Impact of the Early Life Virome Development on Bronchopulmonary Dysplasia in Preterm Neonates (ELVIRE)

Bronchopulmonary dysplasia (BPD) is the most frequent respiratory complication in extremely preterm infants. It leads to significant mortality and long-term morbidity. The pathophysiology of BPD is multifactorial, involving inflammation and oxidative stress due to neonatal exposures such as mechanical ventilation and infections.

Previous studies have highlighted the role of respiratory bacterial microbiota in BPD development, with causal effects having been demonstrated in murine models. Moreover, the gut-lung axis is implicated in BPD, with alterations to the gut bacteriome and mycobiome observed in preterm infants in the first weeks of life who later develop BPD.

Despite its critical role in shaping immunity and microbial ecology, the virome has been largely understudied in preterm infants. Our recent observations have revealed the existence of a detectable respiratory virome at birth in most very preterm infants, and certain virome and bacteriome profiles have been found to be associated with different risks of developing BPD.

Hypothesis:

The early acquisition and dynamics of the respiratory and gut virome in the first weeks of life influence microbiome structure and pulmonary immune development, contributing to BPD pathogenesis. These dynamics may define distinct endotypes of BPD with implications for prognosis and therapy.

Objectives:

• Primary: Characterize the evolution of the respiratory and gut virome during the first 3 weeks of life in infants born <30 weeks of gestation, comparing those who develop BPD to those who do not.

• Secondary:

  • Define different BPD endotypes and assess their association with demographic and clinical characteristics
  • Characterise the structure of the microbiome within each endotype.
  • Compare the evolution of the virome, bacteriome and mycobiome within and between anatomical sites.

Study Design:

A monocentric, prospective observational cohort of 40 preterm infants (<30 weeks GA) requiring respiratory support at birth. Infants are classified at 36 weeks' postmenstrual age (PMA) into BPD and non-BPD groups based on oxygen dependency.

Sample Collection:

• Oropharyngeal aspirates: Collected at days 0, 7, 14, and 21.
• Stool samples: Collected at days 7, 14, and 21.

Methods:

• Virome analysis: Viral metagenomics
• Metatranscriptomics: Assess transcriptionally active bacteria/fungi and host gene expression.
• Data integration: Multi-omics factor analysis and unsupervised clustering to identify BPD endotypes; ecological network analysis to evaluate microbiome structure and interactions.

Outcomes:

• Primary: Qualitative and quantitative assessment of virome composition and diversity, including dynamics and persistence across timepoints.
• Secondary: Definition of microbiome-based endotypes; interaction networks between viruses, bacteria, and fungi; and longitudinal comparisons of microbial diversity and composition across anatomical sites.

Study Overview

• Status: Not yet recruiting
• Conditions: Bronchopulmonary Dysplasia (BPD)
• Intervention / Treatment: Other: Viral metagenomics and metatranscriptomics analysis of oropharyngeal and stool samples

Detailed Description

Bronchopulmonary dysplasia (BPD) is the most frequent respiratory complication in extremely preterm infants. It leads to significant mortality and long-term morbidity. The pathophysiology of BPD is multifactorial, involving inflammation and oxidative stress due to neonatal exposures such as mechanical ventilation and infections.

Previous studies have highlighted the role of respiratory bacterial microbiota in BPD development, with causal effects having been demonstrated in murine models. Moreover, the gut-lung axis is implicated in BPD, with alterations to the gut bacteriome and mycobiome observed in preterm infants in the first weeks of life who later develop BPD.

Despite its critical role in shaping immunity and microbial ecology, the virome has been largely understudied in preterm infants. Our recent observations have revealed the existence of a detectable respiratory virome at birth in most very preterm infants, and certain virome and bacteriome profiles have been found to be associated with different risks of developing BPD.

Hypothesis:

The early acquisition and dynamics of the respiratory and gut virome in the first weeks of life influence microbiome structure and pulmonary immune development, contributing to BPD pathogenesis. These dynamics may define distinct endotypes of BPD with implications for prognosis and therapy.

Objectives:

• Primary: Characterize the evolution of the respiratory and gut virome during the first 3 weeks of life in infants born <30 weeks of gestation, comparing those who develop BPD to those who do not.

• Secondary:

  • Define different BPD endotypes and assess their association with demographic and clinical characteristics
  • Characterise the structure of the microbiome within each endotype.
  • Compare the evolution of the virome, bacteriome and mycobiome within and between anatomical sites.

Study Design:

A monocentric, prospective observational cohort of 40 preterm infants (<30 weeks GA) requiring respiratory support at birth. Infants are classified at 36 weeks' postmenstrual age (PMA) into BPD and non-BPD groups based on oxygen dependency.

Sample Collection:

• Oropharyngeal aspirates: Collected at days 0, 7, 14, and 21.
• Stool samples: Collected at days 7, 14, and 21.

Methods:

• Virome analysis: Viral metagenomics
• Metatranscriptomics: Assess transcriptionally active bacteria/fungi and host gene expression.
• Data integration: Multi-omics factor analysis and unsupervised clustering to identify BPD endotypes; ecological network analysis to evaluate microbiome structure and interactions.

Outcomes:

• Primary: Qualitative and quantitative assessment of virome composition and diversity, including dynamics and persistence across timepoints.
• Secondary: Definition of microbiome-based endotypes; interaction networks between viruses, bacteria, and fungi; and longitudinal comparisons of microbial diversity and composition across anatomical sites.

• Study Type: Observational
• Enrollment (Estimated): 40

Contacts and Locations

• Study Contact: Name: JOSSET L Pr, MD; Phone Number: 33 04 72 07 10 22; Email: laurence.josset@chu-lyon.fr

Participation Criteria

Eligibility Criteria

• Ages Eligible for Study: Child
• Accepts Healthy Volunteers: No

• Sampling Method: Non-Probability Sample

Study Population

Neonates hospitalised in the neonatal intensive care unit (NICU) of Lyon University Hospital, France.

Description

Inclusion Criteria:

• Birth < 30 SA
• Respiratory support at birth (invasive or non-invasive ventilation, or oxygen supplementation).

Exclusion Criteria:

• - Major congenital anomalies of the lung or airways.
• Death, transfer or discharge before 36 weeks' postmenstrual age (PMA) (not allowing progression to BPD to be known).
• Number of respiratory samples collected < 3

Study Plan

How is the study designed?

Number of groups / cohorts

2

Cohorts and Interventions

Group / Cohort	Intervention / Treatment
BPD group; The BPD group is defined as infants with moderate or severe BPD, evaluated at 36 weeks' postmenstrual age according to oxygen dependence. BPD is moderate when the infant requires O2 supplementation with FiO2 < 30% at 36 weeks' PMA and severe when the infant requires O2 supplementation with FiO2 ≥ 30% and/or positive pressure ventilation.	Other: Viral metagenomics and metatranscriptomics analysis of oropharyngeal and stool samples; Viral metagenomics and metatranscriptomics will be performed following standardised protocol (published https://doi.org/10.1186/s12879-018-3446-5 and https://doi.org/10.3389/fmicb.2025.1685035) on oropharyngeal aspirates collected at days 0, 7, 14, and 21 and on stool samples collected at days 7, 14, and 21.
Control group; The control group is defined as infants who did not develop BPD (i.e. who were not oxygen-dependent at 36 weeks' postmenstrual age (PMA)).	Other: Viral metagenomics and metatranscriptomics analysis of oropharyngeal and stool samples; Viral metagenomics and metatranscriptomics will be performed following standardised protocol (published https://doi.org/10.1186/s12879-018-3446-5 and https://doi.org/10.3389/fmicb.2025.1685035) on oropharyngeal aspirates collected at days 0, 7, 14, and 21 and on stool samples collected at days 7, 14, and 21.

What is the study measuring?

Primary Outcome Measures

Outcome Measure	Measure Description	Time Frame
Qualitative and quantitative variations in the composition and diversity of the oropharyngeal and digestive viromes in DBP and control patients.	Composition is defined as the relative and absolute abundance of viral species, including both prokaryotic (e.g. bacteriophages) and eukaryotic (e.g. Anelloviridae and Herpesviridae) viruses. Analysis of compositional dynamics is defined by variations in the abundance of each species between samples, as well as by the persistence time of each viral species for each patient. Diversity is defined by richness (the number of species present) and the Shannon index. Diversity analysis is performed on the entire virome and on eukaryotic viruses, temperate bacteriophages and virulent bacteriophages separately. DBP presence is defined as oxygen dependence at 36 weeks PMA.	through study completion, an average of 1 year

Collaborators and Investigators

• Sponsor: Hospices Civils de Lyon

Study record dates

Study Major Dates

• Study Start (Estimated): April 1, 2026
• Primary Completion (Estimated): July 1, 2027
• Study Completion (Estimated): July 1, 2028

Study Registration Dates

• First Submitted: March 17, 2026
• First Submitted That Met QC Criteria: March 17, 2026
• First Posted (Actual): March 23, 2026

Study Record Updates

• Last Update Posted (Actual): March 23, 2026
• Last Update Submitted That Met QC Criteria: March 17, 2026
• Last Verified: March 1, 2026

More Information

Terms related to this study

• Keywords: Microbiome; Bronchopulmonary dysplasia; Virome; Premature neonates
• Additional Relevant MeSH Terms: Respiratory Tract Diseases; Lung Diseases; Infant, Premature, Diseases; Infant, Newborn, Diseases; Lung Injury; Ventilator-Induced Lung Injury; Congenital, Hereditary, and Neonatal Diseases and Abnormalities; Bronchopulmonary Dysplasia
• Other Study ID Numbers: 25-5465

Plan for Individual participant data (IPD)

• Plan to Share Individual Participant Data (IPD)?: UNDECIDED

Drug and device information, study documents

• Studies a U.S. FDA-regulated drug product: No
• Studies a U.S. FDA-regulated device product: No