Clinical trial NCT06037421: Metagenomic Analysis of Bacterial Microbiota in Breast Milk
Official title: Metagenomic Analysis of Bacterial Microbiota in Breast Milk
Study type: OBSERVATIONAL
Overall status: NOT_YET_RECRUITING
Conditions: Bacteria in Breast Milk
Keywords: Bacterial
newborn breast milk
neonates
infectious risk
virulence genes
agar culture methods
shotgun metagenomics
targeted metagenomics
microbiota
Lead sponsor: Centre Hospitalier Sud Francilien
Sponsor class: OTHER
First posted: 2023-09-14
Enrollment: 120
Sex: ALL
Minimum age (years): 1
Standard ages: CHILD
ADULT
OLDER_ADULT
Accepts healthy volunteers: no
Observational model: COHORT
Time perspective: PROSPECTIVE
Sampling method: NON_PROBABILITY_SAMPLE
Study population: Mother-infant pairs whose newborn(s) are being cared for in the CHSF's Neonatal Medicine and Intensive Care Unit.

Brief summary: The aim of this study is to determine the extent to which bacteria in the breast milk microbiota represent an infectious risk for premature infants, by investigating whether they possess virulence genes, and if so, whether these are expressed or repressed.

Detailed description: There are still many unknowns about the exact bacterial composition of breast milk, and the theoretical and real risks represented by its microbiota. In addition to determining the Total Aerobic Flora (TAF) and the Staphylococcus aureus presence, the most commonly isolated enterobacterales species identified by agar culture by the Prevention and Infection Control department are also among those potentially found in diagnostic samples: Enterobacter cloacae, Klebsiella pneumoniae, Klebsiella aerogenes, Klebsiella oxytoca and Escherichia coli. However, it is not yet known whether these are identical strains or not. It is therefore legitimate to ask whether there are any differences between the strains present in the microbiota of breast milk and those responsible for newborn infections.

Conventional methods for enumerating and identifying the bacteria making up the milk microbiota are not standardized, which makes it difficult to draw up a precise, multicentric inventory of its composition. It is therefore impossible to know whether exceeding a threshold value defined by expert consensus represents a real danger for newborns who must receive breast milk.

At the Centre National de Recherche en Génomique Humaine (CNRGH), a metagenomic sequencing approach makes it possible to study the microbiota using two complementary methodologies. Either by sequencing the genomes of organisms (bacteria, viruses, fungi, etc.) present in the environment to be analyzed (shotgun metagenomics), or by sequencing one or more genes specific to each bacterial species (targeted metagenomics). The gene that codes for 16S ribosomal RNA (rRNA) has sequence regions common to different bacterial species, as well as variable regions that can be used to distinguish the bacteria present in a sample.

A comparison of the composition of the bacterial microbiota in breast milk using conventional agar culture methods and metagenomic analysis methods would enable us to make progress in understanding its potential involvement in infectious pathologies in premature infants. It is in this scientific and medical context that a collaborative project was initiated for the first time between the departments of Neonatal Medicine and Intensive Care and of Prevention and Infection Control, and the CNRGH. This was a pilot study with the aim of perpetuating this collaboration, which combines scientific knowledge of the metagenome with the CNRGH's high-performance technological tools, as well as potential applications in the medical environment in the CHSF's care departments.

Eligibility criteria: Inclusion Criteria:

* Women of legal age who have given birth at the CHSF (or in another establishment) and whose newborn(s) are being cared for in the CHSF's Neonatal Medicine and Intensive Care Unit,
* Women wishing to give their milk to their child,
* Parents who have given their consent for the mother-child couple to take part in the study.

Exclusion Criteria:

* Mother having received antibiotic therapy in the 3 months prior to delivery, except for those who received injectable antibiotic prophylaxis during delivery.

Primary outcomes:
measure: Assessing the potential pathogenic risk of certain bacteria in breast milk.
timeFrame: at day 0
Secondary outcomes:
Other outcomes:
measure: Comparing the microbial ecologies of breast milk by bacterial culture and metagenomics.
timeFrame: at day 0
measure: If bacteria isolated from breast milk contain virulence genes, establish whether they are activated or repressed.
timeFrame: at day 0
measure: Establish whether strains of bacteria with pathogenic potential (S. aureus, K. aerogenes, E. coli, K. pneumoniae, K. oxytoca, E. cloacae) found in breast milk contain antibiotic resistance genes.
timeFrame: at day 0
measure: If so, establish whether these are activated or repressed.
timeFrame: at day 0
measure: Compare the microbial ecology of different ecosystems: intestinal, oral and cutaneous with that of breast milk, using bacterial culture and metagenomics.
timeFrame: at day 0
measure: Check maternal blood for the presence of essentially anaerobic bacteria such as bifidobacteria and/or mononuclear cells such as dendritic cells or macrophages, a potential reflection of the entero-mammary pathway.
timeFrame: at day 0
Locations:
city: Corbeil-Essonnes
country: France
facility: Centre Hospitalier Sud Francilien
Study officials:
References: