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

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, 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 regularly collected from 147 participants aged ≤12 years enrolled in the Australian Respiratory Early Surveillance Team for Cystic Fibrosis (AREST CF) program.

The frequency of colonisation per visit was 4.6% for Hi and 32.1% for Hpi, 80.3% of participants had Hi and/or Hpi detected on at least one visit, and using genomic data we estimate 15.6% of participants had persistent colonisation with the same strain for at least two consecutive visits. Colonising strains were genetically highly diverse and AMR was common, with 52% of Hi and 82% of Hpi displaying resistance to at least one drug.

The genetic basis for AMR could be identified in most cases; novel determinants include a new plasmid encoding bla_TEM-1 (ampicillin resistance), a new inhibitor-resistant bla_TEM allele (augmentin resistance), and previously unreported mutations in chromosomally-encoded genes (pbp3, ampicillin resistance; folA and folP, co-trimoxazole resistance; rpoB, rifampicin resistance). Acquired AMR genes were significantly more common in Hpi than Hi (51% vs 21%, p=0.0107) and were mostly associated with the ICEHin mobile element carrying bla_TEM-1, resulting in higher rates of ampicillin resistance in Hpi (73% vs 30%, p=0.0004).

The genome data identified six potential instances of Haemophilus transmission between participants, three of which involved participant pairs who attended the clinic on the same day. The high prevalence of Haemophilus colonisation and high burden of antimicrobial use in children with CF likely provides a reservoir for emergence and spread of AMR as well as a source of infections.