Natural Occurrence of Escherichia coli-Infecting Bacteriophages in Clinical Samples

The interaction between bacteriophages, bacteria and the human host as a tripartite system has recently captured attention. The taxonomic diversity of bacteriophages, as a natural parasite of bacteria, still remains obscure in human body biomes, representing a so-called “viral dark matter.” Here, we...

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Autores principales: Pacífico, Cátia, Hilbert, Miriam, Sofka, Dmitrij, Dinhopl, Nora, Pap, Ildiko-Julia, Aspöck, Christoph, Carriço, João André, Hilbert, Friederike
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6834657/
https://www.ncbi.nlm.nih.gov/pubmed/31736918
http://dx.doi.org/10.3389/fmicb.2019.02484
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author Pacífico, Cátia
Hilbert, Miriam
Sofka, Dmitrij
Dinhopl, Nora
Pap, Ildiko-Julia
Aspöck, Christoph
Carriço, João André
Hilbert, Friederike
author_facet Pacífico, Cátia
Hilbert, Miriam
Sofka, Dmitrij
Dinhopl, Nora
Pap, Ildiko-Julia
Aspöck, Christoph
Carriço, João André
Hilbert, Friederike
author_sort Pacífico, Cátia
collection PubMed
description The interaction between bacteriophages, bacteria and the human host as a tripartite system has recently captured attention. The taxonomic diversity of bacteriophages, as a natural parasite of bacteria, still remains obscure in human body biomes, representing a so-called “viral dark matter.” Here, we isolated and characterized coliphages from blood, urine and tracheal aspirates samples collected at a tertiary care hospital in Austria. Phages were more often isolated from blood, followed by urine and tracheal aspirates. Phylogenetic analysis and genome comparisons allowed the identification of phages belonging to the Tunavirinae subfamily, and to the Peduovirus and Tequintavirus genera. Tunavirinae phages cluster together and are found in samples from 14 patients, suggesting their prevalence across a variety of human samples. When compared with other phage genomes, the highest similarity level was at 87.69% average nucleotide identity (ANI), which suggests that these are in fact a newly isolated phage species. Tequintavirus phages share a 95.90% with phage 3_29, challenging the ANI threshold currently accepted to differentiate phage species. The isolated phages appear to be virulent, with the exception of the Peduovirus members, which are integrative and seem to reside as prophages in bacterial genomes.
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spelling pubmed-68346572019-11-15 Natural Occurrence of Escherichia coli-Infecting Bacteriophages in Clinical Samples Pacífico, Cátia Hilbert, Miriam Sofka, Dmitrij Dinhopl, Nora Pap, Ildiko-Julia Aspöck, Christoph Carriço, João André Hilbert, Friederike Front Microbiol Microbiology The interaction between bacteriophages, bacteria and the human host as a tripartite system has recently captured attention. The taxonomic diversity of bacteriophages, as a natural parasite of bacteria, still remains obscure in human body biomes, representing a so-called “viral dark matter.” Here, we isolated and characterized coliphages from blood, urine and tracheal aspirates samples collected at a tertiary care hospital in Austria. Phages were more often isolated from blood, followed by urine and tracheal aspirates. Phylogenetic analysis and genome comparisons allowed the identification of phages belonging to the Tunavirinae subfamily, and to the Peduovirus and Tequintavirus genera. Tunavirinae phages cluster together and are found in samples from 14 patients, suggesting their prevalence across a variety of human samples. When compared with other phage genomes, the highest similarity level was at 87.69% average nucleotide identity (ANI), which suggests that these are in fact a newly isolated phage species. Tequintavirus phages share a 95.90% with phage 3_29, challenging the ANI threshold currently accepted to differentiate phage species. The isolated phages appear to be virulent, with the exception of the Peduovirus members, which are integrative and seem to reside as prophages in bacterial genomes. Frontiers Media S.A. 2019-10-31 /pmc/articles/PMC6834657/ /pubmed/31736918 http://dx.doi.org/10.3389/fmicb.2019.02484 Text en Copyright © 2019 Pacífico, Hilbert, Sofka, Dinhopl, Pap, Aspöck, Carriço and Hilbert. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Microbiology
Pacífico, Cátia
Hilbert, Miriam
Sofka, Dmitrij
Dinhopl, Nora
Pap, Ildiko-Julia
Aspöck, Christoph
Carriço, João André
Hilbert, Friederike
Natural Occurrence of Escherichia coli-Infecting Bacteriophages in Clinical Samples
title Natural Occurrence of Escherichia coli-Infecting Bacteriophages in Clinical Samples
title_full Natural Occurrence of Escherichia coli-Infecting Bacteriophages in Clinical Samples
title_fullStr Natural Occurrence of Escherichia coli-Infecting Bacteriophages in Clinical Samples
title_full_unstemmed Natural Occurrence of Escherichia coli-Infecting Bacteriophages in Clinical Samples
title_short Natural Occurrence of Escherichia coli-Infecting Bacteriophages in Clinical Samples
title_sort natural occurrence of escherichia coli-infecting bacteriophages in clinical samples
topic Microbiology
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6834657/
https://www.ncbi.nlm.nih.gov/pubmed/31736918
http://dx.doi.org/10.3389/fmicb.2019.02484
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