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Huang YC, Chen FJ, Huang IW, Wu HC, Kuo SC, Huang TW, Lauderdale TL. Clonal expansion of Tn1546-like transposon-carrying vancomycin-resistant Enterococcus faecium, a nationwide study in Taiwan, 2004-2018. J Glob Antimicrob Resist 2024:S2213-7165(24)00117-6. [PMID: 38996869 DOI: 10.1016/j.jgar.2024.06.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Revised: 05/29/2024] [Accepted: 06/07/2024] [Indexed: 07/14/2024] Open
Abstract
OBJECTIVES The prevalence of vancomycin-resistant Enterococcus faecium (VREfm) has increased significantly in Taiwan. We investigated the molecular epidemiology of clinical VREfm isolates to increase our understanding on their spread and changes in population structure over a 14-year span. METHODS A total of 1113 E. faecium isolates were collected biennially from 2004 to 2018 in Taiwan. MICs were determined by broth microdilution. Whole-genome sequencing (WGS) was performed on 229 VREfm isolates to characterize their genetic environment of vancomycin resistance and wgMLST was used to investigate their clonal relationship. RESULTS Among the 229 isolates, ST17 and ST78 predominated, especially during the later years, and their prevalences increased from 14.6% (7/48) and 25.0% (12/48) in 2004-2010 to 47.5% (87/181) and 29.8% (54/181) in 2012-2018, respectively. Four types of vanA-carrying Tn1546 variants were detected, with type 1 and type 2 predominated. Type 1 Tn1546 contained an addition of IS1251, while type 2 resembled type 1 but had an addition of IS1678. wgMLST revealed several distinct clusters of ST17 and ST78 isolates, with type 1 Tn1546-harbouring ST17-Cluster 16 being the largest and most widespread clones throughout the study years. Type 2 Tn1546-carrying ST78 became a predominant clone (Cluster 21) after 2012. Isolates within these clusters are highly similar despite being from different hospitals, regions, and study year. CONCLUSION The increase of VREfm in Taiwan was attributed to horizontal transfer of vanA-carrying Tn1546 variants between different STs and spread of persistent clones. This study highlights the importance of integrating WGS into surveillance to combat antimicrobial resistance.
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Affiliation(s)
- Ying-Chi Huang
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Zhunan, Taiwan
| | - Feng-Jui Chen
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Zhunan, Taiwan
| | - I-Wen Huang
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Zhunan, Taiwan
| | - Han-Chieh Wu
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Zhunan, Taiwan
| | - Shu-Chen Kuo
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Zhunan, Taiwan
| | - Tzu-Wen Huang
- Department of Microbiology and Immunology, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan; Graduate Institute of Medical Sciences, College of Medicine, Taipei Medical University, Taipei, Taiwan.
| | - Tsai-Ling Lauderdale
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Zhunan, Taiwan.
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Founou RC, Founou LL, Allam M, Ismail A, Essack SY. Genome analysis of multidrug resistant Enterococcus faecium and Enterococcus faecalis circulating among hospitalized patients in uMgungundlovu District, KwaZulu-Natal, South Africa. BMC Infect Dis 2024; 24:671. [PMID: 38965470 PMCID: PMC11225414 DOI: 10.1186/s12879-024-09380-3] [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: 01/16/2024] [Accepted: 05/05/2024] [Indexed: 07/06/2024] Open
Abstract
BACKGROUND Vancomycin-resistant enterococci (VRE) are important pathogens categorized as high-priority bacteria in the Global Priority List of Antibiotic-Resistant Bacteria to Guide Research, Discovery, and Development of New Antibiotics published by the World Health Organization. The aim of this study was to determine the risk factors, resistance, virulence, mobilomes associated with multidrug-resistant and clonal lineages of Enterococcus faecium and faecalis circulating among hospitalized patients following the health system in South Africa, using whole genome sequencing (WGS). METHODS A cross-sectional study was conducted during a two-month periods among hospitalized patients in 2017. Rectal swabs were collected from patients admitted to medical and surgical wards in an urban tertiary hospital, and a rural district hospital in uMgungundlovu district, South Africa. Enterococci were screened for vancomycin resistance on bile esculin azide agar supplemented with 6 mg/L of vancomycin and confirmation of VRE was done using ROSCO kits. Conventional and real-time PCR methods were used to ascertain the presence of VanA, VanB, VanC-2/3 and VanC-1 genes. All six multidrug-resistant Enterococcus faecalis and faecium selected were identified using multiplexed paired-end libraries (2 × 300 bp) with the Nextera XT DNA sample preparation kit (Illumina, San Diego, CA, USA) and genome sequencing was done using Illumina MiSeq instrument with 100× coverage at the National Institute of Communicable Diseases Sequencing Core Facility, South Africa. Antibiotic resistance genes, virulence factors, plasmids, integrons and CRISPR were characterized using RAST, ResFinder, VirulenceFinder, PlasmidFinder, PHAST and ISFinder respectively. RESULTS Sequencing analysis revealed that these strains harbouring numerous resistance genes to glycopeptides (vanC[100%], vex3[100%], vex2[83,33%] and vanG[16,66%]), macrolides, lincosamides, sterptogramine B (ermB[33,32%], Isa[16,66%], emeA[16,66%]) and tetracyclines (tetM[33,32%]) in both district and tertiary hospitals. Multidrug efflux pumps including MATE, MFS and pmrA conferring resistance to several classes of antibiotics were also identified. The main transposable elements observed were in the Tn3 family, specifically Tn1546. Four single sequence types (STs) were identified among E. faecium in the district hospital, namely ST822, ST636, ST97 along with a novel ST assigned ST1386, while one lineage, ST29 was detected in the tertiary hospital. CONCLUSION The study reveals the genetic diversity and high pathogenicity of multidrug-resistant Enterococcus faecalis and faecium circulating among hospitalized patients. It underlines the necessity to implement routine screening of admitted patients coupled with infection control procedures, antimicrobial stewardship and awareness should be strengthened to prevent and/or contain the carriage and spread of multidrug resistant E. faecium and E. faecalis in hospitals and communities in South Africa.
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Affiliation(s)
- Raspail Carrel Founou
- Antimicrobial Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban, 4000, South Africa.
- Department of Microbiology-Haematology and Immunology, Faculty of Medicine and Pharmaceutical Sciences, University of Dschang, Dschang, Cameroon.
- Antimicrobial Resistance and Infectious Disease Research Unit, Research Institute of Centre of Expertise and Biological Diagnostic of Cameroon (CEDBCAM-RI), Yaoundé, Cameroon.
| | - Luria Leslie Founou
- Antimicrobial Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban, 4000, South Africa
- Reproductive, Maternal, Newborn and Child Health (ReMARCH) Research Unit, Research Institute of the Centre of Expertise and Biological Diagnostic of Cameroon (CEDBCAM-RI), Yaoundé, Cameroon
- Bioinformatics & Applied Machine Learning Research Unit, EDEN Biosciences Research Institute (EBRI), EDEN Foundation, Yaoundé, Cameroon
| | - Mushal Allam
- Sequencing Core Facility, National Institute for Communicable Diseases a Division of the National Health Laboratory Service, Johannesburg, 2131, South Africa
| | - Arshad Ismail
- Sequencing Core Facility, National Institute for Communicable Diseases a Division of the National Health Laboratory Service, Johannesburg, 2131, South Africa
- Department of Biochemistry and Microbiology, Faculty of Science, Engineering and Agriculture, University of Venda, Thohoyandou, 0950, South Africa
- Institute for Water and Wastewater Technology, Durban University of Technology, Durban, 4000, South Africa
| | - Sabiha Yusuf Essack
- Antimicrobial Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban, 4000, South Africa
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Tang YF, Lin YS, Su LH, Liu JW. Increasing trend of healthcare-associated infections due to vancomycin-resistant Enterococcus faecium (VRE-fm) paralleling escalating community-acquired VRE-fm infections in a medical center implementing strict contact precautions: An epidemiologic and pathogenic genotype analysis and its implications. JOURNAL OF MICROBIOLOGY, IMMUNOLOGY, AND INFECTION = WEI MIAN YU GAN RAN ZA ZHI 2023; 56:1045-1053. [PMID: 37599123 DOI: 10.1016/j.jmii.2023.07.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 07/24/2023] [Accepted: 07/31/2023] [Indexed: 08/22/2023]
Abstract
OBJECTIVE To clarify whether there were clandestine intra-hospital spreads of vancomycin-resistant Enterococcus faecium (VRE-fm) isolates that led to specific strain of VRE lingering in the hospital and/or developing outbreaks that rendered a progressively increasing trend of healthcare-associated infections due to VRE-fm (VRE-fm-HAIs). SETTING Despite implementing strict contact precautions for hospitalized patients with VRE-fm-infection/colonization, number of VRE-fm-HAIs in a medical centre in southern Taiwan were escalating in 2009-2019, paralleling an increasing trend of community-acquired VRE-fm- infections. METHODS We analyzed epidemiologic data and genotypes of non-duplicate VRE-fm isolates each grown from a normally sterile site of 89 patients between December 2016 and October 2018; multilocus sequence typing (MLST) and pulse-field gel electrophoresis (PFGE) typing were performed. RESULTS Totally 13 sequence types (STs) were found, and the 3 leading STs were ST17 (44%), ST78 (37%), and ST18 (6%); 66 pulsotypes were generated by PFGE. Four VRE-fm isolates grouped as ST17/pulsotype S, 2 as ST17/pulsotype AS, 2 as ST17/pulsotype AU, and 3 as ST78/pulsotype V grew from clinical specimens sampled less than one week apart from patients staying at different wards/departments and/or on different floors of the hospital. CONCLUSIONS Despite possible small transitory clusters of intra-hospital VRE-fm spreads, there was no specific VRE-fm strain lingering in the hospital leading to increasing trend of VRE-fm-HAIs during the study period. Strict contact precautions were able to curb intra-hospital VRE-fm spreads, but unable to curb the increasing trend of VRE-fm-HAIs with the backdrop of progressively increasing VRE-fm-infections/colorizations in the community.
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Affiliation(s)
- Ya-Fen Tang
- Infection Control Team, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung, Taiwan; Department of Laboratory Medicine, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung, Taiwan
| | - Yin-Shiou Lin
- Infection Control Team, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung, Taiwan
| | - Li-Hsiang Su
- Infection Control Team, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung, Taiwan
| | - Jien-Wei Liu
- Infection Control Team, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung, Taiwan; Division of Infectious Diseases, Department of Internal Medicine, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung, Taiwan; Chang Gung University College of Medicine, Taoyuan, Taiwan.
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Kim SH, Cho SY, Kim HM, Huh K, Kang CI, Peck KR, Chung DR. Sequence type 17 is a predictor of subsequent bacteremia in vancomycin-resistant Enterococcus faecium-colonized patients: a retrospective cohort study. Antimicrob Resist Infect Control 2021; 10:108. [PMID: 34294150 PMCID: PMC8299594 DOI: 10.1186/s13756-021-00980-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Accepted: 07/13/2021] [Indexed: 11/25/2022] Open
Abstract
Background Sequence type (ST) 17 vancomycin-resistant Enterococcus faecium (VREF) is frequently isolated in nosocomial settings. The aim of this study was to identify whether ST17 contributes to subsequent bacteremia more often than other STs among hospitalized patients carrying VREF. Methods A retrospective cohort study was conducted in patients carrying ST17 VREF and those with non-ST17 VREF. Rectal screening according to hospital policy was used to identify patients with VREF. Subsequent VREF bacteremia events within a year of detection of colonization were recorded. Cox regression analysis was used to adjust the covariates involved in determining the association between ST17 and subsequent bacteremia events. Results The cohorts comprised 52 patients with ST17 and 169 patients with non-ST17 VREF. One-year VREF bacteremia-free rates were 85.9% and 90.2%, respectively. In multivariate analysis, ST17 was associated with subsequent bacteremia at an adjusted hazard risk (aHR) of 4.02 (95% confidence interval [CI], 1.32–12.29). Liver transplantation (aHR, 40.08; 95% CI, 4.87–329.76) and hematologic malignancy (aHR, 20.97; 95% CI, 4.87–87.82) were also significant. All cases of subsequent bacteremia in ST17 VREF carriers were caused by ST17; however, subsequent bacteremia in non-ST17 carriers was often caused by ST17 or another ST variant. Conclusions A specific genotype, ST17 is a predictor of subsequent bacteremia in hospitalized patients carrying VREF. Patients with a hematologic malignancy and those receiving a liver transplant are also at high risk. More targeted strategies may be needed to prevent VREF infection in hospitals. Supplementary Information The online version contains supplementary material available at 10.1186/s13756-021-00980-1.
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Affiliation(s)
- Si-Ho Kim
- Division of Infectious Diseases, Samsung Medical Center, Sungkyunkwan University School of Medicine, 81 Irwon-ro, Gangnam-gu, Seoul, 06351, South Korea.,Division of Infectious Diseases, Samsung Changwon Hospital, Sungkyunkwan University School of Medicine, Changwon, Korea
| | - Sun Young Cho
- Division of Infectious Diseases, Samsung Medical Center, Sungkyunkwan University School of Medicine, 81 Irwon-ro, Gangnam-gu, Seoul, 06351, South Korea.,Center for Infection Prevention and Control, Samsung Medical Center, Seoul, Korea
| | - Hye Mee Kim
- Division of Infectious Diseases, Samsung Medical Center, Sungkyunkwan University School of Medicine, 81 Irwon-ro, Gangnam-gu, Seoul, 06351, South Korea.,Asia Pacific Foundation for Infectious Diseases, Seoul, Korea
| | - Kyungmin Huh
- Division of Infectious Diseases, Samsung Medical Center, Sungkyunkwan University School of Medicine, 81 Irwon-ro, Gangnam-gu, Seoul, 06351, South Korea.,Asia Pacific Foundation for Infectious Diseases, Seoul, Korea
| | - Cheol-In Kang
- Division of Infectious Diseases, Samsung Medical Center, Sungkyunkwan University School of Medicine, 81 Irwon-ro, Gangnam-gu, Seoul, 06351, South Korea
| | - Kyong Ran Peck
- Division of Infectious Diseases, Samsung Medical Center, Sungkyunkwan University School of Medicine, 81 Irwon-ro, Gangnam-gu, Seoul, 06351, South Korea
| | - Doo Ryeon Chung
- Division of Infectious Diseases, Samsung Medical Center, Sungkyunkwan University School of Medicine, 81 Irwon-ro, Gangnam-gu, Seoul, 06351, South Korea. .,Center for Infection Prevention and Control, Samsung Medical Center, Seoul, Korea. .,Asia Pacific Foundation for Infectious Diseases, Seoul, Korea.
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Chen YH, Lin SY, Lin YT, Tseng SP, Chang CC, Yu SY, Hung WW, Jao YT, Lin CY, Chen YH, Hung WC. Emergence of aac(6')-Ie-aph(2'')-Ia-positive enterococci with non-high-level gentamicin resistance mediated by IS1216V: adaptation to decreased aminoglycoside usage in Taiwan. J Antimicrob Chemother 2021; 76:1689-1697. [PMID: 33822062 DOI: 10.1093/jac/dkab071] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Accepted: 02/18/2021] [Indexed: 12/17/2022] Open
Abstract
OBJECTIVES To explore the mechanisms mediating the different levels of gentamicin resistance in enterococci. METHODS Susceptibility testing with gentamicin and PCR of resistance determinants were performed in 149 enterococcal isolates. Genetic relatedness was characterized by MLST and PFGE analysis. Sequences of the aac(6')-Ie-aph(2'')-Ia gene and its surrounding environment were determined by Illumina sequencing. Stability assays of gentamicin resistance were carried out to evaluate the probability of loss of the high-level gentamicin resistance (HLGR) phenotype. RESULTS A total of 17 (11.4%) aac(6')-Ie-aph(2'')-Ia-positive enterococcal isolates (2 Enterococcus faecalis and 15 Enterococcus faecium) with non-HLGR phenotype were found. MLST analysis revealed that the 2 E. faecalis belonged to ST116 and ST618, while all the 15 E. faecium belonged to clonal complex 17. Sequence analysis demonstrated that IS1216V was inserted into the 5'-end of aac(6')-Ie-aph(2'')-Ia, leading to loss of HLGR phenotype. Three IS1216V insertion types were found, and type II and III were frequently found in E. faecium. Interestingly, a total of 38 aac(6')-Ie-aph(2'')-Ia-positive E. faecium with HLGR phenotype also had type II or type III IS1216V insertion. Sequencing of the aac(6')-Ie-aph(2'')-Ia-positive HLGR E. faecium E37 revealed that an intact aac(6')-Ie-aph(2'')-Ia was located adjacent to IS1216V-disrupted aac(6')-Ie-aph(2'')-Ia. In a non-antibiotic environment, E37 tended to lose HLGR phenotype with a probability of 1.57 × 10-4, which was largely attributed to homologous recombination between the intact and disrupted aac(6')-Ie-aph(2'')-Ia. CONCLUSIONS This is first study to elucidate that the E. faecium is capable of changing its HLGR phenotype, which may contribute to adaptation to hospital environments with decreased usage of gentamicin.
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Affiliation(s)
- You-Han Chen
- Department of Microbiology and Immunology, College of Medicine, Kaohsiung Medical University, Taiwan
| | - Shang-Yi Lin
- Division of Infectious Diseases, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
| | - Yu-Tzu Lin
- Department of Medical Laboratory Science and Biotechnology, China Medical University, Taichung, Taiwan
| | - Sung-Pin Tseng
- Department of Medical Laboratory Science and Biotechnology, College of Health Sciences, Kaohsiung Medical University, Kaohsiung, Taiwan.,Drug Development and Value Creation Research Center, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Chen-Chia Chang
- Department of Microbiology and Immunology, College of Medicine, Kaohsiung Medical University, Taiwan
| | - Song-Yih Yu
- Department of Pharmacy, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
| | - Wei-Wen Hung
- Division of Endocrine and Metabolism, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
| | - Ya-Ting Jao
- Infection Control Center, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
| | - Chun-Yu Lin
- Division of Infectious Diseases, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan.,Infection Control Center, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
| | - Yen-Hsu Chen
- Division of Infectious Diseases, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan.,School of Medicine, Graduate Institute of Medicine, Sepsis Research Center, Center of Tropical Medicine and Infectious Diseases, Kaohsiung Medical University, Kaohsiung, Taiwan.,Department of Biological Science and Technology, College of Biological Science and Technology, National Chiao Tung University, HsinChu, Taiwan.,Institute of Medical Science and Technology, National Sun Yat-Sen University, Kaohsiung, Taiwan
| | - Wei-Chun Hung
- Department of Microbiology and Immunology, College of Medicine, Kaohsiung Medical University, Taiwan.,Department of Medical Research, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
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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: 0.7] [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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Gast KB, van Oudheusden AJG, Murk JL, Stohr JJJM, Buiting AG, Verweij JJ. Successful containment of two vancomycin-resistant Enterococcus faecium (VRE) outbreaks in a Dutch teaching hospital using environmental sampling and whole-genome sequencing. J Hosp Infect 2021; 111:132-139. [PMID: 33582200 DOI: 10.1016/j.jhin.2021.02.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 02/02/2021] [Accepted: 02/04/2021] [Indexed: 01/18/2023]
Abstract
BACKGROUND Vancomycin-resistant enterococci (VRE) may cause nosocomial outbreaks. This article describes all VRE carriers that were identified in 2018 at Elisabeth-Tweesteden Hospital, Tilburg, The Netherlands. AIM To investigate the genetic relatedness of VRE isolates and the possibility of a common environmental reservoir using environmental sampling and whole-genome sequencing (WGS). METHODS Infection control measures consisted of contact isolation, contact surveys, point prevalence screening, environmental sampling, cleaning and disinfection. VRE isolates were sequenced using a MiSeq sequencer (Illumina, San Diego, CA, USA), and assembled using SPAdes v.3.10.1. A minimal spanning tree and a neighbour joining tree based on allelic diversity of core-genome multi-locus sequence typing and accessory genes were created using Ridom SeqSphere+ software (Ridom GmbH, Münster, Germany). FINDINGS Over a 1-year period, 19 VRE carriers were identified; of these, 17 were part of two outbreaks. Before environmental cleaning and disinfection, 55 (14%) environmental samples were VRE-positive. Fifty-one isolates (23 patient samples and 28 environmental samples) were available for WGS analysis. Forty-four isolates were assigned to ST117-vanB, five were assigned to ST17-vanB, and two were assigned to ST80-vanB. Isolates from Outbreak 1 (N=22) and Outbreak 2 (N=22) belonged to ST117-vanB; however, WGS showed a different cluster type with 257 allelic differences. CONCLUSION WGS of two outbreak strains provided discriminatory information regarding genetic relatedness, and rejected the hypothesis of a common environmental reservoir. A high degree of environmental contamination was associated with higher VRE transmission. Quantification of environmental contamination may reflect the potential for VRE transmission and could therefore support the infection control measures.
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Affiliation(s)
- K B Gast
- Microvida Laboratory of Medical Microbiology and Immunology, Elisabeth-TweeSteden Hospital, Tilburg, The Netherlands.
| | - A J G van Oudheusden
- Department of Infection Prevention, Elisabeth-TweeSteden Hospital, Tilburg, The Netherlands
| | - J L Murk
- Microvida Laboratory of Medical Microbiology and Immunology, Elisabeth-TweeSteden Hospital, Tilburg, The Netherlands
| | - J J J M Stohr
- Microvida Laboratory of Medical Microbiology and Immunology, Elisabeth-TweeSteden Hospital, Tilburg, The Netherlands
| | - A G Buiting
- Microvida Laboratory of Medical Microbiology and Immunology, Elisabeth-TweeSteden Hospital, Tilburg, The Netherlands; Department of Infection Prevention, Elisabeth-TweeSteden Hospital, Tilburg, The Netherlands
| | - J J Verweij
- Microvida Laboratory of Medical Microbiology and Immunology, Elisabeth-TweeSteden Hospital, Tilburg, The Netherlands
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8
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Xu Z, Wei Y, Wang Y, Xu G, Cheng H, Chen J, Yu Z, Chen Z, Zheng J. In vitro activity of radezolid against Enterococcus faecium and compared with linezolid. J Antibiot (Tokyo) 2020; 73:845-851. [PMID: 32678335 DOI: 10.1038/s41429-020-0345-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 06/14/2020] [Accepted: 06/16/2020] [Indexed: 11/09/2022]
Abstract
This study aims to explore the antimicrobial activity and resistance mechanism of radezolid against Enterococcus faecium, and to compare it with linezolid. A total of 232 E. faecium isolates were collected, and the minimal inhibitory concentrations of radezolid and linezolid were determined. The radezolid- or linezolid-nonsusceptible isolates were selected by passage in vitro under antibiotic pressure. Oxazolidinone-resistant chromosomal genes and plasmid-borne genes cfr, optrA, and poxtA were detected by PCR and sequenced. Radezolid MIC90 was 4 times lower than linezolid in the 232 E. faecium isolates, including the linezolid-nonsusceptible isolates. This study found that 6.5% (15/232) of the E. faecium isolates carried the plasmid-borne genes cfr and 9.5% (22/232) carried the optrA gene, but only one of these isolates had a linezolid MIC ≥ 4 mg l-1. Among the 13 isolates with linezolid MIC ≥ 4 mg l-1 or radezolid MIC ≥ 1 mg l-1, genetic mutations in the V domain of 23S rRNA were only found in four isolates. The MICs of linezolid or radezolid against three E. faecium isolates increased to 4-16 times of the initial MICs after 140 days of daily passage in drug-containing medium. The radezolid MICs remained 8-16 times lower than linezolid in those linezolid-induced resistant isolates. Conversely, the radezolid MICs increased while the linezolid MICs remained unchanged in the most of the radezolid-induced resistant isolates. Radezolid exhibits excellent antimicrobial activity against E. faecium, and has minimal cross resistance with linezolid.
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Affiliation(s)
- Zhichao Xu
- Department of Infectious Diseases and Shenzhen key laboratory for endogenous infections, Shenzhen Nanshan people's Hospital, Shenzhen University of School Medicine, No 89, Taoyuan Road, Nanshan district, Shenzhen, 518052, China.,Quality Control Center of Hospital Infection management of Shenzhen, Guang Dong Medical University, No 89, Taoyuan Road, Nanshan district, Shenzhen, 518052, China
| | - Ying Wei
- Heilongjiang Medical Service Management Evaluation Center, Harbin, Heilongjiang, 150031, China
| | - Yu Wang
- Department of Infectious Diseases and Shenzhen key laboratory for endogenous infections, Shenzhen Nanshan people's Hospital, Shenzhen University of School Medicine, No 89, Taoyuan Road, Nanshan district, Shenzhen, 518052, China
| | - Guangjian Xu
- Department of Infectious Diseases and Shenzhen key laboratory for endogenous infections, Shenzhen Nanshan people's Hospital, Shenzhen University of School Medicine, No 89, Taoyuan Road, Nanshan district, Shenzhen, 518052, China
| | - Hang Cheng
- Department of Infectious Diseases and Shenzhen key laboratory for endogenous infections, Shenzhen Nanshan people's Hospital, Shenzhen University of School Medicine, No 89, Taoyuan Road, Nanshan district, Shenzhen, 518052, China.,Quality Control Center of Hospital Infection management of Shenzhen, Guang Dong Medical University, No 89, Taoyuan Road, Nanshan district, Shenzhen, 518052, China
| | - Junwen Chen
- Department of Infectious Diseases and Shenzhen key laboratory for endogenous infections, Shenzhen Nanshan people's Hospital, Shenzhen University of School Medicine, No 89, Taoyuan Road, Nanshan district, Shenzhen, 518052, China.,Quality Control Center of Hospital Infection management of Shenzhen, Guang Dong Medical University, No 89, Taoyuan Road, Nanshan district, Shenzhen, 518052, China
| | - Zhijian Yu
- Department of Infectious Diseases and Shenzhen key laboratory for endogenous infections, Shenzhen Nanshan people's Hospital, Shenzhen University of School Medicine, No 89, Taoyuan Road, Nanshan district, Shenzhen, 518052, China.,Quality Control Center of Hospital Infection management of Shenzhen, Guang Dong Medical University, No 89, Taoyuan Road, Nanshan district, Shenzhen, 518052, China
| | - Zhong Chen
- Department of Infectious Diseases and Shenzhen key laboratory for endogenous infections, Shenzhen Nanshan people's Hospital, Shenzhen University of School Medicine, No 89, Taoyuan Road, Nanshan district, Shenzhen, 518052, China. .,Quality Control Center of Hospital Infection management of Shenzhen, Guang Dong Medical University, No 89, Taoyuan Road, Nanshan district, Shenzhen, 518052, China.
| | - Jinxin Zheng
- Department of Infectious Diseases and Shenzhen key laboratory for endogenous infections, Shenzhen Nanshan people's Hospital, Shenzhen University of School Medicine, No 89, Taoyuan Road, Nanshan district, Shenzhen, 518052, China. .,Quality Control Center of Hospital Infection management of Shenzhen, Guang Dong Medical University, No 89, Taoyuan Road, Nanshan district, Shenzhen, 518052, China.
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9
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He YH, Ruan GJ, Hao H, Xue F, Ma YK, Zhu SN, Zheng B. Real-time PCR for the rapid detection of vanA, vanB and vanM genes. JOURNAL OF MICROBIOLOGY, IMMUNOLOGY, AND INFECTION = WEI MIAN YU GAN RAN ZA ZHI 2019; 53:746-750. [PMID: 30926279 DOI: 10.1016/j.jmii.2019.02.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Revised: 02/02/2019] [Accepted: 02/13/2019] [Indexed: 10/27/2022]
Abstract
BACKGROUND/PURPOSE To evaluate the ability of quadruple Taqman probe real-time PCR to the detection of vanA, vanB and vanM in enterococcal isolates. METHODS A total of 343 strains, including 253 vancomycin-resistant enterococcus (VRE) strains and 90 non-VRE strains, were tested by both quadruple Taqman probe real-time PCR and gel-based PCR assay. RESULTS When differentiating among three genotypes of vanA, vanB and vanM in VRE strains, the sensitivity, specificity, positive predictive value (PPV), negative predictive value (NPV), diagnostic accuracy and consistency of the quadruple Taqman probe real-time PCR were all 100%. Minimum. Inhibitory concentration (MIC) results showed that there was a wide MIC range of vancomycin and teicoplanin for the strains that harboring vanA/vanM gene respectively or harboring vanA and vanM genes simultaneously. However, the VRE strains with vanB genotype all were sensitive to teicoplanin. CONCLUSION Considering the excellent PPV and low NPV, real-time PCR would be useful to monitor VRE-colonized or infected patients. However, further evaluation of the assay's performance in the clinical specimens is required, especially when considering that high level of PCR inhibitors present in these samples.
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Affiliation(s)
- Yuan-Hui He
- Institute of Clinical Pharmacology, Peking University First Hospital, Beijing, China
| | - Gen-Jie Ruan
- Institute of Clinical Pharmacology, Peking University First Hospital, Beijing, China
| | - Hui Hao
- IPE Biotechnology Co. Ltd, Beijing, China
| | - Feng Xue
- Institute of Clinical Pharmacology, Peking University First Hospital, Beijing, China
| | - Ya-Kun Ma
- Institute of Clinical Pharmacology, Peking University First Hospital, Beijing, China
| | - Sai-Nan Zhu
- Department of Biostatistics, Peking University First Hospital, Beijing, China
| | - Bo Zheng
- Institute of Clinical Pharmacology, Peking University First Hospital, Beijing, China.
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10
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Survival of Patients With Vancomycin-Resistant Enterococcus faecium Bacteremia Treated With Conventional or High Doses of Daptomycin or Linezolid Is Associated With the Rate of Bacterial Clearance*. Crit Care Med 2018; 46:1634-1642. [DOI: 10.1097/ccm.0000000000003264] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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11
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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: 3.3] [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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12
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Lim SY, Teh CSJ, Thong KL. Biofilm-Related Diseases and Omics: Global Transcriptional Profiling of Enterococcus faecium Reveals Different Gene Expression Patterns in the Biofilm and Planktonic Cells. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2018; 21:592-602. [PMID: 29049010 DOI: 10.1089/omi.2017.0119] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Enterococcus faecium is an opportunistic pathogen with a remarkable ability to acquire resistance toward multiple antibiotics, including those of last-resort drugs such as vancomycin and daptomycin. The occurrence of vancomycin-resistant E. faecium is on the rise and there is a need to understand the virulence of this organism. One of the factors that contributes to the virulence is the ability to form biofilms. Since bacteria in biofilm state are more resistant to antibiotics and host immune response, understanding the molecular mechanism of biofilm development is important to control biofilm-related diseases. The aim of this study was to determine the global gene expression profiles of an E. faecium strain, VREr5, during the early event of sessile growth compared with its planktonic phase through RNA-sequencing approach. The results clearly illustrated distinct expression profiles of the planktonic and biofilm cells. A total of 177 genes were overexpressed in the biofilm cells. Most of them encode for proteins involved in adherence, such as the ebpABCfm locus. Genes associated with plasmid replication, gene exchange, and protein synthesis were also upregulated during the early event of biofilm development. Furthermore, the transcriptome analysis also identified genes such as fsrB, luxS, and spx that might suppress biofilm formation in VREr5. The putative biofilm-related bee locus was found to be downregulated. These new findings could provide caveats for future studies on the regulation and maintenance of biofilm and development of biomarkers for biofilm-related diseases.
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Affiliation(s)
- Shu Yong Lim
- 1 Institute of Biological Sciences, Faculty of Science, University of Malaya , Kuala Lumpur, Malaysia
| | - Cindy Shuan Ju Teh
- 2 Department of Medical Microbiology, Faculty of Medicine, University of Malaya , Kuala Lumpur, Malaysia
| | - Kwai Lin Thong
- 1 Institute of Biological Sciences, Faculty of Science, University of Malaya , Kuala Lumpur, Malaysia
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13
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Ye JJ, Shie SS, Cheng CW, Yang JH, Huang PY, Wu TS, Lee MH, Huang CT. Clinical characteristics and treatment outcomes of vancomycin-resistant Enterococcus faecium bacteremia. JOURNAL OF MICROBIOLOGY, IMMUNOLOGY, AND INFECTION = WEI MIAN YU GAN RAN ZA ZHI 2017; 51:705-716. [PMID: 29046248 DOI: 10.1016/j.jmii.2017.08.025] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Revised: 08/28/2017] [Accepted: 08/31/2017] [Indexed: 02/07/2023]
Abstract
BACKGROUND Vancomycin-resistant Enterococcus faecium (VRE-fm) bacteremia causes significant mortality in hospitalized patients. We sought to investigate clinical characteristics, treatment outcomes, and microbiological eradication associated with VRE-fm bacteremia. METHODS A retrospective cohort study was conducted and included 210 adult patients admitted between January 1, 2011 and December 31, 2015. RESULTS The mean Pitt bacteremia score was 4.7. ICU stay (48.6%) and mechanical ventilation (46.2%) were common. Diabetes mellitus was the most common concomitant disease (43.3%), followed by malignancies, including hematologic malignancies (14.3%) and solid cancers (28.1%). The 14-day and 28-day mortality rates were 37.1% and 50.5%, respectively. Linezolid or daptomycin treatment for at least 10 days and higher Pitt bacteremia scores were independently associated with 14-day and 28-day mortality. Longer treatment duration of linezolid or daptomycin predicted microbiological eradication independently. Daptomycin-treated patients tended to have higher 14-day and 28-day mortality, and lower microbial eradication rates (20.8% versus 8.7%; 40.6% versus 26.1%; 14.1% versus 26.1%; respectively) than linezolid-treated patients, and cumulative survival rates at 14 and 28 days tended to be lower in patients who received low-dose daptomycin (<10 mg/kg/day) than that in those who received linezolid and high-dose daptomycin (≥10 mg/kg/day); however, the differences were not statistically significant. CONCLUSION Higher disease severity and inappropriate treatment were associated with increased mortality and longer treatment duration of linezolid or daptomycin was associated with microbial eradication for the patient with VRE-fm bacteremia.
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Affiliation(s)
- Jung-Jr Ye
- Division of Infectious Diseases, Department of Internal Medicine, Chang Gung Memorial Hospital at Kee-Lung, Kee-Lung, Taiwan.
| | - Shian-Sen Shie
- Division of Infectious Diseases, Department of Internal Medicine, Chang Gung Memorial Hospital at Linkou, Chang Gung University College of Medicine, Taoyuan, Taiwan.
| | - Chun-Wen Cheng
- Division of Infectious Diseases, Department of Internal Medicine, Chang Gung Memorial Hospital at Linkou, Chang Gung University College of Medicine, Taoyuan, Taiwan.
| | - Jeng-How Yang
- Division of Infectious Diseases, Department of Internal Medicine, Chang Gung Memorial Hospital at Linkou, Chang Gung University College of Medicine, Taoyuan, Taiwan.
| | - Po-Yen Huang
- Division of Infectious Diseases, Department of Internal Medicine, Chang Gung Memorial Hospital at Linkou, Chang Gung University College of Medicine, Taoyuan, Taiwan; Infection Control Committee, Chang Gung Memorial Hospital at Linkou, Taoyuan, Taiwan.
| | - Ting-Shu Wu
- Division of Infectious Diseases, Department of Internal Medicine, Chang Gung Memorial Hospital at Linkou, Chang Gung University College of Medicine, Taoyuan, Taiwan; Infection Control Committee, Chang Gung Memorial Hospital at Linkou, Taoyuan, Taiwan.
| | - Ming-Hsun Lee
- Division of Infectious Diseases, Department of Internal Medicine, Chang Gung Memorial Hospital at Linkou, Chang Gung University College of Medicine, Taoyuan, Taiwan.
| | - Ching-Tai Huang
- Division of Infectious Diseases, Department of Internal Medicine, Chang Gung Memorial Hospital at Linkou, Chang Gung University College of Medicine, Taoyuan, Taiwan.
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14
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Resistance mechanisms and clinical characteristics of linezolid-resistant Enterococcus faecium isolates: A single-centre study in South Korea. J Glob Antimicrob Resist 2017; 12:44-47. [PMID: 28941790 DOI: 10.1016/j.jgar.2017.09.009] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2017] [Revised: 08/15/2017] [Accepted: 09/13/2017] [Indexed: 11/23/2022] Open
Abstract
OBJECTIVES This study aimed to determine the prevalence of linezolid-resistant (LR) vancomycin-resistant enterococci and to investigate the mechanisms of linezolid resistance with clinical and microbiological characterisation. METHODS All vancomycin-resistant Enterococcus faecium (VREF) isolated from blood and rectal swab cultures during 2012-2015 were tested for linezolid resistance. LR-VREF isolates were tested for antimicrobial susceptibility, glycopeptide resistance genes and virulence genes. Multilocus sequence typing (MLST) and pulsed-field gel electrophoresis (PFGE) were performed. Isolates were tested for known mechanisms of linezolid resistance. RESULTS Among 389 VREF isolates, 7 (1.8%) were found to be resistant to linezolid. All LR-VREF isolates carried the vanA gene. Five isolates had both hyl and esp genes. The isolates were susceptible to tigecycline, daptomycin and quinupristin/dalfopristin, except for one isolate with daptomycin resistance. Two LR-VREF isolates recovered from patients with previous linezolid exposure contained the G2576T mutation in 23S rRNA and exhibited high-level resistance to linezolid (MIC>64mg/L). The other five isolates recovered from linezolid-naïve patients revealed no known linezolid resistance mechanism and exhibited low-level resistance to linezolid (MICs=8-16mg/L). Plasmid-mediated genes encoding cfr or optrA were not detected. LR-VREF isolates were represented by six different sequence types, belonging to hospital lineages, and were assigned to seven PFGE types. CONCLUSIONS The prevalence of LR-VREF in this centre was low. Both linezolid exposure and horizontal transmission appear to be responsible for acquisition of LR-VREF in hospitalised patients. Prudent use of linezolid and improved infection control strategies are needed to limit the spread of LR-VREF.
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15
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Lim SY, Yap KP, Teh CSJ, Jabar KA, Thong KL. Comparative genome analysis of multiple vancomycin-resistant Enterococcus faecium isolated from two fatal cases. INFECTION GENETICS AND EVOLUTION 2017; 49:55-65. [PMID: 28039075 DOI: 10.1016/j.meegid.2016.12.029] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Revised: 12/22/2016] [Accepted: 12/25/2016] [Indexed: 12/31/2022]
Abstract
Enterococcus faecium is both a commensal of the human intestinal tract and an opportunistic pathogen. The increasing incidence of enterococcal infections is mainly due to the ability of this organism to develop resistance to multiple antibiotics, including vancomycin. The aim of this study was to perform comparative genome analyses on four vancomycin-resistant Enterococcus faecium (VREfm) strains isolated from two fatal cases in a tertiary hospital in Malaysia. Two sequence types, ST80 and ST203, were identified which belong to the clinically important clonal complex (CC) 17. This is the first report on the emergence of ST80 strains in Malaysia. Three of the studied strains (VREr5, VREr6, VREr7) were each isolated from different body sites of a single patient (patient Y) and had different PFGE patterns. While VREr6 and VREr7 were phenotypically and genotypically similar, the initial isolate, VREr5, was found to be more similar to VRE2 isolated from another patient (patient X), in terms of the genome contents, sequence types and phylogenomic relationship. Both the clinical records and genome sequence data suggested that patient Y was infected by multiple strains from different clones and the strain that infected patient Y could have derived from the same clone from patient X. These multidrug resistant strains harbored a number of virulence genes such as the epa locus and pilus-associated genes which could enhance their persistence. Apart from that, a homolog of E. faecalis bee locus was identified in VREr5 which might be involved in biofilm formation. Overall, our comparative genomic analyses had provided insight into the genetic relatedness, as well as the virulence potential, of the four clinical strains.
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Affiliation(s)
- Shu Yong Lim
- Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
| | - Kien-Pong Yap
- Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
| | - Cindy Shuan Ju Teh
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Kartini Abdul Jabar
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Kwai Lin Thong
- Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia.
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16
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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: 4.3] [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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17
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Draft Genome Sequence of Multidrug-Resistant Enterococcus faecium Clinical Isolate VRE3, with a Sequence Type 16 Pattern and Novel Structural Arrangement of Tn1546. GENOME ANNOUNCEMENTS 2015; 3:3/4/e00871-15. [PMID: 26272564 PMCID: PMC4536675 DOI: 10.1128/genomea.00871-15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Multidrug-resistant Enterococcus faecium has emerged as a nosocomial pathogen that may infect the body at various sites, including the gastrointestinal tract, and has serious implications in human health and disease. Here, we present the draft genome sequence of clinical strain VRE3, which exhibited a sequence type 16 (ST16) pattern and carried truncated Tn1546, a mobile genetic element encoding a high level of vancomycin resistance.
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