Surveillance of antibiotic resistance in natural commensal Neisseria populations: Reservoirs of resistance for important human pathogens

Antibiotic resistance in Neisseria gonorrhoeae is an urgent threat to public health, with the emergence of strains resistant to current clinically-approved antibiotics, and infection rates simultaneously rising. Substantial effort has been spent on identifying resistance mechanisms to antibiotic therapies currently circulating within the gonococcal population. However, these surveys often overlook a known source of resistance for gonococci – the commensal Neisseria. Neisseria promiscuously share DNA with one another, which has been demonstrated to facilitate rapid adaptation and evolutionary change. For example, the majority of reduced susceptibility to both azithromycin and ceftriaxone in N. gonorrhoeae populations has been acquired though horizontal transfer and subsequent spread of commensal alleles. As resistance has been shown to be directly selected for in commensals after antibiotic usage in patients, these species will always be a persistent threat for resistance donation to N. gonorrhoeae. Thus, the overall goal of this project is to profile the Neisseria resistome, or the total collection of antibiotic resistance mechanisms available to members within the genus. The knowledge gained from this proposal may directly support the development of improved surveillance methods that may aid future resistance outbreak prevention as a result of DNA donation. In Aim 1, we will profile resistance of 1,000 commensal isolates to nine drugs, including the novel drugs (i.e., gentamicin, gepotidacin, and zoliflodacin). We will also determine if resistance is associated with host-specific factors. This builds on our prior work in which we show doxycycline use promotes the emergence of doxycycline resistance in commensals during a preliminary analysis of a subset of this dataset. In Aim 2, we will expand our novel commensal isolate panel using a new commensal Neisseria collection protocol, and collect additional host metadata. Aim 2 is unique in that we will collect new isolates from faculty, students, and staff at the Rochester Institute of Technology, enabling us to both recruit participants, while educating them about important public health issues. In Aim 3, we will use whole genome sequencing of novel commensal isolates to i) confirm species identify, 2) link resistance phenotypes collected in Aim 1 to underlying genotypes using guided and unguided approaches (i.e., database-driven and genome-wide association studies (GWAS), and 3) characterize the within and between-host diversity of collected Neisseria isolates. The PI has demonstrated that these experiments are feasible at the undergraduate and graduate student levels, in both the research laboratory and in the classroom, and will provide exceptional educational and training opportunities for RIT students. Furthermore, this proposal will allow for educational opportunities about the global crisis of antibiotic resistance for study participants across the RIT campus while simultaneously collecting meaningful data. Project Number: 1R15AI197130-01 | Fiscal Year: 2026 | NIH Institute/Center: National Institute of Allergy and Infectious Diseases (NIAID) | Principal Investigator: Crista Wadsworth | Institution: ROCHESTER INSTITUTE OF TECHNOLOGY, ROCHESTER, NY | Award Amount: $561,410 | Activity Code: R15 | Study Section: Anti-Infective Resistance and Targets Study Section [AIRT] View on NIH RePORTER: https://reporter.nih.gov/project-details/1R15AI19713001