Genomic Epidemiology of Vancomycin-Resistant Enterococcus faecium (VREfm) in Latin America: Revisiting The Global VRE Population Structure

Abstract

Little is known about the population structure of vancomycin-resistant Enterococcus faecium (VREfm) in Latin America (LATAM). Here, we provide a complete genomic characterization of 55 representative Latin American VREfm recovered from 1998-2015 in 5 countries. The LATAM VREfm population is structured into two main clinical clades without geographical clustering. Using the LAtAM genomes, we reconstructed the global population of VREfm by including 285 genomes from 36 countries spanning from 1946 to 2017. In contrast to previous studies, our results show an early branching of animal related isolates and a further split of clinical isolates into two sub-clades within clade A. the overall phylogenomic structure of clade A was highly dependent on recombination (54% of the genome) and the split between clades A and B was estimated to have occurred more than 2,765 years ago. furthermore, our molecular clock calculations suggest the branching of animal isolates and clinical clades occurred ~502 years ago whereas the split within the clinical clade occurred ~302 years ago (previous studies showed a more recent split between clinical an animal branches around ~74 years ago). By including isolates from Latin America, we present novel insights into the population structure of VREfm and revisit the evolution of these pathogens. Enterococci are predominantly non-pathogenic gastrointestinal commensal bacteria that occasionally cause human infections. Among them, Enterococcus faecalis and Enterococcus faecium represent the species that account for most clinically relevant infections. In particular, E. faecium has been able to adapt to the hospital environment, emerging during the last few decades as a leading cause of health-care infections worldwide and becoming the most challenging enterococcal species to treat 1,2 .

Targeting ESKAPE pathogens with anti-infective medicinal plants from the Greater Mpigi region in Uganda

“…Our study identified certain extracts of these stem barks as being highly effective in inhibiting bacterial growth of multidrug-resistant strains of E. faecium and S. aureus. Enterococci are mostly commensal non-pathogenic bacteria, present in the GI tract without causing human infections 60 . However, in past decades, E. faecium strains have emerged as one of the most pervasive nosocomial pathogens worldwide that caused numerous outbreaks of serious infections 61,62 .…”

Enterococci, from Harmless Bacteria to a Pathogen

“…In the U.S., colonization of hospitalized patients with VRE rapidly increased since the first VRE detection, up to the current endemic levels in many hospitals. On the contrary, in Europe, the prevalence rates in hospitals have remained much lower and only started to increase since the year 2000 [ 17 , 20 ]. The initial reports of VRE in Europe were of organisms that were frequently isolated from healthy people, farm animals, pets, and retail food products, suggesting a large community reservoir [ 14 , 21 ], whereas such a community reservoir seemed absent in the US.…”

Vigilancia nacional de aislamientos clínicos de Enterococcus faecalis resistentes al linezolid portadores del gen optrA en Colombia, 2014-2019

“…Aunque todos los aislamientos optrA positivos de este estudio fueron E. faecalis resistentes al linezolid, cabe resaltar que un estudio que evaluó la estructura poblacional de E. faecium resistente a la vancomicina (EfmRV) en Latinoamérica ( 35 ) reportó en Colombia un aislamiento de EfmRV portador de optrA pero sensible al linezolid; este fenómeno se ha descrito previamente en China ( 14 ). A la fecha, en la vigilancia nacional solo se recibe aislamientos no sensibles al linezolid para detección de optrA , por lo cual sería necesario evaluar este gen en nuestros aislamientos de Enterococcus spp.…”