Genomic epidemiology of Staphylococcus aureus isolated from bloodstream infections in South America during 2019 supports regional surveillance (original) (raw)
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Staphylococcus aureusremains one of the leading causes of infections worldwide and a common cause of bacteremia. However, studies documenting the epidemiology ofS. aureusin South America (SA) using genomics are scarce. We hereby report on the largest to date genomic epidemiology study of both methicillin-resistantS. aureus(MRSA) and methicillin-susceptibleS. aureus(MSSA) in SA, conducted by the StaphNET-SA network. We characterised 404 genomes recovered from a prospective observational study ofS. aureusbacteremia in 58 hospitals from Argentina, Bolivia, Brazil, Paraguay and Uruguay between April and October 2019.We show that a minority ofS. aureusisolates 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 threeS. aureusgenotypes dominating the MRSA popu...
Antimicrobial agents and chemotherapy, 2017
Staphylococcus aureus are important pathogens causing a spectrum of diseases ranging from mild skin and soft tissue infections to life-threatening conditions. Bloodstream infections are particularly important and the treatment approach is complicated by the presence of methicillin resistance among S. aureus isolates (MRSA). Emergence of new genetic lineages of MRSA has occurred in Latin America (LA) with the rise and dissemination of the community-associated USA300 Latin American Variant (USA300-LV). Here, we prospectively characterized bloodstream MRSA recovered from selected hospitals in 9 Latin American countries. All isolates were typed by pulsed field gel electrophoresis (PFGE) and subjected to antibiotic susceptibility testing. Whole genome sequencing was performed in 96 MRSA representatives. MRSA represented 45% of all isolates (out of 1,185 S. aureus). The majority of MRSA isolates belonged to clonal cluster (CC) 5. In Colombia and Ecuador, most isolates (≥ 72%) belonged to ...
Methicillin-resistant Staphylococcus aureus (MRSA) is a pathogen of public health importance. In Chile, the Cordobes/Chilean clone was the predominant healthcareassociated MRSA (HA-MRSA) clone in 1998. Since then, the molecular epidemiological surveillance of MRSA has not been performed in Southern Chile.We aimed to investigate the molecular epidemiology of HA-MRSA infections in Southern Chile to identify the MRSA clones involved, and their evolutionary relationships with epidemic international MRSA lineages. A total of 303 single inpatient isolates of S. aureus were collected in the Valdivia County Hospital (2007–2008), revealing 33 % (100 MRSA/303) prevalence for HA-MRSA infections. The SCCmec types I and IV were identified in 97 % and 3 % of HA-MRSA, respectively. All isolates lacked the pvl genes. A random sample (n = 29) of all MRSAwas studied by pulsed-field gel electrophoresis (PFGE), multilocus sequence typing (MLST), SCCmec subtyping, agr and spa typing, and virulence genes profiling. PFGE analysis revealed the predominance (89 %, 26/29) of pulsotype A and three additional pulsotypes, designated H1, I33, and G1. Pulsotype A (ST5-SCCmecI-spa-t149) is clonally related to the Cordobes/Chilean clone. Pulsotype H1 (ST5-SCC mecIVNT-spa-t002) is genetically related to the Pediatric clone (ST5-SCCmecIV). Pulsotype I33 (ST5-SCCmecIVc-spa-t002) is clonally related by PFGE to the community-associated MRSA (CA-MRSA) clone spread in Argentina, I-ST5-IVa-PVL+. The G1 pulsotype (ST8-SCCmecIVc-spa-t024) is clonally related to the epidemic USA300 CA-MRSA. Here, we demonstrate the stability of the Cordobes/Chilean clone over time as the major HA-MRSA clone in Southern Chile. The identification of two CA-MRSA clones might suggest that these clones have entered into the healthcare setting from the community. These results emphasize the importance of the local surveillance of MRSA infections in the community and hospital settings.
International Journal of Infectious Diseases, 2013
Methicillin-resistant Staphylococcus aureus (MRSA) is a pathogen mainly associated with hospitals (HA-MRSA). In South America, the two predominant HA-MRSA clones are the Brazilian clone (sequence type ST239), which bears the staphylococcal cassette chromosome (SCC) mec III (MRSA-ST239-III), 1 and the Chilean/Cordobes clone (MRSA-ST5-I). 2 However, in recent years, MRSA has become an important cause of community-acquired infections (CA-MRSA). USA300 is one of the main clones representing CA-MRSA and has disseminated throughout Latin America as well as some European countries. 1,3 In Uruguay and Brazil, CA-MRSA isolates have been reported that display distinct genetic characteristics (MRSA-ST30-IVc). 4 The dissemination of CA-MRSA isolates in hospital environments was reported in Colombia in 2009. In the Andean countries (Colombia, Venezuela,
Genome Research, 2014
Methicillin-resistant Staphylococcus aureus (MRSA) is a major cause of nosocomial infection. Whole-genome sequencing of MRSA has been used to define phylogeny and transmission in well-resourced healthcare settings, yet the greatest burden of nosocomial infection occurs in resource-restricted settings where barriers to transmission are lower. Here, we study the flux and genetic diversity of MRSA on ward and individual patient levels in a hospital where transmission was common. We repeatedly screened all patients on two intensive care units for MRSA carriage over a 3-mo period. All MRSA belonged to multilocus sequence type 239 (ST 239). We defined the population structure and charted the spread of MRSA by sequencing 79 isolates from 46 patients and five members of staff, including the first MRSA-positive screen isolates and up to two repeat isolates where available. Phylogenetic analysis identified a flux of distinct ST 239 clades over time in each intensive care unit. In total, five main clades were identified, which varied in the carriage of plasmids encoding antiseptic and antimicrobial resistance determinants. Sequence data confirmed intra-and interwards transmission events and identified individual patients who were colonized by more than one clade. One patient on each unit was the source of numerous transmission events, and deep sampling of one of these cases demonstrated colonization with a ''cloud'' of related MRSA variants. The application of whole-genome sequencing and analysis provides novel insights into the transmission of MRSA in under-resourced healthcare settings and has relevance to wider global health.
2020
Methicillin Resistant Staphylococcus aureus (MRSA) remains one of the leading causes of both nosocomial and community infections worldwide. In the Philippines, MRSA rates have remained above 50% since 2010, but resistance to other antibiotics, including vancomycin, is low. The MRSA burden can be partially attributed to pathogen-specific characteristics of the circulating clones, but little was known about the S. aureus circulating clones in the Philippines. We sequenced the whole genomes of 116 S. aureus isolates collected in 2013-2014 by the Antimicrobial Resistance Surveillance Program. The multi-locus sequence type, spa type, SCC-mec type, presence of antimicrobial resistance (AMR) determinants and virulence genes, and relatedness between the isolates were all derived from the sequence data. The concordance between phenotypic and genotypic resistance was also determined. The MRSA population in the Philippines was composed of a limited number of genetic clones, including several international epidemic clones, such as CC30-spa-t019-SCCmec-IV-PVL+, CC5-SCCmec-typeIV, and ST239-spa-t030-SCCmec-typeIII. The CC30 genomes were related to the South West Pacific clone, but formed a distinct and diverse lineage, with evidence of global dissemination. We showed the independent acquisition of resistance to sulfamethoxazole/trimethoprim across different locations and genetic clones, but mostly in pediatric patients with invasive infections. The concordance between phenotypic and genotypic resistance was 99.68% overall for 8 antibiotics in 7 classes. We produced the first comprehensive genomic survey of S. aureus in the Philippines, which bridges the gap in genomic data from the Western Pacific region and will constitute the genetic background to contextualize ongoing prospective surveillance. .
BMC infectious diseases, 2017
Community-genotype methicillin-resistant Staphylococcus aureus (CG-MRSA) clones are a global concern due to their resistance and increased virulence and their ability to cause infections both hospitalized patients and healthy people in the community. Here, we characterize 32 isolates of a new CG-MRSA clone. These isolates were identified in four cities in Colombia, South America. The isolates were recovered from four different epidemiological and prospective studies that were conducted in several regions of Colombia. Molecular characterizations included multilocus sequence typing; pulsed-field gel electrophoresis; SCCmec, agr and spa typing; and whole-genome sequencing. All isolates belonged to ST923 (clonal complex 8), harbouring SCCmec IVa and a spa type t1635 and lacking an arginine catabolism mobile element. The isolates were classified as COL923, were resistant to at least one non-beta-lactam antibiotic, and exhibited high frequencies (>60%) of resistance to macrolides and t...
Genome Research, 2013
The widespread use of antibiotics in association with high-density clinical care has driven the emergence of drug-resistant bacteria that are adapted to thrive in hospitalized patients. Of particular concern are globally disseminated methicillin-resistant Staphylococcus aureus (MRSA) clones that cause outbreaks and epidemics associated with health care. The most rapidly spreading and tenacious health-care-associated clone in Europe currently is EMRSA-15, which was first detected in the UK in the early 1990s and subsequently spread throughout Europe and beyond. Using phylogenomic methods to analyze the genome sequences for 193 S. aureus isolates, we were able to show that the current pandemic population of EMRSA-15 descends from a health-care-associated MRSA epidemic that spread throughout England in the 1980s, which had itself previously emerged from a primarily community-associated methicillin-sensitive population. The emergence of fluoroquinolone resistance in this EMRSA-15 subclo...
Genomic surveillance of methicillin-resistant Staphylococcus aureus in the Philippines, 2013–2014
2021
Methicillin-resistant Staphylococcus aureus (MRSA) remains one of the leading causes of both nosocomial and community infections worldwide. In the Philippines, MRSA rates have remained above 50% since 2010, but resistance to other antibiotics, including vancomycin, is low. The MRSA burden can be partially attributed to pathogen-specific characteristics of the circulating clones, but little was known about the S. aureus clones circulating in the Philippines. We sequenced the whole genomes of 116 S. aureus isolates collected in 2013–2014 within the Antimicrobial Resistance Surveillance Program. The multilocus sequence type, spa type, SCCmec type, presence of antimicrobial resistance (AMR) determinants and virulence genes and relatedness between the isolates were all derived from the sequence data. The concordance between phenotypic and genotypic resistance was also determined. The MRSA population in the Philippines comprised a limited number of genetic clones, including several intern...