 30 min. The optimum stability of the phage was observed at 37 °C. pH 7 is the most suitable condition to maintain phage stability. The 15 kDa protein encoded by pIsf-AB02 was detected to have endolysin activity. pIsf-AB02 did not show cytotoxicity to HeLa cells, and it can save HeLa cells from A. baumannii infection. CONCLUSION In this study, we isolated a novel lytic MDR A. baumannii bacteriophage, pIsf-AB02. This phage showed suitable stability at different temperatures and pHs, and demonstrated potent in vitro endolysin activity. pIsf-AB02 may be a good candidate as a therapeutic agent to control nosocomial infections caused by MDR A. baumannii.
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Affiliation(s)
- Behnam Sisakhtpour
- Department of Bacteriology and Virology, Faculty of Medicine, Isfahan University of Medical Sciences, 81744-176, Isfahan, Iran
| | - Arezoo Mirzaei
- Department of Bacteriology and Virology, Faculty of Medicine, Isfahan University of Medical Sciences, 81744-176, Isfahan, Iran
| | - Vajihe Karbasizadeh
- Department of Bacteriology and Virology, Faculty of Medicine, Isfahan University of Medical Sciences, 81744-176, Isfahan, Iran
| | - Nafiseh Hosseini
- Department of Bacteriology and Virology, Faculty of Medicine, Isfahan University of Medical Sciences, 81744-176, Isfahan, Iran
| | - Mehdi Shabani
- Department of Bacteriology and Virology, Faculty of Medicine, Isfahan University of Medical Sciences, 81744-176, Isfahan, Iran
| | - Sharareh Moghim
- Department of Bacteriology and Virology, Faculty of Medicine, Isfahan University of Medical Sciences, 81744-176, Isfahan, Iran.
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Wienhold SM, Brack MC, Nouailles G, Krishnamoorthy G, Korf IHE, Seitz C, Wienecke S, Dietert K, Gurtner C, Kershaw O, Gruber AD, Ross A, Ziehr H, Rohde M, Neudecker J, Lienau J, Suttorp N, Hippenstiel S, Hocke AC, Rohde C, Witzenrath M. Preclinical Assessment of Bacteriophage Therapy against Experimental Acinetobacter baumannii Lung Infection. Viruses 2021; 14:33. [PMID: 35062236 PMCID: PMC8778864 DOI: 10.3390/v14010033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 12/19/2021] [Accepted: 12/21/2021] [Indexed: 11/16/2022] Open
Abstract
Respiratory infections caused by multidrug-resistant Acinetobacter baumannii are difficult to treat and associated with high mortality among critically ill hospitalized patients. Bacteriophages (phages) eliminate pathogens with high host specificity and efficacy. However, the lack of appropriate preclinical experimental models hampers the progress of clinical development of phages as therapeutic agents. Therefore, we tested the efficacy of a purified lytic phage, vB_AbaM_Acibel004, against multidrug-resistant A. baumannii clinical isolate RUH 2037 infection in immunocompetent mice and a human lung tissue model. Sham- and A. baumannii-infected mice received a single-dose of phage or buffer via intratracheal aerosolization. Group-specific differences in bacterial burden, immune and clinical responses were compared. Phage-treated mice not only recovered faster from infection-associated hypothermia but also had lower pulmonary bacterial burden, lower lung permeability, and cytokine release. Histopathological examination revealed less inflammation with unaffected inflammatory cellular recruitment. No phage-specific adverse events were noted. Additionally, the bactericidal effect of the purified phage on A. baumannii was confirmed after single-dose treatment in an ex vivo human lung infection model. Taken together, our data suggest that the investigated phage has significant potential to treat multidrug-resistant A. baumannii infections and further support the development of appropriate methods for preclinical evaluation of antibacterial efficacy of phages.
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Affiliation(s)
- Sandra-Maria Wienhold
- Division of Pulmonary Inflammation, Charité–Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, 10115 Berlin, Germany; (S.-M.W.); (M.C.B.); (G.N.); (G.K.); (J.L.); (A.C.H.)
| | - Markus C. Brack
- Division of Pulmonary Inflammation, Charité–Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, 10115 Berlin, Germany; (S.-M.W.); (M.C.B.); (G.N.); (G.K.); (J.L.); (A.C.H.)
- Department of Infectious Diseases and Respiratory Medicine, Charité–Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, 10115 Berlin, Germany; (N.S.); (S.H.)
| | - Geraldine Nouailles
- Division of Pulmonary Inflammation, Charité–Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, 10115 Berlin, Germany; (S.-M.W.); (M.C.B.); (G.N.); (G.K.); (J.L.); (A.C.H.)
| | - Gopinath Krishnamoorthy
- Division of Pulmonary Inflammation, Charité–Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, 10115 Berlin, Germany; (S.-M.W.); (M.C.B.); (G.N.); (G.K.); (J.L.); (A.C.H.)
| | - Imke H. E. Korf
- Department of Microorganisms, Leibniz Institute DSMZGerman Collection of Microorganisms and Cell Cultures, 38124 Braunschweig, Germany; (I.H.E.K.); (C.R.)
- Department of Pharmaceutical Biotechnology, Fraunhofer Institute for Toxicology and Experimental Medicine (ITEM), 38124 Braunschweig, Germany; (C.S.); (S.W.); (A.R.); (H.Z.)
| | - Claudius Seitz
- Department of Pharmaceutical Biotechnology, Fraunhofer Institute for Toxicology and Experimental Medicine (ITEM), 38124 Braunschweig, Germany; (C.S.); (S.W.); (A.R.); (H.Z.)
| | - Sarah Wienecke
- Department of Pharmaceutical Biotechnology, Fraunhofer Institute for Toxicology and Experimental Medicine (ITEM), 38124 Braunschweig, Germany; (C.S.); (S.W.); (A.R.); (H.Z.)
| | - Kristina Dietert
- Department of Veterinary Pathology, Freie Universität Berlin, 14163 Berlin, Germany; (K.D.); (C.G.); (O.K.); (A.D.G.)
- Veterinary Centre for Resistance Research, Freie Universität Berlin, 14163 Berlin, Germany
| | - Corinne Gurtner
- Department of Veterinary Pathology, Freie Universität Berlin, 14163 Berlin, Germany; (K.D.); (C.G.); (O.K.); (A.D.G.)
| | - Olivia Kershaw
- Department of Veterinary Pathology, Freie Universität Berlin, 14163 Berlin, Germany; (K.D.); (C.G.); (O.K.); (A.D.G.)
| | - Achim D. Gruber
- Department of Veterinary Pathology, Freie Universität Berlin, 14163 Berlin, Germany; (K.D.); (C.G.); (O.K.); (A.D.G.)
| | - Anton Ross
- Department of Pharmaceutical Biotechnology, Fraunhofer Institute for Toxicology and Experimental Medicine (ITEM), 38124 Braunschweig, Germany; (C.S.); (S.W.); (A.R.); (H.Z.)
| | - Holger Ziehr
- Department of Pharmaceutical Biotechnology, Fraunhofer Institute for Toxicology and Experimental Medicine (ITEM), 38124 Braunschweig, Germany; (C.S.); (S.W.); (A.R.); (H.Z.)
| | - Manfred Rohde
- Central Facility for Microscopy, Helmholtz-Centre for Infection Research (HZI), 38124 Braunschweig, Germany;
| | - Jens Neudecker
- Department of General, Visceral, Vascular and Thoracic Surgery, Charité–Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, 10115 Berlin, Germany;
| | - Jasmin Lienau
- Division of Pulmonary Inflammation, Charité–Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, 10115 Berlin, Germany; (S.-M.W.); (M.C.B.); (G.N.); (G.K.); (J.L.); (A.C.H.)
| | - Norbert Suttorp
- Department of Infectious Diseases and Respiratory Medicine, Charité–Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, 10115 Berlin, Germany; (N.S.); (S.H.)
| | - Stefan Hippenstiel
- Department of Infectious Diseases and Respiratory Medicine, Charité–Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, 10115 Berlin, Germany; (N.S.); (S.H.)
| | - Andreas C. Hocke
- Division of Pulmonary Inflammation, Charité–Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, 10115 Berlin, Germany; (S.-M.W.); (M.C.B.); (G.N.); (G.K.); (J.L.); (A.C.H.)
- Department of Infectious Diseases and Respiratory Medicine, Charité–Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, 10115 Berlin, Germany; (N.S.); (S.H.)
| | - Christine Rohde
- Department of Microorganisms, Leibniz Institute DSMZGerman Collection of Microorganisms and Cell Cultures, 38124 Braunschweig, Germany; (I.H.E.K.); (C.R.)
| | - Martin Witzenrath
- Division of Pulmonary Inflammation, Charité–Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, 10115 Berlin, Germany; (S.-M.W.); (M.C.B.); (G.N.); (G.K.); (J.L.); (A.C.H.)
- Department of Infectious Diseases and Respiratory Medicine, Charité–Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, 10115 Berlin, Germany; (N.S.); (S.H.)
- German Center for Lung Research (DZL), Partner Site Charité, 10117 Berlin, Germany
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Phenotypic and Genomic Comparison of Klebsiella pneumoniae Lytic Phages: vB_KpnM-VAC66 and vB_KpnM-VAC13. Viruses 2021; 14:v14010006. [PMID: 35062209 PMCID: PMC8778798 DOI: 10.3390/v14010006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Revised: 12/15/2021] [Accepted: 12/17/2021] [Indexed: 12/25/2022] Open
Abstract
Klebsiella pneumoniae is a human pathogen that worsens the prognosis of many immunocompromised patients. Here, we annotated and compared the genomes of two lytic phages that infect clinical strains of K. pneumoniae (vB_KpnM-VAC13 and vB_KpnM-VAC66) and phenotypically characterized vB_KpnM-VAC66 (time of adsorption of 12 min, burst size of 31.49 ± 0.61 PFU/infected cell, and a host range of 20.8% of the tested strains). Transmission electronic microscopy showed that vB_KpnM-VAC66 belongs to the Myoviridae family. The genomic analysis of the phage vB_KpnM-VAC66 revealed that its genome encoded 289 proteins. When compared to the genome of vB_KpnM-VAC13, they showed a nucleotide similarity of 97.56%, with a 93% of query cover, and the phylogenetic study performed with other Tevenvirinae phages showed a close common ancestor. However, there were 21 coding sequences which differed. Interestingly, the main differences were that vB_KpnM-VAC66 encoded 10 more homing endonucleases than vB_KpnM-VAC13, and that the nucleotidic and amino-acid sequences of the L-shaped tail fiber protein were highly dissimilar, leading to different three-dimensional protein predictions. Both phages differed significantly in their host range. These viruses may be useful in the development of alternative therapies to antibiotics or as a co-therapy increasing its antimicrobial potential, especially when addressing multidrug resistant (MDR) pathogens.
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25
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Wójcicki M, Średnicka P, Błażejak S, Gientka I, Kowalczyk M, Emanowicz P, Świder O, Sokołowska B, Juszczuk-Kubiak E. Characterization and Genome Study of Novel Lytic Bacteriophages against Prevailing Saprophytic Bacterial Microflora of Minimally Processed Plant-Based Food Products. Int J Mol Sci 2021; 22:12460. [PMID: 34830335 PMCID: PMC8624825 DOI: 10.3390/ijms222212460] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 11/14/2021] [Accepted: 11/16/2021] [Indexed: 12/13/2022] Open
Abstract
The food industry is still searching for novel solutions to effectively ensure the microbiological safety of food, especially fresh and minimally processed food products. Nowadays, the use of bacteriophages as potential biological control agents in microbiological food safety and preservation is a promising strategy. The aim of the study was the isolation and comprehensive characterization of novel bacteriophages with lytic activity against saprophytic bacterial microflora of minimally processed plant-based food products, such as mixed leaf salads. From 43 phages isolated from municipal sewage, four phages, namely Enterobacter phage KKP 3263, Citrobacter phage KKP 3664, Enterobacter phage KKP 3262, and Serratia phage KKP 3264 have lytic activity against Enterobacter ludwigii KKP 3083, Citrobacter freundii KKP 3655, Enterobacter cloacae KKP 3082, and Serratia fonticola KKP 3084 bacterial strains, respectively. Transmission electron microscopy (TEM) and whole-genome sequencing (WGS) identified Enterobacter phage KKP 3263 as an Autographiviridae, and Citrobacter phage KKP 3664, Enterobacter phage KKP 3262, and Serratia phage KKP 3264 as members of the Myoviridae family. Genome sequencing revealed that these phages have linear double-stranded DNA (dsDNA) with sizes of 39,418 bp (KKP 3263), 61,608 bp (KKP 3664), 84,075 bp (KKP 3262), and 148,182 bp (KKP 3264). No antibiotic resistance genes, virulence factors, integrase, recombinase, or repressors, which are the main markers of lysogenic viruses, were annotated in phage genomes. Serratia phage KKP 3264 showed the greatest growth inhibition of Serratia fonticola KKP 3084 strain. The use of MOI 1.0 caused an almost 5-fold decrease in the value of the specific growth rate coefficient. The phages retained their lytic activity in a wide range of temperatures (from -20 °C to 50 °C) and active acidity values (pH from 4 to 11). All phages retained at least 70% of lytic activity at 60 °C. At 80 °C, no lytic activity against tested bacterial strains was observed. Serratia phage KKP 3264 was the most resistant to chemical factors, by maintaining high lytic activity across a broader range of pH from 3 to 11. The results indicated that these phages could be a potential biological control agent against saprophytic bacterial microflora of minimally processed plant-based food products.
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Affiliation(s)
- Michał Wójcicki
- Laboratory of Biotechnology and Molecular Engineering, Department of Microbiology, Prof. Wacław Dabrowski Institute of Agricultural and Food Biotechnology—State Research Institute, Rakowiecka 36 Street, 02-532 Warsaw, Poland; (M.W.); (P.Ś.); (M.K.); (P.E.)
| | - Paulina Średnicka
- Laboratory of Biotechnology and Molecular Engineering, Department of Microbiology, Prof. Wacław Dabrowski Institute of Agricultural and Food Biotechnology—State Research Institute, Rakowiecka 36 Street, 02-532 Warsaw, Poland; (M.W.); (P.Ś.); (M.K.); (P.E.)
| | - Stanisław Błażejak
- Department of Biotechnology and Food Microbiology, Institute of Food Sciences, Warsaw University of Life Sciences (WULS-SGGW), Nowoursynowska 166 Street, 02-776 Warsaw, Poland; (S.B.); (I.G.)
| | - Iwona Gientka
- Department of Biotechnology and Food Microbiology, Institute of Food Sciences, Warsaw University of Life Sciences (WULS-SGGW), Nowoursynowska 166 Street, 02-776 Warsaw, Poland; (S.B.); (I.G.)
| | - Monika Kowalczyk
- Laboratory of Biotechnology and Molecular Engineering, Department of Microbiology, Prof. Wacław Dabrowski Institute of Agricultural and Food Biotechnology—State Research Institute, Rakowiecka 36 Street, 02-532 Warsaw, Poland; (M.W.); (P.Ś.); (M.K.); (P.E.)
| | - Paulina Emanowicz
- Laboratory of Biotechnology and Molecular Engineering, Department of Microbiology, Prof. Wacław Dabrowski Institute of Agricultural and Food Biotechnology—State Research Institute, Rakowiecka 36 Street, 02-532 Warsaw, Poland; (M.W.); (P.Ś.); (M.K.); (P.E.)
| | - Olga Świder
- Department of Food Safety and Chemical Analysis, Prof. Wacław Dąbrowski Institute of Agricultural and Food Biotechnology—State Research Institute, Rakowiecka 36 Street, 02-532 Warsaw, Poland;
| | - Barbara Sokołowska
- Department of Microbiology, Prof. Wacław Dabrowski Institute of Agricultural and Food Biotechnology—State Research Institute, Rakowiecka 36 Street, 02-532 Warsaw, Poland;
| | - Edyta Juszczuk-Kubiak
- Laboratory of Biotechnology and Molecular Engineering, Department of Microbiology, Prof. Wacław Dabrowski Institute of Agricultural and Food Biotechnology—State Research Institute, Rakowiecka 36 Street, 02-532 Warsaw, Poland; (M.W.); (P.Ś.); (M.K.); (P.E.)
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26
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Patel SR, Pratap CB, Nath G. Evaluation of bacteriophage cocktail on septicaemia caused by colistin-resistant Acinetobacter baumannii in immunocompromised mice model. Indian J Med Res 2021; 154:141-149. [PMID: 34782540 PMCID: PMC8715691 DOI: 10.4103/ijmr.ijmr_2271_18] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Background & objectives: Since the bacterium, Acinetobacter baumannii (AB) has acquired resistance to almost all commercially available antibiotics, the search for alternative treatment options continues to be need of the hour. Bacteriophage therapy seems to be the most promising amongst various proposed alternatives (e.g. antimicrobial peptides, bacteriocin, probiotics, etc.). The present study, therefore, aimed to evaluate the effect of different dosages of specific phages in immunocompromised rodents in a septicaemia model caused by AB mimicking real clinical situations. Methods: The three most active and unique phages (ɸAb4, ɸAb7 and ɸAb14) were selected for this study. A constant dose (100 µl of 108 pfu/ml) of AB was given in all the experiments. Five different sets of experiments were designed: prophylactic administration of phage cocktail in the volume of 100 µl (109 pfu/ml) before and simultaneous with the bacterial challenge; and therapeutic i.e. administration of phage cocktail six, 12 and 24 h after bacterial challenge. Since there were deaths in mice when phage was given 24 h after bacterial challenge, the reduced dosage i.e. 100 µl of 107, 106, 105 pfu/ml of phage cocktail was also evaluated. Results: The administration of 100 µl (109 pfu/ml) of phage cocktail after six, 12 and 24 h of the bacterial challenge resulted in the mortality ranging between 20 to 60 per cent. However, no mortality could be observed with simultaneous or prophylactic administration of phages with the bacterial challenge. No mortality was observed with reduced doses of the cocktail (106 and105 pfu/ml). Interpretation & conclusions: As per the results of this study, it may be concluded that even if patients with acute infections report late to the hospital, a relatively low dose of the phage cocktail may be therapeutically beneficial.
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Affiliation(s)
- Shesh Raj Patel
- Department of Microbiology, Institute of Medical Sciences, Banaras Hindu University, Varanasi, Uttar Pradesh, India
| | - Chandra Bhan Pratap
- Department of Microbiology, Institute of Medical Sciences, Banaras Hindu University, Varanasi, Uttar Pradesh, India
| | - Gopal Nath
- Department of Microbiology, Institute of Medical Sciences, Banaras Hindu University, Varanasi, Uttar Pradesh, India
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Antoine C, Laforêt F, Blasdel B, Fall A, Duprez JN, Mainil J, Delcenserie V, Thiry D. In Vitro Characterization and In Vivo Efficacy Assessment in Galleria mellonella Larvae of Newly Isolated Bacteriophages against Escherichia coli K1. Viruses 2021; 13:2005. [PMID: 34696434 PMCID: PMC8541614 DOI: 10.3390/v13102005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 09/16/2021] [Accepted: 09/21/2021] [Indexed: 01/04/2023] Open
Abstract
Extra-intestinal Escherichia coli express several virulence factors that increase their ability to colonize and survive in different localizations. The K1 capsular type is involved in several infections, including meningitis, urinary tract, and bloodstream infections. The aims of this work were to isolate, characterize, and assess the in vivo efficacy of phages targeting avian pathogenic E. coli (APEC) O18:K1, which shares many similarities with the human strains responsible for neonatal meningitis. Eleven phages were isolated against APEC O18:K1, and four of them presenting a narrow spectrum targeting E. coli K1 strains were further studied. The newly isolated phages vB_EcoS_K1-ULINTec2 were similar to the Siphoviridae family, and vB_EcoP_K1-ULINTec4, vB_EcoP_K1-ULINTec6, and vB_EcoP_K1-ULINTec7 to the Autographiviridae family. They are capsular type (K1) dependent and present several advantages characteristic of lytic phages, such as a short adsorption time and latent period. vB_EcoP_K1-ULINTec7 is able to target both K1 and K5 strains. This study shows that these phages replicate efficiently, both in vitro and in vivo in the Galleria mellonella model. Phage treatment increases the larvae survival rates, even though none of the phages were able to eliminate the bacterial load.
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Affiliation(s)
- Céline Antoine
- Bacteriology Laboratory, Department of Infectious and Parasitic Diseases, FARAH and Faculty of Veterinary Medicine, University of Liège, 4000 Liège, Belgium; (C.A.); (F.L.); (J.-N.D.); (J.M.)
- Food Science Department, FARAH and Faculty of Veterinary Medicine, ULiège, 4000 Liège, Belgium;
| | - Fanny Laforêt
- Bacteriology Laboratory, Department of Infectious and Parasitic Diseases, FARAH and Faculty of Veterinary Medicine, University of Liège, 4000 Liège, Belgium; (C.A.); (F.L.); (J.-N.D.); (J.M.)
- Food Science Department, FARAH and Faculty of Veterinary Medicine, ULiège, 4000 Liège, Belgium;
| | - Bob Blasdel
- Vésale Bioscience, Vésale Pharmaceutica, 5310 Noville-sur-Mehaigne, Belgium;
| | - Abdoulaye Fall
- Genalyse Partner SA, En Hayeneux 62, 4040 Herstal, Belgium;
| | - Jean-Noël Duprez
- Bacteriology Laboratory, Department of Infectious and Parasitic Diseases, FARAH and Faculty of Veterinary Medicine, University of Liège, 4000 Liège, Belgium; (C.A.); (F.L.); (J.-N.D.); (J.M.)
| | - Jacques Mainil
- Bacteriology Laboratory, Department of Infectious and Parasitic Diseases, FARAH and Faculty of Veterinary Medicine, University of Liège, 4000 Liège, Belgium; (C.A.); (F.L.); (J.-N.D.); (J.M.)
| | - Véronique Delcenserie
- Food Science Department, FARAH and Faculty of Veterinary Medicine, ULiège, 4000 Liège, Belgium;
| | - Damien Thiry
- Bacteriology Laboratory, Department of Infectious and Parasitic Diseases, FARAH and Faculty of Veterinary Medicine, University of Liège, 4000 Liège, Belgium; (C.A.); (F.L.); (J.-N.D.); (J.M.)
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28
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Duyvejonck H, Merabishvili M, Vaneechoutte M, de Soir S, Wright R, Friman VP, Verbeken G, De Vos D, Pirnay JP, Van Mechelen E, Vermeulen SJT. Evaluation of the Stability of Bacteriophages in Different Solutions Suitable for the Production of Magistral Preparations in Belgium. Viruses 2021; 13:v13050865. [PMID: 34066841 PMCID: PMC8151234 DOI: 10.3390/v13050865] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 04/28/2021] [Accepted: 05/04/2021] [Indexed: 01/20/2023] Open
Abstract
In Belgium, the incorporation of phages into magistral preparations for human application has been permitted since 2018. The stability of such preparations is of high importance to guarantee quality and efficacy throughout treatments. We evaluated the ability to preserve infectivity of four different phages active against three different bacterial species in five different buffer and infusion solutions commonly used in medicine and biotechnological manufacturing processes, at two different concentrations (9 and 7 log pfu/mL), stored at 4 °C. DPBS without Ca2+ and Mg2+ was found to be the best option, compared to the other solutions. Suspensions with phage concentrations of 7 log pfu/mL were unsuited as their activity dropped below the effective therapeutic dose (6–9 log pfu/mL), even after one week of storage at 4 °C. Strong variability between phages was observed, with Acinetobacter baumannii phage Acibel004 being stable in four out of five different solutions. We also studied the long term storage of lyophilized staphylococcal phage ISP, and found that the titer could be preserved during a period of almost 8 years when sucrose and trehalose were used as stabilizers. After rehydration of the lyophilized ISP phage in saline, the phage solutions remained stable at 4 °C during a period of 126 days.
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Affiliation(s)
- Hans Duyvejonck
- Research Center Health & Water Technology, University College Ghent, Keramiekstraat 80, B-9000 Gent, Belgium; (H.D.); (E.V.M.)
- Laboratory Bacteriology Research, Faculty of Medicine & Health Sciences, Ghent University, C. Heymanslaan 10, B-9000 Gent, Belgium; (M.M.); (M.V.)
| | - Maya Merabishvili
- Laboratory Bacteriology Research, Faculty of Medicine & Health Sciences, Ghent University, C. Heymanslaan 10, B-9000 Gent, Belgium; (M.M.); (M.V.)
- Laboratory for Molecular and Cellular Technology, Queen Astrid Military Hospital, Bruynstraat 1, 1120 Brussel, Belgium; (S.d.S.); (G.V.); (D.D.V.); (J.-P.P.)
| | - Mario Vaneechoutte
- Laboratory Bacteriology Research, Faculty of Medicine & Health Sciences, Ghent University, C. Heymanslaan 10, B-9000 Gent, Belgium; (M.M.); (M.V.)
| | - Steven de Soir
- Laboratory for Molecular and Cellular Technology, Queen Astrid Military Hospital, Bruynstraat 1, 1120 Brussel, Belgium; (S.d.S.); (G.V.); (D.D.V.); (J.-P.P.)
| | - Rosanna Wright
- Department of Biology, University of York, Wentworth Way, York YO10 5DD, UK; (R.W.); (V.-P.F.)
- Division of Evolution and Genomic Sciences, University of Manchester, Dover Street, Manchester M13 9PT, UK
| | - Ville-Petri Friman
- Department of Biology, University of York, Wentworth Way, York YO10 5DD, UK; (R.W.); (V.-P.F.)
| | - Gilbert Verbeken
- Laboratory for Molecular and Cellular Technology, Queen Astrid Military Hospital, Bruynstraat 1, 1120 Brussel, Belgium; (S.d.S.); (G.V.); (D.D.V.); (J.-P.P.)
| | - Daniel De Vos
- Laboratory for Molecular and Cellular Technology, Queen Astrid Military Hospital, Bruynstraat 1, 1120 Brussel, Belgium; (S.d.S.); (G.V.); (D.D.V.); (J.-P.P.)
| | - Jean-Paul Pirnay
- Laboratory for Molecular and Cellular Technology, Queen Astrid Military Hospital, Bruynstraat 1, 1120 Brussel, Belgium; (S.d.S.); (G.V.); (D.D.V.); (J.-P.P.)
| | - Els Van Mechelen
- Research Center Health & Water Technology, University College Ghent, Keramiekstraat 80, B-9000 Gent, Belgium; (H.D.); (E.V.M.)
| | - Stefan J. T. Vermeulen
- Research Center Health & Water Technology, University College Ghent, Keramiekstraat 80, B-9000 Gent, Belgium; (H.D.); (E.V.M.)
- Correspondence: ; Tel.: +32-498-496-997
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Abstract
Viruses are ubiquitous and abundant in the oceans, and viral metagenomes (viromes) have been investigated extensively via several large-scale ocean sequencing projects. However, there have not been any systematic viromic studies in estuaries. Here, we investigated the viromes of the Delaware Bay and Chesapeake Bay, two Mid-Atlantic estuaries. Deep sequencing generated a total of 48,190 assembled viral sequences (>5 kb) and 26,487 viral populations (9,204 virus clusters and 17,845 singletons), including 319 circular viral contigs between 7.5 kb and 161.8 kb. Unknown viruses represented the vast majority of the dominant populations, while the composition of known viruses, such as pelagiphage and cyanophage, appeared to be relatively consistent across a wide range of salinity gradients and in different seasons. A difference between estuarine and ocean viromes was reflected by the proportions of Myoviridae, Podoviridae, Siphoviridae, Phycodnaviridae, and a few well-studied virus representatives. The difference in viral community between the Delaware Bay and Chesapeake Bay is significantly more pronounced than the difference caused by temperature or salinity, indicating strong local profiles caused by the unique ecology of each estuary. Interestingly, a viral contig similar to phages infecting Acinetobacter baumannii (“Iraqibacter”) was found to be highly abundant in the Delaware Bay but not in the Chesapeake Bay, the source of which is yet to be identified. Highly abundant viruses in both estuaries have close hits to viral sequences derived from the marine single-cell genomes or long-read single-molecule sequencing, suggesting that important viruses are still waiting to be discovered in the estuarine environment. IMPORTANCE This is the first systematic study about spatial and temporal variation of virioplankton communities in estuaries using deep metagenomics sequencing. It is among the highest-quality viromic data sets to date, showing remarkably consistent sequencing depth and quality across samples. Our results indicate that there exists a large pool of abundant and diverse viruses in estuaries that have not yet been cultivated, their genomes only available thanks to single-cell genomics or single-molecule sequencing, demonstrating the importance of these methods for viral discovery. The spatiotemporal pattern of these abundant uncultivated viruses is more variable than that of cultured viruses. Despite strong environmental gradients, season and location had surprisingly little impact on the viral community within an estuary, but we saw a significant distinction between the two estuaries and also between estuarine and open ocean viromes.
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Efficacy of isolated bacteriophage against biofilm embedded colistin-resistant Acinetobacter baumannii. GENE REPORTS 2021. [DOI: 10.1016/j.genrep.2020.100984] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Specific Interaction of Novel Friunavirus Phages Encoding Tailspike Depolymerases with Corresponding Acinetobacter baumannii Capsular Types. J Virol 2021; 95:JVI.01714-20. [PMID: 33268523 PMCID: PMC8092837 DOI: 10.1128/jvi.01714-20] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Acinetobacter baumannii is one of the most clinically important nosocomial pathogens. The World Health Organisation refers it to its «critical priority» category to develop new strategies for effective therapy. This microorganism is capable of producing structurally diverse capsular polysaccharides (CPSs), which serve as primary receptors for A. baumannii bacteriophages carrying polysaccharide-depolymerasing enzymes. In this study, eight novel bacterial viruses that specifically infect A. baumannii strains belonging to K2/K93, K32, K37, K44, K48, K87, K89 and K116 capsular types were isolated and characterized. The overall genomic architecture demonstrated that these viruses are representatives of the Friunavirus genus of the family Autographiviridae The linear double-stranded DNA phage genomes of 41,105-42,402 bp share high nucleotide sequence identity, except for genes encoding structural depolymerases or tailspikes which determine the host specificity. Deletion mutants lacking N-terminal domains of tailspike proteins were cloned, expressed and purified. The structurally defined CPSs of the phage bacterial hosts were cleaved with the specific recombinant depolymerases, and the resultant oligosaccharides that corresponded to monomers or/and dimers of the CPS repeats (K-units) were isolated. Structures of the derived oligosaccharides were established by nuclear magnetic resonance spectroscopy and high-resolution electrospray ionization mass spectrometry. The data obtained showed that all depolymerases studied were glycosidases that cleave specifically the A. baumannii CPSs by the hydrolytic mechanism, in most cases, by the linkage between the K-units.IMPORTANCE Acinetobacter baumannii, a nonfermentative, Gram-negative, aerobic bacterium, is one of the most significant nosocomial pathogens. The pathogenicity of A. baumannii is based on the cooperative action of many factors, one of them being the production of capsular polysaccharides (CPSs) that surround bacterial cells with a thick protective layer. Polymorphism of the chromosomal capsule loci is responsible for the observed high structural diversity of the CPSs. In this study, we describe eight novel lytic phages which have different tailspike depolymerases (TSDs) determining the interaction of the viruses with corresponding A. baumannii capsular types (K-types). Moreover, we elucidate the structures of oligosaccharide products obtained by cleavage of the CPSs by the recombinant depolymerases. We believe that as the TSDs determine phage specificity, the diversity of their structures should be taken into consideration as selection criteria for inclusion of certain phage candidate to the cocktail designed to control A. baumannii with different K-types.
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Lysin LysMK34 of Acinetobacter baumannii Bacteriophage PMK34 Has a Turgor Pressure-Dependent Intrinsic Antibacterial Activity and Reverts Colistin Resistance. Appl Environ Microbiol 2020; 86:AEM.01311-20. [PMID: 32709718 DOI: 10.1128/aem.01311-20] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 07/16/2020] [Indexed: 12/20/2022] Open
Abstract
The prevalence of extensively and pandrug-resistant strains of Acinetobacter baumannii leaves little or no therapeutic options for treatment for this bacterial pathogen. Bacteriophages and their lysins represent attractive alternative antibacterial strategies in this regard. We used the extensively drug-resistant A. baumannii strain MK34 to isolate the bacteriophage PMK34 (vB_AbaP_PMK34). This phage shows fast adsorption and lacks virulence genes; nonetheless, its narrow host spectrum based on capsule recognition limits broad application. PMK34 is a Fri1virus member of the Autographiviridae and has a 41.8-kb genome (50 open reading frames), encoding an endolysin (LysMK34) with potent muralytic activity (1,499.9 ± 131 U/μM), a typical mesophilic thermal stability up to 55°C, and a broad pH activity range (4 to 10). LysMK34 has an intrinsic antibacterial activity up to 4.8 and 2.4 log units for A. baumannii and Pseudomonas aeruginosa strains, respectively, but only when a high turgor pressure is present. The addition of 0.5 mM EDTA or application of an osmotic shock after treatment can compensate for the lack of a high turgor pressure. The combination of LysMK34 and colistin results in up to 32-fold reduction of the MIC of colistin, and colistin-resistant strains are resensitized in both Mueller-Hinton broth and 50% human serum. As such, LysMK34 may be used to safeguard the applicability of colistin as a last-resort antibiotic.IMPORTANCE A. baumannii is one of the most challenging pathogens for which development of new and effective antimicrobials is urgently needed. Colistin is a last-resort antibiotic, and even colistin-resistant A. baumannii strains exist. Here, we present a lysin that sensitizes A. baumannii for colistin and can revert colistin resistance to colistin susceptibility. The lysin also shows a strong, turgor pressure-dependent intrinsic antibacterial activity, providing new insights in the mode of action of lysins with intrinsic activity against Gram-negative bacteria.
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Vukotic G, Obradovic M, Novovic K, Di Luca M, Jovcic B, Fira D, Neve H, Kojic M, McAuliffe O. Characterization, Antibiofilm, and Depolymerizing Activity of Two Phages Active on Carbapenem-Resistant Acinetobacter baumannii. Front Med (Lausanne) 2020; 7:426. [PMID: 32974360 PMCID: PMC7461965 DOI: 10.3389/fmed.2020.00426] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 07/01/2020] [Indexed: 01/21/2023] Open
Abstract
Acinetobacter baumannii is a leading cause of healthcare-associated infections worldwide. Its various intrinsic and acquired mechanisms of antibiotic resistance make the therapeutic challenge even more serious. One of the promising alternative treatments that is increasingly highlighted is phage therapy, the therapeutic use of bacteriophages to treat bacterial infections. Two phages active against nosocomial carbapenem-resistant A. baumannii strain 6077/12, vB_AbaM_ISTD, and vB_AbaM_NOVI, were isolated from Belgrade wastewaters, purified, and concentrated using CsCl gradient ultracentrifugation. The phages were screened against 103 clinical isolates of A. baumannii from a laboratory collection and characterized based on plaque and virion morphology, host range, adsorption rate, and one-step growth curve. Given that phage ISTD showed a broader host range, better adsorption rate, shorter latent period, and larger burst size, its ability to lyse planktonic and biofilm-embedded cells was tested in detail. Phage ISTD yielded a 3.5- and 2-log reduction in planktonic and biofilm-associated viable bacterial cell count, respectively, but the effect was time-dependent. Both phages produced growing turbid halos around plaques indicating the synthesis of depolymerases, enzymes capable of degrading bacterial exopolysaccharides. Halos tested positive for presence of phages in the proximity of the plaque, but not further from the plaque, which indicates that the observed halo enlargement is a consequence of enzyme diffusion through the agar, independently of the phages. This notion was also supported by the growing halos induced by phage preparations applied on pregrown bacterial lawns, indicating that depolymerizing effect was achieved also on non-dividing sensitive cells. Overall, good rates of growth, fast adsorption rate, broad host range, and high depolymerizing activity, as well as antibacterial effectiveness against planktonic and biofilm-associated bacteria, make these phages good candidates for potential application in combating A. baumannii infections.
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Affiliation(s)
- Goran Vukotic
- Laboratory for Molecular Microbiology, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia.,Chair of Biochemistry and Molecular Biology, Faculty of Biology, University of Belgrade, Belgrade, Serbia
| | - Mina Obradovic
- Laboratory for Molecular Microbiology, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
| | - Katarina Novovic
- Laboratory for Molecular Microbiology, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
| | | | - Branko Jovcic
- Laboratory for Molecular Microbiology, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia.,Chair of Biochemistry and Molecular Biology, Faculty of Biology, University of Belgrade, Belgrade, Serbia
| | - Djordje Fira
- Chair of Biochemistry and Molecular Biology, Faculty of Biology, University of Belgrade, Belgrade, Serbia
| | - Horst Neve
- Department of Microbiology and Biotechnology, Max Rubner-Institut, Kiel, Germany
| | - Milan Kojic
- Laboratory for Molecular Microbiology, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
| | - Olivia McAuliffe
- Department of Food Biosciences, Teagasc Food Research Centre, Fermoy, Ireland
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Antibiotic Resistance Profiles, Molecular Mechanisms and Innovative Treatment Strategies of Acinetobacter baumannii. Microorganisms 2020; 8:microorganisms8060935. [PMID: 32575913 PMCID: PMC7355832 DOI: 10.3390/microorganisms8060935] [Citation(s) in RCA: 85] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 06/19/2020] [Accepted: 06/19/2020] [Indexed: 12/18/2022] Open
Abstract
Antibiotic resistance is one of the biggest challenges for the clinical sector and industry, environment and societal development. One of the most important pathogens responsible for severe nosocomial infections is Acinetobacter baumannii, a Gram-negative bacterium from the Moraxellaceae family, due to its various resistance mechanisms, such as the β-lactamases production, efflux pumps, decreased membrane permeability and altered target site of the antibiotic. The enormous adaptive capacity of A. baumannii and the acquisition and transfer of antibiotic resistance determinants contribute to the ineffectiveness of most current therapeutic strategies, including last-line or combined antibiotic therapy. In this review, we will present an update of the antibiotic resistance profiles and underlying mechanisms in A. baumannii and the current progress in developing innovative strategies for combating multidrug-resistant A. baumannii (MDRAB) infections.
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TAC1, an unclassified bacteriophage of the family Myoviridae infecting Acinetobacter baumannii with a large burst size and a short latent period. Arch Virol 2019; 165:419-424. [DOI: 10.1007/s00705-019-04483-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Accepted: 10/26/2019] [Indexed: 10/25/2022]
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36
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Cheng H, Cheng D, Mao J, Lu T, Hong PY. Identification and characterization of core sludge and biofilm microbiota in anaerobic membrane bioreactors. ENVIRONMENT INTERNATIONAL 2019; 133:105165. [PMID: 31520957 DOI: 10.1016/j.envint.2019.105165] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Revised: 08/15/2019] [Accepted: 09/05/2019] [Indexed: 05/20/2023]
Abstract
An analysis of sludge (i.e., 63 samples) and biofilm (i.e., 79 samples) sampled from 13 anaerobic membrane bioreactors (AnMBR) was conducted. Predominant microbial community identification and multivariate analysis indicate that these reactors showed different microbial community structure, but these differences had no impact on the overall AnMBR performance. Instead, core microbial genera which occurred in ≥90% of sludge (20 genera) and biofilm (12 genera) samples could potentially account for the AnMBR performance. A further calculation on net growth rate (NGR) of core genera in sludge suggested distribution into two main groups (i.e., I: low relative abundance and NGR, II: high relative abundance or high NGR). Consistent positive correlations between bacterial genera were observed among those that exhibited either high relative abundance or high NGR. The anaerobic microbial consortium in both sludge and biofilm were largely affected by stochastic dispersal and migration processes (i.e., neutral assembly). However, Acinetobacter spp. and Methanobacterium spp. occurred consistently in higher frequency in the biofilm but in lower occurrence frequency in the AnMBR permeate. Findings from this study suggest first, specific core microorganisms exist in the sludge regardless of the operating conditions of the AnMBRs, and second, prevention of biofoulant layer on anaerobic membranes can be devised by minimizing attachment of microbes on surfaces in a non-selective manner.
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Affiliation(s)
- Hong Cheng
- King Abdullah University of Science and Technology (KAUST), Water Desalination and Reuse Center (WDRC), Biological and Environmental Sciences & Engineering Division (BESE), Thuwal 23955-6900, Saudi Arabia
| | - Dan Cheng
- Singapore Centre for Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, Singapore 637551, Singapore
| | - Junwen Mao
- Department of Physics, Huzhou University, Zhejiang 313000, China; Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Ting Lu
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Pei-Ying Hong
- King Abdullah University of Science and Technology (KAUST), Water Desalination and Reuse Center (WDRC), Biological and Environmental Sciences & Engineering Division (BESE), Thuwal 23955-6900, Saudi Arabia.
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Blasco L, Ambroa A, Lopez M, Fernandez-Garcia L, Bleriot I, Trastoy R, Ramos-Vivas J, Coenye T, Fernandez-Cuenca F, Vila J, Martinez-Martinez L, Rodriguez-Baño J, Pascual A, Cisneros JM, Pachon J, Bou G, Tomas M. Combined Use of the Ab105-2φΔCI Lytic Mutant Phage and Different Antibiotics in Clinical Isolates of Multi-Resistant Acinetobacter baumannii. Microorganisms 2019; 7:microorganisms7110556. [PMID: 31726694 PMCID: PMC6921023 DOI: 10.3390/microorganisms7110556] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 11/08/2019] [Accepted: 11/09/2019] [Indexed: 12/21/2022] Open
Abstract
Phage therapy is an abandoned antimicrobial therapy that has been resumed in recent years. In this study, we mutated a lysogenic phage from Acinetobacter baumannii into a lytic phage (Ab105-2phiΔCI) that displayed antimicrobial activity against A. baumannii clinical strain Ab177_GEIH-2000 (isolated in the GEIH-REIPI Spanish Multicenter A. baumannii Study II 2000/2010, Umbrella Genbank Bioproject PRJNA422585, and for which meropenem and imipenem MICs of respectively, 32 µg/mL, and 16 µg/mL were obtained). We observed an in vitro synergistic antimicrobial effect (reduction of 4 log–7 log CFU/mL) between meropenem and the lytic phage in all combinations analyzed (Ab105-2phiΔCI mutant at 0.1, 1 and 10 MOI and meropenem at 1/4 and 1/8 MIC). Moreover, bacterial growth was reduced by 8 log CFU/mL for the combination of imipenem at 1/4 MIC plus lytic phage (Ab105-2phiΔCI mutant) and by 4 log CFU/mL for the combination of imipenem at 1/8 MIC plus lytic phage (Ab105-2phiΔCI mutant) at both MOI 1 and 10. These results were confirmed in an in vivo model (G. mellonella), and the combination of imipenem and mutant Ab105-2phiΔCI was most effective (p < 0.05). This approach could help to reduce the emergence of phage resistant bacteria and restore sensitivity to antibiotics used to combat multi-resistant strains of Acinetobacter baumannii.
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Affiliation(s)
- Lucia Blasco
- Microbiology Department-Research Institute Biomedical A Coruña (INIBIC), Hospital A Coruña (CHUAC), University of A Coruña (UDC), 15495 A Coruña, Spain; (L.B.); (A.A.); (M.L.); (L.F.-G.); (I.B.); (R.T.); (G.B.)
| | - Anton Ambroa
- Microbiology Department-Research Institute Biomedical A Coruña (INIBIC), Hospital A Coruña (CHUAC), University of A Coruña (UDC), 15495 A Coruña, Spain; (L.B.); (A.A.); (M.L.); (L.F.-G.); (I.B.); (R.T.); (G.B.)
| | - Maria Lopez
- Microbiology Department-Research Institute Biomedical A Coruña (INIBIC), Hospital A Coruña (CHUAC), University of A Coruña (UDC), 15495 A Coruña, Spain; (L.B.); (A.A.); (M.L.); (L.F.-G.); (I.B.); (R.T.); (G.B.)
| | - Laura Fernandez-Garcia
- Microbiology Department-Research Institute Biomedical A Coruña (INIBIC), Hospital A Coruña (CHUAC), University of A Coruña (UDC), 15495 A Coruña, Spain; (L.B.); (A.A.); (M.L.); (L.F.-G.); (I.B.); (R.T.); (G.B.)
| | - Ines Bleriot
- Microbiology Department-Research Institute Biomedical A Coruña (INIBIC), Hospital A Coruña (CHUAC), University of A Coruña (UDC), 15495 A Coruña, Spain; (L.B.); (A.A.); (M.L.); (L.F.-G.); (I.B.); (R.T.); (G.B.)
| | - Rocio Trastoy
- Microbiology Department-Research Institute Biomedical A Coruña (INIBIC), Hospital A Coruña (CHUAC), University of A Coruña (UDC), 15495 A Coruña, Spain; (L.B.); (A.A.); (M.L.); (L.F.-G.); (I.B.); (R.T.); (G.B.)
| | - Jose Ramos-Vivas
- Microbiology Department-Research Institute Biomedical Valdecilla (IDIVAL), Hospital Marques de Valdecilla, 39008 Santander, Spain;
| | - Tom Coenye
- Laboratory of Pharmaceutical Microbiology, Ghent University, 9000 Gent, Belgium;
| | - Felipe Fernandez-Cuenca
- Clinical Unit for Infectious Diseases, Microbiology and Preventive Medicine, Hospital Universitario Virgen Macarena/Department of Microbiology and Medicine, University of Seville/Biomedicine Institute of Seville (IBIS), 41009 Seville, Spain; (F.F.-C.); (J.R.-B.); (A.P.)
| | - Jordi Vila
- Institute of Global Health of Barcelona (ISGlobal), Hospital Clínic-Universitat de Barcelona, 170, 08036 Barcelona, Spain;
| | - Luis Martinez-Martinez
- Unit of Microbiology, University Hospital Reina Sofía, Department of Microbiology, University of Córdoba, Maimonides Biomedical Research Institute of Cordoba (IMIBIC), 14004 Cordoba, Spain;
| | - Jesus Rodriguez-Baño
- Clinical Unit for Infectious Diseases, Microbiology and Preventive Medicine, Hospital Universitario Virgen Macarena/Department of Microbiology and Medicine, University of Seville/Biomedicine Institute of Seville (IBIS), 41009 Seville, Spain; (F.F.-C.); (J.R.-B.); (A.P.)
| | - Alvaro Pascual
- Clinical Unit for Infectious Diseases, Microbiology and Preventive Medicine, Hospital Universitario Virgen Macarena/Department of Microbiology and Medicine, University of Seville/Biomedicine Institute of Seville (IBIS), 41009 Seville, Spain; (F.F.-C.); (J.R.-B.); (A.P.)
| | - Jose Miguel Cisneros
- Clinical Unit for Infectious Diseases, Microbiology and Preventive Medicine, Hospital Universitario Virgen del Rocío/Department of Microbiology and Medicine, University of Seville/Biomedicine Institute of Seville (IBIS), 41009 Seville, Spain; (J.M.C.); (J.P.)
| | - Jeronimo Pachon
- Clinical Unit for Infectious Diseases, Microbiology and Preventive Medicine, Hospital Universitario Virgen del Rocío/Department of Microbiology and Medicine, University of Seville/Biomedicine Institute of Seville (IBIS), 41009 Seville, Spain; (J.M.C.); (J.P.)
| | - German Bou
- Microbiology Department-Research Institute Biomedical A Coruña (INIBIC), Hospital A Coruña (CHUAC), University of A Coruña (UDC), 15495 A Coruña, Spain; (L.B.); (A.A.); (M.L.); (L.F.-G.); (I.B.); (R.T.); (G.B.)
| | - Maria Tomas
- Microbiology Department-Research Institute Biomedical A Coruña (INIBIC), Hospital A Coruña (CHUAC), University of A Coruña (UDC), 15495 A Coruña, Spain; (L.B.); (A.A.); (M.L.); (L.F.-G.); (I.B.); (R.T.); (G.B.)
- Correspondence: ; Tel.: +34-981-176-399; Fax: +34-981-178-273
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Duyvejonck H, Merabishvili M, Pirnay JP, De Vos D, Verbeken G, Van Belleghem J, Gryp T, De Leenheer J, Van der Borght K, Van Simaey L, Vermeulen S, Van Mechelen E, Vaneechoutte M. Development of a qPCR platform for quantification of the five bacteriophages within bacteriophage cocktail 2 (BFC2). Sci Rep 2019; 9:13893. [PMID: 31554892 PMCID: PMC6761158 DOI: 10.1038/s41598-019-50461-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Accepted: 09/05/2019] [Indexed: 11/09/2022] Open
Abstract
To determine phage titers accurately, reproducibly and in a non-laborious and cost-effective manner, we describe the development of a qPCR platform for molecular quantification of five phages present in bacteriophage cocktail 2 (BFC2). We compared the performance of this molecular approach, with regard to quantification and reproducibility, with the standard culture-based double agar overlay method (DAO). We demonstrated that quantification of each of the five phages in BFC2 was possible by means of qPCR, without prior DNA extraction, but yields were significantly higher in comparison to DAO. Although DAO is assumed to provide an indication of the number of infective phage particles, whereas qPCR only provides information on the number of phage genomes, the difference in yield (qPCR/DAO ratio) was observed to be phage-dependent and appeared rather constant for all phages when analyzing different (freshly prepared) stocks of these phages. While DAO is necessary to determine sensitivity of clinical strains against phages in clinical applications, qPCR might be a valid alternative for rapid and reproducible quantification of freshly prepared stocks, after initial establishment of a correction factor towards DAO.
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Affiliation(s)
- Hans Duyvejonck
- Laboratory Bacteriology Research (LBR), Department of Diagnostic Sciences, Faculty of Medicine and Health Sciences, Ghent University, Corneel Heymanslaan 10, 9000, Ghent, Belgium. .,Department of Biosciences, Faculty of Education, Health and Social Work, University College Ghent, Keramiekstraat 80, 9000, Ghent, Belgium.
| | - Maya Merabishvili
- Laboratory Bacteriology Research (LBR), Department of Diagnostic Sciences, Faculty of Medicine and Health Sciences, Ghent University, Corneel Heymanslaan 10, 9000, Ghent, Belgium.,Laboratory for Molecular and Cellular Technology (LabMCT), Burn Wound Center, Queen Astrid Military Hospital, Bruynstraat 1, 1120, Brussels, Belgium.,The Eliava Institute of Bacteriophages, Microbiology and Virology, Gotua 3, Tbilisi, 0160, Georgia
| | - Jean-Paul Pirnay
- Laboratory for Molecular and Cellular Technology (LabMCT), Burn Wound Center, Queen Astrid Military Hospital, Bruynstraat 1, 1120, Brussels, Belgium
| | - Daniel De Vos
- Laboratory for Molecular and Cellular Technology (LabMCT), Burn Wound Center, Queen Astrid Military Hospital, Bruynstraat 1, 1120, Brussels, Belgium
| | - Gilbert Verbeken
- Laboratory for Molecular and Cellular Technology (LabMCT), Burn Wound Center, Queen Astrid Military Hospital, Bruynstraat 1, 1120, Brussels, Belgium
| | - Jonas Van Belleghem
- Laboratory Bacteriology Research (LBR), Department of Diagnostic Sciences, Faculty of Medicine and Health Sciences, Ghent University, Corneel Heymanslaan 10, 9000, Ghent, Belgium
| | - Tessa Gryp
- Laboratory Bacteriology Research (LBR), Department of Diagnostic Sciences, Faculty of Medicine and Health Sciences, Ghent University, Corneel Heymanslaan 10, 9000, Ghent, Belgium
| | - Julie De Leenheer
- Department of Biosciences, Faculty of Education, Health and Social Work, University College Ghent, Keramiekstraat 80, 9000, Ghent, Belgium
| | - Kelly Van der Borght
- Department of Biosciences, Faculty of Education, Health and Social Work, University College Ghent, Keramiekstraat 80, 9000, Ghent, Belgium
| | - Leen Van Simaey
- Laboratory Bacteriology Research (LBR), Department of Diagnostic Sciences, Faculty of Medicine and Health Sciences, Ghent University, Corneel Heymanslaan 10, 9000, Ghent, Belgium
| | - Stefan Vermeulen
- Department of Biosciences, Faculty of Education, Health and Social Work, University College Ghent, Keramiekstraat 80, 9000, Ghent, Belgium
| | - Els Van Mechelen
- Department of Biosciences, Faculty of Education, Health and Social Work, University College Ghent, Keramiekstraat 80, 9000, Ghent, Belgium
| | - Mario Vaneechoutte
- Laboratory Bacteriology Research (LBR), Department of Diagnostic Sciences, Faculty of Medicine and Health Sciences, Ghent University, Corneel Heymanslaan 10, 9000, Ghent, Belgium
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Characterization and complete genome sequence analysis of phage GP4, a novel lytic Bcep22-like podovirus. Arch Virol 2019; 164:2339-2343. [DOI: 10.1007/s00705-019-04309-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Accepted: 05/06/2019] [Indexed: 11/30/2022]
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Specific and Selective Bacteriophages in the Fight against Multidrug-resistant Acinetobacter baumannii. Virol Sin 2019; 34:347-357. [PMID: 31093881 DOI: 10.1007/s12250-019-00125-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Accepted: 03/29/2019] [Indexed: 01/21/2023] Open
Abstract
Acinetobacter baumannii causes serious infections especially in immunocompromised and/or hospitalized patients. Several A. baumannii strains are multidrug resistant and infect wounds, bones, and the respiratory tract. Current studies are focused on finding new effective agents against A. baumannii. Phage therapy is a promising means to fight this bacterium and many studies on procuring and applying new phages against A. baumannii are currently being conducted. As shown in animal models, phages against multidrug-resistant A. baumannii may control bacterial infections caused by this pathogen and may be a real hope to solve this dangerous health problem.
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Djebara S, Maussen C, De Vos D, Merabishvili M, Damanet B, Pang KW, De Leenheer P, Strachinaru I, Soentjens P, Pirnay JP. Processing Phage Therapy Requests in a Brussels Military Hospital: Lessons Identified. Viruses 2019; 11:v11030265. [PMID: 30884879 PMCID: PMC6466067 DOI: 10.3390/v11030265] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 03/10/2019] [Accepted: 03/14/2019] [Indexed: 12/18/2022] Open
Abstract
There is a growing interest in phage therapy as a complementary tool against antimicrobial resistant infections. Since 2007, phages have been used sporadically to treat bacterial infections in well-defined cases in the Queen Astrid military hospital (QAMH) in Brussels, Belgium. In the last two years, external requests for phage therapy have increased significantly. From April 2013 to April 2018, 260 phage therapy requests were addressed to the QAMH. Of these 260 requests, only 15 patients received phage therapy. In this paper, we analyze the phage therapy requests and outcomes in order to improve upon the overall capacity for phage therapy at the QAMH.
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Affiliation(s)
- Sarah Djebara
- Center for Infectious diseases ID4C, Queen Astrid military hospital, Bruynstraat 1, B-1120 Brussels, Belgium.
| | - Christiane Maussen
- Center for Infectious diseases ID4C, Queen Astrid military hospital, Bruynstraat 1, B-1120 Brussels, Belgium.
| | - Daniel De Vos
- Laboratory for molecular and cellular technology, Queen Astrid military hospital, Bruynstraat 1, B-1120 Brussels, Belgium.
| | - Maya Merabishvili
- Laboratory for molecular and cellular technology, Queen Astrid military hospital, Bruynstraat 1, B-1120 Brussels, Belgium.
| | - Benjamin Damanet
- Center for Infectious diseases ID4C, Queen Astrid military hospital, Bruynstraat 1, B-1120 Brussels, Belgium.
| | - Kim Win Pang
- Center for Infectious diseases ID4C, Queen Astrid military hospital, Bruynstraat 1, B-1120 Brussels, Belgium.
| | - Peggy De Leenheer
- Center for Infectious diseases ID4C, Queen Astrid military hospital, Bruynstraat 1, B-1120 Brussels, Belgium.
| | - Isabella Strachinaru
- Center for Infectious diseases ID4C, Queen Astrid military hospital, Bruynstraat 1, B-1120 Brussels, Belgium.
| | - Patrick Soentjens
- Center for Infectious diseases ID4C, Queen Astrid military hospital, Bruynstraat 1, B-1120 Brussels, Belgium.
| | - Jean-Paul Pirnay
- Laboratory for molecular and cellular technology, Queen Astrid military hospital, Bruynstraat 1, B-1120 Brussels, Belgium.
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Global In-Silico Scenario of tRNA Genes and Their Organization in Virus Genomes. Viruses 2019; 11:v11020180. [PMID: 30795514 PMCID: PMC6409571 DOI: 10.3390/v11020180] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Revised: 01/28/2019] [Accepted: 01/30/2019] [Indexed: 12/22/2022] Open
Abstract
Viruses are known to be highly dependent on the host translation machinery for their protein synthesis. However, tRNA genes are occasionally identified in such organisms, and in addition, few of them harbor tRNA gene clusters comprising dozens of genes. Recently, tRNA gene clusters have been shown to occur among the three domains of life. In such a scenario, the viruses could play a role in the dispersion of such structures among these organisms. Thus, in order to reveal the prevalence of tRNA genes as well as tRNA gene clusters in viruses, we performed an unbiased large-scale genome survey. Interestingly, tRNA genes were predicted in ssDNA (single-stranded DNA) and ssRNA (single-stranded RNA) viruses as well in many other dsDNA viruses of families from Caudovirales order. In the latter group, tRNA gene clusters composed of 15 to 37 tRNA genes were characterized, mainly in bacteriophages, enlarging the occurrence of such structures within viruses. These bacteriophages were from hosts that encompass five phyla and 34 genera. This in-silico study presents the current global scenario of tRNA genes and their organization in virus genomes, contributing and opening questions to be explored in further studies concerning the role of the translation apparatus in these organisms.
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43
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Fan N, Yang M, Jin R, Qi R. Isolation and Genomic Characterization of an Acinetobacter johnsonii Bacteriophage AJO2 From Bulking Activated Sludge. Front Microbiol 2019; 10:266. [PMID: 30873130 PMCID: PMC6401600 DOI: 10.3389/fmicb.2019.00266] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Accepted: 02/01/2019] [Indexed: 11/13/2022] Open
Abstract
A novel Podoviridae lytic phage AJO2, specifically infecting Acinetobacter johnsonii, was isolated from bulking activated sludge. The one-step growth experiment showed that the latent period and burst size of AJO2 were estimated to be 30 min and 78.1 phages per infected cell, respectively. The viability test indicated that neutral conditions (pH 6-8) were table for AJO2 survival, while it was sensitive to high temperature (≥60°C) and ultraviolet treatment (254 nm). Genomic sequencing revealed that the AJO2 had a linearly permuted, double-stranded (ds) DNA consisting of 38,124 bp, with the G+C content of 41 mol%. A total of 58 putative open reading frames (ORFs), 11 pairs of repeats and 11 promoters were identified. The AJO2 genome had a modular gene structure which shared some similarities to those of A. baumanii phages. However, genomic comparative analysis revealed many differences among them, and novel genes were identified in the AJO2 genome. These results contribute to subsequent researches on the interaction between bacteriophages and hosts in wastewater treatment, especially during the bulking period. Additionally, the newly isolated phage could be a good candidate as a therapeutic agent to control nosocomial infections caused by A. johnsonii.
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Affiliation(s)
- Niansi Fan
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Min Yang
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Rencun Jin
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Rong Qi
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, University of Chinese Academy of Sciences, Beijing, China
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Functional Analysis and Antivirulence Properties of a New Depolymerase from a Myovirus That Infects Acinetobacter baumannii Capsule K45. J Virol 2019; 93:JVI.01163-18. [PMID: 30463964 DOI: 10.1128/jvi.01163-18] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Accepted: 11/08/2018] [Indexed: 12/15/2022] Open
Abstract
Acinetobacter baumannii is an important pathogen causative of health care-associated infections and is able to rapidly develop resistance to all known antibiotics, including colistin. As an alternative therapeutic agent, we have isolated a novel myovirus (vB_AbaM_B9) which specifically infects and makes lysis from without in strains of the K45 and K30 capsule types, respectively. Phage B9 has a genome of 93,641 bp and encodes 167 predicted proteins, of which 29 were identified by mass spectrometry. This phage holds a capsule depolymerase (B9gp69) able to digest extracted exopolysaccharides of both K30 and K45 strains and remains active in a wide range of pH values (5 to 9), ionic strengths (0 to 500 mM), and temperatures (20 to 80°C). B9gp69 was demonstrated to be nontoxic in a cell line model of the human lung and to make the K45 strain fully susceptible to serum killing in vitro Contrary to the case with phage, no resistance development was observed by bacteria targeted with the B9gp69. Therefore, capsular depolymerases may represent attractive antimicrobial agents against A. baumannii infections.IMPORTANCE Currently, phage therapy has revived interest for controlling hard-to-treat bacterial infections. Acinetobacter baumannii is an emerging Gram-negative pathogen able to cause a variety of nosocomial infections. Additionally, this species is becoming more resistant to several classes of antibiotics. Here we describe the isolation of a novel lytic myophage B9 and its recombinant depolymerase. While the phage can be a promising alternative antibacterial agent, its success in the market will ultimately depend on new regulatory frameworks and general public acceptance. We therefore characterized the phage-encoded depolymerase, which is a natural enzyme that can be more easily managed and used. To our knowledge, the therapeutic potential of phage depolymerase against A. baumannii is still unknown. We show for the first time that the K45 capsule type is an important virulence factor of A. baumannii and that capsule removal via the recombinant depolymerase activity helps the host immune system to combat the bacterial infection.
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45
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Saha D, Mukherjee R. Ameliorating the antimicrobial resistance crisis: phage therapy. IUBMB Life 2019; 71:781-790. [DOI: 10.1002/iub.2010] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Revised: 12/22/2018] [Accepted: 01/05/2019] [Indexed: 01/21/2023]
Affiliation(s)
- Dibya Saha
- Department of Biology; Indian Institute of Science Education and Research; Tirupati India
| | - Raju Mukherjee
- Department of Biology; Indian Institute of Science Education and Research; Tirupati India
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Complete Genome Sequences of Five Acinetobacter baumannii Phages from Abidjan, Côte d'Ivoire. Microbiol Resour Announc 2019; 8:MRA01358-18. [PMID: 30637387 PMCID: PMC6318358 DOI: 10.1128/mra.01358-18] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Accepted: 11/19/2018] [Indexed: 01/24/2023] Open
Abstract
Five bacteriophages of Acinetobacter baumannii were isolated from sewage water in Abidjan, Côte d’Ivoire. Phages Aci01-1, Aci02-2, and Aci05 belong to an unclassified genus of the Myoviridae family, with double-stranded DNA (dsDNA) genomes, whereas Aci07 and Aci08 belong to the Fri1virus genus of the Podoviridae family of phages. Five bacteriophages of Acinetobacter baumannii were isolated from sewage water in Abidjan, Côte d’Ivoire. Phages Aci01-1, Aci02-2, and Aci05 belong to an unclassified genus of the Myoviridae family, with double-stranded DNA (dsDNA) genomes, whereas Aci07 and Aci08 belong to the Fri1virus genus of the Podoviridae family of phages.
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Wang R, Xing S, Zhao F, Li P, Mi Z, Shi T, Liu H, Tong Y. Characterization and genome analysis of novel phage vB_EfaP_IME195 infecting Enterococcus faecalis. Virus Genes 2018; 54:804-811. [PMID: 30387031 DOI: 10.1007/s11262-018-1608-6] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Accepted: 10/12/2018] [Indexed: 01/17/2023]
Abstract
Enterococcus faecalis is one of the main bacteria in the human and animal intestine but is also classed as an opportunistic pathogen. During normal growth, E. faecalis produces natural antibiotics and is conducive to human health. As ectopic parasites, E. faecalis is capable of causing infective endocarditis, neonatal sepsis, bloodstream infections, bacteremia, and intraabdominal infections. With the incidence of antibiotic resistance reaching crisis point, it is imperative to find alternative treatments for multidrug-resistant infections. Using phage for pathogen control is a promising treatment option to combat bacterial resistance. In this study, a lytic phage, designated vB_EfaP_IME195, was isolated from hospital sewage using a clinical multidrug-resistant Enterococcus faecalis strain as an indicator. The one-step growth curve with the optimal multiplicity of infection of (MOI) 0.01 revealed a latent period of ~ 30 min and a burst size of ~ 120 plaque-forming units (pfu) per cell. Transmission electron microscopy showed that the phage belongs to the family Podoviridae. Phage vB_EfaP_IME195 has a linear, double-stranded DNA genome of 18,607 bp with a G + C content of 33% and 27 coding sequences (GenBank accession no. KT932700). Run-off sequencing experiments showed that the phage has a unique 59-bp inverted repeat sequences at the terminal ends. BLASTn analysis revealed that vB_EfaP_IME195 shares 92% identity (93% genome coverage) with unpublished E. faecalis phage Idefix. This study reported a novel E. faecalis phage with unique genome termini containing inverted repeats. The isolation and characterization of this novel lytic E. faecalis phage provides the basis for the development of new therapeutic agents like phage cocktails for multidrug-resistant E. faecalis infection, and its unique genomic feature would also provide valuable knowledge and insight for further phage genome analysis.
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Affiliation(s)
- Ronghuan Wang
- School of Public Health, Lanzhou University, Lanzhou, 730000, China
| | - Shaozhen Xing
- Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong, China
| | - Feiyang Zhao
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China
| | - Ping Li
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China
| | - Zhiqiang Mi
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China
| | - Taoxing Shi
- Academy of Military Medical Sciences, Beijing, 100085, China
| | - Hui Liu
- School of Public Health, Lanzhou University, Lanzhou, 730000, China.
| | - Yigang Tong
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China.
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100071, China.
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Manohar P, Tamhankar AJ, Lundborg CS, Ramesh N. Isolation, characterization and in vivo efficacy of Escherichia phage myPSH1131. PLoS One 2018; 13:e0206278. [PMID: 30356310 PMCID: PMC6200275 DOI: 10.1371/journal.pone.0206278] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Accepted: 10/10/2018] [Indexed: 12/14/2022] Open
Abstract
Phage therapy is the use of lytic bacteriophages to cure infections caused by bacteria. The aim of this study is to isolate and to characterize the bacteriophages against Escherichia coli isolated from clinical samples. For isolation of bacteriophages, water samples were collected from the Ganges River, and phage enrichment method was followed for phage isolation. Microbiological, genomic and lyophilization experiments were carried out to characterize the bacteriophage. Galleria mellonella was used to study the potential of phages against E. coli infection. Escherichia phage myPSH1131 belonging to Podoviridae family and found to have broad host range infectivity (n = 31) to infect Enterohemorrhagic E. coli (n = 9), Enteropathogenic E. coli (n = 6), Enterotoxigenic E. coli (n = 3), Enteroaggregative E. coli (n = 3), Uropathogenic E. coli (n = 9) and one unknown E. coli. The genome size is 76,163 base pairs (97 coding regions) and their genes show high similarity to SU10 phage. Lyophilization studies showed that the use of 1M sucrose, 2% gelatin and the combination of both 0.5M sucrose plus 1% gelatin could restore phage viability up to 20 months at 4°C. For in vivo studies, it was observed that a single phage dose can reduce the E. coli infection but to achieve 100% survival rate the infected larvae should be treated with three phage doses (20 μL, 103 PFU/mL) at 6 hours interval. The characterized Escherichia phage myPSH1131 was found to have broad host range activity against E. coli pathogens and in vivo studies showed that multiple doses are required for effective treatment.
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Affiliation(s)
- Prasanth Manohar
- Antibiotic Resistance and Phage Therapy Laboratory, School of Bioscience and Technology, Vellore Institute of Technology (VIT), Vellore, Tamil Nadu, India
| | - Ashok J. Tamhankar
- Global Health-Health Systems and Policy (HSP): Medicines, focusing antibiotics, Department of Public Health Sciences, Karolinska Institutet, Stockholm, Sweden
- Indian Initiative for Management of Antibiotic Resistance, Deonar, Mumbai, India
| | - Cecilia Stalsby Lundborg
- Global Health-Health Systems and Policy (HSP): Medicines, focusing antibiotics, Department of Public Health Sciences, Karolinska Institutet, Stockholm, Sweden
| | - Nachimuthu Ramesh
- Antibiotic Resistance and Phage Therapy Laboratory, School of Bioscience and Technology, Vellore Institute of Technology (VIT), Vellore, Tamil Nadu, India
- * E-mail:
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Enhanced antibacterial effect of the novel T4-like bacteriophage KARL-1 in combination with antibiotics against multi-drug resistant Acinetobacter baumannii. Sci Rep 2018; 8:14140. [PMID: 30237558 PMCID: PMC6147977 DOI: 10.1038/s41598-018-32344-y] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Accepted: 09/06/2018] [Indexed: 01/08/2023] Open
Abstract
The continuing rise of infections caused by multi-drug resistant bacteria has led to a renewed interest in bacteriophage therapy. Here we characterize phage vB_AbaM-KARL-1 with lytic activity against multi-drug resistant clinical isolates of Acinetobacter baumannii (AB). Besides genomic and phenotypic phage analysis, the objective of our study was to investigate the antibacterial outcome when the phage acts in concert with distinct antibiotics. KARL-1 belongs to the family of Myoviridae and is able to lyse 8 of 20 (40%) tested clinical isolates. Its double-stranded DNA genome consists of 166,560 bp encoding for 253 open reading frames. Genome wide comparison suggests that KARL-1 is a novel species within the subfamily Tevenvirinae, sharing 77% nucleotide identity (coverage 58%) with phage ZZ1. The antibacterial efficacy at various multiplicities of infection (MOI) was monitored either alone or in combination with meropenem, ciprofloxacin, and colistin. A complete clearance of liquid cultures was achieved with KARL-1 at an MOI of 10-1 and meropenem (>128 mg/l). KARL-1 was still effective at an MOI of 10-7, but antibacterial activity was significantly augmented with meropenem. While ciprofloxacin did generally not support phage activity, the application of KARL-1 at an MOI of 10-7 and therapeutic doses of colistin significantly elevated bacterial suppression. Hence, KARL-1 represents a novel candidate for use against multi-drug resistant AB and the therapeutic outcome may be positively influenced by the addition of traditional antibiotics.
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Characterization of vB_Kpn_F48, a Newly Discovered Lytic Bacteriophage for Klebsiella pneumoniae of Sequence Type 101. Viruses 2018; 10:v10090482. [PMID: 30205588 PMCID: PMC6163469 DOI: 10.3390/v10090482] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Revised: 09/05/2018] [Accepted: 09/07/2018] [Indexed: 02/06/2023] Open
Abstract
Resistance to carbapenems in Enterobacteriaceae, including Klebsiella pneumoniae, represents a major clinical problem given the lack of effective alternative antibiotics. Bacteriophages could provide a valuable tool to control the dissemination of antibiotic resistant isolates, for the decolonization of colonized individuals and for treatment purposes. In this work, we have characterized a lytic bacteriophage, named vB_Kpn_F48, specific for K. pneumoniae isolates belonging to clonal group 101. Phage vB_Kpn_F48 was classified as a member of Myoviridae, order Caudovirales, on the basis of transmission electron microscopy analysis. Physiological characterization demonstrated that vB_Kpn_F48 showed a narrow host range, a short latent period, a low burst size and it is highly stable to both temperature and pH variations. High throughput sequencing and bioinformatics analysis revealed that the phage is characterized by a 171 Kb dsDNA genome that lacks genes undesirable for a therapeutic perspective such integrases, antibiotic resistance genes and toxin encoding genes. Phylogenetic analysis suggests that vB_Kpn_F48 is a T4-like bacteriophage which belongs to a novel genus within the Tevenvirinae subfamily, which we tentatively named "F48virus". Considering the narrow host range, the genomic features and overall physiological parameters phage vB_Kpn_F48 could be a promising candidate to be used alone or in cocktails for phage therapy applications.
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