A genomic perspective on the near-term impact of doxycycline post-exposure prophylaxis on Neisseria gonorrhoeae antimicrobial resistance

Post-exposure prophylaxis with doxycycline (doxyPEP) is being introduced to prevent bacterial sexually transmitted infections (STIs). Pre-existing tetracycline resistance in Neisseria gonorrhoeae limits doxyPEP effectiveness against gonorrhea, and selection for tetracycline resistant lineages may influence prevalence of resistance to other antimicrobials via selection for multi-drug resistant strains. Using genomic and antimicrobial susceptibility data from 5,644 clinical isolates of N. gonorrhoeae, we assessed the near-term impact of doxyPEP on N. gonorrhoeae antimicrobial resistance. We found that the impact on antimicrobial resistance is likely to be influenced by the strength of selection for plasmid-encoded and chromosomally-encoded tetracycline resistance, as isolates with high-level, plasmid-encoded resistance had lower minimum inhibitory concentrations to other antimicrobials compared to isolates with low-level tetracycline resistance. The impact of doxyPEP may differ across demographic groups and geographic regions within the United States due to variation in pre-existing tetracycline resistance.

Post-exposure prophylaxis with doxycycline (doxyPEP) has been shown to decrease rates of bacterial sexually transmitted infections (STIs) in clinical trials, [1][2][3] and doxyPEP is recommended by some public health departments in the United States. Official guidelines from the US Centers for Disease Control and Prevention (CDC) and other public health institutions are pending.
A concern around doxyPEP is its impact on antibiotic resistance. Pre-existing tetracycline resistance in the Neisseria gonorrhoeae population resulted in lower doxyPEP effectiveness against gonorrhea than against syphilis and chlamydia 2 and reflects tetracycline and multidrug resistant strains of N. gonorrhoeae that may be selected for by doxyPEP. Given this concern, we evaluated the potential near-term impacts of doxyPEP on antimicrobial resistance in N. gonorrhoeae using whole genome sequencing (WGS) data and minimum inhibitory concentrations (MICs) from a global collection of 5,644 N. gonorrhoeae isolates (Supplementary  Tables 1-2), including 1,041 isolates from 2018 collected and sequenced by CDC's Gonococcal Isolate Surveillance Program (GISP) 4 .
Interpretative breakpoints for N. gonorrhoeae susceptibility and resistance to doxycycline have not been defined; however, treatment failures have been observed when isolates have doxycycline MICs ≥ 1 µg/ml, 5 and doxycycline MICs correlate with tetracycline MICs. 6 Tetracycline resistance can be mediated by plasmid-encoded tetM, which confers high-level resistance, and chromosomally-encoded mutations in rpsJ, porB, and the mtr operon. 7 We excluded isolates that had tetracycline MICs that most likely represented reporting errors (Supplementary Text).
We found that co-resistance to other antimicrobials was most common in isolates with chromosomally-encoded tetracycline resistance ( Figure 1). Ceftriaxone, azithromycin, and ciprofloxacin MICs were significantly higher in isolates with tetracycline MICs of 2-8 µg/ml compared to isolates not resistant to tetracycline and to isolates with high-level tetracycline resistance (p < 0.0001, Mann-Whitney test). Ceftriaxone reduced susceptibility (MIC ≥ 0.125 µg/mL) was rare in GISP isolates (n=2), but the global data suggested that reduced susceptibility is most often acquired by strains with chromosomally-mediated tetracycline resistance, including strains encoding the penA 60 allele, which confers ceftriaxone reduced susceptibility. 8 Azithromycin resistance appeared in 23.5% (56/238) of GISP isolates resistant to tetracycline; all that were tetracycline and azithromycin co-resistant had chromosomally encoded tetracycline resistance. Ciprofloxacin resistance appeared in 33.6% (80/238) of GISP isolates resistant to tetracycline; however, only 12.9% (13/101) of isolates with tetM were also ciprofloxacin resistant.
In the United States, doxyPEP is primarily recommended for men who have sex with men (MSM) and transgender persons who have sex with men. The composition of N. gonorrhoeae isolates was not homogeneous across the United States, and the percentage of tetracycline resistant isolates collected across HHS regions ranged from 17.4% -52.0% (Supplementary Figure 1). Mechanisms of resistance also varied, and high-level resistance was not evenly distributed across geographic regions, with the lowest proportion of isolates with high-level resistance in HHS regions from the east coast and southeastern United States (1.7% -4.4%). This indicates that doxyPEP will likely have regionally varying effectiveness and impact on circulating N. gonorrhoeae.
In our study, the genomic data representing the N. gonorrhoeae population in the United States were from isolates collected in 2018, and recent changes in treatment guidelines 9 and introductions of resistant lineages, such as isolates encoding penA 60, 10 may have shifted the landscape of antimicrobial resistance in the United States. The number of genomes meeting quality thresholds from the southeastern United States was low (Supplementary Figure 1), so these data may not accurately capture lineages transmitting in this region. We emphasize that the long-term impacts of doxyPEP on the N. gonorrhoeae population in the United States are unknown, as lineages may acquire new resistance alleles and introduction of lineages from other geographic regions is possible. 11,12 For example, a recent study found that strains encoding tetM are highly prevalent among women in Kenya, 13 and phylogenetic analysis of our global dataset identified several lineages with high-level tetracycline resistance not represented among GISP isolates (Supplementary Figure 2).
The near-term impact of doxyPEP on N. gonorrhoeae antimicrobial resistance and circulating lineages will be influenced by the strength of selection for tetracycline resistance. If doxyPEP use selects for all tetracycline resistant lineages, there is potential for increased resistance to other antimicrobials as well. However, if doxyPEP use primarily selects for lineages with tetMmediated resistance, we may observe a temporary decline in resistance to other antimicrobials due to relatively less co-resistance in these lineages. Timely genomic surveillance, with a focus on doxyPEP users, is needed to distinguish between these outcomes. . CC-BY 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (which was not certified by peer review) The copyright holder for this preprint this version posted March 17, 2023. ; https://doi.org/10.1101/2023.03.14.23287223 doi: medRxiv preprint