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Bezdicek M, Hanslikova J, Nykrynova M, Dufkova K, Kocmanova I, Kubackova P, Mayer J, Lengerova M. New Multilocus Sequence Typing Scheme for Enterococcus faecium Based on Whole Genome Sequencing Data. Microbiol Spectr 2023; 11:e0510722. [PMID: 37306567 PMCID: PMC10434285 DOI: 10.1128/spectrum.05107-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 05/24/2023] [Indexed: 06/13/2023] Open
Abstract
The MLST scheme currently used for Enterococcus faecium typing was designed in 2002 and is based on putative gene functions and Enterococcus faecalis gene sequences available at that time. As a result, the original MLST scheme does not correspond to the real genetic relatedness of E. faecium strains and often clusters genetically distant strains to the same sequence types (ST). Nevertheless, typing has a significant impact on the subsequent epidemiological conclusions and introduction of appropriate epidemiological measures, thus it is crucial to use a more accurate MLST scheme. Based on the genome analysis of 1,843 E. faecium isolates, a new scheme, consisting of 8 highly discriminative loci, was created in this study. These strains were divided into 421 STs using the new MLST scheme, as opposed to 223 STs assigned by the original MLST scheme. The proposed MLST has a discriminatory power of D = 0.983 (CI95% 0.981 to 0.984), compared to the original scheme's D = 0.919 (CI95% 0.911 to 0.927). Moreover, we identified new clonal complexes with our newly designed MLST scheme. The scheme proposed here is available within the PubMLST database. Although whole genome sequencing availability has increased rapidly, MLST remains an integral part of clinical epidemiology, mainly due to its high standardization and excellent robustness. In this study, we proposed and validated a new MLST scheme for E. faecium, which is based on genome-wide data and thus reflects the tested isolates' more accurate genetic similarity. IMPORTANCE Enterococcus faecium is one of the most important pathogens causing health care associated infections. One of the main reasons for its clinical importance is a rapidly spreading resistance to vancomycin and linezolid, which significantly complicates antibiotic treatment of infections caused by such resistant strains. Monitoring the spread and relationships between resistant strains causing severe conditions represents an important tool for implementing appropriate preventive measures. Therefore, there is an urgent need to establish a robust method enabling strain monitoring and comparison at the local, national, and global level. Unfortunately, the current, extensively used MLST scheme does not reflect the real genetic relatedness between individual strains and thus does not provide sufficient discriminatory power. This can lead directly to incorrect epidemiological measures due to insufficient accuracy and biased results.
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Affiliation(s)
- Matej Bezdicek
- Department of Internal Medicine - Haematology and Oncology, University Hospital Brno, Brno, Czech Republic
- Department of Internal Medicine - Haematology and Oncology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Jana Hanslikova
- Department of Internal Medicine - Haematology and Oncology, University Hospital Brno, Brno, Czech Republic
| | - Marketa Nykrynova
- Department of Internal Medicine - Haematology and Oncology, University Hospital Brno, Brno, Czech Republic
- Department of Biomedical Engineering, Brno University of Technology, Brno, Czech Republic
| | - Kristyna Dufkova
- Department of Internal Medicine - Haematology and Oncology, University Hospital Brno, Brno, Czech Republic
- Department of Internal Medicine - Haematology and Oncology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Iva Kocmanova
- Department of Clinical Microbiology and Immunology, University Hospital Brno, Brno, Czech Republic
| | - Petra Kubackova
- Department of Clinical Microbiology and Immunology, University Hospital Brno, Brno, Czech Republic
| | - Jiri Mayer
- Department of Internal Medicine - Haematology and Oncology, University Hospital Brno, Brno, Czech Republic
- Department of Internal Medicine - Haematology and Oncology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Martina Lengerova
- Department of Internal Medicine - Haematology and Oncology, University Hospital Brno, Brno, Czech Republic
- Department of Internal Medicine - Haematology and Oncology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
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Wen Z, Liu F, Zhang P, Wei Y, Shi Y, Zheng J, Li G, Yu Z, Xu Z, Deng Q, Chen Z. In vitro activity and adaptation strategies of eravacycline in clinical Enterococcus faecium isolates from China. J Antibiot (Tokyo) 2022; 75:498-508. [PMID: 35896611 DOI: 10.1038/s41429-022-00546-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 06/30/2022] [Accepted: 07/03/2022] [Indexed: 11/09/2022]
Abstract
Eravacycline (Erava) is a synthetic fluorocycline with potent antimicrobial activity against a wide range of Gram-positive bacteria. This study aimed to investigate the in vitro antimicrobial activity and resistance mechanism of Erava in clinical E. faecium isolates from China. Erava minimum inhibitory concentrations (MICs) against clinical E. faecium isolates-including those resistant to linezolid (LZD) or harboring the tetracycline (Tet) resistance genes was ≤0.25 mg l-1. Moreover, our data indicated that clinical isolates of E. faecium with Erava MIC 0.25 mg l-1 were predominantly shown to belong to Sequence-type 78 (ST78) and ST80. The prevalence of Erava heteroresistance in clinical E. faecium strain was 2.46% (3/122). The increased Erava MIC values of heteroresistance-derived E. faecium clones could be significantly reduced by efflux pump inhibitors (EPIs). Furthermore, comparative proteomics results showed that efflux pumps lmrA, mdlA, and mdlB contributed significantly to the acquisition of Erava resistance in E. faecium. In addition, a genetic mutation in 16 S rRNA (G190A) were detected in resistant E. faecium isolates induced by Erava. In summary, Erava exhibits potent in vitro antimicrobial activity against E. faecium, but mutation of Tet target sites and elevated expression of efflux pumps under Erava selection results in Erava resistance.
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Affiliation(s)
- Zewen Wen
- Department of Infectious Diseases and Shenzhen Key Lab of Endogenous Infection, Shenzhen Nanshan People's Hospital and the 6th affiliated hospital of Guangdong Medical University, Shenzhen, 518052, China.,Quality Control Center of Hospital Infection Management of Shenzhen, Huazhong University of Science and Technology Union Shenzhen Hospital, Shenzhen, 518052, China
| | - Fangfang Liu
- Department of Infectious Diseases and Shenzhen Key Lab of Endogenous Infection, Shenzhen Nanshan People's Hospital and the 6th affiliated hospital of Guangdong Medical University, Shenzhen, 518052, China.,Quality Control Center of Hospital Infection Management of Shenzhen, Huazhong University of Science and Technology Union Shenzhen Hospital, Shenzhen, 518052, China
| | - Peixing Zhang
- Department of Infectious Diseases and Shenzhen Key Lab of Endogenous Infection, Shenzhen Nanshan People's Hospital and the 6th affiliated hospital of Guangdong Medical University, Shenzhen, 518052, China.,Quality Control Center of Hospital Infection Management of Shenzhen, Huazhong University of Science and Technology Union Shenzhen Hospital, Shenzhen, 518052, China
| | - Ying Wei
- Heilongjiang Medical Service Management Evaluation Center, Harbin, Heilongjiang, 150031, China
| | - Yiyi Shi
- Department of Infectious Diseases and Shenzhen Key Lab of Endogenous Infection, Shenzhen Nanshan People's Hospital and the 6th affiliated hospital of Guangdong Medical University, Shenzhen, 518052, China.,Quality Control Center of Hospital Infection Management of Shenzhen, Huazhong University of Science and Technology Union Shenzhen Hospital, Shenzhen, 518052, China
| | - Jinxin Zheng
- Department of Infectious Diseases and Shenzhen Key Lab of Endogenous Infection, Shenzhen Nanshan People's Hospital and the 6th affiliated hospital of Guangdong Medical University, Shenzhen, 518052, China.,Quality Control Center of Hospital Infection Management of Shenzhen, Huazhong University of Science and Technology Union Shenzhen Hospital, Shenzhen, 518052, China
| | - Guiqiu Li
- Quality Control Center of Hospital Infection Management of Shenzhen, Huazhong University of Science and Technology Union Shenzhen Hospital, Shenzhen, 518052, China.,The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, 150001, China
| | - Zhijian Yu
- Department of Infectious Diseases and Shenzhen Key Lab of Endogenous Infection, Shenzhen Nanshan People's Hospital and the 6th affiliated hospital of Guangdong Medical University, Shenzhen, 518052, China.,Quality Control Center of Hospital Infection Management of Shenzhen, Huazhong University of Science and Technology Union Shenzhen Hospital, Shenzhen, 518052, China
| | - Zhicao Xu
- Department of Infectious Diseases and Shenzhen Key Lab of Endogenous Infection, Shenzhen Nanshan People's Hospital and the 6th affiliated hospital of Guangdong Medical University, Shenzhen, 518052, China. .,Quality Control Center of Hospital Infection Management of Shenzhen, Huazhong University of Science and Technology Union Shenzhen Hospital, Shenzhen, 518052, China.
| | - Qiwen Deng
- Department of Infectious Diseases and Shenzhen Key Lab of Endogenous Infection, Shenzhen Nanshan People's Hospital and the 6th affiliated hospital of Guangdong Medical University, Shenzhen, 518052, China. .,Quality Control Center of Hospital Infection Management of Shenzhen, Huazhong University of Science and Technology Union Shenzhen Hospital, Shenzhen, 518052, China.
| | - Zhong Chen
- Department of Infectious Diseases and Shenzhen Key Lab of Endogenous Infection, Shenzhen Nanshan People's Hospital and the 6th affiliated hospital of Guangdong Medical University, Shenzhen, 518052, China. .,Quality Control Center of Hospital Infection Management of Shenzhen, Huazhong University of Science and Technology Union Shenzhen Hospital, Shenzhen, 518052, China.
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Wongnak K, Pattanachaiwit S, Rattanasirirat W, Limsrivanichakorn S, Kiratisin P, Assanasen S, Leelaporn A. First characterization of Tn1546-like structures of vancomycin-resistant Enterococcus faecium Thai isolates. J Infect Chemother 2021; 27:991-998. [PMID: 33663929 DOI: 10.1016/j.jiac.2021.02.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Revised: 02/07/2021] [Accepted: 02/10/2021] [Indexed: 10/22/2022]
Abstract
INTRODUCTION Vancomycin-resistant Enterococcus faecium (VREfm) carrying vanA was first isolated from patient at Siriraj Hospital, Thailand in 2004. Since then, VREfm isolates have been detected increasingly in this 2500-bed university hospital. To understand the epidemiology of vanA VREfm in this setting, the isolates collected during 2004-2013 were characterized. METHODS A total of 49 vanA VREfm isolates previously confirmed by multiplex PCR were characterized by determining resistance phenotypes to vancomycin, teicoplanin, ampicillin and ciprofloxacin by broth microdilution method. Multilocus sequence typing (MLST) and virulence genes of those isolates were investigated. The Tn1546 structure diversity was studied by long-range overlapping PCR and primer walking sequencing. RESULTS Of all isolates studied, 9 sequence types (ST17, ST80, ST78, ST730, ST203, ST18, ST280, ST64, ST323) in clonal complex 17 and a novel ST1051 were revealed. The esp-positive isolates were 73.5%. Of all vanA operons characterized, at least 9 types of Tn1546-like structures were detected. All of vanA determinants contained 5'-end different from the Tn1546 prototype. Approximately 47% of them also carried the insertion sequence IS1251 at the intergenic region between vanS and vanH. Interestingly, another IS (ISEfa4) was found to be inside the sequence of IS1251 in ST17 isolate. CONCLUSION Heterogeneity of vanA VREfm was observed. Nearly all of isolates studied belonged to CC17. One novel ST1051 strain was detected. Isolates in the initial period carried vanA operon similar to the prototype. The diversity of vanA determinants has been increased in the recent isolates. A novel vanA operon structure was detected.
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Affiliation(s)
- Kornikar Wongnak
- Department of Microbiology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkoknoi, Bangkok, 10700, Thailand
| | - Supanit Pattanachaiwit
- Department of Microbiology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkoknoi, Bangkok, 10700, Thailand
| | - Wasinee Rattanasirirat
- Department of Microbiology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkoknoi, Bangkok, 10700, Thailand
| | - Sunee Limsrivanichakorn
- Department of Microbiology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkoknoi, Bangkok, 10700, Thailand
| | - Pattarachai Kiratisin
- Department of Microbiology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkoknoi, Bangkok, 10700, Thailand
| | - Susan Assanasen
- Department of Medicine, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkoknoi, Bangkok, 10700, Thailand
| | - Amornrut Leelaporn
- Department of Microbiology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkoknoi, Bangkok, 10700, Thailand.
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Zhou X, Willems RJL, Friedrich AW, Rossen JWA, Bathoorn E. Enterococcus faecium: from microbiological insights to practical recommendations for infection control and diagnostics. Antimicrob Resist Infect Control 2020; 9:130. [PMID: 32778149 PMCID: PMC7418317 DOI: 10.1186/s13756-020-00770-1] [Citation(s) in RCA: 96] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Accepted: 07/02/2020] [Indexed: 02/08/2023] Open
Abstract
Early in its evolution, Enterococcus faecium acquired traits that allowed it to become a successful nosocomial pathogen. E. faecium inherent tenacity to build resistance to antibiotics and environmental stressors that allows the species to thrive in hospital environments. The continual wide use of antibiotics in medicine has been an important driver in the evolution of E. faecium becoming a highly proficient hospital pathogen.For successful prevention and reduction of nosocomial infections with vancomycin resistant E. faecium (VREfm), it is essential to focus on reducing VREfm carriage and spread. The aim of this review is to incorporate microbiological insights of E. faecium into practical infection control recommendations, to reduce the spread of hospital-acquired VREfm (carriage and infections). The spread of VREfm can be controlled by intensified cleaning procedures, antibiotic stewardship, rapid screening of VREfm carriage focused on high-risk populations, and identification of transmission routes through accurate detection and typing methods in outbreak situations. Further, for successful management of E. faecium, continual innovation in the fields of diagnostics, treatment, and eradication is necessary.
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Affiliation(s)
- Xuewei Zhou
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.
| | - Rob J L Willems
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Alexander W Friedrich
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - John W A Rossen
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Erik Bathoorn
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
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Scaccia N, Vaz-Moreira I, Manaia CM. Persistence of wastewater antibiotic resistant bacteria and their genes in human fecal material. FEMS Microbiol Ecol 2020; 96:5815073. [PMID: 32239211 DOI: 10.1093/femsec/fiaa058] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Accepted: 03/27/2020] [Indexed: 01/11/2023] Open
Abstract
Domestic wastewater is a recognized source of antibiotic resistant bacteria and antibiotic resistance genes (ARB&ARGs), whose risk of transmission to humans cannot be ignored. The fitness of wastewater ARB in the complex fecal microbiota of a healthy human was investigated in feces-based microcosm assays (FMAs). FMAs were inoculated with two wastewater isolates, Escherichia coli strain A2FCC14 (MLST ST131) and Enterococcus faecium strain H1EV10 (MLST ST78), harboring the ARGs blaTEM, blaCTX, blaOXA-A and vanA, respectively. The FMAs, incubated in the presence or absence of oxygen or in the presence or absence of the antibiotics cefotaxime or vancomycin, were monitored based on cultivation, ARGs quantification and bacterial community analysis. The fecal bacterial community was dominated by members of the phyla Firmicutes, Bacteroidetes, Actinobacteria, Proteobacteria and Verrucomicrobia. The ARGs harbored by the wastewater isolates could be quantified after one week, in FMAs incubated under both aerobic and anaerobic conditions. These observations were not significantly different in FMAs incubated anaerobically, supplemented with sub-inhibitory concentrations of cefotaxime or vancomycin. The observation that ARGs of wastewater ARB persisted in presence of the human fecal microbiota for at least one week supports the hypothesis of a potential transmission to humans, a topic that deserves further investigation.
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Affiliation(s)
- Nazareno Scaccia
- Universidade Católica Portuguesa, CBQF - Centro de Biotecnologia e Química Fina - Laboratório Associado, Escola Superior de Biotecnologia, Rua Diogo Botelho 1327, 4169-005 Porto, Portugal
| | - Ivone Vaz-Moreira
- Universidade Católica Portuguesa, CBQF - Centro de Biotecnologia e Química Fina - Laboratório Associado, Escola Superior de Biotecnologia, Rua Diogo Botelho 1327, 4169-005 Porto, Portugal
| | - Célia M Manaia
- Universidade Católica Portuguesa, CBQF - Centro de Biotecnologia e Química Fina - Laboratório Associado, Escola Superior de Biotecnologia, Rua Diogo Botelho 1327, 4169-005 Porto, Portugal
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Bayjanov JR, Baan J, Rogers MRC, Troelstra A, Willems RJL, van Schaik W. Enterococcus faecium genome dynamics during long-term asymptomatic patient gut colonization. Microb Genom 2019; 5:e000277. [PMID: 31166888 PMCID: PMC6700664 DOI: 10.1099/mgen.0.000277] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Accepted: 05/24/2019] [Indexed: 11/18/2022] Open
Abstract
Enterococcus faecium is a gut commensal of humans and animals. In addition, it has recently emerged as an important nosocomial pathogen through the acquisition of genetic elements that confer resistance to antibiotics and virulence. We performed a whole-genome sequencing-based study on 96 multidrug-resistant E. faecium strains that asymptomatically colonized five patients with the aim of describing the genome dynamics of this species. The patients were hospitalized on multiple occasions and isolates were collected over periods ranging from 15 months to 6.5 years. Ninety-five of the sequenced isolates belonged to E. faecium clade A1, which was previously determined to be responsible for the vast majority of clinical infections. The clade A1 strains clustered into six clonal groups of highly similar isolates, three of which consisted entirely of isolates from a single patient. We also found evidence of concurrent colonization of patients by multiple distinct lineages and transfer of strains between patients during hospitalization. We estimated the evolutionary rate of two clonal groups that each colonized single patients at 12.6 and 25.2 single-nucleotide polymorphisms (SNPs)/genome/year. A detailed analysis of the accessory genome of one of the clonal groups revealed considerable variation due to gene gain and loss events, including the chromosomal acquisition of a 37 kbp prophage and the loss of an element containing carbohydrate metabolism-related genes. We determined the presence and location of 12 different insertion sequence (IS) elements, with ISEfa5 showing a unique pattern of location in 24 of the 25 isolates, suggesting widespread ISEfa5 excision and insertion into the genome during gut colonization. Our findings show that the E. faecium genome is highly dynamic during asymptomatic colonization of the human gut. We observed considerable genomic flexibility due to frequent horizontal gene transfer and recombination, which can contribute to the generation of genetic diversity within the species and, ultimately, can contribute to its success as a nosocomial pathogen.
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Affiliation(s)
- Jumamurat R. Bayjanov
- Department of Medical Microbiology, University Medical Center Utrecht, 3584CX Utrecht, The Netherlands
| | - Jery Baan
- Department of Medical Microbiology, University Medical Center Utrecht, 3584CX Utrecht, The Netherlands
| | - Malbert R. C. Rogers
- Department of Medical Microbiology, University Medical Center Utrecht, 3584CX Utrecht, The Netherlands
| | - Annet Troelstra
- Department of Medical Microbiology, University Medical Center Utrecht, 3584CX Utrecht, The Netherlands
| | - Rob J. L. Willems
- Department of Medical Microbiology, University Medical Center Utrecht, 3584CX Utrecht, The Netherlands
| | - Willem van Schaik
- Department of Medical Microbiology, University Medical Center Utrecht, 3584CX Utrecht, The Netherlands
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
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Vancomycin-resistant Enterococcus faecium at a university hospital in Taiwan, 2002-2015: Fluctuation of genetic populations and emergence of a new structure type of the Tn1546-like element. JOURNAL OF MICROBIOLOGY, IMMUNOLOGY, AND INFECTION = WEI MIAN YU GAN RAN ZA ZHI 2018; 51:821-828. [PMID: 30201132 DOI: 10.1016/j.jmii.2018.08.008] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Revised: 08/17/2018] [Accepted: 08/18/2018] [Indexed: 11/24/2022]
Abstract
BACKGROUND/PURPOSES Vancomycin resistance increased significantly to 31.3% among Enterococcus faecium in 2006 and remained high thereafter at a university hospital in Taiwan. A longitudinal study was retrospectively conducted to characterize these vancomycin-resistant E. faecium (VRE-fm). METHODS A total of 378 non-repetitive VRE-fm blood isolates collected during 2002-2015 were studied. Multilocus sequence typing, pulsed-field gel electrophoresis, analysis of van genes and the Tn1546 structure, and conjugation experiments were performed. RESULTS The majority (78.0%) of the isolates were associated with hospital-acquired infections. Molecular typing revealed nine major pulsotypes and five predominant sequence types (STs): ST17 (33.9%), ST78 (18.3%), ST414 (14.6%), ST18 (10.6%), and ST203 (7.4%). Fluctuation of these prevailing STs among the study years in association with some major pulsotypes was noted. All isolates carried vanA genes, except that in four isolates vanB genes were found. Among the vanA-carrying Tn1546-like elements, one predominant structure type (Type I, 55.9%) was noted throughout the study years. Since 2009, another predominant structure type (Type II, 40.1%) has emerged firstly in ST414 and gradually spread to other 11 STs in subsequent years. Isolates carrying these Type II Tn1546-like elements have become the most predominant population since 2014, majorly found in ST78 and ST17. Preliminary experiments indicated that plasmids carrying the Type II Tn1546-like elements demonstrated ten-fold higher efficiency than those carrying the Type I Tn1546-like elements. CONCLUSION Dissemination of some major STs and horizontal transfer of plasmids carrying two major structure types of Tn1546-like elements may have together contributed to the increase of VRE-fm infection.
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Akpaka PE, Kissoon S, Jayaratne P, Wilson C, Golding GR, Nicholson AM, Lewis DB, Hermelijn SM, Wilson-Pearson A, Smith A. Genetic characteristics and molecular epidemiology of vancomycin-resistant Enterococci isolates from Caribbean countries. PLoS One 2017; 12:e0185920. [PMID: 29020115 PMCID: PMC5636112 DOI: 10.1371/journal.pone.0185920] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Accepted: 09/21/2017] [Indexed: 12/20/2022] Open
Abstract
Emergence of vancomycin-resistant Enterococci (VRE) that first appeared on the stage about three decades ago is now a major concern worldwide as it has globally reached every continent. Our aim was to simply undertake a multinational study to delineate the resistance and virulence genes of clinical isolates of VRE isolates from the Caribbean. We employed both conventional (standard microbiological methods including use of E-test strips, chromogenic agar) and molecular methods (polymerase chain reactions–PCR, pulsed-field gel electrophoresis–PFGE and multilocus sequence typing–MLST) to analyze and characterize 245 Enterococci species and 77 VRE isolates from twelve hospitals from eight countries in the Caribbean. The PCR confirmed and demonstrated the resistance and virulence genes (vanA and esp) among all confirmed VRE isolates. The PFGE delineated clonally related isolates from patients from the same country and other countries in the region. The main sequence types of the VRE isolates from the region included STs 412, 750, 203, 736 and 18, all from the common ancestor for clonal complex 17 (CC17). Despite this common ancestor and association of outbreaks of this lineage clones, there has been no reports of outbreaks of infection by VRE in several hospitals in the Caribbean.
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Affiliation(s)
- Patrick Eberechi Akpaka
- The University of the West Indies, Paraclinical Sciences, St. Augustine, Trinidad & Tobago
- * E-mail:
| | - Shivnarine Kissoon
- The University of the West Indies, Paraclinical Sciences, St. Augustine, Trinidad & Tobago
| | - Padman Jayaratne
- McMaster University, Department of Pathological Sciences, Hamilton, Canada
| | - Clyde Wilson
- King Edward VII Memorial Hospital, Department of Pathology and Microbiology, Hamilton, Bermuda
| | - George R. Golding
- Public Health Agency of Canada, National Microbiology Laboratory, Winnipeg, Canada
| | - Alison M. Nicholson
- The University of the West Indies, Department of Microbiology, Mona—Kingston, Jamaica
| | - Delores B. Lewis
- The University of the West Indies, Faculty of Medical Sciences, Cave Hill, Barbados
| | - Sandra M. Hermelijn
- Academic Hospital Paramaribo, Medical Microbiology Laboratory, Paramaribo, Suriname
| | | | - Ashley Smith
- King Edward VII Memorial Hospital, Department of Pharmacy, Hamilton, Bermuda
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Wardal E, Kuch A, Gawryszewska I, Żabicka D, Hryniewicz W, Sadowy E. Diversity of plasmids and Tn1546-type transposons among VanA Enterococcus faecium in Poland. Eur J Clin Microbiol Infect Dis 2016; 36:313-328. [PMID: 27752789 PMCID: PMC5253160 DOI: 10.1007/s10096-016-2804-8] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Accepted: 09/26/2016] [Indexed: 10/26/2022]
Abstract
The objective of this study was to investigate the antimicrobial resistance, Tn1546 transposon variability and plasmid diversity among Polish vancomycin-resistant Enterococcus faecium (VREfm) isolates of VanA phenotype in the context of their clonal structure. Two hundred sixteen clinical VREfm isolates collected between 1997 and 2010 were studied by antimicrobial susceptibility testing, MLST, MLVA and detection of IS16, esp Efm, pilA, intA and plasmid-specific genes by PCR. Tn1546 structure was revealed by overlapping PCR and sequencing. Selected isolates were subjected to PFGE-S1 and Southern hybridization analyses. The vast majority of the isolates (95.8 %) belonged to lineages 17/18 (during the whole study period 1997-2010) and 78 (mostly in 2006-2010) of hospital-adapted meroclone of E. faecium. All isolates displayed a multi-drug resistance phenotype. Twenty-eight Tn1546 types (including 26 novel ones) were associated with eight different ISs (IS1216, IS1251, ISEfa4, ISEfa5, ISEfm2, ISEf1, IS3-like, ISEfm1-like). The vanA-determinant was typically located on plasmids, which most commonly carried rep2pRE25, rep17pRUM, rep18pEF418, rep1pIP501, ω-ε-ζ and axe-txe genes. VanA isolates from 1997-2005 to 2006-2010 differed in clonal composition, prevalence of gentamicin- and tetracycline-resistance and plasmidome. Our analysis revealed high complexity of Tn1546-type transposons and vanA-plasmids, and suggested that diverse genetic events, such as conjugation transfer, recombination, chromosomal integration and DNA mutations shaped the structure of these elements among Polish VREfm.
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Affiliation(s)
- E Wardal
- Department of Molecular Microbiology, National Medicines Institute, Chełmska 30/34, 00-725, Warsaw, Poland
| | - A Kuch
- Department of Epidemiology and Clinical Microbiology, National Medicines Institute, Chełmska 30/34, 00-725, Warsaw, Poland
| | - I Gawryszewska
- Department of Molecular Microbiology, National Medicines Institute, Chełmska 30/34, 00-725, Warsaw, Poland
| | - D Żabicka
- Department of Epidemiology and Clinical Microbiology, National Medicines Institute, Chełmska 30/34, 00-725, Warsaw, Poland
| | - W Hryniewicz
- Department of Epidemiology and Clinical Microbiology, National Medicines Institute, Chełmska 30/34, 00-725, Warsaw, Poland
| | - E Sadowy
- Department of Molecular Microbiology, National Medicines Institute, Chełmska 30/34, 00-725, Warsaw, Poland.
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Pinholt M, Gumpert H, Bayliss S, Nielsen JB, Vorobieva V, Pedersen M, Feil E, Worning P, Westh H. Genomic analysis of 495 vancomycin-resistant Enterococcus faecium reveals broad dissemination of a vanA plasmid in more than 19 clones from Copenhagen, Denmark. J Antimicrob Chemother 2016; 72:40-47. [PMID: 27605596 DOI: 10.1093/jac/dkw360] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Revised: 07/23/2016] [Accepted: 08/02/2016] [Indexed: 01/21/2023] Open
Abstract
OBJECTIVES From 2012 to 2014, there has been a huge increase in vancomycin-resistant (vanA) Enterococcus faecium (VREfm) in Copenhagen, Denmark, with 602 patients infected or colonized with VREfm in 2014 compared with just 22 in 2012. The objective of this study was to describe the genetic epidemiology of VREfm to assess the contribution of clonal spread and horizontal transfer of the vanA transposon (Tn1546) and plasmid in the dissemination of VREfm in hospitals. METHODS VREfm from Copenhagen, Denmark (2012-14) were whole-genome sequenced. The clonal structure was determined and the structure of Tn1546-like transposons was characterized. One VREfm isolate belonging to the largest clonal group was sequenced using long-read technology to close a 37 kb vanA plasmid. RESULTS Phylogeny revealed a polyclonal structure where 495 VREfm isolates were divided into 13 main groups and 7 small groups. The majority of the isolates were located in three groups (n = 44, 100 and 218) and clonal spread of VREfm between wards and hospitals was identified. Five Tn1546-like transposon types were identified. A dominant truncated transposon (type 4, 92%) was spread across all but one VREfm group. The closed vanA plasmid was highly covered by reads from isolates containing the type 4 transposon. CONCLUSIONS This study suggests that it was the dissemination of the type 4 Tn1546-like transposon and plasmid via horizontal transfer to multiple populations of E. faecium, followed by clonal spread of new VREfm clones, that contributed to the increase in and diversity of VREfm in Danish hospitals.
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Affiliation(s)
- Mette Pinholt
- Department of Clinical Microbiology, Hvidovre University Hospital, Hvidovre, Denmark .,Institute of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Heidi Gumpert
- Department of Clinical Microbiology, Hvidovre University Hospital, Hvidovre, Denmark
| | - Sion Bayliss
- Department of Biology and Biochemistry, University of Bath, Bath, UK
| | - Jesper B Nielsen
- Department of Clinical Microbiology, Hvidovre University Hospital, Hvidovre, Denmark
| | - Veronika Vorobieva
- Department of Clinical Microbiology, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Michael Pedersen
- Department of Clinical Microbiology, Herlev University Hospital, Herlev, Denmark
| | - Edward Feil
- Department of Biology and Biochemistry, University of Bath, Bath, UK
| | - Peder Worning
- Department of Clinical Microbiology, Hvidovre University Hospital, Hvidovre, Denmark
| | - Henrik Westh
- Department of Clinical Microbiology, Hvidovre University Hospital, Hvidovre, Denmark.,Institute of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
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11
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Freitas AR, Tedim AP, Francia MV, Jensen LB, Novais C, Peixe L, Sánchez-Valenzuela A, Sundsfjord A, Hegstad K, Werner G, Sadowy E, Hammerum AM, Garcia-Migura L, Willems RJ, Baquero F, Coque TM. Multilevel population genetic analysis ofvanAandvanB Enterococcus faeciumcausing nosocomial outbreaks in 27 countries (1986–2012). J Antimicrob Chemother 2016; 71:3351-3366. [DOI: 10.1093/jac/dkw312] [Citation(s) in RCA: 112] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2016] [Revised: 06/11/2016] [Accepted: 07/05/2016] [Indexed: 01/17/2023] Open
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12
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Detection of Vancomycin-Resistant Enterococci. Mol Microbiol 2016. [DOI: 10.1128/9781555819071.ch18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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13
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Molecular characterization of resistance, virulence and clonality in vancomycin-resistant Enterococcus faecium and Enterococcus faecalis : A hospital-based study in Beijing, China. INFECTION GENETICS AND EVOLUTION 2015; 33:253-60. [DOI: 10.1016/j.meegid.2015.05.012] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2015] [Revised: 05/10/2015] [Accepted: 05/11/2015] [Indexed: 11/21/2022]
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14
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Mikalsen T, Pedersen T, Willems R, Coque TM, Werner G, Sadowy E, van Schaik W, Jensen LB, Sundsfjord A, Hegstad K. Investigating the mobilome in clinically important lineages of Enterococcus faecium and Enterococcus faecalis. BMC Genomics 2015; 16:282. [PMID: 25885771 PMCID: PMC4438569 DOI: 10.1186/s12864-015-1407-6] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2014] [Accepted: 02/27/2015] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND The success of Enterococcus faecium and E. faecalis evolving as multi-resistant nosocomial pathogens is associated with their ability to acquire and share adaptive traits, including antimicrobial resistance genes encoded by mobile genetic elements (MGEs). Here, we investigate this mobilome in successful hospital associated genetic lineages, E. faecium sequence type (ST)17 (n=10) and ST78 (n=10), E. faecalis ST6 (n=10) and ST40 (n=10) by DNA microarray analyses. RESULTS The hybridization patterns of 272 representative targets including plasmid backbones (n=85), transposable elements (n=85), resistance determinants (n=67), prophages (n=29) and clustered regularly interspaced short palindromic repeats (CRISPR)-cas sequences (n=6) separated the strains according to species, and for E. faecalis also according to STs. RCR-, Rep_3-, RepA_N- and Inc18-family plasmids were highly prevalent and with the exception of Rep_3, evenly distributed between the species. There was a considerable difference in the replicon profile, with rep 17/pRUM , rep 2/pRE25 , rep 14/EFNP1 and rep 20/pLG1 dominating in E. faecium and rep 9/pCF10 , rep 2/pRE25 and rep 7 in E. faecalis strains. We observed an overall high correlation between the presence and absence of genes coding for resistance towards antibiotics, metals, biocides and their corresponding MGEs as well as their phenotypic antimicrobial susceptibility pattern. Although most IS families were represented in both E. faecalis and E. faecium, specific IS elements within these families were distributed in only one species. The prevalence of IS256-, IS3-, ISL3-, IS200/IS605-, IS110-, IS982- and IS4-transposases was significantly higher in E. faecium than E. faecalis, and that of IS110-, IS982- and IS1182-transposases in E. faecalis ST6 compared to ST40. Notably, the transposases of IS981, ISEfm1 and IS1678 that have only been reported in few enterococcal isolates were well represented in the E. faecium strains. E. faecalis ST40 strains harboured possible functional CRISPR-Cas systems, and still resistance and prophage sequences were generally well represented. CONCLUSIONS The targeted MGEs were highly prevalent among the selected STs, underlining their potential importance in the evolution of hospital-adapted lineages of enterococci. Although the propensity of inter-species horizontal gene transfer (HGT) must be emphasized, the considerable species-specificity of these MGEs indicates a separate vertical evolution of MGEs within each species, and for E. faecalis within each ST.
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Affiliation(s)
- Theresa Mikalsen
- Research group for Host-microbe Interactions, Department of Medical Biology, Faculty of Health Science, UiT - The Arctic University of Norway, Tromsø, Norway.
| | - Torunn Pedersen
- Norwegian National Advisory Unit on Detection of Antimicrobial Resistance, Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsø, Norway.
| | - Rob Willems
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands.
| | - Teresa M Coque
- Servicio de Microbiologia, Hospital Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain. .,Centro de Investigación Biomédica en Red de Epidemiología y Salud Pública (CIBER-ESP), Madrid, Spain.
| | - Guido Werner
- Division of Nosocomial Pathogens and Antibiotic Resistance, Robert Koch Institute, Wernigerode Branch, Wernigerode, Germany.
| | - Ewa Sadowy
- Department of Molecular Microbiology, National Medicines Institute, ul, Chełmska 30/34, 00-725, Warsaw, Poland.
| | - Willem van Schaik
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands.
| | - Lars Bogø Jensen
- Division of Food Microbiologyt, National Food Institute, Danish Technical University, Copenhagen V, Denmark.
| | - Arnfinn Sundsfjord
- Research group for Host-microbe Interactions, Department of Medical Biology, Faculty of Health Science, UiT - The Arctic University of Norway, Tromsø, Norway. .,Norwegian National Advisory Unit on Detection of Antimicrobial Resistance, Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsø, Norway.
| | - Kristin Hegstad
- Research group for Host-microbe Interactions, Department of Medical Biology, Faculty of Health Science, UiT - The Arctic University of Norway, Tromsø, Norway. .,Norwegian National Advisory Unit on Detection of Antimicrobial Resistance, Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsø, Norway.
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15
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Kuo AJ, Su LH, Shu JC, Wang JT, Wang JH, Fung CP, Chia JH, Lu JJ, Wu TL. National surveillance on vancomycin-resistant Enterococcus faecium in Taiwan: emergence and widespread of ST414 and a Tn1546-like element with simultaneous insertion of IS1251-like and IS1678. PLoS One 2014; 9:e115555. [PMID: 25549328 PMCID: PMC4280182 DOI: 10.1371/journal.pone.0115555] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2014] [Accepted: 11/24/2014] [Indexed: 12/22/2022] Open
Abstract
Cases of bacteremia caused by vancomycin-resistant E. faecium (VRE-fm) increased significantly in Taiwan. The present multicenter surveillance study was performed to reveal the associated epidemiological characteristics. In 2012, 134 non-repetitive VRE-fm isolates were prospectively collected from 12 hospitals in Taiwan. Antimicrobial susceptibility, pulsed-field gel electrophoresis (PFGE), multilocus sequence typing (MLST), and analysis of van genes and Tn1546 structures were investigated. Two isolates carried vanB genes, while all the remaining isolates carried vanA genes. Three isolates demonstrated a specific vanA genotype - vanB phenotype. Nine (6.7%) isolates demonstrated tigecycline resistance, and all were susceptible to daptomycin and linezolid. Molecular typing revealed 58 pulsotypes and 13 sequence types (STs), all belonged to three major lineages 17, 18, and 78. The most frequent STs were ST17 (n = 48, 35.8%), ST414 (n = 22, 16.4%), and ST78 (n = 16, 11.9%). Among the vanA harboring isolates, eight structure types of the Tn1546-like element were demonstrated. Type I (a partial deletion in the orf1 and insertion of IS1251-like between the vanS - vanH genes) and Type II (Type I with an additional insertion of IS1678 between orf2 - vanS genes) were the most predominant, consisted of 60 (45.5%) and 62 (47.0%) isolates, respectively. The increase of VRE-fm bacteremia in Taiwan may be associated with the inter- and intra-hospital spread of some major STs and horizontal transfer of vanA genes mostly carried on two efficient Tn1546-like elements. The prevailing ST414 and widespread of the Type II Tn1546-like elements are an emerging problem that requires continuous monitoring.
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Affiliation(s)
- An-Jing Kuo
- Department of Laboratory Medicine, Chang Gung Memorial Hospital, Linkou, Taoyuan, Taiwan, ROC
- Department of Medical Biotechnology and Laboratory Science, College of Medicine, Chang Gung University, Taoyuan, Taiwan, ROC
| | - Lin-Hui Su
- Department of Laboratory Medicine, Chang Gung Memorial Hospital, Linkou, Taoyuan, Taiwan, ROC
- Department of Medical Biotechnology and Laboratory Science, College of Medicine, Chang Gung University, Taoyuan, Taiwan, ROC
| | - Jwu-Ching Shu
- Department of Medical Biotechnology and Laboratory Science, College of Medicine, Chang Gung University, Taoyuan, Taiwan, ROC
- Research Center for Pathogenic Bacteria, Chang Gung University, Taoyuan, Taiwan, ROC
| | - Jann-Tay Wang
- Division of Infectious Diseases, Department of Medicine, National Taiwan University Hospital, Taipei, Taiwan, ROC
| | - Jen-Hsien Wang
- Division of Infectious Diseases, Department of Internal Medicine, China Medical University Hospital, Taichung, Taiwan, ROC
| | - Chang-Phone Fung
- Section of Infectious Diseases, Department of Medicine, Taipei Veterans General Hospital, National Yan-Ming University, Taipei, Taiwan, ROC
| | - Ju-Hsin Chia
- Department of Laboratory Medicine, Chang Gung Memorial Hospital, Linkou, Taoyuan, Taiwan, ROC
- Department of Medical Biotechnology and Laboratory Science, College of Medicine, Chang Gung University, Taoyuan, Taiwan, ROC
| | - Jang-Jih Lu
- Department of Laboratory Medicine, Chang Gung Memorial Hospital, Linkou, Taoyuan, Taiwan, ROC
- Department of Medical Biotechnology and Laboratory Science, College of Medicine, Chang Gung University, Taoyuan, Taiwan, ROC
| | - Tsu-Lan Wu
- Department of Laboratory Medicine, Chang Gung Memorial Hospital, Linkou, Taoyuan, Taiwan, ROC
- Department of Medical Biotechnology and Laboratory Science, College of Medicine, Chang Gung University, Taoyuan, Taiwan, ROC
- * E-mail:
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16
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Molecular characterization of vancomycin-resistant Enterococcus spp. clinical isolates recovered from hospitalized patients among several medical institutions in China. Diagn Microbiol Infect Dis 2012; 74:399-403. [DOI: 10.1016/j.diagmicrobio.2012.09.006] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2012] [Revised: 09/06/2012] [Accepted: 09/07/2012] [Indexed: 01/20/2023]
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17
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da Silva LPP, Pitondo-Silva A, Martinez R, da Costa Darini AL. Genetic features and molecular epidemiology of Enterococcus faecium isolated in two university hospitals in Brazil. Diagn Microbiol Infect Dis 2012; 74:267-71. [DOI: 10.1016/j.diagmicrobio.2012.07.012] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2012] [Revised: 07/19/2012] [Accepted: 07/30/2012] [Indexed: 10/27/2022]
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18
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New type F lineage-related Tn1546and avanA/vanBtype vancomycin-resistantEnterococcus faeciumisolated from patients in Dammam, Saudi Arabia during 2006–2007. Epidemiol Infect 2012; 141:1109-14. [DOI: 10.1017/s0950268812001574] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
SUMMARYKnowledge regarding vancomycin-resistant enterococci (VRE) from Middle Eastern countries is scarce. We therefore investigated the antimicrobial resistance profiles and genetic relationships of VREEnterococcus faeciumisolates obtained from patients attending the King Fahad Specialist Hospital, Dammam, during 2006–2007. The predominant VRE comprised 20vanB, fivevanAand onevanA/vanBtype isolates, which tended to fall into two genetic clusters that were identifiable phenotypically by their susceptibility to tetracycline. Multi-locus sequence typing of a random selection of isolates showed that they were part of clonal cluster 17, showing the importance of this genotype in nosocomial VRE infections in Saudi Arabia. Further analysis showed that four of thevanAgenotype isolates possessed a new type F Tn1546transposon, associated with IS1216Vand IS1251. Finally,E. faecium vanA/Bisolates are rarely reported in the clinical setting including in Saudi Arabia.
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Abstract
Enterococcus faecium has recently emerged as an important multiresistant nosocomial pathogen. Defining population structure in this species is required to provide insight into the existence, distribution, and dynamics of specific multiresistant or pathogenic lineages in particular environments, like the hospital. Here, we probe the population structure of E. faecium using Bayesian-based population genetic modeling implemented in Bayesian Analysis of Population Structure (BAPS) software. The analysis involved 1,720 isolates belonging to 519 sequence types (STs) (491 for E. faecium and 28 for Enterococcus faecalis). E. faecium isolates grouped into 13 BAPS (sub)groups, but the large majority (80%) of nosocomial isolates clustered in two subgroups (2-1 and 3-3). Phylogenetic and eBURST analysis of BAPS groups 2 and 3 confirmed the existence of three separate hospital lineages (17, 18, and 78), highlighting different evolutionary trajectories for BAPS 2-1 (lineage 78) and 3-3 (lineage 17 and lineage 18) isolates. Phylogenomic analysis of 29 E. faecium isolates showed agreement between BAPS assignment of STs and their relative positions in the phylogenetic tree. Odds ratio calculation confirmed the significant association between hospital isolates with BAPS 3-3 and lineages 17, 18, and 78. Admixture analysis showed a scarce number of recombination events between the different BAPS groups. For the E. faecium hospital population, we propose an evolutionary model in which strains with a high propensity to colonize and infect hospitalized patients arise through horizontal gene transfer. Once adapted to the distinct hospital niche, this subpopulation becomes isolated, and recombination with other populations declines. Multiresistant Enterococcus faecium has become one of the most important nosocomial pathogens, causing increasing numbers of nosocomial infections worldwide. Here, we used Bayesian population genetic analysis to identify groups of related E. faecium strains and show a significant association of hospital and farm animal isolates to different genetic groups. We also found that hospital isolates could be divided into three lineages originating from sequence types (STs) 17, 18, and 78. We propose that, driven by the selective pressure in hospitals, the three hospital lineages have arisen through horizontal gene transfer, but once adapted to the distinct pathogenic niche, this population has become isolated and recombination with other populations declines. Elucidation of the population structure is a prerequisite for effective control of multiresistant E. faecium since it provides insight into the processes that have led to the progressive change of E. faecium from an innocent commensal to a multiresistant hospital-adapted pathogen.
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Molecular epidemiology of vancomycin-resistant Enterococcus faecium: a prospective, multicenter study in South American hospitals. J Clin Microbiol 2010; 48:1562-9. [PMID: 20220167 DOI: 10.1128/jcm.02526-09] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Enterococcus faecium has emerged as an important nosocomial pathogen worldwide, and this trend has been associated with the dissemination of a genetic lineage designated clonal cluster 17 (CC17). Enterococcal isolates were collected prospectively (2006 to 2008) from 32 hospitals in Colombia, Ecuador, Perú, and Venezuela and subjected to antimicrobial susceptibility testing. Genotyping was performed with all vancomycin-resistant E. faecium (VREfm) isolates by pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing. All VREfm isolates were evaluated for the presence of 16 putative virulence genes (14 fms genes, the esp gene of E. faecium [espEfm], and the hyl gene of E. faecium [hylEfm]) and plasmids carrying the fms20-fms21 (pilA), hylEfm, and vanA genes. Of 723 enterococcal isolates recovered, E. faecalis was the most common (78%). Vancomycin resistance was detected in 6% of the isolates (74% of which were E. faecium). Eleven distinct PFGE types were found among the VREfm isolates, with most belonging to sequence types 412 and 18. The ebpAEfm-ebpBEfm-ebpCEfm (pilB) and fms11-fms19-fms16 clusters were detected in all VREfm isolates from the region, whereas espEfm and hylEfm were detected in 69% and 23% of the isolates, respectively. The fms20-fms21 (pilA) cluster, which encodes a putative pilus-like protein, was found on plasmids from almost all VREfm isolates and was sometimes found to coexist with hylEfm and the vanA gene cluster. The population genetics of VREfm in South America appear to resemble those of such strains in the United States in the early years of the CC17 epidemic. The overwhelming presence of plasmids encoding putative virulence factors and vanA genes suggests that E. faecium from the CC17 genogroup may disseminate in the region in the coming years.
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