Simultaneous profiling of sexually transmitted bacterial pathogens, microbiome, and concordant host response in cervical samples using whole transcriptome sequencing analysis

Abstract

Pelvic inflammatory disease (PID) is a female upper genital tract inflammatory disorder that arises after sexually transmitted bacterial infections (STI). Factors modulating risk for reproductive sequelae include co-infection, microbiota, host genetics and physiology. In a pilot study of cervical samples obtained from women at high risk for STIs, we examined the potential for unbiased characterization of host, pathogen and microbiome interactions using whole transcriptome sequencing analysis of ribosomal RNA-depleted total RNAs (Total RNA-Seq). Only samples from women with STI infection contained pathogen-specific sequences (3 to 38% transcriptome coverage). Simultaneously, we identified and quantified their active microbial communities. After integration with host-derived reads from the same data, we detected clustering of host transcriptional profiles that reflected microbiome differences and STI infection. Together, our study suggests that total RNA profiling will advance understanding of the interplay of pathogen, host and microbiota during natural infection and may reveal novel, outcome-relevant biomarkers.

Human Fallopian Tube Epithelial Cell Culture Model To Study Host Responses to Chlamydia trachomatis Infection

“…Once internalized, the chlamydial developmental cycle appeared normal with respect to inclusion formation, differentiation to RB, gene transcription, and generation of new EB within polarized FTE. The mildly elevated expression of the late genes glgA and hctA by chlamydiae in FTE cells may reflect chlamydial sensing of the cellular environment; highly abundant glgA transcripts have been detected in a clinical cervical specimen (41), and anti-chlamydial glycogen synthase antibody was prevalent in a large human cohort (42). Alternatively, these increases may be artifacts of RNA carryover from the high MOI needed to achieve infection.…”

Endocervical miRNA Expression Profiles in Women Positive for Chlamydia trachomatis with Clinical Signs and/or Symptoms Are Distinct from Those in Women Positive for Chlamydia trachomatis without Signs and Symptoms

“…It is currently unknown if the CT-infected women have different genetic compositions of chlamydiae. It is also possible that microbiota changes (23)(24)(25) and hormonal changes at the time of infection could dictate the miR expression pattern or result in differences in the development of symptoms. Future studies should include women with signs and symptoms without Chlamydia infection and also coinfection groups (NG/TV/bacterial vaginosis) to determine if miRNA expression patterns are specific to chlamydial infection.…”

Understanding and interpreting community sequencing measurements of the vaginal microbiome

“…Community sequencing is furthering the study of how BV‐associated microbes increase HIV and HPV risk and reduce efficacy of antiretrovirals for HIV prevention . Metatranscriptomic sequencing of the vaginal microbiome during BV and STI is being used to find pathways related to aetiology, treatment targets, and treatment evasion, as well as to determine the dominant pathogen in STI co‐infection …”