1
|
Mills EG, Smith AB, Griffith MP, Hewlett K, Pless L, Sundermann AJ, Harrison LH, Zackular JP, Van Tyne D. Bacteriocin production facilitates nosocomial emergence of vancomycin-resistant Enterococcus faecium. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.08.01.24311290. [PMID: 39132485 PMCID: PMC11312660 DOI: 10.1101/2024.08.01.24311290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/13/2024]
Abstract
Vancomycin-resistant Enterococcus faecium (VREfm) is a prevalent healthcare-acquired pathogen. Gastrointestinal colonization can lead to difficult-to-treat bloodstream infections with high mortality rates. Prior studies have investigated VREfm population structure within healthcare centers. However, little is known about how and why hospital-adapted VREfm populations change over time. We sequenced 710 healthcare-associated VREfm clinical isolates from 2017-2022 from a large tertiary care center as part of the Enhanced Detection System for Healthcare-Associated Transmission (EDS-HAT) program. Although the VREfm population in our center was polyclonal, 46% of isolates formed genetically related clusters, suggesting a high transmission rate. We compared our collection to 15,631 publicly available VREfm genomes spanning 20 years. Our findings describe a drastic shift in lineage replacement within nosocomial VREfm populations at both the local and global level. Functional and genomic analysis revealed, antimicrobial peptide, bacteriocin T8 may be a driving feature of strain emergence and persistence in the hospital setting.
Collapse
Affiliation(s)
- Emma G. Mills
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Alexander B. Smith
- Division of Protective Immunity, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Marissa P. Griffith
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- Microbial Genomic Epidemiology Laboratory, Center for Genomic Epidemiology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Department of Epidemiology, School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Katharine Hewlett
- Division of Protective Immunity, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Lora Pless
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- Microbial Genomic Epidemiology Laboratory, Center for Genomic Epidemiology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Alexander J. Sundermann
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- Department of Epidemiology, School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Lee H. Harrison
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- Microbial Genomic Epidemiology Laboratory, Center for Genomic Epidemiology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Department of Epidemiology, School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Joseph P. Zackular
- Division of Protective Immunity, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Center for Microbial Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Daria Van Tyne
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- Center for Evolutionary Biology and Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| |
Collapse
|
2
|
Boutin S, Welker S, Gerigk M, Miethke T, Heeg K, Nurjadi D. Molecular surveillance of carbapenem-resistant Enterobacterales in two nearby tertiary hospitals to identify regional spread of high-risk clones in Germany, 2019-2020. J Hosp Infect 2024; 149:126-134. [PMID: 38723905 DOI: 10.1016/j.jhin.2024.04.014] [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: 01/30/2024] [Revised: 04/02/2024] [Accepted: 04/16/2024] [Indexed: 06/09/2024]
Abstract
BACKGROUND Understanding the transmission dynamics of carbapenem-resistant Enterobacterales (CRE) is critical to addressing the escalating global threat of antimicrobial resistance (AMR). Although hospital transmission of CRE has been extensively studied, information on community transmission is lacking. AIM To identify genomic clusters of CRE from two nearby institutions that may be indicative of community or inter-facility transmission. METHODS CRE isolates between January 1st, 2019 and December 31st, 2020 from two tertiary hospitals, detected in the respective routine microbiology laboratories, were collected and characterized by short-read whole-genome sequencing. FINDINGS A total of 272 CRE were collected, with Enterobacter cloacae complex (71/192, 37%) predominant in Heidelberg and Escherichia coli (19/80, 24%) in Mannheim. The most common carbapenem resistance gene, blaOXA-48, was detected in 38% of CRE from both centres. Several putative transmission clusters were found, including six clusters of E. cloacae complex, five clusters of Klebsiella pneumoniae, four clusters of Citrobacter freundii, and two clusters each of Escherichia coli and K. aerogenes. No clusters involved isolates from both study centres, except for an ST22 C. freundii cluster. Globally circulating clones were identified between the two centres for ST131 E. coli, ST66 E. hormaechei, and ST22 C. freundii. CONCLUSION This study found no widespread transmission clusters among isolates from both centres, suggesting a hospital-specific clonal structure. This suggests that CRE clusters involving both institutions may indicate emerging or circulating clones in the community, highlighting the need for intersectoral surveillance and data sharing.
Collapse
Affiliation(s)
- S Boutin
- Medical Microbiology and Hygiene, Department of Infectious Diseases, Heidelberg University Hospital, Heidelberg, Germany; Department of Infectious Diseases and Microbiology, University of Lübeck and University Hospital Schleswig Holstein Campus Lübeck, Lübeck, Germany; German Center for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, Lübeck, Germany
| | - S Welker
- Institute of Medical Microbiology and Hygiene, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - M Gerigk
- Institute of Medical Microbiology and Hygiene, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - T Miethke
- Institute of Medical Microbiology and Hygiene, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany; Mannheim Institute for Innate Immunoscience (MI3), Mannheim, Germany; Center of Experimental Medicine, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - K Heeg
- Medical Microbiology and Hygiene, Department of Infectious Diseases, Heidelberg University Hospital, Heidelberg, Germany
| | - D Nurjadi
- Medical Microbiology and Hygiene, Department of Infectious Diseases, Heidelberg University Hospital, Heidelberg, Germany; Department of Infectious Diseases and Microbiology, University of Lübeck and University Hospital Schleswig Holstein Campus Lübeck, Lübeck, Germany; German Center for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, Lübeck, Germany.
| |
Collapse
|
3
|
Sundermann AJ, Rangachar Srinivasa V, Mills EG, Griffith MP, Evans E, Chen J, Waggle KD, Snyder GM, Pless LL, Harrison LH, Van Tyne D. Genomic sequencing surveillance of patients colonized with vancomycin-resistant Enterococcus (VRE) improves detection of hospital-associated transmission. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.05.01.24306710. [PMID: 38746387 PMCID: PMC11092704 DOI: 10.1101/2024.05.01.24306710] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Background Vancomycin-resistant enterococcal (VRE) infections pose significant challenges in healthcare. Transmission dynamics of VRE are complex, often involving patient colonization and subsequent transmission through various healthcare-associated vectors. We utilized a whole genome sequencing (WGS) surveillance program at our institution to better understand the contribution of clinical and colonizing isolates to VRE transmission. Methods We performed whole genome sequencing on 352 VRE clinical isolates collected over 34 months and 891 rectal screening isolates collected over a 9-month nested period, and used single nucleotide polymorphisms to assess relatedness. We then performed a geo-temporal transmission analysis considering both clinical and rectal screening isolates compared with clinical isolates alone, and calculated 30-day outcomes of patients. Results VRE rectal carriage constituted 87.3% of VRE acquisition, with an average monthly acquisition rate of 7.6 per 1000 patient days. We identified 185 genetically related clusters containing 2-42 isolates and encompassing 69.6% of all isolates in the dataset. The inclusion of rectal swab isolates increased the detection of clinical isolate clusters (from 53% to 67%, P<0.01). Geo-temporal analysis identified hotspot locations of VRE transmission. Patients with clinical VRE isolates that were closely related to previously sampled rectal swab isolates experienced 30-day ICU admission (17.5%), hospital readmission (9.2%), and death (13.3%). Conclusions Our findings describe the high burden of VRE transmission at our hospital and shed light on the importance of using WGS surveillance of both clinical and rectal screening isolates to better understand the transmission of this pathogen. This study highlights the potential utility of incorporating WGS surveillance of VRE into routine hospital practice for improving infection prevention and patient safety.
Collapse
|
4
|
Vancomycin-resistant Enterococcus sequence type 1478 spread across hospitals participating in the Canadian Nosocomial Infection Surveillance Program from 2013 to 2018. Infect Control Hosp Epidemiol 2023; 44:17-23. [PMID: 35264277 DOI: 10.1017/ice.2022.7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
OBJECTIVE To analyze the spread of a novel sequence type (ST1478) of vancomycin-resistant Enterococcus faecium across Canadian hospitals. DESIGN Retrospective chart review of patients identified as having ST1478 VRE bloodstream infection. SETTING Canadian hospitals that participate in the Canadian Nosocomial Infection Surveillance Program (CNISP). METHODS From 2013 to 2018, VRE bloodstream isolates collected from participating CNISP hospitals were sent to the National Microbiology Laboratory (NML). ST1478 isolates were identified using multilocus sequence typing, and whole-genome sequencing was performed. Patient characteristics and location data were collected for patients with ST1478 bloodstream infection (BSI). The sequence and patient location information were used to generate clusters of infections and assess for intrahospital and interhospital spread. RESULTS ST1478 VRE BSI occurred predominantly in a small number of hospitals in central and western Canada. Within these hospitals, infections were clustered on certain wards, and isolates often had <20 single-nucleotide variants (SNV) differences from one another, suggesting a large component of intrahospital spread. Furthermore, some patients with bloodstream infections were identified as moving from one hospital to another, potentially having led to interhospital spread. Genomic analysis of all isolates revealed close relatedness between isolates at multiple different hospitals (<20 SNV) not predicted from our epidemiologic data. CONCLUSIONS Both intrahospital and regional interhospital spread have contributed to the emergence of VRE ST1478 infections across Canada. Whole-genome sequencing provides evidence of spread that might be missed with epidemiologic investigation alone.
Collapse
|
5
|
Maechler F, Weber A, Schwengers O, Schwab F, Denkel L, Behnke M, Gastmeier P, Kola A. Split k-mer analysis compared to cgMLST and SNP-based core genome analysis for detecting transmission of vancomycin-resistant enterococci: results from routine outbreak analyses across different hospitals and hospitals networks in Berlin, Germany. Microb Genom 2023; 9:mgen000937. [PMID: 36748706 PMCID: PMC9973845 DOI: 10.1099/mgen.0.000937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 11/22/2022] [Indexed: 01/31/2023] Open
Abstract
The increase of Vancomycin-resistant Enterococcus faecium (VREfm) in recent years has been partially attributed to the rise of specific clonal lineages, which have been identified throughout Germany. To date, there is no gold standard for the interpretation of genomic data for outbreak analyses. New genomic approaches such as split k-mer analysis (SKA) could support cluster attribution for routine outbreak investigation. The aim of this project was to investigate frequent clonal lineages of VREfm identified during suspected outbreaks across different hospitals, and to compare genomic approaches including SKA in routine outbreak investigation. We used routine outbreak laboratory data from seven hospitals and three different hospital networks in Berlin, Germany. Short-read libraries were sequenced on the Illumina MiSeq system. We determined clusters using the published Enterococcus faecium-cgMLST scheme (threshold ≤20 alleles), and assigned sequence and complex types (ST, CT), using the Ridom SeqSphere+ software. For each cluster as determined by cgMLST, we used pairwise core-genome SNP-analysis and SKA at thresholds of ten and seven SNPs, respectively, to further distinguish cgMLST clusters. In order to investigate clinical relevance, we analysed to what extent epidemiological linkage backed the clusters determined with different genomic approaches. Between 2014 and 2021, we sequenced 693 VREfm strains, and 644 (93 %) were associated within cgMLST clusters. More than 74 % (n=475) of the strains belonged to the six largest cgMLST clusters, comprising ST117, ST78 and ST80. All six clusters were detected across several years and hospitals without apparent epidemiological links. Core SNP analysis identified 44 clusters with a median cluster size of three isolates (IQR 2-7, min-max 2-63), as well as 197 singletons (41.4 % of 475 isolates). SKA identified 67 clusters with a median cluster size of two isolates (IQR 2-4, min-max 2-19), and 261 singletons (54.9 % of 475 isolates). Of the isolate pairs attributed to clusters, 7 % (n=3064/45 596) of pairs in clusters determined by standard cgMLST, 15 % (n=1222/8500) of pairs in core SNP-clusters and 51 % (n=942/1880) of pairs in SKA-clusters showed epidemiological linkage. The proportion of epidemiological linkage differed between sequence types. For VREfm, the discriminative ability of the widely used cgMLST based approach at ≤20 alleles difference was insufficient to rule out hospital outbreaks without further analytical methods. Cluster assignment guided by core genome SNP analysis and the reference free SKA was more discriminative and correlated better with obvious epidemiological linkage, at least recently published thresholds (ten and seven SNPs, respectively) and for frequent STs. Besides higher overall discriminative power, the whole-genome approach implemented in SKA is also easier and faster to conduct and requires less computational resources.
Collapse
Affiliation(s)
- Friederike Maechler
- Institute of Hygiene and Environmental Medicine, Charité – Universitätsmedizin Berlin, Berlin, Germany
| | - Anna Weber
- Institute of Hygiene and Environmental Medicine, Charité – Universitätsmedizin Berlin, Berlin, Germany
| | - Oliver Schwengers
- Bioinformatics and Systems Biology, Justus Liebig University Giessen, Giessen, Germany
| | - Frank Schwab
- Institute of Hygiene and Environmental Medicine, Charité – Universitätsmedizin Berlin, Berlin, Germany
| | - Luisa Denkel
- Institute of Hygiene and Environmental Medicine, Charité – Universitätsmedizin Berlin, Berlin, Germany
| | - Michael Behnke
- Institute of Hygiene and Environmental Medicine, Charité – Universitätsmedizin Berlin, Berlin, Germany
| | - Petra Gastmeier
- Institute of Hygiene and Environmental Medicine, Charité – Universitätsmedizin Berlin, Berlin, Germany
| | - Axel Kola
- Institute of Hygiene and Environmental Medicine, Charité – Universitätsmedizin Berlin, Berlin, Germany
| |
Collapse
|
6
|
Eichel VM, Boutin S, Frank U, Weigand MA, Heininger A, Mutters NT, Büchler MW, Heeg K, Nurjadi D. The Impact of Discontinuing Contact Precautions and Enforcement of Basic Hygiene Measures on Nosocomial Vancomycin-Resistant Enterococcus faecium Transmission. J Hosp Infect 2021; 121:120-127. [PMID: 34861314 DOI: 10.1016/j.jhin.2021.11.020] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 11/17/2021] [Accepted: 11/18/2021] [Indexed: 11/26/2022]
Abstract
OBJECTIVES Vancomycin-resistant Enterococcus faecium (VREfm) has emerged as a pathogen of major public health concern. Although definitive evidence is lacking, contact precautions have been a crucial element in infection prevention and control (IPC) strategies designed to limit nosocomial VRE transmissions. This study investigates the effect of discontinuing contact precautions while enforcing basic hygiene measures, including hand hygiene, environmental cleaning, and antiseptic body washing, for VRE patients at ICUs on prevention of nosocomial VRE transmission causing bacteraemia. METHODS Contact precaution was discontinued in January 2018. A total of 96 VREfm isolates from 61 ICU patients with VREfm bacteraemia and/or colonization from 8 ICUs in 2016 and 2019 in a tertiary care hospital were characterized by whole genome sequenicng. VRE transmission was investigated using patient movement data and admission screening for reliable identification of nosocomial acquisition. RESULTS Discontinuation of contact precautions did not increase VREfm transmission events (8 in 2016 vs 1 in 2019). While the rate of endogenous VREfm was similar in both years (38% vs 31%), the number of non-colonized patients prior to VREfm bacteraemia was 16 (16/29; 55%) in 2019, which was significantly higher than in 2016 (8/32; 25%). The mean incidence density for VREfm bacteraemia was similar for both years; 0.26 versus 0.31 per 1000 patient days in 2016 and 2019, respectively. CONCLUSION Our data suggest that discontinuation of contact precaution, while enforcing the basic hygiene measures did not lead to an increase of nosocomial bloodstream infection rates due to transmissions of VREfm in hyperendemic ICU settings.
Collapse
Affiliation(s)
- Vanessa M Eichel
- Department of Infectious Diseases, Medical Microbiology and Hygiene, Heidelberg University Hospital, Im Neuenheimer Feld 324, D-69120 Heidelberg, Germany.
| | - Sébastien Boutin
- Department of Infectious Diseases, Medical Microbiology and Hygiene, Heidelberg University Hospital, Im Neuenheimer Feld 324, D-69120 Heidelberg, Germany
| | - Uwe Frank
- Department of Infectious Diseases, Medical Microbiology and Hygiene, Heidelberg University Hospital, Im Neuenheimer Feld 324, D-69120 Heidelberg, Germany; Institute for Infection Prevention and Hospital Epidemiology, Medical Center, University of Freiburg, Breisacher Str. 115B, D-79106 Freiburg i.Br., Germany
| | - Markus A Weigand
- Department of Anaesthesiology, Heidelberg University Hospital, Im Neuenheimer Feld 420, 69120 Heidelberg, Germany
| | - Alexandra Heininger
- Department of Infectious Diseases, Medical Microbiology and Hygiene, Heidelberg University Hospital, Im Neuenheimer Feld 324, D-69120 Heidelberg, Germany; Department of Hospital Hygiene, University Medical Center Mannheim,Theodor-Kutzer-Ufer 1-3, 68167 Mannheim, Germany
| | - Nico T Mutters
- Department of Infectious Diseases, Medical Microbiology and Hygiene, Heidelberg University Hospital, Im Neuenheimer Feld 324, D-69120 Heidelberg, Germany; Institute of Hygiene and Public Health, University Hospital Bonn, Venusberg-Campus 1, 53127 Bonn, Germany
| | - Markus W Büchler
- Department of General, Visceral and Transplantation Surgery, Im Neuenheimer Feld 6420, 69120 Heidelberg University Hospital, Heidelberg, Germany
| | - Klaus Heeg
- Department of Infectious Diseases, Medical Microbiology and Hygiene, Heidelberg University Hospital, Im Neuenheimer Feld 324, D-69120 Heidelberg, Germany
| | - Dennis Nurjadi
- Department of Infectious Diseases, Medical Microbiology and Hygiene, Heidelberg University Hospital, Im Neuenheimer Feld 324, D-69120 Heidelberg, Germany
| |
Collapse
|
7
|
Kocer K, Klein S, Hildebrand D, Krall J, Heeg K, Boutin S, Nurjadi D. Pitfalls in genotypic antimicrobial susceptibility testing caused by low expression of blaKPC in Escherichia coli. J Antimicrob Chemother 2021; 76:2795-2801. [PMID: 34324652 DOI: 10.1093/jac/dkab267] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2021] [Accepted: 07/05/2021] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND There is a growing interest in the rapid genotypic identification of antimicrobial resistance (AMR). In routine diagnostics, we detected multiple KPC-positive Escherichia coli (KPC-Ec) with discordant phenotypic meropenem susceptibility from a single patient's blood cultures, which prompted a more thorough investigation. OBJECTIVES We investigated the potential clinical relevance of, and the mechanism behind, discordant phenotypic and genotypic meropenem susceptibility in KPC-Ec. METHODS WGS was used to perform a comparative analysis of the isolates' genetic characteristics and their blaKPC-2 locus. Expression of blaKPC-2 was determined by quantitative PCR and the potency of meropenem hydrolysis was determined using a semi-quantitative carbapenem inactivation method. An in vivo infection assay using Galleria mellonella was performed to assess the potential clinical relevance of KPC expression in E. coli. RESULTS Despite the presence of blaKPC-2, three of five isolates were susceptible to meropenem (MICVITEK2 ≤ 0.25 mg/L), while two isolates were resistant (MICVITEK2 ≥ 16 mg/L). The isolates with high MICs had significantly higher blaKPC-2 expression, which corresponds to phenotypic meropenem inactivation. The genetic environment of blaKPC-2, which may impact KPC production, was identical in all isolates. In vivo infection assay with G. mellonella suggested that meropenem was effective in reducing mortality following infection with low-expressing KPC-Ec. CONCLUSIONS Our findings clearly highlight a limitation of genotypic AMR prediction for blaKPC. For the time being, genotypic AMR prediction requires additional analysis for accurate antibiotic therapy decision-making.
Collapse
Affiliation(s)
- Kaan Kocer
- Department of Infectious Diseases, Medical Microbiology and Hygiene, Heidelberg University Hospital, Im Neuenheimer Feld 324, 69120 Heidelberg, Germany
| | - Sabrina Klein
- Department of Infectious Diseases, Medical Microbiology and Hygiene, Heidelberg University Hospital, Im Neuenheimer Feld 324, 69120 Heidelberg, Germany
| | - Dagmar Hildebrand
- Department of Infectious Diseases, Medical Microbiology and Hygiene, Heidelberg University Hospital, Im Neuenheimer Feld 324, 69120 Heidelberg, Germany
| | - Johannes Krall
- Department of Infectious Diseases, Medical Microbiology and Hygiene, Heidelberg University Hospital, Im Neuenheimer Feld 324, 69120 Heidelberg, Germany
| | - Klaus Heeg
- Department of Infectious Diseases, Medical Microbiology and Hygiene, Heidelberg University Hospital, Im Neuenheimer Feld 324, 69120 Heidelberg, Germany
| | - Sébastien Boutin
- Department of Infectious Diseases, Medical Microbiology and Hygiene, Heidelberg University Hospital, Im Neuenheimer Feld 324, 69120 Heidelberg, Germany
| | - Dennis Nurjadi
- Department of Infectious Diseases, Medical Microbiology and Hygiene, Heidelberg University Hospital, Im Neuenheimer Feld 324, 69120 Heidelberg, Germany
| |
Collapse
|
8
|
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.
Collapse
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
| |
Collapse
|
9
|
Kjær Hansen S, Andersen L, Detlefsen M, Holm A, Roer L, Antoniadis P, Skov MN, Hammerum AM, Kemp M. Using core genome multilocus sequence typing (cgMLST) for vancomycin-resistant Enterococcus faecium isolates to guide infection control interventions and end an outbreak. J Glob Antimicrob Resist 2021; 24:418-423. [PMID: 33618041 DOI: 10.1016/j.jgar.2021.02.007] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2020] [Revised: 12/11/2020] [Accepted: 02/05/2021] [Indexed: 11/15/2022] Open
Abstract
OBJECTIVES Until July 2016, vancomycin-resistantEnterococcus faecium (VREfm) was sporadically detected in Odense University Hospital, Denmark. After July 2016, the number of VREfm cases increased. This study aimed to apply a core genome multilocus sequence typing (cgMLST) scheme for E. faecium to type and analyse VREfm isolates collected at a single Danish hospital and to compare the results with cgMLST data from other regions of Denmark to trace transmission. METHODS A total of 38 VREfm clinical isolates from inpatients at the hospital in the period January 2014 through June 2017 were included in the study and analysed using whole-genome sequencing. Use of SeqSphere + software was initiated from the beginning of June 2017 to obtain MLST, cgMLST and epi curves. Admission histories were incorporated and national surveillance data on cgMLST were used to identify transmission routes. RESULTS Six different sequence types (STs) were identified, the most frequent being ST80, ST117 and ST203. cgMLST subdivided the 38 isolates into 18 different complex types (CTs) with 13 isolates (34%) belonging to ST80-CT993. Epi curves indicated transmission of ST80-CT993 in several departments. Transmission from patients transferred from other hospitals was not identifiable. Infection control interventions launched in one department ended the outbreak. CONCLUSION The high resolution of cgMLST allowed for detailed interpretation with evidence of nosocomial transmission of specific CTs. cgMLST made it easy to compare our local isolates with national findings, thereby clarifying transmission routes. Supplemented with admission histories, cgMLST targeted the epidemiological investigation and delineated the expensive and time-consuming infection control interventions.
Collapse
Affiliation(s)
- Sanne Kjær Hansen
- Research Unit for Department of Clinical Microbiology, Odense University Hospital, University of Southern Denmark, Odense, Denmark; Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen S, Denmark.
| | - Lise Andersen
- Department of Clinical Microbiology, Odense University Hospital, Odense C, Denmark
| | - Mette Detlefsen
- Department of Clinical Microbiology, Odense University Hospital, Odense C, Denmark
| | - Anette Holm
- Research Unit for Department of Clinical Microbiology, Odense University Hospital, University of Southern Denmark, Odense, Denmark; Department of Clinical Microbiology, Odense University Hospital, Odense C, Denmark
| | - Louise Roer
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen S, Denmark
| | - Panagiotis Antoniadis
- Research Unit for Department of Clinical Microbiology, Odense University Hospital, University of Southern Denmark, Odense, Denmark
| | - Marianne Nielsine Skov
- Research Unit for Department of Clinical Microbiology, Odense University Hospital, University of Southern Denmark, Odense, Denmark; Department of Clinical Microbiology, Odense University Hospital, Odense C, Denmark
| | - Anette M Hammerum
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen S, Denmark
| | - Michael Kemp
- Research Unit for Department of Clinical Microbiology, Odense University Hospital, University of Southern Denmark, Odense, Denmark
| |
Collapse
|
10
|
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.
Collapse
Affiliation(s)
- Guido Werner
- National Reference Centre for Staphylococci and Enterococci, Division Nosocomial Pathogens and Antibiotic Resistances, Department of Infectious Diseases, Robert Koch Institute, Wernigerode Branch, Germany.
| | - Bernd Neumann
- National Reference Centre for Staphylococci and Enterococci, Division Nosocomial Pathogens and Antibiotic Resistances, Department of Infectious Diseases, Robert Koch Institute, Wernigerode Branch, Germany
| | - Robert E Weber
- National Reference Centre for Staphylococci and Enterococci, Division Nosocomial Pathogens and Antibiotic Resistances, Department of Infectious Diseases, Robert Koch Institute, Wernigerode Branch, Germany
| | | | | | - Jennifer K Bender
- National Reference Centre for Staphylococci and Enterococci, Division Nosocomial Pathogens and Antibiotic Resistances, Department of Infectious Diseases, Robert Koch Institute, Wernigerode Branch, Germany
| |
Collapse
|
11
|
Kocer K, Boutin S, Probst K, Heeg K, Nurjadi D. Whole-genome sequencing disproves two suspected transmission events of bla NDM between Pseudomonas aeruginosa and Enterobacterales in hospitalized patients. J Hosp Infect 2020; 106:372-375. [PMID: 32652213 DOI: 10.1016/j.jhin.2020.07.006] [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: 05/22/2020] [Accepted: 07/06/2020] [Indexed: 11/18/2022]
Abstract
New Delhi metallo-β-lactamase (blaNDM) acquisition by Gram-negative bacteria is a primary concern due to its broad-host-range distribution. This study investigated two potential in-vivo horizontal gene transfers (HGTs) of blaNDM between Enterobacterales and Pseudomonas aeruginosa, initially indicated by polymerase chain reaction. Whole-genome sequencing showed independent parallel acquisition of two different blaNDM variants (NDM-1 and NDM-5) in P. aeruginosa and Enterobacterales, respectively. The data show that short-read sequencing provides the necessary resolution to confirm or dispute HGT by the comparison of genetic elements surrounding the gene of interest, and thus provide a timely response to potential outbreaks.
Collapse
Affiliation(s)
- K Kocer
- Heidelberg University Hospital, Department of Infectious Diseases, Medical Microbiology and Hygiene, Heidelberg, Germany.
| | - S Boutin
- Heidelberg University Hospital, Department of Infectious Diseases, Medical Microbiology and Hygiene, Heidelberg, Germany; Translational Lung Research Centre Heidelberg, Member of the German Centre for Lung Research, Heidelberg University Hospital, Heidelberg, Germany
| | - K Probst
- Heidelberg University Hospital, Department of Infectious Diseases, Medical Microbiology and Hygiene, Heidelberg, Germany
| | - K Heeg
- Heidelberg University Hospital, Department of Infectious Diseases, Medical Microbiology and Hygiene, Heidelberg, Germany
| | - D Nurjadi
- Heidelberg University Hospital, Department of Infectious Diseases, Medical Microbiology and Hygiene, Heidelberg, Germany
| |
Collapse
|
12
|
Heininger A, Zimmermann S, Bootsveld C, Boutin S, Nurjadi D. Low prevalence of combined linezolid- and vancomycin-resistant Enterococcus faecium from hospital admission screening in an endemic region in Germany. J Glob Antimicrob Resist 2020; 22:646-650. [PMID: 32439568 DOI: 10.1016/j.jgar.2020.05.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 04/16/2020] [Accepted: 05/08/2020] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND The emergence and spread of linezolid and combined linezolid/vancomycin resistance in Enterococcus faecium (LVRE) is a major therapeutic challenge. Due to the unavailability of standardized selective culture media for LVRE screening, the detection of LVRE is laborious and costly. Systematic data on LVRE prevalence are scarce, and therefore, supportive evidence for the correct implementation of preemptive strategies is lacking. OBJECTIVE We investigated the prevalence of LVRE in a vancomycin-resistant enterococci (VRE) endemic area in Germany in admission screening of high-risk patients for multidrug-resistant organisms to assess the necessity of LVRE screening. METHODS We performed phenotypic testing for linezolid susceptibility in all patients (n = 2572) admitted to our hospital in the months of January, April, July and October 2018 with a positive VRE culture in their rectal admission screening swab. Eight isolates from seven patients with LVRE colonization were characterized by whole genome sequencing. RESULTS Twenty-eight percent (712/2572) of screened patients were colonized by VRE. Seventy percent (497/712) of the isolates were available for testing and whole genome sequencing. A total of 1.4% (7/497) of VRE were LVRE, predominantly due to mutations of 23S rRNA. optrA, poxtA or cfr genes were not detected. Patients with LVRE colonization did not develop LVRE infections during their stay. CONCLUSION LVRE prevalence was low, and there was no evidence for the dissemination of linezolid resistance genes. Due to the low prevalence and the low risk of infection due to endogenous LVRE, we do not see the immediate necessity to introduce routine LVRE screening in our hospital.
Collapse
Affiliation(s)
- Alexandra Heininger
- Department of Infectious Diseases, Medical Microbiology and Hygiene, Heidelberg University Hospital, Heidelberg, Germany
| | - Stefan Zimmermann
- Department of Infectious Diseases, Medical Microbiology and Hygiene, Heidelberg University Hospital, Heidelberg, Germany
| | - Carolin Bootsveld
- Department of Infectious Diseases, Medical Microbiology and Hygiene, Heidelberg University Hospital, Heidelberg, Germany
| | - Sébastien Boutin
- Department of Infectious Diseases, Medical Microbiology and Hygiene, Heidelberg University Hospital, Heidelberg, Germany
| | - Dennis Nurjadi
- Department of Infectious Diseases, Medical Microbiology and Hygiene, Heidelberg University Hospital, Heidelberg, Germany.
| |
Collapse
|