Targeted next-generation sequencing in diagnosing reproductive tract infections: a comparative study

Targeted next-generation sequencing (tNGS), which utilizes multiplex PCR amplification or probe capture for pathogen nucleic acid enrichment, is gaining attention in the clinical management of infectious diseases. This study aims to assess the clinical efficacy of tNGS in patients with suspected reproductive tract infections.

A total of 181 patients with suspected reproductive tract infection between June 2024 and August 2024 were enrolled at the second Xiangya Hospital, Changsha, China. Vaginal discharge samples from all participants were tested for tNGS and Human Papillomavirus (HPV) testing, with a subset also analyzed for microecology. A comparative analysis of diagnostic efficacy and concordance was conducted.

For HPV detection, tNGS had a broader coverage of HPV types compared to traditional HPV testing, with higher detection sensitivity for most sub-types. The rate of complete agreement between tNGS and HPV testing was 71%, 12% for partial agreement, and 17% for mismatched. Among the 129 cases exhibiting complete concordance, tNGS identified an additional 12 pathogens, predominantly Ureaplasma parvum, Ureaplasma urealyticum, and Cytomegalovirus (CMV). Moreover, tNGS shows a significant advantage in detecting mixed infections. When comparing vaginal microecology testing results, bacterial vaginosis (BV) affected patients exhibited a higher prevalence of HPV, CMV, Candida albicans, M. hominis, Chlamydia trachomatis, U. urealyticum and U. parvum.

tNGS offers a broader spectrum of HPV subtypes, enhanced sensitivity, and the capability to identify mixed infections, making it a competitive alternative to traditional HPV detection assays. Additionally, tNGS serves as a robust complement to vaginal microecology assays.