A Prospective Cohort Multicenter Study of Molecular Epidemiology and Phylogenomics of Staphylococcus aureus Bacteremia in Nine Latin American Countries

Abstract

Staphylococcus aureus is an important pathogen 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-resistant S. aureus (MRSA) isolates. The 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 on 96 MRSA representatives. MRSA represented 45% of all (1,185 S. aureus) isolates. The majority of MRSA isolates belonged to clonal cluster (CC) 5. In Colombia and Ecuador, most isolates (≥72%) belonged to the USA300-LV lineage (CC8). Phylogenetic reconstructions indicated that MRSA isolates from participating hospitals belonged to three major clades. Clade A grouped isolates with sequence type 5 (ST5), ST105, and ST1011 (mostly staphylococcal chromosomal cassette mec [SCCmec] I and II). Clade B included ST8, ST88, ST97, and ST72 strains (SCCmec IV, subtypes a, b, and c/E), and clade C grouped mostly Argentinian MRSA belonging to ST30. In summary, CC5 MRSA was prevalent in bloodstream infections in LA with the exception of Colombia and Ecuador, where USA300-LV is now the dominant lineage. Clonal replacement appears to be a common phenomenon, and continuous surveillance is crucial to identify changes in the molecular epidemiology of MRSA.

Keywords: Latin America; Staphylococcus aureus; bacteremia.

FIG 1

Clonal distribution of MRSA isolates in Latin American hospitals included in the study. Specific genetic lineages derived from pulsed-field gel electrophoresis, SCCmec typing, and antimicrobial susceptibility testing are indicated by colors in each corresponding country. ST, sequence type; LV, Latin American variant.

FIG 2

Whole-genome maximum likelihood phylogeny of MRSA isolates. The circular representations in the phylogenetic tree show the three main clades designated A, B, and C (highlighted in gray). Major clades (A, B, and C) are composed mainly of strains from CC5, CC8, and CC30, respectively (sequence types [ST] are indicated). Each branch tip is labeled by a colored circle according to the country of isolation or if it was considered a reference strain (black). The box at the bottom shows the representation of the true distance of the phylogenetic tree.

FIG 3

Site of isolation and molecular characteristics of MRSA lineages. The rectangular transformed representation shows the three main clades (A, B, and C) highlighted in green, blue, and orange, respectively. Molecular typing characteristics of the evaluated strains are shown, including multi locus sequence type (ST), pulse field gel electrophoresis type (PFGE), staphylococcal chromosomal cassette mec type (SCCmec), and presence (+) or absence (−) of the Panton-Valentine leukocidin (PVL). ARG, Argentina; AUS, Australia; BRA, Brazil; CHL, Chile; COL, Colombia; DEU, Germany; DNK, Denmark; ECU, Ecuador; GBR, Great Britain; GTM, Guatemala; JPN, Japan; MEX, Mexico; NDL, The Netherlands; PER, Peru; SWE, Sweden; USA, United States of America; VEN, Venezuela; ARG30, Argentinian clone ST30; ARG5, Argentinian clone ST5; CH, Chilean clone; NY/JP, New York/Japan-USA100 clone; BR, Brazilian clone; NT, nontypeable; UNR, unrelated by PFGE.

FIG 4

Genomic characteristics of Latin American MRSA strains. (A) Presence (dark) and absence (light) of 2,132 antibiotic resistance genes from the ResFinder 2.1 database, and (B) the presence (black) and absence (white) of the genes in the genetic locus “copper and mercury resistance” (COMER) and “arginine catabolic mobile element” (ACME). The strains are organized according to the phylogenetic reconstruction of these strains, and the three main clades (A, B, and C) are highlighted in green, blue, and orange, respectively. (A) The genes are grouped according to the type antibiotic they confer resistance to: aminoglycosides, glycopeptides, macrolides-lincosamides-streptogramin B (MLS_B), trimethoprim (TMP), tetracyclines, beta-lactams, phenicols-lincosamides-oxazolidinones-pleuromutilins-streptogramin A (PhLOPSA), and fluoroquinolones. (B) The genetic organization of the loci COMER and ACME is shown; reference sequences were obtained from the strains CA12 (accession no. CP007672.1, regions 53520 to 77705) and USA300FPR3757 (accession no. CP000255.1, regions 63100 to 88681), respectively. TR, transcriptional regulator; Cc, cytochrome c.