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The development of a national surveillance system for hospital-acquired infections in Denmark the Hospital Acquired Infections Database - HAIBA Sophie Gubbels MD MSc Department of Infectious Disease Epidemiology Statens Serum Institut Artillerivej 5 2300 Copenhagen S Denmark PhD thesis University of Copenhagen Denmark 2016 Supervisors Kåre Mølbak, Associate professor, MD DMSc Department of Infectious Disease Epidemiology Statens Serum Institut, Copenhagen, Denmark Brian Kristensen MD PhD Department of Microbiology Surveillance and Research Statens Serum Institut, Copenhagen, Denmark Marianne Voldstedlund MD PhD Department of Infectious Disease Epidemiology Statens Serum Institut, Copenhagen, Denmark Assessment committee Thomas Benfield, Professor, MD DMSc (Chairperson) Department of Clinical Medicine University of Copenhagen, Denmark Mette Nørgaard, Associate professor, MD PhD Department of Clinical Epidemiology, Institute of Clinical Medicine Aarhus University Hospital, Denmark Marc J.M. Bonten, Professor, MD PhD Department of Medical Microbiology, University Medical Center Utrecht, the Netherlands Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, the Netherlands This thesis has been submitted to the Graduate School of The Faculty of Health and Medical Sciences, University of Copenhagen on 9 August 2016. Defence date and venue: 27 January 2017 at the Lecture Hall, Statens Serum Institut, Artillerivej 5, Copenhagen, Denmark Cover: Hand hygiene, by Oliver Gubbels-Khalifé Printed in Denmark ISBN 978-87-999602-0-0 Preface It is an honour to have had the chance to be part of the fascinating journey of building the Danish Hospital Acquired Infections Database (HAIBA). The fact that every person in Denmark has a personal identification number (CPR-number), which is registered everywhere – from the general practitioner, to the tax services, the bank account, the telephone contract and the library – can be quite a shock for persons coming from other countries. Indeed, I had to get used to giving out my number so often. Somehow, it brought me a certain apprehension and fear for misuse of the data. However, I got to know the Danish society as one where trust is a very highly cherished value – although challenged sometimes – and through my work at the Statens Serum Institut I have had the chance to experience the benefits and possibilities this systematic registration can bring. HAIBA is the perfect example of this. It is the first surveillance system for HAI, which is countrywide and requires no additional data entry from any physician, infection control specialist or microbiologist. Building HAIBA required a set of skills, which branched over a wide range of areas of expertise – epidemiologists, statisticians, microbiologists, infection control nurses, clinical specialists, software developers, it-architects, lawyers, politicians and managers – each with their own jargon and expectations. We all had to try to understand each other and build a system that was optimal for each of us. Communication was the key word. The fact that I did not speak sufficient Danish at the beginning of the project did not make it easier! It has been a great pleasure to work with so many motivated and knowledgeable persons over the years. In the first place, I would like to thank the HAIBA group that worked on the development and now on the maintenance of HAIBA on a daily basis. My principal supervisor Kåre Mølbak for being such an inspiration and for all the support; from the overall visions and strategies to the tiniest technical details, from scientific questions to administrative issues. Your door is always open. Brian Kristensen and Marianne Voldstedlund, thank you for giving me more insight in microbiology. It is not an easy field to catch in computer algorithms that leave no space for human interpretations. Thanks to Jens Nielsen for the great collaboration on the coding of the algorithms. While making so many drawings to make sure that we really captured all situations we possibly could think of, we often had heated discussions, but these always led to an even better result. Kenn Schultz Nielsen, your optimism, even when we face big challenges is phenomenal. Your understanding of surveillance and epidemiology, while also having great insight in IT-architecture provided that bridge between what was needed from a surveillance point of view and the best IT- solutions to get there. Manon Chaine, you started with us as a master student and made yourself indispensable by teaching yourself how to develop the output of HAIBA that is now online. You also did very important work on the development of the case definition for Clostridium difficile. Søren Jakobsen, it was pleasure working with you on the project management of HAIBA and discussing different strategies, risk assessments and road maps. Orla Condell, Laura Espenhain, Silvia Funke, Lara Ricotta, Victoria Fernandez de Casadevante and Jonas Kähler, you have strengthened the team at different points in time to assist in validation studies, bringing new ideas and looking at issues from different angles. The work of HAIBA would, however, not have been possible, had we not had support from many other persons. I will attempt to mention those that were involved since the start in 2011. During the proof of concept period and the early development of HAIBA Lars Steen Anker, Marlene Haahr and Bodil Bjerg were instrumental. The National Center for Infection Control has given us valuable advice regarding the point prevalence surveys and infection control: Christian Stab Jensen, Elsebeth Tvenstrup Jensen and Jette Holt. In addition, colleagues from the Department of Infectious Disease Epidemiology have supported in many ways: Henrik Bang, Michael Galle, Louise Køhler Olsen, Sofie Holtemann. Others from around the institute shared their valuable experiences with us, particularly Jakob Sandegaard, Nete Nielsen, Katharina Olsen, Mette Fogh Ho-Lanng, Anni Buhr and Camilla Wiberg Danielsen. The Advisory Forum provided the important link to the regions and kept us sharp with their valuable feedback: Preben Ditlev Cramon, Svend Ellermann-Eriksen, Jørgen H. Engberg, Morten Freundlich, Henrik Friis, Ulrik Gerdes, Annemarie Hellebek, Anette Holm, Elin Kallestrup, Jan Koldbro, Gitte Køtter, Annmarie Lassen, Jesper Laustsen, Bettina Lundgren, Elin Lyngsø, Jens Kjølseth Møller, Henrik C. Schønheyder, Jens Kjær Rasmussen, Jan Utzon and Christian Østergaard. Also others in the regions have played important roles in the development, validation and implementation of HAIBA: Leif Percival Andersen, Jacob Anhøj, Magnus Arpi, Jonas Rosendal Bager-Elsborg, Paul Daniels Bartels, Lisbeth Kyndi Bergen, María Kristín Björnsdóttir, Ram Dessau, Trine Frederiksen, Per Gundtoft, Kim Oren Gradel, Hans Peder Graversen, Dennis Schrøder Hansen, Anne-Marie Sigsgaard Hansen, Anne-Marie Blok Hellesøe, Ole Heltberg, Jens Otto Jarløv, Thøger Gorm Jensen, Jette Nygaard Jensen, Christoffer Calov Jørgensen, Henrik Kehlet, Poul Kjældgaard, Nina Kling, Jenny Dahl Knudsen, Søren From Knudsen, Annabel Lee Krarup, Jeppe Lange, Lars Lemming, Rita Andersen Leth, Martin Lindbergs-Larsen, Niels Frimodt Møller, Helle Neustrup, Bente Olesen, Kirsten Pedersen, Lasse Pirk, Arne Poulstrup, Steen Rasmussen, Jakob Redder, Thor Schmidt, Lars M. Storm and Lea Toftegaard Weisdorf. In addition, Christina Vandenbroucke-Grauls from the VU University Medical Center in Amsterdam provided useful perspectives in an early stage of the development of the case definitions and always followed the development with interest. Several committees supported the coordination of HAIBA. The steering committee that oversaw the development of HAIBA: Bodil Bjerg, Søren Brostrøm, Birgitte Drewes, Frederik Gerstoft, Mette Grønholt Harbo, Helle Engslund Krarup, Asja Kunøe, Jesper Myrup, Lisbeth Nielsen, Lars Villiam Pallesen, John Erik Pedersen and Tove Rønne. The internal steering committee that secured collaboration at Statens Serum Institut during the development: Birgitte Drewes, Elsebeth Tvenstrup Jensen, Maria Friis Larsen, Lars Villiam Pallesen, Robert Leo Skov and Heidi Søltoft. The current coordination group for the production system: Anders Brahm, Dorte Vesterholm Lind, Karen Marie Lyng, Jan Poulsen, Vahid Raben, Jean Rygaard and Flemming Per Voss. For legal and political clarifications, we have had advice from Martin Bagger Brandt, Sara Fini, Ole Jensen, Pia Jespersen, Tyra Grove Krause, Anja Sofie Nielsen, Marie-Louise Paludan, Tove Rønne, and Erika Wolf. For technical support to different aspects, both IT-development of management of IT- systems, many persons were and still are involved: Judy Eskildsen, Milan Fajber, Mark Hanger, Henrik Mulvad Hansen, Lars Rylander Holm, Stine Holm, Jens Hvidberg, Anders Jensen, Steen Eide Joensen, Dorte Vesterholm Lind, Thomas Tjørnelund Nielsen, Charlotte Nobel, Lise Kristine Højsgaard Schmidt, Peter Spanggaard and Erik Villadsen. I would like to thank all my colleagues from the Department of Infectious Disease Epidemiology, for being such a positive and inspiring group of people. Special thanks to Tyra Grove Krause for advice and support and to Katrin Gaardbo Kuhn, who became a dear friend. Of course, I would also like to thank my family for their support. My mother for her interest in my work and for travelling to Denmark, whenever we needed help. Jade, thank you for all your encouragement. With your knowledge of hospital performance and quality indicators and my experiences with HAIBA, we had some very interesting
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  • Kocuria Spp. in Foods: Biotechnological Uses and Risks for Food Safety

    Kocuria Spp. in Foods: Biotechnological Uses and Risks for Food Safety

    Review Article APPLIED FOOD BIOTECHNOLOGY, 2021, 8 (2):79-88 pISSN: 2345-5357 Journal homepage: www.journals.sbmu.ac.ir/afb eISSN: 2423-4214 Kocuria spp. in Foods: Biotechnological Uses and Risks for Food Safety Gustavo Luis de Paiva Anciens Ramos1, Hilana Ceotto Vigoder2, Janaina dos Santos Nascimento2* 1- Department of Bromatology, Universidade Federal Fluminense (UFF), Brazil. 2- Department of Microbiology, Instituto Federal de Educação, Ciência e Tecnologia do Rio de Janeiro (IFRJ), Brazil. Article Information Abstract Article history: Background and Objective: Bacteria of the Genus Kocuria are found in several Received 4 June 2020 environments and their isolation from foods has recently increased due to more Revised 17 Aug 2020 precise identification protocols using molecular and instrumental techniques. This Accepted 30 Sep 2020 review describes biotechnological properties and food-linked aspects of these bacteria, which are closely associated with clinical cases. Keywords: ▪ Kocuria spp. Results and Conclusion: Kocuria spp. are capable of production of various enzymes, ▪ Gram-positive cocci being potentially used in environmental treatment processes and clinics and ▪ Biotechnological potential production of antimicrobial substances. Furthermore, these bacteria show desirable ▪ Biofilm enzymatic activities in foods such as production of catalases and proteases. Beneficial ▪ Antimicrobial resistance interactions with other microorganisms have been reported on increased production of enzymes and volatile compounds in foods. However, there are concerns about the *Corresponding author: Janaina dos Santos Nascimento, bacteria, including their biofilm production, which generates technological and safety Department of Microbiology, problems. The bacterial resistance to antimicrobials is another concern since isolates Instituto Federal de Educação, of this genus are often resistant or multi-resistant to antimicrobials, which increases Ciência e Tecnologia do Rio de the risk of gene transfer to pathogens of foods.