Predicting neonatal infection in preterm premature rupture of membranes with vaginal microbiology and metagenomics: a prospective cohort study

Laurent Mandelbrot; Sean Kennedy; Jessica Rousseau; François Goffinet; Luce Landraud; Céline Plainvert; Valérie Marcou; Luc Desfrère; Tiphaine Barral; Lahçene Allal; Agnès Baud; Nathalie Grall; Claire Poyart; Pierre-Yves Ancel; Asmaa Tazi

doi:10.1016/j.ajog.2025.12.042

Predicting neonatal infection in preterm premature rupture of membranes with vaginal microbiology and metagenomics: a prospective cohort study

Am J Obstet Gynecol. 2025 Dec 18:S0002-9378(25)00939-1. doi: 10.1016/j.ajog.2025.12.042. Online ahead of print.

Authors

Affiliations

¹ Assistance Publique-Hôpitaux de Paris, Department of Obstetrics and Gynecology, Hôpital Louis Mourier, Colombes, France; Université Paris Cité and Université Sorbonne Paris Nord, Inserm, Paris, France; FHU Prem'Impact, Paris, France. Electronic address: laurent.mandelbrot@aphp.fr.
² Computational Biology Department, Institut Pasteur, Université Paris Cité, Paris, France. Electronic address: sean.kennedy@pasteur.fr.
³ Assistance Publique- Hôpitaux de Paris, URC-CIC Paris Descartes Necker/Cochin, Paris, France.
⁴ FHU Prem'Impact, Paris, France; Université Paris Cité and Université Sorbonne Paris Nord, INSERM, INRAE, Centre de Recherche Epidémiologie et StatistiqueS (CRESS), Obstetrical, Perinatal and Pediatric Life Course Epidemiology (OPPALE Team), Paris, France; Assistance Publique-Hôpitaux de Paris, Department of Obstetrics and Gynecology, Hôpital Cochin-Port Royal, Paris, France.
⁵ Université Paris Cité and Université Sorbonne Paris Nord, Inserm, Paris, France; Assistance Publique-Hôpitaux de Paris, Department of Microbiology, Hôpital Louis Mourier, Colombes, France.
⁶ Assistance Publique-Hôpitaux de Paris, Department of Bacteriology, National Reference Center for Streptococci, Hôpital Cochin, Paris, France.
⁷ FHU Prem'Impact, Paris, France; Assistance Publique-Hôpitaux de Paris, Department of Neonatal Medicine, Hôpital Cochin-Port Royal, Paris, France.
⁸ FHU Prem'Impact, Paris, France; Assistance Publique-Hôpitaux de Paris, Department of Neonatal Medicine, Hôpital Louis Mourier, Colombes, France.
⁹ Assistance Publique-Hôpitaux de Paris, Department of Obstetrics and Gynecology, Hopital Bichat, Paris, France.
¹⁰ Assistance Publique-Hôpitaux de Paris, Neonatal Medicine Unit, Hôpital Bichat, Paris, France.
¹¹ Computational Biology Department, Institut Pasteur, Université Paris Cité, Paris, France.
¹² Assistance Publique-Hôpitaux de Paris, Department of Microbiology, Hôpital Bichat, Paris, France.
¹³ FHU Prem'Impact, Paris, France; Assistance Publique-Hôpitaux de Paris, Department of Bacteriology, National Reference Center for Streptococci, Hôpital Cochin, Paris, France; Inserm U1016, CNRS UMR 8104, Université Paris Cité, Institut Cochin, Paris, France.
¹⁴ Assistance Publique- Hôpitaux de Paris, URC-CIC Paris Descartes Necker/Cochin, Paris, France; Université Paris Cité and Université Sorbonne Paris Nord, INSERM, INRAE, Centre de Recherche Epidémiologie et StatistiqueS (CRESS), Obstetrical, Perinatal and Pediatric Life Course Epidemiology (OPPALE Team), Paris, France.

PMID: 41421745
DOI: 10.1016/j.ajog.2025.12.042

Abstract

Objective: Early-onset neonatal sepsis due to ascending infection is a potentially preventable complication of preterm premature rupture of membranes. Our objective was to determine whether the analysis of bacteria from vaginal swab samples is predictive of the risk of early-onset neonatal sepsis in preterm premature rupture of membranes.

Study design: In a prospective 3-center observational cohort, patients with preterm premature rupture of membranes were enrolled between 22 and 36 weeks of gestation + 6 days. Vaginal swab samples at delivery were analyzed using 2 different approaches, classical bacterial cultures and shotgun metagenomic sequencing analysis. A metagenomics score was constructed combining the characterization of the vaginal microbiome and the presence of pathogens and the optimal cutoff to predict early-onset neonatal sepsis was tested on a receiver operating curve.

Results: Five hundred sixty-three preterm premature rupture of membranes cases were enrolled, with 646 live-born neonates. Preterm premature rupture of membranes occurred<32 weeks of gestation in 41.9% and deliveries were<34 weeks of gestation in 41.0%. The incidence of early-onset neonatal sepsis was 29/646 (4.5%). When considering all central and peripheral microbiological samples available for 26 neonates, the main pathogens isolated were Escherichia coli in 14 cases (53.8%), other gram-negatives in 5 (19.2%), strict anaerobes in 3 (11.5%); there was a single case (3.8%) each with Group B Streptococcus, Streptococcus anginosus, Staphylococcus aureus, and Ureaplasma urealyticum. We studied the prediction of early-onset neonatal sepsis among 272 mothers and their 310 neonates (20 early-onset neonatal sepsis, 6.4%) with both culture and metagenomic data available. A culture positive for a major or intermediate pathogen in the vaginal sample at delivery had a sensitivity of 80.0% (95% confidence interval=56.3-94.3) and a specificity of 37.9% (95% confidence interval=32.3-43.8), adjusted odds ratio of 1.6 (95% confidence interval [0.5-5.0]) to predict early-onset neonatal sepsis. The presence of E. coli was associated with an early-onset neonatal sepsis risk of 10.6% vs 4.9%, in the absence of E. coli (P=0.07). The metagenomics score was highly associated with early-onset neonatal sepsis, with an area under the receiver operating curve of 0.75 (95% confidence interval, 0.61-0.90). At the optimal cutoff value, sensitivity was 70% (95% confidence interval, 64%% to 95%), specificity was 85% (95% confidence interval, 81%% to 89%). A metagenomics score greater than 40 was associated with a significantly increased risk of early-onset neonatal sepsis with an adjusted odds ratio of 8.9 (95% confidence interval [3.5; 22.3]) in multivariate analysis adjusted for latency period and gestational age, P<0.001.

Conclusion: In preterm premature rupture of membranes, conventional microbial culture of maternal vaginal samples was associated with early-onset neonatal sepsis, but its predictive values remain insufficient to guide perinatal care. Metagenomic microbial signatures improved predictive values. This opens the perspective for a rapid point-of-care test.

Keywords: Nugent score; ascending-route infection; bacterial culture; early-onset neonatal sepsis; metagenomics; pregnancy, preterm premature rupture of membranes (PPROM); vaginal microbiota; vaginal swab sampling.