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Jati AP, Sola-Campoy PJ, Bosch T, Schouls LM, Hendrickx APA, Bautista V, Lara N, Raangs E, Aracil B, Rossen JWA, Friedrich AW, Navarro Riaza AM, Cañada-García JE, Ramírez de Arellano E, Oteo-Iglesias J, Pérez-Vázquez M, García-Cobos S. Widespread Detection of Yersiniabactin Gene Cluster and Its Encoding Integrative Conjugative Elements (ICE Kp) among Nonoutbreak OXA-48-Producing Klebsiella pneumoniae Clinical Isolates from Spain and the Netherlands. Microbiol Spectr 2023; 11:e0471622. [PMID: 37310221 PMCID: PMC10434048 DOI: 10.1128/spectrum.04716-22] [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: 11/18/2022] [Accepted: 05/22/2023] [Indexed: 06/14/2023] Open
Abstract
In this study, we determined the presence of virulence factors in nonoutbreak, high-risk clones and other isolates belonging to less common sequence types associated with the spread of OXA-48-producing Klebsiella pneumoniae clinical isolates from The Netherlands (n = 61) and Spain (n = 53). Most isolates shared a chromosomally encoded core of virulence factors, including the enterobactin gene cluster, fimbrial fim and mrk gene clusters, and urea metabolism genes (ureAD). We observed a high diversity of K-Locus and K/O loci combinations, KL17 and KL24 (both 16%), and the O1/O2v1 locus (51%) being the most prevalent in our study. The most prevalent accessory virulence factor was the yersiniabactin gene cluster (66.7%). We found seven yersiniabactin lineages-ybt 9, ybt 10, ybt 13, ybt 14, ybt 16, ybt 17, and ybt 27-which were chromosomally embedded in seven integrative conjugative elements (ICEKp): ICEKp3, ICEKp4, ICEKp2, ICEKp5, ICEKp12, ICEKp10, and ICEKp22, respectively. Multidrug-resistant lineages-ST11, ST101, and ST405-were associated with ybt 10/ICEKp4, ybt 9/ICEKp3, and ybt 27/ICEKp22, respectively. The fimbrial adhesin kpi operon (kpiABCDEFG) was predominant among ST14, ST15, and ST405 isolates, as well as the ferric uptake system kfuABC, which was also predominant among ST101 isolates. No convergence of hypervirulence and resistance was observed in this collection of OXA-48-producing K. pneumoniae clinical isolates. Nevertheless, two isolates, ST133 and ST792, were positive for the genotoxin colibactin gene cluster (ICEKp10). In this study, the integrative conjugative element, ICEKp, was the major vehicle for yersiniabactin and colibactin gene clusters spreading. IMPORTANCE Convergence of multidrug resistance and hypervirulence in Klebsiella pneumoniae isolates has been reported mostly related to sporadic cases or small outbreaks. Nevertheless, little is known about the real prevalence of carbapenem-resistant hypervirulent K. pneumoniae since these two phenomena are often separately studied. In this study, we gathered information on the virulent content of nonoutbreak, high-risk clones (i.e., ST11, ST15, and ST405) and other less common STs associated with the spread of OXA-48-producing K. pneumoniae clinical isolates. The study of virulence content in nonoutbreak isolates can help us to expand information on the genomic landscape of virulence factors in K. pneumoniae population by identifying virulence markers and their mechanisms of spread. Surveillance should focus not only on antimicrobial resistance but also on virulence characteristics to avoid the spread of multidrug and (hyper)virulent K. pneumoniae that may cause untreatable and more severe infections.
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Affiliation(s)
- Afif P. Jati
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology and Infection Prevention, Groningen, The Netherlands
- Indonesian Society of Bioinformatics and Biodiversity, Indonesia
| | - Pedro J. Sola-Campoy
- Laboratorio de Referencia e Investigación en Resistencia a Antibióticos e Infecciones Relacionadas con la Asistencia Sanitaria, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Thijs Bosch
- Infectious Diseases Research, Diagnostics and Laboratory Surveillance, Centre for Infectious Disease Control Netherlands, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Leo M. Schouls
- Infectious Diseases Research, Diagnostics and Laboratory Surveillance, Centre for Infectious Disease Control Netherlands, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Antoni P. A. Hendrickx
- Infectious Diseases Research, Diagnostics and Laboratory Surveillance, Centre for Infectious Disease Control Netherlands, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Verónica Bautista
- Laboratorio de Referencia e Investigación en Resistencia a Antibióticos e Infecciones Relacionadas con la Asistencia Sanitaria, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Noelia Lara
- Laboratorio de Referencia e Investigación en Resistencia a Antibióticos e Infecciones Relacionadas con la Asistencia Sanitaria, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Erwin Raangs
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology and Infection Prevention, Groningen, The Netherlands
| | - Belén Aracil
- Laboratorio de Referencia e Investigación en Resistencia a Antibióticos e Infecciones Relacionadas con la Asistencia Sanitaria, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
- CIBER de Enfermedades Infecciosas, Spanish Network for Research in Infectious Diseases, Instituto de Salud Carlos III, Madrid, Spain
| | - John W. A. Rossen
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology and Infection Prevention, Groningen, The Netherlands
- Laboratory of Medical Microbiology and Infectious Diseases, Isala Hospital, Zwolle, The Netherlands
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, Utah, USA
| | - Alex W. Friedrich
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology and Infection Prevention, Groningen, The Netherlands
- University Hospital Münster, Institute of European Prevention Networks in Infection Control, Münster, Germany
| | - Ana M. Navarro Riaza
- Laboratorio de Referencia e Investigación en Resistencia a Antibióticos e Infecciones Relacionadas con la Asistencia Sanitaria, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Javier E. Cañada-García
- Laboratorio de Referencia e Investigación en Resistencia a Antibióticos e Infecciones Relacionadas con la Asistencia Sanitaria, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Eva Ramírez de Arellano
- Laboratorio de Referencia e Investigación en Resistencia a Antibióticos e Infecciones Relacionadas con la Asistencia Sanitaria, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
- CIBER de Enfermedades Infecciosas, Spanish Network for Research in Infectious Diseases, Instituto de Salud Carlos III, Madrid, Spain
| | - Jesús Oteo-Iglesias
- Laboratorio de Referencia e Investigación en Resistencia a Antibióticos e Infecciones Relacionadas con la Asistencia Sanitaria, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
- CIBER de Enfermedades Infecciosas, Spanish Network for Research in Infectious Diseases, Instituto de Salud Carlos III, Madrid, Spain
| | - María Pérez-Vázquez
- Laboratorio de Referencia e Investigación en Resistencia a Antibióticos e Infecciones Relacionadas con la Asistencia Sanitaria, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
- CIBER de Enfermedades Infecciosas, Spanish Network for Research in Infectious Diseases, Instituto de Salud Carlos III, Madrid, Spain
| | - Silvia García-Cobos
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology and Infection Prevention, Groningen, The Netherlands
- Laboratorio de Referencia e Investigación en Resistencia a Antibióticos e Infecciones Relacionadas con la Asistencia Sanitaria, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - The Dutch and Spanish Collaborative Working Groups on Surveillance on Carbapenemase-Producing Enterobacterales
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology and Infection Prevention, Groningen, The Netherlands
- Indonesian Society of Bioinformatics and Biodiversity, Indonesia
- Laboratorio de Referencia e Investigación en Resistencia a Antibióticos e Infecciones Relacionadas con la Asistencia Sanitaria, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
- Infectious Diseases Research, Diagnostics and Laboratory Surveillance, Centre for Infectious Disease Control Netherlands, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
- CIBER de Enfermedades Infecciosas, Spanish Network for Research in Infectious Diseases, Instituto de Salud Carlos III, Madrid, Spain
- Laboratory of Medical Microbiology and Infectious Diseases, Isala Hospital, Zwolle, The Netherlands
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, Utah, USA
- University Hospital Münster, Institute of European Prevention Networks in Infection Control, Münster, Germany
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Cimen C, Berends MS, Bathoorn E, Lokate M, Voss A, Friedrich AW, Glasner C, Hamprecht A. Vancomycin-resistant enterococci (VRE) in hospital settings across European borders: a scoping review comparing the epidemiology in the Netherlands and Germany. Antimicrob Resist Infect Control 2023; 12:78. [PMID: 37568229 PMCID: PMC10422769 DOI: 10.1186/s13756-023-01278-0] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 07/19/2023] [Indexed: 08/13/2023] Open
Abstract
The rising prevalence of vancomycin-resistant enterococci (VRE) is a matter of concern in hospital settings across Europe without a distinct geographical pattern. In this scoping review, we compared the epidemiology of vancomycin-resistant Enterococcus spp. in hospitals in the Netherlands and Germany, between 1991 and 2022. We searched PubMed and summarized the national antibiotic resistance surveillance data of the two countries. We included 46 studies and summarized national surveillance data from the NethMap in the Netherlands, the National Antimicrobial Resistance Surveillance database in Germany, and the EARS-Net data. In total, 12 studies were conducted in hospitals in the Netherlands, 32 were conducted in German hospitals, and an additional two studies were conducted in a cross-border setting. The most significant difference between the two countries was that studies in Germany showed an increasing trend in the prevalence of VRE in hospitals, and no such trend was observed in studies in the Netherlands. Furthermore, in both Dutch and German hospitals, it has been revealed that the molecular epidemiology of VREfm has shifted from a predominance of vanA towards vanB over the years. According to national surveillance reports, vancomycin resistance in Enterococcus faecium clinical isolates fluctuates below 1% in Dutch hospitals, whereas it follows an increasing trend in German hospitals (above 20%), as supported by individual studies. This review demonstrates that VRE is more frequently encountered in German than in Dutch hospitals and discusses the underlying factors for the difference in VRE occurrence in these two neighboring countries by comparing differences in healthcare systems, infection prevention control (IPC) guidelines, and antibiotic use in the Netherlands and Germany.
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Affiliation(s)
- Cansu Cimen
- Institute for Medical Microbiology and Virology, University of Oldenburg, Oldenburg, Germany
- Department of Medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Matthijs S Berends
- Department of Medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
- Department of Medical Epidemiology, Certe Medical Diagnostics and Advice Foundation, Groningen, The Netherlands
| | - Erik Bathoorn
- 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
| | - Andreas Voss
- Department of Medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Alex W Friedrich
- Department of Medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
- University Hospital Muenster, University of Muenster, Muenster, Germany
| | - Corinna Glasner
- Department of Medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.
| | - Axel Hamprecht
- Institute for Medical Microbiology and Virology, University of Oldenburg, Oldenburg, Germany
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Luz CF, Berends MS, Zhou X, Lokate M, Friedrich AW, Sinha B, Glasner C. Better antimicrobial resistance data analysis and reporting in less time. JAC Antimicrob Resist 2023; 5:dlac143. [PMID: 36686270 PMCID: PMC9847555 DOI: 10.1093/jacamr/dlac143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 12/21/2022] [Indexed: 01/19/2023] Open
Abstract
Objectives Insights about local antimicrobial resistance (AMR) levels and epidemiology are essential to guide decision-making processes in antimicrobial use. However, dedicated tools for reliable and reproducible AMR data analysis and reporting are often lacking. We aimed to compare traditional data analysis and reporting versus a new approach for reliable and reproducible AMR data analysis in a clinical setting. Methods Ten professionals who routinely work with AMR data were provided with blood culture test results including antimicrobial susceptibility results. Participants were asked to perform a detailed AMR data analysis in a two-round process: first using their software of choice and next using our newly developed software tool. Accuracy of the results and time spent were compared between both rounds. Finally, participants rated the usability using the System Usability Scale (SUS). Results The mean time spent on creating the AMR report reduced from 93.7 to 22.4 min (P < 0.001). Average task completion per round changed from 56% to 96% (P < 0.05). The proportion of correct answers in the available results increased from 37.9% in the first to 97.9% in the second round (P < 0.001). Usability of the new tools was rated with a median of 83.8 (out of 100) on the SUS. Conclusions This study demonstrated the significant improvement in efficiency and accuracy in standard AMR data analysis and reporting workflows through open-source software. Integrating these tools in clinical settings can democratize the access to fast and reliable insights about local microbial epidemiology and associated AMR levels. Thereby, our approach can support evidence-based decision-making processes in the use of antimicrobials.
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Affiliation(s)
| | | | - Xuewei Zhou
- Department of Medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, Hanzeplein 1, 9713 GZ, Groningen, Netherlands
| | - Mariëtte Lokate
- Department of Medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, Hanzeplein 1, 9713 GZ, Groningen, Netherlands
| | - Alex W Friedrich
- Department of Medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, Hanzeplein 1, 9713 GZ, Groningen, Netherlands
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Stolberg-Stolberg J, Jacob E, Kuehn J, Hennies M, Hafezi W, Freistuehler M, Koeppe J, Friedrich AW, Katthagen JC, Raschke MJ. COVID-19 rapid molecular point-of-care testing is effective and cost-beneficial for the acute care of trauma patients. Eur J Trauma Emerg Surg 2023; 49:487-493. [PMID: 36066585 PMCID: PMC9447950 DOI: 10.1007/s00068-022-02091-x] [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] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Accepted: 08/16/2022] [Indexed: 11/25/2022]
Abstract
PURPOSE To evaluate the accuracy and cost benefit of a rapid molecular point-of-care testing (POCT) device detecting COVID-19 within a traumatological emergency department. BACKGROUND Despite continuous withdrawal of COVID-19 restrictions, hospitals will remain particularly vulnerable to local outbreaks which is reflected by a higher institution-specific basic reproduction rate. Patients admitted to the emergency department with unknown COVID-19 infection status due to a- or oligosymptomatic COVID-19 infection put other patients and health care workers at risk, while fast diagnosis and treatment is necessary. Delayed testing results in additional costs to the health care system. METHODS From the 8th of April 2021 until 31st of December 2021, all patients admitted to the emergency department were tested with routine RT-PCR and rapid molecular POCT device (Abbott ID NOW™ COVID-19). COVID-19-related additional costs for patients admitted via shock room or emergency department were calculated based on internal cost allocations. RESULTS 1133 rapid molecular tests resulted in a sensitivity of 83.3% (95% CI 35.9-99.6%), specificity of 99.8% (95% CI 99.4-100%), a positive predictive value of 71.4% (95% CI 29-96.3%) and a negative predictive value of 99.9% (95% CI 99.5-100%) as compared to RT-PCR. Without rapid COVID-19 testing, each emergency department and shock room admission with subsequent surgery showed additional direct costs of 2631.25€, without surgery of 729.01€. CONCLUSION Although rapid molecular COVID-19 testing can initially be more expensive than RT-PCR, subsequent cost savings, improved workflows and workforce protection outweigh this effect by far. The data of this study support the use of a rapid molecular POCT device in a traumatological emergency department.
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Affiliation(s)
- Josef Stolberg-Stolberg
- Department of Trauma, Hand and Reconstructive Surgery, University Hospital Muenster, Albert-Schweitzer-Campus 1, Building W1, 48149, Muenster, Germany.
| | - Elena Jacob
- Department of Trauma, Hand and Reconstructive Surgery, University Hospital Muenster, Albert-Schweitzer-Campus 1, Building W1, 48149, Muenster, Germany
| | - Joachim Kuehn
- Department of Clinical Virology, Institute of Virology, University Hospital Muenster, 48149, Muenster, Germany
| | - Marc Hennies
- Department of Clinical Virology, Institute of Virology, University Hospital Muenster, 48149, Muenster, Germany
| | - Wali Hafezi
- Department of Clinical Virology, Institute of Virology, University Hospital Muenster, 48149, Muenster, Germany
| | - Moritz Freistuehler
- Medical Management Division-Medical Controlling, University Hospital Muenster, Niels-Stensen-Straße 8, 48149, Muenster, Germany
| | - Jeanette Koeppe
- Institute of Biostatistics and Clinical Research, University of Muenster, Schmeddingstrasse 56, 48149, Muenster, Germany
| | - Alex W Friedrich
- Medical Executive Board, University Hospital Muenster, Albert-Schweitzer-Campus 1, Building D5, 48149, Muenster, Germany
| | - J Christoph Katthagen
- Department of Trauma, Hand and Reconstructive Surgery, University Hospital Muenster, Albert-Schweitzer-Campus 1, Building W1, 48149, Muenster, Germany
| | - Michael J Raschke
- Department of Trauma, Hand and Reconstructive Surgery, University Hospital Muenster, Albert-Schweitzer-Campus 1, Building W1, 48149, Muenster, Germany
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5
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Raineri EJM, Maaß S, Wang M, Brushett S, Palma Medina LM, Sampol Escandell N, Altulea D, Raangs E, de Jong A, Vera Murguia E, Feil EJ, Friedrich AW, Buist G, Becher D, García-Cobos S, Couto N, van Dijl JM. Staphylococcus aureus populations from the gut and the blood are not distinguished by virulence traits-a critical role of host barrier integrity. Microbiome 2022; 10:239. [PMID: 36567349 PMCID: PMC9791742 DOI: 10.1186/s40168-022-01419-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 11/09/2022] [Indexed: 06/17/2023]
Abstract
BACKGROUND The opportunistic pathogen Staphylococcus aureus is an asymptomatically carried member of the microbiome of about one third of the human population at any given point in time. Body sites known to harbor S. aureus are the skin, nasopharynx, and gut. In particular, the mechanisms allowing S. aureus to pass the gut epithelial barrier and to invade the bloodstream were so far poorly understood. Therefore, the objective of our present study was to investigate the extent to which genetic differences between enteric S. aureus isolates and isolates that caused serious bloodstream infections contribute to the likelihood of invasive disease. RESULTS Here, we present genome-wide association studies (GWAS) that compare the genome sequences of 69 S. aureus isolates from enteric carriage by healthy volunteers and 95 isolates from bloodstream infections. We complement our GWAS results with a detailed characterization of the cellular and extracellular proteomes of the representative gut and bloodstream isolates, and by assaying the virulence of these isolates with infection models based on human gut epithelial cells, human blood cells, and a small animal infection model. Intriguingly, our results show that enteric and bloodstream isolates with the same sequence type (ST1 or ST5) are very similar to each other at the genomic and proteomic levels. Nonetheless, bloodstream isolates are not necessarily associated with an invasive profile. Furthermore, we show that the main decisive factor preventing infection of gut epithelial cells in vitro is the presence of a tight barrier. CONCLUSIONS Our data show that virulence is a highly variable trait, even within a single clone. Importantly, however, there is no evidence that blood stream isolates possess a higher virulence potential than those from the enteric carriage. In fact, some gut isolates from healthy carriers were more virulent than bloodstream isolates. Based on our present observations, we propose that the integrity of the gut epithelial layer, rather than the pathogenic potential of the investigated enteric S. aureus isolates, determines whether staphylococci from the gut microbiome will become invasive pathogens. Video Abstract.
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Affiliation(s)
- Elisa J. M. Raineri
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Sandra Maaß
- Department of Microbial Proteomics, Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Min Wang
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Siobhan Brushett
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Laura M. Palma Medina
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
- Present address: Department of Medicine Huddinge, Present Address: Center for Infectious Medicine, Karolinska Institute, Huddinge, Sweden
| | - Neus Sampol Escandell
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Dania Altulea
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
- Present address: Division of Nephrology, Department of Internal Medicine, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Erwin Raangs
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Anne de Jong
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
| | - Elias Vera Murguia
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Edward J. Feil
- Department of Biology and Biochemistry, The Milner Centre for Evolution, University of Bath, Bath, UK
| | - Alex W. Friedrich
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Girbe Buist
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Dörte Becher
- Department of Microbial Proteomics, Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Silvia García-Cobos
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
- Present address: Reference and Research Laboratory On Antimicrobial Resistance and Healthcare Associated Infections, Centro Nacional de Microbiología, Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - Natacha Couto
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
- Department of Biology and Biochemistry, The Milner Centre for Evolution, University of Bath, Bath, UK
| | - Jan Maarten van Dijl
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
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6
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Righi E, Mutters NT, Guirao X, Del Toro MD, Eckmann C, Friedrich AW, Giannella M, Kluytmans J, Presterl E, Christaki E, Cross ELA, Visentin A, Sganga G, Tsioutis C, Tacconelli E. ESCMID/EUCIC clinical practice guidelines on perioperative antibiotic prophylaxis in patients colonized by multidrug-resistant Gram-negative bacteria before surgery. Clin Microbiol Infect 2022; 29:463-479. [PMID: 36566836 DOI: 10.1016/j.cmi.2022.12.012] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [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: 09/12/2022] [Revised: 12/10/2022] [Accepted: 12/11/2022] [Indexed: 12/24/2022]
Abstract
SCOPE The aim of the guidelines is to provide recommendations on perioperative antibiotic prophylaxis (PAP) in adult inpatients who are carriers of multidrug-resistant Gram-negative bacteria (MDR-GNB) before surgery. METHODS These evidence-based guidelines were developed after a systematic review of published studies on PAP targeting the following MDR-GNB: extended-spectrum cephalosporin-resistant Enterobacterales, carbapenem-resistant Enterobacterales (CRE), aminoglycoside-resistant Enterobacterales, fluoroquinolone-resistant Enterobacterales, cotrimoxazole-resistant Stenotrophomonas maltophilia, carbapenem-resistant Acinetobacter baumannii (CRAB), extremely drug-resistant Pseudomonas aeruginosa, colistin-resistant Gram-negative bacteria, and pan-drug-resistant Gram-negative bacteria. The critical outcomes were the occurrence of surgical site infections (SSIs) caused by any bacteria and/or by the colonizing MDR-GNB, and SSI-attributable mortality. Important outcomes included the occurrence of any type of postsurgical infectious complication, all-cause mortality, and adverse events of PAP, including development of resistance to targeted (culture-based) PAP after surgery and incidence of Clostridioides difficile infections. The last search of all databases was performed until April 30, 2022. The level of evidence and strength of each recommendation were defined according to the Grading of Recommendations Assessment, Development and Evaluation approach. Consensus of a multidisciplinary expert panel was reached for the final list of recommendations. Antimicrobial stewardship considerations were included in the recommendation development. RECOMMENDATIONS The guideline panel reviewed the evidence, per bacteria, of the risk of SSIs in patients colonized with MDR-GNB before surgery and critically appraised the existing studies. Significant knowledge gaps were identified, and most questions were addressed by observational studies. Moderate to high risk of bias was identified in the retrieved studies, and the majority of the recommendations were supported by low level of evidence. The panel conditionally recommends rectal screening and targeted PAP for fluoroquinolone-resistant Enterobacterales before transrectal ultrasound-guided prostate biopsy and for extended-spectrum cephalosporin-resistant Enterobacterales in patients undergoing colorectal surgery and solid organ transplantation. Screening for CRE and CRAB is suggested before transplant surgery after assessment of the local epidemiology. Careful consideration of the laboratory workload and involvement of antimicrobial stewardship teams before implementing the screening procedures or performing changes in PAP are warranted. High-quality prospective studies to assess the impact of PAP among CRE and CRAB carriers performing high-risk surgeries are advocated. Future well-designed clinical trials should assess the effectiveness of targeted PAP, including the monitoring of MDR-GNB colonization through postoperative cultures using European Committee on Antimicrobial Susceptibility Testing clinical breakpoints.
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Affiliation(s)
- Elda Righi
- Division of Infectious Diseases, Department of Diagnostics and Public Health, University of Verona, Verona, Italy
| | - Nico T Mutters
- University Hospital Bonn, Institute for Hygiene and Public Health, Bonn, Germany
| | - Xavier Guirao
- Surgical Endocrine Unit, Department of General Surgery, Surgical Site Prevention Unit, Parc Tauli, Hospital Universitari Sabadell, Spain
| | - Maria Dolores Del Toro
- Division of Infectious Diseases and Microbiology, University Hospital Virgen Macarena, Seville, Spain; Department of Medicine, University of Sevilla. Biomedicine Institute of Sevilla, Seville, Spain; Centro de Investigación Biomédica en Red en Enfermedades Infecciosas, Spain
| | - Christian Eckmann
- Klinikum Hannoversch-Muenden, Academic Hospital of Goettingen University, Germany
| | - Alex W Friedrich
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology and Infection Prevention, Groningen, the Netherlands; Institute for European Prevention Networks in Infection Control, University Hospital Münster, Münster, Germany
| | - Maddalena Giannella
- Infectious Diseases Unit, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Azienda Ospedaliero Universitaria di Bologna, Bologna, Italy; Department of Medical and Surgical Sciences, University of Bologna, Italy
| | - Jan Kluytmans
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht University, the Netherlands
| | - Elisabeth Presterl
- Department of Infection Control and Hospital Epidemiology, Medical University of Vienna, Vienna, Austria
| | - Eirini Christaki
- Department of Internal Medicine, Faculty of Medicine, School of Health Sciences, University of Ioannina, Ioannina, Greece
| | - Elizabeth L A Cross
- Department of Global Health and Infection, Brighton and Sussex Medical School, Brighton, United Kingdom
| | - Alessandro Visentin
- Division of Infectious Diseases, Department of Diagnostics and Public Health, University of Verona, Verona, Italy
| | - Gabriele Sganga
- Emergency Surgery and Trauma, Fondazione Policlinico Universitario A. Gemelli IRCCS, Università Cattolica del Sacro Cuore, Rome, Italy
| | | | - Evelina Tacconelli
- Division of Infectious Diseases, Department of Diagnostics and Public Health, University of Verona, Verona, Italy; Division of Infectious Diseases, Department of Internal Medicine I, University of Tübingen, Tübingen, Germany.
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7
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Tami A, van der Gun BTF, Wold KI, Vincenti-González MF, Veloo ACM, Knoester M, Harmsma VPR, de Boer GC, Huckriede ALW, Pantano D, Gard L, Rodenhuis-Zybert IA, Upasani V, Smit J, Dijkstra AE, de Haan JJ, van Elst JM, van den Boogaard J, O’ Boyle S, Nacul L, Niesters HGM, Friedrich AW. The COVID HOME study research protocol: Prospective cohort study of non-hospitalised COVID-19 patients. PLoS One 2022; 17:e0273599. [PMID: 36327223 PMCID: PMC9632784 DOI: 10.1371/journal.pone.0273599] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 09/05/2022] [Indexed: 11/06/2022] Open
Abstract
BACKGROUND Guidelines on COVID-19 management are developed as we learn from this pandemic. However, most research has been done on hospitalised patients and the impact of the disease on non-hospitalised and their role in transmission are not yet well understood. The COVID HOME study conducts research among COVID-19 patients and their family members who were not hospitalised during acute disease, to guide patient care and inform public health guidelines for infection prevention and control in the community and household. METHODS An ongoing prospective longitudinal observational study of COVID-19 outpatients was established in March 2020 at the beginning of the COVID-19 pandemic in the Netherlands. Laboratory confirmed SARS-CoV-2 infected individuals of all ages that did not merit hospitalisation, and their household (HH) members, were enrolled after written informed consent. Enrolled participants were visited at home within 48 hours after initial diagnosis, and then weekly on days 7, 14 and 21 to obtain clinical data, a blood sample for biochemical parameters/cytokines and serological determination; and a nasopharyngeal/throat swab plus urine, stool and sperm or vaginal secretion (if consenting) to test for SARS-CoV-2 by RT-PCR (viral shedding) and for viral culturing. Weekly nasopharyngeal/throat swabs and stool samples, plus a blood sample on days 0 and 21 were also taken from HH members to determine whether and when they became infected. All participants were invited to continue follow-up at 3-, 6-, 12- and 18-months post-infection to assess long-term sequelae and immunological status.
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Affiliation(s)
- Adriana Tami
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Bernardina T. F. van der Gun
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Karin I. Wold
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - María F. Vincenti-González
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Alida C. M. Veloo
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Marjolein Knoester
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Valerie P. R. Harmsma
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Gerolf C. de Boer
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Anke L. W. Huckriede
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Daniele Pantano
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Lilli Gard
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Izabela A. Rodenhuis-Zybert
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Vinit Upasani
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Jolanda Smit
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Akkelies E. Dijkstra
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Jacco J. de Haan
- Department of Medical Oncology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Jip M. van Elst
- Department of Medical Oncology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | | | - Shennae O’ Boyle
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Luis Nacul
- Department of Clinical Research, Faculty of Medicine and London School of Hygiene and Tropical Medicine, University of British Columbia, Vancouver, Canada
| | - Hubert G. M. Niesters
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Alex W. Friedrich
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
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8
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Tacconelli E, Gorska A, Carrara E, Davis RJ, Bonten M, Friedrich AW, Glasner C, Goossens H, Hasenauer J, Abad JMH, Peñalvo JL, Sanchez-Niubo A, Sialm A, Scipione G, Soriano G, Yazdanpanah Y, Vorstenbosch E, Jaenisch T. Challenges of data sharing in European Covid-19 projects: A learning opportunity for advancing pandemic preparedness and response. Lancet Reg Health Eur 2022; 21:100467. [PMID: 35942201 PMCID: PMC9351292 DOI: 10.1016/j.lanepe.2022.100467] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
The COVID-19 pandemic saw a massive investment into collaborative research projects with a focus on producing data to support public health decisions. We relay our direct experience of four projects funded under the Horizon2020 programme, namely ReCoDID, ORCHESTRA, unCoVer and SYNCHROS. The projects provide insight into the complexities of sharing patient level data from observational cohorts. We focus on compliance with the General Data Protection Regulation (GDPR) and ethics approvals when sharing data across national borders. We discuss procedures for data mapping; submission of new international codes to standards organisation; federated approach; and centralised data curation. Finally, we put forward recommendations for the development of guidelines for the application of GDPR in case of major public health threats; mandatory standards for data collection in funding frameworks; training and capacity building for data owners; cataloguing of international use of metadata standards; and dedicated funding for identified critical areas.
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9
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van der Pol S, Jansen DEMC, van der Velden AW, Butler CC, Verheij TJM, Friedrich AW, Postma MJ, van Asselt ADI. The Opportunity of Point-of-Care Diagnostics in General Practice: Modelling the Effects on Antimicrobial Resistance. Pharmacoeconomics 2022; 40:823-833. [PMID: 35764913 PMCID: PMC9243781 DOI: 10.1007/s40273-022-01165-3] [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] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Accepted: 05/29/2022] [Indexed: 06/15/2023]
Abstract
OBJECTIVES Antimicrobial resistance (AMR) is a public health threat associated with antibiotic consumption. Community-acquired acute respiratory tract infections (CA-ARTIs) are a major driver of antibiotic consumption in primary care. We aimed to quantify the investments required for a large-scale rollout of point-of care (POC) diagnostic testing in Dutch primary care, and the impact on AMR due to reduced use of antibiotics. METHODS We developed an individual-based model that simulates consultations for CA-ARTI at GP practices in the Netherlands and compared a scenario where GPs test all CA-ARTI patients with a hypothetical diagnostic strategy to continuing the current standard-of-care for the years 2020-2030. We estimated differences in costs and future AMR rates caused by testing all patients consulting for CA-ARTI with a hypothetical diagnostic strategy, compared to the current standard-of-care in GP practices. RESULTS Compared to the current standard-of-care, the diagnostic algorithm increases the total costs of GP consultations for CA-ARTI by 9% and 19%, when priced at €5 and €10, respectively. The forecast increase in Streptococcus pneumoniae resistance against penicillins can be partly restrained by the hypothetical diagnostic strategy from 3.8 to 3.5% in 2030, albeit with considerable uncertainty. CONCLUSIONS Our results show that implementing a hypothetical diagnostic strategy for all CA-ARTI patients in primary care raises the costs of consultations, while lowering antibiotic consumption and AMR. Novel health-economic methods to assess and communicate the potential benefits related to AMR may be required for interventions with limited gains for individual patients, but considerable potential related to antibiotic consumption and AMR.
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Affiliation(s)
- Simon van der Pol
- Department of Health Sciences, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands.
- Health-Ecore, Zeist, The Netherlands.
| | - Danielle E M C Jansen
- Department of General Practice and Elderly Care Medicine, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
- Department of Sociology, Interuniversity Center for Social Science Theory and Methodology (ICS), University of Groningen, Groningen, The Netherlands
| | - Alike W van der Velden
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Christopher C Butler
- Nuffield Department of Primary Care and Public Health, School of Medicine, Cardiff Sciences, University, Cardiff of Oxford, Oxford, UK
| | - Theo J M Verheij
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Alex W Friedrich
- Department of Medical Microbiology and Infection Control, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
- Institute of European Prevention Networks in Infection Control, University Hospital Münster, Münster, Germany
| | - Maarten J Postma
- Department of Health Sciences, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
- Health-Ecore, Zeist, The Netherlands
- Department of Economics, Econometrics and Finance, University of Groningen, Groningen, The Netherlands
| | - Antoinette D I van Asselt
- Department of Health Sciences, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
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10
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Blanford JI, Jong NBD, Schouten SE, Friedrich AW, Araújo-Soares V. Navigating travel in Europe during the pandemic: from mobile apps, certificates and quarantine to traffic-light system. J Travel Med 2022; 29:6520892. [PMID: 35134215 PMCID: PMC9155998 DOI: 10.1093/jtm/taac006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 12/14/2021] [Accepted: 01/26/2022] [Indexed: 11/21/2022]
Abstract
BACKGROUND Ever since 2020, travelling has become complex, and increasingly so as the COVID-19 pandemic continues. To reopen Europe safely, a consensus of travel measures has been agreed between countries to enable movement between countries with as few restrictions as possible. However, communication of these travel measures and requirements for entry are not always clear and easily available. The aim of this study was to assess the availability, accessibility and harmonization of current travel information available in Europe. METHODS We performed a systematic documental analysis of online publicly available information and synthesized travel entry requirements for all countries in the European Union and Schengen Area (N = 31). For each country we assessed entry requirements, actions after entry, how risk was assessed, and how accessible the information was. RESULTS We found varying measures implemented across Europe for entry and a range of exemptions and restrictions, some of which were consistent between countries. Information was not always easy to find taking on average 10 clicks to locate. Twenty-one countries required pre-travel forms to be completed. Forty apps were in use, 11 serving as digital certification checkers. All countries required some form of COVID-19 certification for entry with some exemptions (e.g. children). Nineteen percent (n = 6) of countries used the ECDC risk assessment system; 80% (n = 25) defined their own. Forty-eight percent (n = 15) of countries used a traffic-light system with 2-5 risk classifications. CONCLUSION A comprehensive set of measures has been developed to enable continued safe travel in Europe. However further refinements and coordination is needed to align travel measures throughout the EU to minimize confusion and maximize adherence to requested measures. We recommend that, along with developing travel measures based on a common set of rules, a standard approach is taken to communicate what these measures are.
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Affiliation(s)
- Justine I Blanford
- Faculty of Geoinformation Science and Earth Observation, University of Twente, Enschede, the Netherlands
| | - Nienke Beerlage-de Jong
- Section of Health Technology and Services Research, Technical Medical Centre, University of Twente, Enschede, the Netherlands
| | - Stephanie E Schouten
- Section of Health Technology and Services Research, Technical Medical Centre, University of Twente, Enschede, the Netherlands
| | - Alex W Friedrich
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, Groningen, the Netherlands
| | - Vera Araújo-Soares
- Section of Health Technology and Services Research, Technical Medical Centre, University of Twente, Enschede, the Netherlands
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11
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Glasner C, Berends MS, Becker K, Esser J, Gieffers J, Jurke A, Kampinga G, Kampmeier S, Klont R, Köck R, von Müller L, Al Naemi N, Ott A, Ruijs G, Saris K, Tami A, Voss A, Waar K, van Zeijl J, Friedrich AW. A prospective multicentre screening study on multidrug-resistant organisms in intensive care units in the Dutch-German cross-border region, 2017 to 2018: the importance of healthcare structures. Euro Surveill 2022; 27. [PMID: 35115078 PMCID: PMC8815100 DOI: 10.2807/1560-7917.es.2022.27.5.2001660] [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] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Background Antimicrobial resistance poses a risk for healthcare, both in the community and hospitals. The spread of multidrug-resistant organisms (MDROs) occurs mostly on a local and regional level, following movement of patients, but also occurs across national borders. Aim The aim of this observational study was to determine the prevalence of MDROs in a European cross-border region to understand differences and improve infection prevention based on real-time routine data and workflows. Methods Between September 2017 and June 2018, 23 hospitals in the Dutch (NL)–German (DE) cross-border region (BR) participated in the study. During 8 consecutive weeks, patients were screened upon admission to intensive care units (ICUs) for nasal carriage of meticillin-resistant Staphylococcus aureus (MRSA) and rectal carriage of vancomycin-resistant Enterococcus faecium/E. faecalis (VRE), third-generation cephalosporin-resistant Enterobacteriaceae (3GCRE) and carbapenem-resistant Enterobacteriaceae (CRE). All samples were processed in the associated laboratories. Results A total of 3,365 patients were screened (median age: 68 years (IQR: 57–77); male/female ratio: 59.7/40.3; NL-BR: n = 1,202; DE-BR: n = 2,163). Median screening compliance was 60.4% (NL-BR: 56.9%; DE-BR: 62.9%). MDRO prevalence was higher in DE-BR than in NL-BR, namely 1.7% vs 0.6% for MRSA (p = 0.006), 2.7% vs 0.1% for VRE (p < 0.001) and 6.6% vs 3.6% for 3GCRE (p < 0.001), whereas CRE prevalence was comparable (0.2% in DE-BR vs 0.0% in NL-BR ICUs). Conclusions This first prospective multicentre screening study in a European cross-border region shows high heterogenicity in MDRO carriage prevalence in NL-BR and DE-BR ICUs. This indicates that the prevalence is probably influenced by the different healthcare structures.
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Affiliation(s)
- Corinna Glasner
- Department of Medical Microbiology and Infection Control, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Matthijs S Berends
- Department of Medical Microbiology and Infection Control, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.,Certe Medical Diagnostics and Advice Foundation, Groningen, the Netherlands
| | - Karsten Becker
- Institute of Medical Microbiology, University Hospital Münster, Münster, Germany.,Friedrich Loeffler-Institute of Medical Microbiology, University Medicine Greifswald, Greifswald, Germany
| | - Jutta Esser
- Practice of Laboratory Medicine and University Osnabrück, Department of Dermatology, Environmental Medicine and Health Theory, Osnabrück, Germany
| | - Jens Gieffers
- Institute for Microbiology, Hygiene and Laboratory Medicine, Klinikum Lippe, Detmold, Germany
| | - Annette Jurke
- North Rhine-Westphalian Centre for Health, Section Infectious Disease Epidemiology, Bochum, Germany
| | - Greetje Kampinga
- Department of Medical Microbiology and Infection Control, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | | | - Rob Klont
- Laboratory Microbiology Twente Achterhoek, Hengelo, the Netherlands
| | - Robin Köck
- Institute of Hygiene, DRK Kliniken Berlin, Berlin, Germany.,Institute of Hygiene, University Hospital Münster, Münster, Germany
| | - Lutz von Müller
- Institute for Laboratory Medicine, Microbiology and Hygiene, Christophorus-Kliniken GmbH, Coesfeld, Germany
| | - Nashwan Al Naemi
- Laboratory Microbiology Twente Achterhoek, Hengelo, the Netherlands
| | - Alewijn Ott
- Certe Medical Diagnostics and Advice Foundation, Groningen, the Netherlands
| | - Gijs Ruijs
- Laboratory for Medical Microbiology and Infectious Diseases, Isala, Zwolle, the Netherlands
| | - Katja Saris
- Department of Medical Microbiology, Radboud University Medical Centre and Canisius-Wilhelmina Hospital, Nijmegen, the Netherlands
| | - Adriana Tami
- Department of Medical Microbiology and Infection Control, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Andreas Voss
- Department of Medical Microbiology, Radboud University Medical Centre and Canisius-Wilhelmina Hospital, Nijmegen, the Netherlands
| | - Karola Waar
- Izore, Centre for Infectious Diseases Friesland, Leeuwarden, the Netherlands.,Certe Medical Diagnostics and Advice Foundation, Groningen, the Netherlands
| | - Jan van Zeijl
- Izore, Centre for Infectious Diseases Friesland, Leeuwarden, the Netherlands.,Certe Medical Diagnostics and Advice Foundation, Groningen, the Netherlands
| | - Alex W Friedrich
- Department of Medical Microbiology and Infection Control, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.,European Prevention Networks in Infection Control, University Hospital Münster, Münster, Germany
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12
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Cassidy H, Schuele L, Lizarazo-Forero E, Couto N, Rossen JWA, Friedrich AW, van Leer-Buter C, Niesters HGM. OUP accepted manuscript. Virus Evol 2022; 8:veab109. [PMID: 35317350 PMCID: PMC8932292 DOI: 10.1093/ve/veab109] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 12/16/2021] [Accepted: 02/16/2022] [Indexed: 11/12/2022] Open
Abstract
Chronic enterovirus infections can cause significant morbidity, particularly in immunocompromised patients. This study describes a fatal case associated with a chronic untypeable enterovirus infection in an immunocompromised patient admitted to a Dutch university hospital over nine months. We aimed to identify the enterovirus genotype responsible for the infection and to determine potential evolutionary changes. Long-read sequencing was performed using viral targeted sequence capture on four respiratory and one faecal sample. Phylogenetic analysis was performed using a maximum likelihood method, along with a root-to-tip regression and time-scaled phylogenetic analysis to estimate evolutionary changes between sample dates. Intra-host variant detection, using a Fixed Ploidy algorithm, and selection pressure, using a Fixed Effect Likelihood and a Mixed Effects Model of Evolution, were also used to explore the patient samples. Near-complete genomes of enterovirus C104 (EV-C104) were recovered in all respiratory samples but not in the faecal sample. The recovered genomes clustered with a recently reported EV-C104 from Belgium in August 2018. Phylodynamic analysis including ten available EV-C104 genomes, along with the patient sequences, estimated the most recent common ancestor to occur in the middle of 2005 with an overall estimated evolution rate of 2.97 × 10−3 substitutions per year. Although positive selection pressure was identified in the EV-C104 reference sequences, the genomes recovered from the patient samples alone showed an overall negative selection pressure in multiple codon sites along the genome. A chronic infection resulting in respiratory failure from a relatively rare enterovirus was observed in a transplant recipient. We observed an increase in single-nucleotide variations between sample dates from a rapidly declining patient, suggesting mutations are weakly deleterious and have not been purged during selection. This is further supported by the persistence of EV-C104 in the patient, despite the clearance of other viral infections. Next-generation sequencing with viral enrichment could be used to detect and characterise challenging samples when conventional workflows are insufficient.
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Affiliation(s)
| | | | - Erley Lizarazo-Forero
- Department of Medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, Hanzeplein 1, Groningen 9713 GZ, The Netherlands
| | - Natacha Couto
- Department of Medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, Hanzeplein 1, Groningen 9713 GZ, The Netherlands
- Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath BA2 7AY, UK
| | - John W A Rossen
- Department of Medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, Hanzeplein 1, Groningen 9713 GZ, The Netherlands
- Department of Pathology, University of Utah School of Medicine, 15 North Medical Drive East, Salt Lake City, UT 84112, USA
| | - Alex W Friedrich
- Department of Medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, Hanzeplein 1, Groningen 9713 GZ, The Netherlands
| | - Coretta van Leer-Buter
- Department of Medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, Hanzeplein 1, Groningen 9713 GZ, The Netherlands
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13
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Sadok N, Tiwow ID, Roo-Brand G, Friedrich AW, Werker PM. The Effect of Extra Safety Measures on Incidence of Surgical Site Infection After Alloplastic Breast Reconstruction. J Plast Reconstr Aesthet Surg 2022; 75:2197-2204. [DOI: 10.1016/j.bjps.2022.01.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 11/27/2021] [Accepted: 01/09/2022] [Indexed: 10/19/2022]
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14
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Chisari E, Wouthuyzen-Bakker M, Friedrich AW, Parvizi J. The relation between the gut microbiome and osteoarthritis: A systematic review of literature. PLoS One 2021; 16:e0261353. [PMID: 34914764 PMCID: PMC8675674 DOI: 10.1371/journal.pone.0261353] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [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: 07/07/2021] [Accepted: 11/30/2021] [Indexed: 02/07/2023] Open
Abstract
Background Along with mechanical and genetic factors, emerging evidence suggests that the presence of low-grade inflammation has a role in the pathogenesis of osteoarthritis (OA) and seems to be related to the microbiome composition of the gut. Purpose To provide evidence whether there is clinical or preclinical evidence of gut-joint axis in the pathogenesis and symptoms of OA. Methods An extensive review of the current literature was performed using three different databases. Human, as well as animal studies, were included. The risk of bias was identified using ROBINS and SYRCLE tools, while the quality of evidence was assessed using GRADE and CAMADARES criteria. Results A total of nineteen articles were included. Multiple animal studies demonstrated that both obesity, and high-fat and high-sugar diets resulted in a gut dysbiosis status characterized by increased Firmicutes/Bacteroidetes (F/B) phyla ratio and increased permeability. These changes were associated with increased lipopolysaccharide serum levels, which consequently resulted in synovitis and OA severity. The administration of pre-and probiotics partially reversed this bacterial composition. In addition, in human studies, a decreased amount of gut Bacteroidetes, subsequent increased F/B ratio, have also been observed in OA patients. Conclusions Our review confirms preliminary yet sound evidence supporting a gut-joint axis in OA in primarily preclinical models, by showing an association between diet, gut dysbiosis and OA radiological severity and self-reported symptoms. Clinical studies are needed to confirm these findings, and to investigate whether interventions targeting the composition of the microbiome will have a beneficial clinical effect.
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Affiliation(s)
- Emanuele Chisari
- Rothman Orthopaedic Institute at Thomas Jefferson University, Philadelphia, Pennsylvania, United States of America.,Department of Medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, RB, Groningen, Netherlands
| | - Marjan Wouthuyzen-Bakker
- Department of Medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, RB, Groningen, Netherlands
| | - Alex W Friedrich
- Department of Medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, RB, Groningen, Netherlands
| | - Javad Parvizi
- Rothman Orthopaedic Institute at Thomas Jefferson University, Philadelphia, Pennsylvania, United States of America
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15
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Frie M, Havinga LM, Wiersema-Buist J, Veldman CG, de Vries MJ, Rurenga-Gard L, Friedrich AW, Knoester M. Effect of school reopening on SARS-CoV-2 incidence in a low-prevalence region: Prospective SARS-CoV-2 testing in healthcare workers with primary school-attending children versus without children living at home. J Infect Prev 2021; 22:269-274. [PMID: 34880949 PMCID: PMC8647639 DOI: 10.1177/17571774211012469] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Accepted: 03/24/2021] [Indexed: 01/08/2023] Open
Abstract
Coronavirus disease 2019 (COVID-19) often presents asymptomatically or milder in
children compared to adults. The role of young children in the transmission of
severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) remains largely
unknown. In the Netherlands, the first action of loosening the partial lockdown
that had been implemented to reduce SARS-CoV-2 transmission was the reopening of
primary schools on 1 May 2020. We subsequently conducted a prospective cohort
study among healthcare workers (HCWs) with primary school-attending children
versus HCWs without children living at home. We tested each HCW three times for
SARS-CoV-2 from May 20 to June 15 2020 at 1-week intervals. In total, 832
nasopharyngeal swabs were taken from 283 HCWs with primary school-attending
children living at home and 864 nasopharyngeal swabs from 285 HCWs without
children living at home. All nasopharyngeal swabs tested negative for
SARS-CoV-2. In our region with a low population density and low SARS-CoV-2
prevalence, reopening of primary schools did not lead to an increase in
infections. The results of this study may serve as an example for the
implementation of regional strategies to reduce SARS-CoV-2 transmission in
countries with large variations in both population density and SARS-CoV-2
prevalence.
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Affiliation(s)
- Melvin Frie
- Department of Medical Microbiology and Infection Control, University of Groningen, University Medical Center Groningen, The Netherlands
| | - Lisa M Havinga
- Department of Medical Microbiology and Infection Control, University of Groningen, University Medical Center Groningen, The Netherlands
| | - Janneke Wiersema-Buist
- Department of Surgery, University of Groningen, University Medical Center Groningen, The Netherlands
| | - Charlotte G Veldman
- Department of Medical Sciences, University of Groningen, University Medical Center Groningen, The Netherlands
| | - Marjan Jt de Vries
- Department of Occupational Health Service, University of Groningen, University Medical Center Groningen, The Netherlands
| | - Lilli Rurenga-Gard
- Department of Medical Microbiology and Infection Control, University of Groningen, University Medical Center Groningen, The Netherlands
| | - Alex W Friedrich
- Department of Medical Microbiology and Infection Control, University of Groningen, University Medical Center Groningen, The Netherlands
| | - Marjolein Knoester
- Department of Medical Microbiology and Infection Control, University of Groningen, University Medical Center Groningen, The Netherlands
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16
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Symanzik C, Hillenbrand J, Stasielowicz L, Greie JC, Friedrich AW, Pulz M, John SM, Esser J. Novel insights into pivotal risk factors for rectal carriage of extended-spectrum-β-lactamase-producing enterobacterales within the general population in Lower Saxony, Germany. J Appl Microbiol 2021; 132:3256-3264. [PMID: 34856042 DOI: 10.1111/jam.15399] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 11/26/2021] [Accepted: 11/30/2021] [Indexed: 11/29/2022]
Abstract
AIMS To estimate the prevalence of extended-spectrum-β-lactamase (ESBL)-producing enterobacterales (ESBL-E) carriage in the general population of Lower Saxony, Germany, and to identify risk factors for being colonized. METHODS AND RESULTS Participants were recruited through local press and information events. Detection of ESBL-E by culture was conducted using ESBL-selective chromagar plates containing third-generation cephalosporins. Identification of pathogens was performed using matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF)_technology on Vitek mass spectrometry. Antibiotic susceptibility testing was conducted by microdilution (Vitek II) and an ESBL confirmation assay was carried out using a combination disk test. Of 527 randomly collected stool samples from healthy volunteers, 5.5% were tested positive for ESBL-E. Post-stratification for age and gender yielded a similar population estimate (5.9%). People traveling abroad and taking antibiotics had the greatest rectal ESBL-E carriage. CONCLUSIONS Potential risk factors (eg, working in healthcare facilities, recent inpatient stay) did not attribute to rectal ESBL-E carriage as other factors (eg, travelling, taking antibiotics). Rectal ESBL-E carriage within the general population seems to be high. SIGNIFICANCE AND IMPACT OF THE STUDY The known risk factors for carriage with MDRO might not be fully applicable to ESBL-E and require further examination in order to develop effective strategies for the prevention of ESBL-E dissemination within the general population.
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Affiliation(s)
- Cara Symanzik
- Institute for Interdisciplinary Dermatological Prevention and Rehabilitation (iDerm) at the Osnabrueck University, Osnabrueck, Germany.,Department of Dermatology, Environmental Medicine and Health Theory, Osnabrueck University, Osnabrueck, Germany
| | - Jacqueline Hillenbrand
- Department of Dermatology, Environmental Medicine and Health Theory, Osnabrueck University, Osnabrueck, Germany
| | | | - Jörg-Christian Greie
- Department of Dermatology, Environmental Medicine and Health Theory, Osnabrueck University, Osnabrueck, Germany.,Laboratory Medical Practice Osnabrueck, Georgsmarienhuette/Osnabrueck, Germany
| | - Alex W Friedrich
- Department of Medical Microbiology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Matthias Pulz
- Public Health Agency of Lower Saxony, Hannover, Germany
| | - Swen Malte John
- Institute for Interdisciplinary Dermatological Prevention and Rehabilitation (iDerm) at the Osnabrueck University, Osnabrueck, Germany.,Department of Dermatology, Environmental Medicine and Health Theory, Osnabrueck University, Osnabrueck, Germany
| | - Jutta Esser
- Department of Dermatology, Environmental Medicine and Health Theory, Osnabrueck University, Osnabrueck, Germany.,Laboratory Medical Practice Osnabrueck, Georgsmarienhuette/Osnabrueck, Germany
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17
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Schuele L, Lizarazo-Forero E, Strutzberg-Minder K, Schütze S, Löbert S, Lambrecht C, Harlizius J, Friedrich AW, Peter S, Rossen JWA, Couto N. Application of shotgun metagenomics sequencing and targeted sequence capture to detect circulating porcine viruses in the Dutch-German border region. Transbound Emerg Dis 2021; 69:2306-2319. [PMID: 34347385 PMCID: PMC9540031 DOI: 10.1111/tbed.14249] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [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: 04/06/2021] [Accepted: 07/16/2021] [Indexed: 12/22/2022]
Abstract
Porcine viruses have been emerging in recent decades, threatening animal and human health, as well as economic stability for pig farmers worldwide. Next‐generation sequencing (NGS) can detect and characterize known and unknown viruses but has limited sensitivity when an unbiased approach, such as shotgun metagenomics sequencing, is used. To increase the sensitivity of NGS for the detection of viruses, we applied and evaluated a broad viral targeted sequence capture (TSC) panel and compared it to an unbiased shotgun metagenomic approach. A cohort of 36 pooled porcine nasal swab and blood serum samples collected from both sides of the Dutch–German border region were evaluated. Overall, we detected 46 different viral species using TSC, compared to 40 viral species with a shotgun metagenomics approach. Furthermore, we performed phylogenetic analysis on recovered influenza A virus (FLUAV) genomes from Germany and revealed a close similarity to a zoonotic influenza strain previously detected in the Netherlands. Although TSC introduced coverage bias within the detected viruses, it improved sensitivity, genome sequence depth and contig length. In‐depth characterization of the swine virome, coupled with developing new enrichment techniques, can play a crucial role in the surveillance of circulating porcine viruses and emerging zoonotic pathogens.
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Affiliation(s)
- Leonard Schuele
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands.,Institute of Medical Microbiology and Hygiene, University of Tübingen, Tübingen, Germany
| | - Erley Lizarazo-Forero
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | | | - Sabine Schütze
- Animal Health Services, Chamber of Agriculture of North Rhine-Westphalia, Bad Sassendorf, Germany
| | - Sandra Löbert
- Animal Health Services, Chamber of Agriculture of North Rhine-Westphalia, Bad Sassendorf, Germany
| | - Claudia Lambrecht
- Animal Health Services, Chamber of Agriculture of North Rhine-Westphalia, Bad Sassendorf, Germany
| | - Jürgen Harlizius
- Animal Health Services, Chamber of Agriculture of North Rhine-Westphalia, Bad Sassendorf, Germany
| | - Alex W Friedrich
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Silke Peter
- Institute of Medical Microbiology and Hygiene, University of Tübingen, Tübingen, Germany
| | - John W A Rossen
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands.,Department of Pathology, University of Utah School of Medicine, Salt Lake City, Utah, USA
| | - Natacha Couto
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands.,The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, UK
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18
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Schuele L, Lizarazo-Forero E, Cassidy H, Strutzberg-Minder K, Boehmer J, Schuetze S, Loebert S, Lambrecht C, Harlizius J, Friedrich AW, Peter S, Rossen JWA, Couto N. First detection of porcine respirovirus 1 in Germany and the Netherlands. Transbound Emerg Dis 2021; 68:3120-3125. [PMID: 33837672 PMCID: PMC9292642 DOI: 10.1111/tbed.14100] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [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: 11/10/2020] [Revised: 03/10/2021] [Accepted: 04/06/2021] [Indexed: 01/10/2023]
Abstract
Porcine respirovirus 1, also referred to as porcine parainfluenza virus 1 (PPIV‐1), was first detected in deceased pigs from Hong Kong in 2013. It has since then been found in the USA, Chile and most recently in Hungary. Information on the pathogenicity and global spread is sparse. However, it has been speculated to play a role in the porcine respiratory disease complex. To investigate the porcine virome, we screened 53 pig samples from 26 farms within the Dutch–German border region using shotgun metagenomics sequencing (SMg). After detecting PPIV‐1 in five farms through SMg, a real‐time reverse transcriptase PCR (RT‐qPCR) assay was designed, which not only confirmed the presence of the virus in 1 of the 5 farms but found an additional 6 positive farms. Phylogenetic analysis found the closest match to be the first detected PPIV‐1 strain in Hong Kong. The Dutch‐German region represents a significant area of pig farming within Europe and could provide important information on the characterization and circulation of porcine viruses, such as PPIV‐1. With its recent detection in Hungary, these findings suggest widespread circulation of PPIV‐1 in Central Europe, highlighting the need for further research on persistence, pathogenicity and transmission in Europe.
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Affiliation(s)
- Leonard Schuele
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology and Infection Prevention, Groningen, The Netherlands.,Institute of Medical Microbiology and Hygiene, University of Tübingen, Tübingen, Germany
| | - Erley Lizarazo-Forero
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology and Infection Prevention, Groningen, The Netherlands
| | - Hayley Cassidy
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology and Infection Prevention, Groningen, The Netherlands
| | | | - Jan Boehmer
- IVD Innovative Veterinary Diagnostics (IVD GmbH), Seelze, Germany
| | - Sabine Schuetze
- Animal Health Services, Chamber of Agriculture of North Rhine-Westphalia, Bad Sassendorf, Germany
| | - Sandra Loebert
- Animal Health Services, Chamber of Agriculture of North Rhine-Westphalia, Bad Sassendorf, Germany
| | - Claudia Lambrecht
- Animal Health Services, Chamber of Agriculture of North Rhine-Westphalia, Bad Sassendorf, Germany
| | - Juergen Harlizius
- Animal Health Services, Chamber of Agriculture of North Rhine-Westphalia, Bad Sassendorf, Germany
| | - Alex W Friedrich
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology and Infection Prevention, Groningen, The Netherlands
| | - Silke Peter
- Institute of Medical Microbiology and Hygiene, University of Tübingen, Tübingen, Germany
| | - John W A Rossen
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology and Infection Prevention, Groningen, The Netherlands.,Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Natacha Couto
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology and Infection Prevention, Groningen, The Netherlands.,The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, UK
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19
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Verburg I, van Veelen HPJ, Waar K, Rossen JWA, Friedrich AW, Hernández Leal L, García-Cobos S, Schmitt H. Effects of Clinical Wastewater on the Bacterial Community Structure from Sewage to the Environment. Microorganisms 2021; 9:718. [PMID: 33807193 PMCID: PMC8065902 DOI: 10.3390/microorganisms9040718] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [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: 03/03/2021] [Revised: 03/21/2021] [Accepted: 03/26/2021] [Indexed: 12/30/2022] Open
Abstract
This study pertains to measure differences in bacterial communities along the wastewater pathway, from sewage sources through the environment. Our main focus was on taxa which include pathogenic genera, and genera harboring antibiotic resistance (henceforth referred to as "target taxa"). Our objective was to measure the relative abundance of these taxa in clinical wastewaters compared to non-clinical wastewaters, and to investigate what changes can be detected along the wastewater pathway. The study entailed a monthly sampling campaign along a wastewater pathway, and taxa identification through 16S rRNA amplicon sequencing. Results indicated that clinical and non-clinical wastewaters differed in their overall bacterial composition, but that target taxa were not enriched in clinical wastewater. This suggests that treatment of clinical wastewater before release into the wastewater system would only remove a minor part of the potential total pathogen load in wastewater treatment plants. Additional findings were that the relative abundance of most target taxa was decreased after wastewater treatment, yet all investigated taxa were detected in 68% of the treated effluent samples-meaning that these bacteria are continuously released into the receiving surface water. Temporal variation was only observed for specific taxa in surface water, but not in wastewater samples.
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Affiliation(s)
- Ilse Verburg
- Wetsus, European Centre of Excellence for Sustainable Water Technology, 8900 CC Leeuwarden, The Netherlands; (I.V.); (H.P.J.v.V.); (L.H.L.)
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, 9713 GZ Groningen, The Netherlands; (J.W.A.R.); (A.W.F.); (S.G.-C.)
| | - H. Pieter J. van Veelen
- Wetsus, European Centre of Excellence for Sustainable Water Technology, 8900 CC Leeuwarden, The Netherlands; (I.V.); (H.P.J.v.V.); (L.H.L.)
| | - Karola Waar
- Izore, Centrum Infectieziekten Friesland, 8900 JA Leeuwarden, The Netherlands;
| | - John W. A. Rossen
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, 9713 GZ Groningen, The Netherlands; (J.W.A.R.); (A.W.F.); (S.G.-C.)
| | - Alex W. Friedrich
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, 9713 GZ Groningen, The Netherlands; (J.W.A.R.); (A.W.F.); (S.G.-C.)
| | - Lucia Hernández Leal
- Wetsus, European Centre of Excellence for Sustainable Water Technology, 8900 CC Leeuwarden, The Netherlands; (I.V.); (H.P.J.v.V.); (L.H.L.)
| | - Silvia García-Cobos
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, 9713 GZ Groningen, The Netherlands; (J.W.A.R.); (A.W.F.); (S.G.-C.)
| | - Heike Schmitt
- Wetsus, European Centre of Excellence for Sustainable Water Technology, 8900 CC Leeuwarden, The Netherlands; (I.V.); (H.P.J.v.V.); (L.H.L.)
- Institute for Risk Assessment Sciences, Utrecht University, 3508 TD Utrecht, The Netherlands
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), 3721 MA Bilthoven, The Netherlands
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20
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van der Pol S, Dik JWH, Glasner C, Postma MJ, Sinha B, Friedrich AW. The tripartite insurance model (TIM): a financial incentive to prevent outbreaks of infections due to multidrug-resistant microorganisms in hospitals. Clin Microbiol Infect 2021; 27:S1198-743X(21)00046-X. [PMID: 33524590 DOI: 10.1016/j.cmi.2021.01.019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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: 08/28/2020] [Revised: 01/15/2021] [Accepted: 01/19/2021] [Indexed: 12/17/2022]
Abstract
Healthcare-associated infections caused by multidrug-resistant organisms (MDROs) constitute a major challenge worldwide, but care providers are often not sufficiently incentivized to implement recommended infection prevention measures to prevent the spread of such infections. We propose a new approach which creates incentives for hospitals, external laboratories and insurers to collaborate on preventing MDRO outbreaks by testing more and implementing infection prevention measures. This tripartite insurance model (TIM) redistributes the costs of preventing and combating MDRO outbreaks in a way that all parties benefit from reducing the number of outbreaks.
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Affiliation(s)
- Simon van der Pol
- University of Groningen, University Medical Centre Groningen, Department of Health Sciences, Groningen, the Netherlands.
| | - Jan-Willem H Dik
- University of Groningen, University Medical Centre Groningen, Department of Medical Microbiology and Infection Control, Groningen, the Netherlands; National Health Care Institute, Diemen, the Netherlands
| | - Corinna Glasner
- University of Groningen, University Medical Centre Groningen, Department of Medical Microbiology and Infection Control, Groningen, the Netherlands
| | - Maarten J Postma
- University of Groningen, University Medical Centre Groningen, Department of Health Sciences, Groningen, the Netherlands; University of Groningen, Department of Economics, Econometrics and Finance, Groningen, the Netherlands
| | - Bhanu Sinha
- University of Groningen, University Medical Centre Groningen, Department of Medical Microbiology and Infection Control, Groningen, the Netherlands
| | - Alex W Friedrich
- University of Groningen, University Medical Centre Groningen, Department of Medical Microbiology and Infection Control, Groningen, the Netherlands
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21
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Gunnink LB, Arouri DJ, Jolink FE, Lokate M, de Jonge K, Kampmeier S, Kreis C, Raschke M, Kleinjan M, ter Maaten JC, Friedrich AW, Bathoorn E, Glasner C. Compliance to Screening Protocols for Multidrug-Resistant Microorganisms at the Emergency Departments of Two Academic Hospitals in the Dutch-German Cross-Border Region. Trop Med Infect Dis 2021; 6:tropicalmed6010015. [PMID: 33530494 PMCID: PMC7838951 DOI: 10.3390/tropicalmed6010015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 01/19/2021] [Accepted: 01/21/2021] [Indexed: 12/12/2022] Open
Abstract
Infections caused by multidrug-resistant organisms (MDROs) are associated with prolonged hospitalization and higher risk of mortality. Patients arriving in the hospital via the emergency department (ED) are screened for the presence of MDROs in compliance with the screening protocols in order to apply the correct isolation measures. In the Dutch–German border region, local hospitals apply their own screening protocols which are based upon national screening protocols. The contents of the national and local MDRO screening protocols were compared on vancomycin-resistant enterococci (VRE), methicillin-resistant Staphylococcus aureus (MRSA), and carbapenemase-producing and carbapenem-resistant Enterobacteriaceae (CPE/CRE). The practicality of the screening protocols was evaluated by performing an audit. As a result, the content of the MDRO screening protocols differed regarding risk factors for MDRO carriage, swab site, personal protective equipment, and isolation measures. The observations and questionnaires showed that the practicality was sufficient; however, the responsibility was not designated clearly and education regarding the screening protocols was deemed inappropriate. The differences between the MDRO screening protocols complicate patient care in the Dutch–German border region. Arrangements have to be made about the responsibility of the MDRO screening, and improvements are necessary concerning education regarding the MDRO screening protocols.
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Affiliation(s)
- Lisa B. Gunnink
- Department of Medical Microbiology and Infection Control, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands; (L.B.G.); (D.J.A.); (F.E.J.J.); (M.L.); (K.d.J.); (A.W.F.); (E.B.)
| | - Donia J. Arouri
- Department of Medical Microbiology and Infection Control, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands; (L.B.G.); (D.J.A.); (F.E.J.J.); (M.L.); (K.d.J.); (A.W.F.); (E.B.)
| | - Floris E.J. Jolink
- Department of Medical Microbiology and Infection Control, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands; (L.B.G.); (D.J.A.); (F.E.J.J.); (M.L.); (K.d.J.); (A.W.F.); (E.B.)
| | - Mariëtte Lokate
- Department of Medical Microbiology and Infection Control, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands; (L.B.G.); (D.J.A.); (F.E.J.J.); (M.L.); (K.d.J.); (A.W.F.); (E.B.)
| | - Klaas de Jonge
- Department of Medical Microbiology and Infection Control, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands; (L.B.G.); (D.J.A.); (F.E.J.J.); (M.L.); (K.d.J.); (A.W.F.); (E.B.)
| | - Stefanie Kampmeier
- Institute of Hygiene, University Hospital Münster, Robert-Koch-Straße 41, 48149 Münster, Germany;
| | - Carolin Kreis
- Department of Trauma, Hand and Reconstructive Surgery, University Hospital Münster, Albert-Schweitzer-Campus 1, Building W1, 48149 Münster, Germany; (C.K.); (M.R.)
| | - Michael Raschke
- Department of Trauma, Hand and Reconstructive Surgery, University Hospital Münster, Albert-Schweitzer-Campus 1, Building W1, 48149 Münster, Germany; (C.K.); (M.R.)
| | - Mirjam Kleinjan
- Department of Emergency Medicine, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands;
| | - Jan C. ter Maaten
- Department of Internal Medicine, Emergency Medicine, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands;
| | - Alex W. Friedrich
- Department of Medical Microbiology and Infection Control, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands; (L.B.G.); (D.J.A.); (F.E.J.J.); (M.L.); (K.d.J.); (A.W.F.); (E.B.)
| | - Erik Bathoorn
- Department of Medical Microbiology and Infection Control, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands; (L.B.G.); (D.J.A.); (F.E.J.J.); (M.L.); (K.d.J.); (A.W.F.); (E.B.)
| | - Corinna Glasner
- Department of Medical Microbiology and Infection Control, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands; (L.B.G.); (D.J.A.); (F.E.J.J.); (M.L.); (K.d.J.); (A.W.F.); (E.B.)
- Correspondence: ; Tel.: +31-(0)-50-36-13480
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22
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Schuele L, Cassidy H, Lizarazo E, Strutzberg-Minder K, Schuetze S, Loebert S, Lambrecht C, Harlizius J, Friedrich AW, Peter S, Niesters HGM, Rossen JWA, Couto N. Assessment of Viral Targeted Sequence Capture Using Nanopore Sequencing Directly from Clinical Samples. Viruses 2020; 12:E1358. [PMID: 33260903 PMCID: PMC7759923 DOI: 10.3390/v12121358] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 11/23/2020] [Accepted: 11/25/2020] [Indexed: 12/18/2022] Open
Abstract
Shotgun metagenomic sequencing (SMg) enables the simultaneous detection and characterization of viruses in human, animal and environmental samples. However, lack of sensitivity still poses a challenge and may lead to poor detection and data acquisition for detailed analysis. To improve sensitivity, we assessed a broad scope targeted sequence capture (TSC) panel (ViroCap) in both human and animal samples. Moreover, we adjusted TSC for the Oxford Nanopore MinION and compared the performance to an SMg approach. TSC on the Illumina NextSeq served as the gold standard. Overall, TSC increased the viral read count significantly in challenging human samples, with the highest genome coverage achieved using the TSC on the MinION. TSC also improved the genome coverage and sequencing depth in clinically relevant viruses in the animal samples, such as influenza A virus. However, SMg was shown to be adequate for characterizing a highly diverse animal virome. TSC on the MinION was comparable to the NextSeq and can provide a valuable alternative, offering longer reads, portability and lower initial cost. Developing new viral enrichment approaches to detect and characterize significant human and animal viruses is essential for the One Health Initiative.
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Affiliation(s)
- Leonard Schuele
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, 9713 RC Groningen, The Netherlands; (H.C.); (E.L.); (A.W.F.); (H.G.M.N.); (J.W.A.R.); (N.C.)
- Institute of Medical Microbiology and Hygiene, University of Tübingen, 72076 Tübingen, Germany;
| | - Hayley Cassidy
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, 9713 RC Groningen, The Netherlands; (H.C.); (E.L.); (A.W.F.); (H.G.M.N.); (J.W.A.R.); (N.C.)
| | - Erley Lizarazo
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, 9713 RC Groningen, The Netherlands; (H.C.); (E.L.); (A.W.F.); (H.G.M.N.); (J.W.A.R.); (N.C.)
| | | | - Sabine Schuetze
- Animal Health Services, Chamber of Agriculture of North Rhine-Westphalia, 59505 Bad Sassendorf, Germany; (S.S.); (S.L.); (C.L.); (J.H.)
| | - Sandra Loebert
- Animal Health Services, Chamber of Agriculture of North Rhine-Westphalia, 59505 Bad Sassendorf, Germany; (S.S.); (S.L.); (C.L.); (J.H.)
| | - Claudia Lambrecht
- Animal Health Services, Chamber of Agriculture of North Rhine-Westphalia, 59505 Bad Sassendorf, Germany; (S.S.); (S.L.); (C.L.); (J.H.)
| | - Juergen Harlizius
- Animal Health Services, Chamber of Agriculture of North Rhine-Westphalia, 59505 Bad Sassendorf, Germany; (S.S.); (S.L.); (C.L.); (J.H.)
| | - Alex W. Friedrich
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, 9713 RC Groningen, The Netherlands; (H.C.); (E.L.); (A.W.F.); (H.G.M.N.); (J.W.A.R.); (N.C.)
| | - Silke Peter
- Institute of Medical Microbiology and Hygiene, University of Tübingen, 72076 Tübingen, Germany;
| | - Hubert G. M. Niesters
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, 9713 RC Groningen, The Netherlands; (H.C.); (E.L.); (A.W.F.); (H.G.M.N.); (J.W.A.R.); (N.C.)
| | - John W. A. Rossen
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, 9713 RC Groningen, The Netherlands; (H.C.); (E.L.); (A.W.F.); (H.G.M.N.); (J.W.A.R.); (N.C.)
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT 84108, USA
| | - Natacha Couto
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, 9713 RC Groningen, The Netherlands; (H.C.); (E.L.); (A.W.F.); (H.G.M.N.); (J.W.A.R.); (N.C.)
- Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath BA2 7AY, UK
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Campos ACC, Andrade NL, Ferdous M, Chlebowicz MA, Santos CC, Correal JCD, Lo Ten Foe JR, Rosa ACP, Damasco PV, Friedrich AW, Rossen JWA. Corrigendum: Comprehensive Molecular Characterization of Escherichia coli Isolates from Urine Samples of Hospitalized Patients in Rio de Janeiro, Brazil. Front Microbiol 2020; 11:599031. [PMID: 33193282 PMCID: PMC7662894 DOI: 10.3389/fmicb.2020.599031] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Accepted: 09/15/2020] [Indexed: 11/13/2022] Open
Abstract
[This corrects the article DOI: 10.3389/fmicb.2018.00243.].
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Affiliation(s)
- Ana Carolina C Campos
- Departamento de Microbiologia, Imunologia e Parasitologia, Faculdade de Ciências Médicas, Universidade Do Estado Do Rio de Janeiro, Rio de Janeiro, Brazil.,Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Nathália L Andrade
- Departamento de Microbiologia, Imunologia e Parasitologia, Faculdade de Ciências Médicas, Universidade Do Estado Do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Mithila Ferdous
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Monika A Chlebowicz
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Carla C Santos
- Departamento de Controle de Infecções, Hospital Rio Laranjeiras, Rio de Janeiro, Brazil
| | - Julio C D Correal
- Departamento de Microbiologia, Imunologia e Parasitologia, Faculdade de Ciências Médicas, Universidade Do Estado Do Rio de Janeiro, Rio de Janeiro, Brazil.,Departamento de Controle de Infecções, Hospital Rio Laranjeiras, Rio de Janeiro, Brazil
| | - Jerome R Lo Ten Foe
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Ana Cláudia P Rosa
- Departamento de Microbiologia, Imunologia e Parasitologia, Faculdade de Ciências Médicas, Universidade Do Estado Do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Paulo V Damasco
- Departamento de Doenças Infecciosas e Parasitárias, Universidade Federal Do Estado Do Rio de Janeiro, Rio de Janeiro, Brazil.,Departamento de Doenças Infecciosas e Parasitárias, Universidade Do Estado Do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Alex W Friedrich
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - John W A Rossen
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
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24
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Purba AKR, Luz CF, Wulandari RR, van der Gun I, Dik JW, Friedrich AW, Postma MJ. The Impacts of Deep Surgical Site Infections on Readmissions, Length of Stay, and Costs: A Matched Case-Control Study Conducted in an Academic Hospital in the Netherlands. Infect Drug Resist 2020; 13:3365-3374. [PMID: 33061483 PMCID: PMC7533242 DOI: 10.2147/idr.s264068] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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: 06/09/2020] [Accepted: 08/04/2020] [Indexed: 11/23/2022] Open
Abstract
OBJECTIVE This study aimed to evaluate the impacts of deep surgical site infections (dSSIs) regarding hospital readmissions, prolonged length of stay (LoS), and estimated costs. PATIENTS AND METHODS We designed and applied a matched case-control observational study using the electronic health records at the University Medical Center Groningen in the Netherlands. We compared patients with dSSI and non-SSI, matched on the basis of having similar procedures. A prevailing topology of surgeries categorized as clean, clean-contaminated, contaminated, and dirty was applied. RESULTS Out of a total of 12,285 patients, 393 dSSI were identified as cases, and 2864 patients without SSIs were selected as controls. A total of 343 dSSI patients (87%) and 2307 (81%) controls required hospital readmissions. The median LoS was 7 days (P25-P75: 2.5-14.5) for dSSI patients and 5 days (P25-P75: 1-9) for controls (p-value: <0.001). The estimated mean cost per hospital admission was €9,016 (SE±343) for dSSI patients and €5,409 (SE±120) for controls (p<0.001). Independent variables associated with dSSI were patient's age ≥65 years (OR: 1.334; 95% CI: 1.036-1.720), the use of prophylactic antibiotics (OR: 0.424; 95% CI: 0.344-0.537), and neoplasms (OR: 2.050; 95% CI: 1.473-2.854). CONCLUSION dSSI is associated with increased costs, prolonged LoS, and increased readmission rates. Elevated risks were seen for elderly patients and those with neoplasms. Additionally, a protective effect of prophylactic antibiotics was found.
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Affiliation(s)
- Abdul Khairul Rizki Purba
- Department of Health Sciences, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.,University of Groningen, University Medical Center Groningen, Department of Medical Microbiology, Groningen, the Netherlands.,Department of Pharmacology and Therapy, Faculty of Medicine, Universitas Airlangga, Surabaya, Indonesia.,Unit of Pharmacotherapy, -Epidemiology and -Economics (PTE2), Department of Pharmacy, Faculty of Science and Engineering, University of Groningen, Groningen, the Netherlands
| | - Christian F Luz
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology, Groningen, the Netherlands
| | | | - Ieneke van der Gun
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology, Groningen, the Netherlands
| | - Jan-Willem Dik
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology, Groningen, the Netherlands
| | - Alex W Friedrich
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology, Groningen, the Netherlands
| | - Maarten J Postma
- Department of Health Sciences, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.,Department of Pharmacology and Therapy, Faculty of Medicine, Universitas Airlangga, Surabaya, Indonesia.,Unit of Pharmacotherapy, -Epidemiology and -Economics (PTE2), Department of Pharmacy, Faculty of Science and Engineering, University of Groningen, Groningen, the Netherlands.,Department of Economics, Econometrics and Finance, Faculty of Economics & Business, University of Groningen, Groningen, the Netherlands
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25
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Hilt N, Lokate M, OldeLoohuis A, Hulscher MEJL, Friedrich AW, Voss A. Hand hygiene compliance in Dutch general practice offices. Arch Public Health 2020; 78:79. [PMID: 32939264 PMCID: PMC7486593 DOI: 10.1186/s13690-020-00464-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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: 05/06/2020] [Accepted: 09/02/2020] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND Hand hygiene (HH) is considered one of the most important measures to prevent healthcare-associated infections (HAI). Most studies focus on HH compliance within the hospital setting, whereas little is known for the outpatient setting. The aim of this study was to evaluate compliance with HH recommendations in general practitioners (GPs) office, based on World Health Organization (WHO) guideline. METHODS An observational study was conducted at five Dutch GPs-practices in September 2017. We measured HH compliance through direct observation using WHO's 'five moments of hand hygiene' observation tool. All observations were done by one trained professional. RESULTS We monitored a total of 285 HH opportunities for 30 health care workers (HCWs). The overall compliance was 37%. Hand hygiene compliance was 34, 51 and 16% for general practitioners, practice assistants, and nurses, respectively. It varies between 63% after body fluid exposure and no HH performance before-, during and after home visit of a patient (defined as moment 5). The preferred method of HH was soap and water (63%) versus 37% for alcohol-based hand rub (ABHR). The median time of disinfecting hands was 8 s (range 6-11 s) for HCWs in our study. CONCLUSIONS HH compliance among HCWs in Dutch GPs was found to be low, especially with regard to home visits. The WHO recommended switch from hand wash to ABHR was not implemented by the majority of HCWs in 5 observed GPs offices.
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Affiliation(s)
- Nataliya Hilt
- Radboudumc, Department of Medical Microbiology, Geert Grooteplein Zuid 10, 6525 GA Nijmegen, The Netherlands
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands
| | - Mariëtte Lokate
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands
| | - Alfons OldeLoohuis
- Radboudumc, Department of Primary and Community Care, Geert Grooteplein Zuid 10, 6525 GA Nijmegen, the Netherlands
| | - Marlies E. J. L. Hulscher
- Scientific Institute for Quality of Healthcare, Radboud University Nijmegen Medical Centre, Geert Grooteplein Zuid 10, 6525 GA Nijmegen, the Netherlands
| | - Alex W. Friedrich
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands
| | - Andreas Voss
- Radboudumc, Department of Medical Microbiology, Geert Grooteplein Zuid 10, 6525 GA Nijmegen, The Netherlands
- Department of Clinical Microbiology and Infectious Diseases, Canisius-Wilhelmina Hospital (CWZ), Weg door Jonkerbos 100, 6532 SZ Nijmegen, the Netherlands
- Radboudumc, REshape Center for Innovation, Geert Grooteplein Zuid 10, 6525 GA Nijmegen, the Netherlands
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26
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Fleres G, Couto N, Schuele L, Chlebowicz MA, Mendes CI, van der Sluis LWM, Rossen JWA, Friedrich AW, García-Cobos S. Detection of a novel mcr-5.4 gene variant in hospital tap water by shotgun metagenomic sequencing. J Antimicrob Chemother 2020; 74:3626-3628. [PMID: 31504580 PMCID: PMC6857192 DOI: 10.1093/jac/dkz363] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Affiliation(s)
- Giuseppe Fleres
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology, Groningen, The Netherlands
| | - Natacha Couto
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology, Groningen, The Netherlands
| | - Leonard Schuele
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology, Groningen, The Netherlands
| | - Monika A Chlebowicz
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology, Groningen, The Netherlands
| | - Catarina I Mendes
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology, Groningen, The Netherlands
| | - Luc W M van der Sluis
- Center of Dentistry and Oral Hygiene, University Medical Center Groningen, 9712 CP Groningen, The Netherlands
| | - John W A Rossen
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology, Groningen, The Netherlands
| | - Alex W Friedrich
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology, Groningen, The Netherlands
| | - Silvia García-Cobos
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology, Groningen, The Netherlands
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27
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Sama IE, Ravera A, Santema BT, van Goor H, Ter Maaten JM, Cleland JGF, Rienstra M, Friedrich AW, Samani NJ, Ng LL, Dickstein K, Lang CC, Filippatos G, Anker SD, Ponikowski P, Metra M, van Veldhuisen DJ, Voors AA. Circulating plasma concentrations of angiotensin-converting enzyme 2 in men and women with heart failure and effects of renin-angiotensin-aldosterone inhibitors. Eur Heart J 2020; 41:1810-1817. [PMID: 32388565 PMCID: PMC7239195 DOI: 10.1093/eurheartj/ehaa373] [Citation(s) in RCA: 336] [Impact Index Per Article: 84.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/22/2020] [Revised: 04/03/2020] [Accepted: 04/20/2020] [Indexed: 02/07/2023] Open
Abstract
Aims The current pandemic coronavirus SARS-CoV-2 infects a wide age group but predominantly elderly individuals, especially men and those with cardiovascular disease. Recent reports suggest an association with use of renin–angiotensin–aldosterone system (RAAS) inhibitors. Angiotensin-converting enzyme 2 (ACE2) is a functional receptor for coronaviruses. Higher ACE2 concentrations might lead to increased vulnerability to SARS-CoV-2 in patients on RAAS inhibitors. Methods and results We measured ACE2 concentrations in 1485 men and 537 women with heart failure (index cohort). Results were validated in 1123 men and 575 women (validation cohort). The median age was 69 years for men and 75 years for women. The strongest predictor of elevated concentrations of ACE2 in both cohorts was male sex (estimate = 0.26, P < 0.001; and 0.19, P < 0.001, respectively). In the index cohort, use of ACE inhibitors, angiotensin receptor blockers (ARBs), or mineralocorticoid receptor antagonists (MRAs) was not an independent predictor of plasma ACE2. In the validation cohort, ACE inhibitor (estimate = –0.17, P = 0.002) and ARB use (estimate = –0.15, P = 0.03) were independent predictors of lower plasma ACE2, while use of an MRA (estimate = 0.11, P = 0.04) was an independent predictor of higher plasma ACE2 concentrations. Conclusion In two independent cohorts of patients with heart failure, plasma concentrations of ACE2 were higher in men than in women, but use of neither an ACE inhibitor nor an ARB was associated with higher plasma ACE2 concentrations. These data might explain the higher incidence and fatality rate of COVID-19 in men, but do not support previous reports suggesting that ACE inhibitors or ARBs increase the vulnerability for COVID-19 through increased plasma ACE2 concentrations. ![]()
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Affiliation(s)
- Iziah E Sama
- Department of Cardiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Alice Ravera
- Department of Cardiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.,Cardiology, Department of Medical and Surgical Specialties, Radiologic Sciences and Public Health, University of Brescia, Brescia, Italy
| | - Bernadet T Santema
- Department of Cardiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Harry van Goor
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Jozine M Ter Maaten
- Department of Cardiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - John G F Cleland
- Robertson Centre for Biostatistics & Clinical Trials Unit, University of Glasgow and National Heart & Lung Institute, Imperial College, London, UK
| | - Michiel Rienstra
- Department of Cardiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Alex W Friedrich
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Nilesh J Samani
- Department of Cardiovascular Sciences, University of Leicester, Glenfield Hospital, and NIHR Leicester Biomedical Research Centre, Leicester, UK
| | - Leong L Ng
- Department of Cardiovascular Sciences, University of Leicester, Glenfield Hospital, and NIHR Leicester Biomedical Research Centre, Leicester, UK
| | - Kenneth Dickstein
- University of Bergen, Bergen, Norway.,Stavanger University Hospital, Stavanger, Norway
| | - Chim C Lang
- Division of Molecular and Clinical Medicine, School of Medicine, University of Dundee Ninewells Hospital and Medical School, Dundee, UK
| | - Gerasimos Filippatos
- National and Kapodistrian University of Athens, School of Medicine, Athens, Greece.,University of Cyprus, School of Medicine, Nicosia, Cyprus
| | - Stefan D Anker
- Department of Cardiology (CVK) and Berlin Institute of Health Center for Regenerative Therapies (BCRT), Germany.,German Centre for Cardiovascular Research (DZHK) partner site Berlin, Charité Universitätsmedizin Berlin, Germany
| | - Piotr Ponikowski
- Department of Heart Diseases, Medical University, Military Hospital, Wrocław, Poland
| | - Marco Metra
- Cardiology, Department of Medical and Surgical Specialties, Radiologic Sciences and Public Health, University of Brescia, Brescia, Italy
| | - Dirk J van Veldhuisen
- Department of Cardiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Adriaan A Voors
- Department of Cardiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
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Campos ACDC, Andrade NL, Couto N, Mutters NT, de Vos M, Rosa ACDP, Damasco PV, Lo Ten Foe JR, Friedrich AW, Chlebowicz-Flissikowska MA, Rossen JWA. Characterization of fosfomycin heteroresistance among multidrug-resistant Escherichia coli isolates from hospitalized patients in Rio de Janeiro, Brazil. J Glob Antimicrob Resist 2020; 22:584-593. [PMID: 32389792 DOI: 10.1016/j.jgar.2020.04.026] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [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: 11/04/2019] [Revised: 03/06/2020] [Accepted: 04/17/2020] [Indexed: 12/16/2022] Open
Abstract
OBJECTIVES Urinary tract infections (UTIs) caused by multidrug-resistant Escherichia coli have become a major medical concern. Old antibiotics such as fosfomycin have become an alternative therapeutic option due to their effectiveness and, as a result, fosfomycin is now used as a first-line drug for the treatment of UTIs in many countries. Despite low resistance rates, fosfomycin heteroresistance, defined as a phenomenon where subpopulations of bacteria are resistant to high antibiotic concentrations whereas most of the bacteria are susceptible, is an underestimated problem. METHODS The frequency of heteroresistance in E. coli isolated from hospitalized patients in Brazil and its effect on susceptibility of E. coli in biofilms was studied and the isolates were molecularly characterized to reveal the mechanisms behind their fosfomycin heteroresistance using whole-genome sequencing. RESULTS A higher frequency of fosfomycin heteroresistance compared with other studies was found. In biofilms, most heteroresistant isolates were less sensitive to fosfomycin than control isolates and showed overexpression of metabolic genes thereby increasing their survival rate. Molecular characterization showed that some resistant subpopulations derived from heteroresistant isolates had a defect in their fosfomycin uptake system caused by mutations in transporter and regulatory genes, whereas others overexpressed the murA gene. None to minor effects on bacterial fitness were observed. Oxidative stress protection, virulence and metabolic genes were differentially expressed in resistant subpopulations and heteroresistant isolates. CONCLUSION Frequent detection of heteroresistance in UTIs may play a role in the failure of antibiotic treatments and should therefore be more carefully diagnosed.
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Affiliation(s)
- Ana Carolina da C Campos
- Universidade do Estado do Rio de Janeiro, Faculdade de Ciências Médicas, Departamento de Microbiologia, Inmunologia e Parasitologia, Boulevard 28 de Setembro, 77 - Vila Isabel, RJ-20551-030, Rio de Janeiro, Brazil; University of Groningen, University Medical Center Groningen, Department of Medical Microbiology and Infection Prevention, Hanzeplein 1, 9713 GZ, Groningen, The Netherlands
| | - Nathália L Andrade
- Universidade do Estado do Rio de Janeiro, Faculdade de Ciências Médicas, Departamento de Microbiologia, Inmunologia e Parasitologia, Boulevard 28 de Setembro, 77 - Vila Isabel, RJ-20551-030, Rio de Janeiro, Brazil
| | - Natacha Couto
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology and Infection Prevention, Hanzeplein 1, 9713 GZ, Groningen, The Netherlands
| | - Nico T Mutters
- Heidelberg University Hospital, Center for Infectious Diseases, Medical Microbiology and Hygiene, Im Neuenheimer Feld 672, 69120, Heidelberg, Germany
| | - Marjon de Vos
- University of Groningen, Institute for Evolutionary Life Sciences, Linnaeusborg 5(th) floor, Nijenborgh 7, 9747 AG, Groningen, The Netherlands
| | - Ana Cláudia de P Rosa
- Universidade do Estado do Rio de Janeiro, Faculdade de Ciências Médicas, Departamento de Microbiologia, Inmunologia e Parasitologia, Boulevard 28 de Setembro, 77 - Vila Isabel, RJ-20551-030, Rio de Janeiro, Brazil
| | - Paulo V Damasco
- Universidade do Estado do Rio de Janeiro, Departamento de Doenças Infecciosas e Parasitárias, Boulevard 28 de Setembro, 77 - Vila Isabel, RJ-20551-030, Rio de Janeiro, Brazil; Universidade Federal do Estado do Rio de Janeiro, Departamento de Doenças Infecciosas e Parasitárias, R. Voluntários da Pátria, 107 - Botafogo, RJ- 22270-000, Rio de Janeiro, Brazil
| | - Jerome R Lo Ten Foe
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology and Infection Prevention, Hanzeplein 1, 9713 GZ, Groningen, The Netherlands
| | - Alex W Friedrich
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology and Infection Prevention, Hanzeplein 1, 9713 GZ, Groningen, The Netherlands
| | - Monika A Chlebowicz-Flissikowska
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology and Infection Prevention, Hanzeplein 1, 9713 GZ, Groningen, The Netherlands
| | - John W A Rossen
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology and Infection Prevention, Hanzeplein 1, 9713 GZ, Groningen, The Netherlands.
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Miro E, Rossen JWA, Chlebowicz MA, Harmsen D, Brisse S, Passet V, Navarro F, Friedrich AW, García-Cobos S. Core/Whole Genome Multilocus Sequence Typing and Core Genome SNP-Based Typing of OXA-48-Producing Klebsiella pneumoniae Clinical Isolates From Spain. Front Microbiol 2020; 10:2961. [PMID: 32082262 PMCID: PMC7005014 DOI: 10.3389/fmicb.2019.02961] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [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: 09/10/2019] [Accepted: 12/09/2019] [Indexed: 11/17/2022] Open
Abstract
Whole-genome sequencing (WGS)-based typing methods have emerged as promising and highly discriminative epidemiological tools. In this study, we combined gene-by-gene allele calling and core genome single nucleotide polymorphism (cgSNP) approaches to investigate the genetic relatedness of a well-characterized collection of OXA-48-producing Klebsiella pneumoniae isolates. We included isolates from the predominant sequence type ST405 (n = 31) OXA-48-producing K. pneumoniae clone and isolates from ST101 (n = 3), ST14 (n = 1), ST17 (n = 1), and ST1233 (n = 1), obtained from eight Catalan hospitals. Core-genome multilocus sequence typing (cgMLST) schemes from Institut Pasteur’s BIGSdb-Kp (634 genes) and SeqSphere+ (2,365 genes), and a SeqSphere+ whole-genome MLST (wgMLST) scheme (4,891 genes) were used. Allele differences or allelic mismatches and the genetic distance, as the proportion of allele differences, were used to interpret the results from a gene-by-gene approach, whereas the number of SNPs was used for the cgSNP analysis. We observed between 0–10 and 0–14 allele differences among the predominant ST405 using cgMLST and wgMLST from SeqSphere+, respectively, and <2 allelic mismatches when using Institut Pasteur’s BIGSdb-Kp cgMLST scheme. For ST101, we observed 14 and 54 allele differences when using cgMLST and wgMLST SeqSphere+, respectively, and 2–5 allelic mismatches for BIGSdb-Kp cgMLST. A low genetic distance (<0.0035, a previously established threshold for epidemiological link) was generally in concordance with a low number of allele differences (<8) when using the SeqSphere+ cgMLST scheme. The cgSNP analysis showed 6–29 SNPs in isolates with identical allelic SeqSphere+ cgMLST profiles and 16–61 cgSNPs among ST405 isolates. Furthermore, comparison of WGS-based typing results with previously obtained MLST and pulsed-field gel electrophoresis (PFGE) data showed some differences, demonstrating the different molecular principles underlying these techniques. In conclusion, the use of the different WGS-based typing methods that were used to elucidate the genetic relatedness of clonal OXA-48-producing K. pneumoniae all led to the same conclusions. Furthermore, threshold parameters in WGS-based typing methods should be applied with caution and should be used in combination with clinical epidemiological data and population and species characteristics.
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Affiliation(s)
- Elisenda Miro
- Department of Microbiology, Hospital de la Santa Creu i Sant Pau, Institut d'Investigació Biomèdica Sant Pau (IIB Sant Pau), Barcelona, Spain
| | - John W A Rossen
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, Groningen, Netherlands.,ESCMID Study Group for Genomic and Molecular Diagnostics (ESGMD), Basel, Switzerland
| | - Monika A Chlebowicz
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Dag Harmsen
- Department of Periodontology and Restorative Dentistry, University of Münster, Münster, Germany
| | - Sylvain Brisse
- Biodiversity and Epidemiology of Bacterial Pathogens, Institut Pasteur, Paris, France
| | - Virginie Passet
- Biodiversity and Epidemiology of Bacterial Pathogens, Institut Pasteur, Paris, France
| | - Ferran Navarro
- Department of Microbiology, Hospital de la Santa Creu i Sant Pau, Institut d'Investigació Biomèdica Sant Pau (IIB Sant Pau), Barcelona, Spain
| | - Alex W Friedrich
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - S García-Cobos
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
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30
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Aardema H, Lisotto P, Kurilshikov A, Diepeveen JRJ, Friedrich AW, Sinha B, de Smet AMGA, Harmsen HJM. Marked Changes in Gut Microbiota in Cardio-Surgical Intensive Care Patients: A Longitudinal Cohort Study. Front Cell Infect Microbiol 2020; 9:467. [PMID: 32010644 PMCID: PMC6974539 DOI: 10.3389/fcimb.2019.00467] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [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: 10/09/2019] [Accepted: 12/17/2019] [Indexed: 12/12/2022] Open
Abstract
Background: Virtually no studies on the dynamics of the intestinal microbiota in patients admitted to the intensive care unit (ICU) are published, despite the increasingly recognized important role of microbiota on human physiology. Critical care patients undergo treatments that are known to influence the microbiota. However, dynamics and extent of such changes are not yet fully understood. To address this topic, we analyzed the microbiota before, during and after planned major cardio surgery that, for the first time, allowed us to follow the microbial dynamics of critical care patients. In this prospective, observational, longitudinal, single center study, we analyzed the fecal microbiota using 16S rRNA gene sequencing. Results: Samples of 97 patients admitted between April 2015 and November 2016 were included. In 32 patients, data of all three time points (before, during and after admission) were available for analysis. We found a large intra-individual variation in composition of gut microbiota. During admission, a significant change in microbial composition occurred in most patients, with a significant increase in pathobionts combined with a decrease in strictly anaerobic gut bacteria, typically beneficial for health. A lower bacterial diversity during admission was associated with longer hospitalization. In most patients analyzed at all three time points, the change in microbiota during hospital stay reverted to the original composition post-discharge. Conclusions: Our study shows that, even with a short ICU stay, patients present a significant change in microbial composition shortly after admission. The unique longitudinal setup of this study displayed a restoration of the microbiota in most patients to baseline composition post-discharge, which demonstrated its great restorative capacity. A relative decrease in benign or even beneficial bacteria and increase of pathobionts shifts the microbial balance in the gut, which could have clinical relevance. In future studies, the microbiota of ICU patients should be considered a good target for optimisation.
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Affiliation(s)
- Heleen Aardema
- Department of Critical Care, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Paola Lisotto
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Alexander Kurilshikov
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Janneke R J Diepeveen
- Department of Critical Care, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Alex W Friedrich
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Bhanu Sinha
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Anne Marie G A de Smet
- Department of Critical Care, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Hermie J M Harmsen
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
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Purba AK, Ascobat P, Muchtar A, Wulandari L, Rosyid AN, Purwono PB, van der Werf TS, Friedrich AW, Postma MJ. Multidrug-Resistant Infections Among Hospitalized Adults With Community-Acquired Pneumonia In An Indonesian Tertiary Referral Hospital. Infect Drug Resist 2019; 12:3663-3675. [PMID: 31819549 PMCID: PMC6883944 DOI: 10.2147/idr.s217842] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [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: 05/31/2019] [Accepted: 08/12/2019] [Indexed: 01/12/2023] Open
Abstract
Objectives To evaluate the clinical and microbiological appearance among hospitalized pneumonia patients focusing on resistance and risk factors for mortality in a referral hospital. Patients and methods The study was an observational retrospective study on patients with CAP from 2014 to 2016 at Dr Soetomo referral hospital of Surabaya, Indonesia. All positive cultures with antimicrobial susceptibility results from blood and respiratory specimens were included. Patients infected with drug-susceptible pathogens and MDR organisms were also assessed in terms of clinical characteristics, day-3 clinical improvement, and 14-day mortality. Results Of 202 isolates, 181 possessed antimicrobial susceptibility data. S. pneumoniae was the most prevalent pathogen causing CAP (18.3%). Most patients were empirically treated with ceftriaxone (n=75; 41.4%). Among beta-lactam antibiotics, the susceptibility to the third-generation cephalosporins remained relatively high, between 67.4% and 82.3%, compared with the other beta-lactams such as amoxicillin/clavulanate and ampicillin/sulbactam (a sensitivity rate of 36.5% and 47.5, respectively). For carbapenem antibiotics, imipenem and meropenem susceptibility was 69.6% and 82.3% respectively. Approximately 22% of isolates were identified as MDR that showed significant differences in clinical outcomes of 14-day mortality rates (p<0.001). Notably, patients with day-3 improvement had a lower risk of mortality (OR= 0.06; 95% CI= 0.02–0.19). Conclusion One-fifth of causative agents among hospitalized CAP cases were identified as MDR organisms. The pathogens of MDR and non-MDR CAP remain susceptible to the third-generation cephalosporins. Together with additional consideration of culture findings and Pneumonia Severity Index (PSI) assessment, a 3-day clinical assessment is essential to predict the prognosis of 14-day mortality. ![]()
Point your SmartPhone at the code above. If you have a QR code reader the video abstract will appear. Or use: https://youtu.be/QzMqf278Mac
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Affiliation(s)
- Abdul Kr Purba
- Unit of Global Health, Department of Health Sciences, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.,Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.,Department of Pharmacology and Therapy, Faculty of Medicine, Universitas Airlangga - Dr. Soetomo Hospital, Surabaya, Indonesia.,Department of Pharmacology and Therapeutics, Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia.,Unit of PharmacoTherapy, Epidemiology and -economics (PTE2), Department of Pharmacy, Faculty of Science and Engineering, University of Groningen, Groningen, The Netherlands
| | - Purwantyastuti Ascobat
- Department of Pharmacology and Therapeutics, Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia
| | - Armen Muchtar
- Department of Pharmacology and Therapeutics, Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia
| | - Laksmi Wulandari
- Department of Pulmonology and Respiratory Medicine, Faculty of Medicine, Universitas Airlangga - Dr. Soetomo Hospital, Surabaya, Indonesia
| | - Alfian Nur Rosyid
- Department of Pulmonology and Respiratory Medicine, Faculty of Medicine, Universitas Airlangga - Dr. Soetomo Hospital, Surabaya, Indonesia
| | - Priyo Budi Purwono
- Department of Microbiology, Faculty of Medicine, Universitas Airlangga - Dr. Soetomo Hospital, Surabaya, Indonesia
| | - Tjip S van der Werf
- Department of Internal Medicine, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Alex W Friedrich
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Maarten J Postma
- Unit of Global Health, Department of Health Sciences, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.,Department of Pharmacology and Therapy, Faculty of Medicine, Universitas Airlangga - Dr. Soetomo Hospital, Surabaya, Indonesia.,Unit of PharmacoTherapy, Epidemiology and -economics (PTE2), Department of Pharmacy, Faculty of Science and Engineering, University of Groningen, Groningen, The Netherlands.,Department of Economics, Econometrics and Finance, Faculty of Economics & Business, University of Groningen, Groningen, The Netherlands
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da Cruz Campos AC, Cavallo FM, Andrade NL, van Dijl JM, Couto N, Zrimec J, Lo Ten Foe JR, Rosa ACP, Damasco PV, Friedrich AW, Chlebowicz-Flissikowska MA, Rossen JWA. Determining the Virulence Properties of Escherichia coli ST131 Containing Bacteriocin-Encoding Plasmids Using Short- and Long-Read Sequencing and Comparing Them with Those of Other E. coli Lineages. Microorganisms 2019; 7:E534. [PMID: 31698849 PMCID: PMC6920910 DOI: 10.3390/microorganisms7110534] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Revised: 10/29/2019] [Accepted: 11/01/2019] [Indexed: 01/17/2023] Open
Abstract
Escherichia coli ST131 is a clinical challenge due to its multidrug resistant profile and successful global spread. They are often associated with complicated infections, particularly urinary tract infections (UTIs). Bacteriocins play an important role to outcompete other microorganisms present in the human gut. Here, we characterized bacteriocin-encoding plasmids found in ST131 isolates of patients suffering from a UTI using both short- and long-read sequencing. Colicins Ia, Ib and E1, and microcin V, were identified among plasmids that also contained resistance and virulence genes. To investigate if the potential transmission range of the colicin E1 plasmid is influenced by the presence of a resistance gene, we constructed a strain containing a plasmid which had both the colicin E1 and blaCMY-2 genes. No difference in transmission range was found between transformant and wild-type strains. However, a statistically significantly difference was found in adhesion and invasion ability. Bacteriocin-producing isolates from both ST131 and non-ST131 lineages were able to inhibit the growth of other E. coli isolates, including other ST131. In summary, plasmids harboring bacteriocins give additional advantages for highly virulent and resistant ST131 isolates, improving the ability of these isolates to compete with other microbiota for a niche and thereby increasing the risk of infection.
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Affiliation(s)
- Ana Carolina da Cruz Campos
- Departamento de Microbiologia, Imunologia e Parasitologia, Universidade do Estado do Rio de Janeiro, Rio de Janeiro 20550-170, Brazil; (A.C.d.C.C.); (N.L.A.); (A.C.P.R.)
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713GZ Groningen, The Netherlands; (F.M.C.); (J.M.v.D.); (N.C.); (J.R.L.T.F.); (A.W.F.); (M.A.C.-F.)
| | - Francis M. Cavallo
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713GZ Groningen, The Netherlands; (F.M.C.); (J.M.v.D.); (N.C.); (J.R.L.T.F.); (A.W.F.); (M.A.C.-F.)
| | - Nathália L. Andrade
- Departamento de Microbiologia, Imunologia e Parasitologia, Universidade do Estado do Rio de Janeiro, Rio de Janeiro 20550-170, Brazil; (A.C.d.C.C.); (N.L.A.); (A.C.P.R.)
| | - Jan Maarten van Dijl
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713GZ Groningen, The Netherlands; (F.M.C.); (J.M.v.D.); (N.C.); (J.R.L.T.F.); (A.W.F.); (M.A.C.-F.)
| | - Natacha Couto
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713GZ Groningen, The Netherlands; (F.M.C.); (J.M.v.D.); (N.C.); (J.R.L.T.F.); (A.W.F.); (M.A.C.-F.)
| | - Jan Zrimec
- Department of biology and Biological Engineering, Chalmers University of Technology, Chalmersplatsen 4, 412 96 Göteborg, Sweden;
| | - Jerome R. Lo Ten Foe
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713GZ Groningen, The Netherlands; (F.M.C.); (J.M.v.D.); (N.C.); (J.R.L.T.F.); (A.W.F.); (M.A.C.-F.)
| | - Ana C. P. Rosa
- Departamento de Microbiologia, Imunologia e Parasitologia, Universidade do Estado do Rio de Janeiro, Rio de Janeiro 20550-170, Brazil; (A.C.d.C.C.); (N.L.A.); (A.C.P.R.)
| | - Paulo V. Damasco
- Departamento de Doenças Infecciosas e Parasitárias, Universidade Federal do Estado do Rio de Janeiro, Rua Voluntário da Patria, 21, Rio de Janeiro 941-901107, Brazil;
| | - Alex W. Friedrich
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713GZ Groningen, The Netherlands; (F.M.C.); (J.M.v.D.); (N.C.); (J.R.L.T.F.); (A.W.F.); (M.A.C.-F.)
| | - Monika A. Chlebowicz-Flissikowska
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713GZ Groningen, The Netherlands; (F.M.C.); (J.M.v.D.); (N.C.); (J.R.L.T.F.); (A.W.F.); (M.A.C.-F.)
| | - John W. A. Rossen
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713GZ Groningen, The Netherlands; (F.M.C.); (J.M.v.D.); (N.C.); (J.R.L.T.F.); (A.W.F.); (M.A.C.-F.)
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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] [What about the content of this article? (0)] [Affiliation(s)] [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.
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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
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Rubio‐Garcia A, Rossen JWA, Wagenaar JA, Friedrich AW, Zeijl JH. Livestock‐associated meticillin‐resistant Staphylococcus aureusin a young harbour seal ( Phoca vitulina) with endocarditis. Vet rec case rep 2019. [DOI: 10.1136/vetreccr-2019-000886] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Affiliation(s)
- Ana Rubio‐Garcia
- Department of Infectious Diseases and ImmunologyUtrecht University Faculty of Veterinary MedicineUtrechtThe Netherlands
- Veterinary and Research DepartmentSealcentre PieterburenPieterburenThe Netherlands
| | - John W A Rossen
- Department of Medical Microbiology and Infection PreventionUniversity Medical Center GroningenGroningenThe Netherlands
| | - Jaap A Wagenaar
- Department of Infectious Diseases and ImmunologyUtrecht University Faculty of Veterinary MedicineUtrechtThe Netherlands
- Wageningen Bioveterinary ResearchLelystadThe Netherlands
| | - Alex W Friedrich
- Department of Medical Microbiology and Infection PreventionUniversity Medical Center GroningenGroningenThe Netherlands
| | - Jan H Zeijl
- Department of Medical MicrobiologyIzore Center for Infectious DiseasesLeeuwardenThe Netherlands
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Kluytmans-van den Bergh MFQ, Bruijning-Verhagen PCJ, Vandenbroucke-Grauls CMJE, de Brauwer EIGB, Buiting AGM, Diederen BM, van Elzakker EPM, Friedrich AW, Hopman J, Al Naiemi N, Rossen JWA, Ruijs GJHM, Savelkoul PHM, Verhulst C, Vos MC, Voss A, Bonten MJM, Kluytmans JAJW. Contact precautions in single-bed or multiple-bed rooms for patients with extended-spectrum β-lactamase-producing Enterobacteriaceae in Dutch hospitals: a cluster-randomised, crossover, non-inferiority study. Lancet Infect Dis 2019; 19:1069-1079. [PMID: 31451419 DOI: 10.1016/s1473-3099(19)30262-2] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 04/24/2019] [Accepted: 05/21/2019] [Indexed: 02/07/2023]
Abstract
BACKGROUND Use of single-bed rooms for control of extended-spectrum β-lactamase (ESBL)-producing Enterobacteriaceae is under debate; the added value when applying contact precautions has not been shown. We aimed to assess whether an isolation strategy of contact precautions in a multiple-bed room was non-inferior to a strategy of contact precautions in a single-bed room for preventing transmission of ESBL-producing Enterobacteriaceae. METHODS We did a cluster-randomised, crossover, non-inferiority study on medical and surgical wards of 16 Dutch hospitals. During two consecutive study periods, either contact precautions in a single-bed room or contact precautions in a multiple-bed room were applied as the preferred isolation strategy for patients with ESBL-producing Enterobacteriaceae cultured from a routine clinical sample (index patients). Eligible index patients were aged 18 years or older, had no strict indication for barrier precautions in a single-bed room, had a culture result reported within 7 days of culture and before discharge, and had no wardmate known to be colonised or infected with an ESBL-producing Enterobacteriaceae isolate of the same bacterial species with a similar antibiogram. Hospitals were randomly assigned in a 1:1 ratio by computer to one of two sequences of isolation strategies, stratified by university or non-university hospital. Allocation was masked for laboratory technicians who assessed the outcomes but not for patients, treating doctors, and infection-control practitioners enrolling index patients. The primary outcome was transmission of ESBL-producing Enterobacteriaceae to wardmates, which was defined as rectal carriage of an ESBL-producing Enterobacteriaceae isolate that was clonally related to the index patient's isolate in at least one wardmate. The primary analysis was done in the per-protocol population, which included patients who were adherent to the assigned room type. A 10% non-inferiority margin for the risk difference was used to assess non-inferiority. This study is registered with Nederlands Trialregister, NTR2799. FINDINGS 16 hospitals were randomised, eight to each sequence of isolation strategies. All hospitals randomised to the sequence single-bed room then multiple-bed room and five of eight hospitals randomised to the sequence multiple-bed room then single-bed room completed both study periods and were analysed. From April 24, 2011, to Feb 27, 2014, 1652 index patients and 12 875 wardmates were assessed for eligibility. Of those, 693 index patients and 9527 wardmates were enrolled and 463 index patients and 7093 wardmates were included in the per-protocol population. Transmission of ESBL-producing Enterobacteriaceae to at least one wardmate was identified for 11 (4%) of 275 index patients during the single-bed room strategy period and for 14 (7%) of 188 index patients during the multiple-bed room strategy period (crude risk difference 3·4%, 90% CI -0·3 to 7·1). INTERPRETATION For patients with ESBL-producing Enterobacteriaceae cultured from a routine clinical sample, an isolation strategy of contact precautions in a multiple-bed room was non-inferior to a strategy of contact precautions in a single-bed room for preventing transmission of ESBL-producing Enterobacteriaceae. Non-inferiority of the multiple-bed room strategy might change the current single-bed room preference for isolation of patients with ESBL-producing Enterobacteriaceae and, thus, broaden infection-control options for ESBL-producing Enterobacteriaceae in daily clinical practice. FUNDING Netherlands Organisation for Health Research and Development.
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Affiliation(s)
- Marjolein F Q Kluytmans-van den Bergh
- Department of Infection Control, Amphia Hospital, Breda, Netherlands; Amphia Academy Infectious Disease Foundation, Amphia Hospital, Breda, Netherlands; Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, University of Utrecht, Utrecht, Netherlands.
| | - Patricia C J Bruijning-Verhagen
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, University of Utrecht, Utrecht, Netherlands
| | - Christina M J E Vandenbroucke-Grauls
- Department of Medical Microbiology and Infection Control, Amsterdam University Medical Center, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | | | - Anton G M Buiting
- Laboratory for Medical Microbiology and Immunology, Elisabeth-TweeSteden Hospital, Tilburg, Netherlands
| | - Bram M Diederen
- Regional Laboratory of Public Health, Haarlem, Netherlands; Microvida Laboratory for Microbiology, Bravis Hospital, Roosendaal, Netherlands
| | | | - Alex W Friedrich
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Joost Hopman
- Department of Medical Microbiology, Radboud University Medical Center, Nijmegen, Netherlands
| | - Nashwan Al Naiemi
- Department of Medical Microbiology and Infection Control, Ziekenhuisgroep Twente, Almelo/Hengelo, Netherlands
| | - John W A Rossen
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Gijs J H M Ruijs
- Laboratory for Microbiology and Infectious Diseases, Isala Clinics, Zwolle, Netherlands
| | - Paul H M Savelkoul
- Department of Medical Microbiology and Infection Control, Amsterdam University Medical Center, Vrije Universiteit Amsterdam, Amsterdam, Netherlands; Department of Medical Microbiology, Maastricht University Medical Center+, Maastricht, Netherlands
| | - Carlo Verhulst
- Microvida Laboratory for Microbiology, Amphia Hospital, Breda, Netherlands
| | - Margreet C Vos
- Department of Medical Microbiology and Infectious Diseases, Erasmus Medical Center, Rotterdam, Netherlands
| | - Andreas Voss
- Department of Medical Microbiology, Radboud University Medical Center, Nijmegen, Netherlands; Department of Medical Microbiology, Canisius Wilhelmina Hospital, Nijmegen, Netherlands
| | - Marc J M Bonten
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, University of Utrecht, Utrecht, Netherlands; Department of Medical Microbiology, University Medical Center Utrecht, University of Utrecht, Utrecht, Netherlands
| | - Jan A J W Kluytmans
- Department of Infection Control, Amphia Hospital, Breda, Netherlands; Microvida Laboratory for Microbiology, Amphia Hospital, Breda, Netherlands; Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, University of Utrecht, Utrecht, Netherlands
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Peker N, Garcia-Croes S, Dijkhuizen B, Wiersma HH, van Zanten E, Wisselink G, Friedrich AW, Kooistra-Smid M, Sinha B, Rossen JWA, Couto N. A Comparison of Three Different Bioinformatics Analyses of the 16S-23S rRNA Encoding Region for Bacterial Identification. Front Microbiol 2019; 10:620. [PMID: 31040829 PMCID: PMC6476902 DOI: 10.3389/fmicb.2019.00620] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [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: 10/25/2018] [Accepted: 03/12/2019] [Indexed: 11/25/2022] Open
Abstract
Rapid and reliable identification of bacterial pathogens directly from patient samples is required for optimizing antimicrobial therapy. Although Sanger sequencing of the 16S ribosomal RNA (rRNA) gene is used as a molecular method, species identification and discrimination is not always achievable for bacteria as their 16S rRNA genes have sometimes high sequence homology. Recently, next generation sequencing (NGS) of the 16S–23S rRNA encoding region has been proposed for reliable identification of pathogens directly from patient samples. However, data analysis is laborious and time-consuming and a database for the complete 16S–23S rRNA encoding region is not available. Therefore, a better, faster, and stronger approach is needed for NGS data analysis of the 16S–23S rRNA encoding region. We compared speed and diagnostic accuracy of different data analysis approaches: de novo assembly followed by Basic Local Alignment Search Tool (BLAST), operational taxonomic unit (OTU) clustering, or mapping using an in-house developed 16S–23S rRNA encoding region database for the identification of bacterial species. De novo assembly followed by BLAST using the in-house database was superior to the other methods, resulting in the shortest turnaround time (2 h and 5 min), approximately 2 h less than OTU clustering and 4.5 h less than mapping, and a sensitivity of 80%. Mapping was the slowest and most laborious data analysis approach with a sensitivity of 60%, whereas OTU clustering was the least laborious approach with 70% sensitivity. Although the in-house database requires more sequence entries to improve the sensitivity, the combination of de novo assembly and BLAST currently appears to be the optimal approach for data analysis.
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Affiliation(s)
- Nilay Peker
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Sharron Garcia-Croes
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Brigitte Dijkhuizen
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Henry H Wiersma
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Evert van Zanten
- Department of Medical Microbiology, Certe, Groningen, Netherlands
| | - Guido Wisselink
- Department of Medical Microbiology, Certe, Groningen, Netherlands
| | - Alex W Friedrich
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Mirjam Kooistra-Smid
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, Groningen, Netherlands.,Department of Medical Microbiology, Certe, Groningen, Netherlands
| | - Bhanu Sinha
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - John W A Rossen
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Natacha Couto
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
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Jurke A, Daniels-Haardt I, Silvis W, Berends MS, Glasner C, Becker K, Köck R, Friedrich AW. Changing epidemiology of meticillin-resistant Staphylococcus aureus in 42 hospitals in the Dutch-German border region, 2012 to 2016: results of the search-and-follow-policy. Euro Surveill 2019; 24:1800244. [PMID: 30994105 PMCID: PMC6470371 DOI: 10.2807/1560-7917.es.2019.24.15.1800244] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Accepted: 03/03/2019] [Indexed: 11/20/2022] Open
Abstract
IntroductionMeticillin-resistant Staphylococcus aureus (MRSA) is a major cause of healthcare-associated infections.AimWe describe MRSA colonisation/infection and bacteraemia rate trends in Dutch-German border region hospitals (NL-DE-BRH) in 2012-16.MethodsAll 42 NL-DE BRH (8 NL-BRH, 34 DE-BRH) within the cross-border network EurSafety Health-net provided surveillance data (on average ca 620,000 annual hospital admissions, of these 68.0% in Germany). Guidelines defining risk for MRSA colonisation/infection were reviewed. MRSA-related parameters and healthcare utilisation indicators were derived. Medians over the study period were compared between NL- and DE-BRH.ResultsMeasures for MRSA cases were similar in both countries, however defining patients at risk for MRSA differed. The rate of nasopharyngeal MRSA screening swabs was 14 times higher in DE-BRH than in NL-BRH (42.3 vs 3.0/100 inpatients; p < 0.0001). The MRSA incidence was over seven times higher in DE-BRH than in NL-BRH (1.04 vs 0.14/100 inpatients; p < 0.0001). The nosocomial MRSA incidence-density was higher in DE-BRH than in NL-BRH (0.09 vs 0.03/1,000 patient days; p = 0.0002) and decreased significantly in DE-BRH (p = 0.0184) during the study. The rate of MRSA isolates from blood per 100,000 patient days was almost six times higher in DE-BRH than in NL-BRH (1.55 vs 0.26; p = 0.0041). The patients had longer hospital stays in DE-BRH than in NL-BRH (6.8 vs 4.9; p < 0.0001). DE-BRH catchment area inhabitants appeared to be more frequently hospitalised than their Dutch counterparts.ConclusionsOngoing IPC efforts allowed MRSA reduction in DE-BRH. Besides IPC, other local factors, including healthcare systems, could influence MRSA epidemiology.
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Affiliation(s)
- Annette Jurke
- North Rhine-Westphalian Centre for Health, Section Infectious Disease Epidemiology, Bochum, Germany
| | - Inka Daniels-Haardt
- North Rhine-Westphalian Centre for Health, Department Health Promotion, Health Protection, Bochum, Germany
| | - Welmoed Silvis
- Laboratory for Medical Microbiology and Public Health (LabMicTA), Hengelo, Netherlands
| | - Matthijs S Berends
- Certe Medical Diagnostics and Advice, Groningen, Netherlands
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology and Infection Prevention, Groningen, Netherlands
| | - Corinna Glasner
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology and Infection Prevention, Groningen, Netherlands
| | - Karsten Becker
- University Hospital Münster, University of Münster, Institute of Medical Microbiology, Münster, Germany
| | - Robin Köck
- University Hospital Münster, University of Münster, Institute of Medical Microbiology, Münster, Germany
- University Hospital Münster, University of Münster, Institute for Hygiene, Münster, Germany
- Institute of Hygiene, DRK Kliniken Berlin, Berlin, Germany
| | - Alex W Friedrich
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology and Infection Prevention, Groningen, Netherlands
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Friedrich AW. Control of hospital acquired infections and antimicrobial resistance in Europe: the way to go. Wien Med Wochenschr 2019; 169:25-30. [PMID: 30623278 PMCID: PMC6373234 DOI: 10.1007/s10354-018-0676-5] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 11/21/2018] [Indexed: 11/17/2022]
Abstract
One of the major challenges for modern medicine is our ageing society and an increased level of immunocompromised hosts. More invasive and intensive medical interventions will increase the number of healthcare-associated infections (HCAI), which means infection that occur because of or in concomitance, but in any case, during or after healthcare interventions. Such infections are caused usually endogenously from microbial components of the patient’s own microbiome. Usually, the microorganisms of the microbiome show a natural resistance against a few antibiotics. Due to selection processes and epidemic transmission of specific clones, microorganisms that have become resistant to multiple antibiotics become part of the patient’s microbiome and can subsequently cause infections that are difficult or even impossible to treat. The kind of infections that will occur depends on diverse factors. Already today, according to Cassini et al., 2,609,911 new cases of HCAI occur every year in the European Union and European Economic Area (EU/EEA). The cumulative burden of the six HAIs was estimated at 501 disability-adjusted life years (DALYs) per 100,000 general population each year in the EU/EEA. In a recent publication, 426,277 healthcare-associated infections caused by antimicrobial resistant microorganisms were calculated to occur in the EU every year. Attributable deaths in the EU due to antimicrobial resistant microorganisms were estimated to be 33,110 per year. We know that we cannot prevent all HCAI. Because medical innovations will allow for an increased number of novel treatments that will comprise abiotic materials, microorganisms will adapt to this environment and enhance the risk for new HCAI. The challenge for the future will not be to try to prevent all infections, as some of them will remain unavoidable, but to prevent the occurrence of non-treatable microorganisms that would make unavoidable infections additionally untreatable. That means that we need to reflect on how we organize infection prevention, diagnostics and control. While patients with classical infectious diseases present with infectious diseases (ID)-specific symptoms, patients with HCAI present usually with another underlying disease. HCAI are therefore perceived as a secondary damage not following classical clinical and epidemiological rules. However, more recently we have to consider how we should react to HCAI and antimicrobial resistance (AMR) as they are quite different in epidemiology and transmission behavior than classical infectious diseases. Today, the prevalence of AMR is rising all over Europe. Although good success has been seen in many countries, methicillin-resistant Staphylococcus aureus (MRSA) remains an important challenge for many countries. In addition to MRSA, multidrug-resistant Escherichia coli and carbapenem-resistant Enterobacteriaceae are becoming a problem of public health importance. Furthermore, we need to focus more on implementation of known infection prevention measures than trying to solve the problem by observing and describing it. However, in addition to medical factors such as antibiotic use, hand hygiene etc., we tend to forget that there are factors behind these factors that have a major influence and are found in the structures of our different healthcare systems. We need to look more at the context before we try to implement prevention measures and need to learn from each other. A common goal to tackle carbapenem-resistant Enterobacteriaceae (CRE) by 2030 would be an important step to foster collaboration across Europe. As the current funding and remmuneration system does not sufficiently support prevention of HCAI and AMR, it is time for the development of a less production- but more prevention-economic financing system for clinical microbiology and infection control.
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Affiliation(s)
- Alex W Friedrich
- Department of Medical Microbiology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands.
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van Rijt AM, Dik JWH, Lokate M, Postma MJ, Friedrich AW. Cost analysis of outbreaks with Methicillin-resistant Staphylococcus aureus (MRSA) in Dutch long-term care facilities (LTCF). PLoS One 2018; 13:e0208092. [PMID: 30475904 PMCID: PMC6258236 DOI: 10.1371/journal.pone.0208092] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [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: 03/23/2018] [Accepted: 11/12/2018] [Indexed: 12/14/2022] Open
Abstract
Objectives Highly resistant microorganisms (HRMOs) are of high concern worldwide and are becoming increasingly less susceptible for antibiotics. To study the cost effectiveness of infection prevention measures in long-term care, it is essential to first fully understand the impact of HRMOs. The objective of this study is to identify the costs associated with outbreaks caused by Methicillin-resistant Staphylococcus aureus (MRSA) in Dutch long-term care facilities (LTCF). Methods After an outbreak of MRSA, Dutch LTCF can submit a reimbursement form to the Dutch Healthcare Authority (“Nederlandse Zorgautoriteit”; NZa) to get a part of the total costs reimbursed. In this study, we requested NZa forms for financial impact analysis. Details regarding the costs of the outbreak have been extracted from these forms and additionally specific LTCF have been visited in person to validate the data. Results 34 complete reimbursement forms from the period between 2011 and 2016 were received from the NZa and have been included. The median cost per patient per day was estimated at €83.80, varying between €16.89 and €1,820.09. We validated five reimbursement forms by visiting the facility and recalculating the costs. We found a non-significant positive difference of €26.07 compared with the original data (p = 0.068). Conclusions This study is to our knowledge the first to give a national overview of total costs associated with an MRSA outbreak in LTCF in the Netherlands. Overall, costs per patient per day seem lower than in a hospital setting, although total costs are much higher due to the long term of care.
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Affiliation(s)
- Antonius M. van Rijt
- Department of Medical Microbiology, University Medical Center Groningen, Groningen, The Netherlands
| | - Jan-Willem H. Dik
- Department of Medical Microbiology, University Medical Center Groningen, Groningen, The Netherlands
| | - Mariëtte Lokate
- Department of Medical Microbiology, University Medical Center Groningen, Groningen, The Netherlands
| | - Maarten J. Postma
- Faculty of Medical Sciences, University of Groningen, Groningen, The Netherlands
| | - Alex W. Friedrich
- Department of Medical Microbiology, University Medical Center Groningen, Groningen, The Netherlands
- * E-mail:
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Scudeller L, Rodríguez-Baño J, Zinkernagel A, Tacconelli E, Akova M, Friedrich AW, Sanguinetti M, Paul M, Poljak M. ESCMID white paper: a guide on ESCMID guidance documents. Clin Microbiol Infect 2018; 25:155-162. [PMID: 30145398 DOI: 10.1016/j.cmi.2018.08.005] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Revised: 08/03/2018] [Accepted: 08/07/2018] [Indexed: 10/28/2022]
Abstract
BACKGROUND AND AIM The European Society of Clinical Microbiology and Infectious Diseases (ESCMID) aims to further develop its role in international medical and scientific guidance in the field of Clinical Microbiology and Infectious Diseases, where many types of guidance documents exist. The ESCMID Executive Committee and the Clinical Microbiology and Infection (CMI) editorial board wish to clarify the terminology and format to be used in ESCMID guidance documents submitted for publication in CMI, and to highlight the principles behind ESCMID guidance documents. TYPES OF GUIDANCE DOCUMENTS There are five types of ESCMID guidance documents: White Papers, Clinical Practice Guidelines, Consensus Statements, State-of-the-Science Statements, and Position Papers. They differ in scope, methods of development, drafting group composition and preferred publication format. Guidance documents can be proposed, developed and published by ESCMID Study Groups, Committees and individual members; often, other scientific societies are involved. The full disclosure of potential conflicts of interest of all drafting group members is a requirement. FINAL REMARKS Guidance documents constitute a common cultural and scientific background to people in the same and related professions. Also, they are an important educational and training tool. Developing a guidance document is a scientific endeavour, where a sound and transparent development process is needed, requiring multidisciplinary and personal skills.
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Affiliation(s)
- L Scudeller
- IRCCS Policlinic San Matteo Foundation, Pavia, Italy.
| | - J Rodríguez-Baño
- Sección Enfermedades Infecciosas, Hospital Universitario Virgen Macarena, Sevilla, Spain
| | - A Zinkernagel
- FMH Innere Medizin und FMH Infektiologie, Universitätsspital Zürich, Zürich, Switzerland
| | | | - M Akova
- Department of Infectious Diseases, Hacettepe University, School of Medicine, Sihhiye, Ankara, Turkey
| | - A W Friedrich
- UMCG Medical Microbiology, Groningen, The Netherlands
| | | | - M Paul
- Infectious Diseases Institute, Rambam Health Care Campus, The Ruth and Bruce Rappaport Faculty of Medicine, Technion Israel Institute of Technology, Haifa, Israel; CMI Editorial Office, Israel
| | - M Poljak
- Institute of Microbiology and Immunology, University of Ljubljana, Ljubljana, Slovenia
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Purba AKR, Setiawan D, Bathoorn E, Postma MJ, Dik JWH, Friedrich AW. Prevention of Surgical Site Infections: A Systematic Review of Cost Analyses in the Use of Prophylactic Antibiotics. Front Pharmacol 2018; 9:776. [PMID: 30072898 PMCID: PMC6060435 DOI: 10.3389/fphar.2018.00776] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [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: 03/23/2018] [Accepted: 06/26/2018] [Indexed: 12/18/2022] Open
Abstract
Introduction: The preoperative phase is an important period in which to prevent surgical site infections (SSIs). Prophylactic antibiotic use helps to reduce SSI rates, leading to reductions in hospitalization time and cost. In clinical practice, besides effectiveness and safety, the selection of prophylactic antibiotic agents should also consider the evidence with regard to costs and microbiological results. This review assessed the current research related to the use of antibiotics for SSI prophylaxis from an economic perspective and the underlying epidemiology of microbiological findings. Methods: A literature search was carried out through PubMed and Embase databases from 1 January 2006 to 31 August 2017. The relevant studies which reported the use of prophylactic antibiotics, SSI rates, and costs were included for analysis. The causing pathogens for SSIs were categorized by sites of the surgery. The quality of reporting on each included study was assessed with the “Consensus on Health Economic Criteria” (CHEC). Results: We identified 20 eligible full-text studies that met our inclusion criteria, which were subsequently assessed, studies had in a reporting quality scored on the CHEC list averaging 13.03 (8–18.5). Of the included studies, 14 were trial-based studies, and the others were model-based studies. The SSI rates ranged from 0 to 71.1% with costs amounting to US$480-22,130. Twenty-four bacteria were identified as causative agents of SSIs. Gram negatives were the dominant causes of SSIs especially in general surgery, neurosurgery, cardiothoracic surgery, and obstetric cesarean sections. Conclusions: Varying results were reported in the studies reviewed. Yet, information from both trial-based and model-based costing studies could be considered in the clinical implementation of proper and efficient use of prophylactic antibiotics to prevent SSIs and antimicrobial resistance.
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Affiliation(s)
- Abdul K R Purba
- Department of Health Sciences, University of Groningen, University Medical Center Groningen, Groningen, Netherlands.,Department of Pharmacology and Therapy, Faculty of Medicine, Universitas Airlangga, Surabaya, Indonesia.,Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Didik Setiawan
- Unit of PharmacoEpidemiology & Pharmacoeconomics (PE2), Department of Pharmacy, University of Groningen, Groningen, Netherlands.,Department of Pharmacology and Clinical Pharmacy, Faculty of Pharmacy, Universitas Muhammadiyah Purwokerto, Purwokerto, Indonesia
| | - Erik Bathoorn
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Maarten J Postma
- Department of Health Sciences, University of Groningen, University Medical Center Groningen, Groningen, Netherlands.,Department of Pharmacology and Therapy, Faculty of Medicine, Universitas Airlangga, Surabaya, Indonesia.,Unit of PharmacoEpidemiology & Pharmacoeconomics (PE2), Department of Pharmacy, University of Groningen, Groningen, Netherlands.,Department of Economics, Econometrics & Finance, Faculty of Economics & Business, University of Groningen, Groningen, Netherlands
| | - Jan-Willem H Dik
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Alex W Friedrich
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
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Veloo ACM, Jean-Pierre H, Justesen US, Morris T, Urban E, Wybo I, Kostrzewa M, Friedrich AW, On Behalf Of The Enria Workgroup. An overview of the data obtained during the validation of an optimized MALDI-TOF MS Biotyper database for the identification of anaerobic bacteria. Data Brief 2018; 18:1484-1496. [PMID: 29904651 PMCID: PMC5998164 DOI: 10.1016/j.dib.2018.04.070] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Revised: 04/10/2018] [Accepted: 04/18/2018] [Indexed: 12/01/2022] Open
Abstract
This data in brief article presents the data obtained during the validation of the optimized Biotyper Matrix Assisted Laser Desorption Ionization Time-of-Flight Mass Spectrometry (MALDI-TOF MS) database. The validation was performed by the different expertise laboratories, collaborating within the European Network for the Rapid Identification of Anaerobes (ENRIA) project, using 6309 human clinical anaerobic bacterial strains. Different databases were compared with each other; the db 5989 database (V5 database); the V5 database complimented with Main Spectral Profiles (MSPs) of ENRIA strains added to the next update of the database; and the V5 database complimented with the MSPs of all anaerobic clinical isolates collected within the ENRIA project. For a comprehensive discussion of the full dataset, please see the research article that accompanies this data article (Veloo et al., 2018) [1]
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Affiliation(s)
- A C M Veloo
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology, Groningen, The Netherlands
| | - H Jean-Pierre
- Centre Hospitalier Universitaire de Montpellier, Hôpital Arnaud de Villeneuve, Laboratoire de Bactériologie, 371 Avenue du Doyen Gaston Giraud, 34295 Montpellier Cedex 5, France.,Université Montpellier 1, UMR5119 ECOSYM, Equipe Pathogènes Hydriques Santé Environnements, UMR 5569 Hydrosciences, UFR Pharmacie, 15 avenue Charles Flahault, 34093 Montpellier Cedex 5, France
| | - U S Justesen
- Department of Clinical Microbiology, Odense University Hospital, Odense, Denmark
| | - T Morris
- UK Anaerobe Reference Unit, Public Health Wales Microbiology, Cardiff, UK
| | - E Urban
- Institute of Clinical Microbiology, University of Szeged, Hungary
| | - I Wybo
- Department of Microbiology and Infection Control, Universitair Ziekenhuis Brussel, Brussels, Belgium
| | | | - A W Friedrich
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology, Groningen, The Netherlands
| | - On Behalf Of The Enria Workgroup
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology, Groningen, The Netherlands.,Centre Hospitalier Universitaire de Montpellier, Hôpital Arnaud de Villeneuve, Laboratoire de Bactériologie, 371 Avenue du Doyen Gaston Giraud, 34295 Montpellier Cedex 5, France.,Université Montpellier 1, UMR5119 ECOSYM, Equipe Pathogènes Hydriques Santé Environnements, UMR 5569 Hydrosciences, UFR Pharmacie, 15 avenue Charles Flahault, 34093 Montpellier Cedex 5, France.,Department of Clinical Microbiology, Odense University Hospital, Odense, Denmark.,UK Anaerobe Reference Unit, Public Health Wales Microbiology, Cardiff, UK.,Institute of Clinical Microbiology, University of Szeged, Hungary.,Department of Microbiology and Infection Control, Universitair Ziekenhuis Brussel, Brussels, Belgium.,Bruker Daltonics, Bremen, Germany
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Köck R, Daniels-Haardt I, Becker K, Mellmann A, Friedrich AW, Mevius D, Schwarz S, Jurke A. Carbapenem-resistant Enterobacteriaceae in wildlife, food-producing, and companion animals: a systematic review. Clin Microbiol Infect 2018; 24:1241-1250. [PMID: 29654871 DOI: 10.1016/j.cmi.2018.04.004] [Citation(s) in RCA: 182] [Impact Index Per Article: 30.3] [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: 12/18/2017] [Revised: 03/30/2018] [Accepted: 04/04/2018] [Indexed: 01/05/2023]
Abstract
OBJECTIVES The spread of carbapenem-resistant Enterobacteriaceae (CRE) in healthcare settings challenges clinicians worldwide. However, little is known about dissemination of CRE in livestock, food, and companion animals and potential transmission to humans. METHODS We performed a systematic review of all studies published in the PubMed database between 1980 and 2017 and included those reporting the occurrence of CRE in samples from food-producing and companion animals, wildlife, and exposed humans. The primary outcome was the occurrence of CRE in samples from these animals; secondary outcomes included the prevalence of CRE, carbapenemase types, CRE genotypes, and antimicrobial susceptibilities. RESULTS We identified 68 articles describing CRE among pigs, poultry, cattle, seafood, dogs, cats, horses, pet birds, swallows, wild boars, wild stork, gulls, and black kites in Africa, America, Asia, Australia, and Europe. The following carbapenemases have been detected (predominantly affecting the genera Escherichia and Klebsiella): VIM, KPC, NDM, OXA, and IMP. Two studies found that 33-67% of exposed humans on poultry farms carried carbapenemase-producing CRE closely related to isolates from the farm environment. Twenty-seven studies selectively screened samples for CRE and found a prevalence of <1% among livestock and companion animals in Europe, 2-26% in Africa, and 1-15% in Asia. Wildlife (gulls) in Australia and Europe carried CRE in 16-19%. CONCLUSIONS The occurrence of CRE in livestock, seafood, wildlife, pets, and directly exposed humans poses a risk for public health. Prospective prevalence studies using molecular and cultural microbiological methods are needed to better define the scope and transmission of CRE.
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Affiliation(s)
- R Köck
- University Hospital Münster, University of Münster, Institute of Medical Microbiology, Münster, Germany; University Hospital Münster, University of Münster, Institute for Hygiene, Münster, Germany; Institute of Hospital Hygiene Oldenburg, Oldenburg, Germany.
| | - I Daniels-Haardt
- NRW Centre for Health, Section Infectious Disease Epidemiology, Bochum, Germany
| | - K Becker
- University Hospital Münster, University of Münster, Institute of Medical Microbiology, Münster, Germany
| | - A Mellmann
- University Hospital Münster, University of Münster, Institute for Hygiene, Münster, Germany
| | - A W Friedrich
- Department for Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - D Mevius
- Wageningen Bioveterinary Research, Department of Bacteriology and Epidemiology, Lelystad, The Netherlands; Faculty of Veterinary Medicine, Department of Infectious Diseases & Immunology, Utrecht University, Utrecht, The Netherlands
| | - S Schwarz
- Freie Universität Berlin, Institute of Microbiology and Epizootics, Berlin, Germany
| | - A Jurke
- NRW Centre for Health, Section Infectious Disease Epidemiology, Bochum, Germany
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Tacconelli E, Carrara E, Savoldi A, Harbarth S, Mendelson M, Monnet DL, Pulcini C, Kahlmeter G, Kluytmans J, Carmeli Y, Ouellette M, Outterson K, Patel J, Cavaleri M, Cox EM, Houchens CR, Grayson ML, Hansen P, Singh N, Theuretzbacher U, Magrini N, Aboderin AO, Al-Abri SS, Awang Jalil N, Benzonana N, Bhattacharya S, Brink AJ, Burkert FR, Cars O, Cornaglia G, Dyar OJ, Friedrich AW, Gales AC, Gandra S, Giske CG, Goff DA, Goossens H, Gottlieb T, Guzman Blanco M, Hryniewicz W, Kattula D, Jinks T, Kanj SS, Kerr L, Kieny MP, Kim YS, Kozlov RS, Labarca J, Laxminarayan R, Leder K, Leibovici L, Levy-Hara G, Littman J, Malhotra-Kumar S, Manchanda V, Moja L, Ndoye B, Pan A, Paterson DL, Paul M, Qiu H, Ramon-Pardo P, Rodríguez-Baño J, Sanguinetti M, Sengupta S, Sharland M, Si-Mehand M, Silver LL, Song W, Steinbakk M, Thomsen J, Thwaites GE, van der Meer JWM, Van Kinh N, Vega S, Villegas MV, Wechsler-Fördös A, Wertheim HFL, Wesangula E, Woodford N, Yilmaz FO, Zorzet A. Discovery, research, and development of new antibiotics: the WHO priority list of antibiotic-resistant bacteria and tuberculosis. The Lancet Infectious Diseases 2018; 18:318-327. [DOI: 10.1016/s1473-3099(17)30753-3] [Citation(s) in RCA: 2242] [Impact Index Per Article: 373.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Revised: 10/13/2017] [Accepted: 11/01/2017] [Indexed: 12/12/2022]
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Krüger A, Burgán J, Friedrich AW, Rossen JWA, Lucchesi PMA. ArgO145, a Stx2a prophage of a bovine O145:H- STEC strain, is closely related to phages of virulent human strains. Infect Genet Evol 2018; 60:126-132. [PMID: 29476813 DOI: 10.1016/j.meegid.2018.02.024] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Revised: 01/18/2018] [Accepted: 02/17/2018] [Indexed: 01/08/2023]
Abstract
Shiga toxins (Stx) are the main virulence factor of a pathogroup of Escherichia coli strains that cause severe human diseases. These toxins are encoded in prophages (Stx prophages), and generally their expression depends on prophage induction. Several studies have reported high diversity among both Stx prophages and Stx. In particular, the toxin subtype Stx2a is associated with high virulence and HUS. Here, we report the genome of ArgO145, an inducible Stx2a prophage identified in a bovine O145:H- strain which produced high levels of Shiga toxin and Stx phage particles. The ArgO145 genome shared lambda phage organization, with recombination, regulation, replication, lysis, and head and tail structural gene regions, although some lambda genes encoding regulatory proteins could not be identified. Remarkably, some Stx2a phages of strains isolated from patients in other countries showed high similarity to ArgO145.
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Affiliation(s)
- A Krüger
- Centro de Investigación Veterinaria de Tandil (CIVETAN), UNCPBA-CONICET-CIC, Laboratorio de Inmunoquímica y Biotecnología, Argentina.
| | - J Burgán
- Centro de Investigación Veterinaria de Tandil (CIVETAN), UNCPBA-CONICET-CIC, Laboratorio de Inmunoquímica y Biotecnología, Argentina
| | - A W Friedrich
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology, The Netherlands
| | - J W A Rossen
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology, The Netherlands
| | - P M A Lucchesi
- Centro de Investigación Veterinaria de Tandil (CIVETAN), UNCPBA-CONICET-CIC, Laboratorio de Inmunoquímica y Biotecnología, Argentina
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Campos ACC, Andrade NL, Ferdous M, Chlebowicz MA, Santos CC, Correal JCD, Lo Ten Foe JR, Rosa ACP, Damasco PV, Friedrich AW, Rossen JWA. Comprehensive Molecular Characterization of Escherichia coli Isolates from Urine Samples of Hospitalized Patients in Rio de Janeiro, Brazil. Front Microbiol 2018; 9:243. [PMID: 29503639 PMCID: PMC5821075 DOI: 10.3389/fmicb.2018.00243] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [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: 09/22/2017] [Accepted: 01/31/2018] [Indexed: 01/09/2023] Open
Abstract
Urinary tract infections (UTIs) are often caused by Escherichia coli. Their increasing resistance to broad-spectrum antibiotics challenges the treatment of UTIs. Whereas, E. coli ST131 is often multidrug resistant (MDR), ST69 remains susceptible to antibiotics such as cephalosporins. Both STs are commonly linked to community and nosocomial infections. E. coli phylogenetic groups B2 and D are associated with virulence and resistance profiles making them more pathogenic. Little is known about the population structure of E. coli isolates obtained from urine samples of hospitalized patients in Brazil. Therefore, we characterized E. coli isolated from urine samples of patients hospitalized at the university and three private hospitals in Rio de Janeiro, using whole genome sequencing. A high prevalence of E. coli ST131 and ST69 was found, but other lineages, namely ST73, ST648, ST405, and ST10 were also detected. Interestingly, isolates could be divided into two groups based on their antibiotic susceptibility. Isolates belonging to ST131, ST648, and ST405 showed a high resistance rate to all antibiotic classes tested, whereas isolates belonging to ST10, ST73, ST69 were in general susceptible to the antibiotics tested. Additionally, most ST69 isolates, normally resistant to aminoglycosides, were susceptible to this antibiotic in our population. The majority of ST131 isolates were ESBL-producing and belonged to serotype O25:H4 and the H30-R subclone. Previous studies showed that this subclone is often associated with more complicated UTIs, most likely due to their high resistance rate to different antibiotic classes. Sequenced isolates could be classified into five phylogenetic groups of which B2, D, and F showed higher resistance rates than groups A and B1. No significant difference for the predicted virulence genes scores was found for isolates belonging to ST131, ST648, ST405, and ST69. In contrast, the phylogenetic groups B2, D and F showed a higher predictive virulence score compared to phylogenetic groups A and B1. In conclusion, despite the diversity of E. coli isolates causing UTIs, clonal groups O25:H4-B2-ST131 H30-R, O1:H6-B2-ST648, and O102:H6-D-ST405 were the most prevalent. The emergence of highly virulent and MDR E. coli in Brazil is of high concern and requires more attention from the health authorities.
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Affiliation(s)
- Ana Carolina C Campos
- Departamento de Microbiologia, Imunologia e Parasitologia, Faculdade de Ciências Médicas, Universidade do Estado do Rio de Janeiro, Rio de Janeiro, Brazil.,Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Nathália L Andrade
- Departamento de Microbiologia, Imunologia e Parasitologia, Faculdade de Ciências Médicas, Universidade do Estado do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Mithila Ferdous
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Monika A Chlebowicz
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Carla C Santos
- Departamento de Controle de Infecções, Hospital Rio Laranjeiras, Rio de Janeiro, Brazil
| | - Julio C D Correal
- Departamento de Microbiologia, Imunologia e Parasitologia, Faculdade de Ciências Médicas, Universidade do Estado do Rio de Janeiro, Rio de Janeiro, Brazil.,Departamento de Controle de Infecções, Hospital Rio Laranjeiras, Rio de Janeiro, Brazil
| | - Jerome R Lo Ten Foe
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Ana Cláudia P Rosa
- Departamento de Microbiologia, Imunologia e Parasitologia, Faculdade de Ciências Médicas, Universidade do Estado do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Paulo V Damasco
- Departamento de Doenças Infecciosas e Parasitárias, Universidade Federal do Estado do Rio de Janeiro, Rio de Janeiro, Brazil.,Departamento de Doenças Infecciosas e Parasitárias, Universidade do Estado do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Alex W Friedrich
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - John W A Rossen
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
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Gigliucci F, von Meijenfeldt FAB, Knijn A, Michelacci V, Scavia G, Minelli F, Dutilh BE, Ahmad HM, Raangs GC, Friedrich AW, Rossen JWA, Morabito S. Metagenomic Characterization of the Human Intestinal Microbiota in Fecal Samples from STEC-Infected Patients. Front Cell Infect Microbiol 2018; 8:25. [PMID: 29468143 PMCID: PMC5808120 DOI: 10.3389/fcimb.2018.00025] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [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: 10/30/2017] [Accepted: 01/18/2018] [Indexed: 11/20/2022] Open
Abstract
The human intestinal microbiota is a homeostatic ecosystem with a remarkable impact on human health and the disruption of this equilibrium leads to an increased susceptibility to infection by numerous pathogens. In this study, we used shotgun metagenomic sequencing and two different bioinformatic approaches, based on mapping of the reads onto databases and on the reconstruction of putative draft genomes, to investigate possible changes in the composition of the intestinal microbiota in samples from patients with Shiga Toxin-producing E. coli (STEC) infection compared to healthy and healed controls, collected during an outbreak caused by a STEC O26:H11 infection. Both the bioinformatic procedures used, produced similar result with a good resolution of the taxonomic profiles of the specimens. The stool samples collected from the STEC infected patients showed a lower abundance of the members of Bifidobacteriales and Clostridiales orders in comparison to controls where those microorganisms predominated. These differences seemed to correlate with the STEC infection although a flexion in the relative abundance of the Bifidobacterium genus, part of the Bifidobacteriales order, was observed also in samples from Crohn's disease patients, displaying a STEC-unrelated dysbiosis. The metagenomics also allowed to identify in the STEC positive samples, all the virulence traits present in the genomes of the STEC O26 that caused the outbreak as assessed through isolation of the epidemic strain and whole genome sequencing. The results shown represent a first evidence of the changes occurring in the intestinal microbiota of children in the course of STEC infection and indicate that metagenomics may be a promising tool for the culture-independent clinical diagnosis of the infection.
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Affiliation(s)
- Federica Gigliucci
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, Viale Regina Elena, Rome, Italy.,Department of Sciences, University Roma Tre, Rome, Italy
| | | | - Arnold Knijn
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, Viale Regina Elena, Rome, Italy
| | - Valeria Michelacci
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, Viale Regina Elena, Rome, Italy
| | - Gaia Scavia
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, Viale Regina Elena, Rome, Italy
| | - Fabio Minelli
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, Viale Regina Elena, Rome, Italy
| | - Bas E Dutilh
- Theoretical Biology and Bioinformatics, Utrecht University, Utrecht, Netherlands.,Centre for Molecular and Biomolecular Informatics, Radboud University Medical Centre, Nijmegen, Netherlands
| | - Hamideh M Ahmad
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Gerwin C Raangs
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Alex W Friedrich
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - John W A Rossen
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Stefano Morabito
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, Viale Regina Elena, Rome, Italy
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48
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Rossen JWA, Friedrich AW, Moran-Gilad J. Practical issues in implementing whole-genome-sequencing in routine diagnostic microbiology. Clin Microbiol Infect 2017; 24:355-360. [PMID: 29117578 DOI: 10.1016/j.cmi.2017.11.001] [Citation(s) in RCA: 153] [Impact Index Per Article: 21.9] [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: 07/02/2017] [Revised: 10/30/2017] [Accepted: 11/01/2017] [Indexed: 12/15/2022]
Abstract
BACKGROUND Next generation sequencing (NGS) is increasingly being used in clinical microbiology. Like every new technology adopted in microbiology, the integration of NGS into clinical and routine workflows must be carefully managed. AIM To review the practical aspects of implementing bacterial whole genome sequencing (WGS) in routine diagnostic laboratories. SOURCES Review of the literature and expert opinion. CONTENT In this review, we discuss when and how to integrate whole genome sequencing (WGS) in the routine workflow of the clinical laboratory. In addition, as the microbiology laboratories have to adhere to various national and international regulations and criteria for their accreditation, we deliberate on quality control issues for using WGS in microbiology, including the importance of proficiency testing. Furthermore, the current and future place of this technology in the diagnostic hierarchy of microbiology is described as well as the necessity of maintaining backwards compatibility with already established methods. Finally, we speculate on the question of whether WGS can entirely replace routine microbiology in the future and the tension between the fact that most sequencers are designed to process multiple samples in parallel whereas for optimal diagnosis a one-by-one processing of the samples is preferred. Special reference is made to the cost and turnaround time of WGS in diagnostic laboratories. IMPLICATIONS Further development is required to improve the workflow for WGS, in particular to shorten the turnaround time, reduce costs, and streamline downstream data analyses. Only when these processes reach maturity will reliance on WGS for routine patient management and infection control management become feasible, enabling the transformation of clinical microbiology into a genome-based and personalized diagnostic field.
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Affiliation(s)
- J W A Rossen
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology, Groningen, The Netherlands; European Society for Clinical Microbiology and Infectious Diseases (ESCMID) Study Group for Genomic and Molecular Diagnostics (ESGMD), Basel, Switzerland.
| | - A W Friedrich
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology, Groningen, The Netherlands
| | - J Moran-Gilad
- European Society for Clinical Microbiology and Infectious Diseases (ESCMID) Study Group for Genomic and Molecular Diagnostics (ESGMD), Basel, Switzerland; Department of Health Systems Management, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel; Public Health Services, Ministry of Health, Jerusalem, Israel
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49
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Pirii LE, Friedrich AW, Rossen JWA, Vogels W, Beerthuizen GIJM, Nieuwenhuis MK, Kooistra-Smid AMD, Bathoorn E. Extensive colonization with carbapenemase-producing microorganisms in Romanian burn patients: infectious consequences from the Colectiv fire disaster. Eur J Clin Microbiol Infect Dis 2017; 37:175-183. [PMID: 29063446 PMCID: PMC5748401 DOI: 10.1007/s10096-017-3118-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [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: 08/29/2017] [Accepted: 10/09/2017] [Indexed: 02/07/2023]
Abstract
Health care of severe burn patients is highly specialized and may require international patient transfer. Burn patients have an increased risk of developing infections. Patients that have been hospitalized in countries where carbapenemase-producing microorganisms (CPMO) are endemic may develop infections that are difficult to treat. In addition, there is a risk on outbreaks with CPMOs in burn centers. This study underlines that burn patients may extensively be colonized with CPMOs, and it provides best practice recommendations regarding clinical microbiology and infection control. We evaluated CPMO-carriage and wound colonization in a burn patient initially treated in Romania, and transported to the Netherlands. The sequence types and acquired beta-lactamase genes of highly-resistant microorganisms were derived from next generation sequencing data. Next, we searched literature for reports on CPMOs in burn patients. Five different carbapenemase-producing isolates were cultured: two unrelated OXA-48-producing Klebsiella pneumoniae isolates, OXA-23-producing Acinetobacter baumanii, OXA-48-producing Enterobacter cloacae, and NDM-1-producing Providencia stuartii. Also, multi-drug resistant Pseudomonas aeruginosa isolates were detected. Among the sampling sites, there was high variety in CPMOs. We found 46 reports on CPMOs in burn patients. We listed the epidemiology of CPMOs by country of initial treatment, and summarized recommendations for care of these patients based on these reports and our study.
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Affiliation(s)
- L E Pirii
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.
| | - A W Friedrich
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - J W A Rossen
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - W Vogels
- Department of Medical Microbiology, Certe, Groningen, The Netherlands.,Department of Medical Microbiology, Martini Hospital, Groningen, The Netherlands
| | | | - M K Nieuwenhuis
- Association of Dutch Burn Centers, Burn Centre, Martini Hospital Groningen, Groningen, The Netherlands
| | - A M D Kooistra-Smid
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.,Department of Medical Microbiology, Certe, Groningen, The Netherlands
| | - E Bathoorn
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
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50
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Veloo ACM, Jean-Pierre H, Justesen US, Morris T, Urban E, Wybo I, Shah HN, Friedrich AW, Morris T, Shah HN, Jean-Pierre H, Justesen US, Nagy E, Urban E, Kostrzewa M, Veloo A, Friedrich AW. A multi-center ring trial for the identification of anaerobic bacteria using MALDI-TOF MS. Anaerobe 2017; 48:94-97. [PMID: 28797803 DOI: 10.1016/j.anaerobe.2017.07.004] [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: 06/20/2017] [Revised: 07/20/2017] [Accepted: 07/21/2017] [Indexed: 11/15/2022]
Abstract
Inter-laboratory reproducibility of Matrix Assisted Laser Desorption Time-of-Flight Mass Spectrometry (MALDI-TOF MS) of anaerobic bacteria has not been shown before. Therefore, ten anonymized anaerobic strains were sent to seven participating laboratories, an initiative of the European Network for the Rapid Identification of Anaerobes (ENRIA). On arrival the strains were cultured and identified using MALDI-TOF MS. The spectra derived were compared with two different Biotyper MALDI-TOF MS databases, the db5627 and the db6903. The results obtained using the db5627 shows a reasonable variation between the different laboratories. However, when a more optimized database is used, the variation is less pronounced. In this study we show that an optimized database not only results in a higher number of strains which can be identified using MALDI-TOF MS, but also corrects for differences in performance between laboratories.
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Affiliation(s)
- A C M Veloo
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, The Netherlands.
| | - H Jean-Pierre
- Centre Hospitalier Universitaire de Montpellier, Hôpital Arnaud de Villeneuve, Laboratoire de Bactériologie, 371 Avenue du Doyen Gaston Giraud, 34295 Montpellier Cedex 5, France; Université Montpellier 1, UMR5119 ECOSYM, Equipe Pathogènes Hydriques Santé Environnements, UMR 5569 Hydrosciences, UFR Pharmacie, 15 avenue Charles Flahault, 34093 Montpellier Cedex 5, France
| | - U S Justesen
- Department of Clinical Microbiology, Odense University Hospital, Odense, Denmark
| | - T Morris
- UK Anaerobe Reference Unit, Public Health Wales Microbiology, Cardiff, UK
| | - E Urban
- Institute of Clinical Microbiology, University of Szeged, Hungary
| | - I Wybo
- Department of Microbiology and Infection Control, Universitair Ziekenhuis Brussel, Brussels, Belgium
| | - H N Shah
- Department of Natural Sciences, Middlesex University, London NW4 4BT, UK
| | - A W Friedrich
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, The Netherlands
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