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Multidrug-resistant gram-negative (MRGN) bacteria are a serious threat to global health. We used genomics tostudy MRGN obtained from houseflies in a tertiary Rwandan hospital. Our analysis revealed a high abundance ofdifferent MRGN includingE. colipathogenic lineage ST131 suggesting the important role of flies in disseminatinghighly virulent pathogens in clinical settings and beyond