Genomic epidemiology of the primary methicillin-resistant Staphylococcus aureus clones causing invasive infections in Paraguayan children

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Abstract
2. Methicillin-resistant Staphylococcus aureus (MRSA) is one of the major human pathogens, causing a wide range of infections from food poisoning to necrotizing pneumonia, endocarditis, or septicemia. It could carry numerous resistance genes and virulence factors, some of which are related to the severity of the infection, being also regarded as a potential “Super Bug”. In Paraguay, the prevalence of CC30-ST30-IV clones is the leading cause of S. aureus infections both at the regional level and in pediatric population. Here we aimed to deeply analyze the genomic features of MRSA isolates that cause invasive infections in Paraguayan children. An observational, descriptive, cross-sectional study was designed to analyze representative MRSA isolates of the main clones identified between 2009 to 2013 in Paraguayan children. All the genetically linked MRSA isolates were recovered from diverse clinical sources, patients, and hospitals at broad gap periods. Cases were primarily community-acquired, which excludes in-hospital transmission or outbreaks. MRSA isolates were analyzed with short-read paired-end sequencing and assessed for the virulome, resistome, and phylogenetic relationships. The pan-genomic analysis of these clones revealed three major and different clonal complexes (CC8, CC30, and CC5), each composed of clones closely related to each other, despite having different spa types. Furthermore, multiple virulence and resistance genes were identified for the first time in this study, pointing out the complex virulence profiles of MRSA circulating in the country. This study opens a wide range of new possibilities for future projects and trials to improve the existing knowledge on the epidemiology of MRSA circulating in Paraguay. 3. Impact statement: The increasing prevalence of methicillin-resistant Staphylococcus aureus (MRSA) is a public health problem worldwide. The most frequent MRSA clones identified in Paraguay in previous studies were (including community and hospital-acquired) the Pediatric (CC5-ST5-IV), the Cordobes-Chilean (CC5-ST5-I), the SouthWest Pacific (CC30-ST30-IV) and the Brazilian (CC8-ST239-III) clones. In this study, the pan-genomic analysis of the most representative MRSA clones circulating in invasive infection in Paraguayan children over ten years (2009-2019), such as the CC30-ST30-IV, CC5-ST5-IV, and CC8-ST8-IV, were carried out to evaluate their genetic diversity, their virulence factors repertoire, and antimicrobial resistance mechanisms revealed multiple virulences and resistance genes pointing out the complex virulence profiles of MRSA circulating in Paraguay. Our work is the first genomic study of MRSA in Paraguay and will contribute to the development of genomic surveillance in the region and our understanding of this pathogen’s global epidemiology. 4. Data summary: The authors confirm all supporting data, code and protocols have been provided within the article or through supplementary data files.

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