Effect of Azithromycin treatment on the microbial composition, functional dynamics and resistomes of endocervical, vaginal and rectal microbiomes of women in Fiji with Chlamydia trachomatis infection

  1. Sankhya Bommana
  2. Olusola Olagoke
  3. Yi-Juan Hu
  4. Roselle Wang
  5. Mike Kama
  6. Morgan Dehdashti
  7. Reshma Kodimerla
  8. Timothy D. Read
  9. Deborah Dean

Reviewed by

Read the full article See related articles

Listed in

Log in to save this article

Abstract

Antibiotics disrupt mucosal microbial communities, yet the effects on microbiomes with Chlamydia trachomatis ( Ct ) infection remain poorly understood. Some data exist on vaginal microbiomes pre- and post-treatment, but none are available for the endocervix or rectum that are primary sites of infection. We applied metagenomic shotgun sequencing to vaginal, endocervical and rectal samples from women who, overtime, had Ct persistence, clearance, or no infection to evaluate azithromycin-induced changes in microbial composition, function, and the resistome. Our results show a shift in composition and function that support Ct post-treatment with azithromycin resistance mutations in the Ct rpl V gene and significant endocervical enrichment of azithromycin resistance genes in Lactobacillus iners and Gardnerella vaginalis , the strains of which have moderate/high potential for biofilm formation. These findings highlight the unintended ecological consequences of azithromycin, including resistance gene propagation and microbiome shifts that support persistent/recurrent Ct , emphasizing the need for novel treatment and microbiome- preserving strategies.

Article activity feed

  1. Rapid Reviews Infectious Diseases

    Allan Pillay

    Review 2: "Effect of Azithromycin Treatment on the Microbial Composition, Functional Dynamics and Resistomes of Endocervical, Vaginal and Rectal Microbiomes of Women in Fiji with Chlamydia Trachomatis Infection"

    Overall, this preprint offers valuable insights into how antibiotic treatment can unintentionally alter the microbiome and pathogen dynamics.

  2. Rapid Reviews Infectious Diseases

    Calum Walsh

    Review 1: "Effect of Azithromycin Treatment on the Microbial Composition, Functional Dynamics and Resistomes of Endocervical, Vaginal and Rectal Microbiomes of Women in Fiji with Chlamydia Trachomatis Infection"

    Overall, this preprint offers valuable insights into how antibiotic treatment can unintentionally alter the microbiome and pathogen dynamics.

  4. Version published to 10.1101/2025.04.02.646699v2 on bioRxiv
  5. Version published to 10.1101/2025.04.02.646699v1 on bioRxiv