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Bosnjak M, Karpe AV, Van TTH, Kotsanas D, Jenkin GA, Costello SP, Johanesen P, Moore RJ, Beale DJ, Srikhanta YN, Palombo EA, Larcombe S, Lyras D. Multi-omics analysis of hospital-acquired diarrhoeal patients reveals biomarkers of enterococcal proliferation and Clostridioides difficile infection. Nat Commun 2023; 14:7737. [PMID: 38007555 PMCID: PMC10676382 DOI: 10.1038/s41467-023-43671-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2023] [Accepted: 11/16/2023] [Indexed: 11/27/2023] Open
Abstract
Hospital-acquired diarrhoea (HAD) is common, and often associated with gut microbiota and metabolome dysbiosis following antibiotic administration. Clostridioides difficile is the most significant antibiotic-associated diarrhoeal (AAD) pathogen, but less is known about the microbiota and metabolome associated with AAD and C. difficile infection (CDI) with contrasting antibiotic treatment. We characterised faecal microbiota and metabolome for 169 HAD patients (33 with CDI and 133 non-CDI) to determine dysbiosis biomarkers and gain insights into metabolic strategies C. difficile might use for gut colonisation. The specimen microbial community was analysed using 16 S rRNA gene amplicon sequencing, coupled with untargeted metabolite profiling using gas chromatography-mass spectrometry (GC-MS), and short-chain fatty acid (SCFA) profiling using GC-MS. AAD and CDI patients were associated with a spectrum of dysbiosis reflecting non-antibiotic, short-term, and extended-antibiotic treatment. Notably, extended antibiotic treatment was associated with enterococcal proliferation (mostly vancomycin-resistant Enterococcus faecium) coupled with putative biomarkers of enterococcal tyrosine decarboxylation. We also uncovered unrecognised metabolome dynamics associated with concomitant enterococcal proliferation and CDI, including biomarkers of Stickland fermentation and amino acid competition that could distinguish CDI from non-CDI patients. Here we show, candidate metabolic biomarkers for diagnostic development with possible implications for CDI and vancomycin-resistant enterococci (VRE) treatment.
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Affiliation(s)
- Marijana Bosnjak
- Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Victoria, Australia
| | - Avinash V Karpe
- Environment, Commonwealth Scientific and Industrial Research Organisation, Ecosciences Precinct, Dutton Park, Queensland, Australia
- Department of Chemistry and Biotechnology, Swinburne University of Technology, Hawthorn, Victoria, Australia
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, Acton, ACT, Australia
| | - Thi Thu Hao Van
- School of Science, RMIT University, Bundoora, Victoria, Australia
| | - Despina Kotsanas
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, Acton, ACT, Australia
| | - Grant A Jenkin
- Department of Infectious Diseases, Monash Health, Clayton, Victoria, Australia
| | - Samuel P Costello
- Department of Gastroenterology, The Queen Elizabeth Hospital, Woodville South, South Australia, Australia
| | - Priscilla Johanesen
- Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Victoria, Australia
| | - Robert J Moore
- School of Science, RMIT University, Bundoora, Victoria, Australia
| | - David J Beale
- Environment, Commonwealth Scientific and Industrial Research Organisation, Ecosciences Precinct, Dutton Park, Queensland, Australia
| | - Yogitha N Srikhanta
- Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Victoria, Australia
| | - Enzo A Palombo
- Department of Chemistry and Biotechnology, Swinburne University of Technology, Hawthorn, Victoria, Australia
| | - Sarah Larcombe
- Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Victoria, Australia
| | - Dena Lyras
- Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Victoria, Australia.
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Manolitsis I, Feretzakis G, Katsimperis S, Angelopoulos P, Loupelis E, Skarmoutsou N, Tzelves L, Skolarikos A. A 2-Year Audit on Antibiotic Resistance Patterns from a Urology Department in Greece. J Clin Med 2023; 12:jcm12093180. [PMID: 37176622 PMCID: PMC10178956 DOI: 10.3390/jcm12093180] [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: 03/01/2023] [Revised: 04/21/2023] [Accepted: 04/27/2023] [Indexed: 05/15/2023] Open
Abstract
PURPOSE The high incidence of urinary tract infections (UTIs), often in nosocomial environments, is a major cause of antimicrobial resistance (AMR). The dissemination of antibiotic-resistant infections results in very high health and economic burdens for patients and healthcare systems, respectively. This study aims to determine and present the antibiotic resistance profiles of the most common pathogens in a urology department in Greece. METHODS During the period 2019-2020, we included 12,215 clinical samples of blood and urine specimens that tested positive for the following pathogens: Escherichia coli, Enterococcus faecium, Enterococcus faecalis, Proteus mirabilis, Klebsiella pneumoniae, or Pseudomonas aeruginosa, as these are the most commonly encountered microbes in a urology department. RESULTS The analysis revealed a 22.30% mean resistance rate of E. coli strains with a 76.42% resistance to ampicillin and a 54.76% resistance rate to ciprofloxacin in the two-year period. It also showed an approximately 19% resistance rate of P. mirabilis strains and a mean resistance rate of 46.205% of K. pneumoniae strains, with a decreasing trend during the four semesters (p-value < 0.001), which presented an 80% resistance rate to ampicillin/sulbactam and 73.33% to ciprofloxacin. The resistance to carbapenems was reported to be 39.82%. The analysis revealed a 24.17% mean resistance rate of P. aeruginosa with a declining rate over the two-year period (p-value < 0.001). The P. aeruginosa strains were 38% resistant to fluoroquinolones and presented varying resistance against carbapenems (31.58% against doripenem and 19.79% against meropenem). Regarding the Enteroccocal strains, a 46.91% mean resistance was noted for E. faecium with 100% resistance to ampicillin, and a 24.247% mean resistance rate for E. faecalis strains that were 41% resistant to ciprofloxacin. Both types showed 100% sensitivity to linezolid. CONCLUSIONS The dissemination of antibiotic-resistant pathogens poses the need to implement surveillance programs and, consequently, to develop strategies to prevent the emergence of such pathogens in order to optimize patient outcomes.
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Affiliation(s)
- Ioannis Manolitsis
- Second Department of Urology, Sismanogleio General Hospital, 15126 Marousi, Greece
| | - Georgios Feretzakis
- School of Science and Technology, Hellenic Open University, 26335 Patras, Greece
- Department of Quality Control, Research and Continuing Education, Sismanogleio General Hospital, 15126 Marousi, Greece
| | | | | | | | | | - Lazaros Tzelves
- Second Department of Urology, Sismanogleio General Hospital, 15126 Marousi, Greece
| | - Andreas Skolarikos
- Second Department of Urology, Sismanogleio General Hospital, 15126 Marousi, Greece
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3
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Vancomycin-Resistant Enterococcus faecium and the emergence of new Sequence Types associated with Hospital Infection. Res Microbiol 2023; 174:104046. [PMID: 36858192 DOI: 10.1016/j.resmic.2023.104046] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 02/16/2023] [Accepted: 02/20/2023] [Indexed: 03/02/2023]
Abstract
Enterococcus faecium is a major cause of vancomycin-resistant enterococcal (VRE) infection. New variants of the pathogen have emerged and become dominant in healthcare settings. Two such examples, vanB ST796 and vanA ST1421 sequence types, originally arose in Australia and proceeded to cause VRE outbreaks in other countries. Of concern is the detection of a vancomycin variable enterococcal (VVE) variant of ST1421 in Europe that exhibits a vancomycin-susceptible phenotype but which can revert to resistant in the presence of vancomycin. The recent application of genome sequencing for increasing our understanding of the evolution and spread of VRE is also explored here.
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4
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Piezzi V, Wassilew N, Atkinson A, D'Incau S, Kaspar T, Seth-Smith HMB, Casanova C, Bittel P, Jent P, Sommerstein R, Buetti N, Marschall J. Nosocomial outbreak of vancomycin-resistant Enterococcus faecium (VRE) ST796, Switzerland, 2017 to 2020. Euro Surveill 2022; 27:2200285. [PMID: 36695463 PMCID: PMC9716646 DOI: 10.2807/1560-7917.es.2022.27.48.2200285] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
A large clonal outbreak caused by vancomycin-resistant Enterococcus faecium (VRE) affected the Bern University Hospital group from the end of December 2017 until July 2020. We describe the characteristics of the outbreak and the bundle of infection prevention and control (IPC) measures implemented. The outbreak was first recognised when two concomitant cases of VRE bloodstream infection were identified on the oncology ward. During 32 months, 518 patients in the 1,300-bed hospital group were identified as vanB VRE carriers. Eighteen (3.5%) patients developed an invasive infection, of whom seven had bacteraemia. In 2018, a subset of 328 isolates were analysed by whole genome sequencing, 312 of which were identified as sequence type (ST) 796. The initial IPC measures were implemented with a focus on the affected wards. However, in June 2018, ST796 caused another increase in cases, and the management strategy was intensified and escalated to a hospital-wide level. The clinical impact of this large nosocomial VRE outbreak with the emergent clone ST796 was modest. A hospital-wide approach with a multimodal IPC bundle was successful against this highly transmissible strain.
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Affiliation(s)
- Vanja Piezzi
- Department of Infectious Diseases, University Hospital Bern, University of Bern, Bern, Switzerland
| | - Nasstasja Wassilew
- Department of Infectious Diseases, University Hospital Bern, University of Bern, Bern, Switzerland
| | - Andrew Atkinson
- Department of Infectious Diseases, University Hospital Bern, University of Bern, Bern, Switzerland
| | - Stéphanie D'Incau
- Department of Infectious Diseases, Lucerne Cantonal Hospital, Lucerne, Switzerland
| | - Tanja Kaspar
- Department of Infectious Diseases, University Hospital Bern, University of Bern, Bern, Switzerland
| | - Helena MB Seth-Smith
- Division of Clinical Bacteriology and Mycology, University Hospital Basel, Basel, Switzerland and Applied Microbiology Research, Department of Biomedicine, University of Basel, Basel, Switzerland,Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
| | - Carlo Casanova
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Pascal Bittel
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Philipp Jent
- Department of Infectious Diseases, University Hospital Bern, University of Bern, Bern, Switzerland
| | - Rami Sommerstein
- Department of Infectious Diseases, University Hospital Bern, University of Bern, Bern, Switzerland,Department Health Sciences and Medicine, Clinic St. Anna, University of Lucerne, Lucerne, Switzerland
| | - Niccolò Buetti
- Infection Control Programme, University of Geneva Hospitals and Faculty of Medicine, Geneva, Switzerland,INSERM, IAME, Université Paris-Cité, Paris, France
| | - Jonas Marschall
- Department of Infectious Diseases, University Hospital Bern, University of Bern, Bern, Switzerland,Division of Infectious Diseases, Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO, United States
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5
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Sanderson H, Gray KL, Manuele A, Maguire F, Khan A, Liu C, Navanekere Rudrappa C, Nash JHE, Robertson J, Bessonov K, Oloni M, Alcock BP, Raphenya AR, McAllister TA, Peacock SJ, Raven KE, Gouliouris T, McArthur AG, Brinkman FSL, Fink RC, Zaheer R, Beiko RG. Exploring the mobilome and resistome of Enterococcus faecium in a One Health context across two continents. Microb Genom 2022; 8. [PMID: 36129737 DOI: 10.1099/mgen.0.000880] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Enterococcus faecium is a ubiquitous opportunistic pathogen that is exhibiting increasing levels of antimicrobial resistance (AMR). Many of the genes that confer resistance and pathogenic functions are localized on mobile genetic elements (MGEs), which facilitate their transfer between lineages. Here, features including resistance determinants, virulence factors and MGEs were profiled in a set of 1273 E. faecium genomes from two disparate geographic locations (in the UK and Canada) from a range of agricultural, clinical and associated habitats. Neither lineages of E. faecium, type A and B, nor MGEs are constrained by geographic proximity, but our results show evidence of a strong association of many profiled genes and MGEs with habitat. Many features were associated with a group of clinical and municipal wastewater genomes that are likely forming a new human-associated ecotype within type A. The evolutionary dynamics of E. faecium make it a highly versatile emerging pathogen, and its ability to acquire, transmit and lose features presents a high risk for the emergence of new pathogenic variants and novel resistance combinations. This study provides a workflow for MGE-centric surveillance of AMR in Enterococcus that can be adapted to other pathogens.
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Affiliation(s)
- Haley Sanderson
- Vaccine and Infectious Disease Organization, University of Saskatchewan, Saskatoon, Canada
| | - Kristen L Gray
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Colombia, Canada
| | - Alexander Manuele
- Faculty of Computer Science, Dalhousie University, Halifax, Nova Scotia, Canada.,Institute for Comparative Genomics, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Finlay Maguire
- Faculty of Computer Science, Dalhousie University, Halifax, Nova Scotia, Canada.,Institute for Comparative Genomics, Dalhousie University, Halifax, Nova Scotia, Canada.,Department of Community Health & Epidemiology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Amjad Khan
- Faculty of Computer Science, Dalhousie University, Halifax, Nova Scotia, Canada.,Institute for Comparative Genomics, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Chaoyue Liu
- Faculty of Computer Science, Dalhousie University, Halifax, Nova Scotia, Canada.,Institute for Comparative Genomics, Dalhousie University, Halifax, Nova Scotia, Canada.,Department of Mathematics & Statistics, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Chandana Navanekere Rudrappa
- Faculty of Computer Science, Dalhousie University, Halifax, Nova Scotia, Canada.,Institute for Comparative Genomics, Dalhousie University, Halifax, Nova Scotia, Canada
| | - John H E Nash
- National Microbiology Laboratory, Public Health Agency of Canada, Guelph and Toronto, Ontario, Canada
| | - James Robertson
- National Microbiology Laboratory, Public Health Agency of Canada, Guelph and Toronto, Ontario, Canada
| | - Kyrylo Bessonov
- National Microbiology Laboratory, Public Health Agency of Canada, Guelph and Toronto, Ontario, Canada
| | - Martins Oloni
- Michael G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada.,David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada
| | - Brian P Alcock
- Michael G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada.,David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada
| | - Amogelang R Raphenya
- Michael G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada.,David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada
| | - Tim A McAllister
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, Alberta, Canada
| | | | - Kathy E Raven
- Department of Medicine, Cambridge University, Cambridge, UK
| | | | - Andrew G McArthur
- Michael G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada.,David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada
| | - Fiona S L Brinkman
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Colombia, Canada
| | - Ryan C Fink
- Faculty of Computer Science, Dalhousie University, Halifax, Nova Scotia, Canada.,Institute for Comparative Genomics, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Rahat Zaheer
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, Alberta, Canada
| | - Robert G Beiko
- Faculty of Computer Science, Dalhousie University, Halifax, Nova Scotia, Canada.,Institute for Comparative Genomics, Dalhousie University, Halifax, Nova Scotia, Canada
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Krause AL, Stinear TP, Monk IR. Barriers to genetic manipulation of Enterococci: Current Approaches and Future Directions. FEMS Microbiol Rev 2022; 46:6650352. [PMID: 35883217 PMCID: PMC9779914 DOI: 10.1093/femsre/fuac036] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 07/14/2022] [Accepted: 07/22/2022] [Indexed: 01/09/2023] Open
Abstract
Enterococcus faecalis and Enterococcus faecium are Gram-positive commensal gut bacteria that can also cause fatal infections. To study clinically relevant multi-drug resistant E. faecalis and E. faecium strains, methods are needed to overcome physical (thick cell wall) and enzymatic barriers that limit the transfer of foreign DNA and thus prevent facile genetic manipulation. Enzymatic barriers to DNA uptake identified in E. faecalis and E. faecium include type I, II and IV restriction modification systems and CRISPR-Cas. This review examines E. faecalis and E. faecium DNA defence systems and the methods with potential to overcome these barriers. DNA defence system bypass will allow the application of innovative genetic techniques to expedite molecular-level understanding of these important, but somewhat neglected, pathogens.
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Affiliation(s)
- Alexandra L Krause
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, VIC 3000 Australia
| | - Timothy P Stinear
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, VIC 3000 Australia
| | - Ian R Monk
- Corresponding author: Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, VIC 3000 Australia. E-mail:
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Boumasmoud M, Dengler Haunreiter V, Schweizer TA, Meyer L, Chakrakodi B, Schreiber PW, Seidl K, Kühnert D, Kouyos RD, Zinkernagel AS. Genomic Surveillance of Vancomycin-Resistant Enterococcus faecium Reveals Spread of a Linear Plasmid Conferring a Nutrient Utilization Advantage. mBio 2022; 13:e0377121. [PMID: 35343787 PMCID: PMC9040824 DOI: 10.1128/mbio.03771-21] [Citation(s) in RCA: 3] [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: 02/11/2022] [Accepted: 02/25/2022] [Indexed: 12/12/2022] Open
Abstract
Healthcare-associated outbreaks of vancomycin-resistant Enterococcus faecium (VREfm) are a worldwide problem with increasing prevalence. The genomic plasticity of this hospital-adapted pathogen contributes to its efficient spread despite infection control measures. Here, we aimed to identify the genomic and phenotypic determinants of health care-associated transmission of VREfm. We assessed the VREfm transmission networks at the tertiary-care University Hospital of Zurich (USZ) between October 2014 and February 2018 and investigated microevolutionary dynamics of this pathogen. We performed whole-genome sequencing for the 69 VREfm isolates collected during this time frame and assessed the population structure and variability of the vancomycin resistance transposon. Phylogenomic analysis allowed us to reconstruct transmission networks and to unveil external or wider transmission networks undetectable by routine surveillance. Notably, it unveiled a persistent clone, sampled 31 times over a 29-month period. Exploring the evolutionary dynamics of this clone and characterizing the phenotypic consequences revealed the spread of a variant with decreased daptomycin susceptibility and the acquired ability to utilize N-acetyl-galactosamine (GalNAc), one of the primary constituents of the human gut mucins. This nutrient utilization advantage was conferred by a novel plasmid, termed pELF_USZ, which exhibited a linear topology. This plasmid, which was harbored by two distinct clones, was transferable by conjugation. Overall, this work highlights the potential of combining epidemiological, functional genomic, and evolutionary perspectives to unveil adaptation strategies of VREfm. IMPORTANCE Sequencing microbial pathogens causing outbreaks has become a common practice to characterize transmission networks. In addition to the signal provided by vertical evolution, bacterial genomes harbor mobile genetic elements shared horizontally between clones. While macroevolutionary studies have revealed an important role of plasmids and genes encoding carbohydrate utilization systems in the adaptation of Enterococcus faecium to the hospital environment, mechanisms of dissemination and the specific function of many of these genetic determinants remain to be elucidated. Here, we characterize a plasmid providing a nutrient utilization advantage and show evidence for its clonal and horizontal spread at a local scale. Further studies integrating epidemiological, functional genomics, and evolutionary perspectives will be critical to identify changes shaping the success of this pathogen.
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Affiliation(s)
- Mathilde Boumasmoud
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Vanina Dengler Haunreiter
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Tiziano A. Schweizer
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Lilly Meyer
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Bhavya Chakrakodi
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Peter W. Schreiber
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Kati Seidl
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Denise Kühnert
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Roger D. Kouyos
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Annelies S. Zinkernagel
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
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8
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Hsiao CY, Kuo CM, Tuan CL. Island Ecological Tourism: Constructing Indicators of the Tourist Service System in the Penghu National Scenic Area. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.708344] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
It is critical to develop a sustainable ecotourism service system for the fragile Penghu National Scenic Area in Taiwan. This study, therefore, adopted the fuzzy Delphi method and analytic hierarchy process (AHP) to establish an index framework. The results identified four dimensions with 21 service factors. The findings are as follows. Safety management capability is found to be the main factor in the ecotourism service system. Ecological diversity is essential for the marine environment and the core resource for ecotourism; the transportation capacity and environmental quality need to be improved. Marine environmental resources are indispensable to the development of ecotourism. In addition, the local community must support ecotourism, natural resources should be protected, and the development of ecotourism needs to support the sustainability of local conservation. Therefore, encouraging local residents and stakeholders to attend and promote ecotourism, establishing a safety management system for ecotourism, developing environmental protection regulations for tourists in ecotourism, and improving tourist satisfaction are vital. The government needs to develop guidelines for the protection of marine resources, plan an ecotourism service system, and improve public and transportation infrastructure to make it safe and accessible.
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9
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Johnson CN, Sheriff EK, Duerkop BA, Chatterjee A. Let Me Upgrade You: Impact of Mobile Genetic Elements on Enterococcal Adaptation and Evolution. J Bacteriol 2021; 203:e0017721. [PMID: 34370561 PMCID: PMC8508098 DOI: 10.1128/jb.00177-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Enterococci are Gram-positive bacteria that have evolved to thrive as both commensals and pathogens, largely due to their accumulation of mobile genetic elements via horizontal gene transfer (HGT). Common agents of HGT include plasmids, transposable elements, and temperate bacteriophages. These vehicles of HGT have facilitated the evolution of the enterococci, specifically Enterococcus faecalis and Enterococcus faecium, into multidrug-resistant hospital-acquired pathogens. On the other hand, commensal strains of Enterococcus harbor CRISPR-Cas systems that prevent the acquisition of foreign DNA, restricting the accumulation of mobile genetic elements. In this review, we discuss enterococcal mobile genetic elements by highlighting their contributions to bacterial fitness, examine the impact of CRISPR-Cas on their acquisition, and identify key areas of research that can improve our understanding of enterococcal evolution and ecology.
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Affiliation(s)
- Cydney N. Johnson
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Emma K. Sheriff
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Breck A. Duerkop
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Anushila Chatterjee
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, Colorado, USA
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10
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Wyres KL, Hawkey J, Mirčeta M, Judd LM, Wick RR, Gorrie CL, Pratt NF, Garlick JS, Watson KM, Pilcher DV, McGloughlin SA, Abbott IJ, Macesic N, Spelman DW, Jenney AWJ, Holt KE. Genomic surveillance of antimicrobial resistant bacterial colonisation and infection in intensive care patients. BMC Infect Dis 2021; 21:683. [PMID: 34261450 PMCID: PMC8278603 DOI: 10.1186/s12879-021-06386-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 06/21/2021] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Third-generation cephalosporin-resistant Gram-negatives (3GCR-GN) and vancomycin-resistant enterococci (VRE) are common causes of multi-drug resistant healthcare-associated infections, for which gut colonisation is considered a prerequisite. However, there remains a key knowledge gap about colonisation and infection dynamics in high-risk settings such as the intensive care unit (ICU), thus hampering infection prevention efforts. METHODS We performed a three-month prospective genomic survey of infecting and gut-colonising 3GCR-GN and VRE among patients admitted to an Australian ICU. Bacteria were isolated from rectal swabs (n = 287 and n = 103 patients ≤2 and > 2 days from admission, respectively) and diagnostic clinical specimens between Dec 2013 and March 2014. Isolates were subjected to Illumina whole-genome sequencing (n = 127 3GCR-GN, n = 41 VRE). Multi-locus sequence types (STs) and antimicrobial resistance determinants were identified from de novo assemblies. Twenty-three isolates were selected for sequencing on the Oxford Nanopore MinION device to generate completed reference genomes (one for each ST isolated from ≥2 patients). Single nucleotide variants (SNVs) were identified by read mapping and variant calling against these references. RESULTS Among 287 patients screened on admission, 17.4 and 8.4% were colonised by 3GCR-GN and VRE, respectively. Escherichia coli was the most common species (n = 36 episodes, 58.1%) and the most common cause of 3GCR-GN infection. Only two VRE infections were identified. The rate of infection among patients colonised with E. coli was low, but higher than those who were not colonised on admission (n = 2/33, 6% vs n = 4/254, 2%, respectively, p = 0.3). While few patients were colonised with 3GCR- Klebsiella pneumoniae or Pseudomonas aeruginosa on admission (n = 4), all such patients developed infections with the colonising strain. Genomic analyses revealed 10 putative nosocomial transmission clusters (≤20 SNVs for 3GCR-GN, ≤3 SNVs for VRE): four VRE, six 3GCR-GN, with epidemiologically linked clusters accounting for 21 and 6% of episodes, respectively (OR 4.3, p = 0.02). CONCLUSIONS 3GCR-E. coli and VRE were the most common gut colonisers. E. coli was the most common cause of 3GCR-GN infection, but other 3GCR-GN species showed greater risk for infection in colonised patients. Larger studies are warranted to elucidate the relative risks of different colonisers and guide the use of screening in ICU infection control.
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Affiliation(s)
- Kelly L Wyres
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Victoria, Australia.
| | - Jane Hawkey
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Victoria, Australia
| | - Mirianne Mirčeta
- Microbiology Unit, Alfred Health, Melbourne, Victoria, Australia
| | - Louise M Judd
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Victoria, Australia
| | - Ryan R Wick
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Victoria, Australia
| | - Claire L Gorrie
- Department of Microbiology and Immunology, University of Melbourne, Melbourne, Victoria, Australia
| | - Nigel F Pratt
- Infectious Diseases Clinical Research Unit, The Alfred Hospital, Melbourne, Victoria, Australia
| | - Jill S Garlick
- Infectious Diseases Clinical Research Unit, The Alfred Hospital, Melbourne, Victoria, Australia
| | - Kerrie M Watson
- Infectious Diseases Clinical Research Unit, The Alfred Hospital, Melbourne, Victoria, Australia
| | - David V Pilcher
- Intensive Care Unit, The Alfred Hospital, Melbourne, Victoria, Australia
- Australian and New Zealand Intensive Care - Research Centre, School of Public Health and Preventive Medicine, Monash University, Melbourne, Victoria, Australia
| | - Steve A McGloughlin
- Intensive Care Unit, The Alfred Hospital, Melbourne, Victoria, Australia
- Australian and New Zealand Intensive Care - Research Centre, School of Public Health and Preventive Medicine, Monash University, Melbourne, Victoria, Australia
| | - Iain J Abbott
- Department of Infectious Diseases, The Alfred Hospital, Melbourne, Victoria, Australia
| | - Nenad Macesic
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Victoria, Australia
- Department of Infectious Diseases, The Alfred Hospital, Melbourne, Victoria, Australia
| | - Denis W Spelman
- Department of Infectious Diseases, The Alfred Hospital, Melbourne, Victoria, Australia
| | - Adam W J Jenney
- Microbiology Unit, Alfred Health, Melbourne, Victoria, Australia.
- Department of Infectious Diseases, The Alfred Hospital, Melbourne, Victoria, Australia.
| | - Kathryn E Holt
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Victoria, Australia
- London School of Hygiene and Tropical Medicine, London, UK
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11
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Altamirano FLG, Barr JJ. Screening for Lysogen Activity in Therapeutically Relevant Bacteriophages. Bio Protoc 2021; 11:e3997. [PMID: 34124298 DOI: 10.21769/bioprotoc.3997] [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: 09/30/2020] [Revised: 02/05/2021] [Accepted: 02/17/2021] [Indexed: 11/02/2022] Open
Abstract
Lysogenic phages can integrate into their bacterial host's genome, potentially transferring any genetic information they possess including virulence or resistance genes, and are therefore routinely excluded from therapeutic applications. Lysogenic behavior is typically seen in phages that create turbid plaques or possess subpar bactericidal activity; yet, these are not definitive indicators. As a result, the presence of integrase genes is often used as a hallmark for lysogenic behavior; however, the accuracy of genetic screening for lysogeny depends on the quality of the extraction, sequencing and assembly of the phage genome, and database comparison. The present protocol describes a simple phenotypic test that can be used to screen therapeutically relevant phages for lysogenic behavior. This test relies on the identification of spontaneous phage release from their lysogenized host and can be reliably used in cases where no sequencing data are available. The protocol does not require specialized equipment, is not work-intensive, and is broadly applicable to any phage with an easily culturable bacterial host, making it particularly amenable to settings with limited resources. Graphical abstract: Screening pipeline for lysogen activity of a given phage.
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Affiliation(s)
| | - Jeremy J Barr
- School of Biological Sciences, Monash University, Clayton, VIC, Australia
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12
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Antibiotic Resistance of Uropathogens Isolated from Patients Hospitalized in District Hospital in Central Poland in 2020. Antibiotics (Basel) 2021; 10:antibiotics10040447. [PMID: 33923389 PMCID: PMC8071495 DOI: 10.3390/antibiotics10040447] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 04/13/2021] [Accepted: 04/14/2021] [Indexed: 11/17/2022] Open
Abstract
The aim of this study was to determine antibiotic resistance patterns and the prevalence of uropathogenes causing urinary tract infections (UTIs) in patients hospitalized in January–June 2020 in central Poland. Antimicrobial susceptibility testing was performed using the disk-diffusion method. Escherichia coli (52.2%), Klebsiella pneumoniae (13.7%), Enterococcus faecalis (9.3%), E. faecium (6.2%), and Proteus mirabilis (4,3%) were most commonly isolated from urine samples. E. coli was significantly more frequent in women (58.6%) (p = 0.0089) and in the age group 0–18, while K. pneumoniae was more frequent in men (24.4%) (p = 0.0119) and in individuals aged 40–60 and >60. Gram-negative species showed resistance to ampicillin. K. pneumoniae were resistant to amoxicillin plus clavulanic acid (75.0%), piperacillin plus tazobactam (76.2%), cefotaxime (76.2%), cefuroxime (81.0%), ciprofloxacin (81.0%), and trimethoprim plus sulphamethoxazole (81.0%). Carbapenems were effective against all E. coli and P. mirabilis. Some K. pneumoniae (13.6%) produced metallo-β-lactamases (MBLs). E. coli (22.6%), K. pneumoniae (81.8%), and all E. faecium were multidrug-resistant (MDR). Some E. coli (26.2%), K. pneumoniae (63.6%), and P. mirabilis (14.3%) isolates produced extended-spectrum beta-lactamases (ESBL). Vancomycin-resistant E. faecium was also found. This study showed that the possibilities of UTIs therapy using available antibiotics become limited due to the increasing number of antibiotic-resistant uropathogens.
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13
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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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14
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Werner G, Neumann B, Weber RE, Kresken M, Wendt C, Bender JK. Thirty years of VRE in Germany - "expect the unexpected": The view from the National Reference Centre for Staphylococci and Enterococci. Drug Resist Updat 2020; 53:100732. [PMID: 33189998 DOI: 10.1016/j.drup.2020.100732] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 10/12/2020] [Accepted: 10/15/2020] [Indexed: 02/06/2023]
Abstract
Enterococci are commensals of the intestinal tract of many animals and humans. Of the various known and still unnamed new enterococcal species, only isolates of Enterococcus faecium and Enterococcus faecalis have received increased medical and public health attention. According to textbook knowledge, the majority of infections are caused by E. faecalis. In recent decades, the number of enterococcal infections has increased, with the increase being exclusively associated with a rising number of nosocomial E. faecium infections. This increase has been accompanied by the dissemination of certain hospital-acquired strain variants and an alarming progress in the development of antibiotic resistance namely vancomycin resistance. With this review we focus on a description of the specific situation of vancomycin resistance among clinical E. faecium isolates in Germany over the past 30 years. The present review describes three VRE episodes in Germany, each of which is framed by the beginning and end of the respective decade. The first episode is specified by the first appearance of VRE in 1990 and a country-wide spread of specific vanA-type VRE strains (ST117/CT24) until the late 1990s. The second decade was initially marked by regional clusters and VRE outbreaks in hospitals in South-Western Germany in 2004 and 2005, mainly caused by vanA-type VRE of ST203. Against the background of a certain "basic level" of VRE prevalence throughout Germany, an early shift from the vanA genotype to the vanB genotype in clinical isolates already occurred at the end of the 2000s without much notice. With the beginning of the third decade in 2010, VRE rates in Germany have permanently increased, first in some federal states and soon after country-wide. Besides an increase in VRE prevalence, this decade was marked by a sharp increase in vanB-type resistance and a dominance of a few, novel strain variants like ST192 and later on ST117 (CT71, CT469) and ST80 (CT1065). The largest VRE outbreak, which involved about 2,900 patients and lasted over three years, was caused by a novel and until that time, unknown strain type of ST80/CT1013 (vanB). Across all periods, VRE outbreaks were mainly oligoclonal and strain types varied over space (hospital wards) and time. The spread of VRE strains obviously respects political borders; for instance, both vancomycin-variable enterococci which were highly prevalent in Denmark and ST796 VRE which successfully disseminated in Australia and Switzerland, were still completely absent among German hospital patients, until to date.
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Affiliation(s)
- Guido Werner
- National Reference Centre for Staphylococci and Enterococci, Division Nosocomial Pathogens and Antibiotic Resistances, Department of Infectious Diseases, Robert Koch Institute, Wernigerode Branch, Germany.
| | - Bernd Neumann
- National Reference Centre for Staphylococci and Enterococci, Division Nosocomial Pathogens and Antibiotic Resistances, Department of Infectious Diseases, Robert Koch Institute, Wernigerode Branch, Germany
| | - Robert E Weber
- National Reference Centre for Staphylococci and Enterococci, Division Nosocomial Pathogens and Antibiotic Resistances, Department of Infectious Diseases, Robert Koch Institute, Wernigerode Branch, Germany
| | | | | | - Jennifer K Bender
- National Reference Centre for Staphylococci and Enterococci, Division Nosocomial Pathogens and Antibiotic Resistances, Department of Infectious Diseases, Robert Koch Institute, Wernigerode Branch, Germany
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15
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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: 84] [Impact Index Per Article: 21.0] [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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16
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Wist V, Morach M, Schneeberger M, Cernela N, Stevens MJ, Zurfluh K, Stephan R, Nüesch-Inderbinen M. Phenotypic and Genotypic Traits of Vancomycin-Resistant Enterococci from Healthy Food-Producing Animals. Microorganisms 2020; 8:E261. [PMID: 32075283 PMCID: PMC7074742 DOI: 10.3390/microorganisms8020261] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Revised: 02/06/2020] [Accepted: 02/11/2020] [Indexed: 12/14/2022] Open
Abstract
Food-producing animals may be a reservoir of vancomycin-resistant enterococci (VRE), potentially posing a threat to animal and public health. The aims of this study were to estimate the faecal carriage of VRE among healthy cattle (n = 362), pigs (n = 350), sheep (n = 218), and poultry (n = 102 flocks) in Switzerland, and to characterise phenotypic and genotypic traits of the isolates. VRE were isolated from caecum content of six bovine, and 12 porcine samples respectively, and from pooled faecal matter collected from 16 poultry flock samples. All isolates harboured vanA. Three different types of Tn1546-like elements carrying the vanA operon were identified. Conjugal transfer of vanA to human Enterococcus faecalis strain JH2-2 was observed for porcine isolates only. Resistance to tetracycline and erythromycin was frequent among the isolates. Our data show that VRE harbouring vanA are present in healthy food-producing animals. The vanA gene from porcine isolates was transferable to other enterococci and these isolates might play a role in the dissemination of VRE in the food production chain.
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Affiliation(s)
| | | | | | | | | | | | | | - Magdalena Nüesch-Inderbinen
- Institute for Food Safety and Hygiene, Vetsuisse Faculty, University of Zurich, Winterthurerstrasse 272, 8057 Zurich, Switzerland; (V.W.); (M.M.); (M.S.); (N.C.); (K.Z.); (R.S.)
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17
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Abstract
Enterococcus faecium is one of the most frequent nosocomial pathogens of hospital-acquired infections. E. faecium has gained resistance against most commonly available antibiotics, most notably, against ampicillin, gentamicin, and vancomycin, which renders infections difficult to treat. Many antibiotic resistance traits, in particular, vancomycin resistance, can be encoded in autonomous and extrachromosomal elements called plasmids. These sequences can be disseminated to other isolates by horizontal gene transfer and confer novel mechanisms to source specificity. In our study, we elucidated the total plasmid content, referred to as the plasmidome, of 1,644 E. faecium isolates by using short- and long-read whole-genome technologies with the combination of a machine-learning classifier. This was fundamental to investigate the full collection of plasmid sequences present in our collection (pan-plasmidome) and to observe the potential transfer of plasmid sequences between E. faecium hosts. We observed that E. faecium isolates from hospitalized patients carried a larger number of plasmid sequences compared to that from other sources, and they elucidated different configurations of plasmidome populations in the hospital environment. We assessed the contribution of different genomic components and observed that plasmid sequences have the highest contribution to source specificity. Our study suggests that E. faecium plasmids are regulated by complex ecological constraints rather than physical interaction between hosts. Enterococcus faecium is a gut commensal of humans and animals but is also listed on the WHO global priority list of multidrug-resistant pathogens. Many of its antibiotic resistance traits reside on plasmids and have the potential to be disseminated by horizontal gene transfer. Here, we present the first comprehensive population-wide analysis of the pan-plasmidome of a clinically important bacterium, by whole-genome sequence analysis of 1,644 isolates from hospital, commensal, and animal sources of E. faecium. Long-read sequencing on a selection of isolates resulted in the completion of 305 plasmids that exhibited high levels of sequence modularity. We further investigated the entirety of all plasmids of each isolate (plasmidome) using a combination of short-read sequencing and machine-learning classifiers. Clustering of the plasmid sequences unraveled different E. faecium populations with a clear association with hospitalized patient isolates, suggesting different optimal configurations of plasmids in the hospital environment. The characterization of these populations allowed us to identify common mechanisms of plasmid stabilization such as toxin-antitoxin systems and genes exclusively present in particular plasmidome populations exemplified by copper resistance, phosphotransferase systems, or bacteriocin genes potentially involved in niche adaptation. Based on the distribution of k-mer distances between isolates, we concluded that plasmidomes rather than chromosomes are most informative for source specificity of E. faecium.
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18
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Leong KWC, Kalukottege R, Cooley LA, Anderson TL, Wells A, Langford E, O’Toole RF. State-Wide Genomic and Epidemiological Analyses of Vancomycin-Resistant Enterococcus faecium in Tasmania's Public Hospitals. Front Microbiol 2020; 10:2940. [PMID: 32010070 PMCID: PMC6975128 DOI: 10.3389/fmicb.2019.02940] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Accepted: 12/06/2019] [Indexed: 12/26/2022] Open
Abstract
From 2015 onwards, the number of vancomycin-resistant Enterococcus faecium (VREfm) isolates increased in Tasmania. Previously, we examined the transmission of VREfm at the Royal Hobart Hospital (RHH). In this study, we performed a state-wide analysis of VREfm from Tasmania's four public acute hospitals. Whole-genome analysis was performed on 331 isolates collected from screening and clinical specimens of VREfm. In silico multi-locus sequence typing (MLST) was used to determine the relative abundance of broad sequence types (ST) across the state. Core genome MLST (cgMLST) was then applied to identify potential clades within the ST groupings followed by single-nucleotide polymorphic (SNP) analysis. This work revealed that differences in VREfm profiles are evident between the state's two largest hospitals with the dominant vanA types being ST80 at the RHH and ST1421 at Launceston General Hospital (LGH). A higher number of VREfm cases were recorded at LGH (n = 54 clinical, n = 122 colonization) compared to the RHH (n = 14 clinical, n = 67 colonization) during the same time period, 2014-2016. Eleven of the clinical isolates from LGH were vanA and belonged to ST1421 (n = 8), ST1489 (n = 1), ST233 (n = 1), and ST80 (n = 1) whereas none of the clinical isolates from the RHH were vanA. For the recently described ST1421, cgMLST established the presence of individual clusters within this sequence type that were common to more than one hospital and that included isolates with a low amount of SNP variance (≤16 SNPs). A spatio-temporal analysis revealed that VREfm vanA ST1421 was first detected at the RHH in 2014 and an isolate belonging to the same cgMLST cluster was later collected at LGH in 2016. Inclusion of isolates from two smaller hospitals, the North West Regional Hospital (NRH) and the Mersey Community Hospital (MCH) found that ST1421 was present in both of these institutions in 2017. These findings illustrate the spread of a recently described sequence type of VREfm, ST1421, to multiple hospitals in an Australian state within a relatively short time span.
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Affiliation(s)
- Kelvin W. C. Leong
- Department of Pharmacy and Biomedical Sciences, School of Molecular Sciences, College of Science, Health and Engineering, La Trobe University, Albury-Wodonga, VIC, Australia
| | - Ranmini Kalukottege
- Department of Microbiology, Launceston General Hospital, Launceston, TAS, Australia
| | - Louise A. Cooley
- Royal Hobart Hospital, Hobart, TAS, Australia
- School of Medicine, University of Tasmania, Hobart, TAS, Australia
| | - Tara L. Anderson
- Royal Hobart Hospital, Hobart, TAS, Australia
- Tasmanian Infection Prevention and Control Unit, Department of Health and Human Services, Hobart, TAS, Australia
| | - Anne Wells
- Tasmanian Infection Prevention and Control Unit, Department of Health and Human Services, Hobart, TAS, Australia
| | - Emma Langford
- Department of Microbiology, Hobart Pathology, Hobart, TAS, Australia
| | - Ronan F. O’Toole
- Department of Pharmacy and Biomedical Sciences, School of Molecular Sciences, College of Science, Health and Engineering, La Trobe University, Albury-Wodonga, VIC, Australia
- School of Medicine, University of Tasmania, Hobart, TAS, Australia
- Department of Clinical Microbiology, Trinity College Dublin, Dublin, Ireland
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19
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Complete genome and bimodal genomic structure of the amoebal symbiont Neochlamydia strain S13 revealed by ultra-long reads obtained from MinION. J Hum Genet 2019; 65:41-48. [PMID: 31723216 DOI: 10.1038/s10038-019-0684-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Revised: 10/02/2019] [Accepted: 10/03/2019] [Indexed: 12/12/2022]
Abstract
Neochlamydia strain S13 is an amoebal symbiont of an Acanthamoeba sp. The symbiont confers resistance to Legionella pneumophila on its host; however, the molecular mechanism underlying this resistance is not completely understood. Genome analyses have been crucial for understanding the complicated host-symbiont relationship but segregating the host's genome DNA from the symbiont's DNA is often challenging. In this study, we successfully identified a bimodal genomic structure in Neochlamydia strain S13 using PacBio RS II supported by ultra-long reads derived from MinION. One mode consisted of circular sequences of 2,586,667 and 231,307 bp; the other was an integrated sequence of the two via long homologous regions. They encoded 2175 protein-coding regions, some of which were implied to be acquired via horizontal gene transfer. They were specifically conserved in the genus Neochlamydia and formed a cluster in the genome, presumably by multiplication through genome replication. Moreover, it was notable that the sequenced DNA was obtained without segregating the symbiont DNA from the host. This is an easy and versatile technique that facilitates the characterization of diverse hosts and symbionts in nature.
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20
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Lee RS, Gonçalves da Silva A, Baines SL, Strachan J, Ballard S, Carter GP, Kwong JC, Schultz MB, Bulach DM, Seemann T, Stinear TP, Howden BP. The changing landscape of vancomycin-resistant Enterococcus faecium in Australia: a population-level genomic study. J Antimicrob Chemother 2019; 73:3268-3278. [PMID: 30189014 DOI: 10.1093/jac/dky331] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Accepted: 07/23/2018] [Indexed: 12/17/2022] Open
Abstract
Background Vancomycin-resistant Enterococcus faecium (VREfm) represent a major source of nosocomial infection worldwide. In Australia, there has been a recent concerning increase in bacteraemia associated with the vanA genotype, prompting investigation into the genomic epidemiology of VREfm. Methods A population-level study of VREfm (10 November-9 December 2015) was conducted. A total of 321 VREfm isolates (from 286 patients) across Victoria State were collected and sequenced with Illumina NextSeq. SNPs were used to assess relatedness. STs and genes associated with resistance and virulence were identified. The vanA-harbouring plasmid from an isolate from each ST was assembled using long-read data. Illumina reads from remaining isolates were then mapped to these assemblies to identify their probable vanA-harbouring plasmid. Results vanA-VREfm comprised 17.8% of isolates. ST203, ST80 and a pstS(-) clade, ST1421, predominated (30.5%, 30.5% and 37.2%, respectively). Most vanB-VREfm were ST796 (77.7%). vanA-VREfm were more closely related within hospitals versus between them [core SNPs 10 (IQR 1-357) versus 356 (179-416), respectively], suggesting discrete introductions of vanA-VREfm, with subsequent intra-hospital transmission. In contrast, vanB-VREfm had similar core SNP distributions within versus between hospitals, due to widespread dissemination of ST796. Different vanA-harbouring plasmids were found across STs. With the exception of ST78 and ST796, Tn1546 transposons also varied. Phylogenetic analysis revealed Australian strains were often interspersed with those from other countries, suggesting ongoing cross-continental transmission. Conclusions Emerging vanA-VREfm in Australia is polyclonal, indicating repeat introductions of vanA-VREfm into hospitals and subsequent dissemination. The close relationship to global strains reinforces the need for ongoing screening and control of VREfm in Australia and abroad.
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Affiliation(s)
- Robyn S Lee
- The Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne, at The Peter Doherty Institute for Infection and Immunity, 792 Elizabeth Street, Level 1, Melbourne, Victoria, Australia.,Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T. H. Chan School of Public Health, 677 Huntington Avenue, Level 5, Boston, MA, USA
| | - Anders Gonçalves da Silva
- The Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne, at The Peter Doherty Institute for Infection and Immunity, 792 Elizabeth Street, Level 1, Melbourne, Victoria, Australia
| | - Sarah L Baines
- Department of Microbiology and Immunology, The University of Melbourne, at The Peter Doherty Institute for Infection and Immunity, 792 Elizabeth Street, Level 1, Melbourne, Victoria, Australia
| | - Janet Strachan
- The Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne, at The Peter Doherty Institute for Infection and Immunity, 792 Elizabeth Street, Level 1, Melbourne, Victoria, Australia
| | - Susan Ballard
- The Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne, at The Peter Doherty Institute for Infection and Immunity, 792 Elizabeth Street, Level 1, Melbourne, Victoria, Australia
| | - Glen P Carter
- The Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne, at The Peter Doherty Institute for Infection and Immunity, 792 Elizabeth Street, Level 1, Melbourne, Victoria, Australia
| | - Jason C Kwong
- Department of Microbiology and Immunology, The University of Melbourne, at The Peter Doherty Institute for Infection and Immunity, 792 Elizabeth Street, Level 1, Melbourne, Victoria, Australia
| | - Mark B Schultz
- The Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne, at The Peter Doherty Institute for Infection and Immunity, 792 Elizabeth Street, Level 1, Melbourne, Victoria, Australia
| | - Dieter M Bulach
- The Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne, at The Peter Doherty Institute for Infection and Immunity, 792 Elizabeth Street, Level 1, Melbourne, Victoria, Australia
| | - Torsten Seemann
- Melbourne Bioinformatics Group, Lab-14, 700 Swanston Street, Carlton, Victoria, Australia
| | - Timothy P Stinear
- Department of Microbiology and Immunology, The University of Melbourne, at The Peter Doherty Institute for Infection and Immunity, 792 Elizabeth Street, Level 1, Melbourne, Victoria, Australia
| | - Benjamin P Howden
- The Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne, at The Peter Doherty Institute for Infection and Immunity, 792 Elizabeth Street, Level 1, Melbourne, Victoria, Australia.,Infectious Diseases Department, Austin Health, Studley Rd, Heidelberg, Victoria, Australia
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21
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Pidot SJ, Gao W, Buultjens AH, Monk IR, Guerillot R, Carter GP, Lee JYH, Lam MMC, Grayson ML, Ballard SA, Mahony AA, Grabsch EA, Kotsanas D, Korman TM, Coombs GW, Robinson JO, Gonçalves da Silva A, Seemann T, Howden BP, Johnson PDR, Stinear TP. Increasing tolerance of hospital Enterococcus faecium to handwash alcohols. Sci Transl Med 2019; 10:10/452/eaar6115. [PMID: 30068573 DOI: 10.1126/scitranslmed.aar6115] [Citation(s) in RCA: 133] [Impact Index Per Article: 26.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2017] [Revised: 02/10/2018] [Accepted: 04/03/2018] [Indexed: 11/03/2022]
Abstract
Alcohol-based disinfectants and particularly hand rubs are a key way to control hospital infections worldwide. Such disinfectants restrict transmission of pathogens, such as multidrug-resistant Staphylococcus aureus and Enterococcus faecium Despite this success, health care infections caused by E. faecium are increasing. We tested alcohol tolerance of 139 hospital isolates of E. faecium obtained between 1997 and 2015 and found that E. faecium isolates after 2010 were 10-fold more tolerant to killing by alcohol than were older isolates. Using a mouse gut colonization model of E. faecium transmission, we showed that alcohol-tolerant E. faecium resisted standard 70% isopropanol surface disinfection, resulting in greater mouse gut colonization compared to alcohol-sensitive E. faecium We next looked for bacterial genomic signatures of adaptation. Alcohol-tolerant E. faecium accumulated mutations in genes involved in carbohydrate uptake and metabolism. Mutagenesis confirmed the roles of these genes in the tolerance of E. faecium to isopropanol. These findings suggest that bacterial adaptation is complicating infection control recommendations, necessitating additional procedures to prevent E. faecium from spreading in hospital settings.
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Affiliation(s)
- Sacha J Pidot
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Victoria 3010, Australia
| | - Wei Gao
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Victoria 3010, Australia
| | - Andrew H Buultjens
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Victoria 3010, Australia
| | - Ian R Monk
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Victoria 3010, Australia
| | - Romain Guerillot
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Victoria 3010, Australia
| | - Glen P Carter
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Victoria 3010, Australia
| | - Jean Y H Lee
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Victoria 3010, Australia
| | - Margaret M C Lam
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Victoria 3010, Australia
| | - M Lindsay Grayson
- Infectious Diseases Department, Austin Health, Heidelberg, Victoria 3084, Australia.,Department of Medicine, University of Melbourne, Heidelberg, Victoria 3084, Australia.,Department of Epidemiology and Preventive Medicine, Monash University, Victoria 3800, Australia
| | - Susan A Ballard
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Victoria 3010, Australia
| | - Andrew A Mahony
- Infectious Diseases Department, Austin Health, Heidelberg, Victoria 3084, Australia
| | - Elizabeth A Grabsch
- Infectious Diseases Department, Austin Health, Heidelberg, Victoria 3084, Australia
| | - Despina Kotsanas
- Monash Infectious Diseases, Monash Health, Clayton, Victoria 3168, Australia
| | - Tony M Korman
- Monash Infectious Diseases, Monash Health, Clayton, Victoria 3168, Australia
| | - Geoffrey W Coombs
- Antimicrobial Resistance and Infectious Diseases Research Laboratory, School of Veterinary and Life Sciences, Murdoch University, Murdoch, Western Australia 6150, Australia.,Department of Microbiology, PathWest Laboratory Medicine WA, Fiona Stanley Hospital, Murdoch, Western Australia 6150, Australia
| | - J Owen Robinson
- Antimicrobial Resistance and Infectious Diseases Research Laboratory, School of Veterinary and Life Sciences, Murdoch University, Murdoch, Western Australia 6150, Australia.,Department of Microbiology, PathWest Laboratory Medicine WA, Fiona Stanley Hospital, Murdoch, Western Australia 6150, Australia
| | - Anders Gonçalves da Silva
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Victoria 3010, Australia
| | - Torsten Seemann
- Melbourne Bioinformatics, University of Melbourne, Carlton, Victoria 3053, Australia
| | - Benjamin P Howden
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Victoria 3010, Australia.,Infectious Diseases Department, Austin Health, Heidelberg, Victoria 3084, Australia.,Department of Medicine, University of Melbourne, Heidelberg, Victoria 3084, Australia.,Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Victoria 3010, Australia
| | - Paul D R Johnson
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Victoria 3010, Australia. .,Infectious Diseases Department, Austin Health, Heidelberg, Victoria 3084, Australia.,Department of Medicine, University of Melbourne, Heidelberg, Victoria 3084, Australia
| | - Timothy P Stinear
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Victoria 3010, Australia.
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22
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Wassilew N, Seth-Smith HM, Rolli E, Fietze Y, Casanova C, Führer U, Egli A, Marschall J, Buetti N. Outbreak of vancomycin-resistant Enterococcus faecium clone ST796, Switzerland, December 2017 to April 2018. ACTA ACUST UNITED AC 2019; 23. [PMID: 30043725 PMCID: PMC6152203 DOI: 10.2807/1560-7917.es.2018.23.29.1800351] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
A large outbreak of vancomycin-resistant enterococci (VRE) is affecting four hospitals in the Canton of Bern, Switzerland, since December 2017. Of 89 cases identified as carriers, 77 (86.5%) VRE isolates were virtually indistinguishable using whole genome sequencing, and identified as multilocus sequence type (MLST) ST796. This clone, previously only described in Australia and New Zealand, is characterised by rapid spread and the ability to cause bloodstream infections. It requires a multifaceted infection prevention effort.
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Affiliation(s)
- Nasstasja Wassilew
- Department of Infectious Diseases, University Hospital Bern, Bern, Switzerland
| | - Helena Mb Seth-Smith
- Applied Microbiology Research, Department of Biomedicine, University of Basel, Basel, Switzerland.,Division of Clinical Microbiology, University Hospital Basel, Basel, Switzerland
| | - Eveline Rolli
- Department of Infectious Diseases, University Hospital Bern, Bern, Switzerland
| | - Yvonne Fietze
- Department of Infectious Diseases, University Hospital Bern, Bern, Switzerland
| | - Carlo Casanova
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Urs Führer
- Infectious Diseases Department, Biel Hospital, Biel, Switzerland
| | - Adrian Egli
- Applied Microbiology Research, Department of Biomedicine, University of Basel, Basel, Switzerland.,Division of Clinical Microbiology, University Hospital Basel, Basel, Switzerland
| | - Jonas Marschall
- Department of Infectious Diseases, University Hospital Bern, Bern, Switzerland
| | - Niccolò Buetti
- Department of Infectious Diseases, University Hospital Bern, Bern, Switzerland
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23
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Seth-Smith HMB, Bonfiglio F, Cuénod A, Reist J, Egli A, Wüthrich D. Evaluation of Rapid Library Preparation Protocols for Whole Genome Sequencing Based Outbreak Investigation. Front Public Health 2019; 7:241. [PMID: 31508405 PMCID: PMC6719548 DOI: 10.3389/fpubh.2019.00241] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Accepted: 08/12/2019] [Indexed: 12/18/2022] Open
Abstract
Whole genome sequencing (WGS) has become the new gold standard for bacterial outbreak investigation, due to the high resolution available for typing. While sequencing is currently predominantly performed on Illumina devices, the preceding library preparation can be performed using various protocols. Enzymatic fragmentation library preparation protocols are fast, have minimal hands-on time, and work with small quantities of DNA. The aim of our study was to compare three library preparation protocols for molecular typing: Nextera XT (Illumina); Nextera Flex (Illumina); and QIAseq FX (Qiagen). We selected 12 ATCC strains from human Gram-positive and Gram-negative pathogens with %G+C-content ranging from 27% (Fusobacterium nucleatum) to 73% (Micrococcus luteus), each having a high quality complete genome assembly available, to allow in-depth analysis of the resulting Illumina sequence data quality. Additionally, we selected isolates from previously analyzed cases of vancomycin-resistant Enterococcus faecium (VRE) (n = 7) and a local outbreak of Klebsiella aerogenes (n = 5). The number of protocol steps and time required were compared, in order to test the suitability for routine laboratory work. Data analyses were performed with standard tools commonly used in outbreak situations: Ridom SeqSphere+ for cgMLST; CLC genomics workbench for SNP analysis; and open source programs. Nextera Flex and QIAseq FX were found to be less sensitive than Nextera XT to variable %G+C-content, resulting in an almost uniform distribution of read-depth. Therefore, low coverage regions are reduced to a minimum resulting in a more complete representation of the genome. Thus, with these two protocols, more alleles were detected in the cgMLST analysis, producing a higher resolution of closely related isolates. Furthermore, they result in a more complete representation of accessory genes. In particular, the high data quality and relative simplicity of the workflow of Nextera Flex stood out in this comparison. This thorough comparison within an ISO/IEC 17025 accredited environment will be of interest to those aiming to optimize their clinical microbiological genome sequencing.
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Affiliation(s)
- Helena M B Seth-Smith
- Division of Clinical Bacteriology and Mycology, University Hospital Basel, Basel, Switzerland.,Applied Microbiology Research, Department of Biomedicine, University of Basel, Basel, Switzerland.,DBM Bioinformatics Core Facility, SIB Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Ferdinando Bonfiglio
- Applied Microbiology Research, Department of Biomedicine, University of Basel, Basel, Switzerland.,Personalized Health Basel, University of Basel, Basel, Switzerland
| | - Aline Cuénod
- Division of Clinical Bacteriology and Mycology, University Hospital Basel, Basel, Switzerland.,Applied Microbiology Research, Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Josiane Reist
- Applied Microbiology Research, Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Adrian Egli
- Division of Clinical Bacteriology and Mycology, University Hospital Basel, Basel, Switzerland.,Applied Microbiology Research, Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Daniel Wüthrich
- Division of Clinical Bacteriology and Mycology, University Hospital Basel, Basel, Switzerland.,Applied Microbiology Research, Department of Biomedicine, University of Basel, Basel, Switzerland.,DBM Bioinformatics Core Facility, SIB Swiss Institute of Bioinformatics, Basel, Switzerland
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24
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Agricultural Origins of a Highly Persistent Lineage of Vancomycin-Resistant Enterococcus faecalis in New Zealand. Appl Environ Microbiol 2019; 85:AEM.00137-19. [PMID: 31028029 PMCID: PMC6581176 DOI: 10.1128/aem.00137-19] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Accepted: 04/22/2019] [Indexed: 11/26/2022] Open
Abstract
Historical antimicrobial use in NZ agriculture has driven the evolution of ST108, a VRE lineage carrying a range of clinically relevant antimicrobial resistances. The persistence of this lineage in NZ for over a decade indicates that coselection may be an important stabilizing mechanism for its persistence. Enterococcus faecalis and Enterococcus faecium are human and animal gut commensals. Vancomycin-resistant enterococci (VRE) are important opportunistic pathogens with limited treatment options. Historically, the glycopeptide antibiotics vancomycin and avoparcin selected for the emergence of vancomycin resistance in human and animal isolates, respectively, resulting in global cessation of avoparcin use between 1997 and 2000. To better understand human- and animal-associated VRE strains in the postavoparcin era, we sequenced the genomes of 231 VRE isolates from New Zealand (NZ; 75 human clinical, 156 poultry) cultured between 1998 and 2009. E. faecium lineages and their antibiotic resistance carriage patterns strictly delineated between agricultural and human reservoirs, with bacitracin resistance ubiquitous in poultry but absent in clinical E. faecium strains. In contrast, one E. faecalis lineage (ST108) predominated in both poultry and human isolates in the 3 years following avoparcin discontinuation. Both phylogenetic and antimicrobial susceptibility (i.e., ubiquitous bacitracin resistance in both poultry and clinical ST108 isolates) analyses suggest an agricultural origin for the ST108 lineage. VRE isolate resistomes were carried on multiple, heterogeneous plasmids. In some isolate genomes, bacitracin, erythromycin, and vancomycin resistance elements were colocalized, indicating multiple potentially linked selection mechanisms. IMPORTANCE Historical antimicrobial use in NZ agriculture has driven the evolution of ST108, a VRE lineage carrying a range of clinically relevant antimicrobial resistances. The persistence of this lineage in NZ for over a decade indicates that coselection may be an important stabilizing mechanism for its persistence.
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25
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Buetti N, Wassilew N, Rion V, Senn L, Gardiol C, Widmer A, Marschall J. Emergence of vancomycin-resistant enterococci in Switzerland: a nation-wide survey. Antimicrob Resist Infect Control 2019; 8:16. [PMID: 30675343 PMCID: PMC6337856 DOI: 10.1186/s13756-019-0466-x] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Accepted: 01/08/2019] [Indexed: 11/10/2022] Open
Abstract
This nation-wide survey on the epidemiology of vancomycin-resistant enterococci (VRE) included 142 healthcare institutions and showed an increasing number of VRE colonizations and infections in Switzerland, probably for the most part due to nosocomial dissemination. The introduction and spread of a new clone, gaps in VRE screening policies as well as heterogeneity regarding the management of VRE clusters may be possible explanations.
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Affiliation(s)
- Niccolò Buetti
- Department of Infectious Diseases, Bern University Hospital, University of Bern, Freiburgstrasse, 3010 Bern, Switzerland.,Swissnoso, National Center for Infection Control, Bern, Switzerland.,3UMR 1137 - IAME Team 5 - DeSCID: Decision SCiences in Infectious Diseases, control and care Inserm, University Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Nasstasja Wassilew
- Department of Infectious Diseases, Bern University Hospital, University of Bern, Freiburgstrasse, 3010 Bern, Switzerland
| | - Viktorija Rion
- Swissnoso, National Center for Infection Control, Bern, Switzerland
| | - Laurence Senn
- 4Service of Hospital Preventive Medicine, Lausanne University Hospital, Lausanne, Switzerland
| | - Céline Gardiol
- 5Swiss Federal Office of Public Health, Bern, Switzerland
| | - Andreas Widmer
- Division of Infectious Diseases & Hospital Epidemiology, University Hospital Basel, University of Basel, Basel, Switzerland
| | - Jonas Marschall
- Department of Infectious Diseases, Bern University Hospital, University of Bern, Freiburgstrasse, 3010 Bern, Switzerland
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26
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Reconstruction of the Genomes of Drug-Resistant Pathogens for Outbreak Investigation through Metagenomic Sequencing. mSphere 2019; 4:4/1/e00529-18. [PMID: 30651402 PMCID: PMC6336080 DOI: 10.1128/msphere.00529-18] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The study results reported here perfectly demonstrate the power and promise of clinical metagenomics to recover genome sequences of important drug-resistant bacteria and to rapidly provide rich data that inform outbreak investigations and treatment decisions, independently of the need to culture the organisms. Culture-independent methods that target genome fragments have shown promise in identifying certain pathogens, but the holy grail of comprehensive pathogen genome detection from microbiologically complex samples for subsequent forensic analyses remains a challenge. In the context of an investigation of a nosocomial outbreak, we used shotgun metagenomic sequencing of a human fecal sample and a neural network algorithm based on tetranucleotide frequency profiling to reconstruct microbial genomes and tested the same approach using rectal swabs from a second patient. The approach rapidly and readily detected the genome of Klebsiella pneumoniae carbapenemase (KPC)-producing K. pneumoniae in the patient fecal specimen and in the rectal swab sample, achieving a level of strain resolution that was sufficient for confident transmission inference during a highly clonal outbreak. The analysis also detected previously unrecognized colonization of the patient by vancomycin-resistant Enterococcus faecium, another multidrug-resistant bacterium. IMPORTANCE The study results reported here perfectly demonstrate the power and promise of clinical metagenomics to recover genome sequences of important drug-resistant bacteria and to rapidly provide rich data that inform outbreak investigations and treatment decisions, independently of the need to culture the organisms.
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27
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Leong KWC, Cooley LA, Anderson TL, Gautam SS, McEwan B, Wells A, Wilson F, Hughson L, O'Toole RF. Emergence of Vancomycin-Resistant Enterococcus faecium at an Australian Hospital: A Whole Genome Sequencing Analysis. Sci Rep 2018; 8:6274. [PMID: 29674657 PMCID: PMC5908837 DOI: 10.1038/s41598-018-24614-6] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Accepted: 04/06/2018] [Indexed: 11/09/2022] Open
Abstract
In 2015, a marked increase in vancomycin-resistant Enterococcus faecium (VREfm) isolation was detected at the Royal Hobart Hospital, Australia. The primary objective of this work was to examine the dynamics of VREfm transmission using whole genome data mapped to public health surveillance information. Screening and clinical isolates of VREfm from patients were typed for the specific vancomycin-resistance locus present. Of total isolates collected from 2014-2016 (n = 222), 15.3% and 84.7% harboured either the vanA or the vanB vancomycin-resistance locus, respectively. Whole-genome sequencing of 80 isolates was performed in conjunction with single-nucleotide polymorphic (SNP) analysis and in silico multi-locus sequence typing (MLST). Among the isolates sequenced, 5 phylogenetic clades were identified. The largest vanB clade belonged to MLST sequence type ST796 and contained clinical isolates from VREfm infections that clustered closely with isolates from colonised patients. Correlation of VREfm genotypes with spatio-temporal patient movements detected potential points of transmission within the hospital. ST80 emerged as the major vanA sequence type for which the most likely index case of a patient cluster was ascertained from SNP analyses. This work has identified the dominant clones associated with increased VREfm prevalence in a healthcare setting, and their likely direction of transmission.
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Affiliation(s)
- Kelvin W C Leong
- School of Medicine, University of Tasmania, Hobart, Tasmania, Australia
| | - Louise A Cooley
- School of Medicine, University of Tasmania, Hobart, Tasmania, Australia
- Royal Hobart Hospital, Hobart, Tasmania, Australia
| | - Tara L Anderson
- Royal Hobart Hospital, Hobart, Tasmania, Australia
- Tasmanian Infection Prevention and Control Unit, Department of Health and Human Services, Hobart, Tasmania, Australia
| | - Sanjay S Gautam
- School of Medicine, University of Tasmania, Hobart, Tasmania, Australia
| | | | - Anne Wells
- Tasmanian Infection Prevention and Control Unit, Department of Health and Human Services, Hobart, Tasmania, Australia
| | - Fiona Wilson
- Tasmanian Infection Prevention and Control Unit, Department of Health and Human Services, Hobart, Tasmania, Australia
| | - Lucy Hughson
- Tasmanian Infection Prevention and Control Unit, Department of Health and Human Services, Hobart, Tasmania, Australia
| | - Ronan F O'Toole
- School of Medicine, University of Tasmania, Hobart, Tasmania, Australia.
- Trinity College Dublin, Department of Clinical Microbiology, Dublin, Ireland.
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28
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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: 20] [Impact Index Per Article: 3.3] [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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29
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Gao W, Howden BP, Stinear TP. Evolution of virulence in Enterococcus faecium, a hospital-adapted opportunistic pathogen. Curr Opin Microbiol 2017; 41:76-82. [PMID: 29227922 DOI: 10.1016/j.mib.2017.11.030] [Citation(s) in RCA: 138] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Revised: 11/28/2017] [Accepted: 11/30/2017] [Indexed: 12/29/2022]
Abstract
Enterococci are long-standing members of the human microbiome and they are also widely distributed in nature. However, with the surge of antibiotic-resistance in recent decades, two enterococcal species (Enterococcus faecalis and Enterococcus faecium) have emerged to become significant nosocomial pathogens, acquiring extensive antibiotic resistance. In this review, we summarize what is known about the evolution of virulence in E. faecium, highlighting a specific clone of E. faecium called ST796 that has emerged recently and spread globally.
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Affiliation(s)
- Wei Gao
- Department of Microbiology and Immunology, The Doherty Institute for Infection and Immunity, University of Melbourne, Victoria 3010, Australia
| | - Benjamin P Howden
- Department of Microbiology and Immunology, The Doherty Institute for Infection and Immunity, University of Melbourne, Victoria 3010, Australia; Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The Doherty Institute for Infection and Immunity, University of Melbourne, Victoria 3010, Australia; Infectious Diseases Department, Austin Health, Heidelberg, Victoria 3084, Australia
| | - Timothy P Stinear
- Department of Microbiology and Immunology, The Doherty Institute for Infection and Immunity, University of Melbourne, Victoria 3010, Australia.
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30
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Ahmed MO, Baptiste KE. Vancomycin-Resistant Enterococci: A Review of Antimicrobial Resistance Mechanisms and Perspectives of Human and Animal Health. Microb Drug Resist 2017; 24:590-606. [PMID: 29058560 DOI: 10.1089/mdr.2017.0147] [Citation(s) in RCA: 220] [Impact Index Per Article: 31.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Vancomycin-resistant enterococci (VRE) are both of medical and public health importance associated with serious multidrug-resistant infections and persistent colonization. Enterococci are opportunistic environmental inhabitants with a remarkable adaptive capacity to evolve and transmit antimicrobial-resistant determinants. The VRE gene operons show distinct genetic variability and apparently continued evolution leading to a variety of antimicrobial resistance phenotypes and various environmental and livestock reservoirs for the most common van genes. Such complex diversity renders a number of important therapeutic options including "last resort antibiotics" ineffective and poses a particular challenge for clinical management. Enterococci resistance to glycopeptides and multidrug resistance warrants attention and continuous monitoring.
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Affiliation(s)
- Mohamed O Ahmed
- 1 Department of Microbiology and Parasitology, Faculty of Veterinary Medicine, University of Tripoli , Tripoli, Libya
| | - Keith E Baptiste
- 2 Department of Veterinary Medicine, Danish Medicines Agency , Copenhagen South, Denmark
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31
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Draft Genome Sequences of Five Enterococcus Species Isolated from the Gut of Patients with Suspected Clostridium difficile Infection. GENOME ANNOUNCEMENTS 2017; 5:5/20/e00379-17. [PMID: 28522725 PMCID: PMC5477334 DOI: 10.1128/genomea.00379-17] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
We present draft genome sequences of five Enterococcus species from patients suspected of Clostridium difficile infection. Genome completeness was confirmed by presence of bacterial orthologs (97%). Gene searches using Hidden-Markov models revealed that the isolates harbor between seven and 11 genes involved in antibiotic resistance to tetracyclines, beta-lactams, and vancomycin.
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