Follow-up of the Nasal Microbiome and Viral Infections in Newborns Hospitalised in Neonatology.

Study Overview
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Brief Summary
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The goal of this interventional study is to learn about nasal microbiome and viral infections in newborns hospitalised in neonatology. The main questions it aims to answer are : how often are newborns infected by viruses in neonatology ? how does the microbiome develop during first weeks of life ? how does microbiome and viruses interacts together ? is there a link between viral infection, microbiome, and medical complications during hospitalisation in neonatology ? Participants will have a nasal swab taken each week during their hospitalisation in neonatology, and researchers will take medical data from the medical chart.

Official Title
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Follow-up of the Nasal Microbiome and Viral Infections in Newborns Hospitalised in Neonatology in the University Hospital of Caen, France : Metatranscriptomics Approach by Next Generation Sequencing From Nasal Swabs.

Conditions
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Microbial Colonization, Viral Infection, Neonatal Infection

Intervention / Treatment
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* Diagnostic Test: Nasal swab


Participation Criteria
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Eligibility Criteria
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Inclusion Criteria: newborn hospitalised in neonatal intensive care unit during the inclusion period parents have been informed about the study (speaking french) and have signed the informed consent. affiliated to the social security system. Exclusion Criteria: parental refusal minor parents or under judicial protection newborn who already have been discharded home before inclusion hospitalisation after the first 48 hours of life only palliative care

Ages Eligible for Study
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Maximum Age: 48 Hours

Sexes Eligible for Study
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All

Accepts Healthy Volunteers
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No

Study Plan
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How is the study designed?
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Design Details

Primary Purpose: Basic Science
Intervention Model: Single Group Assignment
Masking: None (Open Label)


Arms and Interventions

| Intervention/Treatment |
| --- |
|Diagnostic Test: Nasal swab|We will take nasal swabs from anterior and middle nostril, once a week for each newborn included.|

What is the study measuring?
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Primary Outcome Measures

| Outcome Measure | Measure Description | Time Frame |
| --- | --- | --- |
| Change in microbiome diversity | Shannon diversity index | Day 0, day 7, day 14, and each week until discharge (maximum duration : 3 months for each newborn). | 
| Change in microbiome abundance | Number of reads for a given taxonomy. | Day 0, day 7, day 14, and each week until discharge (maximum duration : 3 months for each newborn). | 
| Virus presence | Molecular detection of respiratory viruses using multiplex PCR. | Day 0, day 7, day 14, and each week until discharge (maximum duration : 3 months for each newborn). | 

Secondary Outcome Measures

| Outcome Measure | Measure Description | Time Frame |
| --- | --- | --- |
| Occurence of bronchopulmonary dysplasia | assessed by clinical recording on discharge from neonatology | At discharge from neonatology. | 
| Change in expression of local innate immunity markers | Mesure of the expression of the interferon-stimulated genes (ISGs), anti-viral genes, and the inflammasome pathway. | Day 0, day 7, day 14, and each week until discharge (maximum duration : 3 months for each newborn). | 

 Terms related to the study
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Keywords Provided by Centre Hospitalier Valida
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Metatranscriptomics, Microbiome, Newborn