Genomic epidemiology of vancomycin resistant Enterococcus faecium (VREfm) in Latin America: Revisiting the global VRE population structure

Abstract

The prevalence of vancomycin-resistant Enterococcus faecium varies across geographical regions yet little is known about its population structure in Latin America. Here, we provide a complete genomic characterization of 55 representative Latin American VREfm recovered from 1998-2015 in 5 countries. We found that VREfm population in the region is structured into two main clinical clades without geographical clustering. To place our regional findings in context, we reconstructed the global population structure of VREfm by including 285 genomes from 36 countries from 1946-2017. Our results differ from previous studies showing an early branching of animal related isolates and a further split of clinical isolates into two sub-clades, all within clade A. The overall phylogenomic structure was highly dependent on recombination (54% of the genome) and the split between clades A and B is estimated to have occurred more than 3585 years BP. Furthermore, while the branching of animal isolates and clinical clades was predicted to have occur [~]894 years BP, our molecular clock calculations suggest that the split within the clinical clade occurred around [~]371 years BP. By including isolates from Latin America, we present novel insights into the population structure of VREfm and revisit the evolution of this pathogen.