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

Abstract

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.

Detection of Vancomycin Resistance among Methicillin-Resistant Staphylococcus aureus Strains Recovered from Children with Invasive Diseases in a Reference Pediatric Hospital

“…However, the hVISA strain recovered in this research, corresponding to ST30, exhibited similar microbiological characteristics to an hVISA strain isolated from a neonate's blood culture in Brazil in 2009 [10]. The ST30 (CC30) has been circulating in the region and Uruguay since the beginning of the burden of community-acquired MRSA (CA-MRSA) infections and remains present today [12][13][14]. Therefore, considering the proposed mechanisms for hVISA emergence, it is plausible that this specific ST had been exposed to vancomycin for an extended period, especially given the documented increase in vancomycin use in this hospital since the 2002 CA-MRSA outbreak in Uruguay [5,8].…”

Demographic fluctuations in bloodstream Staphylococcus aureus lineages configure the mobile gene pool and antimicrobial resistance

“…In large-scale population genomic studies from other parts of the world, CC5 and CC8 are also prevalent in MRSA from bloodstream infections, but other lineages are also major contributors. In a study from Argentina, Bolivia, Brazil, Paraguay, and Uruguay, CC5, CC8, and CC30 were common in 2019 38 . Lineages CC5, CC8, and CC22 were dominant in Spain from 1990 to 2019 39 .…”

Genome-based surveillance reveals cross-transmission of MRSA ST59 between humans and retail livestock products in Hanzhong, China

“…Initially being reported in North America in the early 2000s ( Enright et al, 2002 ), ST59 MRSA has gradually been replacing ST239 and ST5 human clones and become the predominant sequence type in most hospitals of China since 2010 ( Li et al, 2018 ; Jin et al, 2021 ; Wang et al, 2022 ). However, ST59 MRSA remains geographically confined and is low prevalence in Europe and North America ( Pimentel de Araujo et al, 2021 ; Di Gregorio et al, 2023 ). Previous studies have shown ST9 is the dominant LA-MRSA in China and other Asian countries as opposed to ST398 in Europe and North America ( Silva et al, 2023 ).…”