Characteristic male urine microbiomes associate with asymptomatic sexually transmitted infection

Background

The microbiome of the male urogenital tract is poorly described but it has been suggested that bacterial colonization of the male urethra might impact risk of sexually transmitted infection (STI). Previous cultivation-dependent studies showed that a variety of non-pathogenic bacteria colonize the urethra but did not thoroughly characterize these microbiomes or establish links between the compositions of urethral microbiomes and STI.

Methodology/Findings

Here, we used 16S rRNA PCR and sequencing to identify bacteria in urine specimens collected from men who lacked symptoms of urethral inflammation but who differed in status for STI. All of the urine samples contained multiple bacterial genera and many contained taxa that colonize the human vagina. Uncultivated bacteria associated with female genital tract pathology were abundant in specimens from men who had STI.

Conclusions

Urine microbiomes from men with STI were dominated by fastidious, anaerobic and uncultivated bacteria. The same taxa were rare in STI negative individuals. Our findings suggest that the composition of male urine microbiomes is related to STI.     

Bacterial communities of the coronal sulcus and distal urethra of adolescent males

Lactobacillus-dominated vaginal microbiotas are associated with reproductive health and STI resistance in women, whereas altered microbiotas are associated with bacterial vaginosis (BV), STI risk and poor reproductive outcomes. Putative vaginal taxa have been observed in male first-catch urine, urethral swab and coronal sulcus (CS) specimens but the significance of these observations is unclear. We used 16 S rRNA sequencing to characterize the microbiota of the CS and urine collected from 18 adolescent men over three consecutive months. CS microbiotas of most participants were more stable than their urine microbiotas and the composition of CS microbiotas were strongly influenced by circumcision. BV-associated taxa, including Atopobium, Megasphaera, Mobiluncus, Prevotella and Gemella, were detected in CS specimens from sexually experienced and inexperienced participants. In contrast, urine primarily contained taxa that were not abundant in CS specimens. Lactobacilllus and Streptococcus were major urine taxa but their abundance was inversely correlated. In contrast, Sneathia, Mycoplasma and Ureaplasma were only found in urine from sexually active participants. Thus, the CS and urine support stable and distinct bacterial communities. Finally, our results suggest that the penis and the urethra can be colonized by a variety of BV-associated taxa and that some of these colonizations result from partnered sexual activity.     

Asymptomatic gonorrhoea and chlamydial infection in rural Tanzanian men.

OBJECTIVE: To measure the prevalence of urethritis due to Neisseria gonorrhoeae and Chlamydial infection trachomatis in rural Tanzanian men DESIGN: About 500 men aged 15-54 years were selected from each of 12 rural communities by random cluster sampling; interviewed concerning past or present symptoms of sexually transmitted diseases; and asked to provide a first catch urine specimen, which was tested for pyuria with a leucocyte esterase dipstick test. Subjects with symptoms or with a positive result on testing were examined, and urethral swabs were taken for detection of N gonorrhoeae by gram stain and of C trachomatis by antigen detection immunoassay. SETTING: Mwanza region, north western Tanzania. SUBJECTS: 5876 men aged 15-54 years. MAIN OUTCOME MEASURES: Prevalence of urethral symptoms, observed urethral discharge, pyuria, urethritis ( > 4 pus cells per high power field on urethral smear), N gonorrhoeae infection (intracellular gram negative diplococci), and C trachomatis infection (IDEIA antigen detection assay). RESULTS: 1618 (28%) subjects reported ever having a urethral discharge. Current discharge was reported by 149 (2.5%) and observed on examination in 207 (3.5%). Gonorrhoea was found in 128 subjects (2.2%) and chlamydial infection in 39 (0.7%). Only 24 of 158 infected subjects complained of urethral discharge at the time of interview (15%). CONCLUSION: Infection with N gonorrhoeae and C trachomatis is commonly asymptomatic among men in this rural African population. This has important implications for the design of control programmes for sexually transmitted disease.     

Chlamydia trachomatis Load in Population-Based Screening and STI-Clinics: Implications for Screening Policy

Objectives

If the Chlamydia trachomatis (CT) bacterial load is higher in high-risk populations than in the general population, this negatively affects the efficacy of CT screening incentives. In the largest retrospective study to date, we investigated the CT load in specimens collected from 2 cohorts: (1) attendants of a sexually transmitted infection (STI)-clinic and (2) participants of the Dutch population-based screening (PBS).

Methods

CT load was determined using quantitative PCR in CT-positive male urine and female cervicovaginal swabs. CT loads were converted into tertiles. Using multinominal logistic regression, independent association of cohort, symptoms, risk behaviour and human cell count on load were assessed.

Results

CT loads were determined in 889 CT-positives from PBS (n = 529; 71.8% female) and STI-clinics (n = 360; 61.7% female). In men, STI-clinic-cohort, human cell count and urethral discharge were positively associated with CT load. In women, PBS-cohort and cell count were positively associated with CT load. Both cohorts had the same range in CT load.

Conclusions

The general population has a similar range of bacterial CT load as a high-risk population, but a different distribution for cohort and gender, highlighting the relevance of population-based CT-screening. When CT loads are similar, possibly the chances of transmission and sequelae are too.     

Comparison between Culture and a Multiplex Quantitative Real-Time Polymerase Chain Reaction Assay Detecting Ureaplasma urealyticum and U. parvum

A novel multiplex quantitative real-time polymerase chain reaction (qPCR) for simultaneous detection of U. urealyticum and U. parvum was developed and compared with quantitative culture in Shepard''s 10 C medium for ureaplasmas in urethral swabs from 129 men and 66 women, and cervical swabs from 61 women. Using culture as the gold standard, the sensitivity of the qPCR was 96% and 95% for female urethral and cervical swabs, respectively. In male urethral swabs the sensitivity was 89%. The corresponding specificities were 100%, 87% and 99%. The qPCR showed a linear increasing DNA copy number with increasing colour-changing units. Although slightly less sensitive than culture, this multiplex qPCR assay detecting U. urealyticum and U. parvum constitutes a simple and fast alternative to the traditional methods for identification of ureaplasmas and allows simultaneous species differentiation and quantitation in clinical samples. Furthermore, specimens overgrown by other bacteria using the culture method can be evaluated in the qPCR.     

Diagnosis of urogenital Chlamydia trachomatis infection in women based on mailed samples obtained at home: multipractice comparative study.

OBJECTIVE: To compare urine and vaginal flush samples collected by women at home with endocervical and urethral swabs obtained by general practitioners for their efficacy in the diagnosis of urogenital Chlamydia trachomatis infection. DESIGN: Multipractice comparative study. SETTING: 33 general practices and a central department of clinical microbiology in Aarhus County, Denmark. SUBJECTS: 222 women aged 18-25 years who for any reason had a gynaecological examination. INTERVENTIONS: Endocervical and urethral swabs were obtained by the women''s general practitioners. The same women when at home then collected a first void urine sample, a midstream urine sample, and a vaginal flush sample (using a vaginal pipette) and mailed them to the laboratory. MAIN OUTCOME MEASURES: C trachomatis defected by the polymerase chain reaction and the ligase chain reaction. Eight tests for C trachomatis were performed for every woman. When two of the eight yielded positive results the patient was considered infected. RESULTS: The overall prevalence of C trachomatis infection was 11.2% (23/205 women). Test sensitivities in samples obtained by general practitioners, samples obtained at home subjected to polymerase chain reaction, and samples obtained at home subjected to ligase chain reaction were 91%, 96%, and 100% respectively. The corresponding specificities were 100%, 92.9%, and 99.5%. CONCLUSIONS: The diagnostic efficacy of samples obtained by women at home and mailed to the laboratory was as good as for samples obtained by a general practitioner when using the ligase chain reaction. This may have important implications for the practicability of screening for this common, often asymptomatic, and treatable infection.     

A comparison of nonlethal sampling methods for amphibian gut microbiome analyses

Noninvasive sampling methods for studying intestinal microbiomes are widely applied in studies of endangered species and in those conducting temporal monitoring during manipulative experiments. Although existing studies show that noninvasive sampling methods among different taxa vary in their accuracy, no studies have yet been published comparing nonlethal sampling methods in adult amphibians. In this study, we compare microbiomes from two noninvasive sample types (faeces and cloacal swabs) to that of the large intestine in adult cane toads, Rhinella marina. We use 16S rRNA gene sequencing to investigate how microbial communities change along the digestive tract and which nonlethal sampling method better represents large intestinal microbiota. We found that cane toads' intestinal microbiota was dominated by Bacteroidetes, Proteobacteria and Firmicutes and, interestingly, we also saw a high proportion of Fusobacteria, which has previously been associated with marine species and changes in frog immunity. The large and small intestine of cane toads had a similar microbial composition, but the large intestine showed higher diversity. Our results indicate that cloacal swabs were more similar to large intestine samples than were faecal samples, and small intestine samples were significantly different from both nonlethal sample types. Our study provides valuable information for future investigations of the cane toad gut microbiome and validates the use of cloacal swabs as a nonlethal method to study changes in the large intestine microbiome. These data provide insights for future studies requiring nonlethal sampling of amphibian gut microbiota.     

A new automated method for isolation of Chlamydia trachomatis from urine eliminates inhibition and increases robustness for NAAT systems

Chlamydia trachomatis is a leading cause of sexually transmitted infection. Diagnostic methods with easy non-invasive sample collection are important to increase testing and hence to reduce the spread of this infection. To enable more use of urine samples in C. trachomatis diagnostics, automation is an absolute requirement since obtaining high-quality DNA from urine specimens involves extensive processing.

Here, we present a study in which a new automated sample preparation method, BUGS'n BEADS™ STI (BnB STI), was used up-front of the BDProbeTec™ ET end point analysis and compared with the full BDProbeTec™ ET method to analyze C. trachomatis in 1002 urine samples.

The BnB STI system represents a new concept within magnetic sample preparation in which bacteria are first isolated from the sample material followed by purification of bacterial nucleic acid using the same magnetic particles. Similar sensitivity and specificity were obtained with both methods. None of the samples processed with BnB STI inhibited the BDProbeTec™ ET test whereas 1.8% showed inhibition when processed according to the manual BDProbeTec™ ET DNA preparation method. Moreover, the average MOTA scores obtained with the BnB STI system were 48% higher for all amplification controls and 57% higher for positive samples, compared to the manual sample preparation. Based on these results and the significant reduction in hands-on-time for urine sample processing, the automated BnB STI sample preparation method was implemented for routine analysis of C. trachomatis from urine samples.     

Urethral and urachal urine output to the amniotic and allantoic sacs in fetal sheep

A chronic fetal sheep preparation was developed to measure, without interruption in utero, urethral and urachal urine output to the amniotic and allantoic sacs, respectively. Fetal urethral, urachal and total urine output was measured during a 5 day post-operative period, in late gestation. Total fetal urine output increased from day 1 to a volume of 1216 +/- 115 ml/day (SEM) on day 5 post-operative. Urachal urine output increased significantly from 12 ml/day on day 1 to 467 ml/day on day 5 (P less than 0.05). Fetal arterial blood gases, pH and immunoreactive ACTH, cortisol and immunoreactive arginine vasopressin concentrations were stable throughout the 5-day recovery period. Fetal urachal urine output to the allantoic cavity and total fetal urine output appears to require 4-5 days to stabilize post-operatively. Fetal urine is a major source of amniotic and allantoic fluid in late gestation and the volume of these sacs may be influenced, in part, by the distribution of urethral and urachal urine output.     

Comparison of Microbiomes from Different Niches of Upper and Lower Airways in Children and Adolescents with Cystic Fibrosis

Changes in the airway microbiome may be important in the pathophysiology of chronic lung disease in patients with cystic fibrosis. However, little is known about the microbiome in early cystic fibrosis lung disease and the relationship between the microbiomes from different niches in the upper and lower airways. Therefore, in this cross-sectional study, we examined the relationship between the microbiome in the upper (nose and throat) and lower (sputum) airways from children with cystic fibrosis using next generation sequencing. Our results demonstrate a significant difference in both α and β-diversity between the nose and the two other sampling sites. The nasal microbiome was characterized by a polymicrobial community while the throat and sputum communities were less diverse and dominated by a few operational taxonomic units. Moreover, sputum and throat microbiomes were closely related especially in patients with clinically stable lung disease. There was a high inter-individual variability in sputum samples primarily due to a decrease in evenness linked to increased abundance of potential respiratory pathogens such as Pseudomonas aeruginosa. Patients with chronic Pseudomonas aeruginosa infection exhibited a less diverse sputum microbiome. A high concordance was found between pediatric and adult sputum microbiomes except that Burkholderia was only observed in the adult cohort. These results indicate that an adult-like lower airways microbiome is established early in life and that throat swabs may be a good surrogate in clinically stable children with cystic fibrosis without chronic Pseudomonas aeruginosa infection in whom sputum sampling is often not feasible.     

Urethral plugs and urine retention in male mice

Because MM male mice suffer from a high incidence of urinary tract infection, an assessment was made as to whether the urethral plugs, which occur in male rodents, might be involved in its aetiology. When killed, males more commonly retained urine in their bladders than females but there was no significant difference between strains or method of killing. Males also voided urine more often during stressful handling followed by abdominal pressure, but also retained some urine more often than females. The study of sexually immature mice demonstrated no sex differences and no urine was retained in any bladder. It was concluded that the high frequency of urine retention in mature males is attributable to the presence of urethral plugs but these could not be implicated in the cause of MM urinary tract infection because of comparable findings in the controls. However, the possibility was considered that the plugs might facilitate infection of the kidneys once a bladder infection had become established.     

Male Circumcision and STI Acquisition in Britain: Evidence from a National Probability Sample Survey

Background

It is well-established that male circumcision reduces acquisition of HIV, herpes simplex virus 2, chancroid, and syphilis. However, the effect on the acquisition of non-ulcerative sexually transmitted infections (STIs) remains unclear. We examined the relationship between circumcision and biological measures of three STIs: human papillomavirus (HPV), Chlamydia trachomatis and Mycoplasma genitalium.

Methods

A probability sample survey of 15,162 men and women aged 16-74 years (including 4,060 men aged 16-44 years) was carried out in Britain between 2010 and 2012. Participants completed a computer-assisted personal interview, including a computer-assisted self-interview, which asked about experience of STI diagnoses, and circumcision. Additionally, 1,850 urine samples from sexually-experienced men aged 16-44 years were collected and tested for STIs. Multivariable logistic regression was used to calculate adjusted odds ratios (AOR) to quantify associations between circumcision and i) self-reporting any STI diagnosis and ii) presence of STIs in urine, in men aged 16-44 years, adjusting for key socio-demographic and sexual behavioural factors.

Results

The prevalence of circumcision in sexually-experienced men aged 16-44 years was 17.4% (95%CI 16.0-19.0). There was no association between circumcision and reporting any previous STI diagnoses, and specifically previous chlamydia or genital warts. However, circumcised men were less likely to have any HPV type (AOR 0.26, 95% confidence interval (CI) 0.13-0.50) including high-risk HPV types (HPV-16, 18, 31, 33, 35, 39, 45, 51, 52, 56, 58, 59 and/or 68) (AOR 0.14, 95% CI 0.05-0.40) detected in urine.

Conclusions

Circumcised men had reduced odds of HPV detection in urine. These findings have implications for improving the precision of models of STI transmission in populations with different circumcision prevalence and in designing interventions to reduce STI acquisition.     

The effects of hypoxemia with progressive acidemia on fetal renal function in sheep

In order to determine the effects of fetal hypoxemia on renal blood flow, glomerular filtration rate (GFR) and urethral and urachal urine output, we examined the effects of 3 h maternally-induced (9% O2, 3% CO2, 88% N2) fetal hypoxaemia on 10 chronically-instrumented fetal sheep between 127-135 days of gestation. Fetal arterial pH fell significantly during the second and third hours of hypoxia and this coincided with a significant increase in fetal arterial blood pressure (P less than 0.05). During the second hour of hypoxia, with mild acidaemia, fetal GFR decreased significantly and then, during the third hour, fetal GFR, urethral and total urine output were significantly elevated. During the 2-h recovery period urachal and total, but not urethral urine output, were significantly elevated (P less than 0.05). The data suggested that the increase in GFR and urine output measured during the third hour of hypoxia and the recovery period may reflect a pressure diuresis.     

Ion channels of the mammalian urethra

The mammalian urethra is a muscular tube responsible for ensuring that urine remains in the urinary bladder until urination. In order to prevent involuntary urine leakage, the urethral musculature must be capable of constricting the urethral lumen to an extent that exceeds bladder intravesicular pressure during the urine-filling phase. The main challenge in anti-incontinence treatments involves selectively-controlling the excitability of the smooth muscles in the lower urinary tract. Almost all strategies to battle urinary incontinence involve targeting the bladder and as a result, this tissue has been the focus for the majority of research and development efforts. There is now increasing recognition of the value of targeting the urethral musculature in the treatment and management of urinary incontinence. Newly-identified and characterized ion channels and pathways in the smooth muscle of the urethra provides a range of potential therapeutic targets for the treatment of urinary incontinence. This review provides a summary of the current state of knowledge of the ion channels discovered in urethral smooth muscle cells that regulate their excitability.     

Ion channels of the mammalian urethra

The mammalian urethra is a muscular tube responsible for ensuring that urine remains in the urinary bladder until urination. In order to prevent involuntary urine leakage, the urethral musculature must be capable of constricting the urethral lumen to an extent that exceeds bladder intravesicular pressure during the urine-filling phase. The main challenge in anti-incontinence treatments involves selectively-controlling the excitability of the smooth muscles in the lower urinary tract. Almost all strategies to battle urinary incontinence involve targeting the bladder and as a result, this tissue has been the focus for the majority of research and development efforts. There is now increasing recognition of the value of targeting the urethral musculature in the treatment and management of urinary incontinence. Newly-identified and characterized ion channels and pathways in the smooth muscle of the urethra provides a range of potential therapeutic targets for the treatment of urinary incontinence. This review provides a summary of the current state of knowledge of the ion channels discovered in urethral smooth muscle cells that regulate their excitability.     

Urethral closure mechanisms during sneezing-induced stress in anesthetized female cats

During stress-induced increase in abdominal pressure, urinary continence is maintained by urethral closure mechanisms. Active urethral response has been studied in dogs and rats. Such an active urethral response is also believed to occur in humans during stress events. We aimed to investigate urethral closure mechanisms during sneezing in cats. Urethral pressures along the urethra (UP1-UP4), with microtip transducer catheters with UP4 positioned in the distal urethra where the external urethral sphincter (EUS) is located, and intravesical pressure were measured, and abdominal wall, anal sphincter (AS), levator ani (LA), and EUS electromyograms (EMGs) were recorded during sneezing under closed-abdomen and open-abdomen conditions in eight anesthetized adult female cats. Proximal and middle urethral response induced by sneezing was not different from bladder response. Distal urethral response was greater compared with proximal and middle urethral and bladder response. In the open-abdomen bladder, proximal and middle urethral responses were similarly decreased and distal urethral response was unchanged compared with the closed-abdomen bladder. Bladder and urethral responses were positively correlated to sneeze strength. EUS, LA, and AS EMGs increased during sneezing. No urine leakage was observed, regardless of the strength of sneeze. In cats urethral closure mechanisms are partly passive in the proximal and middle urethra and involve an active component in the distal urethra that is believed to result from EUS and possibly LA contractions. Because central serotonin exerts similar effects on the lower urinary tract in cats and humans, the cat may represent a relevant model for pharmacological studies on continence mechanisms.     

TRICHOMONAS URETHRITIS IN MALES

Trichomonas urethritis in the male should be suspected in all chronic cases of urethritis. The diagnosis is easily established by the hanging-drop method of examining the urethral discharge, or the first-glass urine specimen. Curative treatment is readily accomplished by the use of urethral instillations of Carbarsone suspension using 1 capsule of Carbarsone per ounce of distilled water.     

Clinical judgment in the diagnosis and management of frequency and dysuria in general practice.

In a study of 40 women with the urethral syndrome and 46 women with conventional urinary tract infection, none of whom was pregnant, general practitioners predicted the diagnosis correctly before the report on the midstream urine specimen was received, as evidenced by their management. They seemed to do this by balancing the symptom of dysuria with the psychological make up of the patient: patients with the urethral syndrome suffered appreciably less dysuria than patients with urinary tract infection; patients with the urethral syndrome suffered appreciably more psychological illness. This ability to distinguish between the two disorders has important clinical and economic implications.     

The first performance report for the Bio-Rad Dx CT/NG/MG assay for simultaneous detection of Chlamydia trachomatis, Neisseria gonorrhoeae and Mycoplasma genitalium in urogenital samples

We evaluated the clinical performance of the Bio-Rad Dx CT/NG/MG assay for the detection of Chlamydia trachomatis, Mycoplasma genitalium and Neisseria gonorrhoeae in urogenital samples in comparison with the Roche COBAS? TaqMan? CT assay for C. trachomatis and an in-house TaqMan PCR assay for M. genitalium. Swab specimens were cultured for N. gonorrhoeae. In this prospective study, urogenital samples were obtained from symptomatic and asymptomatic patients attending the sexually transmitted disease clinic of Bordeaux, France, from January to April 2010. A total of 658 clinical specimens (259 male and 180 female urines, 191 vaginal, 21 endocervical and 7 urethral swabs) from 453 patients were analyzed. The prevalence of C. trachomatis and M. genitalium infections was 8.1% (21/260) and 1.9% (5/260) in men and 10.4% (20/193) and 2.1% (4/193) in women, respectively. The Bio-Rad Dx CT/NG/MG clinical sensitivity was 100% for C. trachomatis and M. genitalium in men and women. In male urine, the clinical specificity was 99.6% for C. trachomatis and 100% for M. genitalium. In women, the specificity was 99.5% for swabs and 100% for urines for detecting C. trachomatis and M. genitalium. All seven N. gonorrhoeae PCR-positive samples were also positive by culture. Patients were co-infected in 5/57 cases (8.8%), with C. trachomatis and M. genitalium in three cases, and C. trachomatis and N. gonorrhoeae in two cases. In conclusion, the Bio-Rad Dx CT/NG/MG assay can be recommended for the simultaneous detection of C. trachomatis, M. genitalium and N. gonorrhoeae in urogenital specimens of symptomatic and asymptomatic individuals.     

Nonclassical mucosal antibodies predominate in genital secretions of HIV-1 infected chimpanzees

To identify mucosal immunity in HIV-infected chimpanzees, IgG, IgA, and IgM from plasma, saliva, rectal swabs, vaginal washes, semen, and urethral washes were tested from four male and three female HIV-1_IIIB infected chimpanzees. The level of HIV infections in the seven chimpanzees were classified as high, intermediate and low depending on the number of HIV-1 infected cells per 10⁷ peripheral blood mononuclear cells (PBMC). One male chimpanzee had a relatively high viral load, two males and two females had moderate viral loads and one male and one female had low levels of infection. All seven animals had plasma antibody. The principal finding was that nonclassical mucosal antibodies of the IgG isotype were the predominant antibody in the saliva, rectal swabs, vaginal washes, semen, and urethral washes of infected animals. All plasma and mucosal samples were negative for IgM antibodies. The results show that HIV-1 specific IgG responses and not sIgA predominate at mucosal surfaces of HIV-1_IIIB infected chimpanzees. A trend was observed in which high viral loads correlated with high plasma IgG, IgA and sIgA titers. An overall correlation between relatively high virus loads and high amounts of mucosal IgG was also found.