Genomic epidemiology of S. aureus isolated from bloodstream infections in South America during 2019 supports regional surveillance

Staphylococcus aureus remains one of the leading causes of infections worldwide and a common cause of bacteremia. However, studies documenting the epidemiology of S. aureus in South America (SA) using genomics are scarce. We hereby report on the largest to date genomic epidemiology study of both methicillin-resistant S. aureus (MRSA) and methicillin-susceptible S. aureus (MSSA) in SA, conducted by the StaphNET-SA network. We characterised 404 genomes recovered from a prospective observational study of S. aureus bacteremia in 58 hospitals from Argentina, Bolivia, Brazil, Paraguay and Uruguay between April and October 2019. We show that a minority of S. aureus isolates are phenotypically multi-drug resistant (5.2%), but more than a quarter are resistant to macrolide-lincosamide-streptogramin B (MLSb). MSSA were more genetically diverse than MRSA. Lower rates of associated antimicrobial resistance in CA-MRSA vs HA-MRSA were found in association with three S. aureus genotypes dominating the MRSA population: CC30-MRSA-IVc-t019-lukS/F-PV+, CC5-MRSA-IV-t002-lukS/F-PV-, and CC8-MRSA-IVc-t008-lukS/F-PV+-COMER+. These are historically from a CA origin, carry on average less AMR determinants, and often lack key virulence genes. Surprisingly, CC398-MSSA-t1451-lukS/F-PV- related to the CC398 human-associated lineage is widely disseminated throughout the region, and is described here for the first time as the most prevalent MSSA lineage in SA. Moreover, CC398 strains carrying ermT and sh_fabI (related to triclosan resistance) were recovered from both CA and HA origin, and are largely responsible for the MLSb rates of MSSA strains (inducible iMLSb phenotype). The frequency of MRSA and MSSA lineages differed between countries but the most prevalent S. aureus genotypes are high-risk clones widespread in the South American region without clear country-specific phylogeographic structure. Therefore our findings underscore the need for continuous genomic surveillance by regional networks such as StaphNET-SA.