Impact of narrow spectrum Penicillin V on the oral and fecal resistome in a young child treated for otitis media

Abstract Background Antibiotic overuse has led to a global emergence of resistant bacteria, and children are among the frequent users. Most studies with broad-spectrum antibiotics show severe impact on the resistome development of patients. Although narrow-spectrum antibiotics are believed to have less side-effects, their impact on the microbiome and resistome is mostly unknown. The aim of this study was to investigate the impact of the narrow-spectrum antibiotic phenoxymethylpenicillin (Penicillin V) on the microbiome and resistome of a child treated for acute otitis media (OM). Methods Oral and fecal samples were collected from a one-year child before (day 0) and after (day 5 and 30) receiving Penicillin V against OM. Metagenomic sequencing data was analysed to determine taxonomic profiling, using Kraken and Bracken software, and resistance profiling, using KMA in combination with the ResFinder database. Results In the oral samples, antimicrobial resistance genes (ARGs) belonging to four classes were identified at baseline. At day 5, the abundance of some ARGs was increased; some remained unchanged, while others disappeared. At day 30, most ARGs had returned to baseline levels, or lower. In the fecal samples, we observed seven ARGs at baseline and five at day 5. At day 30, the number increased to 21 ARGs from seven different classes. Conclusions Penicillin V had a remarkable impact on the fecal resistome indicating that even narrow-spectrum antibiotics may have important consequences in selecting for a more resistant microbiome.