Doxycycline increases antimicrobial resistance in the gut without disrupting microbiome diversity

New research reveals that doxycycline post-exposure prophylaxis raises resistance gene levels in the gut, but leaves the overall balance of the microbiome largely intact, marking a crucial step forward in understanding antibiotic resistance and STI prevention.

Study: Impact of doxycycline post-exposure prophylaxis for sexually transmitted infections on the gut microbiome and antimicrobial resistome. Image Credit: Kateryna Kon / Shutterstock

In a recent study published in the journal Nature Medicine, researchers investigated the effects of doxycycline post-exposure prophylaxis (doxy-PEP) on the gut microbiome and antimicrobial resistance genes (ARGs) in men who have sex with men (MSM) and transgender women. They found that the use of doxy-PEP increased the proportion and expression of tetracycline ARGs in the gut resistome but did not significantly alter the gut microbiome’s diversity or composition.

Background

Doxy-PEP is known to be effective in preventing sexually transmitted infections (STIs) caused by bacteria in MSM and transgender women. It is now included in the United States Centers for Disease Control and Prevention guidelines and is expected to be included in the World Health Organization’s upcoming guidelines. However, concerns exist about doxy-PEP’s potential to increase antimicrobial resistance, particularly in Neisseria gonorrhoeae, which could complicate treatment and promote resistance to other antibiotics. The rise of antimicrobial resistance globally is driven by antibiotic misuse, and there are concerns about doxy-PEP selecting for resistance in both pathogens and commensal organisms. Past studies on doxycycline’s impact on the human microbiome were limited, focusing mostly on daily use and employing less comprehensive methods. Advanced techniques like metagenomic deoxyribonucleic acid sequencing (DNA-seq) and meta-transcriptomic ribonucleic acid sequencing (RNA-seq) can now provide deeper insights into the resistome and gene activity, helping assess the broader impact of doxy-PEP. In the present study, researchers analyzed rectal swabs from participants in the DoxyPEP clinical trial to investigate the potential effects of doxy-PEP on the gut microbiome and resistome in MSM and transgender women.

About the study

The DoxyPEP trial compared doxy-PEP to standard care in participants at HIV and sexual health clinics in San Francisco and Seattle. Participants were eligible if they were adults, assigned to the male gender at birth, diagnosed to have a human immunodeficiency virus (HIV) infection or were on HIV pre-exposure prophylaxis, and had a recent bacterial STI including gonorrhea, chlamydia, or early syphilis. The study focused on individuals with the highest doxycycline use. The participants were randomized 2:1 to receive doxy-PEP (n = 100) or standard care (n = 50). Rectal swabs were self-collected at enrollment and after six months, and data on demographics and doxycycline use were additionally collected. Metagenomic sequencing was conducted, with a focus on analyzing the gut microbiome and ARGs using DNA-seq and RNA-seq.

Metagenomic sequencing involved the extraction of nucleic acids from rectal swabs, followed by microbial and ARG detection using CZ ID (short for Chan Zuckerberg Initiative for Discovery) pipelines and analysis tools. Microbial mass and ARG mass were calculated, and environmental contaminants were controlled using negative controls. Statistical analyses focused on resistome diversity, ARG class distribution, and microbiome changes, including tetracycline resistance. Significant correlations between microbial taxa and ARGs were analyzed.

Results and discussion

Significant tetracycline resistance genes (ARGs) were detected among the analyzed samples, revealing that tetracycline ARGs were the most prevalent in the resistome, accounting for a substantial portion of the mass. The proportion of tetracycline ARGs increased from 46% to 51% in the DNA-seq analysis (P = 0.023) and from 4% to 15% in the RNA-seq analysis (P = 0.0000045) over the six-month study period. While no overall differences in resistome mass or alpha diversity were noted between the doxy-PEP and standard-of-care arms, significant compositional differences in the expressed resistome were detected by RNA-seq at month six (P = 0.018). The proportion of tetracycline ARGs was found to increase in the doxy-PEP arm over time, while no changes in ARG richness were observed.

Additionally, doxycycline doses were found to correlate positively with expressed tetracycline ARG richness and proportion, particularly in participants taking more than 25 doses. Only participants who took more than 25 doses of doxycycline during the six-month period demonstrated significant increases in tetracycline ARG richness. There were no significant differences in the gut microbiome or its transcriptome between the two arms at either time point, although a possible reduction in Chlamydia trachomatis abundance (P = 0.06) was observed. Positive correlations between tetracycline ARGs and various bacterial genera increased over time, indicating interactions between the resistome and microbiome during doxy-PEP use.

The present study is the largest antimicrobial resistome study of doxycycline to date, strengthened by its in-depth assessment, detailed dose-response data, and the combined use of metagenomics and meta-transcriptomics. However, the study is limited by the selection of participants with higher doxy-PEP use, which may have biased the findings. There is also potential confounding from the standard-of-care arm participants receiving doxycycline for other indications, quality issues with self-collected samples, lack of timing data for doxy-PEP doses relative to sample collection, a focus solely on the gut microbiome, a short follow-up period of six months, and the inability to definitively associate tetracycline ARGs with specific bacterial species due to short-read sequencing limitations.

Conclusion

In conclusion, the study found that doxy-PEP use led to an increase in the relative expression and proportion of tetracycline ARGs, with minimal effects on the gut microbiome ecology. However, significant differences were observed in the composition of the expressed resistome by RNA-seq, indicating potential impacts at the transcriptional level. The findings highlight the ecological impact of doxy-PEP on the gut microbiome and antimicrobial resistome in humans, emphasizing the need for further research and population-based surveillance to monitor the emergence of resistant pathogens.