Co-selection of genetic antibiotic resistance in <em>Streptococcus pneumoniae</em> after repeated Azithromycin mass drug administrations in Niger

We performed long-read whole-genome sequencing and phenotypic resistance analysis on Streptococcus pneumoniae isolated from the nasopharynx of Nigerien children from communities treated with either 6 twice-yearly azithromycin distributions or placebo. This dataset contains the annotated genome files for the 122 samples used in the study, as well as the associated metadata. Methods Isolated pneumococcal colonies were subjected to long-read WGS using the SMRTbell Prep Kit 3.0 and sequenced on the PacBio Revio platform (Pacific Biosciences of California). PacBio HiFi reads were de novo assembled using Canu (version 2.2) with the ‘-pacbio-hifi’ option and evaluated for quality using BUSCO (version 5.7.1). Assemblies achieving a completeness score >90% underwent a ‘Comprehensive Genome Analysis’ using BV-BRC online tools (accessed April 2025). BV-BRC-annotated genomes were subsequently screened for mobile elements utilizing ICEscreen (version 1.3.3). Annotated genomes were saved in genbank format.