Honors & Awards
Dissertation of the Year, Biomedical and Sciences Category, Loyola University Chicago (2018)
Arthur J. Schmitt Dissertation Fellowship, Loyola University (2016-2017)
Bachelor of Science, Calif Polytechnic State Univ, S.L.O. (2008)
Doctor of Philosophy, Loyola University Of Chicago (2017)
Denise Monack, Postdoctoral Faculty Sponsor
Detecting viral genomes in the female urinary microbiome
JOURNAL OF GENERAL VIROLOGY
2018; 99 (8): 1141–46
Viruses are the most abundant component of the human microbiota. Recent evidence has uncovered a rich diversity of viruses within the female bladder, including both bacteriophages and eukaryotic viruses. We conducted whole-genome sequencing of the bladder microbiome of 30 women: 10 asymptomatic 'healthy' women and 20 women with an overactive bladder. These metagenomes include sequences representative of human, bacterial and viral DNA. This analysis, however, focused specifically on viral sequences. Using the bioinformatic tool virMine, we discovered sequence fragments, as well as complete genomes, of bacteriophages and the eukaryotic virus JC polyomavirus. The method employed here is a critical proof of concept: the genomes of viral populations within the low-biomass bladder microbiota can be reconstructed through whole-genome sequencing of the entire microbial community.
View details for DOI 10.1099/jgv.0.001097
View details for Web of Science ID 000440461400019
View details for PubMedID 29889019
Diversity of the midstream urine microbiome in adults with chronic kidney disease
INTERNATIONAL UROLOGY AND NEPHROLOGY
2018; 50 (6): 1123–30
To examine the characteristics of the midstream urine microbiome in adults with stage 3-5 non-dialysis-dependent chronic kidney disease (CKD).Patients with non-dialysis-dependent CKD (estimated glomerular filtration rate [eGFR] < 60 ml/min/1.73 m2) and diuretic use were recruited from outpatient nephrology clinics. Midstream voided urine specimens were collected using the clean-catch method. The bacterial composition was determined by sequencing the hypervariable (V4) region of the bacterial 16S ribosomal RNA gene. Extraction negative controls (no urine) were included to assess the contribution of extraneous DNA from possible sources of contamination. Midstream urine microbiome diversity was assessed with the inverse Simpson, Chao and Shannon indices. The diversity measures were further examined by demographic characteristics and by comorbidities.The cohort of 41 women and 36 men with detectable bacterial DNA in their urine samples had a mean age of 71.5 years (standard deviation [SD] 7.9) years (range 60-91 years). The majority were white (68.0%) and a substantial minority were African-American (29.3%) The mean eGFR was 27.2 (SD 13.6) ml/min/1.73 m2. Most men (72.2%) were circumcised and 16.6% reported a remote history of prostate cancer. Many midstream voided urine specimens were dominated (> 50% reads) by the genera Corynebacterium (n = 11), Staphylococcus (n = 9), Streptococcus (n = 7), Lactobacillus (n = 7), Gardnerella (n = 7), Prevotella (n = 4), Escherichia_Shigella (n = 3), and Enterobacteriaceae (n = 2); the rest lacked a dominant genus. The samples had high levels of diversity, as measured by the inverse Simpson [7.24 (95% CI 6.76, 7.81)], Chao [558.24 (95% CI 381.70, 879.35)], and Shannon indices [2.60 (95% CI 2.51, 2.69)]. Diversity measures were generally higher in participants with urgency urinary incontinence and higher estimated glomerular filtration rate (eGFR). After controlling for demographics and diabetes status, microbiome diversity was significantly associated with estimated eGFR (P < 0.05).The midstream voided urine microbiome of older adults with stage 3-5 non-dialysis-dependent CKD is diverse. Greater microbiome diversity is associated with higher eGFR.
View details for DOI 10.1007/s11255-018-1860-7
View details for Web of Science ID 000434276700017
View details for PubMedID 29651696
View details for PubMedCentralID PMC5986845
Culturing of female bladder bacteria reveals an interconnected urogenital microbiota
2018; 9: 1557
Metagenomic analyses have indicated that the female bladder harbors an indigenous microbiota. However, there are few cultured reference strains with sequenced genomes available for functional and experimental analyses. Here we isolate and genome-sequence 149 bacterial strains from catheterized urine of 77 women. This culture collection spans 78 species, representing approximately two thirds of the bacterial diversity within the sampled bladders, including Proteobacteria, Actinobacteria, and Firmicutes. Detailed genomic and functional comparison of the bladder microbiota to the gastrointestinal and vaginal microbiotas demonstrates similar vaginal and bladder microbiota, with functional capacities that are distinct from those observed in the gastrointestinal microbiota. Whole-genome phylogenetic analysis of bacterial strains isolated from the vagina and bladder in the same women identifies highly similar Escherichia coli, Streptococcus anginosus, Lactobacillus iners, and Lactobacillus crispatus, suggesting an interlinked female urogenital microbiota that is not only limited to pathogens but is also characteristic of health-associated commensals.
View details for DOI 10.1038/s41467-018-03968-5
View details for Web of Science ID 000430389100009
View details for PubMedID 29674608
View details for PubMedCentralID PMC5908796
Bacteriophages of the Urinary Microbiome
JOURNAL OF BACTERIOLOGY
2018; 200 (7)
Bacterial viruses (bacteriophages) play a significant role in microbial community dynamics. Within the human gastrointestinal tract, for instance, associations among bacteriophages (phages), microbiota stability, and human health have been discovered. In contrast to the gastrointestinal tract, the phages associated with the urinary microbiota are largely unknown. Preliminary metagenomic surveys of the urinary virome indicate a rich diversity of novel lytic phage sequences at an abundance far outnumbering that of eukaryotic viruses. These surveys, however, exclude the lysogenic phages residing within the bacteria of the bladder. To characterize this phage population, we examined 181 genomes representative of the phylogenetic diversity of bacterial species within the female urinary microbiota and found 457 phage sequences, 226 of which were predicted with high confidence. Phages were prevalent within the bladder bacteria: 86% of the genomes examined contained at least one phage sequence. Most of these phages are novel, exhibiting no discernible sequence homology to sequences in public data repositories. The presence of phages with substantial sequence similarity within the microbiota of different women supports the existence of a core community of phages within the bladder. Furthermore, the observed variation between the phage populations of women with and without overactive bladder symptoms suggests that phages may contribute to urinary health. To complement our bioinformatic analyses, viable phages were cultivated from the bacterial isolates for characterization; a novel coliphage was isolated, which is obligately lytic in the laboratory strain Escherichia coli C. Sequencing of bacterial genomes facilitates a comprehensive cataloguing of the urinary virome and reveals phage-host interactions.IMPORTANCE Bacteriophages are abundant within the human body. However, while some niches have been well surveyed, the phage population within the urinary microbiome is largely unknown. Our study is the first survey of the lysogenic phage population within the urinary microbiota. Most notably, the abundance of prophage exceeds that of the bacteria. Furthermore, many of the prophage sequences identified exhibited no recognizable sequence homology to sequences in data repositories. This suggests a rich diversity of uncharacterized phage species present in the bladder. Additionally, we observed a variation in the abundances of phages between bacteria isolated from asymptomatic "healthy" individuals and those with urinary symptoms, thus suggesting that, like phages within the gut, phages within the bladder may contribute to urinary health.
View details for DOI 10.1128/JB.00738-17
View details for Web of Science ID 000427113600012
View details for PubMedID 29378882
View details for PubMedCentralID PMC5847656
Urinary Symptoms and Their Associations With Urinary Tract Infections in Urogynecologic Patients
LIPPINCOTT WILLIAMS & WILKINS. 2017: 718–25
To assess urinary symptoms associated with urinary tract infection (UTI) in a urogynecologic population of women.In this cohort study, we enrolled 150 urogynecologic patients who completed the validated UTI Symptom Assessment questionnaire and contributed transurethral catheterized urine samples. The primary measure (UTI diagnosis) was defined in three ways. Self-report (a nonculture-based UTI diagnosis) was defined by a yes or no response to the query "Do you think you have a UTI?" Two culture-based UTI diagnoses also were analyzed: standard urine culture (10 colony-forming units [CFU]/mL or greater) and enhanced quantitative urine culture (10 CFU/mL or greater) of any uropathogen. Statistical analyses were performed on patient demographics and urinary symptom prevalence among patient groups.Although the presence of the urinary symptoms of frequency and urgency (respectively) differ somewhat between UTI-positive and UTI-negative women (self-report [P=.005 and P<.001], standard urine culture [P=.038 and P=.044], or enhanced quantitative urine culture [P=.059 and P=.098]), the presence of dysuria (pain or burning) during urination was significantly more prevalent in UTI-positive women for all UTI definitions (self-report P<.001, standard urine culture P<.001, and enhanced quantitative urine culture P=.010). Furthermore, women reporting dysuria had higher severity and bother scores for all other urinary symptoms assessed by the UTI Symptom Assessment questionnaire compared with women not reporting dysuria (frequency P=.001, urgency P=.006, dysuria P<.001).Our findings show that, in women seeking urogynecologic care, the presence of frequency and urgency of urination does not confirm a culture-based UTI diagnosis. Instead, clinicians can more readily detect UTI using the presence of dysuria, which more effectively discriminates UTI-positive and UTI-negative individuals, regardless of the culture-based method used to diagnose UTI.
View details for DOI 10.1097/AOG.0000000000002239
View details for Web of Science ID 000411453500014
View details for PubMedID 28885414
View details for PubMedCentralID PMC5679107
Microorganisms Identified in the Maternal Bladder: Discovery of the Maternal Bladder Microbiota
2017; 7 (3): e188–e196
Objective The objective of this study was to characterize the bladder microbiota in pregnancy. Methods A prospective observational study of 51 pregnant women, admitted to a tertiary care hospital, who underwent straight catheterization urine collection or transurethral Foley catheter placement. 16S rRNA gene sequencing and enhanced quantitative urine culture assessed the maternal bladder microbiota with comparisons made to standard urine culture results. Results Enhanced quantitative urine culture and 16S rRNA gene sequencing detected bacteria in the majority of participants. Lactobacillus and Gardnerella were the most commonly detected microbes. In contrast, standard urine culture had a 100% false-negative rate and failed to detect several known or emerging urinary pathogens. Conclusion There are live bacteria in the bladders of most pregnant women. This challenges the definition of asymptomatic bacteriuria.
View details for DOI 10.1055/s-0037-1606860
View details for Web of Science ID 000411970200001
View details for PubMedID 28970961
View details for PubMedCentralID PMC5621969
Evaluation of the urinary microbiota of women with uncomplicated stress urinary incontinence
AMERICAN JOURNAL OF OBSTETRICS AND GYNECOLOGY
2017; 216 (1): 55.e1–55.e16
Female urinary microbiota are associated with urgency urinary incontinence and response to medication. The urinary microbiota of women with stress urinary incontinence has not been described.We sought to study the cross-sectional relationships between urinary microbiota features and demographic and clinical characteristics of women undergoing stress urinary incontinence surgery.Preoperative urine specimens were collected from women without urinary tract infection and were available from 197 women (174 voided, 23 catheterized) enrolled in a multicenter prospective randomized trial, the Value of Urodynamic Evaluation study. Demographic and clinical variables were obtained including stress and urgency urinary incontinence symptoms, menopausal status, and hormone use. The bacterial composition of the urine was qualitatively assessed by sequencing the bacterial 16S ribosomal RNA gene. Phylogenetic relatedness and microbial alpha diversity were compared to demographics and symptoms using generalized estimating equation models.The majority of 197 urine samples (86%) had detectable bacterial DNA. Bacterial diversity was significantly associated with higher body mass index (P = .02); increased Medical, Epidemiologic, and Social Aspects of Aging urge index score (P = .04); and hormonal status (P < .001). No associations were detected with stress urinary incontinence symptoms. Increased diversity was also associated with a concomitant lower frequency of Lactobacillus in hormone-negative women.Women undergoing stress urinary incontinence surgery have detectable urinary microbiota. This cross-sectional analysis revealed that increased diversity of the microbiota was associated with urgency urinary incontinence symptoms, hormonal status, and body mass index. In contrast, the female urinary microbiota were not associated with stress urinary incontinence symptoms.
View details for DOI 10.1016/j.ajog.2016.07.049
View details for Web of Science ID 000396381100014
View details for PubMedID 27498309
View details for PubMedCentralID PMC5182144
Incontinence medication response relates to the female urinary microbiota
INTERNATIONAL UROGYNECOLOGY JOURNAL
2016; 27 (5): 723–33
Many adult women have resident urinary bacteria (urinary microbiome/microbiota). In adult women affected by urinary urgency incontinence (UUI), the etiologic and/or therapeutic role of the urinary microbiome/microbiota remains unknown. We hypothesized that microbiome/microbiota characteristics would relate to clinically relevant treatment response to UUI medication per os.Adult women initiating medication treatment orally for UUI and a comparator group of unaffected women were recruited in a tertiary care health-care system. All participants provided baseline clinical data and urine samples. Women with UUI were given 5 mg solifenacin, with potential dose escalation to 10 mg for inadequate UUI symptom control at 4 weeks. Additional data and urine samples were collected from women with UUI at 4 and 12 weeks. The samples were assessed using 16S ribosomal RNA (rRNA) gene sequencing and enhanced quantitative urine culturing. The primary outcome was treatment response as measured by the validated Patient Global Symptom Control (PGSC) questionnaire. Clinically relevant UUI symptom control was defined as a 4 or 5 score on the PGSC.Diversity and composition of the urinary microbiome/microbiota of women with and without UUI differed at baseline. Women with UUI had more bacteria and a more diverse microbiome/microbiota. The clinical response to solifenacin in UUI participants was related to baseline microbiome/microbiota, with responders more likely to have fewer bacteria and a less diverse community at baseline. Nonresponders had a more diverse community that often included bacteria not typically found in responders.Knowledge of an individual's urinary microbiome/microbiota may help refine UUI treatment. Complementary tools, DNA sequencing, and expanded urine culture provide information about bacteria that appear to be related to UUI incontinence status and treatment response in this population of adult women.
View details for DOI 10.1007/s00192-015-2847-x
View details for Web of Science ID 000374572900005
View details for PubMedID 26423260
View details for PubMedCentralID PMC5119460
The Bladder Is Not Sterile: History and Current Discoveries on the Urinary Microbiome
CURRENT BLADDER DYSFUNCTION REPORTS
2016; 11 (1): 18–24
In the human body, there are 10 bacterial cells for every one human cell. This fact highlights the importance of the National institutes of Health's initiative to map the human microbiome. The Human Microbiome Project was the first large-scale mapping of the human microbiome of 5 body sites: GI tract, mouth, vagina, skin and nasal cavity using culture-independent methods. The bladder was not originally tested because it was considered to be sterile and there were complexities regarding sample collection. Over the last couple years our team along with other investigators have shown that a urinary microbiome exists and for most individuals it plays a protective role.
View details for DOI 10.1007/s11884-016-0345-8
View details for Web of Science ID 000385630200004
View details for PubMedID 27182288
View details for PubMedCentralID PMC4864995
The Interaction between Enterobacteriaceae and Calcium Oxalate Deposits
2015; 10 (10): e0139575
The role of calcium oxalate crystals and deposits in UTI pathogenesis has not been established. The objectives of this study were to identify bacteria present in pediatric urolithiasis and, using in vitro and in vivo models, to determine the relevance of calcium oxalate deposits during experimental pyelonephritis.Pediatric kidney stones and urine were collected and both cultured and sequenced for bacteria. Bacterial adhesion to calcium oxalate was compared. Murine kidney calcium oxalate deposits were induced by intraperitoneal glyoxalate injection and kidneys were transurethrally inoculated with uropathogenic Escherichia coli to induce pyelonephritis.E. coli of the family Enterobacteriaceae was identified in patients by calcium oxalate stone culture. Additionally Enterobacteriaceae DNA was sequenced from multiple calcium oxalate kidney stones. E. coli selectively aggregated on and around calcium oxalate monohydrate crystals. Mice inoculated with glyoxalate and uropathogenic E. coli had higher bacterial burdens, increased kidney calcium oxalate deposits and an increased kidney innate immune response compared to mice with only calcium oxalate deposits or only pyelonephritis.In a murine model, the presence of calcium oxalate deposits increases pyelonephritis risk, likely due to preferential aggregation of bacteria on and around calcium oxalate crystals. When both calcium oxalate deposits and uropathogenic bacteria were present, calcium oxalate deposit number increased along with renal gene transcription of inner stone core matrix proteins increased. Therefore renal calcium oxalate deposits may be a modifiable risk factor for infections of the kidney and urinary tract. Furthermore, bacteria may be present in calcium oxalate deposits and potentially contribute to calcium oxalate renal disease.
View details for DOI 10.1371/journal.pone.0139575
View details for Web of Science ID 000362511000035
View details for PubMedID 26448465
View details for PubMedCentralID PMC4598009
The female urinary microbiome in urgency urinary incontinence
AMERICAN JOURNAL OF OBSTETRICS AND GYNECOLOGY
2015; 213 (3): 347.e1–11
The purpose of this study was to characterize the urinary microbiota in women who are planning treatment for urgency urinary incontinence and to describe clinical associations with urinary symptoms, urinary tract infection, and treatment outcomes.Catheterized urine samples were collected from multisite randomized trial participants who had no clinical evidence of urinary tract infection; 16S ribosomal RNA gene sequencing was used to dichotomize participants as either DNA sequence-positive or sequence-negative. Associations with demographics, urinary symptoms, urinary tract infection risk, and treatment outcomes were determined. In sequence-positive samples, microbiotas were characterized on the basis of their dominant microorganisms.More than one-half (51.1%; 93/182) of the participants' urine samples were sequence-positive. Sequence-positive participants were younger (55.8 vs 61.3 years old; P = .0007), had a higher body mass index (33.7 vs 30.1 kg/m(2); P = .0009), had a higher mean baseline daily urgency urinary incontinence episodes (5.7 vs 4.2 episodes; P < .0001), responded better to treatment (decrease in urgency urinary incontinence episodes, -4.4 vs -3.3; P = .0013), and were less likely to experience urinary tract infection (9% vs 27%; P = .0011). In sequence-positive samples, 8 major bacterial clusters were identified; 7 clusters were dominated not only by a single genus, most commonly Lactobacillus (45%) or Gardnerella (17%), but also by other taxa (25%). The remaining cluster had no dominant genus (13%).DNA sequencing confirmed urinary bacterial DNA in many women with urgency urinary incontinence who had no signs of infection. Sequence status was associated with baseline urgency urinary incontinence episodes, treatment response, and posttreatment urinary tract infection risk.
View details for DOI 10.1016/j.ajog.2015.07.009
View details for Web of Science ID 000360551700014
View details for PubMedID 26210757
View details for PubMedCentralID PMC4556587
The Female Urinary Microbiome: a Comparison of Women with and without Urgency Urinary Incontinence
2014; 5 (4): e01283–14
Bacterial DNA and live bacteria have been detected in human urine in the absence of clinical infection, challenging the prevailing dogma that urine is normally sterile. Urgency urinary incontinence (UUI) is a poorly understood urinary condition characterized by symptoms that overlap urinary infection, including urinary urgency and increased frequency with urinary incontinence. The recent discovery of the urinary microbiome warrants investigation into whether bacteria contribute to UUI. In this study, we used 16S rRNA gene sequencing to classify bacterial DNA and expanded quantitative urine culture (EQUC) techniques to isolate live bacteria in urine collected by using a transurethral catheter from women with UUI and, in comparison, a cohort without UUI. For these cohorts, we demonstrated that the UUI and non-UUI urinary microbiomes differ by group based on both sequence and culture evidences. Compared to the non-UUI microbiome, sequencing experiments revealed that the UUI microbiome was composed of increased Gardnerella and decreased Lactobacillus. Nine genera (Actinobaculum, Actinomyces, Aerococcus, Arthrobacter, Corynebacterium, Gardnerella, Oligella, Staphylococcus, and Streptococcus) were more frequently cultured from the UUI cohort. Although Lactobacillus was isolated from both cohorts, distinctions existed at the species level, with Lactobacillus gasseri detected more frequently in the UUI cohort and Lactobacillus crispatus most frequently detected in controls. Combined, these data suggest that potentially important differences exist in the urinary microbiomes of women with and without UUI, which have strong implications in prevention, diagnosis, or treatment of UUI. Importance: New evidence indicates that the human urinary tract contains microbial communities; however, the role of these communities in urinary health remains to be elucidated. Urgency urinary incontinence (UUI) is a highly prevalent yet poorly understood urinary condition characterized by urgency, frequency, and urinary incontinence. Given the significant overlap of UUI symptoms with those of urinary tract infections, it is possible that UUI may have a microbial component. We compared the urinary microbiomes of women affected by UUI to those of a comparison group without UUI, using both high-throughput sequencing and extended culture techniques. We identified statistically significant differences in the frequency and abundance of bacteria present. These differences suggest a potential role for the urinary microbiome in female urinary health.
View details for DOI 10.1128/mBio.01283-14
View details for Web of Science ID 000341588100052
View details for PubMedID 25006228
View details for PubMedCentralID PMC4161260