VRE-crossword, horizontal or vertical? Transmission of vancomycin-resistant Enterococcus faecium in Dutch hospitals.
Projectomschrijving
Antibioticaresistentie aanpakken door toegankelijker maken van bestaande genetische data van resistente bacteriën
De darmbacterie Enterococcus faecium is van nature aanwezig in de darmen van mens en dier en heeft zich ontwikkeld tot een antibiotica-resistente bacterie verantwoordelijk voor ziekenhuisinfecties. Sinds 2012 zijn er in Nederlandse ziekenhuizen 87 uitbraken gerapporteerd geweest met deze bacterie.
Recent hebben onderzoekers in het UMC Utrecht de complete genetische samenstelling van deze bacteriën, die zijn verzameld tijdens ziekenhuisuitbraken, in kaart gebracht. In dit project worden deze genetische gegevens inzichtelijker en bruikbaarder gemaakt voor verder onderzoek naar de verspreiding van deze resistente bacterie in Nederlandse ziekenhuizen. Daarvoor zal o.a. een online app worden ontwikkeld om ziekenhuis uitbraken sneller en beter in kaart te brengen. Dit zal niet alleen het inzicht in de verspreiding van resistentie vergroten maar ook bijdragen aan de bestrijding.
Producten
Auteur: Victoria Pascal Andreu, Janetta Top, Rob Willems, Anita Schurch
Auteur: Anita Schurch
Link: https://eacademy.escmid.org/escmid/2022/escmid-course/366575/faculty.presenters.moving.beyond.single.species.outbreaks.the.role.of.mobile.html?f=listing%3D0%2Abrowseby%3D8%2Asortby%3D1%2Ac_id%3D366575
Auteur: A. Schurch
Link: https://www.scientificspringmeeting.nl/programme/
Auteur: Victoria Pascal Andreu, Janetta Top, Rob Willems and Anita Schurch
Link: https://ice6.org/
Auteur: Anita Schurch
Link: https://uit.no/research/amrbridge
Auteur: Victoria Pascal Andreu, Janetta Top, Rob Willems, Anita Schurch
Link: https://www.escmid.org/dates-events/escmid-conferences/immem-xiii
Auteur: Anita Schurch
Auteur: S. Arredondo-Alonso, J. Top, J. Corander, R. Willems, A. Schürch
Magazine: Genome Medicine
Begin- en eindpagina:
Auteur: Julian A. Paganini, Jesse J. Kerkvliet?, Lisa Vader?, Nienke L. Plantinga?, Rodrigo Meneses?, Jukka Corander?, Rob J. L. Willems?, Sergio Arredondo-Alonso? and Anita C. Schürch
Magazine: Microbial Genomics
Link: https://doi.org/10.1099/mgen.0.001193
Auteur: Sergio Arredondo-Alonso,corresponding author Rebecca A Gladstone, Anna K Pöntinen, João A Gama, Anita C Schürch, Val F Lanza, Pål Jarle Johnsen, Ørjan Samuelsen, Gerry Tonkin-Hill, and Jukka Corander
Magazine: NAR Genom Bioinform
Verslagen
Samenvatting van de aanvraag
Vancomycin-resistant Enterococcus faecium (VRE) are causative agents of health-care-associated infections and are of growing concern worldwide. Since 2012, 87 outbreaks of VRE have been reported in hospitals in the Netherlands. Between 2012 and 2016, 47 laboratories and hospitals submitted, on a voluntary basis, VRE isolates to the UMC Utrecht for typing. In total, 46% of these isolates contained the vanA gene cluster which is typically located on plasmids, and 54% contained the vanB gene cluster according to the NethMap report 2018 [1]. A total of 730 isolates of this collection has been whole-genome sequenced in the context of a population genomics study. For the same study, two different research software applications have been generated. In the project proposed here, we aim to curate the previously generated genomics data by improving the metadata annotation in the ENA database. We will apply FAIR principles also to the research software which are the basis for the desktop analysis by applying the five recommendations for FAIR software. These FAIR data sets will be used to get fine-grained insight into the molecular epidemiology of vancomycin-resistant clones and resistance genes in Dutch hospitals. In addition, we will develop a user-friendly web-based application on the basis of existing genome sequence data and the previously developed research softwares in collaboration with Medical Molecular Microbiologists from clinical laboratories and infectious disease specialists. The newly developed application can be used to rapidly judge whether the emergence of VRE in a particular hospital or in regional networks of hospitals is the result of clonal (vertical) spread or horizontal gene transfer, e.g. by the exchange of plasmids containing vancomycin-resistance genes. This will inform infection control measures for VRE and will allow generating more knowledge on acquisition and transmission of vancomycin resistance.