Genomic diversity and antimicrobial resistance of Haemophilus colonising the airways of young children with cystic fibrosis. Haemophilus

Respiratory infection during childhood is a key risk factor in early cystic fibrosis (CF) lung disease progression. Haemophilus influenzae (Hi) and Haemophilus parainfluenzae (Hpi) are routinely isolated from the lungs of children with CF during periods of exacerbated respiratory symptoms. However, little is known about the frequency and characteristics of Haemophilus colonisation in this context. Here, we describe detection, antimicrobial resistance (AMR) and genome sequencing of Hi/Hpi isolated from sputum, cough swab, and bronchoalveolar lavage samples collected during quarterly clinic visits from 147 participants aged less than 12 years enrolled in the Australian Respiratory Early Surveillance Team for Cystic Fibrosis (AREST CF) program.