This project aims to assess the relationship between the microbiome and virome composition, the immune responses, and the respiratory health of children with protracted bacterial bronchitis (PBB). In addition, we aim to evaluate how the standard treatment with azithromycin interacts with the components of the microbiome, virome and immune biomarkers.

Protracted Bacterial Bronchitis (PBB) is an often underestimated disease, characterized by a persistent cough for more than four weeks, without other significant underlying symptoms. While generally treatable, it can lead to complications such as recurrent infections and airway damage (bronchiectasis). The reasons why some children develop PBB or subsequent complications while others do not remain unclear. Recent research suggests that an impaired immune response and microbiota dysbiosis may play a key role. This study aims to analyze the microbial and viral composition of the airways in children with PBB, its relationship with inflammation, and the effects of azithromycin. Oropharyngeal swabs will be collected from up to 160 children <5 years old diagnosed with PBB at UZA in a longitudinal setup during one year. At each routine consultation (five in total) and during an exacerbation episode, three oropharyngeal swabs will be collected from each child. The three swabs will be used to: (1) determine the microbiome composition using next-generation sequencing, (2) identify the virome composition using multiplex qPCR or similar approaches, and (3) quantify immune biomarkers (RNA and protein-level) and culture microbial isolates. These findings will help to better understand the role of the airway microbiome in young children with PBB and identify microorganisms that may have a pathogenic or protective role. Ultimately, this knowledge may contribute to the development of new and effective diagnostics and treatments for PBB from an early age.

Inclusion Criteria:

• Children with PBB diagnosis according to case definition
• Consent form signed by parents or legal guardians

Exclusion Criteria:

• Comorbidities (HIV, asthma, chronic obstructive pulmonary disease, diabetes)
• Have had serious illnesses (meningitis, pneumonia, bacteremia, empyema, etc) in the previous three months, identified only at the time of enrollment.
• Have chronic respiratory conditions at the time of enrollment (non-PBB bronchiectasis not caused by PBB, CF, allergy, etc.).
• Having received mechanical ventilation.
• Having been hospitalized or used antibiotics in the previous three months at the time of enrollment.

Children under five years old diagnosed with PBB.

The metadata of participants in the study will be made available in a restricted access repository. For samples and data sharing, the researchers will work with the legal department to establish Material/Data Transfer Agreements. Sequencing data are available at the European Nucleotide Archive. Physical samples are their origin will be stored at the decentral hub of the Antwerp biobank.

After the completion of the study (intended in 2029) and before publication, sequences and related metadata will be deposited into the ENA database and made available indefinitely.

After data deposition in ENA, the data will be publicly accessible to anyone using the ENA instructions https://www.ebi.ac.uk/ena/browser/downloading-data