Resistance-Guided Treatment of Gonorrhea: A Prospective Clinical Study.

BACKGROUND: Novel treatment strategies to slow the continued emergence and spread of antimicrobial resistance in Neisseria gonorrhoeae are urgently needed. A molecular assay that predicts in vitro ciprofloxacin susceptibility is now available but has not been systematically studied in human infections. METHODS: Using a genotypic polymerase chain reaction assay to determine the status of the N. gonorrhoeae gyrase subunit A serine 91 codon, we conducted a multisite prospective clinical study of the efficacy of a single oral dose of ciprofloxacin 500 mg in patients with culture-positive gonorrhea. Follow-up specimens for culture were collected to determine microbiological cure 5-10 days post-treatment. RESULTS: Of the 106 subjects possessing culture-positive infections with wild-type gyrA serine N. gonorrhoeae genotype, the efficacy of single-dose oral ciprofloxacin treatment in the per-protocol population was 100% (95% 1-sided confidence interval, 97.5-100%). CONCLUSIONS: Resistance-guided treatment of N. gonorrhoeae infections with single-dose oral ciprofloxacin was highly efficacious. The widespread introduction and scale-up of gyrA serine 91 genotyping in N. gonorrhoeae infections could have substantial medical and public health benefits in settings where the majority of gonococcal infections are ciprofloxacin susceptible. CLINICAL TRIALS REGISTRATION: NCT02961751.

A Silent Epidemic: The Prevalence, Incidence and Persistence of Mycoplasma genitalium Among Young, Asymptomatic High-Risk Women in the United States.

Background: Mycoplasma genitalium can result in pelvic inflammatory disease and adverse pregnancy outcomes. We analyzed data collected from a prospective study of asymptomatic bacterial vaginosis (BV) to determine the natural history of M. genitalium. Methods: Women aged 15-25 years, with asymptomatic BV and ≥2 risk factors for sexually transmitted infection were recruited from 10 sites throughout the United States. Vaginal swab samples were collected at enrollment and through home-based testing every 2 months over 12 months. M. genitalium nucleic acid amplification testing was performed for M. genitalium using transcription-mediated assays (Hologic). The prevalence, incidence, and persistence of M. genitalium, defined as all positive specimens during follow-up, were estimated with 95% confidence intervals (CIs). Adjusted odds ratios (AOR) were calculated using logistic and Poisson regression to evaluate participant characteristics associated with M. genitalium infection. Results: Among 1139 women, 233 were M. genitalium positive, for a prevalence of 20.5% (95% CI, 18.2%-22.9%); 42 of 204 had persistent M. genitalium (20.6%). Among 801 M. genitalium-negative women at baseline, the M. genitalium incidence was 36.6 per 100 person-years (95% CI, 32.4-41.3). Black race (AOR, 1.92; 95% CI, 1.09-3.38), age ≤21 years (1.40; 1.03-1.91), and prior pregnancy (1.36; 1.00-1.85) were associated with prevalent M. genitalium; only black race was associated with incident M. genitalium (P = .03). Conclusions: We identified high rates of prevalent, incident, and persistent M. genitalium infections among young, high-risk women with asymptomatic BV, supporting the need for clinical trials to evaluate the impact of M. genitalium screening on female reproductive health outcomes.

Historical and Current Trends in the Epidemiology of Early Syphilis in San Francisco, 1955 to 2016.

BACKGROUND: Seventeen years into a sustained epidemic, early syphilis (ES) rates in San Francisco (SF) are continuing to increase and the demographics of the affected population are changing. We provide a historical overview of ES in SF among men who have sex with men (MSM) and describe trends in the epidemiology and disease investigation outcomes. METHODS: We examined data from the SF Department of Public Health's patient-based registry of integrated STD surveillance, clinical, and field investigation data to describe demographic and behavioral characteristics of ES cases, as well as outcomes of syphilis partner services (PS). χ Tests were performed to examine categorical differences across periods. Analysis of variance was used to examine differences in continuous variables. RESULTS: In 2016, 1095 ES cases were reported among males in SF, a 219% increase from the 343 cases identified 10 years ago. Between 1996-1999 and 2010-2016, an increasing proportion of ES cases were among MSM younger than 25 years, nonwhite, and HIV negative (P < 0.05). A decreasing proportion of ES cases were assigned for PS, among whom a smaller proportion of reported sex partners were identified by name, resulting in an overall decline in the proportion of cases who had at least one named partner treated as a result of PS (Disease Intervention Rate) from 30.5 in 2000-2004 to 14.8 in 2010-2016. CONCLUSIONS: Syphilis case rates continue to increase in SF and the epidemic is expanding beyond a core population. Additional resources and innovative prevention approaches are needed to reduce the burden of syphilis among MSM.

Home Screening for Bacterial Vaginosis to Prevent Sexually Transmitted Diseases.

BACKGROUND: Longitudinal studies have consistently found a significant association between bacterial vaginosis (BV) and acquisition of sexually transmitted diseases. However, there are limited prospective data to confirm these findings. METHODS: We conducted a prospective, randomized, open-label trial of home screening and treatment of young women with asymptomatic BV who were also at high risk for sexually transmitted diseases. These women were screened every 2 months for 12 months and randomized to treatment with oral metronidazole 500 mg twice daily for 7 days or observation alone. The primary outcome was the incidence of gonorrhea and/or chlamydia. RESULTS: A total of 1365 subjects were enrolled in the study across 10 sites. Adherence with mailing specimens obtained at home was excellent in both groups (84%-88%). The incidence of gonorrhea and/or chlamydia was 19.1 per 100 person-years (95% confidence interval, 15.1-22.1) for the treatment group and 18.5 per 100 person-years (15.1-22.8) for the observation arm, a difference that was not statistically significant. CONCLUSIONS: Young women were very amenable to home screening for BV, gonorrhea, and chlamydia. Treatment of asymptomatic BV with 1 week of oral metronidazole did not decrease the incidence of gonorrhea and/or chlamydia. CLINICAL TRIALS REGISTRATION: NCT00667368.

Trichomonas vaginalis infection among homeless and unstably housed adult women living in a resource-rich urban environment.

OBJECTIVE: The social context of poverty is consistently linked to Trichomonas vaginalis infection, yet few studies regarding T. vaginalis have been conducted exclusively among low-income individuals. We identified social determinants of health associated with prevalent T. vaginalis infection among homeless and unstably housed adult women. METHODS: Between April and October of 2010, we conducted cross-sectional T. vaginalis screening and behavioural interviews in an existing cohort of San Francisco homeless and unstably housed women. Data were analysed using multivariable logistical regression. RESULTS: Among 245 study participants, the median age was 47 years and 72% were of non-Caucasian race/ethnicity. T. vaginalis prevalence was 12%, compared to 3% in the general population, and 33% of infected individuals reported no gynaecological symptoms. In adjusted analysis, the odds of T. vaginalis infection were lower among persons older than 47 years, the population median (OR=0.14, 95% CI 0.04 to 0.38), and higher among those reporting recent short-term homeless shelter stays (OR=5.36, 95% CI 1.57 to 18.26). Race and income did not reach levels of significance. Sensitivity analyses indicated that testing all women who report recent unprotected sex would identify more infections than testing those who report gynaecological symptoms (20/30 vs 10/30; p=0.01). CONCLUSIONS: The prevalence of T. vaginalis is high among homeless and unstably housed adult women, over one-third of infected individuals have no gynaecological symptoms, and correlates of infection differ from those reported in the general population. Targeted screening and treatment among impoverished women reporting recent unprotected sex, particularly young impoverished women and all women experiencing short-term homelessness, may reduce complications related to this treatable infection.

Ecological analysis examining the association between census tract-level incarceration and reported chlamydia incidence among female adolescents and young adults in San Francisco.

OBJECTIVES: Incarceration has been linked to increased risk of sexually transmitted infections (STIs). We conducted a census tract-level ecological analysis to explore the relationship between neighbourhood incarceration rates and chlamydia incidence among adolescent girls and young women under age 25 in San Francisco in 2010 to focus public health efforts in neighbourhoods at risk. METHODS: Female chlamydial cases under age 25 that were reported to the San Francisco Department of Public Health in 2010 were geocoded to census tract, and chlamydia incidence was calculated. Addresses of incarcerated individuals were geocoded, and census tract-specific incarceration was estimated. American Community Survey data from 2005 to 2009 provided tract-specific survey estimates of demographic and socioeconomic characteristics of communities to allow for evaluation of potential census tract-level confounders. A Poisson mixed model was used to assess the relationship of census tract-level incarceration rate with chlamydial case rate. RESULTS: Accounting for spatial dependence in neighbouring regions, there was a positive association between incarceration rates and chlamydia incidence in young women under age 25 in San Francisco, and this association decreased as poverty increased, after controlling for other risk factors in the model. CONCLUSIONS: This ecological analysis supports the neighbourhood role of incarceration in the risk of chlamydia among young women. These results have important implications for directing limited public health resources to local areas at risk in order to geographically focus prevention interventions and provide improved access to STI services in specific neighbourhoods with high incarceration rates.

Detection of Chlamydia trachomatis and Neisseria gonorrhoeae in Rectal and Oropharyngeal Swabs and Urine Specimens from Men Who Have Sex With Men with Abbott's M2000 RealTime.

We evaluated Abbott's RealTime assay for the detection of Chlamydia trachomatis (CT) and Neisseria gonorrhoeae (GC) in the urethra, oropharynx, and rectum of 260 men who have sex with men. Compared with Hologic's AC2, RealTime had good agreement for detecting CT and GC. Overall, there were 25 CT and 44 GC AC2 positives, and 26 CT and 38 GC RealTime positives. For total negatives, there were 742 CT and 725 GC for AC2, 744 CT and 724 GC for RealTime.

Comparison of Antimicrobial Susceptibility of Urogenital Neisseria gonorrhoeae Isolates Obtained From Women and Men.

BACKGROUND: The US system for gonococcal antimicrobial susceptibility surveillance monitors trends exclusively among men with urethral infection, the population from whom the yield of gonococcal culture is highest. Little is known about the susceptibility of female urogenital isolates, and it is unclear whether gonococcal susceptibility among men who report sex exclusively with women (MSW) is representative of susceptibility among women. METHODS: Using isolates collected during a recent treatment trial in 5 US cities, we performed a secondary analysis to compare antimicrobial susceptibilities of Neisseria gonorrhoeae urogenital isolates obtained from women, MSW, and men who have sex with men (MSM). Pretreatment isolates were collected from trial participants; minimum inhibitory concentrations (MICs) were determined by agar dilution. Geometric mean MICs were adjusted for geographic location using general linear models. RESULTS: Susceptibility data for urogenital isolates from 56 women, 252 MSW, and 170 MSM were studied. The adjusted geometric mean ceftriaxone MIC was similar among women (0.0067 µg/mL; 95% confidence interval [CI], 0.0049-0.0092 µg/mL) and MSW (0.0060 µg/mL; 95% CI, 0.0053-0.0066 µg/mL). In contrast, the adjusted geometric mean ceftriaxone MIC was higher among MSM (0.0098 µg/mL; 95% CI, 0.0082-0.0119 µg/mL) than among MSW. This same pattern was observed for other antimicrobials, including cefixime and azithromycin CONCLUSIONS: Ceftriaxone, cefixime, and azithromycin MICs were higher among MSM than among MSW, but were similar among women and MSW. These findings suggest that gonococcal antimicrobial susceptibility surveillance based on urethral isolates from MSW may adequately represent susceptibility of urogenital N. gonorrhoeae in women.

The efficacy and safety of gentamicin plus azithromycin and gemifloxacin plus azithromycin as treatment of uncomplicated gonorrhea.

BACKGROUND: Ceftriaxone is the foundation of currently recommended gonorrhea treatment. There is an urgent need for backup treatment options for patients with cephalosporin allergy or infections due to suspected cephalosporin-resistant Neisseria gonorrhoeae. We evaluated the efficacy and tolerability of 2 combinations of existing noncephalosporin antimicrobials for treatment of patients with urogenital gonorrhea. METHODS: We conducted a randomized, multisite, open-label, noncomparative trial in 5 outpatient sexually transmitted disease clinic sites in Alabama, California, Maryland, and Pennsylvania. Patients aged 15-60 years diagnosed with uncomplicated urogenital gonorrhea were randomly assigned to either gentamicin 240 mg intramuscularly plus azithromycin 2 g orally, or gemifloxacin 320 mg orally plus azithromycin 2 g orally. The primary outcome was microbiological cure of urogenital infections (negative follow-up culture) at 10-17 days after treatment among 401 participants in the per protocol population. RESULTS: Microbiological cure was achieved by 100% (lower 1-sided exact 95% confidence interval [CI] bound, 98.5%) of 202 evaluable participants receiving gentamicin/azithromycin, and 99.5% (lower 1-sided exact 95% CI bound, 97.6%) of 199 evaluable participants receiving gemifloxacin/azithromycin. Gentamicin/azithromycin cured 10 of 10 pharyngeal infections and 1 of 1 rectal infection; gemifloxacin/azithromycin cured 15 of 15 pharyngeal and 5 of 5 rectal infections. Gastrointestinal adverse events were common in both arms. CONCLUSIONS: Gentamicin/azithromycin and gemifloxacin/azithromycin were highly effective for treatment of urogenital gonorrhea. Gastrointestinal adverse events may limit routine use. These non-cephalosporin-based regimens may be useful alternative options for patients who cannot be treated with cephalosporin antimicrobials. Additional treatment options for gonorrhea are needed. Clinical Trials Registration. NCT00926796.

Insurance among patients seeking care at a municipal sexually transmitted disease clinic: implications for health care reform in the United States.

INTRODUCTION: Limited data exist on insured patients who receive care at publically funded sexually transmitted disease (STD) clinics, despite having access to a primary care provider. In this analysis, we compare patients with and without health insurance who sought services at City Clinic, the San Francisco municipal STD clinic. METHODS: We analyzed San Francisco City Clinic patients between August 1, 2011, and December 31, 2012. Insurance was self-reported and included both private and public insurance. Variables from the clinic electronic medical record were examined and included basic demographic and risk behavior questions, as well as positivity among patients tested for chlamydial and gonoccocal infection. We compared the characteristics of insured and uninsured patients using χ test. RESULTS: There were 13,104 patients in this analysis, of whom 4981 (38%) were categorized as insured and 8123 (62%) as uninsured. Overall, insured patients were older, more likely to be male, more likely to be white, and less likely to be Hispanic compared with uninsured patients (all P < 0.05). In addition, insured patients were more likely to be among men who have sex with men and among HIV-infected individuals compared with uninsured patients (all P < 0.0001). Insured patients were less likely to have a diagnosis of chlamydia at any site or a diagnosis of rectal gonorrhea. CONCLUSIONS: In our municipal STD clinic, more than one-third of patients report currently having insurance, yet still choose to seek care at the STD clinic. The different characteristics between insured and uninsured patients may reflect reasons other than affordability; therefore, STD clinics remain an important source of care for at-risk populations. These data suggest that the expansion of access to insurance may not result in a reduced need for categorical STD services. Maintaining access to high-quality sexual health services should remain a priority in the era of expanded health care access.

Identifying syphilis risk networks through venue attendance in San Francisco.

BACKGROUND: Prioritizing interventions for patients with syphilis who are part of large or interconnected sexual networks may be high yield for partner services, and identifying venues named by patients with syphilis who report high numbers of partners may help identify such networks. In this analysis, we explore differences between interviewed patients with early syphilis regarding where they met sex partners. METHODS: With a cross-sectional design, we examined the distribution of total reported sex partners from male index patients with early syphilis interviewed through the San Francisco Department of Public Health partner services program and the self-reported venues named as places they met sex partners. Based on the median number of total partners among male cases of syphilis who named each venue, we categorized venues into 3 levels of partner frequency: high (>15 partners reported), medium (6-15 partners reported), and low (<6 partners reported). Interviewed patients with early syphilis were then classified into these venue categories, and sociodemographic and risk behaviors from electronic medical records and interviews were compared using χ tests. RESULTS: In 2011, 433 male patients with early syphilis named 32 venues. One hundred forty-three (32.3%) patients were categorized as high, 226 (51.0%) as medium, and 74 (16.7%) as low partner frequency venue users. Patients with early syphilis who reported meeting partners at high partner frequency venues were generally older, more likely to be white, have a previous syphilis infection, use methamphetamines in the previous year, and be HIV infected (all P < 0.05) compared with those who reported meeting partners at medium-frequency and low-frequency venues. CONCLUSIONS: Venues where partners are met may be an appropriate proxy for network membership. Targeting additional resources, outreach, and services to clients who attend high-frequency venues may have a positive impact on syphilis prevention efforts.

Characteristics of males infected with common Neisseria gonorrhoeae sequence types in the Gonococcal Isolate Surveillance Project, San Francisco, California, 2009.

We analyzed 265 urethral Neisseria gonorrhoeae specimens collected from symptomatic males at San Francisco's municipal sexually transmitted disease clinic, a participant in the Gonococcal Isolate Surveillance Project, during 2009. We used N. gonorrhoeae multiantigen sequence typing to describe characteristics of patients infected with common sequence type families. Specimens were classified into 6 homology-based families and 1 additional family of all other identified strains. Strain family results were combined with results of culture-based antibiotic sensitivity minimum inhibitory concentration, sociodemographic and behavioral risk data collected at the clinic, and presence or absence of the mosaic penicillin-binding protein 2 (penA) allele. Characteristics of patients were compared across strain families through the use of χ(2) statistics. Among men who have sex with men, strain distribution differed by those reporting receptive oral sex as their only urethral exposure (P = 0.04), by number of sex partners (P = 0.03), and by race/ethnicity (P < 0.001); there were no differences by age or human immunodeficiency virus status. Also, among men who have sex with men, strain family distributions differed for culture specimens with reduced susceptibility to a range of antibiotics, as well as with presence of the mosaic penA allele (all P < 0.001). The combination of molecular, phenotypic, and epidemiologic data on N. gonorrhoeae infection could help develop a more complete epidemiology of gonorrhea in the United States.

Exploring sexual health among female sexually transmitted disease clinic patients, San Francisco 2010.

BACKGROUND: Current data on sexual health in the United States is limited, in part, because of a lack of measurement tools. It is difficult for programs to develop a holistic approach to improving sexual health that is data-driven and evaluable without a tool that encompasses sexual health beyond the absence of disease. The objective of this study was to understand possible factors associated with sexual health and reported differences in sexual health among women. METHODS: We conducted a survey measuring sexual health among women seeking care at the municipal sexually transmitted disease (STD) clinic in San Francisco between January 25, 2010, and June 15, 2010. Records were matched on variables including basic demographics, reason for visit, symptoms at visit, history of an STD, and STD diagnosis at the visit. RESULTS: A total of 822 women completed the questionnaire during the study period. Women reporting no recent sexual activity reported feeling more insecure, angry, isolated, and limited because of health compared with women with recent sexual activity. However, few differences were seen among women based on symptoms and diagnosis at visit. DISCUSSION: Given the minimal differences based on symptoms and disease, this suggests that there are other factors that impact the quality of life and sexual health. Creating tools that can be used to measure sexual health is a necessary first step for programs to understand the sexual health of a community. More broad-based assessments of sexual health in a variety of populations will be critical to identifying points of intervention and progress toward success.

Epidemiologic characteristics of an ongoing syphilis epidemic among men who have sex with men, San Francisco.

BACKGROUND: Since 2001, San Francisco has experienced a sustained syphilis epidemic that has been nearly exclusively limited to men who have sex with men. We examined the characteristics associated with changes in the syphilis epidemic in San Francisco. METHODS: All primary and secondary (P&S) syphilis cases reported to the San Francisco Department of Public Health between 2001 and 2011 were examined using joinpoint analysis to identify periods within the broader epidemic. Characteristics of the index cases were compared across the periods using χ(2) statistics and t tests. RESULTS: Three distinct periods were identified, an acute increase, decline, and then period of resurgence. In the most recent period of resurgence, compared with earlier periods, patients with P&S syphilis were more likely to have a prior syphilis infection, were older, were more likely to meet partners online, and were more likely to have a partner from outside San Francisco. CONCLUSIONS: In an analysis of 11 years of P&S syphilis data, several factors were associated with declines or resurgences. Innovative prevention measures are needed to reduce syphilis morbidity among men who have sex with men.

Effect of risk-reduction counseling with rapid HIV testing on risk of acquiring sexually transmitted infections: the AWARE randomized clinical trial.

IMPORTANCE: To increase human immunodeficiency virus (HIV) testing rates, many institutions and jurisdictions have revised policies to make the testing process rapid, simple, and routine. A major issue for testing scale-up efforts is the effectiveness of HIV risk-reduction counseling, which has historically been an integral part of the HIV testing process. OBJECTIVE: To assess the effect of brief patient-centered risk-reduction counseling at the time of a rapid HIV test on the subsequent acquisition of sexually transmitted infections (STIs). DESIGN, SETTING, AND PARTICIPANTS: From April to December 2010, Project AWARE randomized 5012 patients from 9 sexually transmitted disease (STD) clinics in the United States to receive either brief patient-centered HIV risk-reduction counseling with a rapid HIV test or the rapid HIV test with information only. Participants were assessed for multiple STIs at both baseline and 6-month follow-up. INTERVENTIONS: Participants randomized to counseling received individual patient-centered risk-reduction counseling based on an evidence-based model. The core elements included a focus on the patient's specific HIV/STI risk behavior and negotiation of realistic and achievable risk-reduction steps. All participants received a rapid HIV test. MAIN OUTCOMES AND MEASURES: The prespecified outcome was a composite end point of cumulative incidence of any of the measured STIs over 6 months. All participants were tested for Neisseria gonorrhoeae, Chlamydia trachomatis, Treponema pallidum (syphilis), herpes simplex virus 2, and HIV. Women were also tested for Trichomonas vaginalis. RESULTS: There was no significant difference in 6-month composite STI incidence by study group (adjusted risk ratio, 1.12; 95% CI, 0.94-1.33). There were 250 of 2039 incident cases (12.3%) in the counseling group and 226 of 2032 (11.1%) in the information-only group. CONCLUSION AND RELEVANCE: Risk-reduction counseling in conjunction with a rapid HIV test did not significantly affect STI acquisition among STD clinic patients, suggesting no added benefit from brief patient-centered risk-reduction counseling. TRIAL REGISTRATION: clinicaltrials.gov Identifier: NCT01154296.

Young men's preferences for sexually transmitted disease and reproductive health services in San Francisco, California.

We explored STD (sexually transmitted disease) service preferences among 108 African-American adolescent males recruited from a high-morbidity neighborhood. Participants largely preferred to seek care at traditional STD testing venues (86.5%) rather than nontraditional venues. Additionally, most males preferred receiving STD test results from a clinician (61.1%) rather than online (11.1%) or through email or text message (12.0%). These results highlight the need for continued strengthening of traditional public health clinics to ensure capacity to meet young men's health needs and to improve outreach and access to traditional STD services for young men.

Sentinel surveillance for pharyngeal chlamydia and gonorrhea among men who have sex with men--San Francisco, 2010.

BACKGROUND: Although a potentially important route for transmission, limited data exist on the burden of pharyngeal chlamydia (CT) and gonorrhea (GC) among men who have sex with men (MSM). We examined pharyngeal CT and GC among MSM screened in San Francisco in 2010. METHODS: MSM seeking services in a variety of clinical settings provided clinician-collected pharyngeal specimens that were tested using the APTIMA Combo 2 platform. The prevalence of pharyngeal CT and GC was estimated at 5 sentinel sites: the municipal STD clinic, a gay men's health clinic, an HIV care clinic, an HIV testing site, and primary care clinics supported by the San Francisco Department of Public Health. Positivity for each infection was calculated as the number of positive tests divided by the number of testers with corresponding confidence intervals (CI). RESULTS: In 2010, a total of 12,454 pharyngeal CT specimens and 12,457 pharyngeal GC specimens were tested for an overall CT positivity of 1.69% (95% CI: 1.47-1.93) and GC positivity of 5.76% (95% CI: 5.36-6.19). At the 5 sentinel sites, pharyngeal CT positivity ranged from 1.10% (HIV testing site) to 2.28% (STD clinic); pharyngeal GC positivity ranged from 3.4% (HIV testing site) to 7.01% (STD clinic). CONCLUSION: Sentinel surveillance data indicate that there is a substantial burden of pharyngeal CT and GC infections among MSM in San Francisco. Identification and treatment of pharyngeal infections could prevent ongoing transmission of these bacteria. Increasing access to nucleic acid amplification tests-based pharyngeal screening should be a public health priority.

Selective Whole-Genome Amplification as a Tool to Enrich Specimens with Low Treponema pallidum Genomic DNA Copies for Whole-Genome Sequencing.

Downstream next-generation sequencing (NGS) of the syphilis spirochete Treponema pallidum subspecies pallidum (T. pallidum) is hindered by low bacterial loads and the overwhelming presence of background metagenomic DNA in clinical specimens. In this study, we investigated selective whole-genome amplification (SWGA) utilizing multiple displacement amplification (MDA) in conjunction with custom oligonucleotides with an increased specificity for the T. pallidum genome and the capture and removal of 5'-C-phosphate-G-3' (CpG) methylated host DNA using the NEBNext Microbiome DNA enrichment kit followed by MDA with the REPLI-g single cell kit as enrichment methods to improve the yields of T. pallidum DNA in isolates and lesion specimens from syphilis patients. Sequencing was performed using the Illumina MiSeq v2 500 cycle or NovaSeq 6000 SP platform. These two enrichment methods led to 93 to 98% genome coverage at 5 reads/site in 5 clinical specimens from the United States and rabbit-propagated isolates, containing >14 T. pallidum genomic copies/µL of sample for SWGA and >129 genomic copies/µL for CpG methylation capture with MDA. Variant analysis using sequencing data derived from SWGA-enriched specimens showed that all 5 clinical strains had the A2058G mutation associated with azithromycin resistance. SWGA is a robust method that allows direct whole-genome sequencing (WGS) of specimens containing very low numbers of T. pallidum, which has been challenging until now. IMPORTANCE Syphilis is a sexually transmitted, disseminated acute and chronic infection caused by the bacterial pathogen Treponema pallidum subspecies pallidum. Primary syphilis typically presents as single or multiple mucocutaneous lesions and, if left untreated, can progress through multiple stages with various clinical manifestations. Molecular studies often rely on direct amplification of DNA sequences from clinical specimens; however, this can be impacted by inadequate samples due to disease progression or timing of patients seeking clinical care. While genotyping has provided important data on circulating strains over the past 2 decades, WGS data are needed to better understand strain diversity, perform evolutionary tracing, and monitor antimicrobial resistance markers. The significance of our research is the development of an SWGA DNA enrichment method that expands the range of clinical specimens that can be directly sequenced to include samples with low numbers of T. pallidum.

Disentangling screening and diagnostic Chlamydia test positivity among females testing at title x-funded and adolescent health clinics, san francisco 2009.

By using a reason-for-test code, we compared positivity for female chlamydia and gonorrhea. At family planning clinics, there were no statistically significant differences in screening versus diagnostic positivity for either chlamydia or gonorrhea among women. However, at adolescent health clinics, diagnostic positivity was higher than screening positivity for chlamydia and gonorrhea.