Oral and Middle Ear Delivery of Otitis Media Standard of Care Antibiotics, But Not Biofilm-Targeted Antibodies, Significantly Alter Chinchilla Nasopharyngeal and Fecal Microbiomes

Otitis media (OM) is one of the most globally pervasive pediatric conditions. Translocation of nasopharynx-resident opportunistic pathogens like nontypeable Haemophilus influenzae (NTHi) assimilate into polymicrobial middle ear biofilms which promote OM pathogenesis, recurrence, chronicity, and substantially diminish antibiotic efficacy. Oral or tympanostomy tube (TT)-delivered antibiotics remain the standard of care (SOC) despite consequences including secondary infection, microbiome disruption, and antimicrobial resistance. Monoclonal antibodies (mAb) against two biofilm-associated structural proteins, NTHi-specific type IV pilus PilA (anti-rsPilA) and protective tip-region epitopes of NTHi integration host factor (anti-tip-chimer), were previously shown to disrupt biofilms and restore antibiotic sensitivity in-vitro. However, additional criterion for clinical relevance includes absence of consequential microbiome alterations. Here, nine chinchilla cohorts (n=3/cohort) without disease were established to evaluate whether TT delivery of mAbs would disrupt nasopharyngeal or fecal microbiomes relative to SOC-OM antibiotics. Treatments included a 7d regimen of oral amoxicillin-clavulanate (AC) or 2d regimen of TT-delivered mAb, AC, Trimethoprim-sulfamethoxazole (TS), ofloxacin, or saline. Fecal and nasopharyngeal lavage (NPL) samples were collected before and several days post-treatment (DPT) for 16S sequencing. Fecal and NPL samples displayed significant antibiotic-mediated changes in alpha and beta diversity with distinct clustering of AC cohorts relative to other groups, as well as blooms in opportunistic pathogens that were not observed in mAb-treated cohorts. Collectively, results showed broad-spectrum antibiotics induced significant fecal and nasopharyngeal microbiome disruption regardless of delivery route. Excitingly, biofilm-targeting antibodies had little effect on fecal and nasopharyngeal microbiomes.