The human urine virome in association with urinary tract infections

Abstract

While once believed to represent a sterile environment, the human urinary tract harbors a unique cellular microbiota. We sought to determine whether the human urinary tract also is home to viral communities whose membership might reflect urinary tract health status. We recruited and sampled urine from 20 subjects, 10 subjects with urinary tract infections (UTIs) and 10 without UTIs, and found viral communities in the urine of each subject group. Most of the identifiable viruses were bacteriophage, but eukaryotic viruses also were identified in all subjects. We found reads from human papillomaviruses (HPVs) in 95% of the subjects studied, but none were found to be high-risk genotypes that are associated with cervical and rectal cancers. We verified the presence of some HPV genotypes by quantitative PCR. Some of the HPV genotypes identified were homologous to relatively novel and uncharacterized viruses that previously have been detected on skin in association with cancerous lesions, while others may be associated with anal and genital warts. On a community level, there was no association between the membership or diversity of viral communities based on urinary tract health status. While more data are still needed, detection of HPVs as members of the human urinary virome using viral metagenomics represents a non-invasive technique that could augment current screening techniques to detect low-risk HPVs in the genitourinary tracts of humans.

“Urinary Tract Infection”—Requiem for a Heavyweight

“…The viability of most uncultivable bacteria has been confirmed using more‐sensitive expanded quantitative urine cultures . Intracellular bacterial colonies and a urinary virome, not detected using standard cultures and of unknown pathogenicity, have also been identified …”

Bacteruria and Urinary Tract Infections in the Elderly

“…A recent review by Whiteside and colleagues 39 reports multiple genera including Jonquetella, Parvimonas, Proteiniphilum, and saccharofermentas in the urinary tract of healthy patients over age 70, through polymerase chain reaction (PCR) and detection of 16s rRNA subunits. A study by Santiago-Rodriguez and colleagues 40 also demonstrated viral communities in 20 individuals, including bacteriophages and lowrisk or novel strains of human papiloma virus, but flora components were unassociated with history of urinary tract health. Although the exact role of these symbiotic organisms is still poorly understood, it is postulated that their metabolic byproducts may convey antimicrobial advantages and contribute to urinary health.…”

Female urinary microbiota

“…Although most studies have concentrated on bacteria, there is also preliminary evidence of viral [28] and fungal community members. As this preliminary work is replicated and published, our understanding will be expanded further.…”