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...
Autores principales: | , , , , , , , |
---|---|
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 |
_version_ | 1783466521604915200 |
---|---|
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. |
format | Online Article Text |
id | pubmed-6834657 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2019 |
publisher | Frontiers Media S.A. |
record_format | MEDLINE/PubMed |
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 |
work_keys_str_mv | AT pacificocatia naturaloccurrenceofescherichiacoliinfectingbacteriophagesinclinicalsamples AT hilbertmiriam naturaloccurrenceofescherichiacoliinfectingbacteriophagesinclinicalsamples AT sofkadmitrij naturaloccurrenceofescherichiacoliinfectingbacteriophagesinclinicalsamples AT dinhoplnora naturaloccurrenceofescherichiacoliinfectingbacteriophagesinclinicalsamples AT papildikojulia naturaloccurrenceofescherichiacoliinfectingbacteriophagesinclinicalsamples AT aspockchristoph naturaloccurrenceofescherichiacoliinfectingbacteriophagesinclinicalsamples AT carricojoaoandre naturaloccurrenceofescherichiacoliinfectingbacteriophagesinclinicalsamples AT hilbertfriederike naturaloccurrenceofescherichiacoliinfectingbacteriophagesinclinicalsamples |