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Segawa T, Masuda K, Hisatsune J, Ishida-Kuroki K, Sugawara Y, Kuwabara M, Nishikawa H, Hiratsuka T, Aota T, Tao Y, Iwahashi Y, Ueda K, Mae K, Masumoto K, Kitagawa H, Komatsuzawa H, Ohge H, Sugai M. Genomic analysis of inter-hospital transmission of vancomycin-resistant Enterococcus faecium sequence type 80 isolated during an outbreak in Hiroshima, Japan. Antimicrob Agents Chemother 2024; 68:e0171623. [PMID: 38506550 PMCID: PMC11064488 DOI: 10.1128/aac.01716-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Accepted: 03/01/2024] [Indexed: 03/21/2024] Open
Abstract
Outbreaks caused by vancomycin-resistant enterococci that transcend jurisdictional boundaries are occurring worldwide. This study focused on a vancomycin-resistant enterococcus outbreak that occurred between 2018 and 2021 across two cities in Hiroshima, Japan. The study involved genetic and phylogenetic analyses using whole-genome sequencing of 103 isolates of vancomycin-resistant enterococci to identify the source and transmission routes of the outbreak. Phylogenetic analysis was performed using core genome multilocus sequence typing and core single-nucleotide polymorphisms; infection routes between hospitals were inferred using BadTrIP. The outbreak was caused by Enterococcus faecium sequence type (ST) 80 carrying the vanA plasmid, which was derived from strain A10290 isolated in India. Of the 103 isolates, 93 were E. faecium ST80 transmitted across hospitals. The circular vanA plasmid of the Hiroshima isolates was similar to the vanA plasmid of strain A10290 and transferred from E. faecium ST80 to other STs of E. faecium and other Enterococcus species by conjugation. The inferred transmission routes across hospitals suggest the existence of a central hospital serving as a hub, propagating vancomycin-resistant enterococci to multiple hospitals. Our study highlights the importance of early intervention at the key central hospital to prevent the spread of the infection to small medical facilities, such as nursing homes, with limited medical resources and a high number of vulnerable individuals.
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Affiliation(s)
- Takaya Segawa
- Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, Higashimurayama, Japan
| | - Kanako Masuda
- Hiroshima Prefectural Center for Disease Control and Prevention, Hiroshima, Japan
- Project Research Center for Nosocomial Infectious Diseases, Hiroshima University, Hiroshima, Japan
| | - Junzo Hisatsune
- Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, Higashimurayama, Japan
- Project Research Center for Nosocomial Infectious Diseases, Hiroshima University, Hiroshima, Japan
- Department of Antimicrobial Resistance, Hiroshima University Graduate School of Biomedical & Health Sciences, Hiroshima, Japan
| | - Kasumi Ishida-Kuroki
- Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, Higashimurayama, Japan
| | - Yo Sugawara
- Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, Higashimurayama, Japan
| | - Masao Kuwabara
- Hiroshima Prefectural Center for Disease Control and Prevention, Hiroshima, Japan
| | - Hideki Nishikawa
- Hiroshima Prefectural Center for Disease Control and Prevention, Hiroshima, Japan
| | - Takahiro Hiratsuka
- Hiroshima Prefectural Technology Research Institute, Public Health and Environment Center, Hiroshima, Japan
| | - Tatsuaki Aota
- Hiroshima City Institute of Public Health, Hiroshima, Japan
| | - Yasuo Tao
- Hiroshima City Public Health Center, Hiroshima, Japan
| | | | - Kuniko Ueda
- Hiroshima City Public Health Center, Hiroshima, Japan
| | - Kaori Mae
- Hiroshima City Medical Association Clinical Laboratory, Hiroshima, Japan
| | - Ken Masumoto
- Hiroshima City Medical Association Clinical Laboratory, Hiroshima, Japan
| | - Hiroki Kitagawa
- Project Research Center for Nosocomial Infectious Diseases, Hiroshima University, Hiroshima, Japan
- Department of Infectious Diseases, Hiroshima University Hospital, Hiroshima, Japan
| | - Hitoshi Komatsuzawa
- Project Research Center for Nosocomial Infectious Diseases, Hiroshima University, Hiroshima, Japan
- Department of Bacteriology, Hiroshima University Graduate School of Biomedical and Health Sciences, Hiroshima, Japan
| | - Hiroki Ohge
- Project Research Center for Nosocomial Infectious Diseases, Hiroshima University, Hiroshima, Japan
- Department of Infectious Diseases, Hiroshima University Hospital, Hiroshima, Japan
| | - Motoyuki Sugai
- Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, Higashimurayama, Japan
- Project Research Center for Nosocomial Infectious Diseases, Hiroshima University, Hiroshima, Japan
- Department of Antimicrobial Resistance, Hiroshima University Graduate School of Biomedical & Health Sciences, Hiroshima, Japan
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2
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Rath A, Kieninger B, Caplunik-Pratsch A, Fritsch J, Mirzaliyeva N, Holzmann T, Bender JK, Werner G, Schneider-Brachert W. Concerning emergence of a new vancomycin-resistant Enterococcus faecium strain ST1299/CT1903/vanA at a tertiary university centre in South Germany. J Hosp Infect 2024; 143:25-32. [PMID: 37852539 DOI: 10.1016/j.jhin.2023.10.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 09/22/2023] [Accepted: 10/08/2023] [Indexed: 10/20/2023]
Abstract
BACKGROUND vanB-carrying vancomycin-resistant Enterococcus faecium (VREfm) of the sequence types 80 (ST80) and ST117 have dominated Germany in the past. In 2020, our hospital witnessed a sharp increase in the proportion of vanA-positive VREfm. AIM To attempt to understand these dynamics through whole-genome sequencing (WGS) and analysis of nosocomial transmissions. METHODS At our hospital, the first VREfm isolate per patient, treated during 2020, was analysed retrospectively using specific vanA/vanB PCR, WGS, multi-locus sequence typing (MLST), and core-genome (cg) MLST. Epidemiologic links between VRE-positive patients were assessed using hospital occupancy data. FINDINGS Isolates from 319 out of 356 VREfm patients were available for WGS, of which 181 (56.7%) fulfilled the ECDC definition for nosocomial transmission. The high load of nosocomial cases is reflected in the overall high clonality rate with only three dominating sequence (ST) and complex types (CT), respectively: the new emerging strain ST1299 (100% vanA, 77.4% CT1903), and the well-known ST80 (90.0% vanB, 81.0% CT1065) and ST117 (78.0% vanB, 65.0% CT71). The ST1299 isolates overall, and the subtype CT1903 in particular, showed high isolate clonality, which demonstrates impressively high spreading potential. Overall, 152 out of 319 isolates had an allelic cgMLST difference of ≤3 to another, including 91 (59.6%) ST1299. Occupancy data identified shared rooms (3.7%), shared departments (6.2%), and VRE-colonized prior room occupants (0.6%) within 30 days before diagnosis as solid epidemiological links. CONCLUSION A new emerging VREfm clone, ST1299/CT1903/vanA, dominated our institution in 2020 and has been an important driver of the increasing VREfm rates.
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Affiliation(s)
- A Rath
- Department of Infection Prevention and Infectious Diseases, University Hospital Regensburg, Regensburg, Germany.
| | - B Kieninger
- Department of Infection Prevention and Infectious Diseases, University Hospital Regensburg, Regensburg, Germany
| | - A Caplunik-Pratsch
- Department of Infection Prevention and Infectious Diseases, University Hospital Regensburg, Regensburg, Germany
| | - J Fritsch
- Department of Infection Prevention and Infectious Diseases, University Hospital Regensburg, Regensburg, Germany
| | - N Mirzaliyeva
- Department of Infection Prevention and Infectious Diseases, University Hospital Regensburg, Regensburg, Germany
| | - T Holzmann
- Department of Infection Prevention and Infectious Diseases, University Hospital Regensburg, Regensburg, Germany
| | - J K Bender
- Department of Infectious Diseases, Division of Nosocomial Pathogens and Antibiotic Resistances, Robert Koch Institute, Wernigerode, Germany
| | - G Werner
- Department of Infectious Diseases, Division of Nosocomial Pathogens and Antibiotic Resistances, Robert Koch Institute, Wernigerode, Germany
| | - W Schneider-Brachert
- Department of Infection Prevention and Infectious Diseases, University Hospital Regensburg, Regensburg, Germany
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3
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Freitas AR, Werner G. Nosocomial Pathogens and Antimicrobial Resistance: Modern Challenges and Future Opportunities. Microorganisms 2023; 11:1685. [PMID: 37512858 PMCID: PMC10386484 DOI: 10.3390/microorganisms11071685] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 06/27/2023] [Indexed: 07/30/2023] Open
Abstract
Antimicrobial resistance (AMR) has become a critical global health emergency in the 21st century, with the greatest burden in resource-limited settings [...].
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Affiliation(s)
- Ana R Freitas
- 1H-TOXRUN, One Health Toxicology Research Unit, University Institute of Health Sciences (IUCS), CESPU, CRL, 4585-116 Gandra, Portugal
- Laboratory of Microbiology, UCIBIO-Applied Molecular Biosciences Unit, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal
- Associate Laboratory i4HB-Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal
| | - Guido Werner
- Division of Nosocomial Pathogens and Antibiotic Resistances, Department of Infectious Diseases, Robert Koch Institute, National Reference Centre for Staphylococci and Enterococci, Wernigerode Branch, 38855 Wernigerode, Germany
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4
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Lu J, Shen T, Zhang Y, Ma X, Xu S, Awad S, Du M, Zhong Z. Safety assessment of Enterococcus lactis based on comparative genomics and phenotypic analysis. Front Microbiol 2023; 14:1196558. [PMID: 37283930 PMCID: PMC10239811 DOI: 10.3389/fmicb.2023.1196558] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 04/25/2023] [Indexed: 06/08/2023] Open
Abstract
Enterococcus faecium is sometimes used in food production; however, its acquisition of antibiotic resistance has become an alarming health concern. The E. lactis species is closely related to E. faecium and has good probiotic potential. This study aimed to investigate the antibiotic resistance of E. lactis. We analyzed the antibiotic resistance phenotype and whole-genome sequences of 60 E. lactis isolates (23, 29, and 8 isolates from dairy products, Rice wine Koji, and human feces, respectively). These isolates showed varying degree of resistance to 13 antibiotics, and were sensitive to ampicillin and linezolid. The E. lactis genomes carried only a subset of commonly reported antibiotic resistance genes (ARGs) in E. faecium. Five ARGs were detected across the investigated E. lactis, including two universally present genes (msrC and AAC(6')-Ii) and three rarely detected ARGs (tet(L), tetM, and efmA). To identify other undescribed antibiotic resistance-encoding genes, a genome-wide association study was performed, returning 160 potential resistance genes that were associated with six antibiotics, namely chloramphenicol, vancomycin, clindamycin, erythromycin, quinupristin-dalfopristin, and rifampicin. Only around one-third of these genes encode known biological functions, including cellular metabolism, membrane transport, and DNA synthesis. This work identified interesting targets for future study of antibiotic resistance in E. lactis. The fact that the lower number of ARGs present in E. lactis supports that it may be an alternative to E. faecalis for use in the food industry. Data generated in this work is of interest to the dairy industry.
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Affiliation(s)
- Jingda Lu
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, China
- Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot, China
- Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Hohhot, China
| | - Tingting Shen
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, China
- Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot, China
- Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Hohhot, China
| | - Yixin Zhang
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, China
- Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot, China
- Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Hohhot, China
| | - Xinwei Ma
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, China
- Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot, China
- Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Hohhot, China
| | - Sheng Xu
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, China
- Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot, China
- Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Hohhot, China
| | - Sameh Awad
- Department of Dairy Science and Technology, Faculty of Agriculture, Alexandria University, Alexandria, Egypt
| | - Muying Du
- College of Food Science, Southwest University, Chongqing, China
- Chinese-Hungarian Cooperative Research Centre for Food Science, Southwest University, Chongqing, China
| | - Zhi Zhong
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, China
- Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot, China
- Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Hohhot, China
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5
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Aung MS, Urushibara N, Kawaguchiya M, Ohashi N, Hirose M, Kudo K, Tsukamoto N, Ito M, Kobayashi N. Antimicrobial Resistance, Virulence Factors, and Genotypes of Enterococcus faecalis and Enterococcus faecium Clinical Isolates in Northern Japan: Identification of optrA in ST480 E. faecalis. Antibiotics (Basel) 2023; 12:antibiotics12010108. [PMID: 36671309 PMCID: PMC9855154 DOI: 10.3390/antibiotics12010108] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 01/04/2023] [Accepted: 01/05/2023] [Indexed: 01/10/2023] Open
Abstract
Enterococcus faecalis and E. faecium are the major pathogens causing community- and healthcare-associated infections, with an ability to acquire resistance to multiple antimicrobials. The present study was conducted to determine the prevalence of virulence factors, drug resistance and its genetic determinants, and clonal lineages of E. faecalis and E. faecium clinical isolates in northern Japan. A total of 480 (426 E. faecalis and 54 E. faecium) isolates collected over a four-month period were analyzed. Three virulence factors promoting bacterial colonization (asa1, efaA, and ace) were more prevalent among E. faecalis (46-59%) than E. faecium, while a similar prevalence of enterococcal surface protein gene (esp) was found in these species. Between E. faecalis and E. faecium, an evident difference was noted for resistance to erythromycin, gentamicin, and levofloxacin and its responsible resistance determinants. Oxazolidinone resistance gene optrA and phenicol exporter gene fexA were identified in an isolate of E. faecalis belonging to ST480 and revealed to be located on a cluster similar to those of isolates reported in other Asian countries. The E. faecalis isolates analyzed were differentiated into 12 STs, among which ST179 and ST16 of clonal complex (CC) 16 were the major lineage. Nearly all the E. faecium isolates were assigned into CC17, which consisted of 10 different sequence types (STs), including a dominant ST17 containing multidrug resistant isolates and ST78 with isolates harboring the hyaluronidase gene (hyl). The present study revealed the genetic profiles of E. faecalis and E. faecium clinical isolates, with the first identification of optrA in ST480 E. faecalis in Japan.
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Affiliation(s)
- Meiji Soe Aung
- Department of Hygiene, Sapporo Medical University School of Medicine, Sapporo 060-8556, Japan
- Correspondence: ; Tel.: +81-11-611-2111
| | - Noriko Urushibara
- Department of Hygiene, Sapporo Medical University School of Medicine, Sapporo 060-8556, Japan
| | - Mitsuyo Kawaguchiya
- Department of Hygiene, Sapporo Medical University School of Medicine, Sapporo 060-8556, Japan
| | - Nobuhide Ohashi
- Department of Hygiene, Sapporo Medical University School of Medicine, Sapporo 060-8556, Japan
| | - Mina Hirose
- Division of Pediatric Dentistry, Department of Oral Growth and Development, School of Dentistry, Health Sciences University of Hokkaido, Ishikari-Tobetsu 061-0293, Japan
| | - Kenji Kudo
- Sapporo Mirai Laboratory, Co., Ltd., Sapporo 060-0003, Japan
| | | | - Masahiko Ito
- Sapporo Mirai Laboratory, Co., Ltd., Sapporo 060-0003, Japan
| | - Nobumichi Kobayashi
- Department of Hygiene, Sapporo Medical University School of Medicine, Sapporo 060-8556, Japan
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6
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Maechler F, Weber A, Schwengers O, Schwab F, Denkel L, Behnke M, Gastmeier P, Kola A. Split k-mer analysis compared to cgMLST and SNP-based core genome analysis for detecting transmission of vancomycin-resistant enterococci: results from routine outbreak analyses across different hospitals and hospitals networks in Berlin, Germany. Microb Genom 2023; 9:mgen000937. [PMID: 36748706 PMCID: PMC9973845 DOI: 10.1099/mgen.0.000937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
The increase of Vancomycin-resistant Enterococcus faecium (VREfm) in recent years has been partially attributed to the rise of specific clonal lineages, which have been identified throughout Germany. To date, there is no gold standard for the interpretation of genomic data for outbreak analyses. New genomic approaches such as split k-mer analysis (SKA) could support cluster attribution for routine outbreak investigation. The aim of this project was to investigate frequent clonal lineages of VREfm identified during suspected outbreaks across different hospitals, and to compare genomic approaches including SKA in routine outbreak investigation. We used routine outbreak laboratory data from seven hospitals and three different hospital networks in Berlin, Germany. Short-read libraries were sequenced on the Illumina MiSeq system. We determined clusters using the published Enterococcus faecium-cgMLST scheme (threshold ≤20 alleles), and assigned sequence and complex types (ST, CT), using the Ridom SeqSphere+ software. For each cluster as determined by cgMLST, we used pairwise core-genome SNP-analysis and SKA at thresholds of ten and seven SNPs, respectively, to further distinguish cgMLST clusters. In order to investigate clinical relevance, we analysed to what extent epidemiological linkage backed the clusters determined with different genomic approaches. Between 2014 and 2021, we sequenced 693 VREfm strains, and 644 (93 %) were associated within cgMLST clusters. More than 74 % (n=475) of the strains belonged to the six largest cgMLST clusters, comprising ST117, ST78 and ST80. All six clusters were detected across several years and hospitals without apparent epidemiological links. Core SNP analysis identified 44 clusters with a median cluster size of three isolates (IQR 2-7, min-max 2-63), as well as 197 singletons (41.4 % of 475 isolates). SKA identified 67 clusters with a median cluster size of two isolates (IQR 2-4, min-max 2-19), and 261 singletons (54.9 % of 475 isolates). Of the isolate pairs attributed to clusters, 7 % (n=3064/45 596) of pairs in clusters determined by standard cgMLST, 15 % (n=1222/8500) of pairs in core SNP-clusters and 51 % (n=942/1880) of pairs in SKA-clusters showed epidemiological linkage. The proportion of epidemiological linkage differed between sequence types. For VREfm, the discriminative ability of the widely used cgMLST based approach at ≤20 alleles difference was insufficient to rule out hospital outbreaks without further analytical methods. Cluster assignment guided by core genome SNP analysis and the reference free SKA was more discriminative and correlated better with obvious epidemiological linkage, at least recently published thresholds (ten and seven SNPs, respectively) and for frequent STs. Besides higher overall discriminative power, the whole-genome approach implemented in SKA is also easier and faster to conduct and requires less computational resources.
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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
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7
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Piezzi V, Wassilew N, Atkinson A, D'Incau S, Kaspar T, Seth-Smith HMB, Casanova C, Bittel P, Jent P, Sommerstein R, Buetti N, Marschall J. Nosocomial outbreak of vancomycin-resistant Enterococcus faecium (VRE) ST796, Switzerland, 2017 to 2020. Euro Surveill 2022; 27:2200285. [PMID: 36695463 PMCID: PMC9716646 DOI: 10.2807/1560-7917.es.2022.27.48.2200285] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
A large clonal outbreak caused by vancomycin-resistant Enterococcus faecium (VRE) affected the Bern University Hospital group from the end of December 2017 until July 2020. We describe the characteristics of the outbreak and the bundle of infection prevention and control (IPC) measures implemented. The outbreak was first recognised when two concomitant cases of VRE bloodstream infection were identified on the oncology ward. During 32 months, 518 patients in the 1,300-bed hospital group were identified as vanB VRE carriers. Eighteen (3.5%) patients developed an invasive infection, of whom seven had bacteraemia. In 2018, a subset of 328 isolates were analysed by whole genome sequencing, 312 of which were identified as sequence type (ST) 796. The initial IPC measures were implemented with a focus on the affected wards. However, in June 2018, ST796 caused another increase in cases, and the management strategy was intensified and escalated to a hospital-wide level. The clinical impact of this large nosocomial VRE outbreak with the emergent clone ST796 was modest. A hospital-wide approach with a multimodal IPC bundle was successful against this highly transmissible strain.
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Affiliation(s)
- Vanja Piezzi
- Department of Infectious Diseases, University Hospital Bern, University of Bern, Bern, Switzerland
| | - Nasstasja Wassilew
- Department of Infectious Diseases, University Hospital Bern, University of Bern, Bern, Switzerland
| | - Andrew Atkinson
- Department of Infectious Diseases, University Hospital Bern, University of Bern, Bern, Switzerland
| | - Stéphanie D'Incau
- Department of Infectious Diseases, Lucerne Cantonal Hospital, Lucerne, Switzerland
| | - Tanja Kaspar
- Department of Infectious Diseases, University Hospital Bern, University of Bern, Bern, Switzerland
| | - Helena MB Seth-Smith
- Division of Clinical Bacteriology and Mycology, University Hospital Basel, Basel, Switzerland and Applied Microbiology Research, Department of Biomedicine, University of Basel, Basel, Switzerland,Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
| | - Carlo Casanova
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Pascal Bittel
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Philipp Jent
- Department of Infectious Diseases, University Hospital Bern, University of Bern, Bern, Switzerland
| | - Rami Sommerstein
- Department of Infectious Diseases, University Hospital Bern, University of Bern, Bern, Switzerland,Department Health Sciences and Medicine, Clinic St. Anna, University of Lucerne, Lucerne, Switzerland
| | - Niccolò Buetti
- Infection Control Programme, University of Geneva Hospitals and Faculty of Medicine, Geneva, Switzerland,INSERM, IAME, Université Paris-Cité, Paris, France
| | - Jonas Marschall
- Department of Infectious Diseases, University Hospital Bern, University of Bern, Bern, Switzerland,Division of Infectious Diseases, Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO, United States
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8
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Wen Z, Liu F, Zhang P, Wei Y, Shi Y, Zheng J, Li G, Yu Z, Xu Z, Deng Q, Chen Z. In vitro activity and adaptation strategies of eravacycline in clinical Enterococcus faecium isolates from China. J Antibiot (Tokyo) 2022; 75:498-508. [PMID: 35896611 DOI: 10.1038/s41429-022-00546-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 06/30/2022] [Accepted: 07/03/2022] [Indexed: 11/09/2022]
Abstract
Eravacycline (Erava) is a synthetic fluorocycline with potent antimicrobial activity against a wide range of Gram-positive bacteria. This study aimed to investigate the in vitro antimicrobial activity and resistance mechanism of Erava in clinical E. faecium isolates from China. Erava minimum inhibitory concentrations (MICs) against clinical E. faecium isolates-including those resistant to linezolid (LZD) or harboring the tetracycline (Tet) resistance genes was ≤0.25 mg l-1. Moreover, our data indicated that clinical isolates of E. faecium with Erava MIC 0.25 mg l-1 were predominantly shown to belong to Sequence-type 78 (ST78) and ST80. The prevalence of Erava heteroresistance in clinical E. faecium strain was 2.46% (3/122). The increased Erava MIC values of heteroresistance-derived E. faecium clones could be significantly reduced by efflux pump inhibitors (EPIs). Furthermore, comparative proteomics results showed that efflux pumps lmrA, mdlA, and mdlB contributed significantly to the acquisition of Erava resistance in E. faecium. In addition, a genetic mutation in 16 S rRNA (G190A) were detected in resistant E. faecium isolates induced by Erava. In summary, Erava exhibits potent in vitro antimicrobial activity against E. faecium, but mutation of Tet target sites and elevated expression of efflux pumps under Erava selection results in Erava resistance.
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Affiliation(s)
- Zewen Wen
- Department of Infectious Diseases and Shenzhen Key Lab of Endogenous Infection, Shenzhen Nanshan People's Hospital and the 6th affiliated hospital of Guangdong Medical University, Shenzhen, 518052, China.,Quality Control Center of Hospital Infection Management of Shenzhen, Huazhong University of Science and Technology Union Shenzhen Hospital, Shenzhen, 518052, China
| | - Fangfang Liu
- Department of Infectious Diseases and Shenzhen Key Lab of Endogenous Infection, Shenzhen Nanshan People's Hospital and the 6th affiliated hospital of Guangdong Medical University, Shenzhen, 518052, China.,Quality Control Center of Hospital Infection Management of Shenzhen, Huazhong University of Science and Technology Union Shenzhen Hospital, Shenzhen, 518052, China
| | - Peixing Zhang
- Department of Infectious Diseases and Shenzhen Key Lab of Endogenous Infection, Shenzhen Nanshan People's Hospital and the 6th affiliated hospital of Guangdong Medical University, Shenzhen, 518052, China.,Quality Control Center of Hospital Infection Management of Shenzhen, Huazhong University of Science and Technology Union Shenzhen Hospital, Shenzhen, 518052, China
| | - Ying Wei
- Heilongjiang Medical Service Management Evaluation Center, Harbin, Heilongjiang, 150031, China
| | - Yiyi Shi
- Department of Infectious Diseases and Shenzhen Key Lab of Endogenous Infection, Shenzhen Nanshan People's Hospital and the 6th affiliated hospital of Guangdong Medical University, Shenzhen, 518052, China.,Quality Control Center of Hospital Infection Management of Shenzhen, Huazhong University of Science and Technology Union Shenzhen Hospital, Shenzhen, 518052, China
| | - Jinxin Zheng
- Department of Infectious Diseases and Shenzhen Key Lab of Endogenous Infection, Shenzhen Nanshan People's Hospital and the 6th affiliated hospital of Guangdong Medical University, Shenzhen, 518052, China.,Quality Control Center of Hospital Infection Management of Shenzhen, Huazhong University of Science and Technology Union Shenzhen Hospital, Shenzhen, 518052, China
| | - Guiqiu Li
- Quality Control Center of Hospital Infection Management of Shenzhen, Huazhong University of Science and Technology Union Shenzhen Hospital, Shenzhen, 518052, China.,The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, 150001, China
| | - Zhijian Yu
- Department of Infectious Diseases and Shenzhen Key Lab of Endogenous Infection, Shenzhen Nanshan People's Hospital and the 6th affiliated hospital of Guangdong Medical University, Shenzhen, 518052, China.,Quality Control Center of Hospital Infection Management of Shenzhen, Huazhong University of Science and Technology Union Shenzhen Hospital, Shenzhen, 518052, China
| | - Zhicao Xu
- Department of Infectious Diseases and Shenzhen Key Lab of Endogenous Infection, Shenzhen Nanshan People's Hospital and the 6th affiliated hospital of Guangdong Medical University, Shenzhen, 518052, China. .,Quality Control Center of Hospital Infection Management of Shenzhen, Huazhong University of Science and Technology Union Shenzhen Hospital, Shenzhen, 518052, China.
| | - Qiwen Deng
- Department of Infectious Diseases and Shenzhen Key Lab of Endogenous Infection, Shenzhen Nanshan People's Hospital and the 6th affiliated hospital of Guangdong Medical University, Shenzhen, 518052, China. .,Quality Control Center of Hospital Infection Management of Shenzhen, Huazhong University of Science and Technology Union Shenzhen Hospital, Shenzhen, 518052, China.
| | - Zhong Chen
- Department of Infectious Diseases and Shenzhen Key Lab of Endogenous Infection, Shenzhen Nanshan People's Hospital and the 6th affiliated hospital of Guangdong Medical University, Shenzhen, 518052, China. .,Quality Control Center of Hospital Infection Management of Shenzhen, Huazhong University of Science and Technology Union Shenzhen Hospital, Shenzhen, 518052, China.
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9
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Epidemiological and genetic characteristics of vancomycin-resistant Enterococcus faecium isolates in a University Children's Hospital in Germany: 2019 to 2020. Antimicrob Resist Infect Control 2022; 11:48. [PMID: 35279207 PMCID: PMC8917738 DOI: 10.1186/s13756-022-01081-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 02/12/2022] [Indexed: 12/28/2022] Open
Abstract
Background Vancomycin-resistant Enterococcus faecium (VREfm) strains are one of the most important pathogens causing nosocomial infections in Germany. Due to limited treatment options and an increased risk for acquisition in immunocompromised children, surveillance to monitor occurrence of VREfm in paediatric clinical facilities is of critical importance. Following an unusual accumulation of VREfm positive patients between April 2019 and August 2020 at Dr. von Hauner Children’s Hospital in Munich, Germany, our study aimed to identify dynamics and routes of transmission, and analyse the affected population in view of previously described host risk factors for VREfm colonisation or infection.
Methods The hospital database was used to collect epidemiological and clinical data of VREfm cases. Descriptive statistical analyses were conducted to outline patient characteristics and depict possible differences between VREfm-colonised and -infected children. An outbreak investigation determining genetic relatedness among VREfm isolates was performed by core genome multilocus sequence typing (cgMLST). To examine potential transmission pathways, results of genome analysis were compared with epidemiological and clinical data of VREfm positive patients. Results VREfm acquisition was documented in a total of 33 children (< 18 years). Seven VREfm-colonised patients (21.2%), especially those with a haemato-oncological disease (4/7; p = 0.011), showed signs of clinical infection. cgMLST analysis revealed seven distinct clusters, demonstrating a possible connection within each clonal lineage. Additional eight singletons were identified. Comparison with epidemiological and clinical data provided strong evidence for a link between several VREfm positive patients within the hospital. Conclusions A nosocomial spread—at least in part—was the most likely reason for the unusual accumulation of VREfm cases. The study highlights that there is a constant need to increase efforts in hygiene measures, infection control and antibiotic stewardship to combat VREfm transmission events within German paediatric hospitals. Continuous monitoring of adherence to respective policies might reduce the occurrence of clustered cases and prevent future outbreaks.
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10
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Jozefíková A, Valček A, Šoltys K, Nováková E, Bujdáková H. Persistence and multi-ward dissemination of vancomycin resistant Enterococcus faecium ST17 clone in hospital settings in Slovakia from 2017 to 2020. Int J Antimicrob Agents 2022; 59:106561. [PMID: 35271995 DOI: 10.1016/j.ijantimicag.2022.106561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2021] [Revised: 02/19/2022] [Accepted: 02/27/2022] [Indexed: 11/16/2022]
Abstract
Hospital vancomycin-resistant Enterococcus faecium (VREfm) were evaluated in term of resistance and phylogenetic relatedness to estimate the location and possible route of transmission of resistance determinants. Hospital VREfm (n=49) were collected in the northern part of Slovakia during the years 2017 to 2020. The collection was analyzed for the presence of the van operon and 10 representatives were subjected to whole-genome sequencing using Illumina MiSeq platform. Obtained sequences were de novo assembled and the draft genome assemblies were analyzed with respect to sequence type (ST), plasmid content, resistance and virulence genes, and the phylogenetic relatedness in single nucleotide polymorphisms (SNP). All strains possessed the vanA operon. Ten selected evaluated isolates belonged to the clinically relevant clonal complex (CC) 17 and carried the vanHAX gene cluster conferring vancomycin resistance on mobile genetic elements, except for the isolate M17773 carrying the vanHAX gene cluster chromosomally. All isolates encoded resistance to quinolones (gyrA and parC mutations) and aminoglycosides [aac(6')-aph(2'')]. Four isolates from different wards and patients belonging to ST17 were closely related (6 - 50 SNP), suggesting a long-term persistence of VREfm ST17 in the hospital settings. VREfm proved to harbor many genetic determinants of antimicrobial resistance. The plasmids carrying the vanA genes belonged to the conjugative broad-host families Inc18 and RepA_N posing a threat to human health, especially in hospital settings. Moreover, 4 clinical isolates were phylogenetically related pointing towards a stable circulation of ST17 VREfm clone in the hospital setting underlining the necessity of continuous surveillance of glycopeptide-resistant pathogens.
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Affiliation(s)
- Anna Jozefíková
- Department of Microbiology and Virology, Faculty of Natural Sciences, Comenius University in Bratislava, Slovakia
| | - Adam Valček
- Department of Microbiology and Virology, Faculty of Natural Sciences, Comenius University in Bratislava, Slovakia; Microbial Resistance and Drug Discovery, VIB-VUB Center for Structural Biology, VIB, Flanders Institute for Biotechnology, Brussels, Belgium; Structural Biology Brussels, Vrije Universiteit Brussel (VUB), Brussels, Belgium
| | - Katarína Šoltys
- Department of Microbiology and Virology, Faculty of Natural Sciences, Comenius University in Bratislava, Slovakia
| | - Elena Nováková
- Institute of Microbiology and Immunology, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Slovakia
| | - Helena Bujdáková
- Department of Microbiology and Virology, Faculty of Natural Sciences, Comenius University in Bratislava, Slovakia.
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11
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Correa-Martínez CL, Jurke A, Schmitz J, Schaumburg F, Kampmeier S, Mellmann A. Molecular Epidemiology of Vancomycin-Resistant Enterococci Bloodstream Infections in Germany: A Population-Based Prospective Longitudinal Study. Microorganisms 2022; 10:130. [PMID: 35056579 PMCID: PMC8777844 DOI: 10.3390/microorganisms10010130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 01/03/2022] [Accepted: 01/05/2022] [Indexed: 11/17/2022] Open
Abstract
Vancomycin-resistant enterococci (VRE) pose a public health challenge worldwide. While VRE bloodstream infections (VREBI) increase in Germany and Europe, population-based molecular data are scarce. We aimed to analyze the molecular epidemiology, demographic aspects, and geographical distribution of VREBI in the German Federal State of North-Rhine-Westphalia (NRW), located in the German-Dutch-Belgian border area, representing over 20% of Germany's population. VREBI isolates were collected from hospitals across NRW between 2016 and 2019. Demographic data were gathered and anonymized upon sample collection. Multilocus sequence typing (MLST) and identification of glycopeptide resistance were carried out. Epidemiological analysis and geographical mapping were performed. Single VREBI isolates from 755 patients were analyzed. In total, 38.9% were female, and 80.0% were aged ≥ 60 years. The VREBI incidence per 100,000 inhabitants nearly tripled, from 0.52 (2016) to 1.48 (2019), particularly in male patients aged ≥ 50 years. The proportion of vanB reached 83% (n = 202/243) in 2018, overtaking vanA as the predominant glycopeptide resistance determinant, detected in close relation with ST117 isolates. The proportion of MLST sequence type (ST) 117 peaked in 2018, at 78.2% (n = 190/243). The major role of these emerging strains in invasive infections in central Europe requires novel strategies for their diagnosis, treatment, and prevention.
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Affiliation(s)
| | - Annette Jurke
- Section Infectious Disease Epidemiology, North Rhine-Westphalian Centre for Health, 44801 Bochum, Germany;
| | - Janne Schmitz
- Institute of Hygiene, University Hospital Münster, 48149 Münster, Germany; (J.S.); (S.K.); (A.M.)
| | - Frieder Schaumburg
- Institute of Medical Microbiology, University Hospital Münster, 48149 Münster, Germany;
| | - Stefanie Kampmeier
- Institute of Hygiene, University Hospital Münster, 48149 Münster, Germany; (J.S.); (S.K.); (A.M.)
| | - Alexander Mellmann
- Institute of Hygiene, University Hospital Münster, 48149 Münster, Germany; (J.S.); (S.K.); (A.M.)
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12
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Rodríguez-Lucas C, Fernández J, Raya C, Bahamonde A, Quiroga A, Muñoz R, Rodicio MR. Establishment and Persistence of Glycopeptide-Resistant Enterococcus faecium ST80 and ST117 Clones Within a Health Care Facility Located in a Low-Prevalence Geographical Region. Microb Drug Resist 2021; 28:217-221. [PMID: 34705570 DOI: 10.1089/mdr.2021.0171] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Vancomycin-resistant Enterococcus faecium (VREfm) is one of the most important nosocomial pathogens with limited therapeutic alternatives. In this study, we followed the trends of VREfm and E. faecium causing bloodstream infections (BSIs) in a Spanish hospital, from 2011 to 2020. During this period, 832 E. faecium strains were isolated and 121 (14.5%) were vancomycin resistant. Nineteen of 101 BSIs (18.8%) caused by E. faecium were due to VREfm. The number of BSI-producing E. faecium isolates increased significantly over the past 5 years, with the percentage of invasive VREfm isolates being substantially higher than the average values in Europe and especially in Spain (<3%). VREfm isolates recovered in 2018 (28) and BSI-producing isolates from 2019 (3) and 2020 (2) were molecularly characterized. All were positive for vanA and belonged to sequence type (ST) 80 (28) or ST117 (5), within clonal complex 17. The isolates were only susceptible to linezolid, although most of them were also susceptible (dose dependent) to daptomycin. We report for the first time the establishment and persistence of the VREfm ST80 and ST117 clones in a Spanish hospital. The spread and establishment of hospital-adapted, multidrug-resistant VREfm clones in health care settings are cause for concern and may precede an increment in the BSIs caused by them.
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Affiliation(s)
- Carlos Rodríguez-Lucas
- Servicio de Microbiología, Hospital Universitario de Cabueñes, Gijón, Spain.,Grupo de Microbiología Traslacional, Instituto de Investigación Sanitaria del Principado de Asturias, Oviedo, Spain
| | - Javier Fernández
- Grupo de Microbiología Traslacional, Instituto de Investigación Sanitaria del Principado de Asturias, Oviedo, Spain.,Servicio de Microbiología, Hospital Universitario Central de Asturias, Oviedo, Spain.,Research and Innovation, Artificial Intelligence and Statistics Department, Pragmatech AI Solutions, Oviedo, Spain
| | - Carmen Raya
- Unidad de Microbiología, Hospital El Bierzo, Ponferrada, Spain
| | | | - Antonio Quiroga
- Servicio de Medicina Preventiva, Hospital El Bierzo, Ponferrada, Spain
| | - Rosario Muñoz
- Unidad de Enfermería Servicio de Medicina Interna, Hospital El Bierzo, Ponferrada, Spain
| | - María Rosario Rodicio
- Grupo de Microbiología Traslacional, Instituto de Investigación Sanitaria del Principado de Asturias, Oviedo, Spain.,Departamento de Biología Funcional, Área de Microbiología, Universidad de Oviedo, Oviedo, Spain
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13
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Timmermans M, Bogaerts B, Vanneste K, De Keersmaecker SCJ, Roosens NHC, Kowalewicz C, Simon G, Argudín MA, Deplano A, Hallin M, Wattiau P, Fretin D, Denis O, Boland C. Large diversity of linezolid-resistant isolates discovered in food-producing animals through linezolid selective monitoring in Belgium in 2019. J Antimicrob Chemother 2021; 77:49-57. [PMID: 34673924 PMCID: PMC8730767 DOI: 10.1093/jac/dkab376] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 09/20/2021] [Indexed: 11/14/2022] Open
Abstract
Background Linezolid is a critically important antibiotic used to treat human infections caused by MRSA and VRE. While linezolid is not licensed for food-producing animals, linezolid-resistant (LR) isolates have been reported in European countries, including Belgium. Objectives To: (i) assess LR occurrence in staphylococci and enterococci isolated from different Belgian food-producing animals in 2019 through selective monitoring; and (ii) investigate the genomes and relatedness of these isolates. Methods Faecal samples (n = 1325) and nasal swab samples (n = 148) were analysed with a protocol designed to select LR bacteria, including a 44–48 h incubation period. The presence of LR chromosomal mutations, transferable LR genes and their genetic organizations and other resistance genes, as well as LR isolate relatedness (from this study and the NCBI database) were assessed through WGS. Results The LR rate differed widely between animal host species, with the highest rates occurring in nasal samples from pigs and sows (25.7% and 20.5%, respectively) and faecal samples from veal calves (16.4%). WGS results showed that LR determinants are present in a large diversity of isolates circulating in the agricultural sector, with some isolates closely related to human isolates, posing a human health risk. Conclusions LR dedicated monitoring with WGS analysis could help to better understand the spread of LR. Cross-selection of LR transferable genes through other antibiotic use should be considered in future action plans aimed at combatting antimicrobial resistance and in future objectives for the rational use of antibiotics in a One Health perspective.
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Affiliation(s)
- Michaël Timmermans
- Veterinary Bacteriology, Sciensano, Ixelles, Belgium.,Faculté de Médecine, Université Libre de Bruxelles, Brussels, Belgium
| | - Bert Bogaerts
- Transversal Activities in Applied Genomics, Sciensano, Ixelles, Belgium
| | - Kevin Vanneste
- Transversal Activities in Applied Genomics, Sciensano, Ixelles, Belgium
| | | | - Nancy H C Roosens
- Transversal Activities in Applied Genomics, Sciensano, Ixelles, Belgium
| | | | | | - Maria A Argudín
- National Reference Centre-Staphylococcus aureus, Department of Microbiology, Hôpital Erasme, Université Libre de Bruxelles, Brussels, Belgium
| | - Ariane Deplano
- National Reference Centre-Staphylococcus aureus, Department of Microbiology, Hôpital Erasme, Université Libre de Bruxelles, Brussels, Belgium.,Department of Microbiology, LHUB-ULB, Université Libre de Bruxelles, Brussels, Belgium
| | - Marie Hallin
- National Reference Centre-Staphylococcus aureus, Department of Microbiology, Hôpital Erasme, Université Libre de Bruxelles, Brussels, Belgium.,Department of Microbiology, LHUB-ULB, Université Libre de Bruxelles, Brussels, Belgium.,Ecole de Santé Publique, Université Libre de Bruxelles, Brussels, Belgium
| | | | - David Fretin
- Veterinary Bacteriology, Sciensano, Ixelles, Belgium
| | - Olivier Denis
- Ecole de Santé Publique, Université Libre de Bruxelles, Brussels, Belgium.,Laboratory of Clinical Microbiology, National Reference Center for Monitoring Antimicrobial Resistance in Gram-Negative Bacteria, CHU UCL Namur, Yvoir, Belgium
| | - Cécile Boland
- Veterinary Bacteriology, Sciensano, Ixelles, Belgium
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14
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Lisotto P, Couto N, Rosema S, Lokate M, Zhou X, Bathoorn E, Harmsen HJM, Friedrich AW, Rossen JWA, Chlebowicz-Fliss MA. Molecular Characterisation of Vancomycin-Resistant Enterococcus faecium Isolates Belonging to the Lineage ST117/CT24 Causing Hospital Outbreaks. Front Microbiol 2021; 12:728356. [PMID: 34646248 PMCID: PMC8503688 DOI: 10.3389/fmicb.2021.728356] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 08/27/2021] [Indexed: 12/02/2022] Open
Abstract
Background: Vancomycin-resistant Enterococcus faecium (VREfm) is a successful nosocomial pathogen. The current molecular method recommended in the Netherlands for VREfm typing is based on core genome Multilocus sequence typing (cgMLST), however, the rapid emergence of specific VREfm lineages challenges distinguishing outbreak isolates solely based on their core genome. Here, we explored if a detailed molecular characterisation of mobile genetic elements (MGEs) and accessory genes could support and expand the current molecular typing of VREfm isolates sharing the same genetic background, enhancing the discriminatory power of the analysis. Materials/Methods: The genomes of 39 VREfm and three vancomycin-susceptible E. faecium (VSEfm) isolates belonging to ST117/CT24, as assessed by cgMLST, were retrospectively analysed. The isolates were collected from patients and environmental samples from 2011 to 2017, and their genomes were analysed using short-read sequencing. Pangenome analysis was performed on de novo assemblies, which were also screened for known predicted virulence factors, antimicrobial resistance genes, bacteriocins, and prophages. Two representative isolates were also sequenced using long-read sequencing, which allowed a detailed analysis of their plasmid content. Results: The cgMLST analysis showed that the isolates were closely related, with a minimal allelic difference of 10 between each cluster’s closest related isolates. The vanB-carrying transposon Tn1549 was present in all VREfm isolates. However, in our data, we observed independent acquisitions of this transposon. The pangenome analysis revealed differences in the accessory genes related to prophages and bacteriocins content, whilst a similar profile was observed for known predicted virulence and resistance genes. Conclusion: In the case of closely related isolates sharing a similar genetic background, a detailed analysis of MGEs and the integration point of the vanB-carrying transposon allow to increase the discriminatory power compared to the use of cgMLST alone. Thus, enabling the identification of epidemiological links amongst hospitalised patients.
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Affiliation(s)
- Paola Lisotto
- Department of Medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Natacha Couto
- Department of Medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, Groningen, Netherlands.,The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom
| | - Sigrid Rosema
- Department of Medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Mariëtte Lokate
- Department of Medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Xuewei Zhou
- Department of Medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Erik Bathoorn
- Department of Medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Hermie J M Harmsen
- Department of Medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Alexander W Friedrich
- Department of Medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - John W A Rossen
- Department of Medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, Groningen, Netherlands.,Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT, United States.,IDbyDNA Inc., Salt Lake City, UT, United States
| | - Monika A Chlebowicz-Fliss
- Department of Medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
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15
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Determination of a Tentative Epidemiological Cut-Off Value (ECOFF) for Dalbavancin and Enterococcus faecium. Antibiotics (Basel) 2021; 10:antibiotics10080915. [PMID: 34438965 PMCID: PMC8388697 DOI: 10.3390/antibiotics10080915] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 07/21/2021] [Accepted: 07/22/2021] [Indexed: 02/07/2023] Open
Abstract
Dalbavancin is a lipoglycopeptide antibiotic that shows potent activity against Gram-positive bacteria. It circumvents vanB-type glycopeptide resistance mechanisms; however, data on the in vitro activity of dalbavancin for Enterococcus faecium (E. faecium) are scarce, and thus, no breakpoints are provided. In recent years, there has been a continuing shift from vanA-type to vanB-type vancomycin-resistance in enterococci in Central Europe. Therefore, we aimed to investigate the in vitro activity of dalbavancin against different van-genotypes, with particular focus on vanB-type E. faecium. Dalbavancin susceptibility was determined for 25 van-negative, 50 vanA-positive, and 101 vanB-positive clinical E. faecium isolates (typed by cgMLST). Epidemiological Cut-Off Values (ECOFFs) were determined using ECOFFinder. For vanB-type E. faecium isolates, dalbavancin MICs were similar to those of vancomycin-susceptible isolates reaching values no higher than 0.125 mg/L. ECOFFs for van-negative and vanB-positive isolates were 0.5 mg/l and 0.25 mg/L respectively. In contrast, E. faecium possessing vanA predominantly showed dalbavancin MICs >8 mg/L, therefore preventing the determination of an ECOFF. We demonstrated the potent in vitro activity of dalbavancin against vancomycin-susceptible and vanB-type E. faecium. On the basis of the observed wildtype distribution, a dalbavancin MIC of 0.25 mg/L can be suggested as a tentative ECOFF for E. faecium.
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16
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Xanthopoulou K, Peter S, Tobys D, Behnke M, Dinkelacker AG, Eisenbeis S, Falgenhauer J, Falgenhauer L, Fritzenwanker M, Gölz H, Häcker G, Higgins PG, Imirzalioglu C, Käding N, Kern WV, Kramme E, Kola A, Mischnik A, Rieg S, Rohde AM, Rupp J, Tacconelli E, Vehreschild MJGT, Walker SV, Gastmeier P, Seifert H. Vancomycin-resistant Enterococcus faecium colonizing patients on hospital admission in Germany: prevalence and molecular epidemiology. J Antimicrob Chemother 2021; 75:2743-2751. [PMID: 32699884 DOI: 10.1093/jac/dkaa271] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2020] [Revised: 05/12/2020] [Accepted: 05/20/2020] [Indexed: 12/20/2022] Open
Abstract
OBJECTIVES To analyse the rectal carriage rate and the molecular epidemiology of vancomycin-resistant Enterococcus faecium (VREfm) recovered from patients upon hospital admission. METHODS Adult patients were screened at six German university hospitals from five different federal states upon hospital admission for rectal colonization with VREfm between 2014 and 2018. Molecular characterization of VREfm was performed by WGS followed by MLST and core-genome MLST analysis. RESULTS Of 16350 patients recruited, 263 were colonized with VREfm, with increasing prevalence rates during the 5 year study period (from 0.8% to 2.6%). In total, 78.5% of the VREfm were vanB positive and 20.2% vanA positive, while 1.2% harboured both vanA and vanB. The predominant ST was ST117 (56.7%) followed by ST80 (15%), ST203 (10.9%), ST78 (5.7%) and ST17 (3.2%). ST117/vanB VREfm isolates formed a large cluster of 96 closely related isolates extending across all six study centres and four smaller clusters comprising 13, 5, 4 and 3 isolates each. In contrast, among the other STs inter-regional clonal relatedness was rarely observed. CONCLUSIONS To our knowledge, this is the largest admission prevalence and molecular epidemiology study of VREfm. These data provide insight into the epidemiology of VREfm at six German university hospitals and demonstrate the remarkable inter-regional clonal expansion of the ST117/vanB VREfm clone.
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Affiliation(s)
- Kyriaki Xanthopoulou
- German Centre for Infection Research (DZIF), Braunschweig, Germany.,Institute for Medical Microbiology, Immunology and Hygiene, University of Cologne, Cologne, Germany
| | - Silke Peter
- German Centre for Infection Research (DZIF), Braunschweig, Germany.,Institute of Medical Microbiology and Hygiene, University of Tübingen, Tübingen, Germany
| | - David Tobys
- German Centre for Infection Research (DZIF), Braunschweig, Germany.,Institute for Medical Microbiology, Immunology and Hygiene, University of Cologne, Cologne, Germany
| | - Michael Behnke
- German Centre for Infection Research (DZIF), Braunschweig, Germany.,Institute for Hygiene and Environmental Medicine, National Reference Centre for the Surveillance of Nosocomial Infections, Charité-University Hospital, Berlin, Germany
| | - Ariane G Dinkelacker
- German Centre for Infection Research (DZIF), Braunschweig, Germany.,Institute of Medical Microbiology and Hygiene, University of Tübingen, Tübingen, Germany
| | - Simone Eisenbeis
- German Centre for Infection Research (DZIF), Braunschweig, Germany.,Division of Infectious Disease, Department of Internal Medicine I, Tübingen University Hospital, Tübingen, Germany
| | - Jane Falgenhauer
- German Centre for Infection Research (DZIF), Braunschweig, Germany.,Institute of Medical Microbiology, Justus Liebig University Giessen, Giessen, Germany
| | - Linda Falgenhauer
- German Centre for Infection Research (DZIF), Braunschweig, Germany.,Institute of Hygiene and Environmental Medicine, Justus Liebig University Giessen, Giessen, Germany
| | - Moritz Fritzenwanker
- German Centre for Infection Research (DZIF), Braunschweig, Germany.,Institute of Medical Microbiology, Justus Liebig University Giessen, Giessen, Germany
| | - Hannah Gölz
- German Centre for Infection Research (DZIF), Braunschweig, Germany.,Institute for Medical Microbiology and Hygiene, University Medical Centre Freiburg, Freiburg, Germany
| | - Georg Häcker
- German Centre for Infection Research (DZIF), Braunschweig, Germany.,Institute for Medical Microbiology and Hygiene, University Medical Centre Freiburg, Freiburg, Germany
| | - Paul G Higgins
- German Centre for Infection Research (DZIF), Braunschweig, Germany.,Institute for Medical Microbiology, Immunology and Hygiene, University of Cologne, Cologne, Germany
| | - Can Imirzalioglu
- German Centre for Infection Research (DZIF), Braunschweig, Germany.,Institute of Medical Microbiology, Justus Liebig University Giessen, Giessen, Germany
| | - Nadja Käding
- German Centre for Infection Research (DZIF), Braunschweig, Germany.,Department of Infectious Diseases and Microbiology, University of Lübeck, Lübeck, Germany
| | - Winfried V Kern
- Division of Infectious Diseases, Department of Medicine II, University of Freiburg Medical Centre and Faculty of Medicine, Freiburg, Germany
| | - Evelyn Kramme
- German Centre for Infection Research (DZIF), Braunschweig, Germany.,Department of Infectious Diseases and Microbiology, University of Lübeck, Lübeck, Germany
| | - Axel Kola
- German Centre for Infection Research (DZIF), Braunschweig, Germany.,Institute for Hygiene and Environmental Medicine, National Reference Centre for the Surveillance of Nosocomial Infections, Charité-University Hospital, Berlin, Germany
| | - Alexander Mischnik
- German Centre for Infection Research (DZIF), Braunschweig, Germany.,Department of Infectious Diseases and Microbiology, University of Lübeck, Lübeck, Germany
| | - Siegbert Rieg
- German Centre for Infection Research (DZIF), Braunschweig, Germany.,Division of Infectious Diseases, Department of Medicine II, University of Freiburg Medical Centre and Faculty of Medicine, Freiburg, Germany
| | - Anna M Rohde
- German Centre for Infection Research (DZIF), Braunschweig, Germany.,Institute for Hygiene and Environmental Medicine, National Reference Centre for the Surveillance of Nosocomial Infections, Charité-University Hospital, Berlin, Germany
| | - Jan Rupp
- German Centre for Infection Research (DZIF), Braunschweig, Germany.,Department of Infectious Diseases and Microbiology, University of Lübeck, Lübeck, Germany
| | - Evelina Tacconelli
- German Centre for Infection Research (DZIF), Braunschweig, Germany.,Division of Infectious Disease, Department of Internal Medicine I, Tübingen University Hospital, Tübingen, Germany
| | - Maria J G T Vehreschild
- German Centre for Infection Research (DZIF), Braunschweig, Germany.,University of Cologne, Department I of Internal Medicine, Cologne, Germany.,Department of Internal Medicine, Infectious Diseases, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Sarah V Walker
- German Centre for Infection Research (DZIF), Braunschweig, Germany.,Institute for Medical Microbiology, Immunology and Hygiene, University of Cologne, Cologne, Germany
| | - Petra Gastmeier
- German Centre for Infection Research (DZIF), Braunschweig, Germany.,Institute for Hygiene and Environmental Medicine, National Reference Centre for the Surveillance of Nosocomial Infections, Charité-University Hospital, Berlin, Germany
| | - Harald Seifert
- German Centre for Infection Research (DZIF), Braunschweig, Germany.,Institute for Medical Microbiology, Immunology and Hygiene, University of Cologne, Cologne, Germany
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17
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Pinholt M, Mollerup S, Boye K, Worning P, Holzknecht BJ, Nygaard S, Nielsen KL, Hasman H, Roer L, Hammerum AM, Westh H, Schønning K. Investigation of the introduction and dissemination of vanB Enterococcus faecium in the Capital Region of Denmark and development of a rapid and accurate clone-specific vanB E. faecium PCR. J Antimicrob Chemother 2021; 76:2260-2267. [PMID: 34151364 DOI: 10.1093/jac/dkab198] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 05/17/2021] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND During 2018-19, an increase of vanB vancomycin-resistant Enterococcus faecium (VREfm) was observed in the Capital Region of Denmark. vanA/vanB PCR performed directly on rectal swabs is accurate in detection of vanA; however, the positive predictive value for vanB-positive samples is low because of the presence of vanB in non-enterococcal gut commensals. OBJECTIVES We investigated the epidemiology and clonal relatedness of vanB VREfm from the period 2015-19 and describe the application of a clone-specific vanB VREfm PCR assay for rapid and accurate detection of vanB VREfm in rectal screening samples. METHODS vanB VREfm were investigated using epidemiological data and WGS data. The SeqSphere+ software was used to analyse MLST and cgMLST, and de novo assemblies were annotated to determine insertion sites for the vanB transposon (Tn1549). A clone-specific vanB VREfm PCR assay was designed to detect the sequence bridging Tn1549 and the E. faecium chromosome (araA2) in the dominant cluster. RESULTS Two hundred and seventy-five vanB VREfm isolates were identified, of which 76% were identified in 2019. A dominant cluster (Cluster 1, n = 204, 74%), six minor clusters and 15 singletons were identified. All Cluster 1 isolates and six non-Cluster 1 isolates had Tn1549 integrated into araA2. In 2019, the PCR assay would have detected 92% of all rectal screening samples containing vanB VREfm. CONCLUSIONS vanB VREfm increased due to the introduction and nosocomial transmission of the successful Cluster 1. The clone-specific PCR assay detected vanB VREfm outbreak isolates in rectal screening samples rapidly and accurately.
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Affiliation(s)
- Mette Pinholt
- Department of Clinical Microbiology, Copenhagen University Hospital-Amager and Hvidovre, Copenhagen, Denmark
| | - Sarah Mollerup
- Department of Clinical Microbiology, Copenhagen University Hospital-Amager and Hvidovre, Copenhagen, Denmark
| | - Kit Boye
- Department of Clinical Microbiology, Copenhagen University Hospital-Amager and Hvidovre, Copenhagen, Denmark
| | - Peder Worning
- Department of Clinical Microbiology, Copenhagen University Hospital-Amager and Hvidovre, Copenhagen, Denmark
| | - Barbara Juliane Holzknecht
- Department of Clinical Microbiology, Copenhagen University Hospital-Herlev and Gentofte, Copenhagen, Denmark.,Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Sanne Nygaard
- Department of Clinical Microbiology, Copenhagen University Hospital-Herlev and Gentofte, Copenhagen, Denmark
| | - Karen Leth Nielsen
- Department of Clinical Microbiology, Copenhagen University Hospital-Rigshospitalet, Copenhagen, Denmark
| | - Henrik Hasman
- Department for Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Louise Roer
- Department for Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Anette M Hammerum
- Department for Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Henrik Westh
- Department of Clinical Microbiology, Copenhagen University Hospital-Amager and Hvidovre, Copenhagen, Denmark.,Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Kristian Schønning
- Department of Clinical Microbiology, Copenhagen University Hospital-Amager and Hvidovre, Copenhagen, Denmark.,Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark.,Department of Clinical Microbiology, Copenhagen University Hospital-Rigshospitalet, Copenhagen, Denmark
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18
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Rogers LA, Strong K, Cork SC, McAllister TA, Liljebjelke K, Zaheer R, Checkley SL. The Role of Whole Genome Sequencing in the Surveillance of Antimicrobial Resistant Enterococcus spp.: A Scoping Review. Front Public Health 2021; 9:599285. [PMID: 34178909 PMCID: PMC8222819 DOI: 10.3389/fpubh.2021.599285] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Accepted: 05/04/2021] [Indexed: 12/19/2022] Open
Abstract
Enterococcus spp. have arisen as important nosocomial pathogens and are ubiquitous in the gastrointestinal tracts of animals and the environment. They carry many intrinsic and acquired antimicrobial resistance genes. Because of this, surveillance of Enterococcus spp. has become important with whole genome sequencing emerging as the preferred method for the characterization of enterococci. A scoping review was designed to determine how the use of whole genome sequencing in the surveillance of Enterococcus spp. adds to our knowledge of antimicrobial resistance in Enterococcus spp. Scoping review design was guided by the PRISMA extension and checklist and JBI Reviewer's Guide for scoping reviews. A total of 72 articles were included in the review. Of the 72 articles included, 48.6% did not state an association with a surveillance program and 87.5% of articles identified Enterococcus faecium. The majority of articles included isolates from human clinical or screening samples. Significant findings from the articles included novel sequence types, the increasing prevalence of vancomycin-resistant enterococci in hospitals, and the importance of surveillance or screening for enterococci. The ability of enterococci to adapt and persist within a wide range of environments was also a key finding. These studies emphasize the importance of ongoing surveillance of enterococci from a One Health perspective. More studies are needed to compare the whole genome sequences of human enterococcal isolates to those from food animals, food products, the environment, and companion animals.
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Affiliation(s)
- Lindsay A Rogers
- Department of Ecosystem and Public Health, Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
| | - Kayla Strong
- Department of Ecosystem and Public Health, Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
| | - Susan C Cork
- Department of Ecosystem and Public Health, Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
| | - Tim A McAllister
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB, Canada
| | - Karen Liljebjelke
- Department of Ecosystem and Public Health, Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
| | - Rahat Zaheer
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB, Canada
| | - Sylvia L Checkley
- Department of Ecosystem and Public Health, Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
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19
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Falgenhauer L, Preuser I, Imirzalioglu C, Falgenhauer J, Fritzenwanker M, Mack D, Best C, Heudorf U, Chakraborty T. Changing epidemiology of vancomycin-resistant Enterococcus faecium: Results of a genome-based study at a regional neurological acute hospital with intensive care and early rehabilitation treatment. Infect Prev Pract 2021; 3:100138. [PMID: 34368749 PMCID: PMC8335922 DOI: 10.1016/j.infpip.2021.100138] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 03/22/2021] [Indexed: 12/04/2022] Open
Abstract
Background Vancomycin-resistant Enterococcus faecium (VREfm) are an emerging threat worldwide. In Germany, a VRE-belt with higher VREfm prevalences transversing its central east-west axis and including the state of Hesse was previously described. Recently, we detected a predominant VREfm clone in hospitals throughout the Rhine-Main metropolitan area of Hesse. Aim Here we expanded our study on VREfm to a regional neurological acute hospital outside of the metropolitan area with patient referrals from throughout Hesse and the neighboring federal state of Rhineland-Palatinate. Material/Methods VREfm isolates obtained between 2016-2018 from a regional neurological acute hospital with intensive care and early rehabilitation units were investigated (n=55). Patient data was collected and analyzed together with whole-genome sequencing data to investigate antibiotic resistance and virulence determinants of the VREfm. The population structure of VREfm was investigated using the Core genome-based multilocus sequence typing (cgMLST). Findings The average age of the patients was 67.1 years. For 96% of the patients, a previous hospital stay was reported. 64% of the patients were treated with antibiotics. All VREfm harbored the vanB vancomycin resistance gene. The multilocus sequence types (STs) detected changed abruptly from four different STs in 2016 to a predominant ST in 2017 and 2018 (ST117). Most of the ST117 isolates were members of the cgMLST type CT71. Conclusion The results indicate a sudden shift of the VREfm population structure from a semi-heterogeneous population to a pre-dominant clone within an interval of two years. Further investigations are warranted to understand the epidemiology and emergence of this clone.
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Affiliation(s)
- Linda Falgenhauer
- Institute of Hygiene and Environmental Medicine, Justus Liebig University Giessen, Schubertstrasse 81, Giessen, 35392, Germany.,German Center for Infection Research (DZIF), Site Giessen-Marburg-Langen, Justus Liebig University Giessen, Schubertstrasse 81, Giessen, 35392, Germany
| | - Ingeborg Preuser
- Department of Neurology, Vitos-Weil-Lahn, Weilstrasse 10, Weilmünster, 35789, Germany
| | - Can Imirzalioglu
- German Center for Infection Research (DZIF), Site Giessen-Marburg-Langen, Justus Liebig University Giessen, Schubertstrasse 81, Giessen, 35392, Germany.,Institute of Medical Microbiology, Justus Liebig University Giessen, Schubertstrasse 81, Giessen, 35392, Germany
| | - Jane Falgenhauer
- German Center for Infection Research (DZIF), Site Giessen-Marburg-Langen, Justus Liebig University Giessen, Schubertstrasse 81, Giessen, 35392, Germany.,Institute of Medical Microbiology, Justus Liebig University Giessen, Schubertstrasse 81, Giessen, 35392, Germany
| | - Moritz Fritzenwanker
- German Center for Infection Research (DZIF), Site Giessen-Marburg-Langen, Justus Liebig University Giessen, Schubertstrasse 81, Giessen, 35392, Germany.,Institute of Medical Microbiology, Justus Liebig University Giessen, Schubertstrasse 81, Giessen, 35392, Germany
| | - Dietrich Mack
- Institut für Medizinische Diagnostik GmbH, Bioscientia Labor Ingelheim, Konrad-Adenauer-Straße 17, Ingelheim am Rhein, 55218, Germany
| | - Christoph Best
- Department of Neurology, Vitos-Weil-Lahn, Weilstrasse 10, Weilmünster, 35789, Germany
| | - Ursel Heudorf
- Network on MDRO Rhine-Main, Breite Gasse 28, Frankfurt/Main, 60313, Germany
| | - Trinad Chakraborty
- German Center for Infection Research (DZIF), Site Giessen-Marburg-Langen, Justus Liebig University Giessen, Schubertstrasse 81, Giessen, 35392, Germany.,Institute of Medical Microbiology, Justus Liebig University Giessen, Schubertstrasse 81, Giessen, 35392, Germany
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20
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Nürnberger L, Schmidt D, Szumlanski T, Kirchhoff L, Ross B, Steinmann J, Rath PM. Molecular characterization of vancomycin-resistant Enterococcus faecium isolates from two German hospitals. GMS HYGIENE AND INFECTION CONTROL 2021; 16:Doc13. [PMID: 33796441 PMCID: PMC7983015 DOI: 10.3205/dgkh000384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Introduction: Vancomycin-resistant Enterococcusfaecium accounts for around 10–23% of nosocomial enterococcal infections and constitutes a relevant therapeutic problem due to its limited susceptibility to antibiotics. The resistance towards glycopeptide antibiotics is mediated by the so-called van genes. Currently, the most common resistance type in Germany is the vanB-type. Little data are available on the molecular epidemiology in Germany. Therefore, an epidemiological typing of Enterococcusfaecium isolates with vanB-type resistance from two German hospitals in Essen and Nuremberg was performed. Two outbreaks and 104 sporadic cases were investigated. Methods: All 128 isolates with vanB-type resistance were collected between 2011–2012 and 2017–2018. They were characterized using multilocus sequence typing (MLST) and pulsed-field gel electrophoresis (PFGE). Results: ST 117 was the most common sequence type (ST) in both hospitals, especially since 2017. PFGE divided the isolates of this study into 68 PFGE types and showed a broad genetic diversity. Two epidemiologically assumed in-hospital outbreaks were genetically confirmed. Apart from that, in-hospital transmissions were rare events. Conclusion: The results obtained by MLST confirmed the previously described allocation of STs in Germany. PFGE showed a broad genetic diversity of vanB VRE between the two hospitals and also within each hospital. In-hospital transmissions were rare, but outbreaks did occur. Our data supports the strategy to screen and isolate patients in transmission events in order to detect monoclonality indicating a common source or hygiene mismanagement.
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Affiliation(s)
- Laura Nürnberger
- Institute of Medical Microbiology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Dirk Schmidt
- Institute of Medical Microbiology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Tobias Szumlanski
- Institute for Clinical Hygiene, Medical Microbiology and Clinical Infectiology, Paracelsus Medical University, Nuremberg Hospital, Nuremberg, Germany
| | - Lisa Kirchhoff
- Institute of Medical Microbiology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Birgit Ross
- Department of Hospital Hygiene, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Jörg Steinmann
- Institute of Medical Microbiology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany.,Institute for Clinical Hygiene, Medical Microbiology and Clinical Infectiology, Paracelsus Medical University, Nuremberg Hospital, Nuremberg, Germany
| | - Peter-Michael Rath
- Institute of Medical Microbiology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
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21
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Turner AM, Lee JYH, Gorrie CL, Howden BP, Carter GP. Genomic Insights Into Last-Line Antimicrobial Resistance in Multidrug-Resistant Staphylococcus and Vancomycin-Resistant Enterococcus. Front Microbiol 2021; 12:637656. [PMID: 33796088 PMCID: PMC8007764 DOI: 10.3389/fmicb.2021.637656] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Accepted: 02/25/2021] [Indexed: 12/17/2022] Open
Abstract
Multidrug-resistant Staphylococcus and vancomycin-resistant Enterococcus (VRE) are important human pathogens that are resistant to most clinical antibiotics. Treatment options are limited and often require the use of 'last-line' antimicrobials such as linezolid, daptomycin, and in the case of Staphylococcus, also vancomycin. The emergence of resistance to these last-line antimicrobial agents is therefore of considerable clinical concern. This mini-review provides an overview of resistance to last-line antimicrobial agents in Staphylococcus and VRE, with a particular focus on how genomics has provided critical insights into the emergence of resistant clones, the molecular mechanisms of resistance, and the importance of mobile genetic elements in the global spread of resistance to linezolid.
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Affiliation(s)
- Adrianna M Turner
- Department of Microbiology and Immunology, Doherty Institute, The University of Melbourne, Melbourne, VIC, Australia
| | - Jean Y H Lee
- Department of Microbiology and Immunology, Doherty Institute, The University of Melbourne, Melbourne, VIC, Australia.,Department of Infectious Diseases, Monash Health, Melbourne, VIC, Australia
| | - Claire L Gorrie
- Department of Microbiology and Immunology, Doherty Institute, The University of Melbourne, Melbourne, VIC, Australia.,Antimicrobial Reference and Research Unit, Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, Doherty Institute, The University of Melbourne, Melbourne, VIC, Australia
| | - Benjamin P Howden
- Department of Microbiology and Immunology, Doherty Institute, The University of Melbourne, Melbourne, VIC, Australia.,Antimicrobial Reference and Research Unit, Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, Doherty Institute, The University of Melbourne, Melbourne, VIC, Australia.,Department of Infectious Diseases, Austin Health, Melbourne, VIC, Australia
| | - Glen P Carter
- Department of Microbiology and Immunology, Doherty Institute, The University of Melbourne, Melbourne, VIC, Australia.,Antimicrobial Reference and Research Unit, Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, Doherty Institute, The University of Melbourne, Melbourne, VIC, Australia
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22
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Kessel J, Bender J, Werner G, Griskaitis M, Herrmann E, Lehn A, Serve H, Zacharowski K, Zeuzem S, Vehreschild MJGT, Wichelhaus TA, Kempf VAJ, Hogardt M. Risk factors and outcomes associated with the carriage of tigecycline- and vancomycin-resistant Enterococcus faecium. J Infect 2020; 82:227-234. [PMID: 33285218 DOI: 10.1016/j.jinf.2020.12.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 11/18/2020] [Accepted: 12/03/2020] [Indexed: 02/08/2023]
Abstract
OBJECTIVES Vancomycin-resistant E. faecium (VRE) is a common cause of healthcare-associated infections. The emergence of VRE with tigecycline resistance (TVRE) is increasing but its impact on patient outcome is still not well defined. This study aimed to assess risk factors for the acquisition of TVRE and of patient outcomes associated with TVRE carriage/infection. METHODS At the University Hospital Frankfurt, we conducted a matched pair TVRE-VRE analysis to identify risk factors for TVRE carriage. Bed-to-bed contacts and potential transmission routes were reconstructed. TVRE were whole-genome sequenced to confirm suspected transmission events and to identify tigecycline resistance mechanisms. RESULTS 76 TVRE cases were identified between 02/2014-04/2017 and compared to VRE colonized or infected controls. TVRE carriage was associated with exposure to tigecycline, an increased rate of bloodstream infections (BSI) with VRE or Candida spp., and higher mortality. Whole-genome sequencing-based analysis of 24 TVRE provided evidence for transmissions of TVRE, also across different wards. CONCLUSIONS Tigecycline exposure is the main risk factor for TVRE carriage. VRE/TVRE- and Candida-BSI are associated with worse clinical outcome. Hospital transmission of TVRE may occur despite strict contact precautions, whereas both antimicrobial stewardship and infection control interventions are of high importance to prevent emergence and spread of TVRE.
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Affiliation(s)
- Johanna Kessel
- Department of Internal Medicine, Infectious Diseases, University Hospital Frankfurt, Goethe University, 60590 Frankfurt am Main, Germany; University Center for Infectious Diseases (UCI), University Hospital Frankfurt, Goethe University, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany.
| | - Jennifer Bender
- Unit FG13 Nosocomial Pathogens and Antibiotic Resistances, National Reference Center for Staphylococci and Enterococci, Robert Koch-Institute, Wernigerode Branch, 38855 Wernigerode, Germany
| | - Guido Werner
- Unit FG13 Nosocomial Pathogens and Antibiotic Resistances, National Reference Center for Staphylococci and Enterococci, Robert Koch-Institute, Wernigerode Branch, 38855 Wernigerode, Germany
| | - Matas Griskaitis
- Institute of Biostatistics, Epidemiology and Informatics, University Hospital Mainz, 55131 Mainz, Germany
| | - Eva Herrmann
- Institute of Biostatistics and Mathematical Modelling, Goethe University, 60590 Frankfurt am Main, Germany
| | - Annette Lehn
- Institute of Biostatistics and Mathematical Modelling, Goethe University, 60590 Frankfurt am Main, Germany
| | - Hubert Serve
- University Center for Infectious Diseases (UCI), University Hospital Frankfurt, Goethe University, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany; Department of Internal Medicine, Hematology/Oncology, University Hospital Frankfurt, Goethe University, 60590 Frankfurt am Main, Germany
| | - Kai Zacharowski
- University Center for Infectious Diseases (UCI), University Hospital Frankfurt, Goethe University, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany; Department for Anesthesiology, Intensive Care Medicine and Pain Therapy, University Hospital Frankfurt, Goethe University, 60590 Frankfurt am Main, Germany
| | - Stefan Zeuzem
- University Center for Infectious Diseases (UCI), University Hospital Frankfurt, Goethe University, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany; Department of Internal Medicine, Gastroenterology, University Hospital Frankfurt, Goethe University, 60590 Frankfurt am Main, Germany
| | - Maria J G T Vehreschild
- Department of Internal Medicine, Infectious Diseases, University Hospital Frankfurt, Goethe University, 60590 Frankfurt am Main, Germany; University Center for Infectious Diseases (UCI), University Hospital Frankfurt, Goethe University, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany
| | - Thomas A Wichelhaus
- University Center for Infectious Diseases (UCI), University Hospital Frankfurt, Goethe University, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany; Institute for Medical Microbiology and Infection Control, University Hospital Frankfurt, Goethe University, 60590 Frankfurt am Main, Germany; University Center of Competence for Infection Control, State of Hesse, Germany
| | - Volkhard A J Kempf
- University Center for Infectious Diseases (UCI), University Hospital Frankfurt, Goethe University, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany; Institute for Medical Microbiology and Infection Control, University Hospital Frankfurt, Goethe University, 60590 Frankfurt am Main, Germany; University Center of Competence for Infection Control, State of Hesse, Germany
| | - Michael Hogardt
- University Center for Infectious Diseases (UCI), University Hospital Frankfurt, Goethe University, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany; Institute for Medical Microbiology and Infection Control, University Hospital Frankfurt, Goethe University, 60590 Frankfurt am Main, Germany; University Center of Competence for Infection Control, State of Hesse, Germany.
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23
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Werner G, Neumann B, Weber RE, Kresken M, Wendt C, Bender JK. Thirty years of VRE in Germany - "expect the unexpected": The view from the National Reference Centre for Staphylococci and Enterococci. Drug Resist Updat 2020; 53:100732. [PMID: 33189998 DOI: 10.1016/j.drup.2020.100732] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 10/12/2020] [Accepted: 10/15/2020] [Indexed: 02/06/2023]
Abstract
Enterococci are commensals of the intestinal tract of many animals and humans. Of the various known and still unnamed new enterococcal species, only isolates of Enterococcus faecium and Enterococcus faecalis have received increased medical and public health attention. According to textbook knowledge, the majority of infections are caused by E. faecalis. In recent decades, the number of enterococcal infections has increased, with the increase being exclusively associated with a rising number of nosocomial E. faecium infections. This increase has been accompanied by the dissemination of certain hospital-acquired strain variants and an alarming progress in the development of antibiotic resistance namely vancomycin resistance. With this review we focus on a description of the specific situation of vancomycin resistance among clinical E. faecium isolates in Germany over the past 30 years. The present review describes three VRE episodes in Germany, each of which is framed by the beginning and end of the respective decade. The first episode is specified by the first appearance of VRE in 1990 and a country-wide spread of specific vanA-type VRE strains (ST117/CT24) until the late 1990s. The second decade was initially marked by regional clusters and VRE outbreaks in hospitals in South-Western Germany in 2004 and 2005, mainly caused by vanA-type VRE of ST203. Against the background of a certain "basic level" of VRE prevalence throughout Germany, an early shift from the vanA genotype to the vanB genotype in clinical isolates already occurred at the end of the 2000s without much notice. With the beginning of the third decade in 2010, VRE rates in Germany have permanently increased, first in some federal states and soon after country-wide. Besides an increase in VRE prevalence, this decade was marked by a sharp increase in vanB-type resistance and a dominance of a few, novel strain variants like ST192 and later on ST117 (CT71, CT469) and ST80 (CT1065). The largest VRE outbreak, which involved about 2,900 patients and lasted over three years, was caused by a novel and until that time, unknown strain type of ST80/CT1013 (vanB). Across all periods, VRE outbreaks were mainly oligoclonal and strain types varied over space (hospital wards) and time. The spread of VRE strains obviously respects political borders; for instance, both vancomycin-variable enterococci which were highly prevalent in Denmark and ST796 VRE which successfully disseminated in Australia and Switzerland, were still completely absent among German hospital patients, until to date.
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Affiliation(s)
- Guido Werner
- National Reference Centre for Staphylococci and Enterococci, Division Nosocomial Pathogens and Antibiotic Resistances, Department of Infectious Diseases, Robert Koch Institute, Wernigerode Branch, Germany.
| | - Bernd Neumann
- National Reference Centre for Staphylococci and Enterococci, Division Nosocomial Pathogens and Antibiotic Resistances, Department of Infectious Diseases, Robert Koch Institute, Wernigerode Branch, Germany
| | - Robert E Weber
- National Reference Centre for Staphylococci and Enterococci, Division Nosocomial Pathogens and Antibiotic Resistances, Department of Infectious Diseases, Robert Koch Institute, Wernigerode Branch, Germany
| | | | | | - Jennifer K Bender
- National Reference Centre for Staphylococci and Enterococci, Division Nosocomial Pathogens and Antibiotic Resistances, Department of Infectious Diseases, Robert Koch Institute, Wernigerode Branch, Germany
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