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Bender JK, Fleige C, Funk F, Moretó-Castellsagué C, Fischer MA, Werner G. Linezolid Resistance Genes and Mutations among Linezolid-Susceptible Enterococcus spp.-A Loose Cannon? Antibiotics (Basel) 2024; 13:101. [PMID: 38275330 PMCID: PMC10812394 DOI: 10.3390/antibiotics13010101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 01/16/2024] [Accepted: 01/17/2024] [Indexed: 01/27/2024] Open
Abstract
The National Reference Centre for Enterococci receives an increasing number of linezolid-resistant Enterococcus isolates. Linezolid (LIN) resistance is mediated by G2576T 23S rDNA gene mutations and/or acquisition of resistance genes (cfr, optrA, poxtA). There are anecdotal reports that those resistance traits may be present in phenotypically linezolid-susceptible isolates. We aimed to determine the prevalence of LIN resistance genes and mutations in enterococci with a LIN MIC of 4 mg/L in broth microdilution (EUCAST = susceptible) isolated from German hospital patients 2019-2021. LIN MICs were additionally determined by ETEST® and VITEK2. Selected strains were subjected to LIN selective pressure and growth was monitored with increasing antibiotic concentrations. We received 195 isolates (LIN MIC = 4 mg/L). In total, 78/195 (40%) isolates contained either a putative resistance gene, the G2576T mutation, or a combination thereof. Very major error was high for broth microdilution. The ability to predict phenotypic resistance from genotypic profile was highest for G2576T-mediated resistance. Selection experiments revealed that, in particular, E. faecium isolates with resistance gene mutations or poxtA rapidly adapt to MICs above the clinical breakpoint. In conclusion, LIN resistance genes and mutations can be observed in phenotypically linezolid-susceptible enterococci. Those isolates may rapidly develop resistance under LIN selective pressure potentially leading to treatment failure.
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Affiliation(s)
- Jennifer K. Bender
- Nosocomial Pathogens and Antibiotic Resistances Unit, Department of Infectious Diseases, Robert Koch Institute, 38855 Wernigerode, Germany (F.F.); (C.M.-C.); (M.A.F.); (G.W.)
| | - Carola Fleige
- Nosocomial Pathogens and Antibiotic Resistances Unit, Department of Infectious Diseases, Robert Koch Institute, 38855 Wernigerode, Germany (F.F.); (C.M.-C.); (M.A.F.); (G.W.)
| | - Finn Funk
- Nosocomial Pathogens and Antibiotic Resistances Unit, Department of Infectious Diseases, Robert Koch Institute, 38855 Wernigerode, Germany (F.F.); (C.M.-C.); (M.A.F.); (G.W.)
| | - Clara Moretó-Castellsagué
- Nosocomial Pathogens and Antibiotic Resistances Unit, Department of Infectious Diseases, Robert Koch Institute, 38855 Wernigerode, Germany (F.F.); (C.M.-C.); (M.A.F.); (G.W.)
- Department of Microbiology and Parasitology, University Hospital of Bellvitge, 08907 Barcelona, Spain
| | - Martin A. Fischer
- Nosocomial Pathogens and Antibiotic Resistances Unit, Department of Infectious Diseases, Robert Koch Institute, 38855 Wernigerode, Germany (F.F.); (C.M.-C.); (M.A.F.); (G.W.)
| | - Guido Werner
- Nosocomial Pathogens and Antibiotic Resistances Unit, Department of Infectious Diseases, Robert Koch Institute, 38855 Wernigerode, Germany (F.F.); (C.M.-C.); (M.A.F.); (G.W.)
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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] [What about the content of this article? (0)] [Affiliation(s)] [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.
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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
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Bender JK, Baufeld E, Becker K, Claus H, Dudakova A, Dörre A, Fila N, Fleige C, Hamprecht A, Hoffmann A, Hogardt M, Kaasch AJ, Kola A, Kriebel N, Layer-Nicolaou F, Marschal M, Molitor E, Mutters NT, Liese J, Nelkenbrecher C, Neumann B, Rohde H, Steinmann J, Sörensen M, Thelen P, Weig M, Zautner AE, Werner G. CHROMAgar™ LIN-R as an efficient screening tool to assess the prevalence of linezolid-resistant enterococci in German hospital patients-a multicentre study approach, 2021-2022. J Antimicrob Chemother 2023; 78:2185-2191. [PMID: 37473450 PMCID: PMC10477123 DOI: 10.1093/jac/dkad218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2023] [Accepted: 06/29/2023] [Indexed: 07/22/2023] Open
Abstract
BACKGROUND In recent years, an increasing number of linezolid-resistant enterococci (LRE) was recognized at the German National Reference Centre (NRC) for Enterococci. National guidelines on infection prevention recommend screening for LRE in epidemiologically linked hospital settings without referring to a reliable and rapid diagnostic method. Since 2020, CHROMAgar™ provide a chromogenic linezolid screening agar, LIN-R, suitable to simultaneously screen for linezolid-resistant staphylococci and enterococci. OBJECTIVES To assess the applicability of CHROMAgar™ LIN-R in clinical settings for detecting LRE directly from patient material and to infer prevalence rates of LRE amongst German hospital patients. METHODS During the 3-month trial period, clinical samples were plated on CHROMAgar™ LIN-R. Antimicrobial susceptibility testing was performed using VITEK2 or disc diffusion. At the NRC, linezolid resistance was determined by broth microdilution, multiplex-PCR for cfr/optrA/poxtA and by a restriction-based assay for 23S rDNA mutations. RESULTS The 12 participating study sites used 13 963 CHROMAgar™ LIN-R plates during the study period. Of 442 presumptive LRE, 192 were confirmed by phenotypic methods. Of these, 161 were received by the NRC and 121 (75%) were verified as LRE. Most of LR-E. faecium 53/81 (65%) exhibited a 23S rRNA gene mutation as the sole resistance-mediating mechanism, whereas optrA constituted the dominant resistance trait in LR-E. faecalis [39/40 (98%)]. Prevalence of LRE across sites was estimated as 1% (ranging 0.18%-3.7% between sites). CONCLUSIONS CHROMAgar™ LIN-R represents a simple and efficient LRE screening tool in hospital settings. A high proportion of false-positive results demands validation of linezolid resistance by a reference method.
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Affiliation(s)
- Jennifer K Bender
- Nosocomial Pathogens and Antibiotic Resistances Unit, Department of Infectious Diseases, National Reference Centre for Staphylococci and Enterococci, Robert Koch Institute, Wernigerode, Germany
| | - Elsa Baufeld
- Friedrich Loeffler Institute of Medical Microbiology, University Medicine Greifswald, Greifswald, Germany
| | - Karsten Becker
- Friedrich Loeffler Institute of Medical Microbiology, University Medicine Greifswald, Greifswald, Germany
| | - Heike Claus
- Institute for Hygiene and Microbiology, University of Würzburg, Würzburg, Germany
| | - Anna Dudakova
- Institute for Medical Microbiology and Virology, University Medical Center Göttingen, Göttingen, Germany
| | - Achim Dörre
- Department of Infectious Disease Epidemiology, Robert Koch Institute, Berlin, Germany
| | - Nikoletta Fila
- Institute of Medical Microbiology and Hygiene, University of Tübingen, Tübingen, Germany
| | - Carola Fleige
- Nosocomial Pathogens and Antibiotic Resistances Unit, Department of Infectious Diseases, National Reference Centre for Staphylococci and Enterococci, Robert Koch Institute, Wernigerode, Germany
| | - Axel Hamprecht
- Institute for Medical Microbiology and Virology, Carl von Ossietzky University Oldenburg and Klinikum Oldenburg, Oldenburg, Germany
| | - Armin Hoffmann
- Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Michael Hogardt
- Institute of Medical Microbiology and Infection Control, University Hospital Frankfurt, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Achim J Kaasch
- Faculty of Medicine, Institute of Medical Microbiology and Hospital Hygiene, Otto-von-Guericke-University, Magdeburg, Germany
- Center for Health and Medical Prevention (CHaMP), Otto-von-Guericke University Magdeburg, Magdeburg, Germany
| | - Axel Kola
- Institute of Hygiene and Environmental Medicine, Charité Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Nancy Kriebel
- Nosocomial Pathogens and Antibiotic Resistances Unit, Department of Infectious Diseases, National Reference Centre for Staphylococci and Enterococci, Robert Koch Institute, Wernigerode, Germany
| | - Franziska Layer-Nicolaou
- Nosocomial Pathogens and Antibiotic Resistances Unit, Department of Infectious Diseases, National Reference Centre for Staphylococci and Enterococci, Robert Koch Institute, Wernigerode, Germany
| | - Matthias Marschal
- Institute of Medical Microbiology and Hygiene, University of Tübingen, Tübingen, Germany
| | - Ernst Molitor
- Institute of Medical Microbiology, Immunology and Parasitology, University Hospital Bonn, Bonn, Germany
| | - Nico T Mutters
- Institute for Hygiene and Public Health, University Hospital Bonn, Bonn, Germany
| | - Jan Liese
- Institute of Medical Microbiology and Hygiene, University of Tübingen, Tübingen, Germany
| | - Claudia Nelkenbrecher
- Institute of Hospital Hygiene, Medical Microbiology and Infectious Diseases, Nuremberg General Hospital, Paracelsus Medical University, Nuremberg, Germany
| | - Bernd Neumann
- Institute of Hospital Hygiene, Medical Microbiology and Infectious Diseases, Nuremberg General Hospital, Paracelsus Medical University, Nuremberg, Germany
| | - Holger Rohde
- Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Jörg Steinmann
- Institute of Hospital Hygiene, Medical Microbiology and Infectious Diseases, Nuremberg General Hospital, Paracelsus Medical University, Nuremberg, Germany
| | - Michael Sörensen
- Laboratory Prof. Gisela Enders and Colleagues, Stuttgart, Germany
| | - Philipp Thelen
- Institute for Medical Microbiology and Virology, Carl von Ossietzky University Oldenburg and Klinikum Oldenburg, Oldenburg, Germany
| | - Michael Weig
- Institute for Medical Microbiology and Virology, University Medical Center Göttingen, Göttingen, Germany
| | - Andreas E Zautner
- Faculty of Medicine, Institute of Medical Microbiology and Hospital Hygiene, Otto-von-Guericke-University, Magdeburg, Germany
- Center for Health and Medical Prevention (CHaMP), Otto-von-Guericke University Magdeburg, Magdeburg, Germany
| | - Guido Werner
- Nosocomial Pathogens and Antibiotic Resistances Unit, Department of Infectious Diseases, National Reference Centre for Staphylococci and Enterococci, Robert Koch Institute, Wernigerode, Germany
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Bender JK, Hermes J, Zabel LT, Haller S, Mürter N, Blank HP, Werner G, Hüttner I, Eckmanns T. Controlling an Unprecedented Outbreak with Vancomycin-Resistant Enterococcus faecium in Germany, October 2015 to November 2019. Microorganisms 2022; 10:1603. [PMID: 36014021 PMCID: PMC9412439 DOI: 10.3390/microorganisms10081603] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 08/03/2022] [Accepted: 08/03/2022] [Indexed: 01/18/2023] Open
Abstract
Hospital outbreaks with vancomycin-resistant enterococci (VRE) pose a serious health threat and a challenge to infection prevention and control (IPC). We herein report on a VRE outbreak of unprecedented extent in Southern Germany (October 2015-November 2019). We used descriptive epidemiology and whole-genome sequencing (WGS) for a detailed outbreak investigation. Of the 2905 cases, 2776 (95.3%) were colonized, whereas from 127 (3.7%), VRE could be isolated from otherwise sterile body fluids or sites unlikely for enterococci colonization. Cases had a median age of 78 years (IQR 68-84) and 1339/2905 (46%) were female. The majority of isolates sequenced belonged to the clonal lineage ST80/CT1013 (212/397, 53%). Nosocomial transmission was observed as well as the constant import of VRE into the hospital. Extensive IPC measures were implemented and terminated the outbreak in late 2019, eventually. Our study shows that the combination of epidemiological and genomic analyses is indispensable for comprehensive outbreak investigations. The adaptation of IPC measures to these findings, their timely implementation, and strict execution also allow containment of large VRE outbreaks in hospital settings.
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Affiliation(s)
- Jennifer K. Bender
- Nosocomial Pathogens and Antibiotic Resistances Unit, Department of Infectious Diseases, Robert Koch Institute, 38855 Wernigerode, Germany
| | - Julia Hermes
- Healthcare-Associated Infections, Surveillance of Antibiotic Resistance and Consumption Unit, Department of Infectious Disease Epidemiology, Robert Koch Institute, 13353 Berlin, Germany
| | | | - Sebastian Haller
- Healthcare-Associated Infections, Surveillance of Antibiotic Resistance and Consumption Unit, Department of Infectious Disease Epidemiology, Robert Koch Institute, 13353 Berlin, Germany
| | - Nadja Mürter
- Local Health Authority Göppingen, 73033 Göppingen, Germany
| | | | - Guido Werner
- Nosocomial Pathogens and Antibiotic Resistances Unit, Department of Infectious Diseases, Robert Koch Institute, 38855 Wernigerode, Germany
| | - Ingo Hüttner
- Alb Fils Kliniken GmbH, 73035 Göppingen, Germany
| | - Tim Eckmanns
- Healthcare-Associated Infections, Surveillance of Antibiotic Resistance and Consumption Unit, Department of Infectious Disease Epidemiology, Robert Koch Institute, 13353 Berlin, Germany
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5
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Bender JK, Haller S, Pfeifer Y, Hogardt M, Hunfeld KP, Thürmer A, Zanuzdana A, Werner M, Kunz B, Eisenberger D, Pfennigwerth N, Kempf VAJ, Werner G, Eckmanns T. Combined clinical, epidemiological and genome-based analysis identified a nationwide outbreak of Burkholderia cepacia complex infections caused by contaminated mouthwash solutions. Open Forum Infect Dis 2022; 9:ofac114. [PMID: 35434175 PMCID: PMC9007922 DOI: 10.1093/ofid/ofac114] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Accepted: 03/07/2022] [Indexed: 11/21/2022] Open
Abstract
Background In September 2018, Burkholderia cepacia complex (BCC) infections in 3 patients associated with exposure to a mouthwash solution (MWS) were reported to the Robert Koch Institute (RKI). As the product was still on the market and the scale of the outbreak was unclear, a nation-wide investigation was initiated. Methods We aimed to investigate BCC infections/colonizations associated with MWS. Hospitals, laboratories, and public health services were informed that BCC isolates should be sent to the RKI. These isolates were typed by pulsed-field gel electrophoresis (PFGE) and whole-genome sequencing (WGS) including development of an ad hoc core genome MLST (cgMLST) scheme. Results In total, 36 patients from 6 hospitals met the case definition, the last patient in November 2018. Twenty-nine isolates from 26 of these patients were available for typing. WGS analysis revealed 2 distinct cgMLST clusters. Cluster 1 (Burkholderia arboris) contained isolates from patients and MWS obtained from 4 hospitals and isolates provided by the manufacturer. Patient and MWS isolates from another hospital were assigned to cluster 2 (B. cepacia). Conclusions The combined clinical, epidemiological, and microbiological investigation, including whole-genome analysis, allowed for uncovering a supraregional BCC outbreak in health care settings. Strains of B. arboris and B. cepacia were identified as contaminating species of MWS bottles and subsequent colonization and putative infection of patients in several hospitals. Despite a recall of the product by the manufacturer in August 2018, the outbreak lasted until December 2018. Reporting of contaminated medical products and recalls should be optimized to protect patients.
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Affiliation(s)
- Jennifer K Bender
- Department of Infectious Diseases, Robert Koch Institute, Wernigerode, Germany
| | - Sebastian Haller
- Department for Infectious Disease Epidemiology, Robert Koch Institute, Berlin, Germany
| | - Yvonne Pfeifer
- Department of Infectious Diseases, Robert Koch Institute, Wernigerode, Germany
| | - Michael Hogardt
- Institute of Medical Microbiology and Infection Control, University Hospital Frankfurt, Frankfurt am Main, Germany
- German National Consiliary Laboratory on Cystic Fibrosis Bacteriology, Frankfurt am Main, Germany
| | - Klaus-Peter Hunfeld
- Institute for Laboratory Medicine, Microbiology & Infection Control, Northwest Medical Centre, Medical Faculty, Goethe University, Frankfurt am Main, Germany
| | | | - Arina Zanuzdana
- Department for Infectious Disease Epidemiology, Robert Koch Institute, Berlin, Germany
| | - Markus Werner
- Institute for Clinical Microbiology, Immunology and Hygiene, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nürnberg, Erlangen, Germany
| | - Bernd Kunz
- Institute for Clinical Microbiology, Immunology and Hygiene, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nürnberg, Erlangen, Germany
| | | | - Niels Pfennigwerth
- National Reference Center for Multidrug-resistant Gram-negative Bacteria, Ruhr-University Bochum, Bochum, Germany
| | - Volkhard A J Kempf
- Institute of Medical Microbiology and Infection Control, University Hospital Frankfurt, Frankfurt am Main, Germany
- German National Consiliary Laboratory on Cystic Fibrosis Bacteriology, Frankfurt am Main, Germany
| | - Guido Werner
- Department of Infectious Diseases, Robert Koch Institute, Wernigerode, Germany
| | - Tim Eckmanns
- Department for Infectious Disease Epidemiology, Robert Koch Institute, Berlin, Germany
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Bender JK, Meyer ED, Sandfort M, Matysiak-Klose D, Bojara G, Hellenbrand W. Low sensitivity of rapid antigen tests to detect SARS-CoV-2 infections prior to and on the day of symptom onset in staff and residents of a nursing home, Germany, January-March 2021. J Infect Dis 2021; 224:1987-1989. [PMID: 34648637 PMCID: PMC8524645 DOI: 10.1093/infdis/jiab528] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 10/13/2021] [Indexed: 11/13/2022] Open
Affiliation(s)
- Jennifer K Bender
- Department of Infectious Diseases, Nosocomial Pathogens and Antibiotic Resistances Unit, Robert Koch Institute, Wernigerode, Germany.,European Programme for Public Health Microbiology Training (EUPHEM), European Centre for Disease Prevention and Control (ECDC), Stockholm, Sweden
| | - Emily D Meyer
- Department of Infectious Disease Epidemiology, Postgraduate Training for Applied Epidemiology (PAE), Robert Koch Institute, Berlin, Germany.,European Programme for Intervention Epidemiology Training (EPIET), European Centre for Disease Prevention and Control (ECDC), Stockholm, Sweden
| | - Mirco Sandfort
- Department of Infectious Disease Epidemiology, Postgraduate Training for Applied Epidemiology (PAE), Robert Koch Institute, Berlin, Germany.,European Programme for Intervention Epidemiology Training (EPIET), European Centre for Disease Prevention and Control (ECDC), Stockholm, Sweden
| | - Dorothea Matysiak-Klose
- Department of Infectious Disease Epidemiology, Immunization Unit, Robert Koch Institute, Berlin, Germany
| | | | - Wiebke Hellenbrand
- Department of Infectious Disease Epidemiology, Immunization Unit, Robert Koch Institute, Berlin, Germany
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Bortolaia V, Kaas RS, Ruppe E, Roberts MC, Schwarz S, Cattoir V, Philippon A, Allesoe RL, Rebelo AR, Florensa AF, Fagelhauer L, Chakraborty T, Neumann B, Werner G, Bender JK, Stingl K, Nguyen M, Coppens J, Xavier BB, Malhotra-Kumar S, Westh H, Pinholt M, Anjum MF, Duggett NA, Kempf I, Nykäsenoja S, Olkkola S, Wieczorek K, Amaro A, Clemente L, Mossong J, Losch S, Ragimbeau C, Lund O, Aarestrup FM. ResFinder 4.0 for predictions of phenotypes from genotypes. J Antimicrob Chemother 2021; 75:3491-3500. [PMID: 32780112 PMCID: PMC7662176 DOI: 10.1093/jac/dkaa345] [Citation(s) in RCA: 1309] [Impact Index Per Article: 436.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 06/30/2020] [Indexed: 12/16/2022] Open
Abstract
Objectives WGS-based antimicrobial susceptibility testing (AST) is as reliable as phenotypic AST for several antimicrobial/bacterial species combinations. However, routine use of WGS-based AST is hindered by the need for bioinformatics skills and knowledge of antimicrobial resistance (AMR) determinants to operate the vast majority of tools developed to date. By leveraging on ResFinder and PointFinder, two freely accessible tools that can also assist users without bioinformatics skills, we aimed at increasing their speed and providing an easily interpretable antibiogram as output. Methods The ResFinder code was re-written to process raw reads and use Kmer-based alignment. The existing ResFinder and PointFinder databases were revised and expanded. Additional databases were developed including a genotype-to-phenotype key associating each AMR determinant with a phenotype at the antimicrobial compound level, and species-specific panels for in silico antibiograms. ResFinder 4.0 was validated using Escherichia coli (n = 584), Salmonella spp. (n = 1081), Campylobacter jejuni (n = 239), Enterococcus faecium (n = 106), Enterococcus faecalis (n = 50) and Staphylococcus aureus (n = 163) exhibiting different AST profiles, and from different human and animal sources and geographical origins. Results Genotype–phenotype concordance was ≥95% for 46/51 and 25/32 of the antimicrobial/species combinations evaluated for Gram-negative and Gram-positive bacteria, respectively. When genotype–phenotype concordance was <95%, discrepancies were mainly linked to criteria for interpretation of phenotypic tests and suboptimal sequence quality, and not to ResFinder 4.0 performance. Conclusions WGS-based AST using ResFinder 4.0 provides in silico antibiograms as reliable as those obtained by phenotypic AST at least for the bacterial species/antimicrobial agents of major public health relevance considered.
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Affiliation(s)
- Valeria Bortolaia
- Technical University of Denmark, National Food Institute, European Union Reference Laboratory for Antimicrobial Resistance, WHO Collaborating Centre for Antimicrobial Resistance in Foodborne Pathogens and Genomics, FAO Reference Laboratory for Antimicrobial Resistance, Kgs. Lyngby, Denmark
| | - Rolf S Kaas
- Technical University of Denmark, National Food Institute, European Union Reference Laboratory for Antimicrobial Resistance, WHO Collaborating Centre for Antimicrobial Resistance in Foodborne Pathogens and Genomics, FAO Reference Laboratory for Antimicrobial Resistance, Kgs. Lyngby, Denmark
| | | | - Marilyn C Roberts
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, WA, USA
| | - Stefan Schwarz
- Institute of Microbiology and Epizootics, Centre for Infection Medicine, Department of Veterinary Medicine, Freie Universität Berlin, Berlin, Germany
| | - Vincent Cattoir
- Rennes University Hospital, Department of Clinical Microbiology, Rennes, France.,National Reference Center for Antimicrobial Resistance (lab Enterococci), Rennes, France.,University of Rennes 1, INSERM U1230, Rennes, France
| | - Alain Philippon
- Faculty of Medicine Paris Descartes, Bacteriology, Paris, France
| | - Rosa L Allesoe
- Technical University of Denmark, National Food Institute, European Union Reference Laboratory for Antimicrobial Resistance, WHO Collaborating Centre for Antimicrobial Resistance in Foodborne Pathogens and Genomics, FAO Reference Laboratory for Antimicrobial Resistance, Kgs. Lyngby, Denmark.,Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen N, Denmark
| | - Ana Rita Rebelo
- Technical University of Denmark, National Food Institute, European Union Reference Laboratory for Antimicrobial Resistance, WHO Collaborating Centre for Antimicrobial Resistance in Foodborne Pathogens and Genomics, FAO Reference Laboratory for Antimicrobial Resistance, Kgs. Lyngby, Denmark
| | - Alfred Ferrer Florensa
- Technical University of Denmark, National Food Institute, European Union Reference Laboratory for Antimicrobial Resistance, WHO Collaborating Centre for Antimicrobial Resistance in Foodborne Pathogens and Genomics, FAO Reference Laboratory for Antimicrobial Resistance, Kgs. Lyngby, Denmark
| | - Linda Fagelhauer
- Institute of Medical Microbiolgy, Justus Liebig University Giessen, Giessen, Germany.,German Center for Infection Research, site Giessen-Marburg-Langen, Justus Liebig University Giessen, Giessen, Germany.,Institute of Hygiene and Environmental Medicine, Justus Liebig University Giessen, Giessen, Germany
| | - Trinad Chakraborty
- Institute of Medical Microbiolgy, Justus Liebig University Giessen, Giessen, Germany.,German Center for Infection Research, site Giessen-Marburg-Langen, Justus Liebig University Giessen, Giessen, Germany
| | - Bernd Neumann
- Robert Koch Institute, Wernigerode Branch, Department of Infectious Diseases, Division of Nosocomial Pathogens and Antibiotic Resistances, Wernigerode, Germany
| | - Guido Werner
- Robert Koch Institute, Wernigerode Branch, Department of Infectious Diseases, Division of Nosocomial Pathogens and Antibiotic Resistances, Wernigerode, Germany
| | - Jennifer K Bender
- Robert Koch Institute, Wernigerode Branch, Department of Infectious Diseases, Division of Nosocomial Pathogens and Antibiotic Resistances, Wernigerode, Germany
| | - Kerstin Stingl
- German Federal Institute for Risk Assessment, Department of Biological Safety, National Reference Laboratory for Campylobacter, Berlin, Germany
| | - Minh Nguyen
- Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, University of Antwerp, Belgium
| | - Jasmine Coppens
- Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, University of Antwerp, Belgium
| | - Basil Britto Xavier
- Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, University of Antwerp, Belgium
| | - Surbhi Malhotra-Kumar
- Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, University of Antwerp, Belgium
| | - Henrik Westh
- Department of Clinical Microbiology, Hvidovre University Hospital, Hvidovre, Denmark.,Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Mette Pinholt
- Department of Clinical Microbiology, Hvidovre University Hospital, Hvidovre, Denmark
| | - Muna F Anjum
- Animal and Plant Health Agency, Addlestone, Surrey, UK
| | | | - Isabelle Kempf
- ANSES, Ploufragan-Plouzané-Niort Laboratory, Ploufragan, France
| | | | | | | | - Ana Amaro
- National Institute of Agrarian and Veterinary Research (INIAV), National Reference Laboratory for Animal Health, Oeiras, Portugal
| | - Lurdes Clemente
- National Institute of Agrarian and Veterinary Research (INIAV), National Reference Laboratory for Animal Health, Oeiras, Portugal
| | - Joël Mossong
- Laboratoire National de Santé, Epidemiology and Microbial Genomics, Dudelange, Luxembourg
| | - Serge Losch
- Laboratoire de Médecine Vétérinaire de l'Etat, Veterinary Services Administration, Dudelange, Luxembourg
| | - Catherine Ragimbeau
- Laboratoire National de Santé, Epidemiology and Microbial Genomics, Dudelange, Luxembourg
| | - Ole Lund
- Technical University of Denmark, National Food Institute, European Union Reference Laboratory for Antimicrobial Resistance, WHO Collaborating Centre for Antimicrobial Resistance in Foodborne Pathogens and Genomics, FAO Reference Laboratory for Antimicrobial Resistance, Kgs. Lyngby, Denmark
| | - Frank M Aarestrup
- Technical University of Denmark, National Food Institute, European Union Reference Laboratory for Antimicrobial Resistance, WHO Collaborating Centre for Antimicrobial Resistance in Foodborne Pathogens and Genomics, FAO Reference Laboratory for Antimicrobial Resistance, Kgs. Lyngby, Denmark
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8
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Weber RE, Fuchs S, Layer F, Sommer A, Bender JK, Thürmer A, Werner G, Strommenger B. Corrigendum: Genome-Wide Association Studies for the Detection of Genetic Variants Associated With Daptomycin and Ceftaroline Resistance in Staphylococcus aureus. Front Microbiol 2021; 12:686197. [PMID: 33986737 PMCID: PMC8111692 DOI: 10.3389/fmicb.2021.686197] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 04/01/2021] [Indexed: 11/18/2022] Open
Affiliation(s)
- Robert E Weber
- Department of Infectious Diseases, Robert Koch-Institute, Wernigerode, Germany
| | - Stephan Fuchs
- Methodology and Research Infrastructure, Bioinformatics, Robert Koch-Institute, Berlin, Germany
| | - Franziska Layer
- Department of Infectious Diseases, Robert Koch-Institute, Wernigerode, Germany
| | - Anna Sommer
- Department of Infectious Diseases, Robert Koch-Institute, Wernigerode, Germany
| | - Jennifer K Bender
- Department of Infectious Diseases, Robert Koch-Institute, Wernigerode, Germany
| | - Andrea Thürmer
- Methodology and Research Infrastructure, Genome Sequencing, Robert Koch-Institute, Berlin, Germany
| | - Guido Werner
- Department of Infectious Diseases, Robert Koch-Institute, Wernigerode, Germany
| | - Birgit Strommenger
- Department of Infectious Diseases, Robert Koch-Institute, Wernigerode, Germany
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9
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Abstract
We determined secondary attack rates (SAR) among close contacts of 59 asymptomatic and symptomatic coronavirus disease case-patients by presymptomatic and symptomatic exposure. We observed no transmission from asymptomatic case-patients and highest SAR through presymptomatic exposure. Rapid quarantine of close contacts with or without symptoms is needed to prevent presymptomatic transmission.
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10
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Pulami D, Schauss T, Eisenberg T, Blom J, Schwengers O, Bender JK, Wilharm G, Kämpfer P, Glaeser SP. Acinetobacter stercoris sp. nov. isolated from output source of a mesophilic german biogas plant with anaerobic operating conditions. Antonie Van Leeuwenhoek 2021; 114:235-251. [PMID: 33591460 PMCID: PMC7902594 DOI: 10.1007/s10482-021-01517-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/22/2020] [Accepted: 01/13/2021] [Indexed: 01/21/2023]
Abstract
The Gram-stain-negative, oxidase negative, catalase positive strain KPC-SM-21T, isolated from a digestate of a storage tank of a mesophilic German biogas plant, was investigated by a polyphasic taxonomic approach. Phylogenetic identification based on the nearly full-length 16S rRNA gene revealed highest gene sequence similarity to Acinetobacter baumannii ATCC 19606T (97.0%). Phylogenetic trees calculated based on partial rpoB and gyrB gene sequences showed a distinct clustering of strain KPC-SM-21T with Acinetobacter gerneri DSM 14967T = CIP 107464T and not with A. baumannii, which was also supported in the five housekeeping genes multilocus sequence analysis based phylogeny. Average nucleotide identity values between whole genome sequences of strain KPC-SM-21T and next related type strains supported the novel species status. The DNA G + C content of strain KPC-SM-21T was 37.7 mol%. Whole-cell MALDI-TOF MS analysis supported the distinctness of the strain to type strains of next related Acinetobacter species. Predominant fatty acids were C18:1 ω9c (44.2%), C16:0 (21.7%) and a summed feature comprising C16:1 ω7c and/or iso-C15:0 2-OH (15.3%). Based on the obtained genotypic, phenotypic and chemotaxonomic data we concluded that strain KPC-SM-21T represents a novel species of the genus Acinetobacter, for which the name Acinetobacter stercoris sp. nov. is proposed. The type strain is KPC-SM-21T (= DSM 102168T = LMG 29413T).
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Affiliation(s)
- Dipen Pulami
- Institut für Angewandte Mikrobiologie, Justus-Liebig-Universität Giessen, 35392, Giessen, Germany
| | - Thorsten Schauss
- Institut für Angewandte Mikrobiologie, Justus-Liebig-Universität Giessen, 35392, Giessen, Germany
| | - Tobias Eisenberg
- Department of Veterinary Medicine, Hessian State Laboratory, Giessen, Germany
| | - Jochen Blom
- Institute for Bioinformatics and Systems Biology, Giessen, 35392, Giessen, Germany
| | - Oliver Schwengers
- Institute for Bioinformatics and Systems Biology, Giessen, 35392, Giessen, Germany
| | - Jennifer K Bender
- Division of Nosocomial Pathogens and Antibiotic Resistances, Wernigerode Branch, Robert Koch Institute, 38855, Wernigerode, Germany
| | - Gottfried Wilharm
- Project group P2, Wernigerode Branch, Robert Koch Institute, 38855, Wernigerode, Germany
| | - Peter Kämpfer
- Institut für Angewandte Mikrobiologie, Justus-Liebig-Universität Giessen, 35392, Giessen, Germany
| | - Stefanie P Glaeser
- Institut für Angewandte Mikrobiologie, Justus-Liebig-Universität Giessen, 35392, Giessen, Germany.
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11
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Weber RE, Fuchs S, Layer F, Sommer A, Bender JK, Thürmer A, Werner G, Strommenger B. Genome-Wide Association Studies for the Detection of Genetic Variants Associated With Daptomycin and Ceftaroline Resistance in Staphylococcus aureus. Front Microbiol 2021; 12:639660. [PMID: 33658988 PMCID: PMC7917082 DOI: 10.3389/fmicb.2021.639660] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Accepted: 01/22/2021] [Indexed: 12/29/2022] Open
Abstract
Background As next generation sequencing (NGS) technologies have experienced a rapid development over the last decade, the investigation of the bacterial genetic architecture reveals a high potential to dissect causal loci of antibiotic resistance phenotypes. Although genome-wide association studies (GWAS) have been successfully applied for investigating the basis of resistance traits, complex resistance phenotypes have been omitted so far. For S. aureus this especially refers to antibiotics of last resort like daptomycin and ceftaroline. Therefore, we aimed to perform GWAS for the identification of genetic variants associated with DAP and CPT resistance in clinical S. aureus isolates. Materials/methods To conduct microbial GWAS, we selected cases and controls according to their clonal background, date of isolation, and geographical origin. Association testing was performed with PLINK and SEER analysis. By using in silico analysis, we also searched for rare genetic variants in candidate loci that have previously been described to be involved in the development of corresponding resistance phenotypes. Results GWAS revealed MprF P314L and L826F to be significantly associated with DAP resistance. These mutations were found to be homogenously distributed among clonal lineages suggesting convergent evolution. Additionally, rare and yet undescribed single nucleotide polymorphisms could be identified within mprF and putative candidate genes. Finally, we could show that each DAP resistant isolate exhibited at least one amino acid substitution within the open reading frame of mprF. Due to the presence of strong population stratification, no genetic variants could be associated with CPT resistance. However, the investigation of the staphylococcal cassette chromosome mec (SCCmec) revealed various mecA SNPs to be putatively linked with CPT resistance. Additionally, some CPT resistant isolates revealed no mecA mutations, supporting the hypothesis that further and still unknown resistance determinants are crucial for the development of CPT resistance in S. aureus. Conclusion We hereby confirmed the potential of GWAS to identify genetic variants that are associated with antibiotic resistance traits in S. aureus. However, precautions need to be taken to prevent the detection of spurious associations. In addition, the implementation of different approaches is still essential to detect multiple forms of variations and mutations that occur with a low frequency.
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Affiliation(s)
- Robert E Weber
- Department of Infectious Diseases, Robert Koch-Institute, Wernigerode, Germany.,Methodology and Research Infrastructure, Genome Sequencing, Robert Koch-Institute, Berlin, Germany
| | - Stephan Fuchs
- Methodology and Research Infrastructure, Bioinformatics, Robert Koch-Institute, Berlin, Germany
| | - Franziska Layer
- Department of Infectious Diseases, Robert Koch-Institute, Wernigerode, Germany.,Methodology and Research Infrastructure, Genome Sequencing, Robert Koch-Institute, Berlin, Germany
| | - Anna Sommer
- Department of Infectious Diseases, Robert Koch-Institute, Wernigerode, Germany.,Methodology and Research Infrastructure, Genome Sequencing, Robert Koch-Institute, Berlin, Germany
| | - Jennifer K Bender
- Department of Infectious Diseases, Robert Koch-Institute, Wernigerode, Germany.,Methodology and Research Infrastructure, Genome Sequencing, Robert Koch-Institute, Berlin, Germany
| | - Andrea Thürmer
- Methodology and Research Infrastructure, Bioinformatics, Robert Koch-Institute, Berlin, Germany
| | - Guido Werner
- Department of Infectious Diseases, Robert Koch-Institute, Wernigerode, Germany.,Methodology and Research Infrastructure, Genome Sequencing, Robert Koch-Institute, Berlin, Germany
| | - Birgit Strommenger
- Department of Infectious Diseases, Robert Koch-Institute, Wernigerode, Germany.,Methodology and Research Infrastructure, Genome Sequencing, Robert Koch-Institute, Berlin, Germany
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12
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Werner G, Neumann B, Weber RE, Kresken M, Wendt C, Bender JK. Thirty years of VRE in Germany - "expect the unexpected": The view from the National Reference Centre for Staphylococci and Enterococci. Drug Resist Updat 2020; 53:100732. [PMID: 33189998 DOI: 10.1016/j.drup.2020.100732] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 10/12/2020] [Accepted: 10/15/2020] [Indexed: 02/06/2023]
Abstract
Enterococci are commensals of the intestinal tract of many animals and humans. Of the various known and still unnamed new enterococcal species, only isolates of Enterococcus faecium and Enterococcus faecalis have received increased medical and public health attention. According to textbook knowledge, the majority of infections are caused by E. faecalis. In recent decades, the number of enterococcal infections has increased, with the increase being exclusively associated with a rising number of nosocomial E. faecium infections. This increase has been accompanied by the dissemination of certain hospital-acquired strain variants and an alarming progress in the development of antibiotic resistance namely vancomycin resistance. With this review we focus on a description of the specific situation of vancomycin resistance among clinical E. faecium isolates in Germany over the past 30 years. The present review describes three VRE episodes in Germany, each of which is framed by the beginning and end of the respective decade. The first episode is specified by the first appearance of VRE in 1990 and a country-wide spread of specific vanA-type VRE strains (ST117/CT24) until the late 1990s. The second decade was initially marked by regional clusters and VRE outbreaks in hospitals in South-Western Germany in 2004 and 2005, mainly caused by vanA-type VRE of ST203. Against the background of a certain "basic level" of VRE prevalence throughout Germany, an early shift from the vanA genotype to the vanB genotype in clinical isolates already occurred at the end of the 2000s without much notice. With the beginning of the third decade in 2010, VRE rates in Germany have permanently increased, first in some federal states and soon after country-wide. Besides an increase in VRE prevalence, this decade was marked by a sharp increase in vanB-type resistance and a dominance of a few, novel strain variants like ST192 and later on ST117 (CT71, CT469) and ST80 (CT1065). The largest VRE outbreak, which involved about 2,900 patients and lasted over three years, was caused by a novel and until that time, unknown strain type of ST80/CT1013 (vanB). Across all periods, VRE outbreaks were mainly oligoclonal and strain types varied over space (hospital wards) and time. The spread of VRE strains obviously respects political borders; for instance, both vancomycin-variable enterococci which were highly prevalent in Denmark and ST796 VRE which successfully disseminated in Australia and Switzerland, were still completely absent among German hospital patients, until to date.
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Affiliation(s)
- Guido Werner
- National Reference Centre for Staphylococci and Enterococci, Division Nosocomial Pathogens and Antibiotic Resistances, Department of Infectious Diseases, Robert Koch Institute, Wernigerode Branch, Germany.
| | - Bernd Neumann
- National Reference Centre for Staphylococci and Enterococci, Division Nosocomial Pathogens and Antibiotic Resistances, Department of Infectious Diseases, Robert Koch Institute, Wernigerode Branch, Germany
| | - Robert E Weber
- National Reference Centre for Staphylococci and Enterococci, Division Nosocomial Pathogens and Antibiotic Resistances, Department of Infectious Diseases, Robert Koch Institute, Wernigerode Branch, Germany
| | | | | | - Jennifer K Bender
- National Reference Centre for Staphylococci and Enterococci, Division Nosocomial Pathogens and Antibiotic Resistances, Department of Infectious Diseases, Robert Koch Institute, Wernigerode Branch, Germany
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13
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Klare I, Bender JK, Fleige C, Kriebel N, Hamprecht A, Gatermann S, Werner G. Comparison of VITEK® 2, three different gradient strip tests and broth microdilution for detecting vanB-positive Enterococcus faecium isolates with low vancomycin MICs. J Antimicrob Chemother 2020; 74:2926-2929. [PMID: 31335935 PMCID: PMC6753474 DOI: 10.1093/jac/dkz310] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Revised: 06/12/2019] [Accepted: 06/21/2019] [Indexed: 11/14/2022] Open
Abstract
OBJECTIVES In 2018, EUCAST issued a warning regarding unreliable results of gradient strip tests for confirming vancomycin resistance in enterococci. We compared the performance of various diagnostic standard and confirmatory tests to identify and determine vanB-type vancomycin resistance. METHODS We analysed a collection of vanB-positive Enterococcus faecium isolates (n = 68) with low vancomycin MICs and compared the performance of VITEK® 2 (bioMérieux), broth microdilution and three gradient strip tests from different providers (Oxoid, Liofilchem and bioMérieux). For the latter we compared the standard procedure with a protocol with increased inoculum, a rich agar medium and a longer incubation time ('macromethod'). RESULTS The sensitivity of VITEK® 2 was 81% compared with 72% for broth microdilution and 61%-63% for the three gradient strip tests using standard conditions. The macromethod substantially improved the performance of all strip tests resulting in a sensitivity of 89%-96% after 48 h of incubation. CONCLUSIONS We recommend that EUCAST changes the present warning against the general use of MIC strips. When MIC strips are used to either exclude or confirm suspected vancomycin resistance in E. faecium, and a PCR is not available, the macromethod should be employed. For clinically relevant enterococci, where a rapid therapeutic decision is needed, a molecular test (e.g. PCR) should be favoured in order to save time and to further increase sensitivity.
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Affiliation(s)
- Ingo Klare
- National Reference Centre for Staphylococci and Enterococci (NRC), Division of Nosocomial Pathogens and Antibiotic Resistance, Department of Infectious Diseases, Robert Koch Institut, Wernigerode Branch, Wernigerode, Germany
| | - Jennifer K Bender
- National Reference Centre for Staphylococci and Enterococci (NRC), Division of Nosocomial Pathogens and Antibiotic Resistance, Department of Infectious Diseases, Robert Koch Institut, Wernigerode Branch, Wernigerode, Germany
| | - Carola Fleige
- National Reference Centre for Staphylococci and Enterococci (NRC), Division of Nosocomial Pathogens and Antibiotic Resistance, Department of Infectious Diseases, Robert Koch Institut, Wernigerode Branch, Wernigerode, Germany
| | - Nancy Kriebel
- National Reference Centre for Staphylococci and Enterococci (NRC), Division of Nosocomial Pathogens and Antibiotic Resistance, Department of Infectious Diseases, Robert Koch Institut, Wernigerode Branch, Wernigerode, Germany
| | - Axel Hamprecht
- Institute for Medical Microbiology, Immunology and Hygiene, University of Cologne, Cologne, Germany and DZIF (German Centre for Infection Research), partner site Bonn-Cologne, Germany
| | - Sören Gatermann
- Department of Medical Microbiology, Institute for Medical Microbiology and Hygiene, Ruhr University Bochum, Bochum, Germany
| | - Guido Werner
- National Reference Centre for Staphylococci and Enterococci (NRC), Division of Nosocomial Pathogens and Antibiotic Resistance, Department of Infectious Diseases, Robert Koch Institut, Wernigerode Branch, Wernigerode, Germany
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14
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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] [What about the content of this article? (0)] [Affiliation(s)] [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.
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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
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15
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Bender JK, Klare I, Fleige C, Werner G. A Nosocomial Cluster of Tigecycline- and Vancomycin-Resistant Enterococcus faecium Isolates and the Impact of rpsJ and tet(M) Mutations on Tigecycline Resistance. Microb Drug Resist 2019; 26:576-582. [PMID: 31895641 DOI: 10.1089/mdr.2019.0346] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Tigecycline-resistant enterococci are only rarely detected worldwide. In 2017, the National Reference Centre for Staphylococci and Enterococci noticed a nosocomial cluster of tigecycline- and vancomycin-resistant Enterococcus faecium (TVRE) in a hospital of tertiary care in Northern Germany. Nineteen E. faecium isolates were analyzed by means of antimicrobial susceptibility testing and pulsed-field gel electrophoresis. A subset of isolates was subjected to whole-genome sequencing. The genetic basis of tigecycline resistance was assessed by ResFinder and by comparative analyses to known tetracycline and tigecycline resistance genes. Phylogenetic investigations revealed the clustering of 11 TVRE that exhibited genotype ST117/CT1489. Two tigecycline-susceptible isolates were unrelated. Characterization of the genetic determinant putatively responsible for tigecycline resistance revealed two chromosomal changes in the TVRE population: (1) a deletion within the ribosomal protein gene rpsJ and (2) a serine insertion in and removal of transcriptional regulation of the ribosomal protection protein Tet(M). We here report the first nosocomial cluster of TVRE in a German hospital and disclosed the resistance mechanism that was most likely causative for tigecycline insusceptibility. Clonal spread of TVRE isolates can be assumed because all isolates were highly related and harbored identical chromosomal alterations associated with tigecycline resistance.
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Affiliation(s)
- Jennifer K Bender
- Division of Nosocomial Pathogens and Antibiotic Resistances, Department of Infectious Diseases, National Reference Centre (NRC) for Staphylococci and Enterococci, Robert Koch Institute, Wernigerode, Germany
| | - Ingo Klare
- Division of Nosocomial Pathogens and Antibiotic Resistances, Department of Infectious Diseases, National Reference Centre (NRC) for Staphylococci and Enterococci, Robert Koch Institute, Wernigerode, Germany
| | - Carola Fleige
- Division of Nosocomial Pathogens and Antibiotic Resistances, Department of Infectious Diseases, National Reference Centre (NRC) for Staphylococci and Enterococci, Robert Koch Institute, Wernigerode, Germany
| | - Guido Werner
- Division of Nosocomial Pathogens and Antibiotic Resistances, Department of Infectious Diseases, National Reference Centre (NRC) for Staphylococci and Enterococci, Robert Koch Institute, Wernigerode, Germany
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16
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Abstract
BACKGROUND Linezolid is an alternative treatment option for infections with multidrug-resistant Gram-positive bacteria including vancomycin-resistant enterococci. Some countries report an increasing number of isolates with resistance to linezolid. The recent publication of the Commission for Hospital Hygiene in Germany on enterococci/VRE recommends screening for linezolid-resistant enterococci (LRE). However, a suitable selective medium or a genetic test is not available. Our aim was to establish a selective screening agar for LRE detection and validate its application with a comprehensive collection of clinical LRE and linezolid-susceptible enterococci. METHODS We decided to combine the selective power of an enterococcal screening agar with a supplementation of linezolid. Several rounds of analyses with reference, control and test strains and under varying linezolid concentrations of a wider and a smaller range were investigated and assessed. The collection of linezolid-resistant enterococcal control strains included isolates with different resistance mechanisms (23S rDNA mutations, cfr(B), optrA, poxtA). Finally, we validated our LRE screening agar with 400 samples sent to our National Reference Centre in 2019. RESULTS Several rounds of pre-tests and confirmatory analyses favored Enterococcosel® Agar supplemented with a concentration of 2 mg/L linezolid. A 48 h incubation period was essential for accurate identification of LRE strains. Performance of the LRE screening agar revealed a sensitivity of 96.6% and a specificity of 94.4%. CONCLUSIONS Here we describe preparation of a suitable screening agar and a procedure to identify LRE isolates with high accuracy.
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Affiliation(s)
- Guido Werner
- Division Nosocomial Pathogens and Antibiotic Resistances, Department of Infectious Diseases, National Reference Centre for Staphylococci and Enterococci (NRC), Robert Koch Institute, Wernigerode Branch, Wernigerode, Germany.
| | - Carola Fleige
- Division Nosocomial Pathogens and Antibiotic Resistances, Department of Infectious Diseases, National Reference Centre for Staphylococci and Enterococci (NRC), Robert Koch Institute, Wernigerode Branch, Wernigerode, Germany
| | - Ingo Klare
- Division Nosocomial Pathogens and Antibiotic Resistances, Department of Infectious Diseases, National Reference Centre for Staphylococci and Enterococci (NRC), Robert Koch Institute, Wernigerode Branch, Wernigerode, Germany
| | - Robert E Weber
- Division Nosocomial Pathogens and Antibiotic Resistances, Department of Infectious Diseases, National Reference Centre for Staphylococci and Enterococci (NRC), Robert Koch Institute, Wernigerode Branch, Wernigerode, Germany
| | - Jennifer K Bender
- Division Nosocomial Pathogens and Antibiotic Resistances, Department of Infectious Diseases, National Reference Centre for Staphylococci and Enterococci (NRC), Robert Koch Institute, Wernigerode Branch, Wernigerode, Germany
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17
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Bender JK, Fleige C, Klare I, Werner G. Development of a multiplex-PCR to simultaneously detect acquired linezolid resistance genes cfr, optrA and poxtA in enterococci of clinical origin. J Microbiol Methods 2019; 160:101-103. [PMID: 30940534 DOI: 10.1016/j.mimet.2019.03.025] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Revised: 03/27/2019] [Accepted: 03/29/2019] [Indexed: 10/27/2022]
Abstract
Linezolid-resistant enterococcus spp. are increasingly recognized by diagnostic laboratories. Resistance can be mediated by the expression of cfr, optrA or poxtA. We developed a multiplex-PCR to simultaneously detect all three genes. The PCR is suitable for microbiological diagnostics in order to restrict further spread of resistances in enterococci.
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Affiliation(s)
- Jennifer K Bender
- National Reference Centre for Staphylococci and Enterococci, Division of Nosocomial Pathogens and Antibiotic Resistances, Department of Infectious Diseases, Robert Koch Institute, Wernigerode, Germany.
| | - Carola Fleige
- National Reference Centre for Staphylococci and Enterococci, Division of Nosocomial Pathogens and Antibiotic Resistances, Department of Infectious Diseases, Robert Koch Institute, Wernigerode, Germany
| | - Ingo Klare
- National Reference Centre for Staphylococci and Enterococci, Division of Nosocomial Pathogens and Antibiotic Resistances, Department of Infectious Diseases, Robert Koch Institute, Wernigerode, Germany
| | - Guido Werner
- National Reference Centre for Staphylococci and Enterococci, Division of Nosocomial Pathogens and Antibiotic Resistances, Department of Infectious Diseases, Robert Koch Institute, Wernigerode, Germany
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Bender JK, Fleige C, Lange D, Klare I, Werner G. Rapid emergence of highly variable and transferable oxazolidinone and phenicol resistance gene optrA in German Enterococcus spp. clinical isolates. Int J Antimicrob Agents 2018; 52:819-827. [PMID: 30236952 DOI: 10.1016/j.ijantimicag.2018.09.009] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Revised: 05/07/2018] [Accepted: 09/09/2018] [Indexed: 01/12/2023]
Abstract
The number of linezolid-resistant Enterococcus spp. isolates received by the National Reference Centre for Staphylococci and Enterococci in Germany has been increasing since 2011. Although the majority are E. faecium, clinical linezolid-resistant E. faecalis have also been isolated. With respect to the newly discovered linezolid resistance protein OptrA, the authors conducted a retrospective polymerase chain reaction screening of 698 linezolid-resistant enterococcus clinical isolates. That yielded 43 optrA-positive strains, of which a subset was analysed by whole-genome sequencing in order to infer linezolid resistance-associated mechanisms and phylogenetic relatedness, and to disclose optrA genetic environments. Multiple optrA variants were detected. The originally described variant from China (optrAWT) was the only variant shared between the two Enterococcus spp.; however, distinct optrAWT loci were detected for E. faecium and E. faecalis. Generally, optrA localized to a plethora of genetic backgrounds that differed even for identical optrA variants. This suggests transmission of a mobile genetic element harbouring the resistance locus. Additionally, identical optrA variants detected on presumably identical plasmids, that were present in unrelated strains, indicates dissemination of the entire optrA-containing plasmid. In accordance, in vitro conjugation experiments verified transfer of optrA plasmids between enterococci of the same and of different species. In conclusion, multiple optrA variants located on distinct plasmids and mobile genetic elements with the potential for conjugative transfer are supposedly causative for the emergence of optrA-positive enterococci. Hence, rapid dissemination of the resistance determinant under selective pressure imposed by extensive use of last-resort antibiotics in clinical settings could be expected.
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Affiliation(s)
- Jennifer K Bender
- National Reference Centre for Staphylococci and Enterococci, Division of Nosocomial Pathogens and Antibiotic Resistances, Department of Infectious Diseases, Robert Koch Institute, Wernigerode, Saxony-Anhalt, Germany.
| | - Carola Fleige
- National Reference Centre for Staphylococci and Enterococci, Division of Nosocomial Pathogens and Antibiotic Resistances, Department of Infectious Diseases, Robert Koch Institute, Wernigerode, Saxony-Anhalt, Germany
| | - Dominik Lange
- National Reference Centre for Staphylococci and Enterococci, Division of Nosocomial Pathogens and Antibiotic Resistances, Department of Infectious Diseases, Robert Koch Institute, Wernigerode, Saxony-Anhalt, Germany
| | - Ingo Klare
- National Reference Centre for Staphylococci and Enterococci, Division of Nosocomial Pathogens and Antibiotic Resistances, Department of Infectious Diseases, Robert Koch Institute, Wernigerode, Saxony-Anhalt, Germany
| | - Guido Werner
- National Reference Centre for Staphylococci and Enterococci, Division of Nosocomial Pathogens and Antibiotic Resistances, Department of Infectious Diseases, Robert Koch Institute, Wernigerode, Saxony-Anhalt, Germany
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Wilharm G, Skiebe E, Higgins PG, Poppel MT, Blaschke U, Leser S, Heider C, Heindorf M, Brauner P, Jäckel U, Böhland K, Cuny C, Łopińska A, Kaminski P, Kasprzak M, Bochenski M, Ciebiera O, Tobółka M, Żołnierowicz KM, Siekiera J, Seifert H, Gagné S, Salcedo SP, Kaatz M, Layer F, Bender JK, Fuchs S, Semmler T, Pfeifer Y, Jerzak L. Relatedness of wildlife and livestock avian isolates of the nosocomial pathogenAcinetobacter baumanniito lineages spread in hospitals worldwide. Environ Microbiol 2017; 19:4349-4364. [DOI: 10.1111/1462-2920.13931] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Accepted: 09/14/2017] [Indexed: 11/30/2022]
Affiliation(s)
- Gottfried Wilharm
- Wernigerode Branch; Robert Koch Institute, Burgstr. 37; Wernigerode D-38855 Germany
| | - Evelyn Skiebe
- Wernigerode Branch; Robert Koch Institute, Burgstr. 37; Wernigerode D-38855 Germany
| | - Paul G. Higgins
- Institute for Medical Microbiology, Immunology and Hygiene; University of Cologne; Cologne D-50935 Germany
- Partner site Bonn-Cologne; German Centre for Infection Research (DZIF); Germany
| | - Marie T. Poppel
- Wernigerode Branch; Robert Koch Institute, Burgstr. 37; Wernigerode D-38855 Germany
| | - Ulrike Blaschke
- Wernigerode Branch; Robert Koch Institute, Burgstr. 37; Wernigerode D-38855 Germany
| | - Sarah Leser
- Wernigerode Branch; Robert Koch Institute, Burgstr. 37; Wernigerode D-38855 Germany
| | - Christine Heider
- Wernigerode Branch; Robert Koch Institute, Burgstr. 37; Wernigerode D-38855 Germany
| | - Magdalena Heindorf
- Wernigerode Branch; Robert Koch Institute, Burgstr. 37; Wernigerode D-38855 Germany
| | - Paul Brauner
- Federal Institute for Occupational Safety and Health (BAuA), Nöldnerstr. 40-42; Berlin D-10317 Germany
| | - Udo Jäckel
- Federal Institute for Occupational Safety and Health (BAuA), Nöldnerstr. 40-42; Berlin D-10317 Germany
| | | | - Christiane Cuny
- Wernigerode Branch; Robert Koch Institute, Burgstr. 37; Wernigerode D-38855 Germany
| | - Andżelina Łopińska
- Faculty of Biological Sciences; University of Zielona Góra, Prof. Z. Szafrana Street 1; 65-561 Zielona Góra Poland
| | - Piotr Kaminski
- Faculty of Biological Sciences; University of Zielona Góra, Prof. Z. Szafrana Street 1; 65-561 Zielona Góra Poland
- Nicolaus Copernicus University in Toruń, Collegium Medicum in Bydgoszcz, Faculty of Medicine; Department of Medical Biology, Department of Ecology and Environmental Protection; M. Skłodowska-Curie St. 9, PL 85-094 Bydgoszcz Poland
| | - Mariusz Kasprzak
- Faculty of Biological Sciences; University of Zielona Góra, Prof. Z. Szafrana Street 1; 65-561 Zielona Góra Poland
| | - Marcin Bochenski
- Faculty of Biological Sciences; University of Zielona Góra, Prof. Z. Szafrana Street 1; 65-561 Zielona Góra Poland
| | - Olaf Ciebiera
- Faculty of Biological Sciences; University of Zielona Góra, Prof. Z. Szafrana Street 1; 65-561 Zielona Góra Poland
| | - Marcin Tobółka
- Institute of Zoology; Poznań University of Life Sciences, Wojska Polskiego 71C; 60-625 Poznań Poland
| | - Katarzyna M. Żołnierowicz
- Institute of Zoology; Poznań University of Life Sciences, Wojska Polskiego 71C; 60-625 Poznań Poland
| | | | - Harald Seifert
- Institute for Medical Microbiology, Immunology and Hygiene; University of Cologne; Cologne D-50935 Germany
- Partner site Bonn-Cologne; German Centre for Infection Research (DZIF); Germany
| | - Stéphanie Gagné
- Laboratory of Molecular Microbiology and Structural Biochemistry; University of Lyon, CNRS UMR 5086; Lyon F-69367 France
| | - Suzana P. Salcedo
- Laboratory of Molecular Microbiology and Structural Biochemistry; University of Lyon, CNRS UMR 5086; Lyon F-69367 France
| | - Michael Kaatz
- Vogelschutzwarte Storchenhof Loburg e.V, Chausseestr. 18; Loburg D-39279 Germany
| | - Franziska Layer
- Wernigerode Branch; Robert Koch Institute, Burgstr. 37; Wernigerode D-38855 Germany
| | - Jennifer K. Bender
- Wernigerode Branch; Robert Koch Institute, Burgstr. 37; Wernigerode D-38855 Germany
| | - Stephan Fuchs
- Wernigerode Branch; Robert Koch Institute, Burgstr. 37; Wernigerode D-38855 Germany
| | | | - Yvonne Pfeifer
- Wernigerode Branch; Robert Koch Institute, Burgstr. 37; Wernigerode D-38855 Germany
| | - Leszek Jerzak
- Faculty of Biological Sciences; University of Zielona Góra, Prof. Z. Szafrana Street 1; 65-561 Zielona Góra Poland
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Gerlach RG, Walter S, McClelland M, Schmidt C, Steglich M, Prager R, Bender JK, Fuchs S, Schoerner C, Rabsch W, Lang W, Jantsch J. Comparative whole genome analysis of three consecutive Salmonella diarizonae isolates. Int J Med Microbiol 2017; 307:542-551. [PMID: 28939438 DOI: 10.1016/j.ijmm.2017.09.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Revised: 07/03/2017] [Accepted: 09/03/2017] [Indexed: 10/18/2022] Open
Abstract
Infections of very young children or immunocompromised people with Salmonella of higher subspecies are a well-known phenomenon often associated with contact to cold-blooded animals. We describe the molecular characterization of three S. enterica subsp. diarizonae strains, isolated consecutively over a period of several months from a hospital patient suffering from diarrhea and sepsis with fatal outcome. With the initial isolate the first complete genome sequence of a member of subsp. diarizonae is provided and based on this reference we revealed the genomic differences between the three isolates by use of next-generation sequencing and confirmed by phenotypical tests. Genome comparisons revealed mutations within gpt, hfq and purK in the first isolate as a sign of clonal variation rather than host-directed evolution. Furthermore, our work demonstrates that S. enterica subsp. diarizonae possess, besides a conserved set of known Salmonella Pathogenicity Islands, a variable portfolio of additional genomic islands of unknown function.
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Affiliation(s)
- Roman G Gerlach
- Project Group 5, Robert Koch Institute, Wernigerode, Germany.
| | - Steffi Walter
- Project Group 5, Robert Koch Institute, Wernigerode, Germany
| | - Michael McClelland
- Department of Microbiology and Molecular Genetics, University of California Irvine, Irvine, CA, USA
| | | | - Matthias Steglich
- Division of Nosocomial Pathogens and Antibiotic Resistances, Department of Infectious Diseases, Robert Koch Institute, Wernigerode, Germany
| | - Rita Prager
- National Reference Centre for Salmonella and other Enteric Bacterial Pathogens and Division of Enteropathogenic Bacteria and Legionella, Department of Infectious Diseases, Robert Koch Institute, Wernigerode, Germany
| | - Jennifer K Bender
- Division of Nosocomial Pathogens and Antibiotic Resistances, Department of Infectious Diseases, Robert Koch Institute, Wernigerode, Germany
| | - Stephan Fuchs
- Division of Nosocomial Pathogens and Antibiotic Resistances, Department of Infectious Diseases, Robert Koch Institute, Wernigerode, Germany
| | - Christoph Schoerner
- Institute of Microbiology - Clinical Microbiology, Immunology and Hygiene, University Hospital Erlangen and Friedrich-Alexander-University of Erlangen-Nuremberg, Erlangen, Germany
| | - Wolfgang Rabsch
- National Reference Centre for Salmonella and other Enteric Bacterial Pathogens and Division of Enteropathogenic Bacteria and Legionella, Department of Infectious Diseases, Robert Koch Institute, Wernigerode, Germany
| | - Werner Lang
- Department of Vascular Surgery, University Hospital Erlangen and Friedrich-Alexander-University of Erlangen-Nuremberg, Erlangen, Germany
| | - Jonathan Jantsch
- Institute of Clinical Microbiology and Hygiene, University Hospital Regensburg and University of Regensburg, Regensburg, Germany
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Hoffmann S, Schmidt C, Walter S, Bender JK, Gerlach RG. Scarless deletion of up to seven methyl-accepting chemotaxis genes with an optimized method highlights key function of CheM in Salmonella Typhimurium. PLoS One 2017; 12:e0172630. [PMID: 28212413 PMCID: PMC5315404 DOI: 10.1371/journal.pone.0172630] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Accepted: 02/07/2017] [Indexed: 11/19/2022] Open
Abstract
Site-directed scarless mutagenesis is an essential tool of modern pathogenesis research. We describe an optimized two-step protocol for genome editing in Salmonella enterica serovar Typhimurium to enable multiple sequential mutagenesis steps in a single strain. The system is based on the λ Red recombinase-catalyzed integration of a selectable antibiotics resistance marker followed by replacement of this cassette. Markerless mutants are selected by expressing the meganuclease I-SceI which induces double-strand breaks in bacteria still harboring the resistance locus. Our new dual-functional plasmid pWRG730 allows for heat-inducible expression of the λ Red recombinase and tet-inducible production of I-SceI. Methyl-accepting chemotaxis proteins (MCP) are transmembrane chemoreceptors for a vast set of environmental signals including amino acids, sugars, ions and oxygen. Based on the sensory input of MCPs, chemotaxis is a key component for Salmonella virulence. To determine the contribution of individual MCPs we sequentially deleted seven MCP genes. The individual mutations were validated by PCR and genetic integrity of the final seven MCP mutant WRG279 was confirmed by whole genome sequencing. The successive MCP mutants were functionally tested in a HeLa cell infection model which revealed increased invasion rates for non-chemotactic mutants and strains lacking the MCP CheM (Tar). The phenotype of WRG279 was reversed with plasmid-based expression of CheM. The complemented WRG279 mutant showed also partially restored chemotaxis in swarming assays on semi-solid agar. Our optimized scarless deletion protocol enables efficient and precise manipulation of the Salmonella genome. As demonstrated with whole genome sequencing, multiple subsequent mutagenesis steps can be realized without the introduction of unwanted mutations. The sequential deletion of seven MCP genes revealed a significant role of CheM for the interaction of S. Typhimurium with host cells which might give new insights into mechanisms of Salmonella host cell sensing.
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Affiliation(s)
| | | | - Steffi Walter
- Project Group 5, Robert Koch Institute, Wernigerode, Germany
| | - Jennifer K. Bender
- Division of Nosocomial Pathogens and Antibiotic Resistances, Department of Infectious Diseases, Robert Koch Institute, Wernigerode, Germany
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Bender JK, Kalmbach A, Fleige C, Klare I, Fuchs S, Werner G. Population structure and acquisition of the vanB resistance determinant in German clinical isolates of Enterococcus faecium ST192. Sci Rep 2016; 6:21847. [PMID: 26902259 PMCID: PMC4763178 DOI: 10.1038/srep21847] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Accepted: 01/29/2016] [Indexed: 12/28/2022] Open
Abstract
In the context of the global action plan to reduce the dissemination of antibiotic resistances it is of utmost importance to understand the population structure of resistant endemic bacterial lineages and to elucidate how bacteria acquire certain resistance determinants. Vancomycin resistant enterococci represent one such example of a prominent nosocomial pathogen on which nation-wide population analyses on prevalent lineages are scarce and data on how the bacteria acquire resistance, especially of the vanB genotype, are still under debate. With respect to Germany, an increased prevalence of VRE was noted in recent years. Here, invasive infections caused by sequence type ST192 VRE are often associated with the vanB-type resistance determinant. Hence, we analyzed 49 vanB-positive and vanB-negative E. faecium isolates by means of whole genome sequencing. Our studies revealed a distinct population structure and that spread of the Tn1549-vanB-type resistance involves exchange of large chromosomal fragments between vanB-positive and vanB-negative enterococci rather than independent acquisition events. In vitro filter-mating experiments support the hypothesis and suggest the presence of certain target sequences as a limiting factor for dissemination of the vanB element. Thus, the present study provides a better understanding of how enterococci emerge into successful multidrug-resistant nosocomial pathogens.
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Affiliation(s)
- Jennifer K Bender
- National Reference Centre for Staphylococci and Enterococci, Robert Koch Institute, Department of Infectious Diseases, Wernigerode, 38855, Germany
| | - Alexander Kalmbach
- National Reference Centre for Staphylococci and Enterococci, Robert Koch Institute, Department of Infectious Diseases, Wernigerode, 38855, Germany
| | - Carola Fleige
- National Reference Centre for Staphylococci and Enterococci, Robert Koch Institute, Department of Infectious Diseases, Wernigerode, 38855, Germany
| | - Ingo Klare
- National Reference Centre for Staphylococci and Enterococci, Robert Koch Institute, Department of Infectious Diseases, Wernigerode, 38855, Germany
| | - Stephan Fuchs
- National Reference Centre for Staphylococci and Enterococci, Robert Koch Institute, Department of Infectious Diseases, Wernigerode, 38855, Germany
| | - Guido Werner
- National Reference Centre for Staphylococci and Enterococci, Robert Koch Institute, Department of Infectious Diseases, Wernigerode, 38855, Germany
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Fiedler S, Bender JK, Klare I, Halbedel S, Grohmann E, Szewzyk U, Werner G. Tigecycline resistance in clinical isolates of Enterococcus faecium is mediated by an upregulation of plasmid-encoded tetracycline determinants tet(L) and tet(M). J Antimicrob Chemother 2015; 71:871-81. [PMID: 26682961 DOI: 10.1093/jac/dkv420] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Accepted: 11/05/2015] [Indexed: 11/12/2022] Open
Abstract
OBJECTIVES Tigecycline represents one of the last-line therapeutics to combat multidrug-resistant bacterial pathogens, including VRE and MRSA. The German National Reference Centre for Staphylococci and Enterococci has received 73 tigecycline-resistant Enterococcus faecium and Enterococcus faecalis isolates in recent years. The precise mechanism of how enterococci become resistant to tigecycline remains undetermined. This study documents an analysis of the role of efflux pumps in tigecycline resistance in clinical isolates of Enterococcus spp. METHODS Various tigecycline MICs were found for the different isolates analysed. Tigecycline-resistant strains were analysed with respect to genome and transcriptome differences by means of WGS and RT-qPCR. Genes of interest were cloned and expressed in Listeria monocytogenes for verification of their functionality. RESULTS Detailed comparative whole-genome analyses of three isogenic strains, showing different levels of tigecycline resistance, revealed the major facilitator superfamily (MFS) efflux pump TetL and the ribosomal protection protein TetM as possible drug resistance proteins. Subsequent RT-qPCR confirmed up-regulation of the respective genes. A correlation of gene copy number and level of MIC was inferred from further qPCR analyses. Expression of both tet(L) and tet(M) in L. monocytogenes unequivocally demonstrated the potential to increase tigecycline MICs upon acquisition of either locus. CONCLUSIONS Our results indicate that increased expression of two tetracycline resistance determinants, a tet(L)-encoded MFS pump and a tet(M)-encoded ribosomal protection protein, is capable of conferring tigecycline resistance in enterococcal clinical isolates.
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Affiliation(s)
- S Fiedler
- Division of Nosocomial Pathogens and Antibiotic Resistances, National Reference Centre for Staphylococci and Enterococci, Department of Infectious Diseases, Robert Koch Institute, Wernigerode Branch, Wernigerode, Germany
| | - J K Bender
- Division of Nosocomial Pathogens and Antibiotic Resistances, National Reference Centre for Staphylococci and Enterococci, Department of Infectious Diseases, Robert Koch Institute, Wernigerode Branch, Wernigerode, Germany
| | - I Klare
- Division of Nosocomial Pathogens and Antibiotic Resistances, National Reference Centre for Staphylococci and Enterococci, Department of Infectious Diseases, Robert Koch Institute, Wernigerode Branch, Wernigerode, Germany
| | - S Halbedel
- Division of Enteropathogenic Bacteria and Legionella, Department of Infectious Diseases, Robert Koch Institute, Wernigerode Branch, Wernigerode, Germany
| | - E Grohmann
- Department of Life Sciences and Technology, Beuth University of Applied Sciences, Berlin, Germany Division of Infectious Diseases, University Medical Centre Freiburg, Freiburg, Germany
| | - U Szewzyk
- Environmental Microbiology, Technical University Berlin, Berlin, Germany
| | - G Werner
- Division of Nosocomial Pathogens and Antibiotic Resistances, National Reference Centre for Staphylococci and Enterococci, Department of Infectious Diseases, Robert Koch Institute, Wernigerode Branch, Wernigerode, Germany
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Werner G, Fleige C, Neumann B, Bender JK, Layer F, Klare I. Evaluation of DiversiLab®, MLST and PFGE typing for discriminating clinical Enterococcus faecium isolates. J Microbiol Methods 2015; 118:81-4. [DOI: 10.1016/j.mimet.2015.08.019] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Revised: 08/24/2015] [Accepted: 08/24/2015] [Indexed: 11/16/2022]
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