Endometrial microbial culture in the era of mNGS: a prospective cohort study of endometrial dysbiosis in women with infertility

Abstract

Endometrial dysbiosis (ED) and chronic endometritis (CE) have gained increasing attention as potential risk factors for implantation failure and infertility. However, their diagnostic assessment remains heterogeneous, and the clinical roles of microbial culture and metagenomic next-generation sequencing (mNGS) remain uncertain. This study compared conventional endometrial microbial culture, CD138 immunohistochemistry, hysteroscopy, and mNGS as complementary approaches for evaluating endometrial inflammation and dysbiosis in infertile women. We also assessed agreement between culture and mNGS and examined whether mNGS provided additional microbiological information beyond routine culture-based assessment. This prospective cohort study enrolled 80 infertile women undergoing outpatient hysteroscopy between May 2023 and April 2024. Endometrial samples were obtained using a Pipelle device, with concurrent collection of endocervical swabs. Specimens underwent aerobic and anaerobic microbial culture, CD138 immunohistochemistry, and mNGS profiling. ED was defined as the presence of potentially pathogenic organisms identified by endometrial culture, whereas histopathological CE was assessed using CD138 immunostaining. The mean participant age was 36.6 years. Among 78 culture-evaluable participants, 31 (39.7%) had culture-detected pathogenic endometrial dysbiosis, 24 (30.8%) had Lactobacillus -only growth, and 23 (29.5%) had negative endometrial cultures. A total of 98 microbial isolates were recovered, with Lactobacillus spp. being the most frequent (31/98, 31.6%). Enterococcus faecalis and Bifidobacterium spp. were the most commonly recovered non- Lactobacillus isolates. Among 48 mNGS-evaluable samples, Gardnerella vaginalis was the most commonly detected potentially pathogenic organism. Antimicrobial susceptibility profiles varied across cultured isolates. Women with culture-detected dysbiosis had a greater number of previous embryo transfer failures than those without dysbiosis ( p < 0.05). Overall agreement was 72.9% between endometrial culture and mNGS and 77.1% between endometrial and endocervical cultures. Endometrial microbial culture identified potentially pathogenic dysbiosis in approximately 40% of this infertility cohort and showed partial agreement with mNGS, suggesting complementary roles for these microbiological approaches. Culture identifies viable, cultivable organisms and enables antimicrobial susceptibility testing, supporting its practical use in routine outpatient assessment. Endocervical sampling may provide complementary information when endometrial sampling is not feasible. Prospective interventional studies are needed to determine whether microbiology-guided management improves reproductive outcomes.