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

The spread of antibiotic resistance is a major concern in the setting of azithromycin mass drug distribution for childhood mortality. We performed long-read whole-genome sequencing and phenotypic resistance analysis on <i>Streptococcus pneumoniae</i> isolated from the nasopharynx of Nigerien children from communities treated with either six twice-yearly azithromycin distributions or placebo. Here, we showed that co-selection for macrolide, tetracycline, and trimethoprim-sulfamethoxazole genetic resistance was detected with repeated azithromycin mass drug distributions.CLINICAL TRIALSThis study is registered with ClinicalTrials.gov as NCT02047981.