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Determinants of Listeria Monocytogenes Stress Responses Department of Food Hygiene and Environmental Health Faculty of Veterinary Medicine University of Helsinki Helsinki DETERMINANTS OF LISTERIA MONOCYTOGENES STRESS RESPONSES Anna Pöntinen ACADEMIC DISSERTATION To be presented, with the permission of the Faculty of Veterinary Medicine of the University of Helsinki, for public examination in Auditorium 6, Metsätalo building, Unioninkatu 40, Helsinki, on 14 June 2019, at 12 noon. Helsinki 2019 Supervising Professor Miia Lindström, DVM, Ph.D. Professor Department of Food Hygiene and Environmental Health Faculty of Veterinary Medicine University of Helsinki Helsinki, Finland Supervisors Professor emeritus Hannu Korkeala, DVM, Ph.D., M.Soc.Sc. Department of Food Hygiene and Environmental Health Faculty of Veterinary Medicine University of Helsinki Helsinki, Finland Professor Miia Lindström, DVM, Ph.D. Department of Food Hygiene and Environmental Health Faculty of Veterinary Medicine University of Helsinki Helsinki, Finland Reviewed by Professor Wilhelm Tham, DVM, Ph.D. School of Hospitality, Culinary Arts and Meal Science Örebro University Örebro, Sweden Professor José Vázquez-Boland, DVM, Ph.D. Infection Medicine Edinburgh Medical School University of Edinburgh Edinburgh, United Kingdom Opponent Professor emeritus Atte von Wright, M.Sc., Ph.D. Institute of Public Health and Clinical Nutrition University of Eastern Finland Kuopio, Finland ISBN 978-951-51-5292-3 (paperback) ISBN 978-951-51-5293-0 (PDF) http://ethesis.helsinki.fi Unigrafia Helsinki 2019 ABSTRACT Listeria monocytogenes is a remarkable bacterium, as it is able to shift from a capable environmental saprophyte into a severe intracellular pathogen. As a strictly foodborne pathogen, L. monocytogenes poses a notable risk, particularly to those consumers among the risk groups for whom invasive listeriosis is potentially fatal. Furthermore, modern consumption habits and increasingly favoured ready-to-eat foods, often consumed without proper heating, increase the risk of acquiring the foodborne disease. The aim of this study was to investigate the genetic mechanisms conferring wide-ranging stress tolerance in L. monocytogenes. Two-component systems, comprising a sensor histidine kinase and a cognate response regulator, aid bacteria in sensing and adapting to changes in both surrounding environmental as well as intracellular conditions. The histidine kinases, in particular, have lacked comprehensive studies on their roles in the stress tolerance of L. monocytogenes. Thus, histidine kinases were studied by expressional analyses under cold conditions and by mutationally disrupting each histidine kinase-encoding gene in a parental model strain, L. monocytogenes EGD-e. The modified strains were individually challenged at high (42.5 qC) and low (3.0 qC) temperatures, high (9.4) and low (5.6) pH levels, and high salt (6% NaCl), ethanol (3.5 vol%) and hydrogen peroxide (5 mM) concentrations. Expressional studies and growth experiments on genetically modified strains proved lisK and yycG to respectively play central roles in the acclimation and immediate growth of L. monocytogenes at low temperatures. The most substantial increase in gene expression under cold conditions was that of the chemotaxis gene cheY with 236-fold upregulation at 3 qC. The disrupted ΔliaS strain displayed impaired growth in response to all the other stresses, particularly at a high temperature and under osmotic stress. These studies demonstrated the prominent importance of the histidine kinase-encoding genes yycG and lisK to cold tolerance and liaS, with roles in the growth of L. monocytogenes under multiple stresses. To shed light on the accessory genetic mechanisms that cause large strain variation in L. monocytogenes in withstanding heat treatments, heat resistance-conferring traits were further investigated by means of whole- genome sequencing. Comparing the complete genomes of heat-resistant L. monocytogenes AT3E and -sensitive AL4E strains revealed the heat- resistant strain to harbour a novel 58-kb plasmid, pLM58, which was absent in the sensitive strain. Furthermore, curing of the plasmid in AT3E produced a marked decrease in heat resistance from virtually no reduction to a 1.1 cfu/ml log10 reduction at 55.0 qC. In pLM58, a 2,155-bp open reading frame annotated as an ATP-dependent ClpL protease-encoding gene was identified. Conjugation of the coding sequence and the putative promoter of the clpL 3 gene into a natively heat-sensitive L. monocytogenes 10403S strain, in turn, enhanced the survival of the strain from a 1.2 cfu/ml log10 reduction to a 0.4 cfu/ml log10 reduction in heat challenge at 55.0 qC. In this study, we presented the first evidence of plasmid-mediated heat resistance in L. monocytogenes and identified the protease ClpL to be a novel plasmid- borne heat-resistance mediator. The emerging resistance of L. monocytogenes to benzalkonium chloride, a quaternary ammonium compound widely used as a detergent in food- processing facilities, is a significant concern for food safety and public health. The resistance of 392 L. monocytogenes isolates from Finland (n = 197) and Switzerland (n = 195) to benzalkonium chloride was assessed. A minimal inhibitory concentration of 20 μg/ml was defined. Altogether, 11.5% of the strains proved to be resistant to benzalkonium chloride. Serotype 1/2c harboured the highest prevalence, 32.4% (11/34), of benzalkonium chloride- resistant strains, while in total, most of the resistant strains belonged to serotype 1/2a. Altogether, 68.9% of the resistant strains harboured at least one of the efflux pump system-encoding genes, bcrABC, emrE or qacH, known to confer benzalkonium chloride resistance in L. monocytogenes. We found resistant strains with partially or completely efflux pump-dependent benzalkonium chloride resistance, with the exception of the known resistance-mediating efflux pumps, suggesting the existence of other resistance-contributing efflux pump systems. The lacking of known efflux pump system-encoding genes in addition to efflux pump-independent benzalkonium chloride resistance, in turn, indicates the contribution of completely novel benzalkonium chloride resistance mechanisms. The aim of these studies was to shed light on the genes contributing to the versatile stress tolerance abilities and strain variation of the severe foodborne pathogen, L. monocytogenes. Knowledge of such traits may aid in developing targeted strategies and measures to identify and control the contamination and risks caused, in particular, by stress-tolerant L. monocytogenes strains. 4 ACKNOWLEDGEMENTS This thesis study was conducted at the Department of Food Hygiene and Environmental Health of the Faculty of Veterinary Medicine, University of Helsinki. The Doctoral Programme in Food Chain and Health, the Finnish Ministry of Agriculture and Forestry, the Finnish Veterinary Foundation, the Finnish Foundation of Veterinary Research and the Walter Ehrström Foundation are gratefully acknowledged for their financial support. Professor Miia Lindström and Professor emeritus Hannu Korkeala are warmly acknowledged for their insightful supervision of this thesis. Professors Wilhelm Tham and José Vázquez-Boland are gratefully appreciated for reviewing this thesis in such an expert and prompt manner and Dr Roy Siddall for carefully revising the English language. I wish to equally acknowledge each person at the department for making our study groups a wonderful scientific community. Some of you I must salute one by one, as I am forever in your debt: Many thanks to Annukka Markkula and Mirjami Mattila, who both taught me how to survive in the lab and whose door and email were always open for my questions. My all-time officemates, Mariella Aalto-Araneda, Hanna Castro, Marita Isokallio, Noora Salin and Katja Selby, I sincerely thank for all the support and invigorating conversations. Jari Aho, Anneli Luoti, Henna Niinivirta, Erika Pitkänen, Anu Seppänen and Heimo Tasanen are appreciated for their indispensable work in the lab, and also Hanna Korpunen for the great seminars and origami. I dedicate special thanks to Kirsi Ristkari for efficiently completing the nearly inhuman pipetting sessions and to Esa Penttinen for constantly showing responsibility and initiative far beyond his duties. Johanna Laine deserves praise for around-the-clock assistance with bureaucracy. Mariella Aalto-Araneda, Claudia Guldimann, Annukka Markkula, Anja Meier, Mikael Skurnik and Taurai Tasara are thanked for fruitful co- authoring. Mirko Rossi is acknowledged for all the help in genome analyses, Panu Somervuo for solving many of the mathematical oddities and Per Johansson for sharing his vast knowledge, regardless of the subject. I am truly grateful to have known wonderful mates throughout these years. Mariella, not only a colleague but also a friend: thank you. My training companion Johanna, cheers for ushering me on a run when I needed it the most. My precious friend Heidi, without you I simply could not operate. Darlings Kati-Maria and Adrian, thank you for all the support and all the late nights and early mornings around endless cups of gin and the Finest English Breakfast Tea. Le temps détruit tout – sauf l’amitié. Finally, I warmly thank my endearingly bizarre family for always supporting me in my obstinate choices. And Dad, for giving me a bit of your perseverance and all of your time, this is for you. 5 CONTENTS ABSTRACT ........................................................................................................ 3 ACKNOWLEDGEMENTS..................................................................................
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