Whole Genome Sequencing of N. gonorrhoeae from Non-Culture Based Clinical Specimens to Surveil for Emerging Resistance - Project Summary Drug-resistant Neisseria gonorrhoeae (NG) is listed as one of the 5 Urgent Threats in the US by the CDC and one of 6 pathogens determined as high priority by WHO. Multi-drug resistant NG (MDR-NG) has emerged in the US and globally and there is strong evidence that strains of MDR-NG can spread within dense community networks of men who have sex with men. While urogenital NG infections typically dominate surveillance data due to ease of sampling (urine, non-invasive vaginal swabs) and high frequency of exposure at these sites, extra-genital sites of infection (i.e., throat, rectal) are critical to detect emerging strains of NG with reduced antimicrobial susceptibility. During the COVID-19 pandemic, NG rates dramatically increased, with heightening racial and ethnic disparities. To effectively disrupt NG transmission and increasing rates of resistance, we need to improve our surveillance of emerging resistance and understanding of community spread. Whole genome sequencing (WGS) is a powerful epidemiologic tool for a range of pathogens. While WGS for bacterial cultures is streamlined and performed readily by labs, applying this methodology to NG-an organism for which cultures are not regularly used in clinical care-is challenging, leading to a significant gap in knowledge of NG spread. Furthermore, public health surveillance for antimicrobial-resistant NG largely relies on cultures for a narrowly defined population, limiting representativeness. Creating a pipeline to make WGS of NG directly available from non-culture based urine and extragenital clinical specimens would improve surveillance for emerging resistance and in future work, significantly alter the landscape of understanding NG spread. Funds are requested to use WGS for non-culture based clinical urine and extragenital specimens to enhance detection of emerging resistance in strains of NG. We anticipate that sequencing of routinely collected clinical NG specimens, including those from extragenital sites, will allow for surveillance of populations often excluded from traditional culture-based surveillance, thus enhancing our ability to detect NG strains with reduced antimicrobial susceptibility. Our study will utilize NAAT-positive NG specimens from Cook County Health-the county's safety-net healthcare network and its dedicated Sexual Health Clinic. The proposal has two aims: (1) Establish workflows for rapid and inexpensive WGS of NG directly from urine, throat, and rectal specimens collected as part of clinical care, and (2) Evaluate non-culture based molecular surveillance as an approach to enhance detection of emerging strains of NG with reduced antimicrobial susceptibility. Our findings will be broadly generalizable to healthcare centers across the US, most of whom routinely employ NAAT testing as their first-line method for NG testing. Knowledge gained would inform the merits of different strategies for enhanced NG surveillance, increase the timeliness of detection of emerging variants of concern, and maximize reach to communities most at risk. Since NG is a high priority CDC and WHO pathogen, our proposal has significant public health impact.
