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•One of the first whole genome analyses of Staphylococcus aureuscarriage isolates in an African country.•Genome data allowed to place S. aureusisolates 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.

•First antimicrobial resistance survey in clinical isolates in Cabo Verde•Increase in methicillin and extendedspectrum beta-lactamase resistance•Generation of baseline data for implementation of the national action plan•Overall susceptibility profile in Cabo Verde comparable to countries of the region

ABSTRACTOptochin (Opt) susceptibility is used largely for the identification of Streptococcus pneumoniaein diagnostic laboratories. Opt-resistant (Optr) S. pneumoniaeisolates have been reported, however, indicating the potential for misidentification of this important pathogen. Point mutations in the atpCgene have been associated with the emergence of OptrS. pneumoniae, but data on the characterization of such atypical variants of S. pneumoniaeare still limited. The present report describes the results of a polyphasic approach to identifying and characterizing 26 OptrS. pneumoniaeisolates recovered from patients or carriers living in Brazil. Sixteen isolates consisted of heterogeneous populations, and 10 isolates were homogeneously Optr. The isolates had different serotypes and antimicrobial susceptibility profiles. They also presented diverse genetic characteristics, as indicated by pulsed-field gel electrophoresis (PFGE), multilocus variable-number tandem-repeat analysis (MLVA), and pspAgene typing. Except for Opt MICs (4- to 64-fold higher among Optrvariants), Optrand Opt-susceptible (Opts) subpopulations originating from the same culture had identical characteristics. Sequencing of the atpCgene of the Optrvariants revealed 13 different nucleotide changes distributed among eight different codons. Changes in codon 49 were the most frequent, suggesting that this might be a hot spot for optochin resistance-conferring mutations. On the other hand, five novel types of mutations in the atpCgene (Met13Ile, Gly18Ser, Gly20Ala, Ala31Val, and Ala49Gly) were identified. In silicoprediction modeling indicated that the atpCgene mutations corresponded to alterations in the transmembrane region of the ATPase, leading to a higher hydrophobicity profile in a-helix 1 and to a lower hydrophobicity profile in a-helix 2.