Put your money where your mouth is: surveillance of antibiotic resistance within the commensal Neisseria

Commensal Neisseria species are major reservoirs of adaptive genetic variation, including antimicrobial resistance, for their pathogenic relatives, yet they remain poorly characterized. This gap limits our ability to anticipate resistance mechanisms that may ultimately emerge in Neisseria gonorrhoeae and Neisseria meningitidis . Here, we analyzed 166 novel commensal Neisseria isolates collected from 31 study participants and measured minimum inhibitory concentrations (MICs) for seven antimicrobials: azithromycin, cefixime, ceftriaxone, ciprofloxacin, doxycycline, penicillin, and gentamicin. Resistance, defined using the Clinical and Laboratory Standards Institute guidelines, was highly prevalent for azithromycin (76%) and doxycycline (52%), while no resistance to gentamicin was observed. High-level doxycycline resistance was always associated with the inheritance of tetM . Reduced susceptibility to azithromycin was linked to an MtrD K823E substitution, and reduced susceptibility to ciprofloxacin was associated with GyrA T91I ( Neisseria subflava ) or S91V ( Neisseria mucosa ). Across all antimicrobials, MICs varied widely, indicating the presence of additional modulating mutations. Finally, the genetic determinants underlying low-level doxycycline resistance and reduced penicillin susceptibility remain unresolved. Overall, here, we continue to build on the foundation of surveillance efforts in the commensal Neisseria and continue to flesh out what is known and unknown about this early warning system—or canary in the coal mine—for emerging resistance and clinically consequential evolution in pathogenic Neisseria . IMPORTANCE Commensal Neisseria species constitute a vast and dynamic reservoir of genetic diversity that can be exchanged with pathogenic relatives, Neisseria gonorrhoeae and Neisseria meningitidis . However, these commensals remain substantially undercharacterized, limiting our ability to anticipate the evolutionary trajectories of antimicrobial resistance in clinically important species. By systematically analyzing commensal isolates and defining phenotypic resistance patterns alongside their genetic determinants, this study, and others like it, function as an early warning system for the emergence and spread of antimicrobial resistance. The high prevalence of azithromycin and doxycycline resistance, identification of specific mutations associated with reduced susceptibility, and evidence of additional unexplained contributors to minimum inhibitory concentration variation highlight both known and cryptic pathways of adaptation. These findings underscore the necessity of integrating commensal surveillance into resistance monitoring frameworks, improving our capacity to forecast clinically consequential evolution and to inform stewardship, diagnostics, and therapeutic development before resistance becomes entrenched in pathogenic Neisseria .