The Urethral Microbiota of Men with and without Idiopathic Urethritis.

Nongonococcal urethritis (NGU) is a common genital tract syndrome in men, and up to 50% of cases are considered idiopathic, i.e., no etiological agent is identified. This poses challenges for clinicians in the diagnosis and treatment of NGU and often results in antibiotic misuse and overuse. Therefore, to identify potential infectious causes of urethritis and inform clinical management of urethritis cases, we characterized and compared the urethral microbiota of men with and without idiopathic urethritis. Participants were derived from a case-control study that examined viral and bacterial pathogens and sexual practices associated with NGU. Men with NGU who tested negative for established causes of NGU (Chlamydia trachomatis, Mycoplasma genitalium, Trichomonas vaginalis, adenoviruses, herpes simplex virus [HSV]-1, and/or HSV-2) were classified as idiopathic cases, and the controls were men reporting no current urethral symptoms. Men provided a urine sample that was used to characterize the urethral microbiota using 16S rRNA gene sequencing. Bacterial taxa associated with idiopathic urethritis were identified using analysis of compositions of microbiomes with bias correction. When stratified by sex of sexual partner, we found that the abundance of Haemophilus influenzae was significantly increased in men who have sex with men with idiopathic urethritis, and the abundance of Corynebacterium was significantly increased in men who have sex with women with idiopathic urethritis. Other taxa, including Ureaplasma, Staphylococcus haemolyticus, Streptococcus pyogenes, Escherichia, and Streptococcus pneumoniae/pseudopneumoniae, dominated the urethral microbiota of idiopathic urethritis cases but not controls, suggesting that these organisms may also contribute to urethritis. Importantly, the taxa we identified represent biologically plausible causes of urethritis and should be prioritized for future study. IMPORTANCE Nongonococcal urethritis (NGU) is the commonest genital tract syndrome in men and is nearly universally presumptively treated with an antibiotic. Common causes of NGU include Chlamydia trachomatis and Mycoplasma genitalium, but in more than 50% of cases, an infectious cause is not identified. In this case-control study, we found that the urethral microbiota composition differed between men with and without idiopathic urethritis and differed by sex of sexual partner. We identified specific bacterial taxa that were associated with idiopathic urethritis, including Haemophilus influenzae and Corynebacterium. These data, together with the finding that key bacterial taxa were found to dominate the urethral microbiota of cases but not controls, suggest that a range of bacteria contribute to urethritis and that these organisms may be influenced by sexual practices. Through identifying the infectious causes of urethritis, we can inform appropriate targeted diagnostic and treatment practices and importantly reduce misuse and overuse of antibiotics.

Gardnerella vaginalis Clade Distribution Is Associated With Behavioral Practices and Nugent Score in Women Who Have Sex With Women.

BACKGROUND: Gardnerella vaginalis is detected in women with and without bacterial vaginosis (BV). Identification of 4 G. vaginalis clades raised the possibility that pathogenic and commensal clades exist. We investigated the association of behavioral practices and Nugent Score with G. vaginalis clade distribution in women who have sex with women (WSW). METHODS: Longitudinal self-collected vaginal specimens were analyzed using established G. vaginalis species-specific and clade-typing polymerase chain reaction assays. Logistic regression assessed factors associated with detection of G. vaginalis clades, and multinomial regression assessed factors associated with number of clades. RESULTS: Clades 1, 2, and 3 and multiclade communities (<2 clades) were associated with Nugent-BV. Clade 1 (odds ratio [OR], 3.36; 95% confidence interval [CI], 1.65-6.84) and multiclade communities (relative risk ratio [RRR], 9.51; 95% CI, 4.36-20.73) were also associated with Lactobacillus-deficient vaginal microbiota. Clade 4 was neither associated with Nugent-BV nor Lactobacillus-deficient microbiota (OR, 1.49; 95% CI, 0.67-3.33). Specific clades were associated with differing behavioral practices. Clade 1 was associated with increasing number of recent sexual partners and smoking, whereas clade 2 was associated with penile-vaginal sex and sharing of sex toys with female partners. CONCLUSIONS: Our results suggest that G. vaginalis clades have varying levels of pathogenicity in WSW, with acquisition occurring through sexual activity. These findings suggest that partner treatment may be an appropriate strategy to improve BV cure.

Anal human papillomavirus infections in young unvaccinated men who have sex with men attending a sexual health clinic for HPV vaccination in Melbourne, Australia.

The Victorian Government introduced a time-limited quadrivalent human papillomavirus (HPV) vaccination catch-up program targeting gay and bisexual men who have sex with men (MSM) aged up to 26 years in 2017. As of 2017, men aged ≥20 years were not eligible for the school-based HPV vaccination program. This study examined the prevalence of anal HPV among 496 MSM aged 20-26 years before they received the first dose of the HPV vaccine at the Melbourne Sexual Health Centre, Australia. More than half (56.5%) had any high-risk HPV genotypes detected in the anus. Almost half (43.1%) had at least one quadrivalent HPV vaccine-preventable genotype (6, 11, 16 or 18) and one-fifth (21.0%) had HPV 16 detected in the anus. These findings suggest that a targeted catch-up HPV vaccination program for MSM is still beneficial to protect against high-risk HPV genotypes associated with anal cancer, as well as low-risk HPV genotypes.

Detection of human papillomavirus in urine among heterosexual men in relation to location of genital warts and circumcision status.

OBJECTIVE: Human papillomavirus (HPV) surveillance is important to monitor the effectiveness of national HPV vaccination programmes. Positivity of HPV in urine in men varies with different sampling methods. We aimed to determine the positivity for detection of HPV-6/11 in urine samples among men in relation to the position of genital warts and circumcision status. METHOD: We analysed stored chlamydia-positive urine specimens in young heterosexual men aged less than 25 years attending Melbourne Sexual Health Centre, Australia, between 2004 and 2015, for HPV genotypes. Positivity of HPV-6/11 and high-risk genotypes were stratified according to the position of genital warts and circumcision status. Positivity of HPV-6/11 was calculated using diagnosis of warts as the gold standard. Warts were classified as proximal penile warts from suprapubic area to midshaft of penis, and distal penile warts from distal shaft of penis to meatus. RESULTS: Of the 934 specimens, 253 (27.1%) men were positive for any HPV and 82 men (8.8%) had genital warts. The ORs of HPV-6/11 detection in urine were 4.63 (95% CI: 1.68 to 12.78) and 40.20 (95% CI: 19.78 to 81.70) times higher among men who had proximal penile warts and distal penile warts, respectively, compared with men who did not have genital warts. Circumcised men were less likely to have high-risk HPV (OR 0.31; 95% CI: 0.14 to 0.65) than uncircumcised men. Uncircumcised men were more likely to have distal penile warts than circumcised men (OR 8.22; 95% CI: 1.34 to 337.46). CONCLUSION: Positivity of HPV-6/11 in urine increases greatly in men with distal penile warts. Circumcised men are less likely to have distal penile warts, any HPV or high-risk HPV detected. Urine is likely to be an alternative sampling method for HPV-6/11 surveillance programme in men in countries with low circumcision rates.

Quadrivalent vaccine-targeted human papillomavirus genotypes in heterosexual men after the Australian female human papillomavirus vaccination programme: a retrospective observational study.

BACKGROUND: Australia introduced a national quadrivalent human papillomavirus (4vHPV) vaccination programme for girls and young women in April, 2007. The HPV genotypes targeted by the female vaccine could also affect the protection afforded to heterosexual men. We examined the prevalence of 4vHPV targeted vaccine genotypes and the nine-valent HPV (9vHPV)-targeted vaccines genotypes among sexually active, predominantly unvaccinated heterosexual men from 2004 to 2015. METHODS: We did a retrospective, observational study of urine and urethral swab specimens from heterosexual men aged 25 years or younger attending the Melbourne Sexual Health Centre between July 1, 2004, and June 30, 2015, who tested positive for Chlamydia trachomatis. We extracted HPV DNA and used the PapType HPV assay to detect 14 high-risk HPV genotypes (16, 18, 31, 33, 35, 39, 45, 51, 52, 56, 58, 59, 66, and 68) and two low-risk genotypes (6 and 11). We calculated the prevalence of any HPV genotype, genotypes 6 or 11, genotypes 16 or 18, genotypes in the 4vHPV group (6, 11, 16, or 18), five additional genotypes in the 9vHPV group (31, 33, 45, 52, or 58), and non-vaccine-targeted genotypes (31, 33, 35, 39, 45, 51, 56, 58, 59, 66, or 68). FINDINGS: We obtained data between July 1, 2004, and June 30, 2015, and did the data analysis in December, 2015. Of 1764 specimens obtained, we included 1466 in our final analysis (the others were excluded because they had indeterminate results or were duplicates). The prevalence of any HPV genotype and genotypes 31, 33, 45, 52, and 58 did not change from 2004-05 to 2014-15, but we noted reductions in genotypes 6 and 11 (from 12% [95% CI 6-21%], to 3% [1-7%], ptrend=0·008), 16 and 18 (from 13% [95% CI 7-22%] to 3% [1-6%], ptrend<0·0001), and 4vHPV-targeted genotypes (from 22% [95% CI 14-33%] to 6% [3-10%], ptrend<0·0001). Prevalence of non-vaccine-targeted genotypes increased from 16% [95% CI 9-26%] to 22% [17-29%], ptrend<0·0001). In Australian-born men, 4vHPV-targeted genotype prevalence decreased from 11 of 55 [20%, 95% CI 10-33%] to two of 74 [3%, 0-11%], ptrend<0·0001); an even greater decline occurred in Australian-born men aged 21 years or younger (from four of 13 [31%, 95% CI 9-61%] to none of 25; ptrend<0·0001). Genotypes 16 and 18 decreased (adjusted prevalence ratio [PR] 0·32, 95% CI 0·14-0·74; p=0·008) but not genotypes 6 and 11 (adjusted PR 0·50, 0·16-1·56; p=0·234) in the postvaccination period among men who had arrived in Australia within 2 years from countries with a bivalent vaccine (2vHPV) programme (England, Scotland, Wales, Cook Islands, Northern Ireland, or the Netherlands), compared with the prevaccination period. No change was noted in 4vHPV genotypes in men born overseas in other countries. INTERPRETATION: The marked reduction in prevalence of 4vHPV genotypes among mainly unvaccinated Australian-born men suggests herd protection has occurred from the female vaccination programme. Additionally, the decline in genotypes 16 and 18, but not genotypes 6 and 11, among overseas-born men predominantly from countries with a 2vHPV vaccine programme suggests that these men received benefits from herd protection for genotypes 16 and 18 from their vaccinated female partners in their own countries. These reductions could translate to reductions in HPV-related malignant conditions in men, even in countries with female-only vaccination programmes. FUNDING: The Australian National Health and Medical Research Council Program.

Human papillomavirus in young women with Chlamydia trachomatis infection 7 years after the Australian human papillomavirus vaccination programme: a cross-sectional study.

BACKGROUND: The national quadrivalent human papillomavirus (4vHPV) vaccination programme was launched in Australia in April, 2007. In this study, we aimed to explore the prevalence of vaccine-targeted human papillomavirus (HPV) types contained in the 4vHPV and nine-valent HPV (9vHPV) vaccines detected in young women diagnosed with chlamydia. METHODS: In this cross-sectional study, we identified specimens from women aged 25 years or younger who attended the Melbourne Sexual Health Centre (Melbourne, VIC, Australia) diagnosed with chlamydia. We calculated the prevalence of 4vHPV types (6, 11, 16, and 18) and the extra five 9vHPV types (31, 33, 45, 52, and 58 alone) excluding 4vHPV types, stratified by Australian financial year (and according to the prevaccination and postvaccination periods) and self-reported vaccination status, for all women, Australian-born women, Australian-born women aged 21 years and younger, and overseas-born women. We calculated adjusted prevalence ratios using binomial log linear regression. FINDINGS: Between July 1, 2004, and June 30, 2014, we included 1202 women. The prevalence of 4vHPV types in Australian-born women decreased during this period (HPV 6 and 11: 2004-05 nine [16%, 95% CI 8-28] of 56 vs 2013-14 one [2%, 0-9] of 57, p<0·0001; HPV 16 and 18: 17 [30%, 19-44] vs two [4%, 0-12], p<0·0001). In Australian-born women aged 21 years and younger, HPV 6 and 11 prevalence remained at 0% for all years after 2008-09, and we detected HPV 16 and 18 in 5% or less of samples for the same period. In unvaccinated Australian-born women, we noted a significant decrease in 4vHPV types from 66 (41%, 95% CI 34-49) of 160 in the prevaccination period (from July 1, 2004, to June 30, 2007) to five (19%, 6-38) of 27 in the postvaccination period (July 1, 2007, to June 30, 2014; p=0·031), but not in the 9vHPV types, excluding 4vHPV (36 [23%, 95% CI 16-30] vs seven [26%, 11-46]; p=0·805). INTERPRETATION: The three-dose vaccination coverage was sufficient for the 4vHPV types to almost disappear in Australian-born women aged 21 years or younger within 3 years of introduction of the national HPV vaccination programme. We noted strong herd protection, with a significant decrease in the prevalence of 4vHPV in unvaccinated women. The 4vHPV vaccination programme in Australia has been successful at protecting women against 4vHPV types. FUNDING: Australian National Health and Medical Research Council.

Human papillomavirus type 6 and 11 genetic variants found in 71 oral and anogenital epithelial samples from Australia.

Genetic variation of 49 human papillomavirus (HPV) 6 and 22 HPV11 isolates from recurrent respiratory papillomatosis (RRP) (n = 17), genital warts (n = 43), anal cancer (n = 6) and cervical neoplasia cells (n = 5), was determined by sequencing the long control region (LCR) and the E6 and E7 genes. Comparative analysis of genetic variability was examined to determine whether different disease states resulting from HPV6 or HPV11 infection cluster into distinct variant groups. Sequence variation analysis of HPV6 revealed that isolates cluster into variants within previously described HPV6 lineages, with the majority (65%) clustering to HPV6 sublineage B1 across the three genomic regions examined. Overall 72 HPV6 and 25 HPV11 single nucleotide variations, insertions and deletions were observed within samples examined. In addition, missense alterations were observed in the E6/E7 genes for 6 HPV6 and 5 HPV11 variants. No nucleotide variations were identified in any isolates at the four E2 binding sites for HPV6 or HPV11, nor were any isolates found to be identical to the HPV6 lineage A or HPV11 sublineage A1 reference genomes. Overall, a high degree of sequence conservation was observed between isolates across each of the regions investigated for both HPV6 and HPV11. Genetic variants identified a slight association with HPV6 and anogenital lesions (p = 0.04). This study provides important information on the genetic diversity of circulating HPV 6 and HPV11 variants within the Australian population and supports the observation that the majority of HPV6 isolates cluster to the HPV6 sublineage B1 with anogenital lesions demonstrating an association with this sublineage (p = 0.02). Comparative analysis of Australian isolates for both HPV6 and HPV11 to those from other geographical regions based on the LCR revealed a high degree of sequence similarity throughout the world, confirming previous observations that there are no geographically specific variants for these HPV types.

Hybrid Capture II testing for high-risk human papillomavirus DNA in the follow-up of women treated for high-grade cervical intraepithelial neoplasia.

OBJECTIVE: This study aimed to estimate and compare the validity of high-risk human papillomavirus DNA (HR-HPV DNA) testing using Hybrid Capture II with and without Pap cytological examination in the detection of incident high-grade cervical intraepithelial neoplasia (CIN 2+) after treatment. MATERIALS AND METHODS: A total of 1,608 women undergoing ablative or excisional treatment were recruited to the study between May 2001 and June 2005, of whom 985 women were treated for CIN 2+. High-risk HPV DNA tests and Pap smears were performed once in every 6 months for 24 months after treatment. RESULTS: A total of 888 women were eligible for analysis. High-grade cervical intraepithelial neoplasia was detected in 22 women (2.5%) for the 24 months after treatment. The sensitivity for CIN 2+ detection with cytological diagnosis ranged from 43% to 100%, from 67% to 100% for HR-HPV DNA test, and from 67% to 100% for both tests combined. The specificity of cytological diagnosis ranged from 94% to 97%, from 75% to 84% for HR-HPV DNA test, and from 80% to 82% for both tests combined. The positive predictive value for cytological diagnosis ranged from 8% to 30%, from 4% to 14% for HR-HPV DNA test, and from 4% to 11% for both tests combined. The negative predictive value was 99% or greater for cytological diagnosis alone, HR-HPV DNA test alone, or for both tests combined. CONCLUSIONS: As histologically proven CIN 2+ after treatment for this group of women was low, adding HR-HPV DNA testing to Pap smear did not increase the detection of CIN 2+ or enhance the negative predictive value of cytological diagnosis alone.

Clearance of human papillomavirus in women treated for cervical dysplasia.

OBJECTIVE: To estimate human papillomavirus (HPV) clearance of women with cervical abnormalities after treatment. METHODS: Women attending dysplasia clinics between 2001 and 2007 with a new diagnosis of high-grade dysplasia or persistent low-grade dysplasia requiring treatment by excision or laser ablation were invited to participate. Cervical cytology, histology of biopsies collected at colposcopy, and HPV DNA detection and genotyping of 37 HPV genotypes on specimens collected at treatment and subsequent routine visits were examined. A log-rank test was used to compare the survival distribution between groups. RESULTS: Of the 1,649 women eligible at treatment (baseline), 1,207 (73%) were included in the analysis; 96% (n=1,159) had three or more posttreatment visits. At baseline and the subsequent three follow-up visits, the prevalence of women with HPV DNA detected was 84%, 53% (on average, 6.3 months after baseline), 44% (on average, 15.7 months after baseline), and 45% (on average, 24.3 months after baseline). The median time to HPV clearance was approximately 6 months for either HPV 16 (n=387) or HPV 18 (n=96), irrespective of concurrent detection of other types. On average, HPV 16 or HPV 18 types cleared faster than other types (P<.001). This association remained significant after adjustment for age, preoperative histology, number of preoperative histology results, and treatment type. CONCLUSION: Clearance times of HPV 16 and HPV 18 infections were similar to each another but shorter than other HPV types. LEVEL OF EVIDENCE: III.