Genomic analysis of community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) causing infections in children: a Spanish multicentre study

Objectives: Staphylococcus aureus is one of the most frequent human pathogens causing skin and soft tissue infections (SSTIs) among children. In this study, we investigated the molecular traits of community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) isolates causing infections in children in Spain. Methods: Ninety-eight CA-MRSA isolates causing infections in children were collected via three Spanish hospitals between 2018 and 2022. Antibiotic susceptibility testing was determined by microdilution. All genomes were fully sequenced to investigate their sequence types (STs), spa-types, staphylococcal cassette chromosome mec (SCCmec) types and their phylogenetic relationship using core genome multilocus sequence typing (cgMLST) and core genome SNP-based analyses. Antibiotic resistance, virulence and plasmid replicon genes were identified in addition to their genetic location: chromosome, plasmid or prophage. Results: Resistance rates were: erythromycin, 42.9%, which could be explained by the presence of erm(C), mph(C) and msr(A) genes; tobramycin, 27.5%, aac(6')-Ie/aph(2'')-Ia, and aadD1 genes; tetracycline, 25.5%, mainly due to tet(K) genes; levofloxacin and moxifloxacin, 19.4%, mainly due to mutations in gyrA and parC; and gentamycin, 15.3%, due to the presence of aac(6')-Ie/aph(2'')-Ia gene. We observed twenty-one different STs and forty different spa-types among the CA-MRSA isolates. The most prevalent lineage was ST8-IVc and t008. Most of the isolates were genetically diverse except for three groups of isolates from the same and from different hospitals, which had = 5 allele differences by cgMLST analysis or = 2 core SNPs by core genome SNP-based analysis. Phage-encoded PVL genes were found in 75.5% of the isolates. Other common virulence genes were related to adhesion (capA, capP), lipid degradation (geh) haemolysis (hlb, hld, hlgABC, hly/hla) and tissue destruction (sspAB). Conclusions: We observed a high genetic diversity among CA-MRSA isolates causing community acquired infections in children in Spain, with ST8-IVc as the most prevalent lineage. Nevertheless, genetic relatedness of some isolates from the same and from different hospitals suggests dissemination of CA-MRSA among children by contact.