Testing for Mycoplasma genitalium and Using Doxycycline as First-Line Therapy at Initial Presentations for Non-Gonococcal Urethritis (NGU) Correlate With Reductions in Persistent NGU.

We found that the odds of return clinic visits for persistent non-gonococcal urethritis (NGU) were significantly lower (odds ratio: .4; 95% confidence interval: .3-.6; P < .0001) after implementing (1) testing for Mycoplasma genitalium during initial evaluations for NGU and (2) switching from azithromycin to doxycycline as first-line NGU treatment.

Contact-Tracing Outcomes Among Household Contacts of Fully Vaccinated Coronavirus Disease 2019 (COVID-19) Patients: San Francisco, California, 29 January-2 July 2021.

BACKGROUND: The extent to which vaccinated persons diagnosed with coronavirus disease 2019 (COVID-19) can transmit to other vaccinated and unvaccinated persons is unclear. METHODS: Using data from the San Francisco Department of Public Health, this report describes outcomes of household contact tracing during 29 January-2 July 2021, where fully vaccinated patients with COVID-19 were the index case in the household. RESULTS: Among 248 fully vaccinated patients with breakthrough infections, 203 (82%) were symptomatic and 105 were identified as the index patient within their household. Among 179 named household contacts, 71 (40%) contacts tested, over half (56%) were fully vaccinated and the secondary attack rate was 28%. Overall transmission from a symptomatic fully vaccinated patient with breakthrough infection to household contacts was suspected in 14 of 105 (13%) of households. Viral genomic sequencing of samples from 44% of fully vaccinated patients showed that 82% of those sequenced were infected by a variant of concern or interest and 77% by a variant carrying mutation(s) associated with resistance to neutralizing antibodies. CONCLUSIONS: Transmission from fully vaccinated symptomatic index patients to vaccinated and unvaccinated household contacts can occur. Indoor face masking and timely testing of all household contacts should be considered when a household member receives a positive test result in order to identify and interrupt transmission chains.

Coronavirus Disease 2019 Outbreak in a San Francisco Homeless Shelter.

We report the public health response to a coronavirus disease 2019 (COVID-19) outbreak in a San Francisco shelter where 67% of residents and 17% of staff tested positive for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). We describe the limited utility of case investigation, person-based contact tracing and symptom screening, and the benefits of mass testing in outbreak response.

Targeting Culture Criteria to Maximize Culture Positivity of Neisseria gonorrhoeae in 3 Sexual Health Clinic Settings.

BACKGROUND: Although most gonorrhea (GC) cases in the United States are detected using nucleic acid amplification tests (NAATs), isolation of Neisseria gonorrhoeae (NG) using culture specimens is needed for antibiotic susceptibility testing (AST). We present data on NAATs and cultures collected before and during the Centers for Disease Control and Prevention demonstration project (Strengthening the US Response to Resistant Gonorrhea [SURRG]) to describe a process to define culture criteria for NG isolation for surveillance of NG with reduced susceptibility. METHODS: For sexually transmitted infection clinics in New York City, NY; San Francisco, CA; and Milwaukee, WI, we calculated NAAT positivity by anatomic site in 2016 (pre-SURRG) across 3 groups: (1) sex partners of persons with GC, (2) patients with symptoms (e.g., urethral or cervical discharge), (3) patients who had tested positive and were returning for GC treatment and compared it with positivity among all other patients. We then examined SURRG-period NAAT positivity among patients from whom a culture was or was not collected, and culture positivity, by specimen site and jurisdiction. RESULTS: Pre-SURRG, NAAT positivity across the 3 select groups was at least twice that of patients who did not meet any criteria. SURRG-period NAAT positivity was higher among patients from whom a culture was also collected. Overall culture positivity was relatively high (New York City, 34.8%; San Francisco, 26.7%; Milwaukee, 24.8%); the proportion of specimens tested varied widely (range, 5.7%-26.5%) by jurisdiction. CONCLUSIONS: Evaluation of NAAT data can inform the establishment of criteria for culture collection for AST. Routine evaluation and quality improvement activities related to culture collection/isolation techniques could increase NG isolation for AST.

Outcomes of Traditional and Enhanced Gonorrhea Partner Services in the Strengthening the US Response to Resistant Gonorrhea Project, 2017 to 2019.

INTRODUCTION: The Centers for Disease Control and Prevention implemented Strengthening the US Response to Resistant Gonorrhea (SURRG) to build local detection and response capacity and evaluate responses to antibiotic-resistant gonorrhea outbreaks, including partner services for gonorrhea. We evaluated outcomes of traditional partner services conducted under SURRG, which involved (1) counseling index patients and eliciting sexual partners; (2) interviewing, testing, and treating partners; and (3) providing partner services to partners newly diagnosed with gonorrhea. We also evaluated outcomes of enhanced partner services, which additionally involved interviewing and testing partners of persons who tested negative, and social contacts of index patients and partners. METHODS: We analyzed partner services investigation data from 8 jurisdictions participating in SURRG from 2017 to 2019. We summed total index patients, partners from traditional partner services, and partners and contacts from enhanced partner services, and calculated partner services outcomes among partners and contacts. We also visualized sexual networks from partner services data. RESULTS: Of 1242 index patients identified, 506 named at least 1 sexual partner. Traditional partner services yielded 1088 sexual partners, and 105 were newly diagnosed with gonorrhea. Enhanced partner services yielded an additional 59 sexual partners and 52 social contacts. Of those partners and contacts, 3 were newly diagnosed with gonorrhea. Network visualization revealed sparse networks with few complex partnership clusters. CONCLUSIONS: Traditional partner services for gonorrhea may be useful for eliciting, notifying, and diagnosing partners of index patients in an outbreak setting. Enhanced partner services are unlikely to be effective for eliciting, notifying, and diagnosing a substantial number of additional people.

Exploring and Comparing the Structure of Sexual Networks Affected by Neisseria gonorrhoeae Using Sexual Partner Services Investigation and Genomic Data.

BACKGROUND: Sexual networks are difficult to construct because of incomplete sexual partner data. The proximity of people within a network may be inferred from genetically similar infections. We explored genomic data combined with partner services investigation (PSI) data to extend our understanding of sexual networks affected by Neisseria gonorrhoeae (NG). METHODS: We used 2017-2019 PSI and whole-genome sequencing (WGS) data from 8 jurisdictions participating in Centers for Disease Control and Prevention's Strengthening the US Response to Resistant Gonorrhea (SURRG) project. Clusters were identified from sexual contacts and through genetically similar NG isolates. Sexual mixing patterns were characterized by describing the clusters by the individual's gender and gender of their sex partners. RESULTS: Our study included 4627 diagnoses of NG infection (81% sequenced), 2455 people received a PSI, 393 people were negative contacts of cases, and 495 were contacts with an unknown NG status. We identified 823 distinct clusters using PSI data combined with WGS data. Of cases that were not linked to any other case using PSI data, 37% were linked when using WGS data. Overall, 40% of PSI cases were allocated to a larger cluster when PSI and WGS data were combined compared with PSI data alone. Mixed clusters containing women, men who report sex with women, and men who report sex with men were common when using the WGS data either alone or in combination with the PSI data. CONCLUSIONS: Combining PSI and WGS data improves our understanding of sexual network connectivity.

Assessment of SARS-CoV-2 Infection Prevalence in Homeless Shelters - Four U.S. Cities, March 27-April 15, 2020.

In the United States, approximately 1.4 million persons access emergency shelter or transitional housing each year (1). These settings can pose risks for communicable disease spread. In late March and early April 2020, public health teams responded to clusters (two or more cases in the preceding 2 weeks) of coronavirus disease 2019 (COVID-19) in residents and staff members from five homeless shelters in Boston, Massachusetts (one shelter); San Francisco, California (one); and Seattle, Washington (three). The investigations were performed in coordination with academic partners, health care providers, and homeless service providers. Investigations included reverse transcription-polymerase chain reaction testing at commercial and public health laboratories for SARS-CoV-2, the virus that causes COVID-19, over approximately 1-2 weeks for residents and staff members at the five shelters. During the same period, the team in Seattle, Washington, also tested residents and staff members at 12 shelters where a single case in each had been identified. In Atlanta, Georgia, a team proactively tested residents and staff members at two shelters with no known COVID-19 cases in the preceding 2 weeks. In each city, the objective was to test all shelter residents and staff members at each assessed facility, irrespective of symptoms. Persons who tested positive were transported to hospitals or predesignated community isolation areas.

Predominance of antibody-resistant SARS-CoV-2 variants in vaccine breakthrough cases from the San Francisco Bay Area, California.

Associations between vaccine breakthrough cases and infection by different SARS coronavirus 2 (SARS-CoV-2) variants have remained largely unexplored. Here we analysed SARS-CoV-2 whole-genome sequences and viral loads from 1,373 persons with COVID-19 from the San Francisco Bay Area from 1 February to 30 June 2021, of which 125 (9.1%) were vaccine breakthrough infections. Vaccine breakthrough infections were more commonly associated with circulating antibody-resistant variants carrying ≥1 mutation associated with decreased antibody neutralization (L452R/Q, E484K/Q and/or F490S) than infections in unvaccinated individuals (78% versus 48%, P = 1.96 × 10-8). Differences in viral loads were non-significant between unvaccinated and fully vaccinated cases overall (P = 0.99) and according to lineage (P = 0.09-0.78). Symptomatic vaccine breakthrough infections had comparable viral loads (P = 0.64), whereas asymptomatic breakthrough infections had decreased viral loads (P = 0.023) compared with infections in unvaccinated individuals. In 5 cases with serial samples available for serologic analyses, vaccine breakthrough infections were found to be associated with low or undetectable neutralizing antibody levels attributable to an immunocompromised state or infection by an antibody-resistant lineage. Taken together, our results show that vaccine breakthrough infections are overrepresented by antibody-resistant SARS-CoV-2 variants, and that symptomatic breakthrough infections may be as efficient in spreading COVID-19 as unvaccinated infections, regardless of the infecting lineage.