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McIver CJ, Pratama R, Jose G, Caagbay D, Montgomery L, Bhardwaj N, Mukerjee C, Taylor PC, Stevens R. A novel molecular assay conducted on the BD Max system to facilitate reflex testing for vanA and vanB in clinical isolates of enterococci. Pathology 2024:S0031-3025(24)00144-2. [PMID: 38981818 DOI: 10.1016/j.pathol.2024.04.005] [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: 09/20/2023] [Revised: 03/18/2024] [Accepted: 04/03/2024] [Indexed: 07/11/2024]
Abstract
Infections caused by vancomycin-resistant enterococci (VRE) are common. Real-time PCR assays targeting vanA and vanB facilitate screening of patients in healthcare settings to limit the risk of dissemination, especially amongst those at high-risk of infection or with limited treatment options. Such assays are commonly performed as reflex testing procedures where they augment phenotypic techniques and shorten turnaround time to benefit timely clinical management. 'Random access' and 'sample-to-result' real-time PCR platforms are suited for this application as they are of low complexity and less technically demanding. Modelled on these attributes, we configured a real-time PCR assay (VRE BD) for detection of vanA/B in clinical isolates of enterococci, adapted for the BD Max System (Becton Dickinson). We applied an unconventional approach by testing suspensions of microorganisms in water to circumvent the traditional pre-analytical genomic extraction process. Our objective of this study was to assess the performance of this assay for detection of VRE in cultures by validating against a traditional real-time PCR assay based on the LightCycler 2.0 platform (Roche, VRE RO). A high level of analytical sensitivity and specificity (≥99.0%) for both genes was obtained when testing suspensions derived from blood agar. Results for suspensions obtained from chromID VRE (Edwards Group) showed a similar level of performance for vanA detection (100%), but not for the vanB target (≥90.9%) where a lesser number of isolates were available for testing. However, our results for VRE detection in isolates from these media were repeatable and reproducible, and equated to positive and negative predictive values of ≥95.2% and ≥97.8%, respectively. Furthermore, the VRE BD assay was also able to accurately detect VRE in clinical and spiked BacT/ALERT (bioMérieux) blood cultures. Thus, the technical simplicity, short turnaround time and robustness of this high performing assay for VRE is suitable for reflex testing. In addition, the format developed for the BD Max platform has potential application for reflex testing other molecular targets of clinical importance.
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Affiliation(s)
- Christopher J McIver
- Microbiology Department, New South Wales Health Pathology, St George Hospital, Kogarah, NSW, Australia; School of Biomedical Sciences, University of New South Wales, Sydney, NSW, Australia.
| | - Ryanbi Pratama
- Microbiology Department, New South Wales Health Pathology, St George Hospital, Kogarah, NSW, Australia
| | - Gismin Jose
- Microbiology Department, New South Wales Health Pathology, St George Hospital, Kogarah, NSW, Australia
| | - Dale Caagbay
- Microbiology Department, New South Wales Health Pathology, St George Hospital, Kogarah, NSW, Australia
| | - Leanne Montgomery
- Microbiology Department, New South Wales Health Pathology, St George Hospital, Kogarah, NSW, Australia
| | - Narinder Bhardwaj
- Microbiology Department, New South Wales Health Pathology, St George Hospital, Kogarah, NSW, Australia
| | - Chinmoy Mukerjee
- Microbiology Department, New South Wales Health Pathology, St George Hospital, Kogarah, NSW, Australia; School of Biomedical Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Peter C Taylor
- Microbiology Department, New South Wales Health Pathology, St George Hospital, Kogarah, NSW, Australia; School of Biomedical Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Robert Stevens
- Microbiology Department, New South Wales Health Pathology, St George Hospital, Kogarah, NSW, Australia
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Zaidi SEZ, Zaheer R, Zovoilis A, McAllister TA. Enterococci as a One Health indicator of antimicrobial resistance. Can J Microbiol 2024. [PMID: 38696839 DOI: 10.1139/cjm-2024-0024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/04/2024]
Abstract
The rapid increase of antimicrobial-resistant bacteria in humans and livestock is concerning. Antimicrobials are essential for the treatment of disease in modern day medicine, and their misuse in humans and food animals has contributed to an increase in the prevalence of antimicrobial-resistant bacteria. Globally, antimicrobial resistance is recognized as a One Health problem affecting humans, animals, and environment. Enterococcal species are Gram-positive bacteria that are widely distributed in nature. Their occurrence, prevalence, and persistence across the One Health continuum make them an ideal candidate to study antimicrobial resistance from a One Health perspective. The objective of this review was to summarize the role of enterococci as an indicator of antimicrobial resistance across One Health sectors. We also briefly address the prevalence of enterococci in human, animal, and environmental settings. In addition, a 16S RNA gene-based phylogenetic tree was constructed to visualize the evolutionary relationship among enterococcal species and whether they segregate based on host environment. We also review the genomic basis of antimicrobial resistance in enterococcal species across the One Health continuum.
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Affiliation(s)
- Sani-E-Zehra Zaidi
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB T1J 4B1, Canada
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive, Lethbridge, AB T1K 3M4, Canada
- University of Manitoba, Department of Biochemistry and Medical Genetics, 745 Bannatyne Ave, Winnipeg
| | - Rahat Zaheer
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB T1J 4B1, Canada
| | - Athanasios Zovoilis
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive, Lethbridge, AB T1K 3M4, Canada
- University of Manitoba, Department of Biochemistry and Medical Genetics, 745 Bannatyne Ave, Winnipeg
| | - Tim A McAllister
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB T1J 4B1, Canada
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Janice J, Wagner TM, Olsen K, Hegstad J, Hegstad K. Emergence of vancomycin-resistant enterococci from vancomycin-susceptible enterococci in hospitalized patients under antimicrobial therapy. J Glob Antimicrob Resist 2024; 36:116-122. [PMID: 38128726 DOI: 10.1016/j.jgar.2023.12.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 11/21/2023] [Accepted: 12/01/2023] [Indexed: 12/23/2023] Open
Abstract
OBJECTIVES Enterococci are opportunistic pathogens with plastic genomes that evolve, acquire, and transmit antimicrobial-resistant determinants such as vancomycin resistance clusters. While vancomycin-resistant enterococci (VRE) have emerged as successful nosocomial pathogens, the mechanism by which vancomycin-susceptible enterococci (VSE) transform to VRE in hospitalized patients remains understudied. METHODS Genomes of Enterococcus faecium from two critically ill hospitalized patients subjected to multiple antibiotic therapies, including broad-spectrum antibiotics, were investigated. To identify mechanisms of resistance evolution, genomes of vancomycin-susceptible and -resistant isolates were compared. RESULTS While VSE isolates were initially identified, VRE strains emerged post-vancomycin therapy. Comparative genomics revealed horizontal transmission of mobile genetic elements containing the Tn1549 transposon, which harbours the vanB-type vancomycin resistance gene cluster. This suggests that broad-spectrum antibiotic stress promoted the transfer of resistance-conferring elements, presumably from another gut inhabitant. CONCLUSION This is one of the first studies investigating VSE and VRE isolates from the same patient. The mechanism of transmission and the within-patient evolution of vancomycin resistance via mobile genetic elements under antibiotic stress is illustrated. Our findings serve as a foundation for future studies building on this knowledge which can further elucidate the dynamics of antibiotic stress, resistance determinant transmission, and interactions within the gut microbiota.
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Affiliation(s)
- Jessin Janice
- Research Group for Host-Microbe Interactions, Department of Medical Biology, Faculty of Health Sciences, 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
| | - Theresa Maria Wagner
- Research Group for Host-Microbe Interactions, Department of Medical Biology, Faculty of Health Sciences, UiT The Arctic University of Norway, Tromsø, Norway
| | - Karina Olsen
- Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsø, Norway
| | - Joachim Hegstad
- 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 Sciences, 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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Malin JJ, von Wintersdorff CJH, Penders J, Savelkoul PHM, Wolffs PFG. Longitudinal fluctuations of common antimicrobial resistance genes in the gut microbiomes of healthy Dutch individuals. Int J Antimicrob Agents 2023; 61:106716. [PMID: 36640847 DOI: 10.1016/j.ijantimicag.2023.106716] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 11/22/2022] [Accepted: 12/31/2022] [Indexed: 01/13/2023]
Abstract
The human gut microbiome is an important reservoir of antimicrobial resistance genes (ARGs), collectively termed the 'resistome'. To date, few studies have examined the dynamics of the human gut resistome in healthy individuals. Previously, the authors observed high rates of ARG acquisition and significant abundance shifts during international travel. In order to provide insight into commonly occurring dynamics, this study investigated longitudinal fluctuations in prevalent ARGs (cfxA, tetM and ermB) in the resistomes of non-travelling healthy volunteers. In addition, this study assessed the prevalence of acquirable ARGs (blaCTX-M, qnrB, qnrS, vanA and vanB) over time. Faecal samples from 23 participants were collected at baseline and after 2 and 4 weeks. DNA was isolated, and ARG quantification was performed by quantitative polymerase chain reaction adjusting for the total amount of bacterial 16S rDNA. vanA and qnrS were not detected in any of the samples, while the prevalence rates of vanB of non-enterococcal origin and qnrB were 73.9% and 5.7%, respectively. The ß-lactamase encoding blaCTX-M was detected in 17.4% of healthy participants. The results were compared with previous data from 122 travellers. ARG acquisitions observed in travellers were rare in non-travelling individuals during 4 weeks of follow-up, supporting the hypothesis of ARG acquisition during international travel. However, median -1.04- to 1.04-fold abundance changes were observed for 100% of cfxA, tetM and ermB, which did not differ from those found in travellers. Thus, common abundance shifts in prevalent ARGs of the gut resistome were found to occur independent of travel behaviour.
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Affiliation(s)
- Jakob J Malin
- Department of Medical Microbiology, NUTRIM School of Nutrition and Translational Research in Metabolism, Maastricht University Medical Centre, Maastricht, the Netherlands
| | - Christian J H von Wintersdorff
- Department of Medical Microbiology, NUTRIM School of Nutrition and Translational Research in Metabolism, Maastricht University Medical Centre, Maastricht, the Netherlands.
| | - John Penders
- Department of Medical Microbiology, NUTRIM School of Nutrition and Translational Research in Metabolism, Maastricht University Medical Centre, Maastricht, the Netherlands; Department of Medical Microbiology, Care and Public Health Research Institute CAPHRI, Maastricht University Medical Centre, Maastricht, the Netherlands
| | - Paul H M Savelkoul
- Department of Medical Microbiology, NUTRIM School of Nutrition and Translational Research in Metabolism, Maastricht University Medical Centre, Maastricht, the Netherlands; Department of Medical Microbiology, Care and Public Health Research Institute CAPHRI, Maastricht University Medical Centre, Maastricht, the Netherlands
| | - Petra F G Wolffs
- Department of Medical Microbiology, NUTRIM School of Nutrition and Translational Research in Metabolism, Maastricht University Medical Centre, Maastricht, the Netherlands; Department of Medical Microbiology, Care and Public Health Research Institute CAPHRI, Maastricht University Medical Centre, Maastricht, the Netherlands
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5
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Abstract
Enterococci are major, recalcitrant nosocomial pathogens with a wide repertoire of intrinsic and acquired resistance determinants and the potential of developing resistance to all clinically available antimicrobials. As such, multidrug-resistant enterococci are considered a serious public health threat. Due to limited treatment options and rapid emergence of resistance to all novel agents, the clinical microbiology laboratory plays a critical role in deploying accurate, reproducible, and feasible antimicrobial susceptibility testing methods to guide appropriate treatment of patients with deep-seated enterococcal infections. In this review, we provide an overview of the advantages and disadvantages of existing manual and automated methods that test susceptibility of Enterococcus faecium and Enterococcus faecalis to β-lactams, aminoglycosides, vancomycin, lipoglycopeptides, oxazolidinones, novel tetracycline-derivatives, and daptomycin. We also identify unique problems and gaps with the performance and clinical utility of antimicrobial susceptibility testing for enterococci, provide recommendations for clinical laboratories to circumvent select problems, and address potential future innovations that can bridge major gaps in susceptibility testing.
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Abdullah HM, Marbjerg LH, Andersen L, Hoegh SV, Kemp M. A Simple and Rapid Low-Cost Procedure for Detection of Vancomycin-Resistance Genes in Enterococci Reveals an Outbreak of Vancomycin-Variable Enterococcus faecium. Diagnostics (Basel) 2022; 12:diagnostics12092120. [PMID: 36140520 PMCID: PMC9497569 DOI: 10.3390/diagnostics12092120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 08/11/2022] [Accepted: 08/29/2022] [Indexed: 11/16/2022] Open
Abstract
The detection of resistance to vancomycin in enterococci cultured from patients is important for the treatment of individual patients and for the prevention of hospital transmission. Phenotypic antimicrobial resistance tests may fail to detect potential vancomycin-resistant enterococci. We have developed and tested a PCR based procedure for routine screening for vancomycin-resistance genes in clinical samples with enterococci. Primary cultures from diagnostic samples reported with growth of Enterococcus faecium or E. facalis were tested for vanA and vanB genes by real-time PCR without the isolation of specific bacteria. Up to ten samples were pooled and tested in each real-time PCR reaction, with subsequent individual testing of cultures from positive pools. In a one-month test period in 2017 vanA gene was detected in one out of 340 urine samples with vancomycin-susceptible enterococci reported from diagnostic culture. A second test period in 2018 included 357 urine samples, and vanA gene was detected in samples from eight patients. Subsequently, all urine samples reported with growth of E. faecium during a period of one year were tested. Fifty-eight individuals were identified with enterococci, carrying the vanA gene not previously detected. Routine molecular testing of primary culture material from patient samples may improve the detection of hospitalized patients carrying E. faecium with resistance genes to vancomycin.
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Affiliation(s)
| | - Lis Høy Marbjerg
- Department of Clinical Microbiology, Odense University Hospital, 5000 Odense, Denmark
| | - Lise Andersen
- Department of Clinical Microbiology, Odense University Hospital, 5000 Odense, Denmark
| | - Silje Vermedal Hoegh
- Department of Clinical Microbiology, Odense University Hospital, 5000 Odense, Denmark
| | - Michael Kemp
- Regional Department of Clinical Microbiology, Zealand University Hospital, 4600 Koege, Denmark
- Department of Regional Health Research, University of Southern Denmark, 5000 Odense, Denmark
- Correspondence:
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7
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Population dynamics in colonizing vancomycin-resistant E. faecium isolated from immunosuppressed patients. J Glob Antimicrob Resist 2022; 28:267-273. [DOI: 10.1016/j.jgar.2022.01.027] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 12/23/2021] [Accepted: 01/31/2022] [Indexed: 11/22/2022] Open
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8
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Nagaoka R, Kitagawa H, Koba Y, Tadera K, Hara T, Kashiyama S, Nomura T, Omori K, Shigemoto N, Yokozaki M, Ohge H. Clinical and microbiological characteristics of Eggerthella lenta bacteremia at a Japanese tertiary hospital. J Infect Chemother 2021; 27:1261-1264. [PMID: 33853729 DOI: 10.1016/j.jiac.2021.03.019] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2021] [Revised: 03/06/2021] [Accepted: 03/25/2021] [Indexed: 12/30/2022]
Abstract
Eggerthella lenta is an important cause of anaerobic bloodstream infections and is associated with high mortality. However, there are few reports of E. lenta infection in Japan. This study aimed to evaluate the clinical and microbiological characteristics of bacteremia caused by E. lenta in Hiroshima, Japan. We retrospectively analyzed E. lenta bacteremia patients at the Hiroshima University Hospital between January 2012 and December 2020. During the study period, 14 patients with E. lenta bacteremia were identified. All E. lenta isolates were cultured in anaerobic bottles, and the median time to blood culture positivity was 52.9 h. In most cases (85.6%), the source of E. lenta bacteremia was associated with intra-abdominal infections, and colon perforation was the most frequent source of E. lenta bacteremia (42.9%, n = 6). Antimicrobial susceptibility testing showed high minimal inhibitory concentrations (MIC) of piperacillin-tazobactam (TZP) and 100% susceptibility to ampicillin-sulbactam, carbapenems, and metronidazole. This study demonstrates that E. lenta bacteremia is associated with intra-abdominal infections, particularly colon perforation, and a high MIC of TZP. When gram-positive anaerobes are detected in the blood cultures of patients with severe intra-abdominal infections, clinicians should suspect E. lenta, and it may be better to change antimicrobial agents from TZP.
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Affiliation(s)
- Rie Nagaoka
- Section of Infection Diseases Laboratory, Department of Clinical Support, Hiroshima University Hospital, Hiroshima, 734-8551, Japan; Division of Clinical Laboratory Medicine, Hiroshima University Hospital, Hiroshima, 734-8551, Japan
| | - Hiroki Kitagawa
- Project Research Center for Nosocomial Infectious Diseases, Hiroshima University, Hiroshima, 734-8551, Japan; Department of Infectious Diseases, Hiroshima University Hospital, Hiroshima, 734-8551, Japan; Department of Surgery, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, 734-8551, Japan.
| | - Yumiko Koba
- Section of Infection Diseases Laboratory, Department of Clinical Support, Hiroshima University Hospital, Hiroshima, 734-8551, Japan; Division of Clinical Laboratory Medicine, Hiroshima University Hospital, Hiroshima, 734-8551, Japan; Project Research Center for Nosocomial Infectious Diseases, Hiroshima University, Hiroshima, 734-8551, Japan
| | - Kayoko Tadera
- Section of Infection Diseases Laboratory, Department of Clinical Support, Hiroshima University Hospital, Hiroshima, 734-8551, Japan; Division of Clinical Laboratory Medicine, Hiroshima University Hospital, Hiroshima, 734-8551, Japan; Project Research Center for Nosocomial Infectious Diseases, Hiroshima University, Hiroshima, 734-8551, Japan
| | - Toshinori Hara
- Section of Infection Diseases Laboratory, Department of Clinical Support, Hiroshima University Hospital, Hiroshima, 734-8551, Japan; Division of Clinical Laboratory Medicine, Hiroshima University Hospital, Hiroshima, 734-8551, Japan; Project Research Center for Nosocomial Infectious Diseases, Hiroshima University, Hiroshima, 734-8551, Japan
| | - Seiya Kashiyama
- Section of Infection Diseases Laboratory, Department of Clinical Support, Hiroshima University Hospital, Hiroshima, 734-8551, Japan; Division of Clinical Laboratory Medicine, Hiroshima University Hospital, Hiroshima, 734-8551, Japan; Project Research Center for Nosocomial Infectious Diseases, Hiroshima University, Hiroshima, 734-8551, Japan
| | - Toshihito Nomura
- Department of Infectious Diseases, Hiroshima University Hospital, Hiroshima, 734-8551, Japan
| | - Keitaro Omori
- Department of Infectious Diseases, Hiroshima University Hospital, Hiroshima, 734-8551, Japan
| | - Norifumi Shigemoto
- Project Research Center for Nosocomial Infectious Diseases, Hiroshima University, Hiroshima, 734-8551, Japan; Department of Infectious Diseases, Hiroshima University Hospital, Hiroshima, 734-8551, Japan; Department of Surgery, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, 734-8551, Japan; Translational Research Center, Hiroshima University, Hiroshima, 734-8551, Japan
| | - Michiya Yokozaki
- Division of Clinical Laboratory Medicine, Hiroshima University Hospital, Hiroshima, 734-8551, Japan
| | - Hiroki Ohge
- Project Research Center for Nosocomial Infectious Diseases, Hiroshima University, Hiroshima, 734-8551, Japan; Department of Infectious Diseases, Hiroshima University Hospital, Hiroshima, 734-8551, Japan
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9
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Sadowy E. Mobile genetic elements beyond the VanB-resistance dissemination among hospital-associated enterococci and other Gram-positive bacteria. Plasmid 2021; 114:102558. [PMID: 33472048 DOI: 10.1016/j.plasmid.2021.102558] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 10/16/2020] [Accepted: 10/19/2020] [Indexed: 12/30/2022]
Abstract
An increasing resistance to vancomycin among clinically relevant enterococci, such as Enterococcus faecalis and Enterococcus faecium is a cause of a great concern, as it seriously limits treatment options. The vanB operon is one of most common determinants of this type of resistance. Genes constituting the operon are located in conjugative transposons, such as Tn1549-type transposons or, more rarely, in ICEEfaV583-type structures. Such elements show differences in structure and size, and reside in various sites of bacterial chromosome or, in the case of Tn1549-type transposons, are also occasionally associated with plasmids of divergent replicon types. While conjugative transposition contributes to the acquisition of Tn1549-type transposons from anaerobic gut commensals by enterococci, chromosomal recombination and conjugal transfer of plasmids appear to represent main mechanisms responsible for horizontal dissemination of vanB determinants among hospital E. faecalis and E. faecium. This review focuses on diversity of genetic elements harbouring vanB determinants in hospital-associated strains of E. faecium and E. faecalis, the mechanisms beyond vanB spread in populations of these bacteria, and provides an overview of the vanB-MGE distribution among other enterococci and Gram-positive bacteria as potential reservoirs of vanB genes.
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Affiliation(s)
- Ewa Sadowy
- Department of Molecular Microbiology, National Medicines Institute, Warsaw, Poland.
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10
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Riccardi N, Monticelli J, Antonello RM, Di Lallo G, Frezza D, Luzzati R, Di Bella S. Therapeutic Options for Infections due to vanB Genotype Vancomycin-Resistant Enterococci. Microb Drug Resist 2020; 27:536-545. [PMID: 32799629 DOI: 10.1089/mdr.2020.0171] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Enterococci are ubiquitous, facultative, anaerobic Gram-positive bacteria that mainly reside, as part of the normal microbiota, in the gastrointestinal tracts of several animal species, including humans. These bacteria have the capability to turn from a normal gut commensal organism to an invasive pathogen in patients debilitated by prolonged hospitalization, concurrent illnesses, and/or exposed to broad-spectrum antibiotics. The majority of vancomycin-resistant enterococcus (VRE) infections are linked to the vanA genotype; however, outbreaks caused by vanB-type VREs have been increasingly reported, representing a new challenge for effective antimicrobial treatment. Teicoplanin, daptomycin, fosfomycin, and linezolid are useful antimicrobials for infections due to vanB enterococci. In addition, new drugs have been developed (e.g., dalbavancin, telavancin, and tedizolid), new molecules will soon be available (e.g., eravacycline, omadacycline, and oritavancin), and new treatment strategies are progressively being used in clinical practice (e.g., combination therapies and bacteriophages). The aim of this article is to discuss the pathogenesis of infections due to enterococci harboring the vanB operon (vanBVRE) and their therapeutic, state-of-the-art, and future treatment options and provide a comprehensive and easy to use review for clinical purposes.
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Affiliation(s)
- Niccolò Riccardi
- Department of Infectious-Tropical Diseases and Microbiology, IRCCS Sacro Cuore Don Calabria Hospital, Negrar di Valpolicella, Verona, Italy
| | - Jacopo Monticelli
- Hospital Direction, AULSS6 Euganea Ospedali Riuniti Padova Sud, Monselice, Italy
| | | | - Gustavo Di Lallo
- Department of Biology, University of Rome "Tor Vergata," Rome, Italy
| | - Domenico Frezza
- Department of Biology, University of Rome "Tor Vergata," Rome, Italy
| | - Roberto Luzzati
- Infectious Diseases Department, Azienda Sanitaria Universitaria Integrata di Trieste, Trieste, Italy
| | - Stefano Di Bella
- Infectious Diseases Department, Azienda Sanitaria Universitaria Integrata di Trieste, Trieste, Italy
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11
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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: 81] [Impact Index Per Article: 20.3] [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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12
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Rapid identification of the vanA/vanB resistance determinant in Enterococcus sp. from blood cultures using the Cepheid Xpert vanA/vanB cartridge system. Diagn Microbiol Infect Dis 2020; 96:114977. [DOI: 10.1016/j.diagmicrobio.2019.114977] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Revised: 11/25/2019] [Accepted: 12/20/2019] [Indexed: 12/20/2022]
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13
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Abstract
Vancomycin-resistant Enterococcus faecium (VREfm) is a globally significant public health threat and was listed on the World Health Organization's 2017 list of high-priority pathogens for which new treatments are urgently needed. Treatment options for invasive VREfm infections are very limited, and outcomes are often poor. Whole-genome sequencing is providing important new insights into VREfm evolution, drug resistance and hospital adaptation, and is increasingly being used to track VREfm transmission within hospitals to detect outbreaks and inform infection control practices. This mini-review provides an overview of recent data on the use of genomics to understand and respond to the global problem of VREfm.
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Affiliation(s)
- Claire Gorrie
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Charlie Higgs
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Glen Carter
- Doherty Applied Microbial Genomics, Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia.,Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Timothy P Stinear
- Doherty Applied Microbial Genomics, Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia.,Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Benjamin Howden
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia.,Department of Infectious Diseases, Austin Health, Heidelberg, Australia.,Doherty Applied Microbial Genomics, Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
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14
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Antibiotic resistance genes in the Actinobacteria phylum. Eur J Clin Microbiol Infect Dis 2019; 38:1599-1624. [PMID: 31250336 DOI: 10.1007/s10096-019-03580-5] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Accepted: 05/01/2019] [Indexed: 02/07/2023]
Abstract
The Actinobacteria phylum is one of the oldest bacterial phyla that have a significant role in medicine and biotechnology. There are a lot of genera in this phylum that are causing various types of infections in humans, animals, and plants. As well as antimicrobial agents that are used in medicine for infections treatment or prevention of infections, they have been discovered of various genera in this phylum. To date, resistance to antibiotics is rising in different regions of the world and this is a global health threat. The main purpose of this review is the molecular evolution of antibiotic resistance in the Actinobacteria phylum.
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15
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Hashimoto Y, Kurushima J, Nomura T, Tanimoto K, Tamai K, Yanagisawa H, Shirabe K, Ike Y, Tomita H. Dissemination and genetic analysis of the stealthy vanB gene clusters of Enterococcus faecium clinical isolates in Japan. BMC Microbiol 2018; 18:213. [PMID: 30545294 PMCID: PMC6293572 DOI: 10.1186/s12866-018-1342-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Accepted: 11/14/2018] [Indexed: 12/18/2022] Open
Abstract
Background VanB-type vancomycin (VAN) resistance gene clusters confer VAN resistances on Enterococcus spp. over a wide range of MIC levels (MIC = 4–1000 mg/L). However, the epidemiology and the molecular characteristics of the VAN susceptible VanB-type Enterococcus still remain unclear. Results We characterized 19 isolates of VanB-type Enterococcus faecium that might colonize in the gut and were not phenotypically resistant to VAN (MIC = 3 mg/L). They were obtained from two hospitals in Japan between 2009 and 2010. These isolates had the identical vanB gene cluster and showed same multilocus sequence typing (MLST) (ST78) and the highly related profiles in pulsed-field gel electrophoresis (PFGE). The vanB gene cluster was located on a plasmid, and was transferable to E. faecium and E. faecalis. Notably, from these VanB-type VREs, VAN resistant (MIC≥16 mg/L) mutants could appear at a frequency of 10− 6–10− 7/parent cell in vitro. Most of these revertants acquired mutations in the vanSB gene, while the remainder of the revertants might have other mutations outside of the vanB gene cluster. All of the revertants we tested showed increases in the VAN-dependent expression of the vanB gene cluster, suggesting that the mutations affected the transcriptional activity and increased the VAN resistance. Targeted mutagenesis revealed that three unique nucleotide substitutions in the vanB gene cluster of these strains attenuated VAN resistance. Conclusions In summary, this study indicated that stealthy VanB-type E. faecium strains that have the potential ability to become resistance to VAN could exist in clinical settings. Electronic supplementary material The online version of this article (10.1186/s12866-018-1342-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yusuke Hashimoto
- Department of Bacteriology, Gunma University Graduate School of Medicine, 3-39-22 Showa-machi, Maebashi, Gunma, 371-8511, Japan
| | - Jun Kurushima
- Department of Bacteriology, Gunma University Graduate School of Medicine, 3-39-22 Showa-machi, Maebashi, Gunma, 371-8511, Japan
| | - Takahiro Nomura
- Department of Bacteriology, Gunma University Graduate School of Medicine, 3-39-22 Showa-machi, Maebashi, Gunma, 371-8511, Japan
| | - Koichi Tanimoto
- Laboratory of Bacterial Drug Resistance, Gunma University Graduate School of Medicine, 3-39-22 Showa-machi, Maebashi, Gunma, 371-8511, Japan
| | - Kiyoko Tamai
- MIROKU Medical Laboratory Inc, 659-2 Innai, Saku, Nagano, 384-2201, Japan
| | - Hideji Yanagisawa
- MIROKU Medical Laboratory Inc, 659-2 Innai, Saku, Nagano, 384-2201, Japan
| | - Komei Shirabe
- Yamaguchi Prefectural Institute of Public Health and Environment, 2-5-67 Aoi, Yamaguchi, Yamaguchi, 753-0821, Japan
| | - Yasuyoshi Ike
- Department of Bacteriology, Gunma University Graduate School of Medicine, 3-39-22 Showa-machi, Maebashi, Gunma, 371-8511, Japan
| | - Haruyoshi Tomita
- Department of Bacteriology, Gunma University Graduate School of Medicine, 3-39-22 Showa-machi, Maebashi, Gunma, 371-8511, Japan. .,Laboratory of Bacterial Drug Resistance, Gunma University Graduate School of Medicine, 3-39-22 Showa-machi, Maebashi, Gunma, 371-8511, Japan.
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16
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Santona A, Taviani E, Hoang HM, Fiamma M, Deligios M, Ngo TVQ, Van Le A, Cappuccinelli P, Rubino S, Paglietti B. Emergence of unusual vanA/vanB genotype in a highly mutated vanB-vancomycin-resistant hospital-associated E. faecium background in Vietnam. Int J Antimicrob Agents 2018; 52:586-592. [DOI: 10.1016/j.ijantimicag.2018.07.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Revised: 07/02/2018] [Accepted: 07/07/2018] [Indexed: 11/25/2022]
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17
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Hygienemaßnahmen zur Prävention der Infektion durch Enterokokken mit speziellen Antibiotikaresistenzen. Bundesgesundheitsblatt Gesundheitsforschung Gesundheitsschutz 2018; 61:1310-1361. [DOI: 10.1007/s00103-018-2811-2] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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18
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Sadowy E, Gawryszewska I, Kuch A, Żabicka D, Hryniewicz W. The changing epidemiology of VanB Enterococcus faecium in Poland. Eur J Clin Microbiol Infect Dis 2018; 37:927-936. [PMID: 29442195 PMCID: PMC5916999 DOI: 10.1007/s10096-018-3209-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Accepted: 02/01/2018] [Indexed: 01/02/2023]
Abstract
Increasing prevalence of VanB Enterococcus faecium in Polish hospitals reported to National Reference Centre for Susceptibility Testing (NRCST) prompted us to investigate the basis of this phenomenon. Two-hundred seventy-eight E. faecium isolates of VanB phenotype from the period 1999 to 2010 obtained by NRCST were investigated by multilocus sequence typing (MLST) and multilocus VNTR analysis (MLVA). Localization, transferability, and partial structure of the vanB-carrying Tn1549 transposon were studied by hybridization, PCR mapping, sequencing, and conjugation. VanB isolates almost exclusively represented hospital-associated E. faecium, with a significant shift from representatives of 17/18 lineage to 78 lineage after 2005. The vanB determinant, initially located mostly on transferable plasmids of the pRUM-, pLG1-, and pRE25-replicon types, later on was found almost exclusively on the host chromosome. Fifteen different plasmid and chromosomal insertion sites were identified, typically associated with single transposon coupling sequences, mostly not observed before. Our study demonstrates the significant change in the epidemiology of VanB-E. faecium in Poland, associated with the introduction and spread of the lineage 78 of the hospital-adapted E. faecium. These data point to the importance of the lineage 78 for the spread of vancomycin-resistance, determined by the vanB gene cluster, resulting in an increasing VRE prevalence in hospitals. This study also supports the scenario, in which representatives of the hospital-associated E. faecium independently acquire the vanB determinant de novo and spread within and among hospitals, concomitantly undergoing differentiation.
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Affiliation(s)
- Ewa Sadowy
- Department of Molecular Microbiology, National Medicines Institute, ul. Chełmska 30/34, 00-725, Warsaw, Poland.
| | - Iwona Gawryszewska
- Department of Molecular Microbiology, National Medicines Institute, ul. Chełmska 30/34, 00-725, Warsaw, Poland
| | - Alicja Kuch
- Department of Epidemiology and Clinical Microbiology, National Medicines Institute, Chełmska 30/34, 00-725, Warsaw, Poland
| | - Dorota Żabicka
- Department of Epidemiology and Clinical Microbiology, National Medicines Institute, Chełmska 30/34, 00-725, Warsaw, Poland
| | - Waleria Hryniewicz
- Department of Epidemiology and Clinical Microbiology, National Medicines Institute, Chełmska 30/34, 00-725, Warsaw, Poland
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19
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Mahony AA, Buultjens AH, Ballard SA, Grabsch EA, Xie S, Seemann T, Stuart RL, Kotsanas D, Cheng A, Heffernan H, Roberts SA, Coombs GW, Bak N, Ferguson JK, Carter GC, Howden BP, Stinear TP, Johnson PDR. Vancomycin-resistant Enterococcus faecium sequence type 796 - rapid international dissemination of a new epidemic clone. Antimicrob Resist Infect Control 2018; 7:44. [PMID: 29588851 PMCID: PMC5863837 DOI: 10.1186/s13756-018-0335-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Accepted: 03/14/2018] [Indexed: 02/07/2023] Open
Abstract
Background Vancomycin-resistant Enterococcus faecium (VRE) is a leading cause of hospital-acquired infections. New, presumably better-adapted strains of VRE appear unpredictably; it is uncertain how they spread despite improved infection control. We aimed to investigate the relatedness of a novel sequence type (ST) of vanB E. faecium - ST796 - very near its time of origin from hospitals in three Australian states and New Zealand. Methods Following near-simultaneous outbreaks of ST796 in multiple institutions, we gathered then tested colonization and bloodstream infection isolates’ antimicrobial resistance (AMR) phenotypes, and phylogenomic relationships using whole genome sequencing (WGS). Patient meta-data was explored to trace the spread of ST796. Results A novel clone of vanB E. faecium (ST796) was first detected at one Australian hospital in late 2011, then in two New Zealand hospitals linked by inter-hospital transfers from separate Melbourne hospitals. ST796 also appeared in hospitals in South Australia and New South Wales and was responsible for at least one major colonization outbreak in a Neonatal Intensive Care Unit without identifiable links between centers. No exceptional AMR was detected in the isolates. While WGS analysis showed very limited diversity at the core genome, consistent with recent emergence of the clone, clustering by institution was observed. Conclusions Evolution of new E. faecium clones, followed by recognized or unrecognized movement of colonized individuals then rapid intra-institutional cross-transmission best explain the multi-center, multistate and international outbreak we observed. Electronic supplementary material The online version of this article (10.1186/s13756-018-0335-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Andrew A Mahony
- 1Department of Infectious Diseases, Austin Health, 145 Studley Rd, Heidelberg, VIC 3084 Australia.,2Department of Medicine, The University of Melbourne, Heidelberg, VIC 3084 Australia
| | - Andrew H Buultjens
- 3Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000 Australia
| | - Susan A Ballard
- 1Department of Infectious Diseases, Austin Health, 145 Studley Rd, Heidelberg, VIC 3084 Australia.,4Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000 Australia
| | | | - Shirley Xie
- 5Department of Microbiology, Austin Health, Heidelberg, VIC 3084 Australia
| | - Torsten Seemann
- 6Melbourne Bioinformatics, The University of Melbourne, Parkville, VIC 3010 Australia
| | - Rhonda L Stuart
- 7Monash Infectious Diseases, Monash Health, Clayton, VIC 3168 Australia
| | - Despina Kotsanas
- 7Monash Infectious Diseases, Monash Health, Clayton, VIC 3168 Australia
| | - Allen Cheng
- 8Department of Infectious Diseases, Alfred Health, School of Public Health and Preventive Medicine, Monash University, Prahran, VIC 3181 Australia
| | - Helen Heffernan
- 9Antimicrobial Reference Laboratory, Institute of Environmental Science and Research (ESR), Wellington, 5022 New Zealand
| | - Sally A Roberts
- 10Department of Clinical Microbiology, Auckland District Health Board, Auckland, 1051 New Zealand
| | - Geoffrey W Coombs
- 11School of Veterinary and Life Sciences, Murdoch University, Murdoch, WA 6150 Australia.,12Microbiology Department, PathWest Laboratory Medicine - WA, Fiona Stanley Hospital, Murdoch, WA 6150 Australia
| | - Narin Bak
- 13Department of Infectious Diseases, Royal Adelaide Hospital, Adelaide, South Australia 5000 Australia
| | - John K Ferguson
- Division of Microbiology, Health Pathology, NSW Department of Immunology and Infectious Diseases, John Hunter Hospital, University of Newcastle, Newcastle, NSW 2305 Australia
| | - Glen C Carter
- 4Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000 Australia
| | - Benjamin P Howden
- 3Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000 Australia.,4Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000 Australia
| | - Timothy P Stinear
- 3Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000 Australia
| | - Paul D R Johnson
- 1Department of Infectious Diseases, Austin Health, 145 Studley Rd, Heidelberg, VIC 3084 Australia.,2Department of Medicine, The University of Melbourne, Heidelberg, VIC 3084 Australia.,3Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000 Australia
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20
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Rubio-Cosials A, Schulz EC, Lambertsen L, Smyshlyaev G, Rojas-Cordova C, Forslund K, Karaca E, Bebel A, Bork P, Barabas O. Transposase-DNA Complex Structures Reveal Mechanisms for Conjugative Transposition of Antibiotic Resistance. Cell 2018; 173:208-220.e20. [PMID: 29551265 PMCID: PMC5871717 DOI: 10.1016/j.cell.2018.02.032] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Revised: 01/08/2018] [Accepted: 02/12/2018] [Indexed: 12/28/2022]
Abstract
Conjugative transposition drives the emergence of multidrug resistance in diverse bacterial pathogens, yet the mechanisms are poorly characterized. The Tn1549 conjugative transposon propagates resistance to the antibiotic vancomycin used for severe drug-resistant infections. Here, we present four high-resolution structures of the conserved Y-transposase of Tn1549 complexed with circular transposon DNA intermediates. The structures reveal individual transposition steps and explain how specific DNA distortion and cleavage mechanisms enable DNA strand exchange with an absolute minimum homology requirement. This appears to uniquely allow Tn916-like conjugative transposons to bypass DNA homology and insert into diverse genomic sites, expanding gene transfer. We further uncover a structural regulatory mechanism that prevents premature cleavage of the transposon DNA before a suitable target DNA is found and generate a peptide antagonist that interferes with the transposase-DNA structure to block transposition. Our results reveal mechanistic principles of conjugative transposition that could help control the spread of antibiotic resistance genes. Antibiotic resistance-carrying conjugative transposon integrase structure revealed DNA distortion and special cleavage site allow insertion into diverse genomic sites Key structural features are conserved among numerous conjugative transposons Structures uncover auto-inhibition, allowing transposition antagonist design
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Affiliation(s)
- Anna Rubio-Cosials
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany
| | - Eike C Schulz
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany; Hamburg Outstation, European Molecular Biology Laboratory, 22603 Hamburg, Germany
| | - Lotte Lambertsen
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany
| | - Georgy Smyshlyaev
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany; European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Hinxton CB10 1SD, UK
| | - Carlos Rojas-Cordova
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany
| | - Kristoffer Forslund
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany
| | - Ezgi Karaca
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany; Izmir Biomedicine and Genome Center (IBG), 35340 Izmir, Turkey
| | - Aleksandra Bebel
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany
| | - Peer Bork
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany; Max Delbrück Center for Molecular Medicine, 13125 Berlin, Germany; Molecular Medicine Partnership Unit, 69120 Heidelberg, Germany; Department of Bioinformatics, Biocenter, University of Würzburg, 97074 Würzburg, Germany
| | - Orsolya Barabas
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany.
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21
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Lambertsen L, Rubio-Cosials A, Patil KR, Barabas O. Conjugative transposition of the vancomycin resistance carrying Tn1549: enzymatic requirements and target site preferences. Mol Microbiol 2018; 107:639-658. [PMID: 29271522 DOI: 10.1111/mmi.13905] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Revised: 12/19/2017] [Accepted: 12/19/2017] [Indexed: 11/30/2022]
Abstract
Rapid spread of resistance to vancomycin has generated difficult to treat bacterial pathogens worldwide. Though vancomycin resistance is often conferred by the conjugative transposon Tn1549, it is yet unclear whether Tn1549 moves actively between bacteria. Here we demonstrate, through development of an in vivo assay system, that a mini-Tn1549 can transpose in E. coli away from its natural Gram-positive host. We find the transposon-encoded INT enzyme and its catalytic tyrosine Y380 to be essential for transposition. A second Tn1549 protein, XIS is important for efficient and accurate transposition. We further show that DNA flanking the left transposon end is critical for excision, with changes to nucleotides 7 and 9 impairing movement. These mutations could be partially compensated for by changing the final nucleotide of the right transposon end, implying concerted excision of the two ends. With changes in these essential DNA sequences, or without XIS, a large amount of flanking DNA transposes with Tn1549. This rescues mobility and allows the transposon to capture and transfer flanking genomic DNA. We further identify the transposon integration target sites as TTTT-N6-AAAA. Overall, our results provide molecular insights into conjugative transposition and the adaptability of Tn1549 for efficient antibiotic resistance transfer.
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Affiliation(s)
- Lotte Lambertsen
- European Molecular Biology Laboratory (EMBL), Structural and Computational Biology Unit, Meyerhofstrasse 1, D-69117 Heidelberg, Germany
| | - Anna Rubio-Cosials
- European Molecular Biology Laboratory (EMBL), Structural and Computational Biology Unit, Meyerhofstrasse 1, D-69117 Heidelberg, Germany
| | - Kiran Raosaheb Patil
- European Molecular Biology Laboratory (EMBL), Structural and Computational Biology Unit, Meyerhofstrasse 1, D-69117 Heidelberg, Germany
| | - Orsolya Barabas
- European Molecular Biology Laboratory (EMBL), Structural and Computational Biology Unit, Meyerhofstrasse 1, D-69117 Heidelberg, Germany
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22
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Vancomycin-Resistant Enterococci (VRE) in The Intensive Care Unit in a Nonoutbreak Setting: Identification of Potential Reservoirs and Epidemiological Associations Between Patient and Environmental VRE. Infect Control Hosp Epidemiol 2017; 39:40-45. [DOI: 10.1017/ice.2017.248] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
OBJECTIVEAmong nosocomial bloodstream infections caused by enterococcal species, Ireland has the highest proportion caused by vancomycin-resistant enterococci (VRE) in Europe at 45.8%. The contribution of the near-patient environment to VRE transmission outside of outbreaks was investigated.DESIGNA prospective observational study was conducted during 7 sampling periods.METHODSRecovery of VRE isolates by swabbing the near-patient environment and patients in the intensive care unit (ICU) was conducted to identify reservoirs, clinical and molecular epidemiological associations, and the success of active surveillance cultures (ASCs).RESULTSOf 289 sampling occasions involving 157 patients and their bed spaces, VRE isolates were recovered from patient bed spaces, clinical samples, or both on 114 of 289 sampling occasions (39.4%). The patient and their bed space were positive for VRE on 34 of 114 VRE-associated sampling occasions (29.8%). Of 1,647 environment samples, 107 sites (6.5%) were VRE positive, with significantly greater VRE recovery from isolation rooms than from the open-plan area (9.1% vs 4.1%;P< .0001). The most frequently VRE-contaminated sites were the drip stand, bed control panel, and chart holders, which together accounted for 61% of contaminated sites. The use of ASCs resulted in a 172% increase in identification of VRE-colonized patients. Molecular typing revealed 2 environmental clusters, 1 cluster involving 3 patients and generally greater heterogeneity of patient isolates compared to environmental isolates.CONCLUSIONEven outside of outbreaks, near-patient ICU environmental contamination with VRE is common. Better infection control policies that limit environmental transmission of VRE in the ICU and that are supported by molecular epidemiological studies, in real time, are needed.Infect Control Hosp Epidemiol2018;39:40–45
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23
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Milanović V, Osimani A, Aquilanti L, Tavoletti S, Garofalo C, Polverigiani S, Litta-Mulondo A, Cocolin L, Ferrocino I, Di Cagno R, Turroni S, Lazzi C, Pellegrini N, Clementi F. Occurrence of antibiotic resistance genes in the fecal DNA of healthy omnivores, ovo-lacto vegetarians and vegans. Mol Nutr Food Res 2017; 61. [PMID: 28464483 DOI: 10.1002/mnfr.201601098] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Revised: 04/12/2017] [Accepted: 04/18/2017] [Indexed: 01/08/2023]
Abstract
SCOPE The effects of long-term omnivore, ovo-lacto vegetarian and vegan diets on the occurrence of 12 antibiotic resistance (AR) genes in the human gut were studied. METHODS AND RESULTS The feces of 144 healthy volunteers recruited from Turin, Bari, Bologna, and Parma were screened for the occurrence of genes conferring resistance to tetracyclines, macrolide-lincosamide-streptogramin B, vancomycin, and β-lactams. Overall, erm(B), tet(W) and tet(M) were detected at the highest frequency. A low effect from the diet on the AR gene distribution emerged, with tet(K) and vanB occurring at a lower and higher frequency in vegans and omnivores, respectively. A correlation of the intake of eggs, milk from animal sources and cheese with an increased occurrence of tet(K) was observed, together with a higher incidence of vanB in consumers of eggs, poultry meat, fish and seafood. When the detection frequencies of AR genes in volunteers from Bari and the other sites were comparatively evaluated, a north-to-south gradient was observed, whereas no effect of sex or age was highlighted. Except for tet(K), a negligible three-factor interaction was seen. CONCLUSION A high impact of the geographical location on AR gene distribution was seen in the cohort of subjects analyzed, irrespective of their dietary habits.
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Affiliation(s)
- Vesna Milanović
- Department of Agricultural, Food and Environmental Sciences (D3A), Università Politecnica delle Marche, Ancona, Italy
| | - Andrea Osimani
- Department of Agricultural, Food and Environmental Sciences (D3A), Università Politecnica delle Marche, Ancona, Italy
| | - Lucia Aquilanti
- Department of Agricultural, Food and Environmental Sciences (D3A), Università Politecnica delle Marche, Ancona, Italy
| | - Stefano Tavoletti
- Department of Agricultural, Food and Environmental Sciences (D3A), Università Politecnica delle Marche, Ancona, Italy
| | - Cristiana Garofalo
- Department of Agricultural, Food and Environmental Sciences (D3A), Università Politecnica delle Marche, Ancona, Italy
| | - Serena Polverigiani
- Department of Agricultural, Food and Environmental Sciences (D3A), Università Politecnica delle Marche, Ancona, Italy
| | - Alice Litta-Mulondo
- Department of Agricultural, Food and Environmental Sciences (D3A), Università Politecnica delle Marche, Ancona, Italy
| | - Luca Cocolin
- Department of Agricultural, Forest and Food Science (DISAFA), University of Turin, Grugliasco, Italy
| | - Ilario Ferrocino
- Department of Agricultural, Forest and Food Science (DISAFA), University of Turin, Grugliasco, Italy
| | - Raffaella Di Cagno
- Faculty of Science and Technology, Libera Università di Bolzano, Bolzano, Italy
| | - Silvia Turroni
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum, University of Bologna, Bologna, Italy
| | - Camilla Lazzi
- Department of Food Science, University of Parma, Parma, Italy
| | | | - Francesca Clementi
- Department of Agricultural, Food and Environmental Sciences (D3A), Università Politecnica delle Marche, Ancona, Italy
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24
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Ferreira TG, Moura H, Barr JR, Pilotto Domingues RMC, Ferreira EDO. Ribotypes associated with Clostridium difficile outbreaks in Brazil display distinct surface protein profiles. Anaerobe 2017; 45:120-128. [PMID: 28435010 DOI: 10.1016/j.anaerobe.2017.04.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Revised: 03/28/2017] [Accepted: 04/01/2017] [Indexed: 11/18/2022]
Abstract
Clostridium difficile is a spore-forming anaerobic intestinal pathogen that causes Clostridium difficile infection (CDI). C. difficile is the leading cause of toxin-mediated nosocomial antibiotic-associated diarrhea. The pathogenesis of CDI is attributed to two major virulence factors, TcdA and TcdB toxins, that cause the symptomatic infection. C. difficile also expresses a number of key proteins, including cell wall proteins (CWPs). S-layer proteins (SLPs) are CWPs that form a paracrystalline surface array that coats the surface of the bacterium. SLPs have a role in C. difficile binding to the gastrointestinal tract, but their importance in virulence need to be better elucidated. Here, we describe bottom-up proteomics analysis of surface-enriched proteins fractions obtained through glycine extraction of five C. difficile clinical isolates from Brazil using gel-based and gel-free approaches. We were able to identify approximately 250 proteins for each strain, among them SlpA, Cwp2, Cwp6, CwpV and Cwp84. Identified CWPs presented different amino acid coverage, which might suggest differences in post-translational modifications. Proteomic analysis of SLPs from ribotype 133, agent of C. difficile outbreaks in Brazil, revealed unique proteins and provided additional information towards in depth characterization of the strains causing CDI in Brazil.
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Affiliation(s)
- Thais Gonçalves Ferreira
- Universidade Federal do Rio de Janeiro, Instituto de Microbiologia Paulo de Góes, Laboratório de Biologia de Anaeróbios, Rio de Janeiro, Brazil
| | - Hercules Moura
- Centers for Disease Control and Prevention - CDC, Division of Laboratory Sciences, Atlanta, GA, USA
| | - John R Barr
- Centers for Disease Control and Prevention - CDC, Division of Laboratory Sciences, Atlanta, GA, USA
| | - Regina M C Pilotto Domingues
- Universidade Federal do Rio de Janeiro, Instituto de Microbiologia Paulo de Góes, Laboratório de Biologia de Anaeróbios, Rio de Janeiro, Brazil.
| | - Eliane de Oliveira Ferreira
- Universidade Federal do Rio de Janeiro, Instituto de Microbiologia Paulo de Góes, Laboratório de Biologia de Anaeróbios, Rio de Janeiro, Brazil; Universidade Federal do Rio de Janeiro - Polo Xerém, Rio de Janeiro, Brazil
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Holzknecht B, Hansen D, Nielsen L, Kailow A, Jarløv J. Screening for vancomycin-resistant enterococci with Xpert® vanA/vanB: diagnostic accuracy and impact on infection control decision making. New Microbes New Infect 2017; 16:54-59. [PMID: 28203378 PMCID: PMC5295639 DOI: 10.1016/j.nmni.2016.12.020] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Revised: 12/21/2016] [Accepted: 12/26/2016] [Indexed: 11/24/2022] Open
Abstract
Vancomycin-resistant enterococci (VRE) are increasingly important nosocomial pathogens and screening for colonization status is a mainstay in infection control. We implemented PCR-based screening during vanA-positive Enterococcus faecium outbreaks in four university hospitals in Copenhagen, Denmark. Xpert®vanA/vanB was performed directly on rectal swabs and the vanA PCR result was used to guide infection control measures. Concurrently, all samples were selectively cultured including an overnight enrichment step. Diagnostic accuracy was calculated as well as turnaround time and the impact of the earlier available PCR results on infection control decision making. In all, 1110 samples were analysed. The vanA PCR positivity rate was 13.8% and culture positivity rate was 15.2%. The diagnostic accuracy of the vanA part of the assay was high with a sensitivity of 87.1%, a specificity of 99.7%, and positive and negative predictive values of 98.0% and 97.7%, respectively. The vanB PCR had a considerably lower specificity of 77.6% and a positive predictive value of 0.4%. In 1067 (96.1%) samples, PCR results were reported within 1 day, whereas median culture turnaround time was 3 days. The saving of time to available results corresponded to 141 saved isolation days and 292 saved transmission risk days. False-negative or false-positive PCR results led to six additional transmission risk days and 13 additional isolation days, respectively. The vanA PCR had high diagnostic accuracy and the prompt availability of results gave a considerable benefit for infection control decision making.
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Affiliation(s)
- B.J. Holzknecht
- Department of Clinical Microbiology, Herlev and Gentofte Hospital, University of Copenhagen, Herlev, Denmark
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A Phenotypically Silent vanB2 Operon Carried on a Tn1549-Like Element in Clostridium difficile. mSphere 2016; 1:mSphere00177-16. [PMID: 27536735 PMCID: PMC4980698 DOI: 10.1128/msphere.00177-16] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2016] [Accepted: 07/22/2016] [Indexed: 11/20/2022] Open
Abstract
In the last decade, Clostridium difficile infection (CDI) has reached an epidemic state with increasing incidence and severity in both health care and community settings. Vancomycin is an important first-line therapy for CDI, and the emergence of resistance would have significant clinical consequences. In this study, we describe for the first time a vanB2 vancomycin resistance operon in C. difficile, isolated from an Australian veal calf at slaughter. The operon was carried on an ~42-kb element showing significant homology and synteny to Tn1549, a conjugative transposon linked with the emergence and global dissemination of vancomycin-resistant enterococci (VRE). Notably, the C. difficile strain did not show any reduced susceptibility to vancomycin in vitro (MIC, 1 mg/liter), possibly as a result of an aberrant vanRB gene. As observed for other anaerobic species of the animal gut microbiota, C. difficile may be a reservoir of clinically important vancomycin resistance genes. IMPORTANCE In an era when the development of new antimicrobial drugs is slow, vancomycin remains the preferred antimicrobial therapy for Clostridium difficile infection (CDI), the most important health care-related infection in the world today. The emergence of resistance to vancomycin would have significant consequences in relation to treating patients with CDI. In this paper, we describe for the first time a complete set of vancomycin resistance genes in C. difficile. The genes were very similar to genes found in vancomycin-resistant enterococci (VRE) that were associated with the emergence and global dissemination of this organism. Fortunately, the C. difficile strain did not show any reduced susceptibility to vancomycin in vitro (MIC, 1 mg/liter), possibly because of a small difference in one gene. However, this observation signals that we may be very close to seeing a fully vancomycin-resistant strain of C. difficile.
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Jouhten H, Mattila E, Arkkila P, Satokari R. Reduction of Antibiotic Resistance Genes in Intestinal Microbiota of Patients With Recurrent Clostridium difficile Infection After Fecal Microbiota Transplantation. Clin Infect Dis 2016; 63:710-1. [PMID: 27317794 DOI: 10.1093/cid/ciw390] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Affiliation(s)
- Hanne Jouhten
- Immunobiology Research Program, Faculty of Medicine, University of Helsinki
| | | | - Perttu Arkkila
- Department of Gastroenterology, Helsinki University Central Hospital, Finland
| | - Reetta Satokari
- Immunobiology Research Program, Faculty of Medicine, University of Helsinki
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Bender JK, Kalmbach A, Fleige C, Klare I, Fuchs S, Werner G. Population structure and acquisition of the vanB resistance determinant in German clinical isolates of Enterococcus faecium ST192. Sci Rep 2016; 6:21847. [PMID: 26902259 PMCID: PMC4763178 DOI: 10.1038/srep21847] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Accepted: 01/29/2016] [Indexed: 12/28/2022] Open
Abstract
In the context of the global action plan to reduce the dissemination of antibiotic resistances it is of utmost importance to understand the population structure of resistant endemic bacterial lineages and to elucidate how bacteria acquire certain resistance determinants. Vancomycin resistant enterococci represent one such example of a prominent nosocomial pathogen on which nation-wide population analyses on prevalent lineages are scarce and data on how the bacteria acquire resistance, especially of the vanB genotype, are still under debate. With respect to Germany, an increased prevalence of VRE was noted in recent years. Here, invasive infections caused by sequence type ST192 VRE are often associated with the vanB-type resistance determinant. Hence, we analyzed 49 vanB-positive and vanB-negative E. faecium isolates by means of whole genome sequencing. Our studies revealed a distinct population structure and that spread of the Tn1549-vanB-type resistance involves exchange of large chromosomal fragments between vanB-positive and vanB-negative enterococci rather than independent acquisition events. In vitro filter-mating experiments support the hypothesis and suggest the presence of certain target sequences as a limiting factor for dissemination of the vanB element. Thus, the present study provides a better understanding of how enterococci emerge into successful multidrug-resistant nosocomial pathogens.
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Affiliation(s)
- Jennifer K Bender
- National Reference Centre for Staphylococci and Enterococci, Robert Koch Institute, Department of Infectious Diseases, Wernigerode, 38855, Germany
| | - Alexander Kalmbach
- National Reference Centre for Staphylococci and Enterococci, Robert Koch Institute, Department of Infectious Diseases, Wernigerode, 38855, Germany
| | - Carola Fleige
- National Reference Centre for Staphylococci and Enterococci, Robert Koch Institute, Department of Infectious Diseases, Wernigerode, 38855, Germany
| | - Ingo Klare
- National Reference Centre for Staphylococci and Enterococci, Robert Koch Institute, Department of Infectious Diseases, Wernigerode, 38855, Germany
| | - Stephan Fuchs
- National Reference Centre for Staphylococci and Enterococci, Robert Koch Institute, Department of Infectious Diseases, Wernigerode, 38855, Germany
| | - Guido Werner
- National Reference Centre for Staphylococci and Enterococci, Robert Koch Institute, Department of Infectious Diseases, Wernigerode, 38855, Germany
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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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Abstract
Purpose of review Hand hygiene and isolation are basic, but very effective, means of preventing the spread of pathogens in healthcare. Although the principle may be straightforward, this review highlights some of the controversies regarding the implementation and efficacy of these interventions. Recent findings Hand hygiene compliance is an accepted measure of quality and safety in many countries. The evidence for the efficacy of hand hygiene in directly reducing rates of hospital-acquired infections has strengthened in recent years, particularly in terms of reduced rates of staphylococcal sepsis. Defining the key components of effective implementation strategies and the ideal method(s) of assessing hand hygiene compliance are dependent on a range of factors associated with the healthcare system. Although patient isolation continues to be an important strategy, particularly in outbreaks, it also has some limitations and can be associated with negative effects. Recent detailed molecular epidemiology studies of key healthcare-acquired pathogens have questioned the true efficacy of isolation, alone as an effective method for the routine prevention of disease transmission. Summary Hand hygiene and isolation are key components of basic infection control. Recent insights into the benefits, limitations and even adverse effects of these interventions are important for their optimal implementation.
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Berthet N, Périchon B, Mazuet C, Chapetón-Montes D, Bouchier C, Bouvet P, Legeay C, Popoff MR, Courvalin P. A vanG-type locus in Clostridium argentinense. J Antimicrob Chemother 2015; 70:1942-5. [PMID: 25802283 DOI: 10.1093/jac/dkv073] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2015] [Accepted: 02/24/2015] [Indexed: 11/12/2022] Open
Abstract
OBJECTIVES The objective was to study a new vanG-type locus in Clostridium argentinense vanGCar and to determine its impact on glycopeptide susceptibility of the host. METHODS The whole genome of C. argentinense NCIB 10714 was sequenced using Illumina single-reads sequencing technology. The presence of vanGCar in seven C. argentinense strains was tested by PCR and its expression was tested by quantitative RT-PCR (qRT-PCR). Glycopeptide susceptibility was determined by the Etest procedure. RESULTS The vanGCar locus contained four genes encoding a carboxypeptidase, a d-alanine:d-serine ligase, a serine transporter and a serine racemase, and was present in the seven C. argentinense studied. An AraC-type transcriptional regulator was found upstream from the genes. C. argentinense NCIB 10714 was susceptible to vancomycin and to teicoplanin. qRT-PCR experiments revealed that vanGCar was not expressed without or with induction by a subinhibitory concentration of vancomycin. CONCLUSIONS The new vanGCar locus was cryptic in C. argentinense and intrinsic to this species. Emergence of vancomycin resistance in C. argentinense due to decryptification of the vanGCar gene cluster could occur.
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Affiliation(s)
- Nicolas Berthet
- Centre National de la Recherche Scientifique, UMR3569 Paris, France Centre International de la Recherche Médicale de Franceville, Unité des Zoonoses et Maladies Emergentes, Franceville, Gabon
| | - Bruno Périchon
- Institut Pasteur, Unité des Agents Antibactériens, Paris, France
| | - Christelle Mazuet
- Institut Pasteur, Unité de Recherche et d'Expertise Bactéries Anaérobies et Toxines, Paris, France
| | - Diana Chapetón-Montes
- Institut Pasteur, Unité de Recherche et d'Expertise Bactéries Anaérobies et Toxines, Paris, France
| | | | - Philippe Bouvet
- Institut Pasteur, Unité de Recherche et d'Expertise Bactéries Anaérobies et Toxines, Paris, France
| | - Christine Legeay
- Institut Pasteur, Unité de Recherche et d'Expertise Bactéries Anaérobies et Toxines, Paris, France
| | - Michel-Robert Popoff
- Institut Pasteur, Unité de Recherche et d'Expertise Bactéries Anaérobies et Toxines, Paris, France
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Clinical and microbiological characteristics of Eggerthella lenta bacteremia. J Clin Microbiol 2014; 53:626-35. [PMID: 25520446 DOI: 10.1128/jcm.02926-14] [Citation(s) in RCA: 90] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Eggerthella lenta is an emerging pathogen that has been underrecognized due to historical difficulties with phenotypic identification. Until now, its pathogenicity, antimicrobial susceptibility profile, and optimal treatment have been poorly characterized. In this article, we report the largest cohort of patients with E. lenta bacteremia to date and describe in detail their clinical features, microbiologic characteristics, treatment, and outcomes. We identified 33 patients; the median age was 68 years, and there was no gender predominance. Twenty-seven patients (82%) had serious intra-abdominal pathology, often requiring a medical procedure. Of those who received antibiotics (28/33, 85%), the median duration of treatment was 21.5 days. Mortality from all causes was 6% at 7 days, 12% at 30 days, and 33% at 1 year. Of 26 isolates available for further testing, all were identified as E. lenta by both commercially available matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) systems, and none were found to harbor a vanA or vanB gene. Of 23 isolates which underwent susceptibility testing, all were susceptible to amoxicillin-clavulanate, cefoxitin, metronidazole, piperacillin-tazobactam, ertapenem, and meropenem, 91% were susceptible to clindamycin, 74% were susceptible to moxifloxacin, and 39% were susceptible to penicillin.
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Evaluation of the Xpert vanA/vanB assay using enriched inoculated broths for direct detection of vanB vancomycin-resistant Enterococci. J Clin Microbiol 2014; 52:4293-7. [PMID: 25297325 DOI: 10.1128/jcm.01125-14] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Rapid and accurate detection of VRE (vancomycin-resistant enterococci) is required for adequate antimicrobial treatment and infection prevention measures. Previous studies using PCR for the detection of VRE, including Cepheid's Xpert vanA/vanB assay, reported accurate detection of vanA VRE; however, many false-positive results were found for vanB VRE. This is mainly due to nonenterococcal vanB genes, which can be found in the gut flora. Our goal was to optimize the rapid and accurate detection of vanB VRE and to improve the positive predictive value (PPV) by limiting false-positive results. We evaluated the use of the Xpert vanA/vanB assay on rectal swabs and on enriched inoculated broths for the detection of vanB VRE. By adjusting the cycle threshold (CT) cutoff value to ≤ 25 for positivity by PCR on enriched broths, the sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) were 96.9%, 100%, 100%, and 99.5% for vanB VRE, respectively. As shown in this study, CT values of ≤ 25 acquired from enriched broths can be considered true positive. For broths with CT values between 25 and 30, we recommend confirming the results by culture. CT values of >30 appeared to be true negative. In conclusion, this study shows that the Cepheid's Xpert vanA/vanB assay performed on enriched inoculated broths with an adjusted cutoff CT value is a useful and rapid tool for the detection of vanB VRE.
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Molecular Diagnosis Contributing for Multi-Drug Resistant Infection Control. CURRENT TREATMENT OPTIONS IN INFECTIOUS DISEASES 2014. [DOI: 10.1007/s40506-013-0006-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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Eggerthella lenta bacteremia complicated by spondylodiscitis, psoas abscess, and meningitis. J Clin Microbiol 2014; 52:1278-80. [PMID: 24430458 DOI: 10.1128/jcm.03158-13] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Eggerthella lenta bacteremia is uncommon and generally associated with abdominal sepsis. The organism and its clinical significance have not been well characterized due to historical difficulties with identification. We report a case of severe infection in a paraplegic man complicated by psoas abscess, osteomyelitis, and meningitis and discuss treatment challenges.
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Klare I, Witte W, Wendt C, Werner G. [Vancomycin-resistant enterococci (VRE). Recent results and trends in development of antibiotic resistance]. Bundesgesundheitsblatt Gesundheitsforschung Gesundheitsschutz 2013; 55:1387-400. [PMID: 23114437 DOI: 10.1007/s00103-012-1564-6] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Enterococci (mainly E. faecalis, E. faecium) are important nosocomial pathogens predominantly affecting older and/or immunocompromised patients. The bacteria possess a broad spectrum of intrinsic and acquired antibiotic resistance properties. Among these, the transferrable glycopeptide resistance of the vanA and vanB genotypes in vancomycin-resistant enterococci (VRE; reservoir: E. faecium) as well as resistance to last resort antibiotics (e.g. linezolid and tigecycline) are of special concern. Enterococci (including VRE) are easily transferred in hospitals; however, colonizations are far more frequent than infections. Resistance frequencies for vancomycin in clinical E. faecium isolates have remained at a relatively constant level of 8-15% (but with local or regional variations) in recent years whereas frequencies for teicoplanin resistance have shown a slight decrease. Glycopeptide resistance trends correlate with a spread of hospital-associated E. faecium strains carrying the vanA and, with rising frequency in recent years, the vanB gene cluster, the latter being associated with teicoplanin susceptibility. This increased occurrence of vanB-positive E. faecium strains may be caused by an increased use of antibiotics selecting enterococci and VRE as well as due to methodological reasons (e.g. reduced EUCAST MIC-breakpoints for glycopeptides; increased use and sensitive performance of chromogenic VRE agars, increased use of molecular diagnostic assays).
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Affiliation(s)
- I Klare
- Nationales Referenzzentrum für Staphylokokken und Enterokokken, Robert Koch-Institut, Burgstrasse 37, Wernigerode, Germany.
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ICESluvan, a 94-kilobase mosaic integrative conjugative element conferring interspecies transfer of VanB-type glycopeptide resistance, a novel bacitracin resistance locus, and a toxin-antitoxin stabilization system. J Bacteriol 2013; 195:5381-90. [PMID: 24078615 DOI: 10.1128/jb.02165-12] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A 94-kb integrative conjugative element (ICESluvan) transferable to Enterococcus faecium and Enterococcus faecalis from an animal isolate of Streptococcus lutetiensis consists of a mosaic of genetic fragments from different Gram-positive bacteria. A variant of ICESluvan was confirmed in S. lutetiensis from a patient. A complete Tn5382/Tn1549 with a vanB2 operon is integrated into a streptococcal ICESde3396-like region harboring a putative bacteriophage exclusion system, a putative agglutinin receptor precursor, and key components of a type IV secretion system. Moreover, ICESluvan encodes a putative MobC family mobilization protein and a relaxase and, thus, in total has all genetic components essential for conjugative transfer. A 9-kb element within Tn5382/Tn1549 encodes, among others, putative proteins similar to the TnpX site-specific recombinase in Faecalibacterium and VanZ in Paenibacillus, which may contribute to the detected low-level teicoplanin resistance. Furthermore, ICESluvan encodes a novel bacitracin resistance locus that is associated with reduced susceptibility to bacitracin when transferred to E. faecium. The expression of a streptococcal pezAT toxin-antitoxin-encoding operon of ICESluvan in S. lutetiensis, E. faecium, and E. faecalis was confirmed by reverse transcription (RT)-PCR, indicating an active toxin-antitoxin system which may contribute to stabilizing ICESluvan within new hosts. Junction PCR and DNA sequencing confirmed that ICESluvan excised to form a circular intermediate in S. lutetiensis, E. faecalis, and E. faecium. Transfer between E. faecalis cells was observed in the presence of helper plasmid pIP964. Sequence analysis of the original S. lutetiensis donor and enterococcal transconjugants showed that ICESluvan integrates in a site-specific manner into the C-terminal end of the chromosomal tRNA methyltransferase gene rumA.
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Abstract
UNLABELLED Nosocomial outbreaks of vancomycin-resistant Enterococcus faecium (VREfm) are thought to occur by transmission of VREfm between patients, predicting that infection control interventions will limit cross-transmission. Despite implementation of such strategies, the incidence of VREfm infections continues to rise. We aimed to use genomics to better understand the epidemiology of E. faecium within a large hospital and investigate the reasons for failure of infection control strategies. Whole-genome sequencing was performed on 61 E. faecium (36 VREfm) isolates, predominately from blood cultures collected at a single hospital between 1998 and 2009, and on five vanB-positive anaerobic commensal bacteria isolated from human feces. Phylogenomic analysis and precise mapping of the vanB gene, which contains the Tn1549 transposon, showed that at least 18 of the 36 VREfm isolates had acquired the transposon via independent insertion events, indicating de novo generation of VREfm rather than cross-transmission. Furthermore, Tn1549 sequences found in 15 of the 36 VREfm isolates were the same as the Tn1549 sequence from one of the gut anaerobes. National and international comparator E. faecium isolates were phylogenetically interspersed with isolates from our hospital, suggesting that our findings might be globally representative. These data demonstrate that VREfm generation within a patient is common, presumably occurring in the human bowel during antibiotic therapy, and help explain our inability to reduce VREfm infections. A recommendation from our findings is that infection control practices should include screening patients for specific hospital clones of vancomycin-susceptible E. faecium rather than just VREfm. IMPORTANCE Enterococcus faecium is an increasingly important human pathogen causing predominantly antibiotic-resistant infections in hospitalized patients. Large amounts of health care funding are spent trying to control antibiotic-resistant bacteria in hospitals globally, yet in many institutions around the world, vancomycin-resistant E. faecium (VREfm) infections continue to rise. The new findings from this study help explain the failures of our current approaches to controlling vanB VREfm in health care institutions. Given the importance of this bacterium as a cause of hospital-acquired infections and the difficulties faced by infection control units in trying to prevent colonization in their institutions, the novel findings from this study provide evidence that a new approach to controlling VREfm in hospitals is required. In particular, more attention should be given to understanding the epidemiology of hospital-adapted vancomycin-susceptible E. faecium, and patients at higher risk for de novo generation of VREfm need to be identified and optimally managed.
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Marshall C, Richards M, McBryde E. Do active surveillance and contact precautions reduce MRSA acquisition? A prospective interrupted time series. PLoS One 2013; 8:e58112. [PMID: 23555568 PMCID: PMC3605415 DOI: 10.1371/journal.pone.0058112] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2012] [Accepted: 02/04/2013] [Indexed: 11/19/2022] Open
Abstract
Background Consensus for methicillin-resistant Staphylococcus aureus (MRSA) control has still not been reached. We hypothesised that use of rapid MRSA detection followed by contact precautions and single room isolation would reduce MRSA acquisition. Methods This study was a pre-planned prospective interrupted time series comparing rapid PCR detection and use of long sleeved gowns and gloves (contact precautions) plus single room isolation or cohorting of MRSA colonised patients with a control group. The study took place in a medical-surgical intensive care unit of a tertiary adult hospital between May 21st 2007 and September 21st 2009. The primary outcome was the rate of MRSA acquisition. A segmented regression analysis was performed to determine the trend in MRSA acquisition rates before and after the intervention. Findings The rate of MRSA acquisition was 18.5 per 1000 at risk patient days in the control phase and 7.9 per 1000 at-risk patient days in the intervention phase, with an adjusted hazard ratio 0.39 (95% CI 0.24 to 0.62). Segmented regression analysis showed a decline in MRSA acquisition of 7% per month in the intervention phase, (95%CI 1.9% to 12.8% reduction) which was a significant change in slope compared with the control phase. Secondary analysis found prior exposure to anaerobically active antibiotics and colonization pressure were associated with increased acquisition risk. Conclusion Contact precautions with single room isolation or cohorting were associated with a 60% reduction in MRSA acquisition. While this study was a quasi-experimental design, many measures were taken to strengthen the study, such as accounting for differences in colonisation pressure, hand hygiene compliance and individual risk factors across the groups, and confining the study to one centre to reduce variation in transmission. Use of two research nurses may limit its generalisability to units in which this level of support is available.
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Affiliation(s)
- Caroline Marshall
- Victorian Infectious Diseases Service, Royal Melbourne Hospital and Department of Medicine, University of Melbourne, Parkville, Victoria, Australia.
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Werner G, Coque TM, Franz CMAP, Grohmann E, Hegstad K, Jensen L, van Schaik W, Weaver K. Antibiotic resistant enterococci-tales of a drug resistance gene trafficker. Int J Med Microbiol 2013; 303:360-79. [PMID: 23602510 DOI: 10.1016/j.ijmm.2013.03.001] [Citation(s) in RCA: 116] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Enterococci have been recognized as important hospital-acquired pathogens in recent years, and isolates of E. faecalis and E. faecium are the third- to fourth-most prevalent nosocomial pathogen worldwide. Acquired resistances, especially against penicilin/ampicillin, aminoglycosides (high-level) and glycopeptides are therapeutically important and reported in increasing numbers. On the other hand, isolates of E. faecalis and E. faecium are commensals of the intestines of humans, many vertebrate and invertebrate animals and may also constitute an active part of the plant flora. Certain enterococcal isolates are used as starter cultures or supplements in food fermentation and food preservation. Due to their preferred intestinal habitat, their wide occurrence, robustness and ease of cultivation, enterococci are used as indicators for fecal pollution assessing hygiene standards for fresh- and bathing water and they serve as important key indicator bacteria for various veterinary and human resistance surveillance systems. Enterococci are widely prevalent and genetically capable of acquiring, conserving and disseminating genetic traits including resistance determinants among enterococci and related Gram-positive bacteria. In the present review we aimed at summarizing recent advances in the current understanding of the population biology of enterococci, the role mobile genetic elements including plasmids play in shaping the population structure and spreading resistance. We explain how these elements could be classified and discuss mechanisms of plasmid transfer and regulation and the role and cross-talk of enterococcal isolates from food and food animals to humans.
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Affiliation(s)
- Guido Werner
- National Reference Centre for Stapyhlococci and Enterococci, Division of Nosocomial Pathogens and Antibiotic Resistances, Robert Koch Institute, Wernigerode Branch, Burgstr. 37, 38855 Wernigerode, Germany.
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Twenty-five years of shared life with vancomycin-resistant enterococci: is it time to divorce? J Antimicrob Chemother 2012. [DOI: 10.1093/jac/dks469] [Citation(s) in RCA: 162] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
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Karki S, Houston L, Land G, Bass P, Kehoe R, Borrell S, Watson K, Spelman D, Kennon J, Harrington G, Cheng AC. Prevalence and risk factors for VRE colonisation in a tertiary hospital in Melbourne, Australia: a cross sectional study. Antimicrob Resist Infect Control 2012; 1:31. [PMID: 23039285 PMCID: PMC3523023 DOI: 10.1186/2047-2994-1-31] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2012] [Accepted: 10/01/2012] [Indexed: 11/25/2022] Open
Abstract
UNLABELLED BACKGROUND Vancomycin-resistant Enterococcus (VRE) has been established as a significant health-care associated problem since its first isolation in Australia in 1994. In this study, we measured the point prevalence and identified risk factors associated with vanB VRE colonisation in a tertiary care hospital in Melbourne, Australia where VRE has been endemic for 15 years. METHODS A hospital-wide point prevalence survey was conducted on October 13, 2008 with colonisation detected using rectal swab culture. Patient's demographic and medical information was collected through a review of medical records. Factors associated with VRE colonisation in univariate analysis were included in multivariate logistic regression model to adjust for confounding. RESULTS The prevalence of VRE colonisation on the day of screening was 17.5% (95% CI, 13.7 to 21.9). VRE was detected from patients in each ward with the prevalence ranging from 3% to 29%. Univariate analysis showed the use of any antibiotic, meropenem, ciprofloxacin, diarrhoea and longer length of hospital stay were associated with increased risk of VRE colonisation (p<0.05). However, age, sex, proximity to VRE positive cases, use of other antibiotics including cephalosporins, vancomycin were not associated with increased risk (P>0.05). Multivariate analysis showed the exposure to meropenem (p=0.004), age (≥65 years) (p=0.036) and length of stay ≥7 days (p<0.001) as independent predictors of VRE colonisation. CONCLUSION Our study suggests that exposure to antibiotics may have been more important than recent cross transmission for a high prevalence of vanB VRE colonisation at our hospital.
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Affiliation(s)
- Surendra Karki
- Department of Epidemiology and Preventive Medicine, Infectious Disease Epidemiology Unit, Monash University, Melbourne, Australia
| | | | - Gillian Land
- Infection Prevention and Healthcare Epidemiology Infectious Diseases and Microbiology Unit, Alfred Health, Melbourne, Australia
| | - Pauline Bass
- Infection Prevention and Healthcare Epidemiology Infectious Diseases and Microbiology Unit, Alfred Health, Melbourne, Australia
| | - Rosaleen Kehoe
- Infection Prevention and Healthcare Epidemiology Infectious Diseases and Microbiology Unit, Alfred Health, Melbourne, Australia
| | - Sue Borrell
- Infection Prevention and Healthcare Epidemiology Infectious Diseases and Microbiology Unit, Alfred Health, Melbourne, Australia
| | - Kerrie Watson
- Infection Prevention and Healthcare Epidemiology Infectious Diseases and Microbiology Unit, Alfred Health, Melbourne, Australia
| | | | - Jacqueline Kennon
- Infection Prevention and Healthcare Epidemiology Infectious Diseases and Microbiology Unit, Alfred Health, Melbourne, Australia
| | | | - Allen C Cheng
- Department of Epidemiology and Preventive Medicine, Infectious Disease Epidemiology Unit, Monash University, Melbourne, Australia
- Infection Prevention and Healthcare Epidemiology Infectious Diseases and Microbiology Unit, Alfred Health, Melbourne, Australia
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Klare I, Fleige C, Geringer U, Witte W, Werner G. Performance of three chromogenic VRE screening agars, two Etest(®) vancomycin protocols, and different microdilution methods in detecting vanB genotype Enterococcus faecium with varying vancomycin MICs. Diagn Microbiol Infect Dis 2012; 74:171-6. [PMID: 22901792 DOI: 10.1016/j.diagmicrobio.2012.06.020] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2012] [Revised: 06/12/2012] [Accepted: 06/25/2012] [Indexed: 01/07/2023]
Abstract
Frequencies of vanB-type Enterococcus faecium increased in Europe during the last years. VanB enterococci show various levels of vancomycin MICs even below the susceptible breakpoint challenging a reliable diagnostics. The performance of 3 chromogenic vancomycin-resistant enterococci (VRE) screening agars, 2 Etest® vancomycin protocols, and different microdilution methods to detect 129 clinical vanB E. faecium strains was investigated. Altogether, 112 (87%) were correctly identified as VanB-type Enterococcus by microdilution MICs. An Etest® macromethod protocol was more sensitive than the standard protocol while keeping sufficient specificity in identifying 15 vanA/vanB-negative strains. Three chromogenic VRE agars performed similarly with 121 (94%), 123 (95%), and 124 (96%) vanB isolates that grew on Brilliance™ VRE Agar, CHROMagar™ VRE, and chromID™ VRE agar, respectively. Using identical media and conditions, we did not identify different growth behaviour on agar and in broth. A few vanB strains showed growth of microcolonies inside the Etest® vancomycin inhibition zones, suggesting a VanB heteroresistance phenotype.
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Affiliation(s)
- Ingo Klare
- National Reference Centre for Staphylococci and Enterococci, Division Nosocomial Infections, Department of Infectious Diseases, Robert Koch-Institut, Wernigerode Branch, Germany
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Werner G, Klare I, Fleige C, Geringer U, Witte W, Just HM, Ziegler R. Vancomycin-resistant vanB-type Enterococcus faecium isolates expressing varying levels of vancomycin resistance and being highly prevalent among neonatal patients in a single ICU. Antimicrob Resist Infect Control 2012; 1:21. [PMID: 22958440 PMCID: PMC3533821 DOI: 10.1186/2047-2994-1-21] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2012] [Accepted: 04/14/2012] [Indexed: 11/10/2022] Open
Abstract
UNLABELLED BACKGROUND Vancomycin-resistant isolates of E. faecalis and E. faecium are of special concern and patients at risk of acquiring a VRE colonization/infection include also intensively-cared neonates. We describe here an ongoing high prevalence of VanB type E. faecium in a neonatal ICU hardly to identify by routine diagnostics. METHODS During a 10 months' key period 71 E. faecium isolates including 67 vanB-type isolates from 61 patients were collected non-selectively. Vancomycin resistance was determined by different MIC methods (broth microdilution, Vitek® 2) including two Etest® protocols (McFarland 0.5/2.0. on Mueller-Hinton/Brain Heart Infusion agars). Performance of three chromogenic VRE agars to identify the vanB type outbreak VRE was evaluated (BrillianceTM VRE agar, chromIDTM VRE agar, CHROMagarTM VRE). Isolates were genotyped by SmaI- and CeuI-macrorestriction analysis in PFGE, plasmid profiling, vanB Southern hybridisations as well as MLST typing. RESULTS Majority of vanB isolates (n = 56, 79%) belonged to a single ST192 outbreak strain type showing an identical PFGE pattern and analyzed representative isolates revealed a chromosomal localization of a vanB2-Tn5382 cluster type. Vancomycin MICs in cation-adjusted MH broth revealed a susceptible value of ≤4 mg/L for 31 (55%) of the 56 outbreak VRE isolates. Etest® vancomycin on MH and BHI agars revealed only two vanB VRE isolates with a susceptible result; in general Etest® MIC results were about 1 to 2 doubling dilutions higher than MICs assessed in broth and values after the 48 h readout were 0.5 to 1 doubling dilutions higher for vanB VRE. Of all vanB type VRE only three, three and two isolates did not grow on BrillianceTM VRE agar, chromIDTM VRE agar and CHROMagarTM VRE, respectively. Permanent cross contamination via the patients' surrounding appeared as a possible risk factor for permanent VRE colonization/infection. CONCLUSIONS Low level expression of vanB resistance may complicate a proper routine diagnostics of vanB VRE and mask an ongoing high VRE prevalence. A high inoculum and growth on rich solid media showed the highest sensitivity in identifying vanB type resistance.
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Affiliation(s)
- Guido Werner
- Unit FG13 Nosocomial Infections, Robert Koch-Institute Wernigerode, Wernigerode, Germany
| | - Ingo Klare
- Unit FG13 Nosocomial Infections, Robert Koch-Institute Wernigerode, Wernigerode, Germany
| | - Carola Fleige
- Unit FG13 Nosocomial Infections, Robert Koch-Institute Wernigerode, Wernigerode, Germany
| | - Uta Geringer
- Unit FG13 Nosocomial Infections, Robert Koch-Institute Wernigerode, Wernigerode, Germany
| | - Wolfgang Witte
- Unit FG13 Nosocomial Infections, Robert Koch-Institute Wernigerode, Wernigerode, Germany
| | - Heinz-Michael Just
- Institute for Clinical Hygiene and Infectiology, Hospital Nord der Stadt Nürnberg, Nuremberg, Germany
| | - Renate Ziegler
- Institute for Clinical Hygiene and Infectiology, Hospital Nord der Stadt Nürnberg, Nuremberg, Germany
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45
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Tong SYC, Xie S, Richardson LJ, Ballard SA, Dakh F, Grabsch EA, Grayson ML, Howden BP, Johnson PDR, Giffard PM. High-resolution melting genotyping of Enterococcus faecium based on multilocus sequence typing derived single nucleotide polymorphisms. PLoS One 2011; 6:e29189. [PMID: 22195020 PMCID: PMC3241712 DOI: 10.1371/journal.pone.0029189] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2011] [Accepted: 11/22/2011] [Indexed: 11/18/2022] Open
Abstract
We have developed a single nucleotide polymorphism (SNP) nucleated high-resolution melting (HRM) technique to genotype Enterococcus faecium. Eight SNPs were derived from the E. faecium multilocus sequence typing (MLST) database and amplified fragments containing these SNPs were interrogated by HRM. We tested the HRM genotyping scheme on 85 E. faecium bloodstream isolates and compared the results with MLST, pulsed-field gel electrophoresis (PFGE) and an allele specific real-time PCR (AS kinetic PCR) SNP typing method. In silico analysis based on predicted HRM curves according to the G+C content of each fragment for all 567 sequence types (STs) in the MLST database together with empiric data from the 85 isolates demonstrated that HRM analysis resolves E. faecium into 231 "melting types" (MelTs) and provides a Simpson's Index of Diversity (D) of 0.991 with respect to MLST. This is a significant improvement on the AS kinetic PCR SNP typing scheme that resolves 61 SNP types with D of 0.95. The MelTs were concordant with the known ST of the isolates. For the 85 isolates, there were 13 PFGE patterns, 17 STs, 14 MelTs and eight SNP types. There was excellent concordance between PFGE, MLST and MelTs with Adjusted Rand Indices of PFGE to MelT 0.936 and ST to MelT 0.973. In conclusion, this HRM based method appears rapid and reproducible. The results are concordant with MLST and the MLST based population structure.
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Affiliation(s)
- Steven Y C Tong
- Menzies School of Health Research, Darwin, Northern Territory, Australia.
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46
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Zabicka D, Strzelecki J, Wozniak A, Strzelecki P, Sadowy E, Kuch A, Hryniewicz W. Efficiency of the Cepheid Xpert vanA/vanB assay for screening of colonization with vancomycin-resistant enterococci during hospital outbreak. Antonie van Leeuwenhoek 2011; 101:671-5. [DOI: 10.1007/s10482-011-9681-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2011] [Accepted: 11/18/2011] [Indexed: 11/30/2022]
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47
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Werner G, Serr A, Schütt S, Schneider C, Klare I, Witte W, Wendt C. Comparison of direct cultivation on a selective solid medium, polymerase chain reaction from an enrichment broth, and the BD GeneOhm™ VanR Assay for identification of vancomycin-resistant enterococci in screening specimens. Diagn Microbiol Infect Dis 2011; 70:512-21. [DOI: 10.1016/j.diagmicrobio.2011.04.004] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2011] [Revised: 03/21/2011] [Accepted: 04/06/2011] [Indexed: 11/15/2022]
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48
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Roberts AP, Mullany P. Tn916-like genetic elements: a diverse group of modular mobile elements conferring antibiotic resistance. FEMS Microbiol Rev 2011; 35:856-71. [PMID: 21658082 DOI: 10.1111/j.1574-6976.2011.00283.x] [Citation(s) in RCA: 157] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Antibiotic-resistant Gram-positive bacteria are responsible for morbidity and mortality in healthcare environments. Enterococcus faecium, Enterococcus faecalis, Staphylococcus aureus and Streptococcus pneumoniae can all exhibit clinically relevant multidrug resistance phenotypes due to acquired resistance genes on mobile genetic elements. It is possible that clinically relevant multidrug-resistant Clostridium difficile strains will appear in the future, as the organism is adept at acquiring mobile genetic elements (plasmids and transposons). Conjugative transposons of the Tn916/Tn1545 family, which carry major antibiotic resistance determinants, are transmissible between these different bacteria by a conjugative mechanism during which the elements are excised by a staggered cut from donor cells, converted to a circular form, transferred by cell-cell contact and inserted into recipient cells by a site-specific recombinase. The ability of these conjugative transposons to acquire additional, clinically relevant antibiotic resistance genes importantly contributes to the emergence of multidrug resistance.
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Affiliation(s)
- Adam P Roberts
- Department of Microbial Diseases, UCL Eastman Dental Institute, University College London, London, UK
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49
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Marner ES, Wolk DM, Carr J, Hewitt C, Dominguez LL, Kovacs T, Johnson DR, Hayden RT. Diagnostic accuracy of the Cepheid GeneXpert vanA/vanB assay ver. 1.0 to detect the vanA and vanB vancomycin resistance genes in Enterococcus from perianal specimens. Diagn Microbiol Infect Dis 2011; 69:382-9. [PMID: 21396533 DOI: 10.1016/j.diagmicrobio.2010.11.005] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2010] [Revised: 11/05/2010] [Accepted: 11/07/2010] [Indexed: 11/30/2022]
Abstract
Rapid detection of vancomycin-resistant enterococci (VRE) carriers could be useful to health care facilities to minimize transmission. To that end, we compared the performance of the Cepheid GeneXpert vanA/vanB assay with that of direct and broth-enriched culture methods for detection of VRE from perianal swabs. Enterococci were cultivated on Enterococcosel™ agar with 8 μg/mL vancomycin, Bile Esculin Azide Agar with 6 μg/mL vancomycin, and Bile Esculin Azide Enterococcosel Broth. Compared to the reference standard (combination of direct agar plating, broth-enriched culture, and clinical chart review), the sensitivity, specificity, positive predictive value, and negative predictive value of the vanA/vanB assay were 96.4%, 93.0%, 92.0%, and 96.9%, respectively (n=184). The 95% limit of detection was 100 colony-forming units (CFU)/mL for vanA and 114 CFU/mL for vanB. In summary, the GeneXpert vanA/vanB assay is a rapid and accurate method to identify vanA/vanB-colonized patients for VRE screening programs that use perianal swab specimens.
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50
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Seo JY, Kim PW, Lee JH, Song JH, Peck KR, Chung DR, Kang CI, Ki CS, Lee NY. Evaluation of PCR-based screening for vancomycin-resistant enterococci compared with a chromogenic agar-based culture method. J Med Microbiol 2011; 60:945-949. [DOI: 10.1099/jmm.0.029777-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Ja Young Seo
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Pyung-Whan Kim
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Jang-Ho Lee
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Jae-Hoon Song
- Division of Infectious Disease, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Kyong-Ran Peck
- Division of Infectious Disease, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Doo-Ryeon Chung
- Division of Infectious Disease, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Cheol-In Kang
- Division of Infectious Disease, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Chang-Seok Ki
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Nam Yong Lee
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
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