Characterization of the φCTX-like Pseudomonas aeruginosa phage Dobby isolated from the kidney stone microbiota

Abstract

Bacteriophages (phages) are vital members of the human microbiota. They are abundant even within low biomass niches of the human body, including the lower urinary tract. While several prior studies have cultured bacteria from kidney stones, this is the first study to explore phages within the kidney stone microbiota. Here we report Dobby, a temperate phage isolated from a strain of Pseudomonas aeruginosa cultured from a kidney stone. Dobby is capable of lysing clinical P. aeruginosa strains within our collection from the urinary tract. Sequencing was performed producing a 37 152 bp genome that closely resembles the temperate P. aeruginosa phage φCTX, a member of the P2 phage group. Dobby does not, however, encode for the cytotoxin CTX. Dobby’s genome was queried against publicly available bacterial sequences identifying 44 other φCTX-like prophages. These prophages are integrated within the genomes of P. aeruginosa strains from a variety of environments, including strains isolated from urine samples and other niches of the human body. Phylogenetic analysis suggests that the temperate φCTX phage species is widespread. With the isolation of Dobby, we now have evidence that phages are members of the kidney stone microbiota. Further investigation, however, is needed to determine their abundance and diversity within these communities.

Urinary Microbiome: Yin and Yang of the Urinary Tract

“…Nevertheless, the urinary virome is mainly formed by bacteriophages, viruses which infect urinary bacteria such as Staphylococcus, Escherichia coli or Enterococcus ( Santiago-Rodriguez et al., 2015 ; Garretto et al., 2018 ; Moustafa et al., 2018 ). Many lytic bacteriophages have been identified in the urinary tract, like φCTX-like Pseudomonas aeruginosa -infecting phage isolated from kidney stones ( Johnson et al., 2019 ), or Escherichia coli -infecting phages isolated from the bladder of women suffering UUI ( Malki et al., 2016 ). Lysogenic phages have been also detected in the urinary bladder from both healthy individuals and patients with urinary tract symptoms ( Miller-Ensminger et al., 2018 ).…”

Microbiome and Human Health: Current Understanding, Engineering, and Enabling Technologies

“…144 To date, only one species of archaea (Methanobrevibacter smithii) has been reported to be associated with urinary infection. 154 A urinary virome has also been detected, including lytic bacteriophages such as a Pseudomonas aeruginosa-infecting phage isolated from kidney stones 155 or Escherichia coli-infecting phages isolated from the bladder of females suffering from UUI. UTIs are one of the most common bacterial infections found in humans, especially among women due to the design of the female anatomy.…”

Complete Genome Sequence of a Pseudomonas aeruginosa Isolate from a Kidney Stone

“…aeruginosa colonies, identified via 16S rRNA gene sequencing, were isolated (5). In one of these isolates, UMB2738, the φCTX-like temperate Pseudomonas phage Dobby was isolated and characterized (10). Similarly, a temperate phage was induced from the other P.…”

“…The genome encodes 6,298 protein coding genes, three rRNA operons, and 57 tRNAs. As this strain was the source of the temperate Pseudomonas phage Dobby (10), the genome assembly was queried via blastn (16) for the Dobby sequence (GenBank accession number MK034952) and located in the first, largest contig of the assembly. The P.…”