Doxycycline post-exposure prophylaxis (doxy-PEP) reduces bacterial sexually transmitted infections among men who have sex with men and transgender women. Although poised for widespread clinical implementation, the impact of doxy-PEP on antimicrobial resistance remains a primary concern as its effects on the gut microbiome and resistome, or the antimicrobial resistance genes (ARGs) present in the gut microbiome, are unknown. To investigate these effects, we studied participants from the DoxyPEP trial, a randomized clinical trial comparing doxy-PEP use, a one-time doxycycline 200-mg dose taken after condomless sex (DP arm, n = 100), to standard of care (SOC arm, n = 50) among men who have sex with men and transgender women. From self-collected rectal swabs at enrollment (day-0) and after 6 months (month-6), we performed metagenomic DNA sequencing (DNA-seq) or metatranscriptomic RNA sequencing (RNA-seq). DNA-seq data were analyzable from 127 samples derived from 89 participants, and RNA-seq data were analyzable from 86 samples derived from 70 participants. We compared the bacterial microbiome and resistome between the two study arms and over time. The median number of doxycycline doses taken since enrollment by participants with DNA-seq data was zero (interquartile range (IQR): 0–7 doses) for the SOC arm and 42 (IQR: 27–64 doses) for the DP arm. Tetracycline ARGs were detected in all day-0 DNA-seq samples and in 85% of day-0 RNA-seq samples. The proportional mass of tetracycline ARGs in the resistome increased between day-0 and month-6 in DP participants from 46% to 51% in the metagenome (P = 2.3 × 10⁻²) and from 4% to 15% in the metatranscriptome (P = 4.5 × 10⁻⁶), but no statistically significant increases in other ARG classes were observed. Exposure to a higher number of doxycycline doses correlated with proportional enrichment of tetracycline ARGs in the metagenome (Spearman’s ρ = 0.23, P = 9.0 × 10⁻³) and metatranscriptome (Spearman’s ρ = 0.55, P = 3.7 × 10⁻⁸). Bacterial microbiome alpha diversity, beta diversity and total bacterial mass did not differ between day-0 and month-6 samples from DP participants when assessed by either DNA-seq or RNA-seq. In an abundance-based correlation analysis, we observed an increase over time in the strength of the correlation between tetracycline ARGs and specific bacterial taxa, including some common human pathogens. In sum, doxy-PEP use over a 6-month period was associated with an increase in the proportion of tetracycline ARGs comprising the gut resistome and an increase in the expression of tetracycline ARGs. At 6 months of doxy-PEP use, no residual differences were observed in alpha and beta diversity or taxonomic composition of the gut microbiome. As doxy-PEP is implemented as a public health strategy, further studies and population-level surveillance of doxycycline-resistant pathogens are needed to understand the implications of these findings. ClinicalTrials.gov registration number: NCT03980223.

多西环素暴露后预防 （doxy-PEP） 可减少男男性行为者和跨性别女性的细菌性传播感染。尽管准备在临床上广泛实施，但 doxy-PEP 对抗菌素耐药性的影响仍然是一个主要问题，因为它对肠道微生物组和抵抗组或肠道微生物组中存在的抗菌素耐药基因 （ARG） 的影响尚不清楚。为了调查这些影响，我们研究了 DoxyPEP 试验的参与者，这是一项随机临床试验，比较了 doxy-PEP 的使用，即在无套性行为后服用一次性多西环素 200 毫克剂量（DP 组，n = 100）与标准护理（SOC 组，n = 50）在男男性行为者和跨性别女性中。从入组时 （第 0 天） 和 6 个月后 （第 6 个月） 自行收集的直肠拭子，我们进行了宏基因组 DNA 测序 （DNA-seq） 或宏转录组学 RNA 测序 （RNA-seq）。DNA-seq 数据可从 89 名参与者的 127 个样本中分析，RNA-seq 数据可从 70 名参与者的 86 个样本中分析。我们比较了两个研究组之间以及随着时间的推移的细菌微生物组和抵抗组。具有 DNA-seq 数据的参与者自入组以来服用的多西环素剂量的中位数为 SOC 组为零（四分位距 （IQR）：0-7 剂），DP 组为 42（IQR：27-64 剂）。在所有 day-0 DNA-seq 样本和 85% 的 day-0 RNA-seq 样本中检测到四环素 ARGs。DP 参与者在第 0 天和第 6 个月之间，抵抗组中四环素 ARGs 的比例质量在宏基因组中从 46% 增加到 51% （P = 2.3 × ^10-2），在宏转录组中从 4% 增加到 15% （P = 4.5 × 10⁻⁶），但在其他 ARG 类别中未观察到统计学上的显着增加。暴露于较高剂量的多西环素与宏基因组 （Spearman ρ = 0.23，P = 9.0 × ^10-3） 和宏转录组 （Spearman ρ = 0.55，P = 3.7 × ^10-8） 中四环素 ARGs 的比例富集相关。当通过 DNA-seq 或 RNA-seq 评估时，DP 参与者的第 0 天和第 6 个月样本之间的细菌微生物组 α 多样性、β 多样性和细菌总量没有差异。在基于丰度的相关性分析中，我们观察到四环素 ARGs 与特定细菌类群（包括一些常见的人类病原体）之间的相关性强度随着时间的推移而增加。总之，在 6 个月内使用 doxy-PEP 与构成肠道抵抗组的四环素 ARGs 比例的增加和四环素 ARGs 表达的增加有关。在使用 doxy-PEP 6 个月时，未观察到肠道微生物组的 α 和 β 多样性或分类组成存在残留差异。由于 doxy-PEP 作为一种公共卫生策略实施，因此需要对多西环素耐药病原体进行进一步的研究和人群水平监测，以了解这些发现的含义。ClinicalTrials.gov 注册号：NCT03980223。