Analysis of spounaviruses as a case study for the overdue reclassification of tailed phages

Tailed bacteriophages are the most abundant and diverse viruses in the world, with genome sizes ranging from 10 kbp to over 500 kbp. Yet, due to historical reasons, all this diversity is confined to a single virus order-Caudovirales, composed of just four families: Myoviridae, Siphoviridae, Podoviridae, and the newly created Ackermannviridae family. In recent years, this morphology-based classification scheme has started to crumble under the constant flood of phage sequences, revealing that tailed phages are even more genetically diverse than once thought. This prompted us, the Bacterial and Archaeal Viruses Subcommittee of the International Committee on Taxonomy of Viruses (ICTV), to consider overall reorganization of phage taxonomy. In this study, we used a wide range of complementary methods-including comparative genomics, core genome analysis, and marker gene phylogenetics-to show that the group of Bacillus phage SPO1-related viruses previously classified into the Spounavirinae subfamily, is clearly distinct from other members of the family Myoviridae and its diversity deserves the rank of an autonomous family. Thus, we removed this group from the Myoviridae family and created the family Herelleviridae-a new taxon of the same rank. In the process of the taxon evaluation, we explored the feasibility of different demarcation criteria and critically evaluated the usefulness of our methods for phage classification. The convergence of results, drawing a consistent and comprehensive picture of a new family with associated subfamilies, regardless of method, demonstrates that the tools applied here are particularly useful in phage taxonomy. We are convinced that creation of this novel family is a crucial milestone toward much-needed reclassification in the Caudovirales order.Peer reviewe

Taxonomy of prokaryotic viruses : 2017 update from the ICTV Bacterial and Archaeal Viruses Subcommittee

Peer reviewe

Taxonomy of prokaryotic viruses : 2018-2019 update from the ICTV Bacterial and Archaeal Viruses Subcommittee

This article is a summary of the activities of the ICTV's Bacterial and Archaeal Viruses Subcommittee for the years 2018 and 2019. Highlights include the creation of a new order, 10 families, 22 subfamilies, 424 genera and 964 species. Some of our concerns about the ICTV's ability to adjust to and incorporate new DNA- and protein-based taxonomic tools are discussed.Peer reviewe

Taxonomy of prokaryotic viruses: 2016 update from the ICTV bacterial and archaeal viruses subcommittee

The prokaryotic virus community is represented at the International Committee on Taxonomy of Viruses (ICTV) by the Bacterial and Archaeal Viruses Subcommittee. Since our last report [8], the committee composition has changed, and a large number of taxonomic proposals (TaxoProps) were submitted to the ICTV Executive Committee (EC) for approval.Peer reviewe

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Filamentous Pseudomonas Phage Pf4 in the Context of Therapy-Inducibility, Infectivity, Lysogenic Conversion, and Potential Application

More than 20% of all Pseudomonas aeruginosa are infected with Pf4-related filamentous phage and although their role in virulence of P. aeruginosa strain PAO1 is well documented, its properties related to therapy are not elucidated in detail. The aim of this study was to determine how phage and antibiotic therapy induce Pf4, whether the released virions can infect other strains and how the phage influences the phenotype of new hosts. The subinhibitory concentrations of ciprofloxacin and mitomycin C increased Pf4 production for more than 50% during the first and sixth hour of exposure, respectively, while mutants appearing after infection with obligatory lytic phage at low MOI produced Pf4 more than four times after 12–24 h of treatment. This indicates that production of Pf4 is enhanced during therapy with these agents. The released virions can infect new P. aeruginosa strains, as confirmed for models UCBPP-PA14 (PA14) and LESB58, existing both episomally and in a form of a prophage, as confirmed by PCR, RFLP, and sequencing. The differences in properties of Pf4-infected, and uninfected PA14 and LESB58 strains were obvious, as infection with Pf4 significantly decreased cell autoaggregation, pyoverdine, and pyocyanin production, while significantly increased swimming motility and biofilm production in both strains. In addition, in strain PA14, Pf4 increased cell surface hydrophobicity and small colony variants’ appearance, but also decreased twitching and swarming motility. This indicates that released Pf4 during therapy can infect new strains and cause lysogenic conversion. The infection with Pf4 increased LESB58 sensitivity to ciprofloxacin, gentamicin, ceftazidime, tetracycline, and streptomycin, and PA14 to ciprofloxacin and ceftazidime. Moreover, the Pf4-infected LESB58 was re-sensitized to ceftazidime and tetracycline, with changes from resistant to intermediate resistant and sensitive, respectively. The obtained results open a new field in phage therapy—treatment with selected filamentous phages in order to re-sensitize pathogenic bacteria to certain antibiotics. However, this approach should be considered with precautions, taking into account potential lysogenic conversion

NEW EDUCATION POLICY’S PRIORITIES AS A FUNCTION OF ECONOMIC DEVELOPMENT OF SERBIA

The subject of the analysis is the importance of new education policy of Republic of Serbia, as one of the key factors for economic development, whose dynamics depends on the degree of its realization and capacity of state to implement New Strategy for development of education in Serbia until 2020 (Law on government RS, 2005). In long term, the biggest importance in the process have investments into human capital and education, and research and development. The goal of the paper is to demonstrate that New Strategy for development of education in Serbia until 2020. has responded to requests that educational system should correspond to needs of the economy, to establish active institutional system of linking between science and industry; and that policy of incentives should be focused towards innovation in entrepreneurial sector. The paper starts with hypothesis that level of development of the economy depends on the results of conducted reform in education system, as well as that education system of Republic of Serbia, whose standards lag behind the outstanding legislation standards of European Union, does not satisfy immediate needs of the current economic structure. Defined hypothesis is confirmed in the paper, by the use of comparative legislation analysis of educational policy in European countries and surrounding countries. Basic message of the paper is that establishment of economic development of Republic of Serbia in post-crisis period is closely linked to implementation of education policy whose priorities are given in the New Strategy for educational development in Serbia until 2020, because without reform of education system is impossible to implement structural reforms in the economy

Prevalence of Pf1-like (pro)phage genetic elements among Pseudomonas aeruginosa isolates

Pf1-like bacteriophages (family Inoviridae) of Pseudomonas aeruginosa can contribute to bacterial short term evolution and virulence. Here we examine Pf1-like (pro)phage diversity and prevalence among different P. aeruginosa isolates. Pf1-like prophages in sequenced genomes of P. aeruginosa were analyzed and grouped into four clades: Pf4, Pf5, Pf7 and Pf-LES. P. aeruginosa strains (n=241) were screened for the presence of universal (primers PfUa and PfUb) and specific Pf1-like genetic elements (Pf1, Pf4 and Pf5). More than half of the strains contained at least one Pf1-like genetic element (60%); universal elements were detected in 56% of the strains, Pf4 in 22%, Pf1 in 18% and Pf5 in 7%. Infectivity experiments confirmed that strains yielding PCR products with either universal or Pf4 specific primers can release infective virions. Based on the high prevalence of Pf1-like (pro)phages, it is necessary to further examine their involvement in P. aeruginosa virulence.publisher: Elsevier articletitle: Prevalence of Pf1-like (pro)phage genetic elements among Pseudomonas aeruginosa isolates journaltitle: Virology articlelink: http://dx.doi.org/10.1016/j.virol.2015.04.008 content_type: article copyright: Copyright © 2015 Elsevier Inc. All rights reserved.status: publishe