Patterns of within-host spread of Chlamydia trachomatis between vagina, endocervix and rectum revealed by comparative genomic analysis

• Type of Material: Article
• Authors: Sandeep J. Joseph, Centers for Disease Control and Prevention; Sankhya Bommana, University of California San Francisco; Noa Ziklo, University of California San Francisco; Mike Kama, Ministry of Health and Medical Services; Deborah Dean, University of California San Francisco; Timothy Read, Emory University
• Language: English
• Date: 2023-03-28
• Publisher: FRONTIERS MEDIA SA
• Publication Version: Final Published Version
• Copyright Statement: © 2023 Joseph, Bommana, Ziklo, Kama, Dean and Read.
• License: Creative Commons Attribution 4.0 International
• Final Published Version (URL): http://dx.doi.org/10.3389/fmicb.2023.1154664
• Title of Journal or Parent Work: FRONTIERS IN MICROBIOLOGY
• Volume: 14
• Start Page: 1154664
• End Page: 1154664
• Grant/Funding Information: TR and DD were supported by United States National Institutes of Health awards R21 AI138079 and R01 AI151075.
• Keywords: Chlamydia trachomatis; sexually transmitted diseases; WOMEN; RECOMBINATION; INFECTION; DOXYCYCLINE; AZITHROMYCIN; single nucleotide polymorphisms; chlamydiae; Microbiology; single variable polymorphisms; Life Sciences & Biomedicine; Science & Technology
• Research Categories: Health Sciences, Obstetrics and Gynecology; Biology, Virology; Biology, Microbiology

Abstract

Introduction: Chlamydia trachomatis, a gram-negative obligate intracellular bacterium, commonly causes sexually transmitted infections (STIs). Little is known about C. trachomatis transmission within the host, which is important for understanding disease epidemiology and progression. Methods: We used RNA-bait enrichment and whole-genome sequencing to compare rectal, vaginal and endocervical samples collected at the same time from 26 study participants who attended Fijian Ministry of Health and Medical Services clinics and tested positive for C. trachomatis at each anatomic site. Results: The 78 C. trachomatis genomes from participants resolved into two major clades of the C. trachomatis phylogeny (the “prevalent urogenital and anorectal” clade and “non-prevalent urogenital and anorectal” clade). For 21 participants, genome sequences were almost identical in each anatomic site. For the other five participants, two distinct C. trachomatis strains were present in different sites; in two cases, the vaginal sample was a mixture of strains. Discussion: The absence of large numbers of fixed SNPs between C. trachomatis genomes within many of the participants could indicate recent acquisition of infection prior to the clinic visit without sufficient time to accumulate significant genetic variation in different body sites. This model suggests that many C. trachomatis infections may be resolved relatively quickly in the Fijian population, possibly reflecting common prescription or over-the-counter antibiotics usage.