1
|
Thieme AH, Gertler M, Piening BC, Maechler F, Benzler J, Hartmann C, Heumann P, Seybold J, Kirchberger V, Budach V, Mockenhaupt F, Mittermaier M. Clinical evaluation of a web-based personalized recommendation system with electronic health record interface to optimize healthcare resources during SARS-CoV-2 surges. Sci Rep 2023; 13:22498. [PMID: 38110426 PMCID: PMC10728075 DOI: 10.1038/s41598-023-48325-9] [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: 05/26/2023] [Accepted: 11/24/2023] [Indexed: 12/20/2023] Open
Abstract
During the SARS-CoV-2 pandemic, the German healthcare system faced challenges of efficiently allocating testing resources. To address this, we developed an open-source personalized recommendation system (PRS) called "CovApp". The PRS utilized a questionnaire to estimate the risk of infection, provided personalized recommendations such as testing, self-isolation, or quarantine, and featured QR code data transmission to electronic health records. The PRS served up to 2.5 million monthly users and received 67,000 backlinks from 1800 domains. We clinically evaluated the PRS at the SARS-CoV-2 testing facility at Charité and observed a 21.7% increase in patient throughput per hour and a 22.5% increase in patients per day. Patients using the PRS were twice as likely to belong to the High Risk group eligible for testing (18.6% vs. 8.9%, p < 0.0001), indicating successful compliance with CovApp's recommendations. CovApp served as a digital bridge between the population and medical staff and significantly improved testing efficiency. As an open-source platform, CovApp can be readily customized to address emerging public health crises. Further, given the EHR interface, the app is of great utility for other applications in clinical settings.
Collapse
Affiliation(s)
- Alexander Henry Thieme
- Department of Medicine and Biomedical Data Science, Stanford University, Stanford, CA, 94305, USA.
- Department of Radiation Oncology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Augustenburger Platz 1, 13353, Berlin, Germany.
- Berlin Institute of Health (BIH), 10178, Berlin, Germany.
| | - Maximilian Gertler
- Charité Centre for Global Health, Institute of International Health, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Brar Christian Piening
- Institute of Hygiene and Environmental Medicine, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Friederike Maechler
- Institute of Hygiene and Environmental Medicine, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | | | - Claudia Hartmann
- Department of Psychosomatic Medicine, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Peter Heumann
- Department of Clinical Procedures GB-IT, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Joachim Seybold
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | | | - Volker Budach
- Department of Radiation Oncology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Augustenburger Platz 1, 13353, Berlin, Germany
| | - Frank Mockenhaupt
- Charité Centre for Global Health, Institute of International Health, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Mirja Mittermaier
- Berlin Institute of Health (BIH), 10178, Berlin, Germany
- Department of Infectious Diseases, Respiratory Medicine and Critical Care, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| |
Collapse
|
2
|
Weber A, Neffe L, Diaz LAP, Thoma N, Aghdassi SJS, Denkel LA, Maechler F, Behnke M, Häussler S, Gastmeier P, Kola A. Analysis of transmission-related third-generation cephalosporin-resistant Enterobacterales by electronic data mining and core genome multi-locus sequence typing. J Hosp Infect 2023; 140:96-101. [PMID: 37562589 DOI: 10.1016/j.jhin.2023.07.020] [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: 05/16/2023] [Revised: 07/28/2023] [Accepted: 07/30/2023] [Indexed: 08/12/2023]
Abstract
BACKGROUND To contain intra-hospital transmission of third-generation cephalosporin-resistant Enterobacterales (3GCR-E), contact isolation precautions are recommended. AIM To quantify transmissions of 3GCR Escherichia coli and 3GCR Klebsiella pneumoniae within a hospital. METHODS An automated outbreak detection system (AODS) was used to identify clusters (N≥2) of 3GCR Enterobacterales for the years 2016, 2018 and 2020. Clusters were defined by phenotypic agreement of microbiological results and spatial and temporal relationship. Core genome multi-locus sequence typing (cgMLST) was used to confirm whether the cluster isolates were transmitted between patients. FINDINGS A total of 4343 3GCR E. coli and 1377 K. pneumoniae isolates were analysed. Among the 3GCR E. coli isolates, the AODS identified 304 isolates as cluster isolates, the median cluster size was two (range: 2-5). The cgMLST analysis revealed that a total of 23 (7.5%) 3GCR E. coli cluster isolates were transmission-associated, of which 20 isolates (87%) were detected in intensive care patients. Among the 3GCR K. pneumoniae isolates, the AODS identified 73 isolates as cluster isolates, the median cluster size was two (range: 2-4). CgMLST revealed that 35 (48%) 3GCR K. pneumoniae cluster isolates were transmission associated, of which 27 isolates (77%) were detected in intensive care patients. CONCLUSION For 3GCR K. pneumoniae, cgMLST confirmed the AODS results more frequently than for 3GCR E. coli. Therefore, contact isolation precautions for 3GCR K. pneumoniae may be appropriate on intensive care units, but only in certain circumstances, such as outbreaks, for Enterobacterales with lower transmissibility, such as E. coli.
Collapse
Affiliation(s)
- A Weber
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Hygiene and Environmental Medicine, Berlin, Germany
| | - L Neffe
- Helmholtz Centre for Infection Research, Department of Molecular Bacteriology, Braunschweig, Germany
| | - L A P Diaz
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Hygiene and Environmental Medicine, Berlin, Germany
| | - N Thoma
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Hygiene and Environmental Medicine, Berlin, Germany
| | - S J S Aghdassi
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Hygiene and Environmental Medicine, Berlin, Germany; Berlin Institute of Health at Charité - Universitätsmedizin Berlin, BIH Biomedical Innovation Academy, BIH Charité Digital Clinician Scientist Programme, Berlin, Germany
| | - L A Denkel
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Hygiene and Environmental Medicine, Berlin, Germany
| | - F Maechler
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Hygiene and Environmental Medicine, Berlin, Germany
| | - M Behnke
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Hygiene and Environmental Medicine, Berlin, Germany
| | - S Häussler
- Helmholtz Centre for Infection Research, Department of Molecular Bacteriology, Braunschweig, Germany; TWINCORE, Centre for Experimental and Clinical Infection Research, A Joint Venture of the HZI and the Hannover Medical School, Hannover, Germany
| | - P Gastmeier
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Hygiene and Environmental Medicine, Berlin, Germany
| | - A Kola
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Hygiene and Environmental Medicine, Berlin, Germany.
| |
Collapse
|
3
|
Maechler F, Schwab F, Hansen S, Behnke M, Bonten MJ, Canton R, Diaz Agero C, Fankhauser C, Harbarth S, Huttner BD, Kola A, Gastmeier P. Quantification of time delay between screening and subsequent initiation of contact isolation for carriers of extended-spectrum beta-lactamase (ESBL)-producing Enterobacterales: A post hoc subgroup analysis of the R-GNOSIS WP5 Trial. Infect Control Hosp Epidemiol 2023; 44:1410-1416. [PMID: 36912321 PMCID: PMC10507499 DOI: 10.1017/ice.2022.285] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 10/28/2022] [Accepted: 11/01/2022] [Indexed: 03/14/2023]
Abstract
OBJECTIVES The aim of this study was to quantify the time delay between screening and initiation of contact isolation for carriers of extended-spectrum beta-lactamase (ESBL)-producing Enterobacterales (ESBL-E). METHODS This study was a secondary analysis of contact isolation periods in a cluster-randomized controlled trial that compared 2 strategies to control ESBL-E (trial no. ISRCTN57648070). Patients admitted to 20 non-ICU wards in Germany, the Netherlands, Spain, and Switzerland were screened for ESBL-E carriage on admission, weekly thereafter, and on discharge. Data collection included the day of sampling, the day the wards were notified of the result, and subsequent ESBL-E isolation days. RESULTS Between January 2014 and August 2016, 19,122 patients, with a length of stay ≥2 days were included. At least 1 culture was collected for 16,091 patients (84%), with a median duration between the admission day and the day of first sample collection of 2 days (interquartile range [IQR], 1-3). Moreover, 854 (41%) of all 2,078 ESBL-E carriers remained without isolation during their hospital stay. In total, 6,040 ESBL-E days (32% of all ESBL-E days) accrued for patients who were not isolated. Of 2,078 ESBL-E-carriers, 1,478 ESBL-E carriers (71%) had no previous history of ESBL-E carriage. Also, 697 (34%) were placed in contact isolation with a delay of 4 days (IQR, 2-5), accounting for 2,723 nonisolation days (15% of ESBL-E days). CONCLUSIONS Even with extensive surveillance screening, almost one-third of all ESBL-E days were nonisolation days. Limitations in routine culture-based ESBL-E detection impeded timely and exhaustive implementation of targeted contact isolation.
Collapse
Affiliation(s)
- Friederike Maechler
- Institute of Hygiene and Environmental Medicine, Universitätsmedizin – CharitéBerlin, Germany
| | - Frank Schwab
- Institute of Hygiene and Environmental Medicine, Universitätsmedizin – CharitéBerlin, Germany
| | - Sonja Hansen
- Institute of Hygiene and Environmental Medicine, Universitätsmedizin – CharitéBerlin, Germany
| | - Michael Behnke
- Institute of Hygiene and Environmental Medicine, Universitätsmedizin – CharitéBerlin, Germany
| | - Marc J. Bonten
- Department of Medical Microbiology and Infection Control, University Medical Center Utrecht, Utrecht, Netherlands
| | - Rafael Canton
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria, Madrid
| | - Cristina Diaz Agero
- Servicio de Medicina Preventiva y Salud Pública Hospital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria, Madrid
| | - Carolina Fankhauser
- Infection Control Program, Geneva University Hospitals and Medical School, Geneva, Switzerland
| | - Stephan Harbarth
- Infection Control Program, Geneva University Hospitals and Medical School, Geneva, Switzerland
| | - Benedikt D. Huttner
- Infection Control Program, Geneva University Hospitals and Medical School, Geneva, Switzerland
| | - Axel Kola
- Institute of Hygiene and Environmental Medicine, Universitätsmedizin – CharitéBerlin, Germany
| | - Petra Gastmeier
- Institute of Hygiene and Environmental Medicine, Universitätsmedizin – CharitéBerlin, Germany
| |
Collapse
|
4
|
Wiese-Posselt M, Saydan S, Schwab F, Behnke M, Kola A, Siegfried Kramer T, Gastmeier P, Maechler F. Screening for Methicillin-Resistant Staphylococcus aureus. Dtsch Arztebl Int 2023; 120:447-453. [PMID: 37199029 PMCID: PMC10481939 DOI: 10.3238/arztebl.m2023.0117] [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] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 01/23/2023] [Accepted: 04/27/2023] [Indexed: 05/19/2023]
Abstract
BACKGROUND Methicillin-resistant Staphylococcus aureus (MRSA) has become less common in Germany in recent years. In this paper, we report data from the MRSA module of the Hospital Infection Surveillance System (Krankenhaus-Infektionen- Surveillance-System, KISS) for the years 2006-2021. We also describe the association of MRSA rates with the frequency of patient screening for MRSA and discuss the findings. METHODS Participation in the MRSA KISS module is voluntary. Once a year, the participating hospitals submit structural data, information on cases in which MRSA was detected (both colonizations and infections; both detected on admission and nosocomially acquired), and the number of nasal swabs taken for the detection of MRSA to the German National Reference Center for the Surveillance of Nosocomial Infections. Statistical analyses were performed with R software. RESULTS The number of hospitals participating in the MRSA module rose from 110 in 2006 to 525 in 2021. From 2006 onward, the overall MRSA prevalence in German hospitals increased, reaching a maximum of 1.04 cases per 100 patients in 2012. The prevalence on admission fell by 44% from 0.96 in 2016 to 0.54 in 2021. The incidence density of nosocomial MRSA fell by an average of 12% per year, from 0.27 per 1000 patient-days in 2006 to 0.06 in 2021, while MRSA screening frequency increased sevenfold by 2021. The nosocomial incidence density was stable, independently of the screening frequency. CONCLUSION MRSA rates in German hospitals fell markedly from 2006 to 2021, reflecting a general trend. The incidence density was no higher in hospitals with a low or moderate screening frequency than in those with a high one. Thus, a targeted, riskadapted MRSA screening strategy on hospital admission can be recommended.
Collapse
Affiliation(s)
- Miriam Wiese-Posselt
- Institute of Hygiene and Environmental Medicine, Charité – University Medicine Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Selin Saydan
- Institute of Hygiene and Environmental Medicine, Charité – University Medicine Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Frank Schwab
- Institute of Hygiene and Environmental Medicine, Charité – University Medicine Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- German National Reference Center for the Surveillance of Nosocomial Infections at the Institute of Hygiene and Environmental Medicine, Charité – University Medicine Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Michael Behnke
- Institute of Hygiene and Environmental Medicine, Charité – University Medicine Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- German National Reference Center for the Surveillance of Nosocomial Infections at the Institute of Hygiene and Environmental Medicine, Charité – University Medicine Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Axel Kola
- Institute of Hygiene and Environmental Medicine, Charité – University Medicine Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Tobias Siegfried Kramer
- Institute of Hygiene and Environmental Medicine, Charité – University Medicine Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Petra Gastmeier
- German National Reference Center for the Surveillance of Nosocomial Infections at the Institute of Hygiene and Environmental Medicine, Charité – University Medicine Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Friederike Maechler
- German National Reference Center for the Surveillance of Nosocomial Infections at the Institute of Hygiene and Environmental Medicine, Charité – University Medicine Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| |
Collapse
|
5
|
Maechler F, Weber A, Schwengers O, Schwab F, Denkel L, Behnke M, Gastmeier P, Kola A. Split k-mer analysis compared to cgMLST and SNP-based core genome analysis for detecting transmission of vancomycin-resistant enterococci: results from routine outbreak analyses across different hospitals and hospitals networks in Berlin, Germany. Microb Genom 2023; 9:mgen000937. [PMID: 36748706 PMCID: PMC9973845 DOI: 10.1099/mgen.0.000937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
The increase of Vancomycin-resistant Enterococcus faecium (VREfm) in recent years has been partially attributed to the rise of specific clonal lineages, which have been identified throughout Germany. To date, there is no gold standard for the interpretation of genomic data for outbreak analyses. New genomic approaches such as split k-mer analysis (SKA) could support cluster attribution for routine outbreak investigation. The aim of this project was to investigate frequent clonal lineages of VREfm identified during suspected outbreaks across different hospitals, and to compare genomic approaches including SKA in routine outbreak investigation. We used routine outbreak laboratory data from seven hospitals and three different hospital networks in Berlin, Germany. Short-read libraries were sequenced on the Illumina MiSeq system. We determined clusters using the published Enterococcus faecium-cgMLST scheme (threshold ≤20 alleles), and assigned sequence and complex types (ST, CT), using the Ridom SeqSphere+ software. For each cluster as determined by cgMLST, we used pairwise core-genome SNP-analysis and SKA at thresholds of ten and seven SNPs, respectively, to further distinguish cgMLST clusters. In order to investigate clinical relevance, we analysed to what extent epidemiological linkage backed the clusters determined with different genomic approaches. Between 2014 and 2021, we sequenced 693 VREfm strains, and 644 (93 %) were associated within cgMLST clusters. More than 74 % (n=475) of the strains belonged to the six largest cgMLST clusters, comprising ST117, ST78 and ST80. All six clusters were detected across several years and hospitals without apparent epidemiological links. Core SNP analysis identified 44 clusters with a median cluster size of three isolates (IQR 2-7, min-max 2-63), as well as 197 singletons (41.4 % of 475 isolates). SKA identified 67 clusters with a median cluster size of two isolates (IQR 2-4, min-max 2-19), and 261 singletons (54.9 % of 475 isolates). Of the isolate pairs attributed to clusters, 7 % (n=3064/45 596) of pairs in clusters determined by standard cgMLST, 15 % (n=1222/8500) of pairs in core SNP-clusters and 51 % (n=942/1880) of pairs in SKA-clusters showed epidemiological linkage. The proportion of epidemiological linkage differed between sequence types. For VREfm, the discriminative ability of the widely used cgMLST based approach at ≤20 alleles difference was insufficient to rule out hospital outbreaks without further analytical methods. Cluster assignment guided by core genome SNP analysis and the reference free SKA was more discriminative and correlated better with obvious epidemiological linkage, at least recently published thresholds (ten and seven SNPs, respectively) and for frequent STs. Besides higher overall discriminative power, the whole-genome approach implemented in SKA is also easier and faster to conduct and requires less computational resources.
Collapse
Affiliation(s)
- Friederike Maechler
- Institute of Hygiene and Environmental Medicine, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Anna Weber
- Institute of Hygiene and Environmental Medicine, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Oliver Schwengers
- Bioinformatics and Systems Biology, Justus Liebig University Giessen, Giessen, Germany
| | - Frank Schwab
- Institute of Hygiene and Environmental Medicine, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Luisa Denkel
- Institute of Hygiene and Environmental Medicine, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Michael Behnke
- Institute of Hygiene and Environmental Medicine, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Petra Gastmeier
- Institute of Hygiene and Environmental Medicine, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Axel Kola
- Institute of Hygiene and Environmental Medicine, Charité - Universitätsmedizin Berlin, Berlin, Germany
| |
Collapse
|
6
|
Meyer F, Fritz A, Deng ZL, Koslicki D, Lesker TR, Gurevich A, Robertson G, Alser M, Antipov D, Beghini F, Bertrand D, Brito JJ, Brown CT, Buchmann J, Buluç A, Chen B, Chikhi R, Clausen PTLC, Cristian A, Dabrowski PW, Darling AE, Egan R, Eskin E, Georganas E, Goltsman E, Gray MA, Hansen LH, Hofmeyr S, Huang P, Irber L, Jia H, Jørgensen TS, Kieser SD, Klemetsen T, Kola A, Kolmogorov M, Korobeynikov A, Kwan J, LaPierre N, Lemaitre C, Li C, Limasset A, Malcher-Miranda F, Mangul S, Marcelino VR, Marchet C, Marijon P, Meleshko D, Mende DR, Milanese A, Nagarajan N, Nissen J, Nurk S, Oliker L, Paoli L, Peterlongo P, Piro VC, Porter JS, Rasmussen S, Rees ER, Reinert K, Renard B, Robertsen EM, Rosen GL, Ruscheweyh HJ, Sarwal V, Segata N, Seiler E, Shi L, Sun F, Sunagawa S, Sørensen SJ, Thomas A, Tong C, Trajkovski M, Tremblay J, Uritskiy G, Vicedomini R, Wang Z, Wang Z, Wang Z, Warren A, Willassen NP, Yelick K, You R, Zeller G, Zhao Z, Zhu S, Zhu J, Garrido-Oter R, Gastmeier P, Hacquard S, Häußler S, Khaledi A, Maechler F, Mesny F, Radutoiu S, Schulze-Lefert P, Smit N, Strowig T, Bremges A, Sczyrba A, McHardy AC. Critical Assessment of Metagenome Interpretation: the second round of challenges. Nat Methods 2022; 19:429-440. [PMID: 35396482 PMCID: PMC9007738 DOI: 10.1038/s41592-022-01431-4] [Citation(s) in RCA: 89] [Impact Index Per Article: 44.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 02/14/2022] [Indexed: 12/20/2022]
Abstract
Evaluating metagenomic software is key for optimizing metagenome interpretation and focus of the Initiative for the Critical Assessment of Metagenome Interpretation (CAMI). The CAMI II challenge engaged the community to assess methods on realistic and complex datasets with long- and short-read sequences, created computationally from around 1,700 new and known genomes, as well as 600 new plasmids and viruses. Here we analyze 5,002 results by 76 program versions. Substantial improvements were seen in assembly, some due to long-read data. Related strains still were challenging for assembly and genome recovery through binning, as was assembly quality for the latter. Profilers markedly matured, with taxon profilers and binners excelling at higher bacterial ranks, but underperforming for viruses and Archaea. Clinical pathogen detection results revealed a need to improve reproducibility. Runtime and memory usage analyses identified efficient programs, including top performers with other metrics. The results identify challenges and guide researchers in selecting methods for analyses. This study presents the results of the second round of the Critical Assessment of Metagenome Interpretation challenges (CAMI II), which is a community-driven effort for comprehensively benchmarking tools for metagenomics data analysis.
Collapse
Affiliation(s)
- Fernando Meyer
- Computational Biology of Infection Research, Helmholtz Centre for Infection Research, Braunschweig, Germany.,Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Braunschweig, Germany
| | - Adrian Fritz
- Computational Biology of Infection Research, Helmholtz Centre for Infection Research, Braunschweig, Germany.,Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Braunschweig, Germany.,German Center for Infection Research (DZIF), Hannover-Braunschweig Site, Braunschweig, Germany
| | - Zhi-Luo Deng
- Computational Biology of Infection Research, Helmholtz Centre for Infection Research, Braunschweig, Germany.,Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Braunschweig, Germany.,Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, Hannover, Germany
| | | | - Till Robin Lesker
- German Center for Infection Research (DZIF), Hannover-Braunschweig Site, Braunschweig, Germany.,Helmholtz Centre for Infection Research, Braunschweig, Germany
| | | | - Gary Robertson
- Computational Biology of Infection Research, Helmholtz Centre for Infection Research, Braunschweig, Germany.,Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Braunschweig, Germany
| | - Mohammed Alser
- Department of Information Technology and Electrical Engineering, ETH Zürich, Zurich, Switzerland
| | - Dmitry Antipov
- Center for Algorithmic Biotechnology, Saint Petersburg State University, Saint Petersburg, Russia
| | | | | | | | | | - Jan Buchmann
- Institute for Biological Data Science, Heinrich-Heine-University, Düsseldorf, Germany
| | - Aydin Buluç
- Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,University of California, Berkeley, Berkeley, CA, USA
| | - Bo Chen
- Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,University of California, Berkeley, Berkeley, CA, USA
| | | | - Philip T L C Clausen
- National Food Institute, Division of Global Surveillance, Technical University of Denmark, Lyngby, Denmark
| | - Alexandru Cristian
- Drexel University, Philadelphia, PA, USA.,Google Inc., Philadelphia, PA, USA
| | - Piotr Wojciech Dabrowski
- Robert Koch-Institut, Berlin, Germany.,Hochschule für Technik und Wirtschaft Berlin, Berlin, Germany
| | | | - Rob Egan
- DOE Joint Genome Institute, Berkeley, CA, USA.,Lawrence Berkeley National Laboratories, Berkeley, CA, USA
| | - Eleazar Eskin
- University of California, Los Angeles, Los Angeles, CA, USA
| | | | - Eugene Goltsman
- DOE Joint Genome Institute, Berkeley, CA, USA.,Lawrence Berkeley National Laboratories, Berkeley, CA, USA
| | - Melissa A Gray
- Drexel University, Philadelphia, PA, USA.,Ecological and Evolutionary Signal-Processing and Informatics Laboratory, Philadelphia, PA, USA
| | - Lars Hestbjerg Hansen
- University of Copenhagen, Department of Plant and Environmental Science, Frederiksberg, Denmark
| | - Steven Hofmeyr
- Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,University of California, Berkeley, Berkeley, CA, USA
| | - Pingqin Huang
- School of Computer Science, Fudan University, Shanghai, China
| | - Luiz Irber
- University of California, Davis, Davis, CA, USA
| | - Huijue Jia
- BGI-Shenzhen, Shenzhen, China.,Shenzhen Key Laboratory of Human Commensal Microorganisms and Health Research, BGI-Shenzhen, Shenzhen, China
| | - Tue Sparholt Jørgensen
- Technical University of Denmark, Novo Nordisk Foundation Center for Biosustainability, Lyngby, Denmark.,Aarhus University, Department of Environmental Science, Roskilde, Denmark
| | - Silas D Kieser
- Department of Cell Physiology and Metabolism, Faculty of Medicine, University of Geneva, Geneva, Switzerland.,Swiss Institute of Bioinformatics, Geneva, Switzerland
| | | | - Axel Kola
- Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Mikhail Kolmogorov
- Department of Computer Science and Engineering, University of California San Diego, San Diego, CA, USA
| | - Anton Korobeynikov
- Center for Algorithmic Biotechnology, Saint Petersburg State University, Saint Petersburg, Russia.,Department of Statistical Modelling, Saint Petersburg State University, Saint Petersburg, Russia
| | - Jason Kwan
- University of Wisconsin-Madison, Madison, WI, USA
| | | | | | - Chenhao Li
- Genome Institute of Singapore, Singapore, Singapore
| | | | - Fabio Malcher-Miranda
- Hasso Plattner Institute, Digital Engineering Faculty, University of Potsdam, Potsdam, Germany
| | | | - Vanessa R Marcelino
- Sydney Medical School, The University of Sydney, Sydney, Australia.,Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Australia
| | | | - Pierre Marijon
- Department of Computer Science, Inria, University of Lille, CNRS, Lille, France
| | - Dmitry Meleshko
- Center for Algorithmic Biotechnology, Saint Petersburg State University, Saint Petersburg, Russia
| | - Daniel R Mende
- Amsterdam University Medical Center, Amsterdam, the Netherlands
| | - Alessio Milanese
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich, Zürich, Switzerland.,Structural and Computational Biology Unit, EMBL, Heidelberg, Germany
| | - Niranjan Nagarajan
- Genome Institute of Singapore, A*STAR, Singapore, Singapore.,National University of Singapore, Singapore, Singapore
| | | | - Sergey Nurk
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Leonid Oliker
- Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,University of California, Berkeley, Berkeley, CA, USA
| | - Lucas Paoli
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich, Zürich, Switzerland
| | | | - Vitor C Piro
- Hasso Plattner Institute, Digital Engineering Faculty, University of Potsdam, Potsdam, Germany
| | | | - Simon Rasmussen
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Evan R Rees
- University of Wisconsin-Madison, Madison, WI, USA
| | - Knut Reinert
- Institute for Bioinformatics, FU Berlin, Berlin, Germany
| | - Bernhard Renard
- Hasso Plattner Institute, Digital Engineering Faculty, University of Potsdam, Potsdam, Germany.,Bioinformatics Unit (MF1), Robert Koch Institute, Berlin, Germany
| | | | - Gail L Rosen
- Drexel University, Philadelphia, PA, USA.,Ecological and Evolutionary Signal-Processing and Informatics Laboratory, Philadelphia, PA, USA.,Center for Biological Discovery from Big Data, Philadelphia, PA, USA
| | - Hans-Joachim Ruscheweyh
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich, Zürich, Switzerland
| | - Varuni Sarwal
- University of California, Los Angeles, Los Angeles, CA, USA
| | - Nicola Segata
- Department CIBIO, University of Trento, Trento, Italy
| | - Enrico Seiler
- Institute for Bioinformatics, FU Berlin, Berlin, Germany
| | - Lizhen Shi
- Florida Polytechnic University, Lakeland, FL, USA
| | - Fengzhu Sun
- Quantitative and Computational Biology Department, University of Southern California, Los Angeles, CA, USA
| | - Shinichi Sunagawa
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich, Zürich, Switzerland
| | | | - Ashleigh Thomas
- DOE Joint Genome Institute, Berkeley, CA, USA.,University of British Columbia, Vancouver, British Columbia, Canada
| | | | - Mirko Trajkovski
- Department of Cell Physiology and Metabolism, Faculty of Medicine, University of Geneva, Geneva, Switzerland.,Diabetes Center, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Julien Tremblay
- Energy, Mining and Environment, National Research Council Canada, Montreal, Quebec, Canada
| | | | | | - Zhengyang Wang
- School of Computer Science, Fudan University, Shanghai, China
| | - Ziye Wang
- School of Mathematical Sciences, Fudan University, Shanghai, China
| | - Zhong Wang
- Department of Energy Joint Genome Institute, Berkeley, CA, USA.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,School of Natural Sciences, University of California at Merced, Merced, CA, USA
| | | | | | - Katherine Yelick
- Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,University of California, Berkeley, Berkeley, CA, USA
| | - Ronghui You
- School of Computer Science, Fudan University, Shanghai, China
| | - Georg Zeller
- Structural and Computational Biology Unit, EMBL, Heidelberg, Germany
| | | | - Shanfeng Zhu
- Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, China.,Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence (Fudan University), Ministry of Education, Shanghai, China
| | - Jie Zhu
- BGI-Shenzhen, Shenzhen, China.,Shenzhen Key Laboratory of Human Commensal Microorganisms and Health Research, BGI-Shenzhen, Shenzhen, China
| | | | | | | | - Susanne Häußler
- Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Ariane Khaledi
- Helmholtz Centre for Infection Research, Braunschweig, Germany
| | | | - Fantin Mesny
- Max Planck Institute for Plant Breeding Research, Köln, Germany
| | | | | | - Nathiana Smit
- Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Till Strowig
- Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Andreas Bremges
- Computational Biology of Infection Research, Helmholtz Centre for Infection Research, Braunschweig, Germany.,German Center for Infection Research (DZIF), Hannover-Braunschweig Site, Braunschweig, Germany
| | - Alexander Sczyrba
- Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
| | - Alice Carolyn McHardy
- Computational Biology of Infection Research, Helmholtz Centre for Infection Research, Braunschweig, Germany. .,Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Braunschweig, Germany. .,German Center for Infection Research (DZIF), Hannover-Braunschweig Site, Braunschweig, Germany. .,Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, Hannover, Germany.
| |
Collapse
|
7
|
Leistner R, Schroeter L, Adam T, Poddubnyy D, Stegemann M, Siegmund B, Maechler F, Geffers C, Schwab F, Gastmeier P, Treskatsch S, Angermair S, Schneider T. Corticosteroids as risk factor for COVID-19-associated pulmonary aspergillosis in intensive care patients. Crit Care 2022; 26:30. [PMID: 35090528 PMCID: PMC8796178 DOI: 10.1186/s13054-022-03902-8] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [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: 11/19/2021] [Accepted: 01/16/2022] [Indexed: 12/15/2022] Open
Abstract
PURPOSE Corticosteroids, in particular dexamethasone, are one of the primary treatment options for critically ill COVID-19 patients. However, there are a growing number of cases that involve COVID-19-associated pulmonary aspergillosis (CAPA), and it is unclear whether dexamethasone represents a risk factor for CAPA. Our aim was to investigate a possible association of the recommended dexamethasone therapy with a risk of CAPA. METHODS We performed a study based on a cohort of COVID-19 patients treated in 2020 in our 13 intensive care units at Charité Universitätsmedizin Berlin. We used ECMM/ISHM criteria for the CAPA diagnosis and performed univariate and multivariable analyses of clinical parameters to identify risk factors that could result in a diagnosis of CAPA. RESULTS Altogether, among the n = 522 intensive care patients analyzed, n = 47 (9%) patients developed CAPA. CAPA patients had a higher simplified acute physiology score (SAPS) (64 vs. 53, p < 0.001) and higher levels of IL-6 (1,005 vs. 461, p < 0.008). They more often had severe acute respiratory distress syndrome (ARDS) (60% vs. 41%, p = 0.024), renal replacement therapy (60% vs. 41%, p = 0.024), and they were more likely to die (64% vs. 48%, p = 0.049). The multivariable analysis showed dexamethasone (OR 3.110, CI95 1.112-8.697) and SAPS (OR 1.063, CI95 1.028-1.098) to be independent risk factors for CAPA. CONCLUSION In our study, dexamethasone therapy as recommended for COVID-19 was associated with a significant three times increase in the risk of CAPA. TRIAL REGISTRATION Registration number DRKS00024578, Date of registration March 3rd, 2021.
Collapse
Affiliation(s)
- Rasmus Leistner
- Division of Gastroenterology, Infectious Diseases and Rheumatology, Medical Department, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Berlin, Germany.
- Institute of Hygiene and Environmental Medicine, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Berlin, Germany.
| | - Lisa Schroeter
- Department of Anesthesiology and Intensive Care Medicine, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany, Charité Campus Benjamin Franklin, Berlin, Germany
| | - Thomas Adam
- Labor Berlin, Charité Vivantes GmbH, Berlin, Germany
| | - Denis Poddubnyy
- Division of Gastroenterology, Infectious Diseases and Rheumatology, Medical Department, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Berlin, Germany
| | - Miriam Stegemann
- Department of Infectious Diseases and Respiratory Medicine, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Britta Siegmund
- Division of Gastroenterology, Infectious Diseases and Rheumatology, Medical Department, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Berlin, Germany
| | - Friederike Maechler
- Institute of Hygiene and Environmental Medicine, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Berlin, Germany
| | - Christine Geffers
- Institute of Hygiene and Environmental Medicine, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Berlin, Germany
| | - Frank Schwab
- Institute of Hygiene and Environmental Medicine, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Berlin, Germany
| | - Petra Gastmeier
- Institute of Hygiene and Environmental Medicine, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Berlin, Germany
| | - Sascha Treskatsch
- Department of Anesthesiology and Intensive Care Medicine, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany, Charité Campus Benjamin Franklin, Berlin, Germany
| | - Stefan Angermair
- Department of Anesthesiology and Intensive Care Medicine, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany, Charité Campus Benjamin Franklin, Berlin, Germany
| | - Thomas Schneider
- Division of Gastroenterology, Infectious Diseases and Rheumatology, Medical Department, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Berlin, Germany
| |
Collapse
|
8
|
Klauke P, Schwab F, Gastmeier P, Maechler F. The impact of non-antimicrobial drug agents on the acquisition of ESBL-producing Enterobacterales in non-critical care wards in a German university hospital: an exploratory, matched case-control study. J Antimicrob Chemother 2021; 77:229-236. [PMID: 34791310 DOI: 10.1093/jac/dkab373] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 09/03/2021] [Indexed: 12/20/2022] Open
Abstract
OBJECTIVES To investigate therapeutical drugs other than antimicrobials as risk factors for the acquisition of ESBL-producing Enterobacterales (ESBL-E). METHODS This matched case-control study is based on rectal surveillance screening data obtained during a larger trial between 2014 and 2016 upon patients' admission and at least once before discharge in eight non-ICU wards. Patients with ward-acquired ESBL-E (cases) were matched 1:1 to non-ESBL-E carriers (controls) based on ward, number of screening samples, days at risk and Charlson comorbidity index (CCI). Daily medication data were documented according to the Anatomical Therapeutic Chemical classification system. Multivariable conditional logistic regression models were used to calculate risk factors for ESBL-E acquisition. RESULTS Of the 232 cases and 232 controls analysed, baseline characteristics such as gender (male 56.9%), median age (65 years old, IQR 52-74), number of screening samples (N = 3, IQR 2-4), days to first sample (2, IQR 1-2), days at risk (8, IQR 6-11) and CCI (4, IQR 2-6) were similar. Multivariable analysis showed that glucocorticoids, opium alkaloids and selective β-2-adrenoreceptor agonists increased the chance to detect ESBL-E (OR 1.07, 95% CI 1.001-1.13, P = 0.047; OR 1.06, 95% CI 1.007-1.12, P = 0.027; and OR 1.31, 95% CI 1.105-1.55, P = 0.001, respectively), while antihistamines decreased it (OR 0.61, 95% CI 0.39-0.97, P = 0.034). In a sensitivity analysis, including drugs prescribed to at least 50 patients, proton pump inhibitors remained as risk factors (OR 1.049, 95% CI 1.001-1.100, P = 0.047). CONCLUSIONS In a non-ICU setting, drugs other than antimicrobials were determined as potential independent risk factors for ESBL-E acquisition.
Collapse
Affiliation(s)
- Paula Klauke
- Institute of Hygiene and Environmental Medicine, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Frank Schwab
- Institute of Hygiene and Environmental Medicine, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Petra Gastmeier
- Institute of Hygiene and Environmental Medicine, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Friederike Maechler
- Institute of Hygiene and Environmental Medicine, Charité-Universitätsmedizin Berlin, Berlin, Germany
| |
Collapse
|
9
|
Weber A, Maechler F, Schwab F, Gastmeier P, Kola A. Increase of vancomycin-resistant Enterococcus faecium strain type ST117 CT71 at Charité - Universitätsmedizin Berlin, 2008 to 2018. Antimicrob Resist Infect Control 2020; 9:109. [PMID: 32678047 PMCID: PMC7364619 DOI: 10.1186/s13756-020-00754-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [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: 11/07/2019] [Accepted: 06/10/2020] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND In addition to an overall rise in vancomycin-resistant Enterococcus faecium (VREfm), an increase in certain strain types marked by sequence type (ST) and cluster type (CT) has been reported in Germany over the past few years. Outbreak analyses at Charité - Universitätsmedizin Berlin revealed the frequent occurrence of VREfm ST117 CT71 isolates in 2017 and 2018. To investigate whether ST117 CT71 have emerged in recent years or whether these strains have been circulating for a longer time, we retrospectively analyzed non-outbreak strains that occurred between 2008 and 2018 to identify frequent STs and CTs. METHODS In total, 120 VREfm isolates obtained from clinical and surveillance cultures from the years 2008, 2013, 2015, and 2018 were analyzed. Thirty isolates per year comprising the first 7-8 non-outbreak isolates of each quarter of the respective year were sequenced using whole genome sequencing. MLST and cgMLST were determined as well as resistance genes and virulence factors. Risk factors for VREfm ST117 were analyzed in a multivariable analysis with patient characteristics as possible confounders. RESULTS The percentage of VREfm of type ST117 increased from 17% in 2008 to 57% in 2018 (p = 0.012). In 2008, vanA genotype accounted for 80% of all ST117 isolates compared to 6% in 2018. VanB CT71 first appeared in 2018 and predominated over all other ST117 at 43% (p < 0.0001). The set of resistance genes (msrC, efmA, erm(B), dfrG, aac(6')-Ii, gyrA, parC and pbp5) and virulence factors (acm, esp, hylEfm, ecbA and sgrA) in CT71 was also found in other ST117 non-CT71 strains, mainly in CT36. The study population did not differ among the different calendar years analyzed in terms of age, gender, length of stay, or ward type (each p > 0.2). CONCLUSION This study revealed an increase in ST117 strains from 2008 to 2018, accompanied by a shift toward CT71 strains with the vanB genotype in 2018. We did not detect resistance or virulence traits in CT71 that could confer survival advantage compared to other CTs among ST117 strains. To date, it is not clear why ST117 and in particular strain type ST117 CT71 predominates over other strains.
Collapse
Affiliation(s)
- Anna Weber
- Institute of Hygiene and Environmental Medicine, Charité - Universitätsmedizin Berlin, Hindenburgdamm 27, 12203, Berlin, Germany.
| | - Friederike Maechler
- Institute of Hygiene and Environmental Medicine, Charité - Universitätsmedizin Berlin, Hindenburgdamm 27, 12203, Berlin, Germany
| | - Frank Schwab
- Institute of Hygiene and Environmental Medicine, Charité - Universitätsmedizin Berlin, Hindenburgdamm 27, 12203, Berlin, Germany
| | - Petra Gastmeier
- Institute of Hygiene and Environmental Medicine, Charité - Universitätsmedizin Berlin, Hindenburgdamm 27, 12203, Berlin, Germany
| | - Axel Kola
- Institute of Hygiene and Environmental Medicine, Charité - Universitätsmedizin Berlin, Hindenburgdamm 27, 12203, Berlin, Germany
| |
Collapse
|
10
|
Denkel LA, Maechler F, Schwab F, Kola A, Weber A, Gastmeier P, Pfäfflin F, Weber S, Werner G, Pfeifer Y, Pietsch M, Leistner R. Infections caused by extended-spectrum β-lactamase-producing Enterobacterales after rectal colonization with ESBL-producing Escherichia coli or Klebsiella pneumoniae. Clin Microbiol Infect 2019; 26:1046-1051. [PMID: 31809805 DOI: 10.1016/j.cmi.2019.11.025] [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] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Revised: 11/20/2019] [Accepted: 11/24/2019] [Indexed: 12/30/2022]
Abstract
OBJECTIVES Infections as a result of extended-spectrum β-lactamase-producing Enterobacterales (ESBL-E) are considered infections with a high public health burden. In this study, we aimed to identify incidences of and risk factors for healthcare-associated infections (HAIs) after rectal colonization with ESBL-producing Escherichia coli (ESBL-EC) or Klebsiella pneumoniae (ESBL-KP). METHODS This prospective cohort study was performed in 2014 and 2015. Patients colonized with ESBL-EC or ESBL-KP were monitored for subsequent HAI with ESBL-E and other pathogens. In the case of an ESBL-E infection, rectal and clinical isolates were compared using pulsed-field gel electrophoresis (PFGE), and whole-genome sequencing (WGS) for ESBL-KP isolates. Proportional hazard models were applied to identify risk factors for HAIs, and to analyse competing risks. RESULTS Among all patients admitted to the hospital during the study period, 13.6% were rectally screened for third-generation cephalosporin-resistant Enterobacterales (3GCREB). A total of 2386 rectal carriers of ESBL-EC and 585 of ESBL-KP were included in the study. Incidence density (ID) for HAI with ESBL-E was 2.74 per 1000 patient days at risk (95% confidence interval (CI) 2.16-3.43) among carriers of ESBL-EC, while it was 4.44 per 1000 patient days at risk (95% CI 3.17-6.04) among carriers of ESBL-KP. In contrast, ID for HAI with other pathogens was 4.36 per 1000 patient days at risk (95% CI 3.62-5.21) among carriers of ESBL-EC, and 5.00 per 1000 patient days at risk (95% CI 3.64-6.69) among carriers of ESBL-KP. Cox proportional hazard regression analyses identified colonization with ESBL-KP (HR = 1.58, 95% CI 1.068-2.325) compared with ESBL-EC as independent risk factor for HAI with ESBL-E. The results were consistent over all competing risk analyses. CONCLUSIONS Clinicians should be aware of the increased risk of ESBL-E infections among patients colonized with ESBL-KP compared with ESBL-EC that might be caused by underlying diseases, higher pathogenicity of ESBL-KP and other factors.
Collapse
Affiliation(s)
- L A Denkel
- Institute of Hygiene and Environmental Medicine, Charité Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Berlin, Germany; National Reference Centre for the Surveillance of Nosocomial Infections, Charité Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Berlin, Germany
| | - F Maechler
- Institute of Hygiene and Environmental Medicine, Charité Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Berlin, Germany; National Reference Centre for the Surveillance of Nosocomial Infections, Charité Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Berlin, Germany
| | - F Schwab
- Institute of Hygiene and Environmental Medicine, Charité Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Berlin, Germany; National Reference Centre for the Surveillance of Nosocomial Infections, Charité Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Berlin, Germany
| | - A Kola
- Institute of Hygiene and Environmental Medicine, Charité Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Berlin, Germany; National Reference Centre for the Surveillance of Nosocomial Infections, Charité Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Berlin, Germany
| | - A Weber
- Institute of Hygiene and Environmental Medicine, Charité Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Berlin, Germany; National Reference Centre for the Surveillance of Nosocomial Infections, Charité Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Berlin, Germany
| | - P Gastmeier
- Institute of Hygiene and Environmental Medicine, Charité Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Berlin, Germany; National Reference Centre for the Surveillance of Nosocomial Infections, Charité Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Berlin, Germany
| | - F Pfäfflin
- Department of Infectious Diseases and Respiratory Medicine, Charité Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Berlin, Germany
| | - S Weber
- Institute of Medical Biometry and Statistics (IMBI), Faculty of Medicine and Medical Centre University of Freiburg, Freiburg, Germany
| | - G Werner
- Unit of Nosocomial Pathogens and Antibiotic Resistances, Department of Infectious Diseases, Robert Koch Institute, Wernigerode Branch, Wernigerode, Germany
| | - Y Pfeifer
- Unit of Nosocomial Pathogens and Antibiotic Resistances, Department of Infectious Diseases, Robert Koch Institute, Wernigerode Branch, Wernigerode, Germany
| | - M Pietsch
- Unit of Enteropathogenic Bacteria and Legionella, Department of Infectious Diseases, Robert Koch Institute, Wernigerode Branch, Wernigerode, Germany
| | - R Leistner
- Institute of Hygiene and Environmental Medicine, Charité Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Berlin, Germany; National Reference Centre for the Surveillance of Nosocomial Infections, Charité Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Berlin, Germany.
| |
Collapse
|
11
|
Díaz-Agero Pérez C, López-Fresneña N, Rincon Carlavilla AL, Hernandez Garcia M, Ruiz-Garbajosa P, Aranaz-Andrés JM, Maechler F, Gastmeier P, Bonten MJM, Canton R. Local prevalence of extended-spectrum beta-lactamase (ESBL) producing Enterobacteriaceae intestinal carriers at admission and co-expression of ESBL and OXA-48 carbapenemase in Klebsiella pneumoniae: a prevalence survey in a Spanish University Hospital. BMJ Open 2019; 9:e024879. [PMID: 30826764 PMCID: PMC6429960 DOI: 10.1136/bmjopen-2018-024879] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
OBJECTIVE To assess the prevalence of extended-spectrum beta-lactamase (ESBL)-producing Enterobacteriaceae (ESBL-E) faecal carriers at admission in a University Hospital in Spain. DESIGN Prevalence survey. SETTING Pneumology, gastroenterology, urology and neurosurgery units at a university tertiary hospital in Madrid (Spain). PARTICIPANTS A total of 10 643 patients aged 18 and older admitted from March 2014 to April 2016 with a rectal swab taken at admission or as soon as possible within the first 48 hours. PRIMARY AND SECONDARY OUTCOME MEASURES Prevalence of ESBL-E faecal carriers and prevalence of ESBL-E infections at admission. RESULTS The prevalance of ESBL-E carriers at admission was 7.69% (CI 95% 7.18 to 8.19). Most of the isolates were Escherichia coli (77.51%), followed by Klebsiella pneumoniae (20.71%). Eighty-eight (10.41%) of ESBL-E were simultaneous ESBL and carbapenemase (CP) producers, 1.83% in the case of E. coli and 42.86% among K. pneumoniae isolates. Of the ESBL typed, 52.15% belonged to the cefotaximases (CTX-M-15) type and 91.38% of the CP were oxacillinase (OXA-48) type. Only 0.43% patients presented an active infection by ESBL-E at admission. CONCLUSIONS The prevalence found in our study is very similar to that found in literature. However, we found a high percentage of simultaneous ESBL and CP producers, particularly in K. pneumoniae. Despite the high prevalence of colonised patients, the ESBL-infection rate at admission was very low.
Collapse
Affiliation(s)
- Cristina Díaz-Agero Pérez
- Servicio de Medicina Preventiva y Salud Publica, Hospital Universitario Ramon y Cajal, Madrid, Spain
- Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain
| | - Nieves López-Fresneña
- Servicio de Medicina Preventiva y Salud Publica, Hospital Universitario Ramon y Cajal, Madrid, Spain
- Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain
| | - Angela L Rincon Carlavilla
- Servicio de Medicina Preventiva y Salud Publica, Hospital Universitario Ramon y Cajal, Madrid, Spain
- Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain
| | - Marta Hernandez Garcia
- Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain
- Servicio de Microbiologia, Hospital Universitario Ramon y Cajal, Madrid, Spain
- Red Española de Investigación en Patología Infecciosa (REIPI), Madrid, Spain
| | - Patricia Ruiz-Garbajosa
- Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain
- Servicio de Microbiologia, Hospital Universitario Ramon y Cajal, Madrid, Spain
- Red Española de Investigación en Patología Infecciosa (REIPI), Madrid, Spain
| | - Jesús María Aranaz-Andrés
- Servicio de Medicina Preventiva y Salud Publica, Hospital Universitario Ramon y Cajal, Madrid, Spain
- Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain
| | | | | | - Marc J M Bonten
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Rafael Canton
- Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain
- Servicio de Microbiologia, Hospital Universitario Ramon y Cajal, Madrid, Spain
- Red Española de Investigación en Patología Infecciosa (REIPI), Madrid, Spain
| |
Collapse
|
12
|
Merino I, Hernández-García M, Turrientes MC, Pérez-Viso B, López-Fresneña N, Diaz-Agero C, Maechler F, Fankhauser-Rodriguez C, Kola A, Schrenzel J, Harbarth S, Bonten M, Gastmeier P, Canton R, Ruiz-Garbajosa P, Desilets M, Dul S, Scherrer-Muller F, Huttner B, Uçkay I, Prendki V, Renzi G. Emergence of ESBL-producing Escherichia coli ST131-C1-M27 clade colonizing patients in Europe. J Antimicrob Chemother 2018; 73:2973-2980. [DOI: 10.1093/jac/dky296] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Accepted: 06/26/2018] [Indexed: 01/12/2023] Open
Affiliation(s)
- Irene Merino
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal-IRYCIS, Madrid, Spain
- Red Española de Investigación en Patología Infecciosa (REIPI), Instituto de Salud Carlos III, Madrid, Spain
| | - Marta Hernández-García
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal-IRYCIS, Madrid, Spain
- Red Española de Investigación en Patología Infecciosa (REIPI), Instituto de Salud Carlos III, Madrid, Spain
| | - María-Carmen Turrientes
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal-IRYCIS, Madrid, Spain
- Centro de Investigación Biomédica en Red en Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
| | - Blanca Pérez-Viso
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal-IRYCIS, Madrid, Spain
- Red Española de Investigación en Patología Infecciosa (REIPI), Instituto de Salud Carlos III, Madrid, Spain
| | - Nieves López-Fresneña
- Servicio de Medicina Preventiva, Hospital Universitario Ramón y Cajal-IRYCIS, Madrid, Spain
| | - Cristina Diaz-Agero
- Servicio de Medicina Preventiva, Hospital Universitario Ramón y Cajal-IRYCIS, Madrid, Spain
| | - Friederike Maechler
- Charité University Medicine, Institute of Hygiene and Environmental Medicine, Hindenburgdamm 27, Berlin, Germany
| | | | - Axel Kola
- Charité University Medicine, Institute of Hygiene and Environmental Medicine, Hindenburgdamm 27, Berlin, Germany
| | - Jacques Schrenzel
- Infection Control Program and Genomic Research Laboratory, University of Geneva Hospitals, Geneva, Switzerland
| | - Stephan Harbarth
- Infection Control Program and Genomic Research Laboratory, University of Geneva Hospitals, Geneva, Switzerland
| | - Marc Bonten
- Universitair Medisch Centrum Utrecht, Utrecht, The Netherlands
| | - Petra Gastmeier
- Charité University Medicine, Institute of Hygiene and Environmental Medicine, Hindenburgdamm 27, Berlin, Germany
| | - R Canton
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal-IRYCIS, Madrid, Spain
- Red Española de Investigación en Patología Infecciosa (REIPI), Instituto de Salud Carlos III, Madrid, Spain
| | - P Ruiz-Garbajosa
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal-IRYCIS, Madrid, Spain
- Red Española de Investigación en Patología Infecciosa (REIPI), Instituto de Salud Carlos III, Madrid, Spain
| | | | | | | | | | | | | | | | | |
Collapse
|
13
|
Maechler F, Geffers C, Schwab F, Peña Diaz LA, Behnke M, Gastmeier P. [Development of antimicrobial resistance in Germany : What is the current situation?]. Med Klin Intensivmed Notfmed 2017; 112:186-191. [PMID: 28378152 DOI: 10.1007/s00063-017-0272-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [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: 01/04/2017] [Accepted: 02/13/2017] [Indexed: 11/28/2022]
Abstract
BACKGROUND The frequency of multidrug-resistant organisms (MDRO) is increasing in Germany and worldwide. OBJECTIVES Presentation of MDRO resistance rates and prevalence in Germany MATERIALS AND METHODS: Results from the Antibiotic Resistance Surveillance (ARS) and Hospital Infection Surveillance Systems (Krankenhausinfektions-Surveillance-Systems, KISS) and from recent prevalence surveys are presented. RESULTS MRSA-resistance rates and the prevalence of methicillin-resistant Staphylococcus aureus (MRSA) have remained at a stable level over the last few years. In contrast, vancomycin-resistant enterococci (VRE) and multidrug-resistant gramnegative (MRGN) bacteria have increased considerably. VRE prevalence has more than tripled in the past 5 years, and Escherichia coli resistant to third-generation cephalosporins, acylureidopenicillins, and fluoroquinolones increased by 43% in 2015 compared with the previous year. CONCLUSIONS New policies to control MDRO should focus on VRE and the heterogeneous group of MRGN bacteria. In the case of the latter, the different bacterial species' characteristics should be taken into consideration.
Collapse
Affiliation(s)
- F Maechler
- Institut für Hygiene und Umweltmedizin, Nationales Referenzzentrum für die Surveillance von Nosokomialen Infektionen, Charité Universitätsmedizin Berlin, Hindenburgdamm 27, 12203, Berlin, Deutschland.
| | - C Geffers
- Institut für Hygiene und Umweltmedizin, Nationales Referenzzentrum für die Surveillance von Nosokomialen Infektionen, Charité Universitätsmedizin Berlin, Hindenburgdamm 27, 12203, Berlin, Deutschland
| | - F Schwab
- Institut für Hygiene und Umweltmedizin, Nationales Referenzzentrum für die Surveillance von Nosokomialen Infektionen, Charité Universitätsmedizin Berlin, Hindenburgdamm 27, 12203, Berlin, Deutschland
| | - L-A Peña Diaz
- Institut für Hygiene und Umweltmedizin, Nationales Referenzzentrum für die Surveillance von Nosokomialen Infektionen, Charité Universitätsmedizin Berlin, Hindenburgdamm 27, 12203, Berlin, Deutschland
| | - M Behnke
- Institut für Hygiene und Umweltmedizin, Nationales Referenzzentrum für die Surveillance von Nosokomialen Infektionen, Charité Universitätsmedizin Berlin, Hindenburgdamm 27, 12203, Berlin, Deutschland
| | - P Gastmeier
- Institut für Hygiene und Umweltmedizin, Nationales Referenzzentrum für die Surveillance von Nosokomialen Infektionen, Charité Universitätsmedizin Berlin, Hindenburgdamm 27, 12203, Berlin, Deutschland
| |
Collapse
|
14
|
Abstract
EPIDEMIOLOGY Prevalence of Multidrug-Resistant Organisms (MDROs) varies temporally, geographically, and by healthcare setting. In general MDROs rates are higher in hospitals compared to the outpatient setting. Within the hospital the prevalence of MDRO-patients in ICUs is higher than in non-ICU wards. While the number of MRSA-patients decreased over the last years, there was a continuous increase of Gram-negative bacilli (GNB) in Germany. At present, every 60. patient in the ICU is known as colonized or infected with GNB. SURVEILLANCE Hospitals in Germany are obliged by the "protection against infection act" (REF?)11 to establish a surveillance for MDROs. To improve the informative value of the surveillance it is recommended to participate in one of three surveillance systems for MDROs in Germany, which differ with regard to the effort required and their key messages. IMPORTANCE MDROs may increase healthcare costs as well as patient morbidity and mortality.
Collapse
|
15
|
Maechler F, Thoma N, Dem P, Kola A, Hansen S, Gastmeier P. More than half of ESBL-E are susceptible to fluoroquinolones: admission prevalence data from eight non-ICUs in a German university hospital. Antimicrob Resist Infect Control 2015. [PMCID: PMC4475129 DOI: 10.1186/2047-2994-4-s1-p124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
|
16
|
Schröder C, Schwab F, Behnke M, Breier AC, Maechler F, Piening B, Dettenkofer M, Geffers C, Gastmeier P. Epidemiology of healthcare associated infections in Germany: Nearly 20 years of surveillance. Int J Med Microbiol 2015; 305:799-806. [PMID: 26358916 DOI: 10.1016/j.ijmm.2015.08.034] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
OBJECTIVE To describe the epidemiology of healthcare-associated infections (HAI) in hospitals participating in the German national nosocomial infections surveillance system (KISS). METHOD The epidemiology of HAI was described for the surveillance components for intensive care units (ITS-KISS), non-ICUs (STATIONS-KISS), very low birth weight infants (NEO-KISS) and surgical site infections (OP-KISS) in the period from 2006 to 2013. In addition, risk factor analyses were performed for the most important infections of ICU-KISS, NEO-KISS and OP-KISS. RESULTS Data from a total of 3,454,778 ICU patients from 913 ICUs, 618,816 non-ICU patients from 142 non-ICU wards, 53,676 VLBW from 241 neonatal intensive care units (NICU) and 1,005,064 surgical patients from operative departments from 550 hospitals were used for analysis. Compared with baseline data, a significant reduction of primary bloodstream infections (PBSI) and lower respiratory tract infections (LRTI) was observed in ICUs with the maximum effect in year 5 (or longer participation) (incidence rate ratio 0.60 (CI95 0.50-0.72) and 0.61 (CI95 0.52-0.71) respectively). A significant reduction of PBSI and LRTI was also observed in NEO-KISS when comparing the baseline situation with the 5th year of participation (hazard ratio 0.70 (CI95 0.64-0.76) and 0.43 (CI95 0.35-0.52)). The effect was smaller in operative departments after the introduction of OP-KISS (OR 0.80; CI95 0.64-1.02 in year 5 or later for all procedure types combined). Due to the large database, it has not only been possible to confirm well-known risk factors for HAI, but also to identify some new interesting risk factors like seasonal and volume effects. CONCLUSIONS Participating in a national surveillance system and using surveillance data for internal quality management leads to substantial reduction of HAI. In addition, a surveillance system can identify otherwise not recognized risk factors which should - if possible - be considered for infection control management and for risk adjustment in the benchmarking process.
Collapse
Affiliation(s)
- C Schröder
- Institute for Hygiene and Environmental Medicine, National Reference Centre for the Surveillance of Nosocomial Infections, Charité - University Hospital, Hindenburgdamm 27, 12203 Berlin, Germany.
| | - F Schwab
- Institute for Hygiene and Environmental Medicine, National Reference Centre for the Surveillance of Nosocomial Infections, Charité - University Hospital, Hindenburgdamm 27, 12203 Berlin, Germany
| | - M Behnke
- Institute for Hygiene and Environmental Medicine, National Reference Centre for the Surveillance of Nosocomial Infections, Charité - University Hospital, Hindenburgdamm 27, 12203 Berlin, Germany
| | - A-C Breier
- Institute for Hygiene and Environmental Medicine, National Reference Centre for the Surveillance of Nosocomial Infections, Charité - University Hospital, Hindenburgdamm 27, 12203 Berlin, Germany
| | - F Maechler
- Institute for Hygiene and Environmental Medicine, National Reference Centre for the Surveillance of Nosocomial Infections, Charité - University Hospital, Hindenburgdamm 27, 12203 Berlin, Germany
| | - B Piening
- Institute for Hygiene and Environmental Medicine, National Reference Centre for the Surveillance of Nosocomial Infections, Charité - University Hospital, Hindenburgdamm 27, 12203 Berlin, Germany
| | - M Dettenkofer
- Institute for Environmental Medicine and Hospital Hygiene, University Medical Centre Freiburg, Germany
| | - C Geffers
- Institute for Hygiene and Environmental Medicine, National Reference Centre for the Surveillance of Nosocomial Infections, Charité - University Hospital, Hindenburgdamm 27, 12203 Berlin, Germany
| | - P Gastmeier
- Institute for Hygiene and Environmental Medicine, National Reference Centre for the Surveillance of Nosocomial Infections, Charité - University Hospital, Hindenburgdamm 27, 12203 Berlin, Germany
| |
Collapse
|
17
|
Behnke M, Leistner R, Pena-Diaz LA, Maechler F, Gastmeier P. 904Multidrug-Resistant Gram-Negative Bacteria (MRGN) in Intensive Care Units - Results from the German National Surveillance System for Nosocomial Infections (KISS). Open Forum Infect Dis 2014. [PMCID: PMC5782287 DOI: 10.1093/ofid/ofu052.612] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Affiliation(s)
- Michael Behnke
- German National Reference Center for the Surveillance of Nosocomial Infections, Berlin, Germany
- Institute of Hygiene and Environmental Medicine, Charité – University Medicine Berlin, Berlin, Germany
| | - Rasmus Leistner
- German National Reference Center for the Surveillance of Nosocomial Infections, Berlin, Germany
- Institute of Hygiene and Environmental Medicine, Charité – University Medicine Berlin, Berlin, Germany
| | - Luis Alberto Pena-Diaz
- German National Reference Center for the Surveillance of Nosocomial Infections, Berlin, Germany
- Institute of Hygiene and Environmental Medicine, Charité – University Medicine Berlin, Berlin, Germany
| | - Friederike Maechler
- German National Reference Center for the Surveillance of Nosocomial Infections, Berlin, Germany
- Institute of Hygiene and Environmental Medicine, Charité – University Medicine Berlin, Berlin, Germany
| | - Petra Gastmeier
- German National Reference Center for the Surveillance of Nosocomial Infections, Berlin, Germany
- Institute of Hygiene and Environmental Medicine, Charité – University Medicine Berlin, Berlin, Germany
| |
Collapse
|
18
|
Maechler F, Peña Diaz LA, Schröder C, Geffers C, Behnke M, Gastmeier P. Prevalence of carbapenem-resistant organisms and other Gram-negative MDRO in German ICUs: first results from the national nosocomial infection surveillance system (KISS). Infection 2014; 43:163-8. [PMID: 25395161 DOI: 10.1007/s15010-014-0701-6] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2014] [Accepted: 11/01/2014] [Indexed: 11/24/2022]
Abstract
PURPOSE Standardized prevalence and incidence data on carbapenem-resistant organisms (CRO) and, as a relevant subgroup, carbapenem-resistant Enterobacteriaceae (CRE) are scarce. CRO-surveillance within the German nosocomial infection surveillance system (KISS) aims to provide epidemiological surveillance data on CRO colonizations and infections. METHODS CRO-surveillance is part of a KISS-module for the surveillance of multidrug-resistant organisms (MDRO). MDRO-KISS methods require surveillance of all patients admitted to the ward and standardized documentation of imported and ICU-acquired cases. Data on all MDRO-carriers including colonization and infection with MDRO are collected. All presented data were routine data collected from January 1st 2013 until December 1st 2013 in accordance with the German Protection against Infection Act (IfSG). RESULTS 341 ICUs submitted data on MDRO during the first year. In total, 5,171 cases of multidrug-resistant Gram-negative bacteria (MRGN) were identified. 848 were CRO (16%). 325 CRO-cases were acquired within the ICU (38%), and 373 CRO-patients had an infection (44%). CRO-prevalence was 0.29 per 100 patients. Acquisition rate of MRGN was 1.32 per 1,000 patient days. This rate is more than doubled the acquisition rates of other MDRO under surveillance within MDRO-KISS (0.57 MRSA, 0.49 VRE). CRO-acquisition rate was 0.3 per 1,000 patient days. Incidence density of MRGN infections bacteria was 0.58 per 1,000 patient days (CRO 0.15/1,000 patient days). CONCLUSIONS To date, CRO are common in German ICUs and the relatively large proportions of ICU-acquired CRO and infections emphasize their potential to cause outbreaks. High MRGN infection rates and high ESBL prevalence data from clinical studies suggest a lack of MRGN identification in asymptomatic carriers.
Collapse
Affiliation(s)
- F Maechler
- Institut für Hygiene und Umweltmedizin, Charité Berlin, Hindenburgdamm 27, 12203, Berlin, Germany,
| | | | | | | | | | | |
Collapse
|
19
|
Maechler F, Schwab F, Meyer E, Geffers C, Leistner R, Gastmeier P. P096: Antibiotic stewardship in intensive care units: a cross sectional study of 355 ICUs in Germany. Antimicrob Resist Infect Control 2013. [PMCID: PMC3688414 DOI: 10.1186/2047-2994-2-s1-p96] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
|