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Highlights One of the first whole genome analyses of Staphylococcus aureus carriage isolates in an African country. Genome data allowed to place S. aureus isolates from Cape Verde in a phylogenetic context. Loss of blaZ -carrying plasmids and transposons is not rare, which is also evident in other international MRSA isolates. Steady increase in antimicrobial drug resistance in Cape Verde. Data provide genomic information for the design of intervention measures to decrease antimicrobial resistance.

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