The Urinary Microbiome of Older Adults Residing in a Nursing Home Varies with Duration of Residence and Shows Increases in Potential Pathogens

2021 ◽  
Author(s):  
Evan S Bradley ◽  
Brent Schell ◽  
Doyle V Ward ◽  
Vanni Bucci ◽  
Abigail Zeamer ◽  
...  
Keyword(s):  
Older Adults ◽  
Nursing Home ◽  
Urinary Tract ◽  
16S Rrna Gene Sequencing ◽  
Urine Samples ◽  
Rrna Gene ◽  
Clinical Frailty Scale ◽  
Gastrointestinal Microbiome ◽  
Duration Of Residence ◽  
Urinary Microbiome

Abstract The community of bacteria that colonize the urinary tract, the urinary microbiome, is hypothesized to influence a wide variety of urinary tract conditions. Older adults that reside in nursing homes are frequently diagnosed and treated for urinary tract conditions such as urinary tract infection (UTI). We investigated the urinary microbiome of older adults residing in a nursing home to determine if there are features of the urinary microbiome that are associated specific conditions and exposure in this population. We were also interested in the stability of urinary microbiome over time and in similarities between the urinary and gastrointestinal microbiome. Urine samples were prospectively collected over a period of 10 months from a cohort of 26 older adults (age > 65 years) residing in single nursing home located in Central Massachusetts. Serial samples were obtained from 6 individuals over 10 months and 5 participants were concurrently enrolled in a study of the gastrointestinal microbiome. Information collected on participants included demographics, medical history, duration of residence in the nursing home, frailty, dementia symptoms, urinary symptoms, antibiotic treatment, urinary catherization, and hospitalizations over a 10-month period. Clean catch mid-stream urine samples were collected and stored at -80C. DNA was extracted and 16S rRNA gene sequencing performed. The length of stay in the nursing facility and the Clinical Frailty Scale correlated with significant changes in microbiome composition. An increase in the relative abundance of a putative urinary pathogen, Aerococcus urinae, was the largest factor influencing change that occurred over duration of residence.

scholarly journals Necessity of 16S rRNA gene sequencing for identifying Haemophilus parainfluenzae-like strains associated with opportunistic urinary tract infections

2014 ◽  
Vol 63 (6) ◽  
pp. 805-811 ◽  
Author(s):  
Siu-Kei Chow ◽  
Jill E. Clarridge
Keyword(s):  
Urinary Tract ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Urinary Tract Infections ◽  
Gene Sequencing ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Haemophilus Parainfluenzae ◽  
Rrna Gene Sequencing ◽  
Tract Infections

The identification of Haemophilus spp. from urogenital sites can be challenging due to the lack of appropriate media for culturing the organisms and the poor resolution of biochemical methods. By incorporating chocolate agar and 16S rRNA gene sequence analysis in our protocol to identify Haemophilus spp. from urinary specimens, we isolated and characterized 30 genetically homogeneous strains of a cryptic species that is phylogenetically close to, but distinct from, Haemophilus parainfluenzae. Commercial biochemical kits and VITEK 2 could not distinguish between the two species. Over 90 % of the strains were isolated from urine and the urogenital area, made possible with the inclusion of chocolate agar in our urine culture protocol. In contrast, no Haemophilus strains isolated from respiratory specimens were identified as the cryptic genospecies. The cryptic genospecies was associated with urinary tract infections (UTIs) in certain patient populations. Distinct from Haemophilus quentinii that also causes urogenital infection, the cryptic genospecies required V factor (NAD) but not X factor (haemin) to grow. The data indicated that 16S rRNA gene sequencing may be necessary in identifying Haemophilus species and that inaccurate categorization of Haemophilus strains isolated from urogenital specimens based on phenotypic characteristics may prevent accurate diagnosis of UTIs.

scholarly journals The Female Urinary Microbiome: a Comparison of Women with and without Urgency Urinary Incontinence

mBio ◽  
2014 ◽  
Vol 5 (4) ◽  
Author(s):  
Meghan M. Pearce ◽  
Evann E. Hilt ◽  
Amy B. Rosenfeld ◽  
Michael J. Zilliox ◽  
Krystal Thomas-White ◽  
...  
Keyword(s):  
Urinary Incontinence ◽  
Urinary Tract ◽  
High Throughput Sequencing ◽  
Urgency Urinary Incontinence ◽  
Rrna Gene ◽  
Bacterial Dna ◽  
Content Type ◽  
Urinary Microbiome ◽  
Live Bacteria ◽  
Tract Infections

ABSTRACTBacterial 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 increasedGardnerellaand decreasedLactobacillus. Nine genera (Actinobaculum,Actinomyces,Aerococcus,Arthrobacter,Corynebacterium,Gardnerella,Oligella,Staphylococcus, andStreptococcus) were more frequently cultured from the UUI cohort. AlthoughLactobacilluswas isolated from both cohorts, distinctions existed at the species level, withLactobacillus gasseridetected more frequently in the UUI cohort andLactobacillus crispatusmost 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.IMPORTANCENew 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.

scholarly journals Antimicrobial Susceptibility of Bacteria Isolated from Urine Samples Obtained from Nursing Home Residents

2009 ◽  
Vol 30 (11) ◽  
pp. 1116-1119 ◽  
Author(s):  
Rituparna Das ◽  
Eleanor Perrelli ◽  
Virginia Towle ◽  
Peter H. Van Ness ◽  
Manisha Juthani-Mehta
Keyword(s):  
Urinary Tract Infection ◽  
Nursing Home ◽  
Urinary Tract ◽  
Tract Infection ◽  
Nursing Home Residents ◽  
Urine Samples ◽  
Oral Antibiotics ◽  
Indwelling Catheter ◽  
E Coli ◽  
Resistance Patterns

In our study of nursing home residents with clinically suspected urinary tract infection who did not require the use of an indwelling catheter, we identified bacteria isolated from urine samples, the resistance patterns of these isolated bacteria, and the antibiotic therapy prescribed to the residents. Escherichia coli, the predominant organism isolated, frequently was resistant to commonly prescribed oral antibiotics. Trimethoprim-sulfamethoxazole remains the best empiric antimicrobial therapy for a urinary tract infection, but nitrofurantoin should be considered if E. coli is identified.

scholarly journals Benchmarking DNA isolation kits used in analyses of the urinary microbiome

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Lisa Karstens ◽  
Nazema Y. Siddiqui ◽  
Tamara Zaza ◽  
Alecsander Barstad ◽  
Cindy L. Amundsen ◽  
...  
Keyword(s):  
Beta Diversity ◽  
High Throughput Sequencing ◽  
Dna Isolation ◽  
Urine Samples ◽  
Rrna Gene ◽  
Microbial Composition ◽  
Alpha And Beta Diversity ◽  
Dna Yield ◽  
Urinary Microbiome ◽  
Buffer Control

AbstractThe urinary microbiome has been increasingly characterized using next-generation sequencing. However, many of the technical methods have not yet been specifically optimized for urine. We sought to compare the performance of several DNA isolation kits used in urinary microbiome studies. A total of 11 voided urine samples and one buffer control were divided into 5 equal aliquots and processed in parallel using five commercial DNA isolation kits. DNA was quantified and the V4 segment of the 16S rRNA gene was sequenced. Data were processed to identify the microbial composition and to assess alpha and beta diversity of the samples. Tested DNA isolation kits result in significantly different DNA yields from urine samples. DNA extracted with the Qiagen Biostic Bacteremia and DNeasy Blood & Tissue kits showed the fewest technical issues in downstream analyses, with the DNeasy Blood & Tissue kit also demonstrating the highest DNA yield. Nevertheless, all five kits provided good quality DNA for high throughput sequencing with non-significant differences in the number of reads recovered, alpha, or beta diversity.

scholarly journals Characterization of extended spectrum β-Lactamase producing bactieria isolated from urinary tract infections

2019 ◽  
Vol 45 (1) ◽  
pp. 23-33
Author(s):  
Munawar Sultana ◽  
Anowar Khasru Parvez ◽  
Khandokar Fahmida Sultana ◽  
Sanjoy Kumer Mukharje ◽  
M Anwar Hossain
Keyword(s):  
Urinary Tract ◽  
Multidrug Resistant ◽  
Medical College Hospital ◽  
Urine Samples ◽  
Rrna Gene ◽  
College Hospital ◽  
Unique Challenge ◽  
Medical College ◽  
Extended Spectrum ◽  
Tract Infections

Background: A unique challenge for clinical microbiologists, clinicians, infection control professionals is to deal with extended-spectrum β-lactamase (ESBL) producing pathogens. The study was aims to isolate ESBL producing bacteria from urine samples of Urinary Tract Infection (UTI)-patients and to analyses their phenotypic and genotypic characteristics. Methods: A total of 90 urine samples from UTI patients were collected from Enam Medical College Hospital and Gonoshastha Medical College Hospital, Savar, Dhaka, Bangladesh; between May-2012 to August-2012. A total 75gram negative isolates were retrieved and screened for ESBL production by the Double Disk Diffusion Synergy Test (DDST). Isolates with ESBL phenotype were further characterised by antibiotic susceptibility testing, PCR and sequencing of β-lactamase genes. Results: Cultural and biochemical assay combined with 16S rRNA gene based phylogenetic identification confirmed that Escherichia spp. were predominant pathogens associate with UTI (41%), and the rest were distributed within the genus Enterobacter spp. 26%, Klebsiella spp. 21% , and Pseudomonas spp.10%. Total 31 isolates were phenotypically confirmed as ESBLs through DDST. The multidrug resistant (MDR) and ESBL producing bacteria showed high resistance to cefotaxime (96%), cefixime (90%) and imipenem (32%). PCR reaction was carried out targeting the genes blaTEM, blaCTX. Dominant ESBL class was CTX-M (65%) followed by TEM (52%). All ESBL isolates except 7 possesses multiple plasmids indicating possibility of both chromosomal and plasmid inheritance of ESBLs. Conclusions: This study shows a high prevalence of ESBL producing MDR in UTI patients among these two hospitals of Bangladesh indicating the necessity of alternative therapeutic intervention. Bangladesh Med Res Counc Bull 2019; 45: 23-33

scholarly journals Benchmarking DNA isolation kits used in analyses of the urinary microbiome

2020 ◽  
Author(s):  
Lisa Karstens ◽  
Nazema Y. Siddiqui ◽  
Tamara Zaza ◽  
Alecsander Barstad ◽  
Cindy L. Amundsen ◽  
...  
Keyword(s):  
Beta Diversity ◽  
Dna Isolation ◽  
Urine Samples ◽  
Rrna Gene ◽  
Microbial Composition ◽  
Alpha And Beta Diversity ◽  
Dna Yield ◽  
Urinary Microbiome ◽  
Technical Issues ◽  
Buffer Control

AbstractThe urinary microbiome has been increasingly characterized using next-generation sequencing. However, many of the technical methods have not yet been specifically optimized for urine. We sought to compare the performance of several DNA isolation kits used in urinary microbiome studies. A total of 11 voided urine samples and one buffer control were divided into 5 equal aliquots and processed in parallel using five commercial DNA isolation kits. DNA was quantified and the V4 segment of the 16S rRNA gene was sequenced. Data were processed to identify the microbial composition and to assess alpha and beta diversity of the samples. Tested DNA isolation kits result in significantly different DNA yields from urine samples but non-significant differences in the number of reads recovered, alpha, or beta diversity. DNA extracted with the Qiagen Biostic Bacteremia and DNeasy Blood & Tissue kits showed the fewest technical issues in downstream analyses, with the DNeasy Blood & Tissue kit also demonstrating the highest DNA yield. The Promega kit recovered fewer Gram positive bacteria compared to other kits. The Promega and DNeasy PowerSoil kits also appear to have some important biases towards over-representing certain Gram negative bacteria of biologic relevance within the urinary microbiome.

scholarly journals Culture-Free Detection of Antibiotic Resistance Markers from Native Patient Samples by Hybridization Capture Sequencing

2021 ◽  
Vol 9 (8) ◽  
pp. 1672
Author(s):  
Ines Ferreira ◽  
Sarah Lepuschitz ◽  
Stephan Beisken ◽  
Giuseppe Fiume ◽  
Katharina Mrazek ◽  
...  
Keyword(s):  
Limit Of Detection ◽  
16S Rrna Gene Sequencing ◽  
Primary Objective ◽  
Urine Samples ◽  
Rrna Gene ◽  
Global Challenge ◽  
Hybridization Capture ◽  
Rrna Gene Sequencing ◽  
Next Generation Sequencing Ngs ◽  
Marker Detection

The increasing incidence of antimicrobial resistance (AMR) is a major global challenge. Routine techniques for molecular AMR marker detection are largely based on low-plex PCR and detect dozens to hundreds of AMR markers. To allow for comprehensive and sensitive profiling of AMR markers, we developed a capture-based next generation sequencing (NGS) workflow featuring a novel AMR marker panel based on the curated AMR database ARESdb. Our primary objective was to compare the sensitivity of target enrichment-based AMR marker detection to metagenomics sequencing. Therefore, we determined the limit of detection (LOD) in synovial fluid and urine samples across four key pathogens. We further demonstrated proof-of-concept for AMR marker profiling from septic samples using a selection of urine samples with confirmed monoinfection. The results showed that the capture-based workflow is more sensitive and requires lower sequencing depth compared with metagenomics sequencing, allowing for comprehensive AMR marker detection with an LOD of 1000 CFU/mL. Combining the ARESdb AMR panel with 16S rRNA gene sequencing allowed for the culture-free detection of bacterial taxa and AMR markers directly from septic patient samples at an average sensitivity of 99%. Summarizing, the newly developed ARESdb AMR panel may serve as a valuable tool for comprehensive and sensitive AMR marker detection.

scholarly journals Effect of Pepper-Containing Diets on the Diversity and Composition of Gut Microbiome of Drosophila melanogaster

2020 ◽  
Vol 21 (3) ◽  
pp. 945 ◽  
Author(s):  
Marleny Garcia-Lozano ◽  
Joshua Haynes ◽  
Carlos Lopez-Ortiz ◽  
Purushothaman Natarajan ◽  
Yadira Peña-Garcia ◽  
...  
Keyword(s):  
Drosophila Melanogaster ◽  
Gut Microbiome ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Host Genotype ◽  
Microbial Composition ◽  
Potential Health ◽  
Gastrointestinal Microbiome ◽  
Composition And Structure ◽  
Rrna Gene Sequencing

One of the greatest impacts on the gastrointestinal microbiome is diet because the host and microbiome share the same food source. In addition, the effect of diet can diverge depending on the host genotype. Diets supplemented with phytochemicals found in peppers might cause shifts in the microbiome. Thus, understanding how these interactions occur can reveal potential health implications associated with such changes. This study aims to explore the gut microbiome of different Drosophila genetic backgrounds and the effects of dietary pepper treatments on its composition and structure. We analyzed the gut microbiomes of three Drosophila melanogaster genetic backgrounds (Canton-S, Oregon-RC, and Berlin-K) reared on control and pepper-containing diets (bell, serrano, and habanero peppers). Results of 16S rRNA gene sequencing revealed that the variability of Drosophila gut microbiome can be driven mainly by genetic factors. When the abundance of these communities is considered, pepper-containing diets also appear to have an effect. The most relevant change in microbial composition was the increment of Lactobacillaceae and Acetobacteraceae abundance in the pepper-containing diets in comparison with the controls in Oregon-RC and Berlin-K. Regression analysis demonstrated that this enhancement was associated with the content of phenolic compounds and carotenoids of the peppers utilized in this study; specifically, to the concentration of β-carotene, β-cryptoxanthin, myricetin, quercetin, and apigenin.

scholarly journals Reassessment of Routine Midstream Culture in Diagnosis of Urinary Tract Infection

2018 ◽  
Vol 57 (3) ◽  
Author(s):  
Sanchutha Sathiananthamoorthy ◽  
James Malone-Lee ◽  
Kiren Gill ◽  
Anna Tymon ◽  
Trang K. Nguyen ◽  
...  
Keyword(s):  
Urinary Tract Infection ◽  
Urinary Tract ◽  
Tract Infection ◽  
Bacterial Species ◽  
Significant Proportion ◽  
Genomic Analysis ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Interpretation Criteria ◽  
The Uk

ABSTRACTMidstream urine (MSU) culture remains the gold standard diagnostic test for confirming urinary tract infection (UTI). We previously showed that patients with chronic lower urinary tract symptoms (LUTS) below the diagnostic cutoff on MSU culture may still harbor bacterial infection and that their antibiotic treatment was associated with symptom resolution. Here, we evaluated the results of the United Kingdom’s MSU culture in symptomatic patients and controls. Next, we compared the bacterial enrichment capabilities of the MSU culture with those of a 50-µl uncentrifuged culture, a 30-ml centrifuged sediment culture, and 16S rRNA gene sequencing. This study was conducted on urine specimens from 33 LUTS patients attending their first clinical appointment (mean age, 48.7 years; standard deviation [SD], 16.5 years), 30 LUTS patients on treatment (mean age, 47.8 years; SD, 16.5 years) whose symptoms had relapsed, and 29 asymptomatic controls (mean age, 40.7 years, SD, 15.7 years). We showed that the routine MSU culture, adopting the UK interpretation criteria tailored to acute UTI, failed to detect a variety of bacterial species, including recognized uropathogens. Moreover, the diagnostic MSU culture was unable to discriminate between patients and controls. In contrast, genomic analysis of urine enriched by centrifugation discriminated between the groups, generating a more accurate understanding of species richness. In conclusion, the United Kingdom’s MSU protocol misses a significant proportion of bacteria, which include recognized uropathogens, and may be unsuitable for excluding UTI in patients with LUTS.

scholarly journals ANTIBIOTIC EXPOSURE IN LONG-TERM CARE FACILITIES IS ASSOCIATED WITH URINARY MICROBIOME PERTURBATIONS

2019 ◽  
Vol 3 (Supplement_1) ◽  
pp. S86-S86
Author(s):  
Brent R Schell ◽  
Doyle V Ward ◽  
Evan S Bradley ◽  
Protiva Dutta ◽  
John P Haran
Keyword(s):  
Older Adults ◽  
Long Term Care ◽  
Asymptomatic Bacteriuria ◽  
Urine Samples ◽  
Antibiotic Exposure ◽  
Term Care ◽  
Significant Difference ◽  
Care Facilities ◽  
Urinary Microbiome

Abstract The discovery of the human urinary microbiome, defined as the microbial communities which colonize the human urinary tract, has shed new light on the meaning and clinical significance of bacteriuria. The prevalence of asymptomatic bacteriuria has been reported to be as high as 50% in healthy older adults living in long term care facilities, yet the urinary microbiome of this population has not been reported. The aim of this pilot study was to describe the urinary microbiome of this population and explore the cross-sectional relationship with recent antibiotic exposure. Voided urine samples were obtained from healthy, institutionalized older adults (ages 79 to 95), including non-catheterized men and women without any urinary symptoms. The bacterial genomic content of each urine sample was assessed by 16S rRNA sequencing. Among the 77 genera found across 16 urine samples, there was no significant difference in the microbial diversity across age groups. When grouped by antibiotic exposure, those recently exposed had a significantly lower diversity (Shannon’s index of 2.16 vs. 2.61, p = 0.029), and lower evenness (Pielou’s evenness of 0.58 vs. 0.69, p= 0.017) relative to those who were not recently exposed. Enrichment analysis showed that recent antibiotic exposure was associated with an increased abundance of the genus Bacteroides and decreased abundance of the genus Streptococcus. To our knowledge, this is the first report describing the urinary microbiome of institutionalized older adults and suggests that recent antibiotic exposure should be accounted for in future studies of the urinary microbiome in this population.

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