The Microbial Communities in Male First Catch Urine Are Highly Similar to Those in Paired Urethral Swab Specimens

Dong, Qunfeng; Nelson, David E.; Diao, Lixia; Gao, Xiang; Fortenberry, J. Dennis; Pol, Barbara Van Der

doi:10.1371/journal.pone.0019709

Cited by 173 publications

(158 citation statements)

References 13 publications

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“…Many of the taxa identified in this study either cannot be or are not routinely cultivated by clinical microbiology laboratories (hereinafter called uncultivated bacteria). A related study determined that first-catch urine and urethral swab samples collected from adult men contained highly similar bacterial communities (6). These and other reports suggest that uncultivated bacteria can colonize the male urogenital tract and might be relevant to male urinary and reproductive tract syndromes.…”

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confidence: 68%

“…Near-full-length 16S rRNA alleles were amplified from gDNA of some samples with degenerate eubacterial primers and were TA cloned and Sanger sequenced as we recently described (26). For pyrosequencing, barcoded degenerate primers targeting the hypervariable V1-V3 subregion of eubacterial 16S rRNA were employed, and the resulting amplicons were sequenced in multiplex by using the Roche 454 Titanium platform (6,29,31). Only those sequence reads that perfectly matched primer barcode sequences were decoded into individual samples.…”

Section: Methodsmentioning

confidence: 99%

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Evidence of Uncultivated Bacteria in the Adult Female Bladder

et al. 2012

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c Clinical urine specimens are usually considered to be sterile when they do not yield uropathogens using standard clinical cultivation procedures. Our aim was to test if the adult female bladder might contain bacteria that are not identified by these routine procedures. An additional aim was to identify and recommend the appropriate urine collection method for the study of bacterial communities in the female bladder. Consenting participants who were free of known urinary tract infection provided urine samples by voided, transurethral, and/or suprapubic collection methods. The presence of bacteria in these samples was assessed by bacterial culture, light microscopy, and 16S rRNA gene sequencing. Bacteria that are not or cannot be routinely cultivated (hereinafter called uncultivated bacteria) were common in voided urine, urine collected by transurethral catheter (TUC), and urine collected by suprapubic aspirate (SPA), regardless of whether the subjects had urinary symptoms. Voided urine samples contained mixtures of urinary and genital tract bacteria. Communities identified in parallel urine samples collected by TUC and SPA were similar. Uncultivated bacteria are clearly present in the bladders of some women. It remains unclear if these bacteria are viable and/or if their presence is relevant to idiopathic urinary tract conditions. C ulture-dependent methods are typically used to test if clinical urine specimens contain uropathogens, and the results play a pivotal role in the diagnosis and treatment of urinary tract infection symptoms in women. Clinical urine cultures are considered positive when the colony count of a recognized uropathogen, such as Escherichia coli, Pseudomonas, Klebsiella, or group B Streptococcus reaches a predefined threshold (14). Bacterial urinary tract infections (UTI) caused by these typical uropathogens elicit symptoms that typically improve or resolve in response to appropriate antibiotic therapy. For other common urinary disorders, including overactive bladder, urinary incontinence, and a spectrum of pain disorders, e.g., painful bladder syndrome and interstitial cystitis, the clinical urine culture is negative and antibiotics are not given for clinical treatment. Under these conditions, the etiology is unknown, and research into these conditions so far has not incorporated culture-independent assessments of bladder infection, such as bacterial 16S rRNA PCR and metagenomic sequencing approaches.Recently, a concerted international effort, known as the Human Microbiome Project (http://commonfund.nih.gov/hmp/), has begun to catalogue the core microbial composition of the healthy human body in order to determine if changes to the core microbial communities affect health. Sequence analysis of 16S rRNA, the workhorse of that effort, has been used to determine the microflora composition of healthy skin (12, 13), the gastrointestinal tract (7, 9, 36), the mouth (24, 25, 28), and the vagina (11,16,27,39) and to correlate certain diseases with changes in this composition (9,11,27). A common the...

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confidence: 68%

Section: Methodsmentioning

confidence: 99%

Evidence of Uncultivated Bacteria in the Adult Female Bladder

et al. 2012

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“…ϩ Lactobacillus crispatus (6) ϩ ϩ Lactobacillus delbrueckii (1) ϩ ϩ Lactobacillus fermentum (1) ϩ Lactobacillus gasseri (12) ϩ ϩ ϩ ϩ ϩ Lactobacillus iners (6) ϩ ϩ ϩ ϩ Lactobacillus jensenii (10) ϩ ϩ ϩ ϩ Lactobacillus johnsonii (1) ϩ Lactobacillus rhamnosus (2) ϩ ϩ Micrococcus luteus (9) ϩ ϩ ϩ ϩ Micrococcus lylae (1) ϩ ϩ Neisseria perflava (1) ϩ (Continued on following page)…”

Section: Discussionmentioning

confidence: 99%

“…For example, our group previously reported the use of 16S rRNA gene sequencing to identify bacterial DNA (urinary microbiome) in culture-negative urine specimens collected from women diagnosed with pelvic prolapse and/or urinary incontinence, as well as from urine of women without urinary symptoms (4). Other investigators also have used culture-independent 16S rRNA gene sequencing to obtain evidence of diverse bacteria that are not routinely cultivated by clinical microbiology laboratories in the urine of both women and men (3,6,9,10).…”

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confidence: 99%

Urine Is Not Sterile: Use of Enhanced Urine Culture Techniques To Detect Resident Bacterial Flora in the Adult Female Bladder

et al. 2014

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Our previous study showed that bacterial genomes can be identified using 16S rRNA sequencing in urine specimens of both symptomatic and asymptomatic patients who are culture negative according to standard urine culture protocols. In the present study, we used a modified culture protocol that included plating larger volumes of urine, incubation under varied atmospheric conditions, and prolonged incubation times to demonstrate that many of the organisms identified in urine by 16S rRNA gene sequencing are, in fact, cultivable using an expanded quantitative urine culture (EQUC) protocol. Sixty-five urine specimens (from 41 patients with overactive bladder and 24 controls) were examined using both the standard and EQUC culture techniques. Fifty-two of the 65 urine samples (80%) grew bacterial species using EQUC, while the majority of these (48/52 [92%]) were reported as no growth at 10 3 CFU/ml by the clinical microbiology laboratory using the standard urine culture protocol. Thirty-five different genera and 85 different species were identified by EQUC. The most prevalent genera isolated were Lactobacillus (15%), followed by Corynebacterium (14.2%), Streptococcus (11.9%), Actinomyces (6.9%), and Staphylococcus (6.9%). Other genera commonly isolated include Aerococcus, Gardnerella, Bifidobacterium, and Actinobaculum. Our current study demonstrates that urine contains communities of living bacteria that comprise a resident female urine microbiota. Overactive bladder (OAB) is a highly prevalent syndrome characterized by urinary urgency with or without urge urinary incontinence and is often associated with frequency and nocturia (1). The etiology of OAB is often unclear and antimuscarinic treatments aimed at relaxing the bladder are ineffective in a large percentage of OAB sufferers, thereby suggesting etiologies outside neuromuscular dysfunction (2). One possibility is that OAB symptoms are influenced by microbes that inhabit the lower urinary tract (urinary microbiota).The microbiota of the female urinary tract has been poorly described; primarily, because a "culture-negative" status has been equated with the dogma that normal urine is sterile. Yet, emerging evidence indicates that the lower urinary tract can have a urinary microbiota (3-8). For example, our group previously reported the use of 16S rRNA gene sequencing to identify bacterial DNA (urinary microbiome) in culture-negative urine specimens collected from women diagnosed with pelvic prolapse and/or urinary incontinence, as well as from urine of women without urinary symptoms (4). Other investigators also have used culture-independent 16S rRNA gene sequencing to obtain evidence of diverse bacteria that are not routinely cultivated by clinical microbiology laboratories in the urine of both women and men (3, 6, 9, 10).Most of our previously sequenced urine specimens underwent standard clinical urine cultures that were reported as "no growth" at a 1:1000 dilution by our diagnostic microbiology laboratory (4). On the basis of this sequence-based evidence, which su...

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“…Urine, like feces, has the potential to provide an easily accessed fluid type, whose flora may provide an exquisitely sensitive measure of pathological state. For example, the microbiome of urine can be used to monitor asymptomatic sexually transmitted disease and is highly correlated to data generated from the urethra swabs (Dong et al, 2011;Nelson et al, 2010). As more work is done in this field, it is likely that more examples will be uncovered.…”

Section: Urinementioning

confidence: 99%