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Pourcel C, Essoh C, Ouldali M, Tavares P. Acinetobacter baumannii satellite phage Aci01-2-Phanie depends on a helper myophage for its multiplication. J Virol 2024:e0066724. [PMID: 38829140 DOI: 10.1128/jvi.00667-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2024] [Accepted: 05/06/2024] [Indexed: 06/05/2024] Open
Abstract
We report the discovery of a satellite-helper phage system with a novel type of dependence on a tail donor. The Acinetobacter baumannii satellite podovirus Aci01-2-Phanie (short name Phanie) uses a phage phi29-like DNA replication and packaging mode. Its linear 11,885 bp dsDNA genome bears 171 bp inverted terminal repeats (ITR). Phanie is related to phage DU-PP-III from Pectobacterium and to members of the Astrithrvirus from Salmonella enterica. Together, they form a new clade of phages with 27% to 30% identity over the whole genome. Detailed 3D protein structure prediction and mass spectrometry analyses demonstrate that Phanie encodes its capsid structural genes and genes necessary to form a short tail. However, our study reveals that Phanie virions are non-infectious unless they associate with the contractile tail of an unrelated phage, Aci01-1, to produce chimeric myoviruses. Following the coinfection of Phanie with myovirus Aci01-1, hybrid viral particles composed of Phanie capsids and Aci01-1 contractile tails are assembled together with Phanie and Aci01-1 particles.IMPORTANCEThere are few reported cases of satellite-helper phage interactions but many more may be yet undiscovered. Here we describe a new mode of satellite phage dependence on a helper phage. Phanie, like phage phi29, replicates its linear dsDNA by a protein primed-mechanism and protects it inside podovirus-like particles. However, these particles are defective, requiring the acquisition of the tail from a myovirus helper for production of infectious virions. The formation of chimeras between a phi29-like podovirus and a helper contractile tail reveals an unexpected association between very different bacterial viruses.
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Affiliation(s)
- Christine Pourcel
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Christiane Essoh
- Department of Biochemistry-Genetic, School of Biological Sciences, Université Peleforo Gon Coulibaly, Korhogo, Côte d'Ivoire
| | - Malika Ouldali
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Paulo Tavares
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
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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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Kolsi A, Haukka K, Dougnon V, Agbankpè AJ, Fabiyi K, Virta M, Skurnik M, Kantele A, Kiljunen S. Isolation and characterization of three novel Acinetobacter baumannii phages from Beninese hospital wastewater. Arch Virol 2023; 168:228. [PMID: 37574509 PMCID: PMC10423700 DOI: 10.1007/s00705-023-05845-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 06/19/2023] [Indexed: 08/15/2023]
Abstract
Acinetobacter baumannii is an opportunistic pathogen that is mostly associated with hospital-acquired infections. The rapid emergence of multi- and pan-drug-resistant Acinetobacter strains poses an increasing challenge in hospitals. Phage therapy offers one treatment option for infections caused by A. baumannii. We isolated three phages from Beninese hospital wastewater - fBenAci001, fBenAci002, and fBenAci003 - that infected clinical A. baumannii strains from Finnish patients. Phylogenetic analysis showed that these phages resemble phages of the genus Friunavirus, family Autographiviridae. The isolated phages meet the requirements set for phages used for phage therapy. However, they were found to have a narrow host range, which may limit their therapeutic use.
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Affiliation(s)
- Anna Kolsi
- Human Microbiome Research Program, Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Department of Microbiology, University of Helsinki, Helsinki, Finland
| | - Kaisa Haukka
- Human Microbiome Research Program, Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Department of Microbiology, University of Helsinki, Helsinki, Finland
| | - Victorien Dougnon
- Research Unit in Applied Microbiology and Pharmacology of natural substances, Polytechnic School of Abomey-Calavi, University of Abomey-Calavi, Abomey Calavi, Benin
| | - Alidehou Jerrold Agbankpè
- Research Unit in Applied Microbiology and Pharmacology of natural substances, Polytechnic School of Abomey-Calavi, University of Abomey-Calavi, Abomey Calavi, Benin
| | - Kafayath Fabiyi
- Research Unit in Applied Microbiology and Pharmacology of natural substances, Polytechnic School of Abomey-Calavi, University of Abomey-Calavi, Abomey Calavi, Benin
| | - Marko Virta
- Department of Microbiology, University of Helsinki, Helsinki, Finland
| | - Mikael Skurnik
- Human Microbiome Research Program, Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Division of Clinical Microbiology, HUS Diagnostic Center, Hospital District of Helsinki and Uusimaa, Helsinki, Finland
| | - Anu Kantele
- Human Microbiome Research Program, Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Meilahti Vaccine Research Center MeVac, Infectious Diseases, Helsinki University, Hospital District of Helsinki and Uusimaa, Helsinki, Finland
| | - Saija Kiljunen
- Human Microbiome Research Program, Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland.
- Division of Clinical Microbiology, HUS Diagnostic Center, Hospital District of Helsinki and Uusimaa, Helsinki, Finland.
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Pourcel C, Ouldali M, Tavares P, Essoh C. The saclayvirus Aci01-1 very long and complex fiber and its receptor at the Acinetobacter baumannii surface. Arch Virol 2023; 168:187. [PMID: 37351676 DOI: 10.1007/s00705-023-05817-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 05/16/2023] [Indexed: 06/24/2023]
Abstract
The Acinetobacter baumannii bacteriophage Aci01-1, which belongs to the genus Saclayvirus of the order Caudoviricetes, has an icosahedral head and a contractile rigid tail. We report that Aci01-1 has, attached to the tail conical tip, a remarkable 146-nm-long flexible fiber with seven beads and a terminal knot. Its putative gene coding for a 241.36-kDa tail fiber protein is homologous to genes in Aci01-1-related and unrelated phages. Analysis of its 3D structure using AlphaFold provides a structural model for the fiber observed by electron microscopy. We also identified a putative receptor of the phage on the bacterial capsule that is hypothesized to interact with the Aci01-1 long fiber.
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Affiliation(s)
- Christine Pourcel
- CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, 91198, Gif-sur-Yvette, France.
| | - Malika Ouldali
- CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, 91198, Gif-sur-Yvette, France
| | - Paulo Tavares
- CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, 91198, Gif-sur-Yvette, France
| | - Christiane Essoh
- Department of Biochemistry-Genetic, School of Biological Sciences, Université Peleforo Gon Coulibaly, Korhogo, Côte d'Ivoire
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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:v14020181. [PMID: 35215775 PMCID: PMC8878043 DOI: 10.3390/v14020181] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [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
- Correspondence:
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Jiang L, Tan J, Hao Y, Wang Q, Yan X, Wang D, Tuo L, Wei Z, Huang G. Isolation and Characterization of a Novel Myophage Abp9 Against Pandrug Resistant Acinetobacater baumannii. Front Microbiol 2020; 11:506068. [PMID: 33013774 PMCID: PMC7506109 DOI: 10.3389/fmicb.2020.506068] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2019] [Accepted: 08/12/2020] [Indexed: 01/10/2023] Open
Abstract
Acinetobacter baumannii (A. baumannii) has emerged as one of the most troublesome pathogens in health care institutions. A. baumannii can cause a wide range of diseases in humans, including pneumonia and septicemia. Phage therapy has drawn great interest from medical researchers as a potential way to control infections by antibiotic-resistant A. baumannii. Using a pandrug-resistant clinical A. baumannii isolate ABZY9 as an indicator, we isolated a lytic phage Abp9 from hospital sewage. Abp9 belongs to myoviridae family and shows a wider host range of 12%. Abp9 contains a linear double-stranded DNA genome of 44,820 bp with a G + C content of 37.69%. The Abp9 genome contains 80 open reading frames, but lacks any known virulence genes or lysogen-formation genes. In a systemic A. baumannii infection mouse models, Abp9 treatment showed good therapeutic effects. We have also observed an excellent lytic activity against A. baumannii in biofilm form of growth in vitro. All of these suggest that Abp9 is a good candidate for the phage therapy against drug-resistant A. baumannii infections.
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Affiliation(s)
- Lingli Jiang
- Department of Burn and Plastic, Affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - Jingjie Tan
- Department of Burn and Plastic, Affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - Yi Hao
- Department of Burn and Plastic, Affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - Qi Wang
- Department of Burn and Plastic, Affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - Xiaorui Yan
- Life Sciences Institute, Zunyi Medical University, Zunyi, China
| | - Dali Wang
- Department of Burn and Plastic, Affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - Li Tuo
- Life Sciences Institute, Zunyi Medical University, Zunyi, China
| | - Zairong Wei
- Department of Burn and Plastic, Affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - Guangtao Huang
- Department of Burn and Plastic, Affiliated Hospital of Zunyi Medical University, Zunyi, China
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