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Rios R, Reyes J, Carvajal LP, Rincon S, Panesso D, Echeverri AM, Dinh A, Kolokotronis SO, Narechania A, Tran TT, Munita JM, Murray BE, Planet PJ, Arias CA, Diaz L. Genomic Epidemiology of Vancomycin-Resistant Enterococcus faecium (VREfm) in Latin America: Revisiting The Global VRE Population Structure. Sci Rep 2020; 10:5636. [PMID: 32221315 PMCID: PMC7101424 DOI: 10.1038/s41598-020-62371-7] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Accepted: 03/10/2020] [Indexed: 12/12/2022] Open
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.
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Affiliation(s)
- Rafael Rios
- Molecular Genetics and Antimicrobial Resistance Unit, International Center for Microbial Genomics, Universidad El Bosque, Bogotá, Colombia
| | - Jinnethe Reyes
- Molecular Genetics and Antimicrobial Resistance Unit, International Center for Microbial Genomics, Universidad El Bosque, Bogotá, Colombia.,Center for Antimicrobial Resistance and Microbial Genomics, McGovern Medical School, University of Texas Health Science Center, Houston, TX, USA
| | - Lina P Carvajal
- Molecular Genetics and Antimicrobial Resistance Unit, International Center for Microbial Genomics, Universidad El Bosque, Bogotá, Colombia
| | - Sandra Rincon
- Molecular Genetics and Antimicrobial Resistance Unit, International Center for Microbial Genomics, Universidad El Bosque, Bogotá, Colombia
| | - Diana Panesso
- Molecular Genetics and Antimicrobial Resistance Unit, International Center for Microbial Genomics, Universidad El Bosque, Bogotá, Colombia.,Center for Antimicrobial Resistance and Microbial Genomics, McGovern Medical School, University of Texas Health Science Center, Houston, TX, USA.,Division of Infectious Diseases, Department of Internal Medicine, McGovern Medical School, University of Texas Health Science Center, Houston, Texas, USA
| | - Aura M Echeverri
- Molecular Genetics and Antimicrobial Resistance Unit, International Center for Microbial Genomics, Universidad El Bosque, Bogotá, Colombia
| | - An Dinh
- Center for Antimicrobial Resistance and Microbial Genomics, McGovern Medical School, University of Texas Health Science Center, Houston, TX, USA.,Division of Infectious Diseases, Department of Internal Medicine, McGovern Medical School, University of Texas Health Science Center, Houston, Texas, USA
| | - Sergios-Orestis Kolokotronis
- Institute for Comparative Genomics, American Museum of Natural History, New York, NY, USA.,Department of Epidemiology and Biostatistics, School of Public Health, SUNY Downstate Health Sciences University, Brooklyn, NY, USA
| | - Apurva Narechania
- Institute for Comparative Genomics, American Museum of Natural History, New York, NY, USA
| | - Truc T Tran
- Center for Antimicrobial Resistance and Microbial Genomics, McGovern Medical School, University of Texas Health Science Center, Houston, TX, USA.,Division of Infectious Diseases, Department of Internal Medicine, McGovern Medical School, University of Texas Health Science Center, Houston, Texas, USA
| | - Jose M Munita
- Center for Antimicrobial Resistance and Microbial Genomics, McGovern Medical School, University of Texas Health Science Center, Houston, TX, USA.,Division of Infectious Diseases, Department of Internal Medicine, McGovern Medical School, University of Texas Health Science Center, Houston, Texas, USA.,Millennium Initiative for Collaborative Research On Bacterial Resistance (MICROB-R), Santiago, Chile.,Genomics and Resistant Microbes Group, Facultad de Medicina Clinica Alemana, Universidad del Desarrollo, Santiago, Chile
| | - Barbara E Murray
- Center for Antimicrobial Resistance and Microbial Genomics, McGovern Medical School, University of Texas Health Science Center, Houston, TX, USA.,Division of Infectious Diseases, Department of Internal Medicine, McGovern Medical School, University of Texas Health Science Center, Houston, Texas, USA.,Department of Microbiology and Molecular Genetics, McGovern Medical School, University of Texas Health Science Center, Houston, Texas, USA
| | - Paul J Planet
- Institute for Comparative Genomics, American Museum of Natural History, New York, NY, USA.,Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania & Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Cesar A Arias
- Molecular Genetics and Antimicrobial Resistance Unit, International Center for Microbial Genomics, Universidad El Bosque, Bogotá, Colombia.,Center for Antimicrobial Resistance and Microbial Genomics, McGovern Medical School, University of Texas Health Science Center, Houston, TX, USA.,Division of Infectious Diseases, Department of Internal Medicine, McGovern Medical School, University of Texas Health Science Center, Houston, Texas, USA.,Millennium Initiative for Collaborative Research On Bacterial Resistance (MICROB-R), Santiago, Chile.,Department of Microbiology and Molecular Genetics, McGovern Medical School, University of Texas Health Science Center, Houston, Texas, USA
| | - Lorena Diaz
- Molecular Genetics and Antimicrobial Resistance Unit, International Center for Microbial Genomics, Universidad El Bosque, Bogotá, Colombia. .,Center for Antimicrobial Resistance and Microbial Genomics, McGovern Medical School, University of Texas Health Science Center, Houston, TX, USA. .,Millennium Initiative for Collaborative Research On Bacterial Resistance (MICROB-R), Santiago, Chile.
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Arias CA, Contreras GA, Murray BE. Management of multidrug-resistant enterococcal infections. Clin Microbiol Infect 2011; 16:555-62. [PMID: 20569266 DOI: 10.1111/j.1469-0691.2010.03214.x] [Citation(s) in RCA: 268] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Enterococci are organisms with a remarkable ability to adapt to the environment and acquire antibiotic resistance determinants. The evolution of antimicrobial resistance in these organisms poses enormous challenges for clinicians when faced with patients affected with severe infections. The increased prevalence and dissemination of multidrug-resistant Enterococcus faecium worldwide has resulted in a major decrease in therapeutic options because the majority of E. faecium isolates are now resistant to ampicillin and vancomycin, and exhibit high-level resistance to aminoglycosides, which are three of the traditionally most useful anti-enterococcal antibiotics. Newer antibiotics such as linezolid, daptomycin and tigecycline have good in vitro activity against enterococcal isolates, although their clinical use may be limited in certain clinical scenarios as a result of reduced rates of success, possible underdosing for enterococci and low serum levels, respectively, and also by the emergence of resistance. The experimental agent oritavancin may offer some hope for the treatment of vancomycin-resistant enterococci but clinical data are still lacking. Thus, optimal therapies for the treatment of multidrug-resistant enterococcal infections continue to be based on empirical observations and extrapolations from in vitro and animal data. Clinical studies evaluating new strategies, including combination therapies, to treat severe vancomycin-resistant E. faecium infections are urgently needed.
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Affiliation(s)
- C A Arias
- Department of Internal Medicine, Division of Infectious Diseases and Center for the Study of Emerging and Reemerging Pathogens, University of Texas Medical School at Houston, Houston, TX, USA
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