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

Authors:

Catherine M. O’Connell1,#, Hayden Brochu2,#, Jenna Girardi1, Erin Harrell2, Aiden Jones2, Toni Darville1, Arlene C. Seña3 and Xinxia Peng2,4

doi: 10.15698/mic2019.03.672
Volume 6, pp. 177 to 183, published 24/01/2019.

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Affiliations:

1 Department of Pediatrics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.

2 Department of Molecular Biomedical Sciences, North Carolina State University, Raleigh, North Carolina, USA.

3 Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.

4 Bioinformatics Research Center, North Carolina State University, Raleigh, North Carolina, USA.

# These authors contributed equally to this work.

Keywords: 

RNA-seq, chlamydia, gonorrhea, natural infection, microbiome.

Corresponding Author(s):

Catherine O’Connell, PhD, University of North Carolina at Chapel Hill, 8340B MBRB, CB# 7509, 111 Mason Farm Road, Chapel Hill, NC 27599-7509; phone (919) 962-3422; fax:(919) 966-7277; catherine.oconnell@unc.edu Xinxia Peng, PhD, North Carolina State University, Raleigh, NC 27695; phone (919) 515-4481; fax: (919)-513-6464; xpeng5@ncsu.edu

Conflict of interest statement:

None.

Please cite this article as:

Catherine M. O'Connell, Hayden Brochu, Jenna Girardi, Erin Har-rell, Aiden Jones, Toni Darville, Arlene C. Seña and Xinxia Peng (2019). Simultaneous profiling of sexually transmitted bacterial pathogens, microbiome, and concordant host response in cervical samples using whole transcriptome sequencing analy-sis. Microbial Cell 6(3): 177-183. doi: 10.15698/mic2019.03.672

© 2019 O’Connell et al. This is an open-access article released under the terms of the Creative Commons Attribution (CC BY) license, which allows the unrestricted use, distribution, and reproduc-tion in any medium, provided the original author and source are acknowledged.

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.