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da Silva JD, Bens L, Santos AJDC, Lavigne R, Soares J, Melo LDR, Vallino M, Dias RS, Drulis-Kawa Z, de Paula SO, Wagemans J. Isolation and Characterization of the Acadevirus Members BigMira and MidiMira Infecting a Highly Pathogenic Proteus mirabilis Strain. Microorganisms 2023; 11:2141. [PMID: 37763984 PMCID: PMC10537623 DOI: 10.3390/microorganisms11092141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 08/14/2023] [Accepted: 08/20/2023] [Indexed: 09/29/2023] Open
Abstract
Proteus mirabilis is an opportunistic pathogen and is responsible for more than 40% of all cases of catheter-associated urinary tract infections (CAUTIs). Healthcare-associated infections have been aggravated by the constant emergence of antibiotic-resistant bacterial strains. Because of this, the use of phages to combat bacterial infections gained renewed interest. In this study, we describe the biological and genomic features of two P. mirabilis phages, named BigMira and MidiMira. These phages belong to the Acadevirus genus (family Autographiviridae). BigMira and MidiMira are highly similar, differing only in four missense mutations in their phage tail fiber. These mutations are sufficient to impact the phages' depolymerase activity. Subsequently, the comparative genomic analysis of ten clinical P. mirabilis strains revealed differences in their antibiotic resistance profiles and lipopolysaccharide locus, with the latter potentially explaining the host range data of the phages. The massive presence of antimicrobial resistance genes, especially in the phages' isolation strain P. mirabilis MCS, highlights the challenges in treating infections caused by multidrug-resistant bacteria. The findings reinforce BigMira and MidiMira phages as candidates for phage therapy purposes.
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Affiliation(s)
- Jéssica Duarte da Silva
- Laboratory of Molecular Immunovirology, Department of Microbiology, Federal University of Viçosa, Viçosa 36570-900, MG, Brazil; (J.D.d.S.); (A.J.d.C.S.); (J.S.); (S.O.d.P.)
| | - Lene Bens
- Laboratory of Gene Technology, Department of Biosystems, Division of Animal and Human Health Engineering, KU Leuven, 3000 Leuven, Belgium; (L.B.); (R.L.)
| | - Adriele J. do Carmo Santos
- Laboratory of Molecular Immunovirology, Department of Microbiology, Federal University of Viçosa, Viçosa 36570-900, MG, Brazil; (J.D.d.S.); (A.J.d.C.S.); (J.S.); (S.O.d.P.)
| | - Rob Lavigne
- Laboratory of Gene Technology, Department of Biosystems, Division of Animal and Human Health Engineering, KU Leuven, 3000 Leuven, Belgium; (L.B.); (R.L.)
| | - José Soares
- Laboratory of Molecular Immunovirology, Department of Microbiology, Federal University of Viçosa, Viçosa 36570-900, MG, Brazil; (J.D.d.S.); (A.J.d.C.S.); (J.S.); (S.O.d.P.)
| | - Luís D. R. Melo
- Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal;
- LABBELS—Associate Laboratory, 4710-057 Braga, Portugal
| | - Marta Vallino
- Institute for Sustainable Plant Protection, National Research Council of Italy, 10135 Torino, Italy;
| | - Roberto Sousa Dias
- Department of General Biology, Federal University of Viçosa, Viçosa 36570-900, MG, Brazil;
| | - Zuzanna Drulis-Kawa
- Department of Pathogen Biology and Immunology, University of Wroclaw, 50-335 Wroclaw, Poland;
| | - Sérgio Oliveira de Paula
- Laboratory of Molecular Immunovirology, Department of Microbiology, Federal University of Viçosa, Viçosa 36570-900, MG, Brazil; (J.D.d.S.); (A.J.d.C.S.); (J.S.); (S.O.d.P.)
- Department of General Biology, Federal University of Viçosa, Viçosa 36570-900, MG, Brazil;
| | - Jeroen Wagemans
- Laboratory of Gene Technology, Department of Biosystems, Division of Animal and Human Health Engineering, KU Leuven, 3000 Leuven, Belgium; (L.B.); (R.L.)
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Ismail A, Saini T, Al Qaffas A, Erill I, Caruso SM, Temple L, Johnson AA. Evidence of a Set of Core-Function Genes in 16 Bacillus Podoviral Genomes with Considerable Genomic Diversity. Viruses 2023; 15. [PMID: 36851489 DOI: 10.3390/v15020276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 01/06/2023] [Accepted: 01/13/2023] [Indexed: 01/20/2023] Open
Abstract
Bacteriophage genomes represent an enormous level of genetic diversity and provide considerable potential to acquire new insights about viral genome evolution. In this study, the genome sequences of sixteen Bacillus-infecting bacteriophages were explored through comparative genomics approaches to reveal shared and unique characteristics. These bacteriophages are in the Salasmaviridae family with small (18,548-27,206 bp) double-stranded DNA genomes encoding 25-46 predicted open reading frames. We observe extensive nucleotide and amino acid sequence divergence among a set of core-function genes that present clear synteny. We identify two examples of sequence directed recombination within essential genes, as well as explore the expansion of gene content in these genomes through the introduction of novel open reading frames. Together, these findings highlight the complex evolutionary relationships of phage genomes that include old, common origins as well as new components introduced through mosaicism.
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Abstract
Numerous bacteriophages-viruses of bacteria, also known as phages-have been described for hundreds of bacterial species. The Gram-negative Shigella species are close relatives of Escherichia coli, yet relatively few previously described phages appear to exclusively infect this genus. Recent efforts to isolate Shigella phages have indicated these viruses are surprisingly abundant in the environment and have distinct genomic and structural properties. In addition, at least one model system used for experimental evolution studies has revealed a unique mechanism for developing faster infection cycles. Differences between these bacteriophages and other well-described model systems may mirror differences between their hosts' ecology and defense mechanisms. In this review, we discuss the history of Shigella phages and recent developments in their isolation and characterization and the structural information available for three model systems, Sf6, Sf14, and HRP29; we also provide an overview of potential selective pressures guiding both Shigella phage and host evolution.
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Affiliation(s)
- Sundharraman Subramanian
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824, USA
| | - Kristin N Parent
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824, USA
| | - Sarah M Doore
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824, USA.,BEACON Center for the Study of Evolution in Action, Michigan State University, East Lansing, Michigan 48824, USA;
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