The antimicrobial resistance landscape of Neisseria gonorrhoeae in New Zealand from November 2018 to March 2019 and the role of sexual orientation in transmission

The increasing use of culture independent diagnostic testing for the diagnosis of Neisseria gonorrhoeae infection has led to gaps in surveillance of antimicrobial resistance (AMR) rates due to limited availability of cultures. Our study reports the findings of a second national survey of N. gonorrhoeae in New Zealand, utilizing whole-genome sequencing (WGS) to study the population structure, prevalence of AMR, epidemiology and transmission of gonorrhoea isolates. We analysed 314 isolates and found a strong correlation between carriage of acquired resistance genes or chromosomal point mutations and phenotypic susceptibility testing results. Overall, the New Zealand rates of azithromycin resistance and decreased susceptibility to ceftriaxone remain lower than in most countries, which are part of the World Health Organization (WHO) Global Gonococcal Antimicrobial Surveillance Programme (GASP). The phylogeny provides evidence of a diverse population significantly associated with sexual behaviour groups. Transmission clustering with a ten single nucleotide polymorphism (SNP) cut-off identified 49 clusters, of which ten were solely associated with men who have sex with men (MSM), whereas remaining clusters included heterosexual patients, as well as MSM, suggesting that bridging of sexual networks is occurring. Utilizing pairwise SNP differences between isolates of the same sequence types we determined genetic variation for the three typing schemes used in this study [Multi locus sequence typing (MLST), multi-antigen sequence typing (NG-MAST), and sequence typing for antimicrobial resistance (NG-STAR)]. A median of 0.0 to 52.5 pairwise SNP differences within a single NG-STAR sequence type underlines previous findings of the superiority of the NG-STAR typing scheme in terms of genomic inherency. With our analysis incorporating epidemiological and genomic data, we were able to show a comprehensive overview of the N. gonorrhoeae population circulating in New Zealand, focussing on AMR and transmission within sexual networks. Regular surveillance studies to understand the origin, evolution and spread of AMR for gonorrhoea remain necessary to make informed decisions about public health guidelines, as the internationally rising rates of ceftriaxone and azithromycin resistance have already led to adaptation of current treatment guidelines in the UK and the USA, highlighting the importance of regular surveillance in individual countries.

Generating a heterosexual bipartite network embedded in social network

We describe an approach to generate a heterosexual network with a prescribed joint-degree distribution embedded in a prescribed large-scale social contact network. The structure of a sexual network plays an important role in how all sexually transmitted infections (STIs) spread. Generating an ensemble of networks that mimics the real-world is crucial to evaluating robust mitigation strategies for controlling STIs. Most of the current algorithms to generate sexual networks only use sexual activity data, such as the number of partners per month, to generate the sexual network. Real-world sexual networks also depend on biased mixing based on age, location, and social and work activities. We describe an approach to use a broad range of social activity data to generate possible heterosexual networks. We start with a large-scale simulation of thousands of people in a city as they go through their daily activities, including work, school, shopping, and activities at home. We extract a social network from these activities where the nodes are the people, and the edges indicate a social interaction, such as working in the same location. This social network captures the correlations between people of different ages, living in different locations, their economic status, and other demographic factors. We use the social contact network to define a bipartite heterosexual network that is embedded within an extended social network. The resulting sexual network captures the biased mixing inherent in the social network, and models based on this pairing of networks can be used to investigate novel intervention strategies based on the social contacts among infected people. We illustrate the approach in a model for the spread of chlamydia in the heterosexual network representing the young sexually active community in New Orleans.

Whole-Genome Enrichment and Sequencing of Chlamydia trachomatis Directly from Patient Clinical Vaginal and Rectal Swabs

ABSTRACT Chlamydia trachomatis, an obligately intracellular bacterium, is the most prevalent cause of bacterial sexually transmitted infections (STIs) worldwide. Numbers of U.S. infections of the urogenital tract and rectum have increased annually. Because C. trachomatis is not easily cultured, comparative genomic studies are limited, restricting our understanding of strain diversity and emergence among populations globally. While Agilent SureSelectXT target enrichment RNA bait libraries have been developed for whole-genome enrichment and sequencing of C. trachomatis directly from clinical urine, vaginal, conjunctival, and rectal samples, public access to these libraries is not available. We therefore designed an RNA bait library (34,795 120-mer probes based on 85 genomes, versus 33,619 probes using 74 genomes in a previous one) to augment organism sequencing from clinical samples that can be shared with the scientific community, enabling comparison studies. We describe the library and limit of detection for genome copy input, and we present results of 100% efficiency and high-resolution determination of recombination and identical genomes within vaginal-rectal specimen pairs in women. This workflow provides a robust approach for discerning genomic diversity and advancing our understanding of the molecular epidemiology of contemporary C. trachomatis STIs across sample types, geographic populations, sexual networks, and outbreaks associated with proctitis/proctocolitis among women and men who have sex with men. IMPORTANCE Chlamydia trachomatis is an obligate intracellular bacterium that is not easily cultured, which limits our understanding of urogenital and rectal C. trachomatis transmission and impact on morbidity. To provide a publicly available workflow for whole-genome target enrichment and sequencing of C. trachomatis directly from clinical urine, vaginal, conjunctival, and rectal specimens, we developed and report on an RNA bait library to enrich the organism from clinical samples for sequencing. We demonstrate an increased efficiency in the percentage of reads mapping to C. trachomatis and identified recombinant and identical C. trachomatis genomes in paired vaginal-rectal samples from women. Our workflow provides a robust genomic epidemiologic approach to advance our understanding of C. trachomatis strains causing ocular, urogenital, and rectal infections and to explore geo-sexual networks, outbreaks of colorectal infections among women and men who have sex with men, and the role of these strains in morbidity.

Giving syphilis and gonorrhea to friends: using in-person friendship networks to find additional cases of gonorrhea and syphilis

Background Syphilis and gonorrhea reached an all-time high in 2018. The resurgence of syphilis and gonorrhea requires innovative methods of sexual contact tracing that encourage disclosure of same-sex sexual contacts that might otherwise be suppressed. Over 75% of Grindr mobile phone application users report seeking “friendship,” so this study asked people diagnosed with syphilis and gonorrhea to identify their friends. Methods Patients at the two Baltimore sexually transmitted infection (STI) clinics and the Baltimore City Health Department were asked 12 questions to elicit members of their friendship networks before eliciting sexual networks. The study included 353 index cases and 172 friendship contacts, yielding a friendship network of 331 non-isolates (n = 331) and sexual-only network of 140 non-isolates. The data were plotted and analyzed using exponential family random graph analysis. Results Eliciting respondents’ in-person social contacts yielded 12 syphilis cases and 6 gonorrhea cases in addition to the 16 syphilis cases and 4 gonorrhea cases that would have been found with sexual contacts alone. Syphilis is clustered within sexual (odds ratio = 2.2, 95% confidence interval (1.36, 3.66)) and social contacts (OR = 1.31, 95% CI (1.02, 1.68)). Gonorrhea is clustered within reported social (OR = 1.56, 95% CI (1.22, 2.00)) but not sexual contacts (OR = 0.98, 95% CI (0.62, 1.53)). Conclusions Eliciting friendship networks of people diagnosed with syphilis and gonorrhea may find members of their sexual networks, drug use networks, or people of similar STI risk. Friendship networks include more diagnosed cases of syphilis and gonorrhea than sexual networks alone, especially among populations with many non-disclosing men who have sex with men (MSM) and women who have sex with women (WSW). Future research should evaluate whether this friendship network method of contact tracing can be implemented by adapting automated mobile phone COVID-19 contact tracing protocols, if these COVID-19 contact tracing methods are able to maintain anonymity and public trust.

The HIV/STI Epidemic Potential of Dynamic Sexual Networks of Men Who Have Sex With Men in Atlanta and San Francisco

ABSTRACTBackgroundThe potential speed through which a pathogen may circulate in a network is a function of network connectivity. Network features like degree (number of ongoing partnerships) determine the cross-sectional network connectivity. The overall transmission potential of a pathogen involves connectivity over time, which can be measured using the forward reachable path (FRP). We modeled dynamic sexual networks of MSM in San Francisco and Atlanta to estimate the FRP as a predictor of HIV/STI epidemic potential.MethodsWe used exponential random graph models to obtain parameter estimates for each city’s sexual network and then simulated the complete networks over time. The FRP was estimated in each city overall and stratified by demographics.ResultsThe overall mean and median FRPs were higher in San Francisco than in Atlanta, suggesting a greater epidemic potential for HIV and STIs in San Francisco. At one year, in both cities, the average FRP among casual partnerships was highest in the youngest age group and lowest in the oldest age group, contrasting with the cross-sectional network parameters we estimated, where the youngest age category had the lowest mean degree and the oldest age category had the highest mean degree.ConclusionsThe FRP results correspond to the observed STI epidemics but not HIV epidemics between the cities. In San Francisco, rates of HIV have been declining over the last few years, whereas they have been steady in Atlanta. The FRP by age group resulted in fundamentally different conclusions about connectivity in the network compared with the cross-sectional network measures.

958. Feasibility and Acceptability of HIV Self-Test Kit Distribution Through PrEP Clients’ Friendship and Sexual Networks

Background Personal networks can influence behaviors, beliefs, attitudes, and values through contact and communication. The University of Miami Mobile PrEP Program offers low-barrier pre-exposure prophylaxis (PrEP)/HIV prevention services through a mobile clinic in five highly impacted neighborhoods in Miami-Dade, the county with the highest HIV incidence in the US. The highest rates are among black and Latino men who have sex with men (MSM). The goal of this study is to understand the acceptability and feasibility of expanding the reach of testing through our clients’ friendship and sexual networks. Methods This study was implemented in five locations across Miami from December 2019 to February 2020. During scheduled PrEP quarterly follow-up clinic visits, participants were offered Ora-Quick oral fluid self test (ST) kits, free of cost for distribution to up to four sexual partners and/or friends. In addition to the information available in the testing kit, brief training regarding the test and resources for post-test engagement were provided. A survey evaluated participants’ distribution plan, comfort level and concerns in offering the test kits to friends/sexual partners. Descriptive statistics included frequencies for categorical variables, and means and ranges for continuous variables. Results A total of 84 participants were offered the ST kits, of which 49 (58%) accepted. Of those accepting kits, 40 (81.63%) of 49 were Latino MSM. Participants requested an average of 3 (mean=2.9, range 1-4) kits, for a total of 144 kits. Overall, 41(84%) felt very comfortable and 47(96%) indicated they felt very comfortable offering this test to their friends/sexual partners. Also, 29(59.2%) planned to distribute kits only to friends, 2(4%) only to sexual partners, 11(22.4%) to both sexual partners and friends and 7(14.2%) to either family or self-test to provide ‘moral support’ to those taking the test. None of the participants expressed any concerns about offering kits to friends or sexual partners. Conclusion Distribution of home based self-test HIV kits through current Mobile PrEP clients’ friendship and sexual networks is acceptable and feasible. Similar social network strategies may be considered to expand reach of HIV testing and PrEP engagement to those with barriers to care. Disclosures All Authors: No reported disclosures