1
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Getahun Strobel A, Prasad P, Prasad V, Naidu R, Young-Sharma T, Suka A, Richards M, Cameron D, Lane CR, Buising K, Howden BP, Autar S. The epidemiology of enterococci in a tertiary hospital and primary healthcare facilities in Fiji (2019-2022). J Glob Antimicrob Resist 2024; 37:102-107. [PMID: 38565419 DOI: 10.1016/j.jgar.2024.03.008] [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: 11/08/2023] [Revised: 02/28/2024] [Accepted: 03/05/2024] [Indexed: 04/04/2024] Open
Abstract
OBJECTIVES We analysed 4 y of laboratory data to characterise the species and determine the antimicrobial susceptibility profiles of enterococci as human pathogens in Fiji. The study also investigated the molecular epidemiology amongst the subset of vancomycin-resistant enterococci (VRE). METHODS This retrospective study reviewed bacteriological data from Colonial War Memorial Hospital (CWMH) and other healthcare facilities in the Central and Eastern divisions of Fiji. Phenotypic, antimicrobial susceptibility and vanA and vanB PCR testing were performed using locally approved protocols. The first clinical isolates per patient with antimicrobial susceptibility testing results in a single year were included in the analysis. Data was analysed using WHONET software and Microsoft Excel. RESULTS A total of 1817 enterococcal isolates were reported, 1415 from CWMH and 402 from other healthcare facilities. The majority of isolates, 75% (n = 1362) were reported as undifferentiated Enterococcus spp., 17.8% (n = 324) were specifically identified as Enterococcus faecalis and 6.7% (n = 122) as E. faecium. Overall, 10% of the enterococci isolates were from blood cultures. Among isolates from CWMH, <15% of E. faecium were susceptible to ampicillin, and 17.2% were vancomycin resistant. Overall, 874 enterococcal isolates (including the undifferentiated species) were tested against vancomycin, of which 4.8% (n = 42) were resistance. All of the VRE isolates tested (n = 15) expressed vanA genes. CONCLUSIONS This study demonstrates the clinical importance of VRE, particularly van A E. faecium in the national referral hospital in Fiji. Enhanced phenotypic and molecular surveillance data are needed to better understand enterococci epidemiology and help guide specific infection prevention and control measures and antibiotic prescribing guidelines.
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Affiliation(s)
- Aneley Getahun Strobel
- Department of Infectious Diseases, The University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia.
| | - Prinika Prasad
- Ministry of Health and Medical Services, Colonial War Memorial Hospital, Suva, Fiji
| | - Vinita Prasad
- Ministry of Health and Medical Services, Colonial War Memorial Hospital, Suva, Fiji
| | - Ravi Naidu
- Ministry of Health and Medical Services, Colonial War Memorial Hospital, Suva, Fiji
| | - Tracey Young-Sharma
- Ministry of Health and Medical Services, Colonial War Memorial Hospital, Suva, Fiji
| | - Ana Suka
- Ministry of Health and Medical Services, Colonial War Memorial Hospital, Suva, Fiji
| | - Matthew Richards
- Infection Prevention and Surveillance Service, The Royal Melbourne Hospital, Melbourne, Australia
| | - Donna Cameron
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at Peter Doherty Institute for infection and Immunity, Melbourne, Australia
| | - Courtney R Lane
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at Peter Doherty Institute for infection and Immunity, Melbourne, Australia
| | - Kirsty Buising
- Department of Infectious Diseases, The University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia; The Royal Melbourne Hospital, Melbourne, Australia
| | - Benjamin P Howden
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at Peter Doherty Institute for infection and Immunity, Melbourne, Australia.
| | - Sanjeshni Autar
- Ministry of Health and Medical Services, Colonial War Memorial Hospital, Suva, Fiji
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2
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Hammerum AM, Karstensen KT, Roer L, Kaya H, Lindegaard M, Porsbo LJ, Kjerulf A, Pinholt M, Holzknecht BJ, Worning P, Nielsen KL, Hansen SGK, Clausen M, Søndergaard TS, Dzajic E, Østergaard C, Wang M, Koch K, Hasman H. Surveillance of vancomycin-resistant enterococci reveals shift in dominating clusters from vanA to vanB Enterococcus faecium clusters, Denmark, 2015 to 2022. Euro Surveill 2024; 29:2300633. [PMID: 38847117 PMCID: PMC11158013 DOI: 10.2807/1560-7917.es.2024.29.23.2300633] [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: 11/15/2023] [Accepted: 03/26/2024] [Indexed: 06/09/2024] Open
Abstract
BackgroundVancomycin-resistant enterococci (VRE) are increasing in Denmark and Europe. Linezolid and vancomycin-resistant enterococci (LVRE) are of concern, as treatment options are limited. Vancomycin-variable enterococci (VVE) harbour the vanA gene complex but are phenotypically vancomycin-susceptible.AimThe aim was to describe clonal shifts for VRE and VVE in Denmark between 2015 and 2022 and to investigate genotypic linezolid resistance among the VRE and VVE.MethodsFrom 2015 to 2022, 4,090 Danish clinical VRE and VVE isolates were whole genome sequenced. We extracted vancomycin resistance genes and sequence types (STs) from the sequencing data and performed core genome multilocus sequence typing (cgMLST) analysis for Enterococcus faecium. All isolates were tested for the presence of mutations or genes encoding linezolid resistance.ResultsIn total 99% of the VRE and VVE isolates were E. faecium. From 2015 through 2019, 91.1% of the VRE and VVE were vanA E. faecium. During 2020, to the number of vanB E. faecium increased to 254 of 509 VRE and VVE isolates. Between 2015 and 2022, seven E. faecium clusters dominated: ST80-CT14 vanA, ST117-CT24 vanA, ST203-CT859 vanA, ST1421-CT1134 vanA (VVE cluster), ST80-CT1064 vanA/vanB, ST117-CT36 vanB and ST80-CT2406 vanB. We detected 35 linezolid vancomycin-resistant E. faecium and eight linezolid-resistant VVEfm.ConclusionFrom 2015 to 2022, the numbers of VRE and VVE increased. The spread of the VVE cluster ST1421-CT1134 vanA E. faecium in Denmark is a concern, especially since VVE diagnostics are challenging. The finding of LVRE, although in small numbers, ia also a concern, as treatment options are limited.
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Affiliation(s)
- Anette M Hammerum
- Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
- These authors contributed equally to this work and share first authorship
| | - Kasper Thystrup Karstensen
- Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
- These authors contributed equally to this work and share first authorship
| | - Louise Roer
- Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Hülya Kaya
- Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Mikkel Lindegaard
- Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Lone Jannok Porsbo
- Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Anne Kjerulf
- Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Mette Pinholt
- Department of Clinical Microbiology, Copenhagen University Hospital - Amager and Hvidovre, Denmark
| | - Barbara Juliane Holzknecht
- Department of Clinical Microbiology, Copenhagen University Hospital - Herlev and Gentofte, Herlev, Denmark
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Peder Worning
- Department of Clinical Microbiology, Copenhagen University Hospital - Amager and Hvidovre, Denmark
| | - Karen Leth Nielsen
- Department of Clinical Microbiology, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | | | - Marianne Clausen
- Department of Clinical Microbiology, Slagelse University Hospital, Slagelse, Denmark
| | - Turid S Søndergaard
- Department of Clinical Microbiology, Sønderjylland Hospital, Aabenraa, Denmark
| | - Esad Dzajic
- Department of Clinical Microbiology, Hospital South West Jutland, Esbjerg, Denmark
| | - Claus Østergaard
- Department of Clinical Microbiology, Lillebaelt Hospital, Vejle, Denmark
| | - Mikala Wang
- Department of Clinical Microbiology, Aarhus University Hospital, Aarhus, Denmark
| | - Kristoffer Koch
- Department of Clinical Microbiology, Aalborg University Hospital, Aalborg, Denmark
| | - Henrik Hasman
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
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3
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Vancomycin-Resistant Enterococcus faecium and the emergence of new Sequence Types associated with Hospital Infection. Res Microbiol 2023; 174:104046. [PMID: 36858192 DOI: 10.1016/j.resmic.2023.104046] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 02/16/2023] [Accepted: 02/20/2023] [Indexed: 03/02/2023]
Abstract
Enterococcus faecium is a major cause of vancomycin-resistant enterococcal (VRE) infection. New variants of the pathogen have emerged and become dominant in healthcare settings. Two such examples, vanB ST796 and vanA ST1421 sequence types, originally arose in Australia and proceeded to cause VRE outbreaks in other countries. Of concern is the detection of a vancomycin variable enterococcal (VVE) variant of ST1421 in Europe that exhibits a vancomycin-susceptible phenotype but which can revert to resistant in the presence of vancomycin. The recent application of genome sequencing for increasing our understanding of the evolution and spread of VRE is also explored here.
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4
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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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5
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Bender JK, Hermes J, Zabel LT, Haller S, Mürter N, Blank HP, Werner G, Hüttner I, Eckmanns T. Controlling an Unprecedented Outbreak with Vancomycin-Resistant Enterococcus faecium in Germany, October 2015 to November 2019. Microorganisms 2022; 10:1603. [PMID: 36014021 PMCID: PMC9412439 DOI: 10.3390/microorganisms10081603] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 08/03/2022] [Accepted: 08/03/2022] [Indexed: 01/18/2023] Open
Abstract
Hospital outbreaks with vancomycin-resistant enterococci (VRE) pose a serious health threat and a challenge to infection prevention and control (IPC). We herein report on a VRE outbreak of unprecedented extent in Southern Germany (October 2015-November 2019). We used descriptive epidemiology and whole-genome sequencing (WGS) for a detailed outbreak investigation. Of the 2905 cases, 2776 (95.3%) were colonized, whereas from 127 (3.7%), VRE could be isolated from otherwise sterile body fluids or sites unlikely for enterococci colonization. Cases had a median age of 78 years (IQR 68-84) and 1339/2905 (46%) were female. The majority of isolates sequenced belonged to the clonal lineage ST80/CT1013 (212/397, 53%). Nosocomial transmission was observed as well as the constant import of VRE into the hospital. Extensive IPC measures were implemented and terminated the outbreak in late 2019, eventually. Our study shows that the combination of epidemiological and genomic analyses is indispensable for comprehensive outbreak investigations. The adaptation of IPC measures to these findings, their timely implementation, and strict execution also allow containment of large VRE outbreaks in hospital settings.
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Affiliation(s)
- Jennifer K. Bender
- Nosocomial Pathogens and Antibiotic Resistances Unit, Department of Infectious Diseases, Robert Koch Institute, 38855 Wernigerode, Germany
| | - Julia Hermes
- Healthcare-Associated Infections, Surveillance of Antibiotic Resistance and Consumption Unit, Department of Infectious Disease Epidemiology, Robert Koch Institute, 13353 Berlin, Germany
| | | | - Sebastian Haller
- Healthcare-Associated Infections, Surveillance of Antibiotic Resistance and Consumption Unit, Department of Infectious Disease Epidemiology, Robert Koch Institute, 13353 Berlin, Germany
| | - Nadja Mürter
- Local Health Authority Göppingen, 73033 Göppingen, Germany
| | | | - Guido Werner
- Nosocomial Pathogens and Antibiotic Resistances Unit, Department of Infectious Diseases, Robert Koch Institute, 38855 Wernigerode, Germany
| | - Ingo Hüttner
- Alb Fils Kliniken GmbH, 73035 Göppingen, Germany
| | - Tim Eckmanns
- Healthcare-Associated Infections, Surveillance of Antibiotic Resistance and Consumption Unit, Department of Infectious Disease Epidemiology, Robert Koch Institute, 13353 Berlin, Germany
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6
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Mohanty S, Behera B. Antibiogram Pattern and Virulence Trait Characterization of Enterococcus Species Clinical Isolates in Eastern India: A Recent Analysis. J Lab Physicians 2022; 14:237-246. [PMID: 36119423 PMCID: PMC9473946 DOI: 10.1055/s-0042-1750085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Abstract
Abstract
Objective We aimed to evaluate the current antimicrobial susceptibility pattern and characterize putative virulence traits among Enterococcus
species isolates from various clinical specimens in view of their increased isolation rates in both community-related and serious nosocomial infections, as well as resistance to many antibiotics.
Methods Study (April 2017–March 2018) included consecutive, nonrepeated, discrete, and clinically significant isolates of enterococci. Susceptibility testing included detection of high-level aminoglycoside-resistant (HLAR) and glycopeptide-resistant enterococci (GRE). All screen-positive GRE isolates were investigated by polymerase chain reaction for species confirmation and presence of vanA/vanB genes. Virulence genes ace, asa1, cyt, efa, esp, gelE, and hyl were investigated by molecular methods. Hemolysin and biofilm production were studied using phenotypic methods.
Results Of 111 isolates, 89 (80.1%), 16 (14.4%), and 6 (5.4%) were from urine, pus, and blood, respectively, consisting predominantly of E. faecalis (67, 60.4%) and E. faecium (32, 28.8%). E. hirae (5, 4.5%) was the predominant non-E. faecalis non-E. faecium isolate. Other species were E. durans (4, 3.6%), E. avium (2, 1.8%), and E. mundtii (1, 0.9%). Seven (6.3%) out of the 111 isolates were GRE, all vanA genotype. HLAR was observed in 70 (63.1%) isolates, significantly higher in E. faecium than E. faecalis (81.2 vs. 58.2%; p < 0.05). All were susceptible to daptomycin. Hemolysin activity and biofilm production were observed in 38 (34.2%) and 36 (32.4%) isolates. Most frequent virulence genes were efa (77, 69.4%), ace (71, 63.9%), asa1 (67, 60.3%), and gelE (66, 59.4%). There was a predominant association of esp and hyl genes with E. faecium and that of the other genes with E. faecalis.
Conclusion The study will contribute to the existing limited data on virulence trait characterization of clinical E. spp. isolates in India. At the same time, it will help to serve as a guide in the choice of empirical therapy in enterococcal infections leading to favorable clinical outcomes by decreasing the clinical failure, microbiological persistence, and associated mortality, and will lead to future studies on controlling the spread of virulent and multiresistant isolates.
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Affiliation(s)
- Srujana Mohanty
- Department of Microbiology, All India Institute of Medical Sciences, Bhubaneswar, Odisha, India
| | - Bijayini Behera
- Department of Microbiology, All India Institute of Medical Sciences, Bhubaneswar, Odisha, India
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7
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Saenhom N, Boueroy P, Chopjitt P, Hatrongjit R, Kerdsin A. Distinguishing Clinical Enterococcus faecium Strains and Resistance to Vancomycin Using a Simple In-House Screening Test. Antibiotics (Basel) 2022; 11:antibiotics11030286. [PMID: 35326750 PMCID: PMC8944677 DOI: 10.3390/antibiotics11030286] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 02/14/2022] [Accepted: 02/18/2022] [Indexed: 12/10/2022] Open
Abstract
Vancomycin-resistant enterococci (VRE) are a major concern as microorganisms with antimicrobial resistance and as a public health threat contributing significantly to morbidity, mortality, and socio-economic costs. Among VREs, vancomycin-resistant Enterococcus faecium (VREfm) is frequently isolated and is resistant to many antibiotics used to treat patients with hospital-acquired infection. Accurate and rapid detection of VREfm results in effective antimicrobial therapy, immediate patient isolation, dissemination control, and appropriate disinfection measures. An in-house VREfm screening broth was developed and compared to the broth microdilution method and multiplex polymerase chain reaction for the detection of 105 enterococci, including 81 VRE isolates (61 E. faecium, 5 E. faecalis, 10 E. gallinarum, and 5 E. casseliflavus). Verification of this screening broth on 61 VREfm, 20 other VRE, and 24 non-VRE revealed greater validity for VREfm detection. The accuracy of this broth was 100% in distinguishing E. faecium from other enterococcal species. Our test revealed 93.3% accuracy, 97.5% sensitivity, and 79.2% specificity compared with broth microdilution and PCR detecting van genes. The kappa statistic to test interrater reliability was 0.8, revealing substantial agreement for this screening test to the broth microdilution method. In addition, the in-house VREfm screening broth produced rapid positivity after at least 8 h of incubation. Application of this assay to screen VREfm should be useful in clinical laboratories and hospital infection control units.
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Affiliation(s)
- Natkamon Saenhom
- Faculty of Public Health, Kasetsart University Chalermphrakiat Sakon Nakhon Province Campus, Sakon Nakhon 47000, Thailand; (N.S.); (P.B.); (P.C.)
| | - Parichart Boueroy
- Faculty of Public Health, Kasetsart University Chalermphrakiat Sakon Nakhon Province Campus, Sakon Nakhon 47000, Thailand; (N.S.); (P.B.); (P.C.)
| | - Peechanika Chopjitt
- Faculty of Public Health, Kasetsart University Chalermphrakiat Sakon Nakhon Province Campus, Sakon Nakhon 47000, Thailand; (N.S.); (P.B.); (P.C.)
| | - Rujirat Hatrongjit
- Faculty of Science and Engineering, Kasetsart University Chalermphrakiat Sakon Nakhon Province Campus, Sakon Nakhon 47000, Thailand;
| | - Anusak Kerdsin
- Faculty of Public Health, Kasetsart University Chalermphrakiat Sakon Nakhon Province Campus, Sakon Nakhon 47000, Thailand; (N.S.); (P.B.); (P.C.)
- Correspondence: ; Tel.: +66-42-725-023
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8
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Zerrouki H, Rebiahi SA, Hadjadj L, Rolain JM, Diene SM. Real-Time PCR Assay for Rapid and Simultaneous Detection of vanA and vanB Genes in Clinical Strains. Diagnostics (Basel) 2021; 11:diagnostics11112081. [PMID: 34829428 PMCID: PMC8618848 DOI: 10.3390/diagnostics11112081] [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: 10/06/2021] [Revised: 11/02/2021] [Accepted: 11/09/2021] [Indexed: 11/29/2022] Open
Abstract
Here, we develop a robust and sensitive real-time PCR assay which allows the simultaneous detection of vanA and vanB genes using common primers. The system was designed using the Primer3 online software. The specificity of primers and probes was first checked by in silico PCR and by BlastN analysis. The genomic DNA of 255 bacterial isolates, including Enterococcus spp., Gram-negative, and Gram-positive strains, as well as a collection of 50 stool and 50 rectal swab samples, were tested to evaluate the specificity of the new real-time PCR (RT-PCR) system. The results of the designed RT-PCR were 100% specific and 100% positive on tested vancomycin resistant isolates harboring either the vanA or vanB gene. RT-PCR assays were negative for all other bacterial species tested including vancomycin-sensitive Enterococci and Enterococcus strains harboring vanC genes. The limit of detection of vanA and vanB genes by RT-PCR assay was 47 CFU/mL and 32 CFU/mL, respectively. The rapid and accurate detection of vancomycin-resistant Enterococci is the cornerstone for minimizing the risk of nosocomial transmissions and outbreaks. We believe that this assay will strengthen routine diagnostics and surveillance programs.
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Affiliation(s)
- Hanane Zerrouki
- Laboratoire de microbiologie appliquée à l’agroalimentaire, au biomédical et à l’environnement, Université de Tlemcen, Tlemcen 13000, Algeria; (H.Z.); (S.-A.R.)
- Aix-Marseille Univ., MEPHI, IRD, APHM, IHU-Méditerranée Infection, 13005 Marseille, France; (L.H.); (J.-M.R.)
| | - Sid-Ahmed Rebiahi
- Laboratoire de microbiologie appliquée à l’agroalimentaire, au biomédical et à l’environnement, Université de Tlemcen, Tlemcen 13000, Algeria; (H.Z.); (S.-A.R.)
| | - Linda Hadjadj
- Aix-Marseille Univ., MEPHI, IRD, APHM, IHU-Méditerranée Infection, 13005 Marseille, France; (L.H.); (J.-M.R.)
| | - Jean-Marc Rolain
- Aix-Marseille Univ., MEPHI, IRD, APHM, IHU-Méditerranée Infection, 13005 Marseille, France; (L.H.); (J.-M.R.)
| | - Seydina M. Diene
- Aix-Marseille Univ., MEPHI, IRD, APHM, IHU-Méditerranée Infection, 13005 Marseille, France; (L.H.); (J.-M.R.)
- Correspondence: ; Tel.: +(33)4-91-83-56-49
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9
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Coolen JPM, Jamin C, Savelkoul PHM, Rossen JWA, Wertheim HFL, Matamoros SP, van Alphen LB, On Behalf Of Sig Bioinformatics In Medical Microbiology Nl Consortium. Centre-specific bacterial pathogen typing affects infection-control decision making. Microb Genom 2021; 7. [PMID: 34356004 PMCID: PMC8549354 DOI: 10.1099/mgen.0.000612] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Whole-genome sequencing is becoming the de facto standard for bacterial outbreak surveillance and infection prevention. This is accompanied by a variety of bioinformatic tools and needs bioinformatics expertise for implementation. However, little is known about the concordance of reported outbreaks when using different bioinformatic workflows. In this multi-centre proficiency testing among 13 major Dutch healthcare-affiliated centres, bacterial whole-genome outbreak analysis was assessed. Centres who participated obtained two randomized bacterial datasets of Illumina sequences, a Klebsiella pneumoniae and a Vancomycin-resistant Enterococcus faecium, and were asked to apply their bioinformatic workflows. Centres reported back on antimicrobial resistance, multi-locus sequence typing (MLST), and outbreak clusters. The reported clusters were analysed using a method to compare landscapes of phylogenetic trees and calculating Kendall–Colijn distances. Furthermore, fasta files were analysed by state-of-the-art single nucleotide polymorphism (SNP) analysis to mitigate the differences introduced by each centre and determine standardized SNP cut-offs. Thirteen centres participated in this study. The reported outbreak clusters revealed discrepancies between centres, even when almost identical bioinformatic workflows were used. Due to stringent filtering, some centres failed to detect extended-spectrum beta-lactamase genes and MLST loci. Applying a standardized method to determine outbreak clusters on the reported de novo assemblies, did not result in uniformity of outbreak-cluster composition among centres.
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Affiliation(s)
- Jordy P M Coolen
- Department of Medical Microbiology and Radboudumc Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Casper Jamin
- Department of Medical Microbiology, Care and Public Health Research Institute (CAPHRI), Maastricht University Medical Center+, Maastricht, The Netherlands
| | - Paul H M Savelkoul
- Department of Medical Microbiology, Care and Public Health Research Institute (CAPHRI), Maastricht University Medical Center+, Maastricht, The Netherlands.,Department of Medical Microbiology & Infection Control, Amsterdam University Medical Centers, location VUmc, Amsterdam, The Netherlands
| | - John W A Rossen
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands.,Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Heiman F L Wertheim
- Department of Medical Microbiology and Radboudumc Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Sébastien P Matamoros
- Department of Medical Microbiology & Infection Control, Amsterdam University Medical Centers, location VUmc, Amsterdam, The Netherlands
| | - Lieke B van Alphen
- Department of Medical Microbiology, Care and Public Health Research Institute (CAPHRI), Maastricht University Medical Center+, Maastricht, The Netherlands
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10
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Hughes A, Sullivan SG, Marshall C. Factors associated with vanA VRE acquisition in Cardiothoracic Surgery patients during an acute outbreak. Infect Dis Health 2021; 26:258-264. [PMID: 34130941 DOI: 10.1016/j.idh.2021.05.003] [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: 02/26/2021] [Revised: 05/12/2021] [Accepted: 05/17/2021] [Indexed: 11/30/2022]
Abstract
BACKGROUND There was an acute outbreak of vanA Enterococcus faecium (VREfm) in a tertiary Melbourne teaching hospital between 2015 and 2016 amongst Cardiothoracic Surgery (CTS) ward and Intensive Care Unit (ICU) patients. Prior to this outbreak vanB VRE had been the predominate genotype encountered. METHODS A retrospective, matched (1:2), case-control study was conducted on CTS patients between 1 August 2015 and 31 May 2016 admitted to a hospital in Melbourne, during an outbreak of vanA VREfm to identify factors associated with colonisation or infection. Factors assessed included undergoing surgery and type of procedure, exposure to antibiotics and admission to ICU. RESULTS During the outbreak, 56 new cases of vanA VREfm out of 802 CTS ward patients were identified. Of these new cases, 52 were included in the case-control analysis, all identified via rectal screening. Cases had significantly longer duration of stay in hospital (p < 0.001) than controls. Multivariable analysis identified exposure to ceftriaxone as an independent factor (OR 4.14, p = 0.018) associated with new vanA VREfm isolates. Other factors such as vancomycin exposure, specific CTS procedures or ICU admission were not identified as independent factors. Ceftriaxone was being used during the outbreak as surgical prophylaxis amongst CTS patients. CONCLUSION Ceftriaxone use was associated with an increased risk of CTS patients acquiring vanA VREfm during an acute outbreak. This highlights the overall importance of antibiotic stewardship to minimise hospital-associated multi-drug resistant infections.
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Affiliation(s)
- Angus Hughes
- University of Melbourne, School of Biomedical Sciences, Parkville, VIC 3010, Australia.
| | - Sheena G Sullivan
- WHO Collaborating Centre for Reference and Research on Influenza, Royal Melbourne Hospital, and Department of Infectious Diseases, University of Melbourne, The Peter Doherty Institute for Infection and Immunity Melbourne, VIC 3000, Australia; Melbourne School of Population and Global Health, University of Melbourne, Australia
| | - Caroline Marshall
- University of Melbourne, Department of Medicine, Royal Melbourne Hospital, Parkville, VIC 3010, Australia; Infection Prevention and Surveillance Service, Royal Melbourne Hospital, Parkville, VIC 3050, Australia; NHMRC National Centre for Antimicrobial Stewardship (NCAS), The Peter Doherty Institute for Infection and Immunity Melbourne, VIC 3000, Australia
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High frequency and diversity of Vancomycin-resistant Enterococci (VRE) in Algerian healthcare settings. INFECTION GENETICS AND EVOLUTION 2021; 92:104889. [PMID: 33933632 DOI: 10.1016/j.meegid.2021.104889] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 04/17/2021] [Accepted: 04/27/2021] [Indexed: 11/23/2022]
Abstract
The spread of vancomycin-resistant Enterococci (VRE) in Algerian hospital settings is poorly reported. Since the first report in 2006, few data have been available on the molecular mechanism of this resistance across the country. In this study, we investigate the frequency and antibiotic resistance mechanisms of Enterococci strains isolated from hospitalised patients in the Tlemcen university hospital. 191 Enterococcus spp. strains were collected from various clinical samples and were identified using MALDI-TOF-MS. The presence of van genes was investigated by standard PCR and sequencing. Results revealed that E. faecium and E. faecalis strains are the main pathogens identified in the study. Antibiotic susceptibility testing revealed that the resistance rate was high for the majority of antibiotic classes, including glycopeptides, and only linezolid was effective on all strains. Molecular analysis revealed that 52.2% of strains from intensive care unit (ICU) were positive for the vanA gene, including 44.44% E. faecium, 5.55% E. faecalis and 2.22% E. avium. 25.5% of these isolates co-harboured both the vanA and vanC genes, including E. gallinarum (n = 16) and E. faecium (n = 6). In surgical wards (SW) 29.70% of strains harboured the van genes, including 4.90% of E. faecalis harbouring the vanB gene, and of the rest of strains, (24.80%) harboured the vanC genes. Indeed, 9.90% E. gallinarum and 4.90% E. faecalis were positive for vanC1 and 9.90% of E. casseliflavus were positive for the vanC2/C3 gene. The glycopeptide resistance rate was higher among strains from the ICU and was mainly composed by E. faecium strains compared with surgical wards where resistant E. faecalis strains were predominant.
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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: 4] [Impact Index Per Article: 1.3] [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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Neumann B, Bender JK, Maier BF, Wittig A, Fuchs S, Brockmann D, Semmler T, Einsele H, Kraus S, Wieler LH, Vogel U, Werner G. Comprehensive integrated NGS-based surveillance and contact-network modeling unravels transmission dynamics of vancomycin-resistant enterococci in a high-risk population within a tertiary care hospital. PLoS One 2020; 15:e0235160. [PMID: 32579600 PMCID: PMC7314025 DOI: 10.1371/journal.pone.0235160] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Accepted: 06/09/2020] [Indexed: 02/07/2023] Open
Abstract
Vancomycin-resistant E. faecium (VRE) are an important cause of nosocomial infections, which are rapidly transmitted in hospitals. To identify possible transmission routes, we applied combined genomics and contact-network modeling to retrospectively evaluate routine VRE screening data generated by the infection control program of a hemato-oncology unit. Over 1 year, a total of 111 VRE isolates from 111 patients were collected by anal swabs in a tertiary care hospital in Southern Germany. All isolated VRE were whole-genome sequenced, followed by different in-depth bioinformatics analyses including genotyping and determination of phylogenetic relations, aiming to evaluate a standardized workflow. Patient movement data were used to overlay sequencing data to infer transmission events and strain dynamics over time. A predominant clone harboring vanB and exhibiting genotype ST117/CT469 (n = 67) was identified. Our comprehensive combined analyses suggested intra-hospital spread, especially of clone ST117/CT469, despite of extensive screening, single room placement, and contact isolation. A new interactive tool to visualize these complex data was designed. Furthermore, a patient-contact network-modeling approach was developed, which indicates both the periodic import of the clone into the hospital and its spread within the hospital due to patient movements. The analyzed spread of VRE was most likely due to placement of patients in the same room prior to positivity of screening. We successfully demonstrated the added value for this combined strategy to extract well-founded knowledge from interdisciplinary data sources. The combination of patient-contact modeling and high-resolution typing unraveled the transmission dynamics within the hospital department and, additionally, a constant VRE influx over time.
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Affiliation(s)
- Bernd Neumann
- Division of Nosocomial Pathogens and Antibiotic Resistance, Robert Koch Institute, Wernigerode, Germany
- * E-mail:
| | - Jennifer K. Bender
- Division of Nosocomial Pathogens and Antibiotic Resistance, Robert Koch Institute, Wernigerode, Germany
| | - Benjamin F. Maier
- Computational Epidemiology, Robert Koch Institute, Berlin, Germany
- Department of Physics, Humboldt University of Berlin, Berlin, Germany
| | - Alice Wittig
- Computational Epidemiology, Robert Koch Institute, Berlin, Germany
- Institute for Theoretical Biology, Humboldt University of Berlin, Berlin, Germany
| | - Stephan Fuchs
- Division of Nosocomial Pathogens and Antibiotic Resistance, Robert Koch Institute, Wernigerode, Germany
| | - Dirk Brockmann
- Computational Epidemiology, Robert Koch Institute, Berlin, Germany
- Institute for Theoretical Biology, Humboldt University of Berlin, Berlin, Germany
| | | | - Hermann Einsele
- Department of Internal Medicine II, University Hospital Würzburg, Wüzburg, Germany
| | - Sabrina Kraus
- Department of Internal Medicine II, University Hospital Würzburg, Wüzburg, Germany
| | | | - Ulrich Vogel
- Institute for Hygiene and Microbiology, Julius-Maximilians University Würzburg, Würzburg, Germany
| | - Guido Werner
- Division of Nosocomial Pathogens and Antibiotic Resistance, Robert Koch Institute, Wernigerode, Germany
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