Introduction: Haemophilus influenzae is one of the most common airway pathogens in Primary Ciliary Dyskinesia (PCD). This study aimed to evaluate the effect of antibiotic treatment on H. influenzae airway colonization and the frequency of in-hospital cross-infections in a paediatric PCD cohort.

Methods: In this prospective, single-centre, observational PCD cohort study, we aimed to illustrate the clonal relationship between different H. influenzae isolates from airway samples from consecutive outpatient visits between January 2020 and September 2021 by using Illumina whole-genome sequencing.

Results: H. influenzae isolates from 15/33 PCD patients (13 females / 20 males, mean age 14.4 ± 6.1 years) were sequenced. The vast majority (13/15 patients) had more than one H. influenzae positive sample. Sequence-identical H. influenzae strains were detected in consecutive samples of 9/13 patients, although 4 patients had received targeted antibiotic treatment after the first isolate. New strains were detected in consecutive samples of 3 patients, all had been treated with antibiotics in the interim. One patient had a new strain after initial antibiotic treatment but regrew the first strain in a following sample. The two sibling pairs in our cohort did not have identical strains. Two unrelated patients had identical strains, which could indicate cross-infection within the hospital setting.

Conclusion: Regrowth of identical H. influenzae strains is common despite targeted antibiotic treatment. In hospital cross-infection was rare in our paediatric PCD cohort. These findings need to be confirmed in a larger cohort, e.g. within the network of the Beat-PCD clinical research collaboration.