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

• DOI: 10.1099/mgen.0.001020
• Publication Date: 2023-05-25T14:17:59Z
• Authors: Sabrina Di Gregorio; Jesús Vielma; María Sol Haim; Lucía Rago; Josefina Campos; Mihir Kekre; Monica Abrudan; Ángela Famiglietti; Liliana Fernandez...; Gabriela Rubinstein; Martha Helena von...; Melina Herrera; Carolina Aro; Marcelo Galas; Norah Balderrama ...; Agnes Figueiredo; Nilton Lincopan; Miryan Falcon; Rosa Guillén; Teresa Camou; Gustavo Varela; David M. Aanensen; Silvia Argimón; Marta Mollerach
• Keywords: 0301 basic medicine; Epidemiology; Antibiotic resistance; Clinical Biochemistry; Bacteremia; MRSA; FOS: Health sciences; Gene; https://purl.org/becyt/ford/3.3; Antibiotics; Staphylococcal infections; Internal medicine; Research Articles; Life Sciences; Genomics; Staphylococcal Infections; Infectious Diseases; Environmental health; Molecular epidemiology; Methicillin-Resistant Staphylococcus aureus Infections; CC30; Medicine; Methicillin-resistant Staphylococcus aureus; Brazil; Methicillin-Resistant Staphylococcus aureus; Staphylococcus aureus; Genotype; Population; CC5; MSSA; CC8; Microbiology; Microbial Identification and Diagnosis; 03 medical and health sciences; Bacterial Biofilms and Quorum Sensing Mechanisms; Sepsis; Biochemistry, Genetics and Molecular Biology; Health Sciences; SOUTH AMERICA; Genetics; Humans; https://purl.org/becyt/ford/3; Panton–Valentine leukocidin; STAPHYLOCOCCUS AUREUS; Molecular Biology; Biology; Bacteria; CC398; Drug resistance; FOS: Biological sciences

Staphylococcus aureus

remains one of the leading causes of infections worldwide and a common cause of bacteraemia. However, studies documenting the epidemiology of

S. aureus

in South America using genomics are scarce. We hereby report on the largest genomic epidemiology study to date of both methicillin-resistant

S. aureus

(MRSA) and methicillin-susceptible

S. aureus

(MSSA) in South America, conducted by the StaphNET-SA network. We characterised 404 genomes recovered from a prospective observational study of

S. aureus

bacteraemia 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 community-associated(CA)-MRSA versus hospital-associated (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 fewer antimicrobial resistance 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 South America. Moreover, CC398 strains carrying ermT (largely responsible for the MLSb resistance rates of MSSA strains: inducible iMLSb phenotype) and sh_fabI (related to triclosan resistance) were recovered from both CA and HA origin. The frequency of MRSA and MSSA lineages differed between countries but the most prevalent

S. aureus

genotypes are high-risk clones widely distributed in the South American region without a clear country-specific phylogeographical structure. Therefore, our findings underline the need for continuous genomic surveillance by regional networks such as StaphNET-SA. This article contains data hosted by Microreact.