Natural Occurrence of Escherichia coli-Infecting Bacteriophages in Clinical Samples

Abstract

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.

Phage Prevalence in the Human Urinary Tract—Current Knowledge and Therapeutic Implications

“…It is unclear whether bacteria acquired phage resistance or phage hosts were not present at the time of sample collection. Yet, this is another example showing that the majority of phage sequences are to be explored in the coming years [ 81 ]. To understand intracommunity interactions in human body inhabited by multiple microorganisms, it is imperative to isolate and characterize phages as they constitute a large and significant subpopulation, including within urobiome.…”

Infection Kinetics and Phylogenetic Analysis of vB_EcoD_SU57, a Virulent T1-Like Drexlerviridae Coliphage

“…The genome nucleotide sequence of SU57 was aligned to genomes showing E-values = 0 in discontinuous MegaBLAST searches against the nucleotide collection database limited to Caudovirales phages, with the addition of the genomes of phage T1, TLS, and F20. Phage genomes from the clinical samples reported by Pacífico et al (2019) were excluded for being too similar between themselves and as they were all 86–88% identical (E-value = 0) to phages vB_Ecos_CEB_EC3a, Rtp, and 2725-N35 (See Supplementary Table 2 for accession numbers to genome sequences).…”

Targeting multicopy prophage genes for the differential diagnosis of Lyme disease

“…Phenol chloroform was also highly efficient in recovering cfDNA from clinical samples 67 . Free phages have been discovered from a range of clinical samples, including blood 68,69 . Their biological significance remains to be understood.…”