1
|
Henriot P, Buelow E, Petit F, Ploy MC, Dagot C, Opatowski L. Modeling the impact of urban and hospital eco-exposomes on antibiotic-resistance dynamics in wastewaters. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 924:171643. [PMID: 38471588 DOI: 10.1016/j.scitotenv.2024.171643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 01/10/2024] [Accepted: 03/09/2024] [Indexed: 03/14/2024]
Abstract
The emergence and selection of antibiotic resistance is a major public health problem worldwide. The presence of antibiotic-resistant bacteria (ARBs) in natural and anthropogenic environments threatens the sustainability of efforts to reduce resistance in human and animal populations. Here, we use mathematical modeling of the selective effect of antibiotics and contaminants on the dynamics of bacterial resistance in water to analyze longitudinal spatio-temporal data collected in hospital and urban wastewater between 2012 and 2015. Samples were collected monthly during the study period at four different sites in Haute-Savoie, France: hospital and urban wastewater, before and after water treatment plants. Three different categories of exposure variables were collected simultaneously: 1) heavy metals, 2) antibiotics and 3) surfactants for a total of 13 drugs/molecules; in parallel to the normalized abundance of 88 individual genes and mobile genetic elements, mostly conferring resistance to antibiotics. A simple hypothesis-driven model describing weekly antibiotic resistance gene (ARG) dynamics was proposed to fit the available data, assuming that normalized gene abundance is proportional to antibiotic resistant bacteria (ARB) populations in water. The detected compounds were found to influence the dynamics of 17 genes found at multiple sites. While mercury and vancomycin were associated with increased ARG and affected the dynamics of 10 and 12 identified genes respectively, surfactants antagonistically affected the dynamics of three genes. The models proposed here make it possible to analyze the relationship between the persistence of resistance genes in the aquatic environment and specific compounds associated with human activities from longitudinal data. Our analysis of French data over 2012-2015 identified mercury and vancomycin as co-selectors for some ARGs.
Collapse
Affiliation(s)
- Paul Henriot
- Epidemiology and Modeling of bacterial Evasion to Antibacterials Unit (EMEA), Institut Paris, France; MESuRS Laboratory, Conservatoire National des Arts et Métiers Paris, France; Université Paris-Saclay, UVSQ, Inserm, CESP, Anti-Infective Evasion and Pharmacoepidemiology Team, Montigny-le-Bretonneux, France.
| | - Elena Buelow
- Université Limoges, INSERM, CHU Limoges, RESINFIT, U1092 Limoges, France; Univ. Grenoble Alpes, CNRS, UMR 5525, VetAgro Sup, Grenoble INP, TIMC, 38000 Grenoble, France
| | - Fabienne Petit
- UNIROUEN, UNICAEN, CNRS, M2C, Normandie Université, Rouen, France; Sorbonne Université, CNRS, EPHE, PSL, UMR METIS, Paris, France
| | - Marie-Cécile Ploy
- Université Limoges, INSERM, CHU Limoges, RESINFIT, U1092 Limoges, France
| | - Christophe Dagot
- Université Limoges, INSERM, CHU Limoges, RESINFIT, U1092 Limoges, France
| | - Lulla Opatowski
- Epidemiology and Modeling of bacterial Evasion to Antibacterials Unit (EMEA), Institut Paris, France; Université Paris-Saclay, UVSQ, Inserm, CESP, Anti-Infective Evasion and Pharmacoepidemiology Team, Montigny-le-Bretonneux, France
| |
Collapse
|
2
|
Caplunik-Pratsch A, Kieninger B, Donauer VA, Brauer JM, Meier VMK, Seisenberger C, Rath A, Loibl D, Eichner A, Fritsch J, Schneider-Brachert W. Introduction and spread of vancomycin-resistant Enterococcus faecium (VREfm) at a German tertiary care medical center from 2004 until 2010: a retrospective whole-genome sequencing (WGS) study of the molecular epidemiology of VREfm. Antimicrob Resist Infect Control 2024; 13:20. [PMID: 38355509 PMCID: PMC10865517 DOI: 10.1186/s13756-024-01379-4] [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: 11/20/2023] [Accepted: 02/07/2024] [Indexed: 02/16/2024] Open
Abstract
BACKGROUND In most of Europe and especially in Germany, there is currently a concerning rise in the number of hospital-acquired infections due to vancomycin-resistant Enterococcus faecium (VREfm). Therefore, there is a need to improve our understanding of the way VREfm spreads in hospitals. In this study, we investigated the molecular epidemiology of VREfm isolates from the first appearance at our university hospital in 2004 until 2010. There is only very scarce information about the molecular epidemiology of VREfm from this early time in Germany. METHODS Our analysis includes all available first VREfm isolates of each patient at our tertiary care center collected during the years 2004-2010. If available, additional consecutive VREfm isolates from some patients were analyzed. We used multilocus sequence typing (MLST) and core genome multilocus sequence typing (cgMLST) for the analysis and description of nosocomial transmission pathways as well as the detection of outbreaks. RESULTS VREfm isolates from 158 patients and 76 additional subsequent patient isolates were included in the analysis. Until 2006, detections of VREfm remained singular cases, followed by a peak in the number of VREfm cases in 2007 and 2008 with a subsequent decline to baseline in 2010. MLST and cgMLST analysis show significant changes in the dominant sequence types (STs) and complex types (CTs) over the study period, with ST192 and ST17 being responsible for the peak in VREfm cases in 2007 and 2008. The four largest clusters detected during the study period are comprised of these two STs. Cluster analysis shows a focus on specific wards and departments for each cluster. In the early years of this study (2004-2006), all analyzed VREfm stemmed from clinical specimens, whereas since 2007, approximately half of the VREfm were detected by screening. Of the 234 VREfm isolates analyzed, 96% had a vanB and only 4% had a vanA resistance genotype. CONCLUSIONS This retrospective study contributes significant knowledge about regional VREfm epidemiology from this early VREfm period in Germany. One remarkable finding is the striking dominance of vanB-positive VREfm isolates over the entire study period, which is in contrast with countrywide data. Analysis of cgMLST shows the transition from sporadic VRE cases at our institution to a sharp increase in VRE numbers triggered by oligoclonal spread and specific outbreak clusters with the dominance of ST192 and ST17.
Collapse
Affiliation(s)
- Aila Caplunik-Pratsch
- Department of Infection Prevention and Infectious Diseases, University Hospital Regensburg, Franz-Josef-Strauß-Allee 11, 93053, Regensburg, Germany.
| | - Bärbel Kieninger
- Department of Infection Prevention and Infectious Diseases, University Hospital Regensburg, Franz-Josef-Strauß-Allee 11, 93053, Regensburg, Germany
| | - Veronika A Donauer
- Department of Infection Prevention and Infectious Diseases, University Hospital Regensburg, Franz-Josef-Strauß-Allee 11, 93053, Regensburg, Germany
| | - Johanna M Brauer
- Department of Infection Prevention and Infectious Diseases, University Hospital Regensburg, Franz-Josef-Strauß-Allee 11, 93053, Regensburg, Germany
| | - Vanessa M K Meier
- Department of Infection Prevention and Infectious Diseases, University Hospital Regensburg, Franz-Josef-Strauß-Allee 11, 93053, Regensburg, Germany
| | - Corinna Seisenberger
- Department of Infection Prevention and Infectious Diseases, University Hospital Regensburg, Franz-Josef-Strauß-Allee 11, 93053, Regensburg, Germany
| | - Anca Rath
- Department of Infection Prevention and Infectious Diseases, University Hospital Regensburg, Franz-Josef-Strauß-Allee 11, 93053, Regensburg, Germany
| | - Daniel Loibl
- Department of Infection Prevention and Infectious Diseases, University Hospital Regensburg, Franz-Josef-Strauß-Allee 11, 93053, Regensburg, Germany
| | - Anja Eichner
- Department of Infection Prevention and Infectious Diseases, University Hospital Regensburg, Franz-Josef-Strauß-Allee 11, 93053, Regensburg, Germany
| | - Jürgen Fritsch
- Department of Infection Prevention and Infectious Diseases, University Hospital Regensburg, Franz-Josef-Strauß-Allee 11, 93053, Regensburg, Germany
| | - Wulf Schneider-Brachert
- Department of Infection Prevention and Infectious Diseases, University Hospital Regensburg, Franz-Josef-Strauß-Allee 11, 93053, Regensburg, Germany
| |
Collapse
|
3
|
Rath A, Kieninger B, Caplunik-Pratsch A, Fritsch J, Mirzaliyeva N, Holzmann T, Bender JK, Werner G, Schneider-Brachert W. Concerning emergence of a new vancomycin-resistant Enterococcus faecium strain ST1299/CT1903/vanA at a tertiary university centre in South Germany. J Hosp Infect 2024; 143:25-32. [PMID: 37852539 DOI: 10.1016/j.jhin.2023.10.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 09/22/2023] [Accepted: 10/08/2023] [Indexed: 10/20/2023]
Abstract
BACKGROUND vanB-carrying vancomycin-resistant Enterococcus faecium (VREfm) of the sequence types 80 (ST80) and ST117 have dominated Germany in the past. In 2020, our hospital witnessed a sharp increase in the proportion of vanA-positive VREfm. AIM To attempt to understand these dynamics through whole-genome sequencing (WGS) and analysis of nosocomial transmissions. METHODS At our hospital, the first VREfm isolate per patient, treated during 2020, was analysed retrospectively using specific vanA/vanB PCR, WGS, multi-locus sequence typing (MLST), and core-genome (cg) MLST. Epidemiologic links between VRE-positive patients were assessed using hospital occupancy data. FINDINGS Isolates from 319 out of 356 VREfm patients were available for WGS, of which 181 (56.7%) fulfilled the ECDC definition for nosocomial transmission. The high load of nosocomial cases is reflected in the overall high clonality rate with only three dominating sequence (ST) and complex types (CT), respectively: the new emerging strain ST1299 (100% vanA, 77.4% CT1903), and the well-known ST80 (90.0% vanB, 81.0% CT1065) and ST117 (78.0% vanB, 65.0% CT71). The ST1299 isolates overall, and the subtype CT1903 in particular, showed high isolate clonality, which demonstrates impressively high spreading potential. Overall, 152 out of 319 isolates had an allelic cgMLST difference of ≤3 to another, including 91 (59.6%) ST1299. Occupancy data identified shared rooms (3.7%), shared departments (6.2%), and VRE-colonized prior room occupants (0.6%) within 30 days before diagnosis as solid epidemiological links. CONCLUSION A new emerging VREfm clone, ST1299/CT1903/vanA, dominated our institution in 2020 and has been an important driver of the increasing VREfm rates.
Collapse
Affiliation(s)
- A Rath
- Department of Infection Prevention and Infectious Diseases, University Hospital Regensburg, Regensburg, Germany.
| | - B Kieninger
- Department of Infection Prevention and Infectious Diseases, University Hospital Regensburg, Regensburg, Germany
| | - A Caplunik-Pratsch
- Department of Infection Prevention and Infectious Diseases, University Hospital Regensburg, Regensburg, Germany
| | - J Fritsch
- Department of Infection Prevention and Infectious Diseases, University Hospital Regensburg, Regensburg, Germany
| | - N Mirzaliyeva
- Department of Infection Prevention and Infectious Diseases, University Hospital Regensburg, Regensburg, Germany
| | - T Holzmann
- Department of Infection Prevention and Infectious Diseases, University Hospital Regensburg, Regensburg, Germany
| | - J K Bender
- Department of Infectious Diseases, Division of Nosocomial Pathogens and Antibiotic Resistances, Robert Koch Institute, Wernigerode, Germany
| | - G Werner
- Department of Infectious Diseases, Division of Nosocomial Pathogens and Antibiotic Resistances, Robert Koch Institute, Wernigerode, Germany
| | - W Schneider-Brachert
- Department of Infection Prevention and Infectious Diseases, University Hospital Regensburg, Regensburg, Germany
| |
Collapse
|
4
|
AL Rubaye M, Janice J, Bjørnholt JV, Kacelnik O, Haldorsen BC, Nygaard RM, Hegstad J, Sundsfjord A, Hegstad K. The population structure of vancomycin-resistant and -susceptible Enterococcus faecium in a low-prevalence antimicrobial resistance setting is highly influenced by circulating global hospital-associated clones. Microb Genom 2023; 9:001160. [PMID: 38112685 PMCID: PMC10763505 DOI: 10.1099/mgen.0.001160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 12/01/2023] [Indexed: 12/21/2023] Open
Abstract
Between 2010 and 2015 the incidence of vancomycin-resistant Enterococcus faecium (VREfm) in Norway increased dramatically. Hence, we selected (1) a random subset of vancomycin-resistant enterococci (VRE) from the Norwegian Surveillance System for Communicable Diseases (2010-15; n=239) and (2) Norwegian vancomycin-susceptible E. faecium (VSEfm) bacteraemia isolates from the national surveillance system for antimicrobial resistance in microbes (2008 and 2014; n=261) for further analysis. Whole-genome sequences were collected for population structure, van gene cluster, mobile genetic element and virulome analysis, as well as antimicrobial susceptibility testing. Comparative genomic and phylogeographical analyses were performed with complete genomes of global E. faecium strains from the National Center for Biotechnology Information (NCBI) (1946-2022; n=272). All Norwegian VREfm and most of the VSEfm clustered with global hospital-associated sequence types (STs) in the phylogenetic subclade A1. The vanB2 subtype carried by chromosomal Tn1549 integrative conjugative elements was the dominant van type. The major Norwegian VREfm cluster types (CTs) were in accordance with concurrent European CTs. The dominant vanB-type VREfm CTs, ST192-CT3/26 and ST117-CT24, were mostly linked to a single hospital in Norway where the clones spread after independent chromosomal acquisition of Tn1549. The less prevalent vanA VRE were associated with more diverse CTs and vanA carrying Inc18 or RepA_N plasmids with toxin-antitoxin systems. Only 5 % of the Norwegian VRE were Enterococcus faecalis, all of which contained vanB. The Norwegian VREfm and VSEfm isolates harboured CT-specific virulence factor (VF) profiles supporting biofilm formation and colonization. The dominant VREfm CTs in general hosted more virulence determinants than VSEfm. The phylogenetic clade B VSEfm isolates (n=21), recently classified as Enterococcus lactis, harboured fewer VFs than E. faecium in general, and particularly subclade A1 isolates. In conclusion, the population structure of Norwegian E. faecium isolates mirrors the globally prevalent clones and particularly concurrent European VREfm/VSEfm CTs. Novel chromosomal acquisition of vanB2 on Tn1549 from the gut microbiota, however, formed a single major hospital VREfm outbreak. Dominant VREfm CTs contained more VFs than VSEfm.
Collapse
Affiliation(s)
- Mushtaq AL Rubaye
- Research group for Host–Microbe Interactions, Department of Medical Biology, UiT The Arctic University of Norway, Tromsø, Norway
| | - Jessin Janice
- Research group for Host–Microbe Interactions, Department of Medical Biology, UiT The Arctic University of Norway, Tromsø, Norway
- Norwegian National Advisory Unit on Detection of Antimicrobial Resistance, Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsø, Norway
- Present address: Section for development, Department of Microbiology, Clinic for Laboratory Medicine, Oslo University Hospital, Oslo, Norway
| | - Jørgen Vildershøj Bjørnholt
- Department of Clinical Microbiology, Oslo University Hospital, Oslo, Norway
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Oliver Kacelnik
- Department of Antibiotic Resistance and Infection Prevention, Norwegian Institute of Public Health, Oslo, Norway
| | - Bjørg C. Haldorsen
- Norwegian National Advisory Unit on Detection of Antimicrobial Resistance, Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsø, Norway
| | - Randi M. Nygaard
- Department of Microbiology, Haukeland University Hospital, Bergen, Norway
| | - Joachim Hegstad
- Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsø, Norway
| | - Arnfinn Sundsfjord
- Research group for Host–Microbe Interactions, Department of Medical Biology, UiT The Arctic University of Norway, Tromsø, Norway
- Norwegian National Advisory Unit on Detection of Antimicrobial Resistance, Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsø, Norway
| | - Kristin Hegstad
- Research group for Host–Microbe Interactions, Department of Medical Biology, UiT The Arctic University of Norway, Tromsø, Norway
- Norwegian National Advisory Unit on Detection of Antimicrobial Resistance, Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsø, Norway
| | - the Norwegian VRE study group
- Research group for Host–Microbe Interactions, Department of Medical Biology, UiT The Arctic University of Norway, Tromsø, Norway
- Norwegian National Advisory Unit on Detection of Antimicrobial Resistance, Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsø, Norway
- Department of Clinical Microbiology, Oslo University Hospital, Oslo, Norway
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Department of Antibiotic Resistance and Infection Prevention, Norwegian Institute of Public Health, Oslo, Norway
- Department of Microbiology, Haukeland University Hospital, Bergen, Norway
- Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsø, Norway
- Present address: Section for development, Department of Microbiology, Clinic for Laboratory Medicine, Oslo University Hospital, Oslo, Norway
| |
Collapse
|
5
|
Permana B, Harris PNA, Runnegar N, Lindsay M, Henderson BC, Playford EG, Paterson DL, Beatson SA, Forde BM. Using Genomics To Investigate an Outbreak of Vancomycin-Resistant Enterococcus faecium ST78 at a Large Tertiary Hospital in Queensland. Microbiol Spectr 2023; 11:e0420422. [PMID: 37191518 PMCID: PMC10269735 DOI: 10.1128/spectrum.04204-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2022] [Accepted: 04/16/2023] [Indexed: 05/17/2023] Open
Abstract
To investigate an outbreak of vancomycin-resistant Enterococcus faecium (VREfm) sequence type 78 (ST78) in a large tertiary Australian hospital. A collection of 63 VREfm ST78 isolates, identified during a routine genomic surveillance program, were subjected to genomic epidemiological analysis based on whole-genome sequencing (WGS) data. The population structure was reconstructed using phylogenetic analysis, and a collection of publicly available VREfm ST78 genomes were used to provide global context. Core genome single nucleotide polymorphism (SNP) distances and available clinical metadata were used to characterize outbreak clusters and reconstruct transmission events. In silico genotyping confirmed that all study isolates were vanB-type VREfm carrying virulence characteristics of the hospital-associated E. faecium. Phylogenetic analysis identified two distinct phylogenetic clades, only one of which was responsible for a hospital outbreak. Four outbreak subtypes could be defined with examples of recent transmissions. Inference on transmission trees suggested complex transmission routes with unknown environmental reservoirs mediating the outbreak. WGS-based cluster analysis with publicly available genomes identified closely related Australian ST78 and ST203 isolates, highlighting the capacity for WGS to resolve complex clonal relationships between the VREfm lineages. Whole genome-based analysis has provided a high-resolution description of an outbreak of vanB-type VREfm ST78 in a Queensland hospital. Combined routine genomic surveillance and epidemiological analysis have facilitated better understanding of the local epidemiology of this endemic strain, providing valuable insight for better targeted control of VREfm. IMPORTANCE Vancomycin-resistant Enterococcus faecium (VREfm) is a leading cause of health care-associated infections (HAIs) globally. In Australia, the spread of hospital-adapted VREfm is largely driven by a single clonal group (clonal complex [CC]), CC17, to which the lineage ST78 belongs. While implementing a genomic surveillance program in Queensland, we observed increased incidence of ST78 colonizations and infections among patients. Here, we demonstrate the use of real-time genomic surveillance as a tool to support and enhance infection control (IC) practices. Our results show that real-time whole-genome sequencing (WGS) can efficiently disrupt outbreaks by identifying transmission routes that in turn can be targeted using resource-limited interventions. Additionally, we demonstrate that by placing local outbreaks in a global context, high-risk clones can be identified and targeted prior to them becoming established within clinical environments. Finally, the persistence of these organism within the hospital highlights the need for routine genomic surveillance as a management tool to control VRE transmission.
Collapse
Affiliation(s)
- Budi Permana
- School of Chemistry and Molecular Biosciences, Faculty of Science, The University of Queensland, Brisbane, Australia
- Australian Centre for Ecogenomics, The University of Queensland, Brisbane, Australia
- Herston Infectious Diseases Institute, Metro North Health, Brisbane, Australia
| | - Patrick N. A. Harris
- Australian Infectious Disease Research Centre, Faculty of Science, The University of Queensland, Brisbane, Australia
- University of Queensland Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Brisbane, Australia
- Pathology Queensland, Central Laboratory, Brisbane, Australia
| | - Naomi Runnegar
- Princess Alexandra–Southside Clinical School, Faculty of Medicine, The University of Queensland, Brisbane, Australia
- Infection Management Services, Princess Alexandra Hospital, Brisbane, Australia
| | - Margaret Lindsay
- Infection Management Services, Princess Alexandra Hospital, Brisbane, Australia
| | | | - E. G. Playford
- Infection Management Services, Princess Alexandra Hospital, Brisbane, Australia
| | - David L. Paterson
- University of Queensland Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Brisbane, Australia
| | - Scott A. Beatson
- School of Chemistry and Molecular Biosciences, Faculty of Science, The University of Queensland, Brisbane, Australia
- Australian Centre for Ecogenomics, The University of Queensland, Brisbane, Australia
- Australian Infectious Disease Research Centre, Faculty of Science, The University of Queensland, Brisbane, Australia
| | - Brian M. Forde
- Australian Infectious Disease Research Centre, Faculty of Science, The University of Queensland, Brisbane, Australia
- University of Queensland Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Brisbane, Australia
| |
Collapse
|
6
|
Sugai M, Yuasa A, Miller RL, Vasilopoulos V, Kurosu H, Taie A, Gordon JP, Matsumoto T. An Economic Evaluation Estimating the Clinical and Economic Burden of Increased Vancomycin-Resistant Enterococcus faecium Infection Incidence in Japan. Infect Dis Ther 2023; 12:1695-1713. [PMID: 37302137 PMCID: PMC10281932 DOI: 10.1007/s40121-023-00826-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 05/19/2023] [Indexed: 06/13/2023] Open
Abstract
INTRODUCTION While incidence rates of vancomycin-resistant Enterococcus faecium have remained comparatively low in Japan, there have been increasing reports of more vancomycin-resistant Enterococcus (VRE) outbreaks, requiring costly measures to contain. Increased incidence of VRE in Japan may lead to more frequent and harder to contain outbreaks with current control measures, causing a significant burden to the healthcare system in Japan. This study aimed to demonstrate the clinical and economic burden of vancomycin-resistant E. faecium infections to the Japanese healthcare system and the impact of increasing rates of vancomycin resistance. METHODS A de novo deterministic analytic model was developed to assess the health economic outcomes of treating hospital-acquired VRE infections; patients are treated according to a two-line treatment strategy, dependent on their resistance status. The model considers hospitalisation costs and the additional cost of infection control. Scenarios investigated the current burden of VRE infections and the additional burden of increased incidence of VRE. Outcomes were assessed over a 1-year and 10-year time horizon from a healthcare payer's perspective in a Japanese setting. Quality-adjusted life years (QALYs) were valued with a willingness-to-pay threshold of ¥5,000,000 ($38,023), and costs and benefits were discounted at a rate of 2%. RESULTS Current VRE incidence levels in enterococcal infections in Japan equates to ¥130,209,933,636 ($996,204,669) in associated costs and a loss of 185,361 life years (LYs) and 165,934 QALYs over 10 years. A three-fold increase (1.83%) is associated with an additional ¥4,745,059,504 ($36,084,651) in total costs on top of the current cost burden as well as an additional loss of 683 LYs over a lifetime, corresponding to 616 QALYs lost. CONCLUSION Despite low incidence rates, VRE infections already represent a substantial economic burden to the Japanese healthcare system. The substantial increase in costs associated with a higher incidence of VRE infections could result in a significant economic challenge for Japan.
Collapse
Affiliation(s)
- Motoyuki Sugai
- Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Akira Yuasa
- Pfizer Japan Inc., Shinjuku Bunka Quint Building, 3-22-7, Yoyogi, Shibuya-Ku, Tokyo, 151-8589, Japan.
| | - Ryan L Miller
- Health Economics and Outcomes Research Ltd., Cardiff, UK
| | | | - Hitomi Kurosu
- Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | | | - Jason P Gordon
- Health Economics and Outcomes Research Ltd., Cardiff, UK
| | - Tetsuya Matsumoto
- Department of Infectious Diseases, School of Medicine, International University of Health and Welfare, Narita, Japan
| |
Collapse
|
7
|
Novais C, Almeida-Santos AC, Paula Pereira A, Rebelo A, Freitas AR, Peixe L. Alert for molecular data interpretation when using Enterococcus faecium reference strains reclassified as Enterococcus lactis. Gene 2023; 851:146951. [PMID: 36261083 DOI: 10.1016/j.gene.2022.146951] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 10/03/2022] [Indexed: 11/06/2022]
Affiliation(s)
- Carla Novais
- UCIBIO-Applied Molecular Biosciences Unit, Laboratory of Microbiology, Department of Biological Sciences, REQUIMTE Faculty of Pharmacy, University of Porto, Rua Jorge de Viterbo Ferreira 228, 4050-313 Porto, Portugal; Associate Laboratory i4HB - Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, Rua Jorge de Viterbo Ferreira 228, 4050-313 Porto, Portugal.
| | - Ana C Almeida-Santos
- UCIBIO-Applied Molecular Biosciences Unit, Laboratory of Microbiology, Department of Biological Sciences, REQUIMTE Faculty of Pharmacy, University of Porto, Rua Jorge de Viterbo Ferreira 228, 4050-313 Porto, Portugal; Associate Laboratory i4HB - Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, Rua Jorge de Viterbo Ferreira 228, 4050-313 Porto, Portugal
| | - Ana Paula Pereira
- UCIBIO-Applied Molecular Biosciences Unit, Laboratory of Microbiology, Department of Biological Sciences, REQUIMTE Faculty of Pharmacy, University of Porto, Rua Jorge de Viterbo Ferreira 228, 4050-313 Porto, Portugal; Associate Laboratory i4HB - Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, Rua Jorge de Viterbo Ferreira 228, 4050-313 Porto, Portugal
| | - Andreia Rebelo
- UCIBIO-Applied Molecular Biosciences Unit, Laboratory of Microbiology, Department of Biological Sciences, REQUIMTE Faculty of Pharmacy, University of Porto, Rua Jorge de Viterbo Ferreira 228, 4050-313 Porto, Portugal; Associate Laboratory i4HB - Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, Rua Jorge de Viterbo Ferreira 228, 4050-313 Porto, Portugal; Abel Salazar Biomedical Sciences Institute (ICBAS), Rua Jorge de Viterbo Ferreira 228, 4050-313 Porto, Portugal; Technical-Scientific Area of Environmental Health, School of Health, Polytechnic Institute of Porto, Rua Dr. António Bernardino de Almeida 400, 420-072 Porto, Portugal
| | - Ana R Freitas
- UCIBIO-Applied Molecular Biosciences Unit, Laboratory of Microbiology, Department of Biological Sciences, REQUIMTE Faculty of Pharmacy, University of Porto, Rua Jorge de Viterbo Ferreira 228, 4050-313 Porto, Portugal; Associate Laboratory i4HB - Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, Rua Jorge de Viterbo Ferreira 228, 4050-313 Porto, Portugal; TOXRUN, Toxicology Research Unit, University Institute of Health Sciences, CESPU, CRL, Rua Central da Gandra, 1317-4585 Gandra, Portugal
| | - Luísa Peixe
- UCIBIO-Applied Molecular Biosciences Unit, Laboratory of Microbiology, Department of Biological Sciences, REQUIMTE Faculty of Pharmacy, University of Porto, Rua Jorge de Viterbo Ferreira 228, 4050-313 Porto, Portugal; Associate Laboratory i4HB - Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, Rua Jorge de Viterbo Ferreira 228, 4050-313 Porto, Portugal
| |
Collapse
|
8
|
Maechler F, Weber A, Schwengers O, Schwab F, Denkel L, Behnke M, Gastmeier P, Kola A. Split k-mer analysis compared to cgMLST and SNP-based core genome analysis for detecting transmission of vancomycin-resistant enterococci: results from routine outbreak analyses across different hospitals and hospitals networks in Berlin, Germany. Microb Genom 2023; 9:mgen000937. [PMID: 36748706 PMCID: PMC9973845 DOI: 10.1099/mgen.0.000937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
The increase of Vancomycin-resistant Enterococcus faecium (VREfm) in recent years has been partially attributed to the rise of specific clonal lineages, which have been identified throughout Germany. To date, there is no gold standard for the interpretation of genomic data for outbreak analyses. New genomic approaches such as split k-mer analysis (SKA) could support cluster attribution for routine outbreak investigation. The aim of this project was to investigate frequent clonal lineages of VREfm identified during suspected outbreaks across different hospitals, and to compare genomic approaches including SKA in routine outbreak investigation. We used routine outbreak laboratory data from seven hospitals and three different hospital networks in Berlin, Germany. Short-read libraries were sequenced on the Illumina MiSeq system. We determined clusters using the published Enterococcus faecium-cgMLST scheme (threshold ≤20 alleles), and assigned sequence and complex types (ST, CT), using the Ridom SeqSphere+ software. For each cluster as determined by cgMLST, we used pairwise core-genome SNP-analysis and SKA at thresholds of ten and seven SNPs, respectively, to further distinguish cgMLST clusters. In order to investigate clinical relevance, we analysed to what extent epidemiological linkage backed the clusters determined with different genomic approaches. Between 2014 and 2021, we sequenced 693 VREfm strains, and 644 (93 %) were associated within cgMLST clusters. More than 74 % (n=475) of the strains belonged to the six largest cgMLST clusters, comprising ST117, ST78 and ST80. All six clusters were detected across several years and hospitals without apparent epidemiological links. Core SNP analysis identified 44 clusters with a median cluster size of three isolates (IQR 2-7, min-max 2-63), as well as 197 singletons (41.4 % of 475 isolates). SKA identified 67 clusters with a median cluster size of two isolates (IQR 2-4, min-max 2-19), and 261 singletons (54.9 % of 475 isolates). Of the isolate pairs attributed to clusters, 7 % (n=3064/45 596) of pairs in clusters determined by standard cgMLST, 15 % (n=1222/8500) of pairs in core SNP-clusters and 51 % (n=942/1880) of pairs in SKA-clusters showed epidemiological linkage. The proportion of epidemiological linkage differed between sequence types. For VREfm, the discriminative ability of the widely used cgMLST based approach at ≤20 alleles difference was insufficient to rule out hospital outbreaks without further analytical methods. Cluster assignment guided by core genome SNP analysis and the reference free SKA was more discriminative and correlated better with obvious epidemiological linkage, at least recently published thresholds (ten and seven SNPs, respectively) and for frequent STs. Besides higher overall discriminative power, the whole-genome approach implemented in SKA is also easier and faster to conduct and requires less computational resources.
Collapse
Affiliation(s)
- Friederike Maechler
- Institute of Hygiene and Environmental Medicine, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Anna Weber
- Institute of Hygiene and Environmental Medicine, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Oliver Schwengers
- Bioinformatics and Systems Biology, Justus Liebig University Giessen, Giessen, Germany
| | - Frank Schwab
- Institute of Hygiene and Environmental Medicine, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Luisa Denkel
- Institute of Hygiene and Environmental Medicine, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Michael Behnke
- Institute of Hygiene and Environmental Medicine, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Petra Gastmeier
- Institute of Hygiene and Environmental Medicine, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Axel Kola
- Institute of Hygiene and Environmental Medicine, Charité - Universitätsmedizin Berlin, Berlin, Germany
| |
Collapse
|
9
|
Attributable mortality of vancomycin resistance in ampicillin-resistant Enterococcus faecium bacteremia in Denmark and the Netherlands: A matched cohort study. Infect Control Hosp Epidemiol 2022; 43:719-727. [PMID: 35670618 DOI: 10.1017/ice.2021.216] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
OBJECTIVE To study whether replacement of nosocomial ampicillin-resistant Enterococcus faecium (ARE) clones by vancomycin-resistant E. faecium (VRE), belonging to the same genetic lineages, increases mortality in patients with E. faecium bacteremia, and to evaluate whether any such increase is mediated by a delay in appropriate antibiotic therapy. DESIGN Retrospective, matched-cohort study. SETTING The study included 20 Dutch and Danish hospitals from 2009 to 2014. PATIENTS Within the study period, 63 patients with VRE bacteremia (36 Dutch and 27 Danish) were identified and subsequently matched to 234 patients with ARE bacteremia (130 Dutch and 104 Danish) for hospital, ward, length of hospital stay prior to bacteremia, and age. For all patients, 30-day mortality after bacteremia onset was assessed. METHODS The risk ratio (RR) reflecting the impact of vancomycin resistance on 30-day mortality was estimated using Cox regression with further analytic control for confounding factors. RESULTS The 30-day mortality rates were 27% and 38% for ARE in the Netherlands and Denmark, respectively, and the 30-day mortality rates were 33% and 48% for VRE in these respective countries. The adjusted RR for 30-day mortality for VRE was 1.54 (95% confidence interval, 1.06-2.25). Although appropriate antibiotic therapy was initiated later for VRE than for ARE bacteremia, further analysis did not reveal mediation of the increased mortality risk. CONCLUSIONS Compared to ARE bacteremia, VRE bacteremia was associated with higher 30-day mortality. One explanation for this association would be increased virulence of VRE, although both phenotypes belong to the same well-characterized core genomic lineage. Alternatively, it may be the result of unmeasured confounding.
Collapse
|
10
|
Descriptive Analysis of Circulating Antimicrobial Resistance Genes in Vancomycin-Resistant Enterococcus (VRE) during the COVID-19 Pandemic. Biomedicines 2022; 10:biomedicines10051122. [PMID: 35625861 PMCID: PMC9138224 DOI: 10.3390/biomedicines10051122] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 04/25/2022] [Accepted: 05/09/2022] [Indexed: 01/07/2023] Open
Abstract
COVID-19 offers ideal premises for bacteria to develop antimicrobial resistance. In this study, we evaluated the presence of several antimicrobial resistance genes (ARG) in vancomycin-resistant Enterococcus (VRE) isolated from rectal swabs from patients at a hospital in Cluj-Napoca, Romania. Rectal swabs were cultivated on CHROMID® VRE (bioMérieux, Marcy—l’ Étoile, France) and positive isolates were identified using MALDI-TOF Mass Spectrometry (Bruker Daltonics, Bremen, Germany) and further analyzed using the PCR technique for the presence of the following ARGs: van A, van B, tet(M), tet(L), ermB, msrA, mefA, aac(6′)-Im, aph(2)-Ib, ant(4′)-Ia, sul1, sul2, sul3, and NDM1. We isolated and identified 68 isolates of Enterococcus faecium and 11 isolates of Enterococcus faecalis. The molecular analysis showed 66 isolates positive for the vanA gene and eight positive for vanB. The most frequent association of ARG in VRE was vanA-tet(M)-ermB. There was no statistically significant difference between Enterococcus faecium and Enterococcus faecalis regarding ARGs. Our work proves that during the COVID-19 pandemic, highly resistant isolates of Enterococcus were present in patients in the intensive care unit; thus, better healthcare policies should be implemented for the management and control of these highly resistant isolates in the future.
Collapse
|
11
|
Population dynamics in colonizing vancomycin-resistant E. faecium isolated from immunosuppressed patients. J Glob Antimicrob Resist 2022; 28:267-273. [DOI: 10.1016/j.jgar.2022.01.027] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 12/23/2021] [Accepted: 01/31/2022] [Indexed: 11/22/2022] Open
|
12
|
Conwell M, Dooley J, Naughton PJ. Enterococcal biofilm - a nidus for antibiotic resistance transfer? J Appl Microbiol 2022; 132:3444-3460. [PMID: 34990042 PMCID: PMC9306868 DOI: 10.1111/jam.15441] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Revised: 08/03/2021] [Accepted: 01/03/2022] [Indexed: 11/30/2022]
Abstract
Enterococci, important agents of hospital acquired infection, are listed on the WHO list of multi-drug resistant pathogens commonly encountered in hospital acquired infections are now of increasing importance, due to the development of strains resistant to multiple antibiotics. Enterococci are also important microorganisms in the environment and their presence is frequently used as an indicator of faecal pollution. Their success is related to their ability to survive within a broad range of habitats and the ease by which they acquire mobile genetic elements, including plasmids, from other bacteria. The enterococci are frequently present within a bacterial biofilm which provides stability and protection to the bacterial population along with an opportunity for a variety of bacterial interactions. Enterococci can accept extrachromosomal DNA both from within its own species and from other bacterial species and this is enhanced by the proximity of the donor and recipient strains. It is this exchange of genetic material that makes the role of biofilm such an important aspect of the success of enterococci. There remain many questions regarding the most suitable model systems to study enterococci in biofilm and regarding the transfer of genetic material including antibiotic resistance in these biofilms. This review focuses on some important aspects of biofilm in the context of horizontal gene transfer (HGT) in enterococci.
Collapse
Affiliation(s)
- M Conwell
- The Nutrition Innovation Centre for Food and Health (NICHE), School of Biomedical Sciences, Ulster University, Cromore Road, Coleraine, Co. Londonderry, BT52 1SA
| | - Jsg Dooley
- The Nutrition Innovation Centre for Food and Health (NICHE), School of Biomedical Sciences, Ulster University, Cromore Road, Coleraine, Co. Londonderry, BT52 1SA
| | - P J Naughton
- The Nutrition Innovation Centre for Food and Health (NICHE), School of Biomedical Sciences, Ulster University, Cromore Road, Coleraine, Co. Londonderry, BT52 1SA
| |
Collapse
|
13
|
Lisotto P, Raangs EC, Couto N, Rosema S, Lokate M, Zhou X, Friedrich AW, Rossen JWA, Harmsen HJM, Bathoorn E, Chlebowicz-Fliss MA. Long-read sequencing-based in silico phage typing of vancomycin-resistant Enterococcus faecium. BMC Genomics 2021; 22:758. [PMID: 34688274 PMCID: PMC8542323 DOI: 10.1186/s12864-021-08080-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Accepted: 10/07/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Vancomycin-resistant enterococci (VRE) are successful nosocomial pathogens able to cause hospital outbreaks. In the Netherlands, core-genome MLST (cgMLST) based on short-read sequencing is often used for molecular typing. Long-read sequencing is more rapid and provides useful information about the genome's structural composition but lacks the precision required for SNP-based typing and cgMLST. Here we compared prophages among 50 complete E. faecium genomes belonging to different lineages to explore whether a phage signature would be usable for typing and identifying an outbreak caused by VRE. As a proof of principle, we investigated if long-read sequencing data would allow for identifying phage signatures and thereby outbreak-related isolates. RESULTS Analysis of complete genome sequences of publicly available isolates showed variation in phage content among different lineages defined by MLST. We identified phage present in multiple STs as well as phages uniquely detected within a single lineage. Next, in silico phage typing was applied to twelve MinION sequenced isolates belonging to two different genetic backgrounds, namely ST117/CT24 and ST80/CT16. Genomic comparisons of the long-read-based assemblies allowed us to correctly identify isolates of the same complex type based on global genome architecture and specific phage signature similarity. CONCLUSIONS For rapid identification of related VRE isolates, phage content analysis in long-read sequencing data is possible. This allows software development for real-time typing analysis of long-read sequencing data, which will generate results within several hours. Future studies are required to assess the discriminatory power of this method in the investigation of ongoing outbreaks over a longer time period.
Collapse
Affiliation(s)
- Paola Lisotto
- Department of Medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Erwin C Raangs
- Department of Medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Natacha Couto
- Department of Medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.,The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, UK
| | - Sigrid Rosema
- Department of Medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Mariëtte Lokate
- Department of Medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Xuewei Zhou
- Department of Medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Alexander W Friedrich
- Department of Medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - John W A Rossen
- Department of Medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.,Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT, USA.,IDbyDNA Inc., Salt Lake City, UT, USA
| | - Hermie J M Harmsen
- Department of Medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Erik Bathoorn
- Department of Medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.
| | - Monika A Chlebowicz-Fliss
- Department of Medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| |
Collapse
|
14
|
Lisotto P, Couto N, Rosema S, Lokate M, Zhou X, Bathoorn E, Harmsen HJM, Friedrich AW, Rossen JWA, Chlebowicz-Fliss MA. Molecular Characterisation of Vancomycin-Resistant Enterococcus faecium Isolates Belonging to the Lineage ST117/CT24 Causing Hospital Outbreaks. Front Microbiol 2021; 12:728356. [PMID: 34646248 PMCID: PMC8503688 DOI: 10.3389/fmicb.2021.728356] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 08/27/2021] [Indexed: 12/02/2022] Open
Abstract
Background: Vancomycin-resistant Enterococcus faecium (VREfm) is a successful nosocomial pathogen. The current molecular method recommended in the Netherlands for VREfm typing is based on core genome Multilocus sequence typing (cgMLST), however, the rapid emergence of specific VREfm lineages challenges distinguishing outbreak isolates solely based on their core genome. Here, we explored if a detailed molecular characterisation of mobile genetic elements (MGEs) and accessory genes could support and expand the current molecular typing of VREfm isolates sharing the same genetic background, enhancing the discriminatory power of the analysis. Materials/Methods: The genomes of 39 VREfm and three vancomycin-susceptible E. faecium (VSEfm) isolates belonging to ST117/CT24, as assessed by cgMLST, were retrospectively analysed. The isolates were collected from patients and environmental samples from 2011 to 2017, and their genomes were analysed using short-read sequencing. Pangenome analysis was performed on de novo assemblies, which were also screened for known predicted virulence factors, antimicrobial resistance genes, bacteriocins, and prophages. Two representative isolates were also sequenced using long-read sequencing, which allowed a detailed analysis of their plasmid content. Results: The cgMLST analysis showed that the isolates were closely related, with a minimal allelic difference of 10 between each cluster’s closest related isolates. The vanB-carrying transposon Tn1549 was present in all VREfm isolates. However, in our data, we observed independent acquisitions of this transposon. The pangenome analysis revealed differences in the accessory genes related to prophages and bacteriocins content, whilst a similar profile was observed for known predicted virulence and resistance genes. Conclusion: In the case of closely related isolates sharing a similar genetic background, a detailed analysis of MGEs and the integration point of the vanB-carrying transposon allow to increase the discriminatory power compared to the use of cgMLST alone. Thus, enabling the identification of epidemiological links amongst hospitalised patients.
Collapse
Affiliation(s)
- Paola Lisotto
- Department of Medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Natacha Couto
- Department of Medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, Groningen, Netherlands.,The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom
| | - Sigrid Rosema
- Department of Medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Mariëtte Lokate
- Department of Medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Xuewei Zhou
- Department of Medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Erik Bathoorn
- Department of Medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Hermie J M Harmsen
- Department of Medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Alexander W Friedrich
- Department of Medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - John W A Rossen
- Department of Medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, Groningen, Netherlands.,Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT, United States.,IDbyDNA Inc., Salt Lake City, UT, United States
| | - Monika A Chlebowicz-Fliss
- Department of Medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| |
Collapse
|
15
|
Pinholt M, Mollerup S, Boye K, Worning P, Holzknecht BJ, Nygaard S, Nielsen KL, Hasman H, Roer L, Hammerum AM, Westh H, Schønning K. Investigation of the introduction and dissemination of vanB Enterococcus faecium in the Capital Region of Denmark and development of a rapid and accurate clone-specific vanB E. faecium PCR. J Antimicrob Chemother 2021; 76:2260-2267. [PMID: 34151364 DOI: 10.1093/jac/dkab198] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 05/17/2021] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND During 2018-19, an increase of vanB vancomycin-resistant Enterococcus faecium (VREfm) was observed in the Capital Region of Denmark. vanA/vanB PCR performed directly on rectal swabs is accurate in detection of vanA; however, the positive predictive value for vanB-positive samples is low because of the presence of vanB in non-enterococcal gut commensals. OBJECTIVES We investigated the epidemiology and clonal relatedness of vanB VREfm from the period 2015-19 and describe the application of a clone-specific vanB VREfm PCR assay for rapid and accurate detection of vanB VREfm in rectal screening samples. METHODS vanB VREfm were investigated using epidemiological data and WGS data. The SeqSphere+ software was used to analyse MLST and cgMLST, and de novo assemblies were annotated to determine insertion sites for the vanB transposon (Tn1549). A clone-specific vanB VREfm PCR assay was designed to detect the sequence bridging Tn1549 and the E. faecium chromosome (araA2) in the dominant cluster. RESULTS Two hundred and seventy-five vanB VREfm isolates were identified, of which 76% were identified in 2019. A dominant cluster (Cluster 1, n = 204, 74%), six minor clusters and 15 singletons were identified. All Cluster 1 isolates and six non-Cluster 1 isolates had Tn1549 integrated into araA2. In 2019, the PCR assay would have detected 92% of all rectal screening samples containing vanB VREfm. CONCLUSIONS vanB VREfm increased due to the introduction and nosocomial transmission of the successful Cluster 1. The clone-specific PCR assay detected vanB VREfm outbreak isolates in rectal screening samples rapidly and accurately.
Collapse
Affiliation(s)
- Mette Pinholt
- Department of Clinical Microbiology, Copenhagen University Hospital-Amager and Hvidovre, Copenhagen, Denmark
| | - Sarah Mollerup
- Department of Clinical Microbiology, Copenhagen University Hospital-Amager and Hvidovre, Copenhagen, Denmark
| | - Kit Boye
- Department of Clinical Microbiology, Copenhagen University Hospital-Amager and Hvidovre, Copenhagen, Denmark
| | - Peder Worning
- Department of Clinical Microbiology, Copenhagen University Hospital-Amager and Hvidovre, Copenhagen, Denmark
| | - Barbara Juliane Holzknecht
- Department of Clinical Microbiology, Copenhagen University Hospital-Herlev and Gentofte, Copenhagen, Denmark.,Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Sanne Nygaard
- Department of Clinical Microbiology, Copenhagen University Hospital-Herlev and Gentofte, Copenhagen, Denmark
| | - Karen Leth Nielsen
- Department of Clinical Microbiology, Copenhagen University Hospital-Rigshospitalet, Copenhagen, Denmark
| | - Henrik Hasman
- Department for Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Louise Roer
- Department for Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Anette M Hammerum
- Department for Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Henrik Westh
- Department of Clinical Microbiology, Copenhagen University Hospital-Amager and Hvidovre, Copenhagen, Denmark.,Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Kristian Schønning
- Department of Clinical Microbiology, Copenhagen University Hospital-Amager and Hvidovre, Copenhagen, Denmark.,Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark.,Department of Clinical Microbiology, Copenhagen University Hospital-Rigshospitalet, Copenhagen, Denmark
| |
Collapse
|
16
|
Makowska N, Bresa K, Koczura R, Philips A, Nowis K, Mokracka J. Urban wastewater as a conduit for pathogenic Gram-positive bacteria and genes encoding resistance to β-lactams and glycopeptides. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 765:144176. [PMID: 33385807 DOI: 10.1016/j.scitotenv.2020.144176] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 11/19/2020] [Accepted: 11/23/2020] [Indexed: 06/12/2023]
Abstract
The emergence and spread of clinical pathogens, antibiotic-resistant bacteria (ARB) and antibiotic resistance genes (ARGs) in the environment pose a direct threat to human and animal health worldwide. In this study, we analyzed qualitatively and quantitatively urban sewage resistome for the occurrence of genes encoding resistance to β-lactams and glycopeptides in the genomes of culturable bacteria, as well as in the wastewater metagenome of the Central Wastewater Treatment Plant in Koziegłowy (Poland). Moreover, we estimated the presence of pathogenic Gram-positive bacteria in wastewater based on analysis of species-specific virulence genes in the wastewater metagenome. The results show that the final effluent contains alarm pathogens with particularly dangerous mechanisms of antibiotic resistance, including methicillin-resistant Staphylococcus aureus (MRSA) and vancomycin-resistant enterococci (VRE). We also noticed that during the wastewater treatment, there is an increase in the frequency of MRSA and VRE. Furthermore, the results prove the effective removal of vanA, but at the same time show that wastewater treatment increases the relative abundance of mecA and virulence genes (groES and sec), indicating the presence of clinical pathogens E. faecalis and S. aureus in the effluent released to surface waters. We also observed an increase in the relative abundance of mecA and vanA genes already in the aeration tank, which suggests accumulation of contaminants affecting enhanced selection and HGT processes in the activated sludge. Moreover, we found a relation between the taxonomic composition and the copy number of ARGs as well as the presence of pathogens at various stages of wastewater treatment. The presence of clinically relevant pathogens, ARB, including multi-resistant bacteria, and ARGs in the effluent indicates that wastewater treatment plant play a key role in the existence of pathogens and antimicrobial resistance spreading pathway in the environment and human communities, which is a direct threat to public health and environmental protection.
Collapse
Affiliation(s)
- Nicoletta Makowska
- Department of Microbiology, Faculty of Biology, Adam Mickiewicz University in Poznań, Poznań, Poland; Department of Molecular Genetics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznań, Poland
| | - Katarzyna Bresa
- Department of Microbiology, Faculty of Biology, Adam Mickiewicz University in Poznań, Poznań, Poland
| | - Ryszard Koczura
- Department of Microbiology, Faculty of Biology, Adam Mickiewicz University in Poznań, Poznań, Poland
| | - Anna Philips
- European Center for Bioinformatics and Genomics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznań, Poland
| | - Katarzyna Nowis
- European Center for Bioinformatics and Genomics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznań, Poland
| | - Joanna Mokracka
- Department of Microbiology, Faculty of Biology, Adam Mickiewicz University in Poznań, Poznań, Poland.
| |
Collapse
|
17
|
van Hal SJ, Willems RJL, Gouliouris T, Ballard SA, Coque TM, Hammerum AM, Hegstad K, Westh HT, Howden BP, Malhotra-Kumar S, Werner G, Yanagihara K, Earl AM, Raven KE, Corander J, Bowden R. The global dissemination of hospital clones of Enterococcus faecium. Genome Med 2021; 13:52. [PMID: 33785076 PMCID: PMC8008517 DOI: 10.1186/s13073-021-00868-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Accepted: 03/15/2021] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND The hospital-adapted A1 group of Enterococcus faecium remains an organism of significant concern in the context of drug-resistant hospital-associated infections. How this pathogen evolves and disseminates remains poorly understood. METHODS A large, globally representative collection of short-read genomic data from the hospital-associated A1 group of Enterococcus faecium was assembled (n = 973). We analysed, using a novel analysis approach, global diversity in terms of both the dynamics of the accessory genome and homologous recombination among conserved genes. RESULTS Two main modes of genomic evolution continue to shape E. faecium: the acquisition and loss of genes, including antimicrobial resistance genes, through mobile genetic elements including plasmids, and homologous recombination of the core genome. These events lead to new clones emerging at the local level, followed by the erosion of signals of clonality through recombination, and in some identifiable cases producing new clonal clusters. These patterns lead to new, emerging lineages which are able to spread globally over relatively short timeframes. CONCLUSIONS The ability of A1 E. faecium to continually present new combinations of genes for potential selection suggests that controlling this pathogen will remain challenging but establishing a framework for understanding genomic evolution is likely to aid in tracking the threats posed by newly emerging lineages.
Collapse
Affiliation(s)
- Sebastiaan J. van Hal
- Department of Infectious Disesase and Microbiology, Royal Prince Alfred Hospital, Sydney, NSW Australia
- University of Sydney, Sydney, NSW Australia
| | - Rob J. L. Willems
- Department of Medical Microbiology, University Medical Center Utrech, Utrecht, The Netherlands
| | | | - Susan A. Ballard
- Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria Australia
| | - Teresa M. Coque
- Department of Microbiology, Ramón y Cajal University Hospital and Ramón y Cajal Health Research Institute (IRYCIS), Madrid, Spain
- Network Research Centre for Epidemiology and Public Health (CIBERESP), Madrid, Spain
| | | | - Kristin Hegstad
- Department of Microbiology and Infection Control, Norwegian National Advisory Unit on Detection of Antimicrobial Resistance, University Hospital of North-Norway, Tromsø, Norway
- Research Group for Host-Microbe Interactions, UiT – the Arctic University of Norway, Tromsø, Norway
| | - Hendrik T. Westh
- MRSA Knowledge Center, Department of Clinical Microbiology, Hvidovre Hospital, Hvidovre, Denmark
| | - Benjamin P. Howden
- Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria Australia
| | - Surbhi Malhotra-Kumar
- Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, Universiteit Antwerpen, Wilrijk, Belgium
| | - Guido Werner
- National Reference Centre for Staphylococci and Enterococci, Division of Nosocomial Pathogens and Antibiotic Resistances, Department of Infectious Diseases, Robert Koch Institute, Wernigerode Branch, Wernigerode, Germany
| | - Katsunori Yanagihara
- Department of Laboratory Medicine, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Ashlee M. Earl
- Infectious Disease & Microbiome Program, Broad Institute, Cambridge, MA USA
| | | | - Jukka Corander
- Department of Biostatistics, University of Oslo, Oslo, Norway
- Parasites and Microbes, Wellcome Sanger Institute, Hinxton, Cambridge, UK
| | - Rory Bowden
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052 Australia
- Department of Medical Biology, University of Melbourne, 1G Royal Parade, Melbourne, Victoria Australia
- Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, OX3 7BN UK
| |
Collapse
|
18
|
Falgenhauer L, Preuser I, Imirzalioglu C, Falgenhauer J, Fritzenwanker M, Mack D, Best C, Heudorf U, Chakraborty T. Changing epidemiology of vancomycin-resistant Enterococcus faecium: Results of a genome-based study at a regional neurological acute hospital with intensive care and early rehabilitation treatment. Infect Prev Pract 2021; 3:100138. [PMID: 34368749 PMCID: PMC8335922 DOI: 10.1016/j.infpip.2021.100138] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 03/22/2021] [Indexed: 12/04/2022] Open
Abstract
Background Vancomycin-resistant Enterococcus faecium (VREfm) are an emerging threat worldwide. In Germany, a VRE-belt with higher VREfm prevalences transversing its central east-west axis and including the state of Hesse was previously described. Recently, we detected a predominant VREfm clone in hospitals throughout the Rhine-Main metropolitan area of Hesse. Aim Here we expanded our study on VREfm to a regional neurological acute hospital outside of the metropolitan area with patient referrals from throughout Hesse and the neighboring federal state of Rhineland-Palatinate. Material/Methods VREfm isolates obtained between 2016-2018 from a regional neurological acute hospital with intensive care and early rehabilitation units were investigated (n=55). Patient data was collected and analyzed together with whole-genome sequencing data to investigate antibiotic resistance and virulence determinants of the VREfm. The population structure of VREfm was investigated using the Core genome-based multilocus sequence typing (cgMLST). Findings The average age of the patients was 67.1 years. For 96% of the patients, a previous hospital stay was reported. 64% of the patients were treated with antibiotics. All VREfm harbored the vanB vancomycin resistance gene. The multilocus sequence types (STs) detected changed abruptly from four different STs in 2016 to a predominant ST in 2017 and 2018 (ST117). Most of the ST117 isolates were members of the cgMLST type CT71. Conclusion The results indicate a sudden shift of the VREfm population structure from a semi-heterogeneous population to a pre-dominant clone within an interval of two years. Further investigations are warranted to understand the epidemiology and emergence of this clone.
Collapse
Affiliation(s)
- Linda Falgenhauer
- Institute of Hygiene and Environmental Medicine, Justus Liebig University Giessen, Schubertstrasse 81, Giessen, 35392, Germany.,German Center for Infection Research (DZIF), Site Giessen-Marburg-Langen, Justus Liebig University Giessen, Schubertstrasse 81, Giessen, 35392, Germany
| | - Ingeborg Preuser
- Department of Neurology, Vitos-Weil-Lahn, Weilstrasse 10, Weilmünster, 35789, Germany
| | - Can Imirzalioglu
- German Center for Infection Research (DZIF), Site Giessen-Marburg-Langen, Justus Liebig University Giessen, Schubertstrasse 81, Giessen, 35392, Germany.,Institute of Medical Microbiology, Justus Liebig University Giessen, Schubertstrasse 81, Giessen, 35392, Germany
| | - Jane Falgenhauer
- German Center for Infection Research (DZIF), Site Giessen-Marburg-Langen, Justus Liebig University Giessen, Schubertstrasse 81, Giessen, 35392, Germany.,Institute of Medical Microbiology, Justus Liebig University Giessen, Schubertstrasse 81, Giessen, 35392, Germany
| | - Moritz Fritzenwanker
- German Center for Infection Research (DZIF), Site Giessen-Marburg-Langen, Justus Liebig University Giessen, Schubertstrasse 81, Giessen, 35392, Germany.,Institute of Medical Microbiology, Justus Liebig University Giessen, Schubertstrasse 81, Giessen, 35392, Germany
| | - Dietrich Mack
- Institut für Medizinische Diagnostik GmbH, Bioscientia Labor Ingelheim, Konrad-Adenauer-Straße 17, Ingelheim am Rhein, 55218, Germany
| | - Christoph Best
- Department of Neurology, Vitos-Weil-Lahn, Weilstrasse 10, Weilmünster, 35789, Germany
| | - Ursel Heudorf
- Network on MDRO Rhine-Main, Breite Gasse 28, Frankfurt/Main, 60313, Germany
| | - Trinad Chakraborty
- German Center for Infection Research (DZIF), Site Giessen-Marburg-Langen, Justus Liebig University Giessen, Schubertstrasse 81, Giessen, 35392, Germany.,Institute of Medical Microbiology, Justus Liebig University Giessen, Schubertstrasse 81, Giessen, 35392, Germany
| |
Collapse
|
19
|
Nürnberger L, Schmidt D, Szumlanski T, Kirchhoff L, Ross B, Steinmann J, Rath PM. Molecular characterization of vancomycin-resistant Enterococcus faecium isolates from two German hospitals. GMS HYGIENE AND INFECTION CONTROL 2021; 16:Doc13. [PMID: 33796441 PMCID: PMC7983015 DOI: 10.3205/dgkh000384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Introduction: Vancomycin-resistant Enterococcusfaecium accounts for around 10–23% of nosocomial enterococcal infections and constitutes a relevant therapeutic problem due to its limited susceptibility to antibiotics. The resistance towards glycopeptide antibiotics is mediated by the so-called van genes. Currently, the most common resistance type in Germany is the vanB-type. Little data are available on the molecular epidemiology in Germany. Therefore, an epidemiological typing of Enterococcusfaecium isolates with vanB-type resistance from two German hospitals in Essen and Nuremberg was performed. Two outbreaks and 104 sporadic cases were investigated. Methods: All 128 isolates with vanB-type resistance were collected between 2011–2012 and 2017–2018. They were characterized using multilocus sequence typing (MLST) and pulsed-field gel electrophoresis (PFGE). Results: ST 117 was the most common sequence type (ST) in both hospitals, especially since 2017. PFGE divided the isolates of this study into 68 PFGE types and showed a broad genetic diversity. Two epidemiologically assumed in-hospital outbreaks were genetically confirmed. Apart from that, in-hospital transmissions were rare events. Conclusion: The results obtained by MLST confirmed the previously described allocation of STs in Germany. PFGE showed a broad genetic diversity of vanB VRE between the two hospitals and also within each hospital. In-hospital transmissions were rare, but outbreaks did occur. Our data supports the strategy to screen and isolate patients in transmission events in order to detect monoclonality indicating a common source or hygiene mismanagement.
Collapse
Affiliation(s)
- Laura Nürnberger
- Institute of Medical Microbiology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Dirk Schmidt
- Institute of Medical Microbiology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Tobias Szumlanski
- Institute for Clinical Hygiene, Medical Microbiology and Clinical Infectiology, Paracelsus Medical University, Nuremberg Hospital, Nuremberg, Germany
| | - Lisa Kirchhoff
- Institute of Medical Microbiology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Birgit Ross
- Department of Hospital Hygiene, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Jörg Steinmann
- Institute of Medical Microbiology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany.,Institute for Clinical Hygiene, Medical Microbiology and Clinical Infectiology, Paracelsus Medical University, Nuremberg Hospital, Nuremberg, Germany
| | - Peter-Michael Rath
- Institute of Medical Microbiology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| |
Collapse
|
20
|
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.
Collapse
Affiliation(s)
- Ewa Sadowy
- Department of Molecular Microbiology, National Medicines Institute, Warsaw, Poland.
| |
Collapse
|
21
|
Whole-genome sequencing analysis reveals the spread of a vanB-carrying transposon among different vancomycin-resistant Enterococcus faecium clinical isolates in a non-endemic setting. J Hosp Infect 2021; 110:52-59. [PMID: 33412230 DOI: 10.1016/j.jhin.2020.12.015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 12/21/2020] [Accepted: 12/23/2020] [Indexed: 11/24/2022]
Abstract
BACKGROUND Vancomycin-resistant enterococci (VRE), particularly Enterococcus faecium (VREfm), can cause serious nosocomial infections, and have been responsible for healthcare-associated outbreaks. Spreading of VREfm can occur both clonally and by the dissemination of mobile genetic elements. AIM To report prospective analysis of whole-genome sequencing (WGS) data, including both core-genome multi-locus sequence typing (cgMLST) and transposon analysis, during a vanB VREfm outbreak. METHODS Screening for vanB-positive VREfm isolates was performed by real-time polymerase chain reaction (PCR) on an overnight enriched broth and, if positive, subculture was performed. vanB-positive VREfm isolates underwent WGS. Generated data were used for molecular typing that was performed by cgMLST using SeqSphere. For transposon characterization, sequence data were mapped against the reference sequence of transposon Tn1549 using CLC Genomics Workbench, or de-novo assemblies were used for BLASTN comparisons. RESULTS In total, 1358 real-time PCRs were performed. Two hundred and fifty-one specimens from 207 patients tested positive on PCR for vanB, of which 13 specimens obtained from six patients were identified as vanB VREfm positive on culture. These six patients harboured seven unique isolates belonging to four cluster types: CT118 (N=2), CT2483 (N=3), CT2500 (N=1) and CT2501 (N=1). Transposon analysis revealed the presence of an identical vanB-carrying transposon in the isolates cultured from all six patients that could be linked based on epidemiological data. CONCLUSION A vanB VREfm outbreak occurred in the study hospital, including six patients with isolates belonging to four cluster types. In-depth transposon analysis revealed that dissemination of transposon Tn1549 rather than clonal spread was the cause of the outbreak.
Collapse
|
22
|
López-Luis BA, Sifuentes-Osornio J, Lambraño-Castillo D, Ortiz-Brizuela E, Ramírez-Fontes A, Tovar-Calderón YE, Leal-Vega FJ, Bobadilla-Del-Valle M, Ponce-de-León A. Risk factors and outcomes associated with vancomycin-resistant Enterococcus faecium and ampicillin-resistant Enterococcus faecalis bacteraemia: A 10-year study in a tertiary-care centre in Mexico City. J Glob Antimicrob Resist 2020; 24:198-204. [PMID: 33359937 DOI: 10.1016/j.jgar.2020.12.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 10/31/2020] [Accepted: 12/06/2020] [Indexed: 12/25/2022] Open
Abstract
OBJECTIVES We sought to identify risk factors associated with vancomycin-resistant Enterococcus faecium (VRE) and ampicillin-resistant Enterococcus faecalis (ARE) bacteraemia, predictors of 30-day mortality, and 90-day recurrence-free survival according to resistance. METHODS We evaluated clinical records of patients with E. faecalis and E. faecium bacteraemia (2007-2017). We performed bivariate and multivariate logistic regression analyses to identify factors associated with VRE and ARE bacteraemia and predictors of 30-day mortality. A Kaplan-Meier estimate of 90-day recurrence-free survival was done. RESULTS We identified 192 and 147 E. faecium and E. faecalis bacteraemia episodes, respectively, of which 55.7% of E. faecium were VRE (94% vanA) and 12.2% of E. faecalis were ARE. Factors related to VRE bacteraemia were previous hospitalisation (aOR, 80.18, 95% CI 1.81-634), history of central venous catheter (aOR, 11.15, 95% CI 2.48-50.2) and endotracheal cannula use (aOR, 17.91, 95% CI 1.22-262.82). There was higher attributable mortality to VRE (28%, 95% CI 14-68%; P < 0.001) and ARE (10%, 95% CI 0.1-36%; P = 0.58) compared with their susceptible counterparts. APACHE II (aOR, 1.45, 95% CI 1.26-1.66) and history of chemotherapy (aOR, 3.52, 95% CI 1.09-11.39) were predictors of E. faecium bacteraemia 30-day mortality. We could not recognise any factor related to ARE bacteraemia or E. faecalis 30-day mortality. CONCLUSION History of hospitalisation and invasive device use were related to VRE bacteraemia. APACHE II and history of chemotherapy were predictors of mortality. We could not identify factors related to ARE or predictors of mortality.
Collapse
Affiliation(s)
- Bruno Ali López-Luis
- Laboratory of Clinical Microbiology, Department of Infectious Diseases, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Avenida Vasco de Quiroga No. 15, Colonia Belisario Domínguez Sección XVI, Delegación Tlalpan, 14080, Mexico City, Mexico
| | - José Sifuentes-Osornio
- Department of Medicine, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Avenida Vasco de Quiroga No. 15, Colonia Belisario Domínguez Sección XVI, Delegación Tlalpan, 14080, Mexico City, Mexico
| | - Darwin Lambraño-Castillo
- Laboratory of Clinical Microbiology, Department of Infectious Diseases, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Avenida Vasco de Quiroga No. 15, Colonia Belisario Domínguez Sección XVI, Delegación Tlalpan, 14080, Mexico City, Mexico
| | - Edgar Ortiz-Brizuela
- Laboratory of Clinical Microbiology, Department of Infectious Diseases, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Avenida Vasco de Quiroga No. 15, Colonia Belisario Domínguez Sección XVI, Delegación Tlalpan, 14080, Mexico City, Mexico
| | - Andrea Ramírez-Fontes
- Laboratory of Clinical Microbiology, Department of Infectious Diseases, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Avenida Vasco de Quiroga No. 15, Colonia Belisario Domínguez Sección XVI, Delegación Tlalpan, 14080, Mexico City, Mexico
| | - Yanet Estrella Tovar-Calderón
- Laboratory of Clinical Microbiology, Department of Infectious Diseases, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Avenida Vasco de Quiroga No. 15, Colonia Belisario Domínguez Sección XVI, Delegación Tlalpan, 14080, Mexico City, Mexico
| | - Francisco Javier Leal-Vega
- Laboratory of Clinical Microbiology, Department of Infectious Diseases, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Avenida Vasco de Quiroga No. 15, Colonia Belisario Domínguez Sección XVI, Delegación Tlalpan, 14080, Mexico City, Mexico
| | - Miriam Bobadilla-Del-Valle
- Laboratory of Clinical Microbiology, Department of Infectious Diseases, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Avenida Vasco de Quiroga No. 15, Colonia Belisario Domínguez Sección XVI, Delegación Tlalpan, 14080, Mexico City, Mexico
| | - Alfredo Ponce-de-León
- Laboratory of Clinical Microbiology, Department of Infectious Diseases, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Avenida Vasco de Quiroga No. 15, Colonia Belisario Domínguez Sección XVI, Delegación Tlalpan, 14080, Mexico City, Mexico.
| |
Collapse
|
23
|
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: 37] [Impact Index Per Article: 9.3] [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.
Collapse
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
| |
Collapse
|
24
|
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: 72] [Impact Index Per Article: 18.0] [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.
Collapse
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
| |
Collapse
|
25
|
Weber A, Maechler F, Schwab F, Gastmeier P, Kola A. Increase of vancomycin-resistant Enterococcus faecium strain type ST117 CT71 at Charité - Universitätsmedizin Berlin, 2008 to 2018. Antimicrob Resist Infect Control 2020; 9:109. [PMID: 32678047 PMCID: PMC7364619 DOI: 10.1186/s13756-020-00754-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Accepted: 06/10/2020] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND In addition to an overall rise in vancomycin-resistant Enterococcus faecium (VREfm), an increase in certain strain types marked by sequence type (ST) and cluster type (CT) has been reported in Germany over the past few years. Outbreak analyses at Charité - Universitätsmedizin Berlin revealed the frequent occurrence of VREfm ST117 CT71 isolates in 2017 and 2018. To investigate whether ST117 CT71 have emerged in recent years or whether these strains have been circulating for a longer time, we retrospectively analyzed non-outbreak strains that occurred between 2008 and 2018 to identify frequent STs and CTs. METHODS In total, 120 VREfm isolates obtained from clinical and surveillance cultures from the years 2008, 2013, 2015, and 2018 were analyzed. Thirty isolates per year comprising the first 7-8 non-outbreak isolates of each quarter of the respective year were sequenced using whole genome sequencing. MLST and cgMLST were determined as well as resistance genes and virulence factors. Risk factors for VREfm ST117 were analyzed in a multivariable analysis with patient characteristics as possible confounders. RESULTS The percentage of VREfm of type ST117 increased from 17% in 2008 to 57% in 2018 (p = 0.012). In 2008, vanA genotype accounted for 80% of all ST117 isolates compared to 6% in 2018. VanB CT71 first appeared in 2018 and predominated over all other ST117 at 43% (p < 0.0001). The set of resistance genes (msrC, efmA, erm(B), dfrG, aac(6')-Ii, gyrA, parC and pbp5) and virulence factors (acm, esp, hylEfm, ecbA and sgrA) in CT71 was also found in other ST117 non-CT71 strains, mainly in CT36. The study population did not differ among the different calendar years analyzed in terms of age, gender, length of stay, or ward type (each p > 0.2). CONCLUSION This study revealed an increase in ST117 strains from 2008 to 2018, accompanied by a shift toward CT71 strains with the vanB genotype in 2018. We did not detect resistance or virulence traits in CT71 that could confer survival advantage compared to other CTs among ST117 strains. To date, it is not clear why ST117 and in particular strain type ST117 CT71 predominates over other strains.
Collapse
Affiliation(s)
- Anna Weber
- Institute of Hygiene and Environmental Medicine, Charité - Universitätsmedizin Berlin, Hindenburgdamm 27, 12203, Berlin, Germany.
| | - Friederike Maechler
- Institute of Hygiene and Environmental Medicine, Charité - Universitätsmedizin Berlin, Hindenburgdamm 27, 12203, Berlin, Germany
| | - Frank Schwab
- Institute of Hygiene and Environmental Medicine, Charité - Universitätsmedizin Berlin, Hindenburgdamm 27, 12203, Berlin, Germany
| | - Petra Gastmeier
- Institute of Hygiene and Environmental Medicine, Charité - Universitätsmedizin Berlin, Hindenburgdamm 27, 12203, Berlin, Germany
| | - Axel Kola
- Institute of Hygiene and Environmental Medicine, Charité - Universitätsmedizin Berlin, Hindenburgdamm 27, 12203, Berlin, Germany
| |
Collapse
|
26
|
Neumann B, Bender JK, Maier BF, Wittig A, Fuchs S, Brockmann D, Semmler T, Einsele H, Kraus S, Wieler LH, Vogel U, Werner G. Comprehensive integrated NGS-based surveillance and contact-network modeling unravels transmission dynamics of vancomycin-resistant enterococci in a high-risk population within a tertiary care hospital. PLoS One 2020; 15:e0235160. [PMID: 32579600 PMCID: PMC7314025 DOI: 10.1371/journal.pone.0235160] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Accepted: 06/09/2020] [Indexed: 02/07/2023] Open
Abstract
Vancomycin-resistant E. faecium (VRE) are an important cause of nosocomial infections, which are rapidly transmitted in hospitals. To identify possible transmission routes, we applied combined genomics and contact-network modeling to retrospectively evaluate routine VRE screening data generated by the infection control program of a hemato-oncology unit. Over 1 year, a total of 111 VRE isolates from 111 patients were collected by anal swabs in a tertiary care hospital in Southern Germany. All isolated VRE were whole-genome sequenced, followed by different in-depth bioinformatics analyses including genotyping and determination of phylogenetic relations, aiming to evaluate a standardized workflow. Patient movement data were used to overlay sequencing data to infer transmission events and strain dynamics over time. A predominant clone harboring vanB and exhibiting genotype ST117/CT469 (n = 67) was identified. Our comprehensive combined analyses suggested intra-hospital spread, especially of clone ST117/CT469, despite of extensive screening, single room placement, and contact isolation. A new interactive tool to visualize these complex data was designed. Furthermore, a patient-contact network-modeling approach was developed, which indicates both the periodic import of the clone into the hospital and its spread within the hospital due to patient movements. The analyzed spread of VRE was most likely due to placement of patients in the same room prior to positivity of screening. We successfully demonstrated the added value for this combined strategy to extract well-founded knowledge from interdisciplinary data sources. The combination of patient-contact modeling and high-resolution typing unraveled the transmission dynamics within the hospital department and, additionally, a constant VRE influx over time.
Collapse
Affiliation(s)
- Bernd Neumann
- Division of Nosocomial Pathogens and Antibiotic Resistance, Robert Koch Institute, Wernigerode, Germany
- * E-mail:
| | - Jennifer K. Bender
- Division of Nosocomial Pathogens and Antibiotic Resistance, Robert Koch Institute, Wernigerode, Germany
| | - Benjamin F. Maier
- Computational Epidemiology, Robert Koch Institute, Berlin, Germany
- Department of Physics, Humboldt University of Berlin, Berlin, Germany
| | - Alice Wittig
- Computational Epidemiology, Robert Koch Institute, Berlin, Germany
- Institute for Theoretical Biology, Humboldt University of Berlin, Berlin, Germany
| | - Stephan Fuchs
- Division of Nosocomial Pathogens and Antibiotic Resistance, Robert Koch Institute, Wernigerode, Germany
| | - Dirk Brockmann
- Computational Epidemiology, Robert Koch Institute, Berlin, Germany
- Institute for Theoretical Biology, Humboldt University of Berlin, Berlin, Germany
| | | | - Hermann Einsele
- Department of Internal Medicine II, University Hospital Würzburg, Wüzburg, Germany
| | - Sabrina Kraus
- Department of Internal Medicine II, University Hospital Würzburg, Wüzburg, Germany
| | | | - Ulrich Vogel
- Institute for Hygiene and Microbiology, Julius-Maximilians University Würzburg, Würzburg, Germany
| | - Guido Werner
- Division of Nosocomial Pathogens and Antibiotic Resistance, Robert Koch Institute, Wernigerode, Germany
| |
Collapse
|
27
|
Zhou X, Chlebowicz MA, Bathoorn E, Rosema S, Couto N, Lokate M, Arends JP, Friedrich AW, Rossen JWA. Elucidating vancomycin-resistant Enterococcus faecium outbreaks: the role of clonal spread and movement of mobile genetic elements. J Antimicrob Chemother 2019; 73:3259-3267. [PMID: 30219855 DOI: 10.1093/jac/dky349] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Accepted: 08/06/2018] [Indexed: 12/27/2022] Open
Abstract
Background Vancomycin-resistant Enterococcus faecium (VREfm) has emerged as a nosocomial pathogen worldwide. The dissemination of VREfm is due to both clonal spread and spread of mobile genetic elements (MGEs) such as transposons. Objectives We aimed to combine vanB-carrying transposon data with core-genome MLST (cgMLST) typing and epidemiological data to understand the pathways of transmission in nosocomial outbreaks. Methods Retrospectively, 36 VREfm isolates obtained from 34 patients from seven VREfm outbreak investigations in 2014 were analysed. Isolates were sequenced on a MiSeq and a MinION instrument. De novo assembly was performed in CLC Genomics Workbench and the hybrid assemblies were obtained through Unicycler v0.4.1. Ridom SeqSphere+ was used to extract MLST and cgMLST data. Detailed analysis of each transposon and their integration points was performed using the Artemis Comparison Tool (ACT) and multiple blast analyses. Results Four different vanB transposons were found among the isolates. cgMLST divided ST80 isolates into three cluster types (CTs); CT16, CT104 and CT106. ST117 isolates were divided into CT24, CT103 and CT105. Within VREfm isolates belonging to CT103, two different vanB transposons were found. In contrast, VREfm isolates belonging to CT104 and CT106 harboured an identical vanB transposon. Conclusions cgMLST provides a high discriminatory power for the epidemiological analysis of VREfm. However, additional transposon analysis is needed to detect horizontal gene transfer. Combining these two methods allows investigation of both clonal spread as well as the spread of MGEs. This leads to new insights and thereby better understanding of the complex transmission routes in VREfm outbreaks.
Collapse
Affiliation(s)
- X Zhou
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology, Groningen, The Netherlands
| | - M A Chlebowicz
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology, Groningen, The Netherlands
| | - E Bathoorn
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology, Groningen, The Netherlands
| | - S Rosema
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology, Groningen, The Netherlands
| | - N Couto
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology, Groningen, The Netherlands
| | - M Lokate
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology, Groningen, The Netherlands
| | - J P Arends
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology, Groningen, The Netherlands
| | - A W Friedrich
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology, Groningen, The Netherlands
| | - J W A Rossen
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology, Groningen, The Netherlands
| |
Collapse
|
28
|
Falgenhauer L, Fritzenwanker M, Imirzalioglu C, Steul K, Scherer M, Heudorf U, Chakraborty T. Near-ubiquitous presence of a vancomycin-resistant Enterococcus faecium ST117/CT71/ vanB -clone in the Rhine-Main metropolitan area of Germany. Antimicrob Resist Infect Control 2019; 8:128. [PMID: 31384433 PMCID: PMC6664515 DOI: 10.1186/s13756-019-0573-8] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Accepted: 07/09/2019] [Indexed: 02/02/2023] Open
Abstract
Whole-genome sequencing analysis of Vancomycin-resistant Enterococcus faecium isolates from the Frankfurt metropolitan region revealed that 78/94 isolates were MLST type ST117, cgMLST complex type CT71 with a common vanB chromosomal insertion site. This indicates circulation of a single VRE clone in a catchment area of 5,000-km2 with 3 million inhabitants.
Collapse
Affiliation(s)
- Linda Falgenhauer
- 1Institute of Medical Microbiology, Justus Liebig University Giessen and German Center for Infection Research (DZIF), Partner Site Giessen-Marburg-Langen, Schubertstrasse 81, 35392 Giessen, Germany
| | - Moritz Fritzenwanker
- 1Institute of Medical Microbiology, Justus Liebig University Giessen and German Center for Infection Research (DZIF), Partner Site Giessen-Marburg-Langen, Schubertstrasse 81, 35392 Giessen, Germany
| | - Can Imirzalioglu
- 1Institute of Medical Microbiology, Justus Liebig University Giessen and German Center for Infection Research (DZIF), Partner Site Giessen-Marburg-Langen, Schubertstrasse 81, 35392 Giessen, Germany
| | - Katrin Steul
- Rhine-Main- Network on MDRO (multidrug-resistant organisms), Breite Gasse 28, 60313 Frankfurt/Main, Germany
| | - Marlene Scherer
- Rhine-Main- Network on MDRO (multidrug-resistant organisms), Breite Gasse 28, 60313 Frankfurt/Main, Germany
| | | | - Ursel Heudorf
- Rhine-Main- Network on MDRO (multidrug-resistant organisms), Breite Gasse 28, 60313 Frankfurt/Main, Germany
| | - Trinad Chakraborty
- 1Institute of Medical Microbiology, Justus Liebig University Giessen and German Center for Infection Research (DZIF), Partner Site Giessen-Marburg-Langen, Schubertstrasse 81, 35392 Giessen, Germany
| |
Collapse
|
29
|
Falgenhauer L, Fritzenwanker M, Imirzalioglu C, Steul K, Scherer M, Heudorf U, Chakraborty T. Near-ubiquitous presence of a vancomycin-resistant Enterococcus faecium ST117/CT71/vanB –clone in the Rhine-Main metropolitan area of Germany. Antimicrob Resist Infect Control 2019. [DOI: 10.1186/s13756-019-0573-8 ecollection 2019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
|
30
|
Abstract
Vancomycin-resistant Enterococcus faecium (VREfm) is a globally significant public health threat and was listed on the World Health Organization's 2017 list of high-priority pathogens for which new treatments are urgently needed. Treatment options for invasive VREfm infections are very limited, and outcomes are often poor. Whole-genome sequencing is providing important new insights into VREfm evolution, drug resistance and hospital adaptation, and is increasingly being used to track VREfm transmission within hospitals to detect outbreaks and inform infection control practices. This mini-review provides an overview of recent data on the use of genomics to understand and respond to the global problem of VREfm.
Collapse
Affiliation(s)
- Claire Gorrie
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Charlie Higgs
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Glen Carter
- Doherty Applied Microbial Genomics, Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia.,Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Timothy P Stinear
- Doherty Applied Microbial Genomics, Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia.,Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Benjamin Howden
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia.,Department of Infectious Diseases, Austin Health, Heidelberg, Australia.,Doherty Applied Microbial Genomics, Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| |
Collapse
|
31
|
Expansion of Vancomycin-Resistant Enterococcus faecium in an Academic Tertiary Hospital in Southwest Germany: a Large-Scale Whole-Genome-Based Outbreak Investigation. Antimicrob Agents Chemother 2019; 63:AAC.01978-18. [PMID: 30782988 DOI: 10.1128/aac.01978-18] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Accepted: 02/13/2019] [Indexed: 12/11/2022] Open
Abstract
Vancomycin-resistant Enterococcus faecium (VREfm) is a frequent cause of nosocomial outbreaks. In the second half of 2015, a sharp increase in the incidence of VREfm was observed at our university medical center. Next-generation sequencing (NGS) was used to analyze the first isolates of VREfm recovered from patients between 2010 and 2016 (n = 773) in order to decipher epidemiological change, outbreak dynamics, and possible transmission routes. VREfm isolates were analyzed using whole-genome sequencing followed by sequence type extraction and phylogenetic analysis. We examined epidemiological data, room occupancy data, and patient transferals and calculated an intensity score for patient-to-patient contact. Phylogenetic analysis revealed the presence of 38 NGS clusters and 110 single clones. The increase of VREfm was caused mainly by the expansion of two newly introduced NGS clusters, comprising VanB-type strains determined by multilocus sequence typing (MLST) as sequence type 80 (ST80) and ST117. By combining phylogenetic information with epidemiological data, intrahospital transmission could be demonstrated, however to a lesser extent than initially expected based solely on epidemiological data. The outbreak clones were continuously imported from other hospitals, suggesting a change in the epidemiological situation at a regional scale. By tracking intrahospital patient transferals, two major axes could be identified that contributed to the spread of VREfm within the hospital. NGS-based outbreak analysis revealed a dramatic change in the local and regional epidemiology of VREfm, emphasizing the role of health care networks in the spread of VREfm.
Collapse
|
32
|
A Core Genome Multilocus Sequence Typing Scheme for Enterococcus faecalis. J Clin Microbiol 2019; 57:JCM.01686-18. [PMID: 30651394 PMCID: PMC6425188 DOI: 10.1128/jcm.01686-18] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Accepted: 12/15/2018] [Indexed: 12/21/2022] Open
Abstract
Among enterococci, Enterococcus faecalis occurs ubiquitously, with the highest incidence of human and animal infections. The high genetic plasticity of E. faecalis complicates both molecular investigations and phylogenetic analyses. Whole-genome sequencing (WGS) enables unraveling of epidemiological linkages and putative transmission events between humans, animals, and food. Core genome multilocus sequence typing (cgMLST) aims to combine the discriminatory power of classical multilocus sequence typing (MLST) with the extensive genetic data obtained by WGS. By sequencing a representative collection of 146 E. faecalis strains isolated from hospital outbreaks, food, animals, and colonization of healthy human individuals, we established a novel cgMLST scheme with 1,972 gene targets within the Ridom SeqSphere+ software. To test the E. faecalis cgMLST scheme and assess the typing performance, different collections comprising environmental and bacteremia isolates, as well as all publicly available genome sequences from the NCBI and SRA databases, were analyzed. In more than 98.6% of the tested genomes, >95% good cgMLST target genes were detected (mean, 99.2% target genes). Our genotyping results not only corroborate the known epidemiological background of the isolates but exceed previous typing resolution. In conclusion, we have created a powerful typing scheme, hence providing an international standardized nomenclature that is suitable for surveillance approaches in various sectors, linking public health, veterinary public health, and food safety in a true One Health fashion.
Collapse
|
33
|
Enterococcus faecium TIR-Domain Genes Are Part of a Gene Cluster Which Promotes Bacterial Survival in Blood. Int J Microbiol 2019; 2018:1435820. [PMID: 30631364 PMCID: PMC6304867 DOI: 10.1155/2018/1435820] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Accepted: 10/14/2018] [Indexed: 11/29/2022] Open
Abstract
Enterococcus faecium has undergone a transition to a multidrug-resistant nosocomial pathogen. The population structure of E. faecium is characterized by a sharp distinction of clades, where the hospital-adapted lineage is primarily responsible for bacteremia. So far, factors that were identified in hospital-adapted strains and that promoted pathogenesis of nosocomial E. faecium mainly play a role in adherence and biofilm production, while less is known about factors contributing to survival in blood. This study identified a gene cluster, which includes genes encoding bacterial Toll/interleukin-1 receptor- (TIR-) domain-containing proteins (TirEs). The cluster was found to be unique to nosocomial strains and to be located on a putative mobile genetic element of phage origin. The three genes within the cluster appeared to be expressed as an operon. Expression was detected in bacterial culture media and in the presence of human blood. TirEs are released into the bacterial supernatant, and TirE2 is associated with membrane vesicles. Furthermore, the tirE-gene cluster promotes bacterial proliferation in human blood, indicating that TirE may contribute to the pathogenesis of bacteremia.
Collapse
|
34
|
Hashimoto Y, Kurushima J, Nomura T, Tanimoto K, Tamai K, Yanagisawa H, Shirabe K, Ike Y, Tomita H. Dissemination and genetic analysis of the stealthy vanB gene clusters of Enterococcus faecium clinical isolates in Japan. BMC Microbiol 2018; 18:213. [PMID: 30545294 PMCID: PMC6293572 DOI: 10.1186/s12866-018-1342-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Accepted: 11/14/2018] [Indexed: 12/18/2022] Open
Abstract
Background VanB-type vancomycin (VAN) resistance gene clusters confer VAN resistances on Enterococcus spp. over a wide range of MIC levels (MIC = 4–1000 mg/L). However, the epidemiology and the molecular characteristics of the VAN susceptible VanB-type Enterococcus still remain unclear. Results We characterized 19 isolates of VanB-type Enterococcus faecium that might colonize in the gut and were not phenotypically resistant to VAN (MIC = 3 mg/L). They were obtained from two hospitals in Japan between 2009 and 2010. These isolates had the identical vanB gene cluster and showed same multilocus sequence typing (MLST) (ST78) and the highly related profiles in pulsed-field gel electrophoresis (PFGE). The vanB gene cluster was located on a plasmid, and was transferable to E. faecium and E. faecalis. Notably, from these VanB-type VREs, VAN resistant (MIC≥16 mg/L) mutants could appear at a frequency of 10− 6–10− 7/parent cell in vitro. Most of these revertants acquired mutations in the vanSB gene, while the remainder of the revertants might have other mutations outside of the vanB gene cluster. All of the revertants we tested showed increases in the VAN-dependent expression of the vanB gene cluster, suggesting that the mutations affected the transcriptional activity and increased the VAN resistance. Targeted mutagenesis revealed that three unique nucleotide substitutions in the vanB gene cluster of these strains attenuated VAN resistance. Conclusions In summary, this study indicated that stealthy VanB-type E. faecium strains that have the potential ability to become resistance to VAN could exist in clinical settings. Electronic supplementary material The online version of this article (10.1186/s12866-018-1342-1) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Yusuke Hashimoto
- Department of Bacteriology, Gunma University Graduate School of Medicine, 3-39-22 Showa-machi, Maebashi, Gunma, 371-8511, Japan
| | - Jun Kurushima
- Department of Bacteriology, Gunma University Graduate School of Medicine, 3-39-22 Showa-machi, Maebashi, Gunma, 371-8511, Japan
| | - Takahiro Nomura
- Department of Bacteriology, Gunma University Graduate School of Medicine, 3-39-22 Showa-machi, Maebashi, Gunma, 371-8511, Japan
| | - Koichi Tanimoto
- Laboratory of Bacterial Drug Resistance, Gunma University Graduate School of Medicine, 3-39-22 Showa-machi, Maebashi, Gunma, 371-8511, Japan
| | - Kiyoko Tamai
- MIROKU Medical Laboratory Inc, 659-2 Innai, Saku, Nagano, 384-2201, Japan
| | - Hideji Yanagisawa
- MIROKU Medical Laboratory Inc, 659-2 Innai, Saku, Nagano, 384-2201, Japan
| | - Komei Shirabe
- Yamaguchi Prefectural Institute of Public Health and Environment, 2-5-67 Aoi, Yamaguchi, Yamaguchi, 753-0821, Japan
| | - Yasuyoshi Ike
- Department of Bacteriology, Gunma University Graduate School of Medicine, 3-39-22 Showa-machi, Maebashi, Gunma, 371-8511, Japan
| | - Haruyoshi Tomita
- Department of Bacteriology, Gunma University Graduate School of Medicine, 3-39-22 Showa-machi, Maebashi, Gunma, 371-8511, Japan. .,Laboratory of Bacterial Drug Resistance, Gunma University Graduate School of Medicine, 3-39-22 Showa-machi, Maebashi, Gunma, 371-8511, Japan.
| |
Collapse
|
35
|
Hygienemaßnahmen zur Prävention der Infektion durch Enterokokken mit speziellen Antibiotikaresistenzen. Bundesgesundheitsblatt Gesundheitsforschung Gesundheitsschutz 2018; 61:1310-1361. [DOI: 10.1007/s00103-018-2811-2] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
|
36
|
Kampmeier S, Kossow A, Clausen LM, Knaack D, Ertmer C, Gottschalk A, Freise H, Mellmann A. Hospital acquired vancomycin resistant enterococci in surgical intensive care patients - a prospective longitudinal study. Antimicrob Resist Infect Control 2018; 7:103. [PMID: 30155243 PMCID: PMC6108103 DOI: 10.1186/s13756-018-0394-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Accepted: 08/14/2018] [Indexed: 11/10/2022] Open
Abstract
Background Vancomycin resistant enterococci (VRE) occur with enhanced frequency in hospitalised patients. This study elucidates the prevalence of VRE on admission among surgical intensive care unit (SICU) patients, whether these patients are at special risk for VRE acquisition and which risk factors support this process. Methods Patients admitted to SICUs of the University Hospital Münster were examined during August-October 2017. VRE screening was performed within 48 h after admission and directly prior to discharge of patients. In parallel risk factors were recorded to estimate their effect on VRE acquisition during SICU stay. Results In total, 374 patients (68% male) with a median age of 66 years were admitted to one of the SICUs during the investigation period. Of all, 336 patients (89.8%) were screened on admission and 268 (71.7%) on discharge. Nine patients were admitted with previously known VRE colonisation. Twelve (3.6%) further patients were VRE positive on admission. During ICU stay, eight (3.0%) additional patients turned out to be VRE colonised. Risk factors found to be significantly associated with VRE acquisition were median length of stay on the ICU (14 vs. 3 days; p = 0.01), long-term dialysis (12.5% vs. 2.0% of patients; p = 0.05), and antibiotic treatment with flucloxacillin (28.6% vs. 7.2% of patients; p = 0.01) or piperacillin/tazobactam (57.1% vs. 26.6% of patients; p = 0.01). Conclusions SICU patients are not at special risk for VRE acquisition. Previous stay on a SICU should therefore not be considered as specific risk factor for VRE colonisation.
Collapse
Affiliation(s)
- Stefanie Kampmeier
- Institute of Hygiene, University Hospital Münster, Robert-Koch-Strasse 41, 48149 Münster, Germany
| | - Annelene Kossow
- Institute of Hygiene, University Hospital Münster, Robert-Koch-Strasse 41, 48149 Münster, Germany
| | - Larissa Monika Clausen
- Institute of Hygiene, University Hospital Münster, Robert-Koch-Strasse 41, 48149 Münster, Germany
| | - Dennis Knaack
- Institute of Medical Microbiology, University Hospital Münster, Münster, Germany
| | - Christian Ertmer
- Department of Anaesthesiology, Intensive Care and Pain Medicine, University Hospital Münster, Münster, Germany
| | - Antje Gottschalk
- Department of Anaesthesiology, Intensive Care and Pain Medicine, University Hospital Münster, Münster, Germany
| | - Hendrik Freise
- Department of Anaesthesiology, Intensive Care and Pain Medicine, University Hospital Münster, Münster, Germany
| | - Alexander Mellmann
- Institute of Hygiene, University Hospital Münster, Robert-Koch-Strasse 41, 48149 Münster, Germany
| |
Collapse
|
37
|
Sadowy E, Gawryszewska I, Kuch A, Żabicka D, Hryniewicz W. The changing epidemiology of VanB Enterococcus faecium in Poland. Eur J Clin Microbiol Infect Dis 2018; 37:927-936. [PMID: 29442195 PMCID: PMC5916999 DOI: 10.1007/s10096-018-3209-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Accepted: 02/01/2018] [Indexed: 01/02/2023]
Abstract
Increasing prevalence of VanB Enterococcus faecium in Polish hospitals reported to National Reference Centre for Susceptibility Testing (NRCST) prompted us to investigate the basis of this phenomenon. Two-hundred seventy-eight E. faecium isolates of VanB phenotype from the period 1999 to 2010 obtained by NRCST were investigated by multilocus sequence typing (MLST) and multilocus VNTR analysis (MLVA). Localization, transferability, and partial structure of the vanB-carrying Tn1549 transposon were studied by hybridization, PCR mapping, sequencing, and conjugation. VanB isolates almost exclusively represented hospital-associated E. faecium, with a significant shift from representatives of 17/18 lineage to 78 lineage after 2005. The vanB determinant, initially located mostly on transferable plasmids of the pRUM-, pLG1-, and pRE25-replicon types, later on was found almost exclusively on the host chromosome. Fifteen different plasmid and chromosomal insertion sites were identified, typically associated with single transposon coupling sequences, mostly not observed before. Our study demonstrates the significant change in the epidemiology of VanB-E. faecium in Poland, associated with the introduction and spread of the lineage 78 of the hospital-adapted E. faecium. These data point to the importance of the lineage 78 for the spread of vancomycin-resistance, determined by the vanB gene cluster, resulting in an increasing VRE prevalence in hospitals. This study also supports the scenario, in which representatives of the hospital-associated E. faecium independently acquire the vanB determinant de novo and spread within and among hospitals, concomitantly undergoing differentiation.
Collapse
Affiliation(s)
- Ewa Sadowy
- Department of Molecular Microbiology, National Medicines Institute, ul. Chełmska 30/34, 00-725, Warsaw, Poland.
| | - Iwona Gawryszewska
- Department of Molecular Microbiology, National Medicines Institute, ul. Chełmska 30/34, 00-725, Warsaw, Poland
| | - Alicja Kuch
- Department of Epidemiology and Clinical Microbiology, National Medicines Institute, Chełmska 30/34, 00-725, Warsaw, Poland
| | - Dorota Żabicka
- Department of Epidemiology and Clinical Microbiology, National Medicines Institute, Chełmska 30/34, 00-725, Warsaw, Poland
| | - Waleria Hryniewicz
- Department of Epidemiology and Clinical Microbiology, National Medicines Institute, Chełmska 30/34, 00-725, Warsaw, Poland
| |
Collapse
|
38
|
Physiological and transcriptome changes induced by Pseudomonas putida acquisition of an integrative and conjugative element. Sci Rep 2018; 8:5550. [PMID: 29615803 PMCID: PMC5882942 DOI: 10.1038/s41598-018-23858-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Accepted: 03/21/2018] [Indexed: 12/27/2022] Open
Abstract
Integrative and conjugative elements (ICEs) comprise ubiquitous large mobile regions in prokaryotic chromosomes that transmit vertically to daughter cells and transfer horizontally to distantly related lineages. Their evolutionary success originates in maximized combined ICE-host fitness trade-offs, but how the ICE impacts on the host metabolism and physiology is poorly understood. Here we investigate global changes in the host genetic network and physiology of Pseudomonas putida with or without an integrated ICEclc, a model ICE widely distributed in proteobacterial genomes. Genome-wide gene expression differences were analyzed by RNA-seq using exponentially growing or stationary phase-restimulated cultures on 3-chlorobenzoate, an aromatic compound metabolizable thanks to specific ICEclc-located genes. We found that the presence of ICEclc imposes a variety of changes in global pathways such as cell cycle and amino acid metabolism, which were more numerous in stationary-restimulated than exponential phase cells. Unexpectedly, ICEclc stimulates cellular motility and leads to more rapid growth on 3-chlorobenzoate than cells carrying only the integrated clc genes. ICEclc also concomitantly activates the P. putida Pspu28-prophage, but this in itself did not provoke measurable fitness effects. ICEclc thus interferes in a number of cellular pathways, inducing both direct benefits as well as indirect costs in P. putida.
Collapse
|
39
|
Bressan R, Knezevich A, Monticelli J, Campanile F, Busetti M, Santagati M, Dolzani L, Milan A, Bongiorno D, Di Santolo M, Tonin EA, Stefani S, Luzzati R, Lagatolla C. Spread of Vancomycin-Resistant Enterococcus faecium Isolates Despite Validated Infection Control Measures in an Italian Hospital: Antibiotic Resistance and Genotypic Characterization of the Endemic Strain. Microb Drug Resist 2018; 24:1148-1155. [PMID: 29373085 DOI: 10.1089/mdr.2017.0314] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
An alarming increase of vancomycin-resistant Enterococcus faecium (VREfm) isolates was detected in an Italian referral hospital subjected to policies of infection control validated by the Joint Commission International. Analysis of the population structure of 122 consecutive, nonreplicate VREfm isolates collected over an 18-month period identified a single major clone that spread around the whole hospital, rapidly establishing an endemic state. It belonged to sequence type (ST) 17 and showed a highly multidrug-resistant phenotype, being resistant to all antimicrobial classes for the carriage of several resistance determinants. Furthermore, some strains with decreased susceptibility to daptomycin were detected. Eighteen out of the 122 isolates did not group in the major clone. They showed a low spreading potential inside the hospital wards, even if most of them displayed a multidrug-resistant phenotype and belonged to a hospital-adapted lineage. Causes that led to the VREfm endemic state have not been fully elucidated. However, it is conceivable that the increase in systemic antibiotic consumption and the use of selective digestive tract decontamination, including vancomycin in critically ill patients during the period before 2014, may have played a role in the ST17 clone dissemination, but additional traits conferring high fitness in hospital environment cannot be excluded.
Collapse
Affiliation(s)
- Raffaela Bressan
- 1 Department of Life Sciences, University of Trieste , Trieste, Italy
| | - Anna Knezevich
- 2 Microbiology Unit, University Hospital of Trieste , Trieste, Italy
| | - Jacopo Monticelli
- 3 Infectious Diseases Unit, University Hospital of Trieste , Trieste, Italy
| | - Floriana Campanile
- 4 Department of Biomedical and Biotechnological Sciences (BIOMETEC), University of Catania , Catania, Italy
| | - Marina Busetti
- 2 Microbiology Unit, University Hospital of Trieste , Trieste, Italy
| | - Maria Santagati
- 4 Department of Biomedical and Biotechnological Sciences (BIOMETEC), University of Catania , Catania, Italy
| | - Lucilla Dolzani
- 1 Department of Life Sciences, University of Trieste , Trieste, Italy
| | - Annalisa Milan
- 1 Department of Life Sciences, University of Trieste , Trieste, Italy
| | - Dafne Bongiorno
- 4 Department of Biomedical and Biotechnological Sciences (BIOMETEC), University of Catania , Catania, Italy
| | | | - Enrico A Tonin
- 1 Department of Life Sciences, University of Trieste , Trieste, Italy
| | - Stefania Stefani
- 4 Department of Biomedical and Biotechnological Sciences (BIOMETEC), University of Catania , Catania, Italy
| | - Roberto Luzzati
- 3 Infectious Diseases Unit, University Hospital of Trieste , Trieste, Italy .,5 Department of Medicine, Surgery and Health Sciences, University of Trieste , Trieste, Italy
| | | |
Collapse
|
40
|
Lambertsen L, Rubio-Cosials A, Patil KR, Barabas O. Conjugative transposition of the vancomycin resistance carrying Tn1549: enzymatic requirements and target site preferences. Mol Microbiol 2018; 107:639-658. [PMID: 29271522 DOI: 10.1111/mmi.13905] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Revised: 12/19/2017] [Accepted: 12/19/2017] [Indexed: 11/30/2022]
Abstract
Rapid spread of resistance to vancomycin has generated difficult to treat bacterial pathogens worldwide. Though vancomycin resistance is often conferred by the conjugative transposon Tn1549, it is yet unclear whether Tn1549 moves actively between bacteria. Here we demonstrate, through development of an in vivo assay system, that a mini-Tn1549 can transpose in E. coli away from its natural Gram-positive host. We find the transposon-encoded INT enzyme and its catalytic tyrosine Y380 to be essential for transposition. A second Tn1549 protein, XIS is important for efficient and accurate transposition. We further show that DNA flanking the left transposon end is critical for excision, with changes to nucleotides 7 and 9 impairing movement. These mutations could be partially compensated for by changing the final nucleotide of the right transposon end, implying concerted excision of the two ends. With changes in these essential DNA sequences, or without XIS, a large amount of flanking DNA transposes with Tn1549. This rescues mobility and allows the transposon to capture and transfer flanking genomic DNA. We further identify the transposon integration target sites as TTTT-N6-AAAA. Overall, our results provide molecular insights into conjugative transposition and the adaptability of Tn1549 for efficient antibiotic resistance transfer.
Collapse
Affiliation(s)
- Lotte Lambertsen
- European Molecular Biology Laboratory (EMBL), Structural and Computational Biology Unit, Meyerhofstrasse 1, D-69117 Heidelberg, Germany
| | - Anna Rubio-Cosials
- European Molecular Biology Laboratory (EMBL), Structural and Computational Biology Unit, Meyerhofstrasse 1, D-69117 Heidelberg, Germany
| | - Kiran Raosaheb Patil
- European Molecular Biology Laboratory (EMBL), Structural and Computational Biology Unit, Meyerhofstrasse 1, D-69117 Heidelberg, Germany
| | - Orsolya Barabas
- European Molecular Biology Laboratory (EMBL), Structural and Computational Biology Unit, Meyerhofstrasse 1, D-69117 Heidelberg, Germany
| |
Collapse
|
41
|
Both A, Franke GC, Mirwald N, Lütgehetmann M, Christner M, Klupp EM, Belmar Campos C, Büttner H, Aepfelbacher M, Rohde H. Two-tier approach combining molecular and culture-based techniques for optimized detection of vancomycin-resistant enterococci. Diagn Microbiol Infect Dis 2017; 89:253-257. [DOI: 10.1016/j.diagmicrobio.2017.08.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Revised: 08/15/2017] [Accepted: 08/17/2017] [Indexed: 11/29/2022]
|
42
|
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: 209] [Impact Index Per Article: 29.9] [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.
Collapse
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
| |
Collapse
|
43
|
Delavat F, Miyazaki R, Carraro N, Pradervand N, van der Meer JR. The hidden life of integrative and conjugative elements. FEMS Microbiol Rev 2017; 41:512-537. [PMID: 28369623 PMCID: PMC5812530 DOI: 10.1093/femsre/fux008] [Citation(s) in RCA: 118] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Accepted: 02/20/2017] [Indexed: 01/01/2023] Open
Abstract
Integrative and conjugative elements (ICEs) are widespread mobile DNA that transmit both vertically, in a host-integrated state, and horizontally, through excision and transfer to new recipients. Different families of ICEs have been discovered with more or less restricted host ranges, which operate by similar mechanisms but differ in regulatory networks, evolutionary origin and the types of variable genes they contribute to the host. Based on reviewing recent experimental data, we propose a general model of ICE life style that explains the transition between vertical and horizontal transmission as a result of a bistable decision in the ICE-host partnership. In the large majority of cells, the ICE remains silent and integrated, but hidden at low to very low frequencies in the population specialized host cells appear in which the ICE starts its process of horizontal transmission. This bistable process leads to host cell differentiation, ICE excision and transfer, when suitable recipients are present. The ratio of ICE bistability (i.e. ratio of horizontal to vertical transmission) is the outcome of a balance between fitness costs imposed by the ICE horizontal transmission process on the host cell, and selection for ICE distribution (i.e. ICE 'fitness'). From this emerges a picture of ICEs as elements that have adapted to a mostly confined life style within their host, but with a very effective and dynamic transfer from a subpopulation of dedicated cells.
Collapse
Affiliation(s)
- François Delavat
- Department of Fundamental Microbiology, University of Lausanne, 1015 Lausanne Switzerland
| | - Ryo Miyazaki
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Ibaraki 305-8566, Japan
| | - Nicolas Carraro
- Department of Fundamental Microbiology, University of Lausanne, 1015 Lausanne Switzerland
| | - Nicolas Pradervand
- Department of Fundamental Microbiology, University of Lausanne, 1015 Lausanne Switzerland
| | | |
Collapse
|
44
|
Kampmeier S, Knaack D, Kossow A, Willems S, Schliemann C, Berdel WE, Kipp F, Mellmann A. Weekly screening supports terminating nosocomial transmissions of vancomycin-resistant enterococci on an oncologic ward - a retrospective analysis. Antimicrob Resist Infect Control 2017; 6:48. [PMID: 28515904 PMCID: PMC5434525 DOI: 10.1186/s13756-017-0206-z] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Accepted: 05/10/2017] [Indexed: 11/17/2022] Open
Abstract
Background To investigate the impact of weekly screening within the bundle of infection control measures to terminate vancomycin-resistant enterococci (VRE) transmissions on an oncologic ward. Methods A cluster of 12 VRE colonisation and five infections was detected on an oncologic ward between January and April 2015. Subsequently, the VRE point prevalence was detected and, as part of a the bundle of infection control strategies to terminate the VRE cluster, we isolated affected patients, performed hand hygiene training among staff on ward, increased observations by infection control specialists, intensified surface disinfection, used personal protective equipment and initiated an admission screening in May 2015. After a further nosocomial VRE infection in August 2015, a weekly screening strategy of all oncology patients on the respective ward was established while admission screening was continued. Whole genome sequencing (WGS)-based typing was applied to determine the clonal relationship of isolated strains. Results Initially, 12 of 29 patients were VRE colonised; of these 10 were hospital-acquired. During May to August, on average 7 of 40 patients were detected to be VRE colonised per week during the admission screening, showing no significant decline compared to the initial situation. WGS-based typing revealed five different clusters of which three were due to vanB- and two vanA-positive enterococci. After an additional weekly screening was established, the number of colonised patients significantly declined to 1/53 and no further nosocomial cases were detected. Conclusions Weekly screening helped to differentiate between nosocomial and community-acquired VRE cases resulting in earlier infection control strategies on epidemic situations for a successful termination of nosocomial VRE transmissions.
Collapse
Affiliation(s)
- Stefanie Kampmeier
- Institute of Hygiene, University Hospital Münster, Robert-Koch-Strasse 41, 48149 Münster, Germany
| | - Dennis Knaack
- Institute of Medical Microbiology, University Hospital Münster, Domagkstrasse 10, 48149 Münster, Germany
| | - Annelene Kossow
- Institute of Hygiene, University Hospital Münster, Robert-Koch-Strasse 41, 48149 Münster, Germany
| | - Stefanie Willems
- Institute of Hygiene, University Hospital Münster, Robert-Koch-Strasse 41, 48149 Münster, Germany.,Present address: Institute of Hygiene, DRK Kliniken Berlin, Drontheimer Str. 39-40, 13359 Berlin, Germany
| | - Christoph Schliemann
- Department of Medicine A, Haematology and Oncology, University Hospital Münster, Albert-Schweitzer-Campus 1, 48149 Münster, Germany
| | - Wolfgang E Berdel
- Department of Medicine A, Haematology and Oncology, University Hospital Münster, Albert-Schweitzer-Campus 1, 48149 Münster, Germany
| | - Frank Kipp
- Institute of Hygiene, University Hospital Münster, Robert-Koch-Strasse 41, 48149 Münster, Germany.,Present address: Institute of Hygiene, DRK Kliniken Berlin, Drontheimer Str. 39-40, 13359 Berlin, Germany
| | - Alexander Mellmann
- Institute of Hygiene, University Hospital Münster, Robert-Koch-Strasse 41, 48149 Münster, Germany
| |
Collapse
|
45
|
Buultjens AH, Lam MMC, Ballard S, Monk IR, Mahony AA, Grabsch EA, Grayson ML, Pang S, Coombs GW, Robinson JO, Seemann T, Johnson PDR, Howden BP, Stinear TP. Evolutionary origins of the emergent ST796 clone of vancomycin resistant Enterococcus faecium. PeerJ 2017; 5:e2916. [PMID: 28149688 PMCID: PMC5267571 DOI: 10.7717/peerj.2916] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Accepted: 12/16/2016] [Indexed: 12/03/2022] Open
Abstract
From early 2012, a novel clone of vancomycin resistant Enterococcus faecium (assigned the multi locus sequence type ST796) was simultaneously isolated from geographically separate hospitals in south eastern Australia and New Zealand. Here we describe the complete genome sequence of Ef_aus0233, a representative ST796 E. faecium isolate. We used PacBio single molecule real-time sequencing to establish a high quality, fully assembled genome comprising a circular chromosome of 2,888,087 bp and five plasmids. Comparison of Ef_aus0233 to other E. faecium genomes shows Ef_aus0233 is a member of the epidemic hospital-adapted lineage and has evolved from an ST555-like ancestral progenitor by the accumulation or modification of five mosaic plasmids and five putative prophage, acquisition of two cryptic genomic islands, accrued chromosomal single nucleotide polymorphisms and a 80 kb region of recombination, also gaining Tn1549 and Tn916, transposons conferring resistance to vancomycin and tetracycline respectively. The genomic dissection of this new clone presented here underscores the propensity of the hospital E. faecium lineage to change, presumably in response to the specific conditions of hospital and healthcare environments.
Collapse
Affiliation(s)
- Andrew H Buultjens
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne , Melbourne , Victoria , Australia
| | - Margaret M C Lam
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne , Melbourne , Victoria , Australia
| | - Susan Ballard
- Microbiology Diagnostic Unit, Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne , Melbourne , Victoria , Australia
| | - Ian R Monk
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne , Melbourne , Victoria , Australia
| | - Andrew A Mahony
- Infectious Diseases Department, Austin Health , Heidelberg , Victoria , Australia
| | - Elizabeth A Grabsch
- Infectious Diseases Department, Austin Health , Heidelberg , Victoria , Australia
| | - M Lindsay Grayson
- Infectious Diseases Department, Austin Health , Heidelberg , Victoria , Australia
| | - Stanley Pang
- School of Veterinary and Life Sciences, Murdoch University, Murdoch, Western Australia, Australia; Department of Microbiology, Pathwest Laboratory Medicine-WA, Fiona Stanley Hospital, Murdoch, Western Australia, Australia
| | - Geoffrey W Coombs
- School of Veterinary and Life Sciences, Murdoch University, Murdoch, Western Australia, Australia; Department of Microbiology, Pathwest Laboratory Medicine-WA, Fiona Stanley Hospital, Murdoch, Western Australia, Australia
| | - J Owen Robinson
- School of Veterinary and Life Sciences, Murdoch University, Murdoch, Western Australia, Australia; Department of Infectious Diseases, Fiona Stanley Hospital, Murdoch, Western Australia, Australia
| | - Torsten Seemann
- Victorian Life Sciences Computation Initiative, University of Melbourne , Carlton , Victoria , Australia
| | - Paul D R Johnson
- Infectious Diseases Department, Austin Health, Heidelberg, Victoria, Australia; Department of Medicine, University of Melbourne, Heidelberg, Victoria, Australia
| | - Benjamin P Howden
- Microbiology Diagnostic Unit, Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne , Melbourne , Victoria , Australia
| | - Timothy P Stinear
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne , Melbourne , Victoria , Australia
| |
Collapse
|
46
|
Guzman Prieto AM, van Schaik W, Rogers MRC, Coque TM, Baquero F, Corander J, Willems RJL. Global Emergence and Dissemination of Enterococci as Nosocomial Pathogens: Attack of the Clones? Front Microbiol 2016; 7:788. [PMID: 27303380 PMCID: PMC4880559 DOI: 10.3389/fmicb.2016.00788] [Citation(s) in RCA: 197] [Impact Index Per Article: 24.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Accepted: 05/09/2016] [Indexed: 12/13/2022] Open
Abstract
Enterococci are Gram-positive bacteria that are found in plants, soil and as commensals of the gastrointestinal tract of humans, mammals, and insects. Despite their commensal nature, they have also become globally important nosocomial pathogens. Within the genus Enterococcus, Enterococcus faecium, and Enterococcus faecalis are clinically most relevant. In this review, we will discuss how E. faecium and E. faecalis have evolved to become a globally disseminated nosocomial pathogen. E. faecium has a defined sub-population that is associated with hospitalized patients and is rarely encountered in community settings. These hospital-associated clones are characterized by the acquisition of adaptive genetic elements, including genes involved in metabolism, biofilm formation, and antibiotic resistance. In contrast to E. faecium, clones of E. faecalis isolated from hospitalized patients, including strains causing clinical infections, are not exclusively found in hospitals but are also present in healthy individuals and animals. This observation suggests that the division between commensals and hospital-adapted lineages is less clear for E. faecalis than for E. faecium. In addition, genes that are reported to be associated with virulence of E. faecalis are often not unique to clinical isolates, but are also found in strains that originate from commensal niches. As a reflection of more ancient association of E. faecalis with different hosts, these determinants Thus, they may not represent genuine virulence genes but may act as host-adaptive functions that are useful in a variety of intestinal environments. The scope of the review is to summarize recent trends in the emergence of antibiotic resistance and explore recent developments in the molecular epidemiology, population structure and mechanisms of adaptation of E. faecium and E. faecalis.
Collapse
Affiliation(s)
- Ana M Guzman Prieto
- Department of Medical Microbiology, University Medical Center Utrecht Utrecht, Netherlands
| | - Willem van Schaik
- Department of Medical Microbiology, University Medical Center Utrecht Utrecht, Netherlands
| | - Malbert R C Rogers
- Department of Medical Microbiology, University Medical Center Utrecht Utrecht, Netherlands
| | - Teresa M Coque
- Hospital Universitario Ramon y Cajal, Instituto Ramón y Cajal de Investigación SanitariaMadrid, Spain; CIBER Epidemiología y Salud PúblicaMadrid, Spain; Unidad de Resistencia a Antibióticos y Virulencia Bacteriana Asociada al Consejo Superior de Investigaciones CientíficasMadrid, Spain
| | - Fernando Baquero
- Hospital Universitario Ramon y Cajal, Instituto Ramón y Cajal de Investigación SanitariaMadrid, Spain; CIBER Epidemiología y Salud PúblicaMadrid, Spain; Unidad de Resistencia a Antibióticos y Virulencia Bacteriana Asociada al Consejo Superior de Investigaciones CientíficasMadrid, Spain
| | - Jukka Corander
- Department of Mathematics and Statistics, University of Helsinki Helsinki, Finland
| | - Rob J L Willems
- Department of Medical Microbiology, University Medical Center Utrecht Utrecht, Netherlands
| |
Collapse
|