Polyomavirus JCPyV and Its Role in the Urinary Tract

Polyomaviruses are the smallest closed-circular supercoiled double-stranded viruses found in the human microbiota. The polyomavirus JC (JCPyV) is most commonly found within the urinary tract, and prior studies estimate that 20-80% of older adults carry JCPyV. In very rare cases, JCPyV leaves the kidneys, causing progressive multifocal leukoencephalopathy. However, the role of JCPyV within the urinary tract remains an open question. In a prior study conducted by our group, the bladder microbiota of females with and without overactive bladder symptoms (OAB) were sequenced. Interestingly, JCPyV was only detected in females with OAB; none of the control (“asymptomatic”) microbiota contained JCPyV. However, the sample size for this study was small (n=30). This thesis is a multidisciplinary approach to explore the presence and prevalence of polyomaviruses in the urinary microbiome (urobiome). In a bioinformatic investigation of JCPyV and BKPyV, a closely related polyomavirus to JCPyV, 165 publicly available urinary virome and urinary metagenome data sets were mined for these two polyomaviruses. Sequence diversity between JCPyV and BKPyV genomes was explored to design a new primer pair to uniquely identify JCPyV in urobiome samples. Using these ultra-specific JCPyV primers, 190 urine samples, including 99 from females with OAB, 33 from females with UTI, and 58 from females without lower urinary tract symptoms, were screened for JCPyV to assess the prevalence of the virus as well as to assess the association of JCPyV with symptom status, age, and race/ethnicity. Additionally, the urobiome of JCPyV+ individuals was sequenced in an effort to identify associations between JCPyV and bacterial taxa. We found no associations between JCPyV presence or abundance and any of the factors when tested individually. However, some associations were found when some of the factors were considered together in predicting JCPyV prevalence. Additionally, both our bioinformatic and molecular survey suggests that JCPyV is less prevalent in the female population than previously thought

Discriminating between jcpyv and bkpyv in urinary virome data sets

Polyomaviruses are abundant in the human body. The polyomaviruses JC virus (JCPyV) and BK virus (BKPyV) are common viruses in the human urinary tract. Prior studies have estimated that JCPyV infects between 20 and 80% of adults and that BKPyV infects between 65 and 90% of individuals by age 10. However, these two viruses encode for the same six genes and share 75% nucleotide sequence identity across their genomes. While prior urinary virome studies have repeatedly reported the presence of JCPyV, we were interested in seeing how JCPyV prevalence compares to BKPyV. We retrieved all publicly available shotgun metagenomic sequencing reads from urinary microbiome and virome studies (n = 165). While one third of the data sets produced hits to JCPyV, upon further investigation were we able to determine that the majority of these were in fact BKPyV. This distinction was made by specifically mining for JCPyV and BKPyV and considering uniform coverage across the genome. This approach provides confidence in taxon calls, even between closely related viruses with significant sequence similarity

Introducing Lu-1, a Novel Lactobacillus jensenii Phage Abundant in the Urogenital Tract

Bacteriophages (phages) play a key role in shaping microbial communities, including those of the human body. Phages are abundant members of the urogenital tract, most often persisting through the lysogenic life cycle as prophages integrated within the genomes of their bacterial hosts. While numerous studies of the urogenital microbiota have focused on the most abundant bacterial member of this niche–Lactobacillus species–very little is known about Lactobacillus phages. Focusing on Lactobacillus jensenii strains from the urinary tract, we identified numerous prophages related to the previously characterized Lv-1 phage from a vaginal L. jensenii strain. Furthermore, we identified a new L. jensenii phage, Lu-1. Evidence suggests that both phages are abundant within the urogenital tract. CRISPR spacer sequences matching to Lv-1 and Lu-1 prophages were identified. While first detected in urinary isolates, the Lu-1 phage was also discovered in L. jensenii isolates from vaginal and perineal swabs, and both phages were found in metagenomic data sets. The prevalence of these phages in the isolates suggests that both phages are active members of the urogenital microbiota

Genomic Survey of E. coli From the Bladders of Women With and Without Lower Urinary Tract Symptoms

Urinary tract infections (UTIs) are one of the most common human bacterial infections. While UTIs are commonly associated with colonization by Escherichia coli, members of this species also have been found within the bladder of individuals with no lower urinary tract symptoms (no LUTS), also known as asymptomatic bacteriuria. Prior studies have found that both uropathogenic E. coli (UPEC) strains and E. coli isolates that are not associated with UTIs encode for virulence factors. Thus, the reason(s) why E. coli sometimes causes UTI-like symptoms remain(s) elusive. In this study, the genomes of 66 E. coli isolates from adult female bladders were sequenced. These isolates were collected from four cohorts, including women: (1) without lower urinary tract symptoms, (2) overactive bladder symptoms, (3) urgency urinary incontinence, and (4) a clinical diagnosis of UTI. Comparative genomic analyses were conducted, including core and accessory genome analyses, virulence and motility gene analyses, and antibiotic resistance prediction and testing. We found that the genomic content of these 66 E. coli isolates does not correspond with the participant’s symptom status. We thus looked beyond the E. coli genomes to the composition of the entire urobiome and found that the presence of E. coli alone was not sufficient to distinguish between the urobiomes of individuals with UTI and those with no LUTS. Because E. coli presence, abundance, and genomic content appear to be weak predictors of UTI status, we hypothesize that UTI symptoms associated with detection of E. coli are more likely the result of urobiome composition

Detecting Polyomaviruses in the Urinary Microbiome

The polyomaviruses JC virus (JCPyV) and BK virus (BKPyV) are thought to be common viruses in the human urinary tract, and prior studies estimate JCPyV infects between 20-80% of older adults and BKPyV infects between 65-90% of individuals by age 10. These estimates largely stem from PCR-based tests. Recent shotgun metagenomes of the urinary microbiota have similarly reported the presence of these two polyomaviruses based on sequence homology searches. However, JCPyV and BKPyV encode for the same six genes and share 75% nucleotide sequence identity across their genomes. This prompted our in-depth investigation into the detection of and distinguishing between these two closely realted viruses within microbiome data. This study examines publicly available whole-genome sequencing reads from urinary microbiome and urinary virome studies (n=165) to ascertain the abundance and prevalence of these two polyomaviruses

Polyomavirus JC Virus and its Prevalence in the Urinary Tract of Women with Overactive Bladder Symptoms

Polyomaviruses are the smallest known double-stranded DNA viruses and are abundant in the human body. The polyomavirus JC virus (JCV) is a common virus of the human urinary tract. In a prior study conducted by the Putonti lab, JCV was found to be present and abundant in the bladder of women with overactive bladder, and absent from a small asymptomatic control group. This suggests that JCV may contribute to urinary tract symptoms. To test this hypothesis, I will screen and quantify JCV in two populations: older women with and without lower urinary tract symptoms (LUTS)