The impact of topical or oral antibiotics in children with acute otitis media on their middle ear, nasopharyngeal, and gut microbiomes

Acute otitis media (AOM) is a major driver of paediatric antibiotic prescriptions. We assessed the impact of oral and topical antibiotics on middle ear, nasopharyngeal, and gut microbiome compositions, and the gut resistome, in children with AOM and ear discharge (AOMd). Fifty-eight children with AOMd and ear pain and/or fever were randomized to oral amoxicillin suspension (n = 31) or hydrocortisone-bacitracin-colistin eardrops (n = 27) for 7 days. From 57 out of 58 children, baseline, and Week-2 middle ear fluid (MEF) and nasopharyngeal (NP) samples were sequenced, along with baseline, Week-2, and Month-3 faecal samples. At baseline, the top 5 MEF genera were Streptococcus, Haemophilus, Turicella, Staphylococcus and Alloiococcus and NP genera Moraxella, Haemophilus, Streptococcus, Corynebacterium, and Dolosigranulum. At Week-2, the ear discharge had resolved in all but four children (oral n = 3, eardrops n = 1). In NP samples, the relative and absolute abundances of Streptococcus decreased to a greater extent after oral than eardrop treatment, but Moraxella and Haemophilus increased only following oral treatment. Neither treatment significantly altered the faecal microbiome or resistome at Week-2 and Month-3. Therefore, both treatments resolved the middle ear discharge in most children, but oral amoxicillin suspension may reduce NP Streptococcus more than hydrocortisone-bacitracin-colistin eardrops at the cost of potentially increasing other NP pathobionts.