Current Topics in Microbiology and Immunology

Volume 431

Series Editors Rafi Ahmed School of , Rollins Research Center, Emory University, Atlanta, GA, USA Shizuo Akira Immunology Frontier Research Center, Osaka University, Suita, Osaka, Japan Klaus Aktories Faculty of Medicine, Institute of Experimental and Clinical Pharmacology and Toxicology, University of Freiburg, Freiburg, Baden-Württemberg, Arturo Casadevall W. Harry Feinstone Department of Molecular Microbiology & Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA Richard W. Compans Department of Microbiology and Immunology, Emory University, Atlanta, GA, USA Jorge E. Galan Boyer Ctr. for Molecular Medicine, School of Medicine, Yale University, New Haven, CT, USA Adolfo Garcia-Sastre Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA Bernard Malissen Parc Scientifique de Luminy, Centre d‘Immunologie de Marseille-Luminy, Marseille, France Rino Rappuoli GSK Vaccines, Siena, Italy The review series Current Topics in Microbiology and Immunology provides a synthesis of the latest research findings in the areas of molecular immunology, bacteriology and virology. Each timely volume contains a wealth of information on the featured subject. This review series is designed to provide access to up-to-date, often previously unpublished information. 2019 Impact Factor: 3.095., 5-Year Impact Factor: 3.895 2019 Eigenfaktor Score: 0.00081, Article Influence Score: 1.363 2019 Cite Score: 6.0, SNIP: 1.023, h5-Index: 43

More information about this series at http://www.springer.com/series/82 Steffen Backert Editor

Fighting Campylobacter Infections Towards a One Health Approach

Responsible Series Editor: Shizuo Akira

123 Editor Steffen Backert Division of Microbiology Department of Biology University of Erlangen-Nuremberg Erlangen, Germany

ISSN 0070-217X ISSN 2196-9965 (electronic) Current Topics in Microbiology and Immunology ISBN 978-3-030-65480-1 ISBN 978-3-030-65481-8 (eBook) https://doi.org/10.1007/978-3-030-65481-8

© The Editor(s) (if applicable) and The Author(s), under exclusive license to Springer Nature Switzerland AG 2021, corrected publication 2021 Chapters “Population Biology and Comparative Genomics of Campylobacter Species” and “Natural Competence and Horizontal Gene Transfer in Campylobacter” are licensed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/). For further details see license information in the chapter. This work is subject to copyright. All rights are solely and exclusively licensed by the Publisher, whether the whole or part of the material is concerned, specifically the rights of translation, reprinting, reuse of illustrations, recitation, broadcasting, reproduction on microfilms or in any other physical way, and transmission or information storage and retrieval, electronic adaptation, computer software, or by similar or dissimilar methodology now known or hereafter developed. The use of general descriptive names, registered names, trademarks, service marks, etc. in this publi- cation does not imply, even in the absence of a specific statement, that such names are exempt from the relevant protective laws and regulations and therefore free for general use. The publisher, the authors and the editors are safe to assume that the advice and information in this book are believed to be true and accurate at the date of publication. Neither the publisher nor the authors or the editors give a warranty, expressed or implied, with respect to the material contained herein or for any errors or omissions that may have been made. The publisher remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

This Springer imprint is published by the registered company Springer Nature Switzerland AG The registered company address is: Gewerbestrasse 11, 6330 Cham, Switzerland Foreword

A Very Personal Foreword: Campylobacter, My First Love in Microbiology

I feel very much honored to be contacted by Steffen Backert for providing a foreword for the Current Topics in Microbiology and Immunology (CTMI) book on Fighting Campylobacter Infections: Towards a One Health Approach that he has edited. After having worked in Campylobacter research area for several decades, I was very impressed by the extraordinary list of chapters and the great collection of internationally recognized experts who contributed to this volume. As a matter of fact, writing the foreword offered to me a perfect opportunity to study the whole book. Thus, I am very happy to write this in a very personal way. In the long history of the Campylobacter research, the pathogenicity of these remarkable bacteria was gradually enlightened. In a first description more than 134 years ago, the German medical doctor and bacteriologist Theodor Escherich described “Vibrio-like” microbes in the colonic mucus of children (Escherich 1886), a study that was not recognized by the international community until 1985 (Kist 1986a). In these early days, Theodor Escherich was working as a pediatrician at a children’s hospital in , where he had seen 72 infants with diarrhea ( infantum) during the summer of 1885. Seventeen of them died from the disease, and in the postmortem examination, Theodor Escherich microscopically detected “Vibrio-like” microbes in the colonic mucosa of 15 infants. He was not able to grow the bacteria under laboratory conditions, but made drawings and described their morphology in detail. The drawings and description clearly fit with Campylobacter bacteria (Kist 1986a). About 45 years after this first report by Theodor Escherich, bacteria isolated from the intestines of sick calves and pigs were named Vibrio jejuni (Jones et al. 1931) and Vibrio coli (Doyle 1944), respectively. In addition, these bacteria were detected in ox bile blood-cultures as a “Vibrio of bovine origin”, when a gastroenteritis outbreak was investigated in a correctional institution of the USA (Levy 1946). “Related Vibrio” species were also discovered elsewhere in patients with diarrheal disease (King 1957). Later, these

v vi Foreword

“related Vibrio-like” microbes, probably all corresponding to and Campylobacter coli as we know them today, were included in the new genus Campylobacter (Sebald and Véron 1963). Subsequently, firstly in 1968, Campylobacter spp. could be isolated and grown from human diarrheal stools (Cooper and Slee 1971; Dekeyser et al. 1972). The development of improved culturing methods in laboratories facilitated the successful isolation and growth of these bacteria from human stool samples, which was the prerequisite that C. jejuni or C. coli could be confirmed as human enteric pathogens (Skirrow 1977). Indeed, C. jejuni and C. coli are extremely fascinating, highly successful, myste- rious and also quite challenging organisms. They are elegantly coiled when they are young and becoming more coccoid in aging stages, a bit like some of us. And yes, Campylobacter was actually my first love in microbiology. And so, for me, this was the beginning of a “love story.” At the time when Martin Skirrow’s communication “Campylobacter enteritis – a new disease” (Skirrow 1977) appeared, I started as a young medical doctor and to my knowledge firstly in Germany implementing cultural and biochemical methods for detection and identification of Campylobacter from stool specimens in our diagnostic laboratory at the Institute of Hygiene and Microbiology at Freiburg University. And in order to prepare a dissertation for a professorship, I launched at the end of 1970 a comprehensive study on incidence, clinics and epidemiological risk factors of infectious enteritis, which covered all causative agents known at that time, including also Campylobacter. In this study, we investigated more than 17,000 patients with diarrhea, and in 945 cases (5.3%) Campylobacter ssp. were isolated from stool specimens (Kist 1986b). In a multivariate analysis, fever and bloody– watery diarrhea were shown as significant clinical symptoms due to Campylobacter infection, with bloody diarrhea more common in younger age-groups and pre- dominantly watery diarrhea in older age-groups. Vomiting, however, was not a typical symptom. Follow-up of the above-mentioned 945 cases revealed the development of a total of three patients with neurological complications, namely two Guillain–Barré syndromes and one Miller Fisher syndrome (Kist 1986b). How I, as the first German microbiologist in this field, got access to the inter- national “Campylobacter community” was then due to a fortunate accident. In 1980 at a meeting of the “Austrian Society for Hygiene, Microbiology and Preventive Medicine,” which took place in Klosterneuburg, a historic monastery nearby , I presented my first Campylobacter-related results of the above study, and I finished my talk with the conclusions “the typical campylobacteriosis patient is a young boy, growing up in a rural area, who drinks raw milk, and likes eating chicken and swimming in natural surface waters.” My presentation was the last before lunch, and some people involved me into a discussion after the end of the session. And nobody got aware that the doors were locked and we were trapped in this wonderful ancient lecture room. So we missed the lunch, but I got in contact with a colleague from the British Public Health Laboratory Service (PHLS). We had a highly stimulating conversation with the result that I was invited to the very first International Workshop on Campylobacter, which took place in Reading, England, in 1981. At that opportunity, I was lucky again because I met there the Foreword vii most prominent protagonists of modern campylobacteriology at that time, namely Jean-Paul Butzler, Martin Skirrow, Hermy Lior, and furthermore Diane Newell, Martin Blaser, Roger Feldman, and later Francis Megraud. Over the years, we became friends and the ties of friendship hold up to now. Already in 1968, Jean-Paul Butzler in collaboration with Paul Joseph Dekeyser had succeeded in Brussels as the first in culturing Campylobacter from a stool specimen of a 20-year-old female (Dekeyser et al. 1972). This prompted Jean-Paul Butzler in the early 1970 to a systematic study at the St. Pierre University in Brussels, where C. jejuni and C. coli were isolated from 5.3% of 3,800 diarrheic stool samples (Butzler 1974). Jean-Paul Butzler published this study in his Ph.D. thesis in Flemish language, but nevertheless it came to the attention of Martin Skirrow in England, who contacted Jean-Paul Butzler in 1976 by phone. This was the beginning of a long-lasting and fruitful collaboration as well as friendship between these head- liners in campylobacteriology. It was highly exciting to me to learn how much further the Campylobacter field developed in recent years. The current volume comprehensively discusses our modern knowledge of research in Campylobacter–human interactions, the natural reservoirs, infection routes and envisaged intervention strategies. Chapter “Human Campylobacteriosis—A Serious Infectious Threat in a One Health Perspective” by Stefan Bereswill and co-workers highlights Campylobacters as the major cause of foodborne bacterial gastroenteritis worldwide, eventually also affecting other organs such as the nervous system and joints, associated with enormous costs in the societies. They also emphasize the urgent need for the so-called One World—One Health concept requiring the combined endeavors of public health authorities, clinicians, veterinarians and basic researchers to better manage the burden of this zoonotic disease in the future. As next, Roswitha Merle reviews the surveillance instruments of Campylobacter infections in humans as well as important control strategies including multiple risk assessment tools. In Chapter “Population Biology and Comparative Genomics of Campylobacter Species”, Torsten Semmler and co-authors discuss the population biology and comparative genomics of various Campylobacter species, including C. jejuni, C. coli, C. upsaliensis, C. concisus and C. lari. They provide an excellent overview of the current technologies like whole-genome sequencing that allow the fast and efficient completion of entire Campylobacter genomes. These approaches lead to the identification of specific genomic features and their proposed impact on host adaptation by Campylobacter spp. The overall management schemes for prevention of Campylobacter infections through the poultry food chain are then comprehensively discussed by Thomas Alter and Felix Reich. In Chapter “Emission Sources of Campylobacter from Agricultural Farms, Impact on Environmental Contamination and Intervention Strategies”, Vanessa Szott and Anika Friese nicely illuminate the emission sources of Campylobacter spp. from agricultural farms, their impact on contamination of the environment and associated intervention measures. In this regard, Sophie Kittler discusses an elegant approach using bacteriophages to reduce Campylobacter loads in poultry. This article focuses on the exciting option as to how certain bacteriophages can be used in practice and discusses the legal biosafety viii Foreword regulations for approval of corresponding treatment schemes in the food industry, which may assist in resolving campylobacteriosis cases in humans. In the following chapter, Nicole Tegtmeyer and Steffen Backert review the molecular virulence properties of C. jejuni. They highlight the known factors and various pathogenicity- linked determinants comprising bacterial motility, chemotaxis, cellular binding, host cell entry, intracellular survival and transmigration into deeper tissues and even other organs, which are discussed in detail. Furthermore, Jörg-Dieter Schulzke and Roland Bücker update us on the diarrheal mechanisms and the role of intestinal barrier dysfunction triggered by Campylobacter infection. In Chapter “Murine Models for the Investigation of Colonization Resistance and Innate Immune Responses in Campylobacter Jejuni Infections”, Markus Heimesaat and colleagues review the various mouse models of C. jejuni infection and the role of the microbiota in this context. They highlight the current validation and standardization procedures in the murine infection model systems, which may provide the basis for future development of more innovative treatment and prevention strategies of C. jejuni infection. In addition, Julia Golz and Kerstin Stingl review the funda- mental concepts of natural transformation and horizontal gene transfer events by Campylobacter spp., which clearly contribute to genome diversity and the spread of antibiotic resistances in the bacteria, which is an enormous problem of the healthcare systems in combating many infectious diseases. Finally, the group of Greta Gölz gives an excellent update of our current knowledge on the molecular mechanisms of biofilm formation and quorum sensing by Campylobacter spp., which are important features that may help the bacteria to survive inside the natural environment. In summary, the book updated me greatly on Campylobacter and provided me with many new ideas. For example, after reading, I saw the previous concepts in a new perspective and also learnt a lot about the most recent developments in the Campylobacter area. The book gave me important new advice where research in the field is standing at this time and in what directions the journey might take us in near future. Together, I highly recommend this book to advanced undergraduates, graduate students, postdocs, medical doctors and other investigators, who are interested in infection biology and zoonoses research.

Freiburg im Breisgau, Germany Manfred Kist October 2020 Foreword ix

References

Butzler JP (1974) Campylobacter, an unrecognized enteropathogen. Ph.D. thesis. Free University of Brussels, Brussels, Belgium (in Flemish). Cooper IA, Slee KJ (1971) Human infection by Vibrio fetus. Med J Aust 1:1263-1267. Escherich T (1886) Beiträge zur Kenntnis der Darmbacterien. Münchener Medizinische Wochenschrift 33:815–835. Dekeyser P, Gossuin-Detrain M, Butzler JP, Sternon J (1972) Acute enteritis due to related vibrio: first positive stool cultures. J Infect Dis 125:390-392. https://doi.org/10.1093/infdis/125.4.390 Doyle LP (1944) A vibrio associated with swine dysentery. Amer J Vet Res 5:3–5. Jones FS, Orcutt M, Little RB (1931) Vibrios (Vibrio jejuni, n.sp.) associated with intestinal disorders of cows and calves. J Exp Med 53:853–863. https://doi.org/10.1084/jem.53.6.853 King EO (1957) Human infections with Vibrio fetus and a closely related vibrio. J Infect Dis 101:119-128. https://doi.org/10.1093/infdis/101.2.119 Kist M (1981) Campylobacter enteritis: epidemiological and data from recent isolations in the region of Freiburg, West Germany. In: Newell DG (ed) Campylobacter – epidemiology, pathogenesis and biochemistry. Proceedings of an International Workshop on Campylobacter Infections held at University of Reading, 24-26th March 1981, pp.138-143 Kist M (1986a) Who discovered Campylobacter jejuni/coli? A review of hitherto disregarded literature. Zentralbl Bakteriol Mikrobiol Hyg A. 261(2):177-186. Kist M (1986b) Vergleichende Untersuchung zu Inzidenz, Klinik und epidemiologischen Risikofaktoren der infektiösen Enteritis. Habilitationsschrift zur Erlangung der Venia legendi der Hohen Medizinischen Fakultät der Albert-Ludwigs-Universität Freiburg im Breisgau (in German). Levy AJ (1946) A gastro-enteritis outbreak probably due to a bovine strain of vibrio. Yale J Biol Med 18: 243-258. Sebald M, Veron M (1963) Base DNA content and classification of Vibrios. Ann Inst Pasteur () 105:897-910. Skirrow MB (1977) Campylobacter enteritis: a ``new'' disease. Br Med J 2:9-11. https://doi.org/10. 1136/bmj.2.6078.9 Contents

Human Campylobacteriosis—A Serious Infectious Threat in a One Health Perspective ...... 1 Markus M. Heimesaat, Steffen Backert, Thomas Alter, and Stefan Bereswill The Data Behind Risk Analysis of Campylobacter Jejuni and Campylobacter Coli Infections ...... 25 Racem Ben Romdhane and Roswitha Merle Population Biology and Comparative Genomics of Campylobacter Species ...... 59 Lennard Epping, Esther-Maria Antão, and Torsten Semmler Management Strategies for Prevention of Campylobacter Infections Through the Poultry Food Chain: A European Perspective ...... 79 Thomas Alter and Felix Reich Emission Sources of Campylobacter from Agricultural Farms, Impact on Environmental Contamination and Intervention Strategies ...... 103 Vanessa Szott and Anika Friese Phage Biocontrol of Campylobacter: A One Health Approach ...... 127 Sophie Kittler, Severin Steffan, Elisa Peh, and Madeleine Plötz Campylobacter Virulence Factors and Molecular Host–Pathogen Interactions ...... 169 Nicole Tegtmeyer, Irshad Sharafutdinov, Aileen Harrer, Delara Soltan Esmaeili, Bodo Linz, and Steffen Backert Diarrheal Mechanisms and the Role of Intestinal Barrier Dysfunction in Campylobacter Infections ...... 203 Fábia Daniela Lobo de Sá,Jörg-Dieter Schulzke, and Roland Bücker

xi xii Contents

Murine Models for the Investigation of Colonization Resistance and Innate Immune Responses in Campylobacter Jejuni Infections .... 233 Soraya Mousavi, Stefan Bereswill, and Markus M. Heimesaat Natural Competence and Horizontal Gene Transfer in Campylobacter ...... 265 Julia Carolin Golz and Kerstin Stingl Molecular Mechanisms of Campylobacter Biofilm Formation and Quorum Sensing ...... 293 Christoph Püning, Yulan Su, Xiaonan Lu, and Greta Gölz Correction to: Fighting Campylobacter Infections ...... C1 Steffen Backert Abbreviations

AC Adenylate cyclase AHL Acylated homoserine lactone AI Autoinducer AIP Autoinducer peptide AMC Activated methyl cycle ANI Average nucleotide identity AspA Aspartate ammonia lyase A AspB Aspartate aminotransferase B ATP Adenosine triphosphate BCCA Brilliance CampyCount agar BumR Butyrate response regulator BumS Butyrate sensor kinase C. Campylobacter Ca2+ Calcium ion CadF Campylobacter adhesin to fibronectin cAMP Cyclic adenosine monophosphate Cas CRISPR-associated protein CASA Campylobacter selective agar CCD Charcoal-cefazolin-sodium deoxycholate CCP Critical control point CCV Campylobacter-containing vacuole CDC2 Cyclin-dependent kinase 2 Cdc42 Cell division control protein 42, a small Rho GTPase CDT Cytolethal distending toxin CetA Campylobacter energy taxis protein A CFA CampyFood Agar CFT Complement fixation tests CFTR Cystic fibrosis transmembrane conductance regulator CFU Colony-forming unit cgMLST Core genome MLST

xiii xiv Abbreviations

CheY Chemotaxis response regulator Y CHO Chinese hamster ovary cell Cia Campylobacter invasion antigen cjA Campylobacter jejuni autoinducer CJIE Campylobacter jejuni integrated element CJT Campylobacter jejuni enterotoxin Cl- Chloride ion CoV Coronavirus COVID-19 Coronavirus disease 2019 CPS Capsular polysaccharide CR Colonization resistance CRISPR Clustered regularly interspaced short palindromic repeats CT Cholera toxin DALY Disability-adjusted life years DegP HtrA ortholog in E. coli DegQ HtrA ortholog in E. coli DegS HtrA ortholog in E. coli dG Deoxyguanosine DNA Deoxyribonucleic acid DOC Desoxycholate Dock180 Dedicator of cytokinesis, a 180 kDa GEF dpa Days post-phage application dPCR Digital PCR DPD 4,5-Dihydroxy-2,3-Pentanedione DRA Downregulated in adenoma dsDNA Double-stranded DNA DSS Dextran sodium sulfate DUS DNA uptake sequence E. Escherichia EC European Commission eDNA Extracellular DNA EEA-1 Early endosome antigen 1 EFSA European Food Safety Authority EGFR Epidermal growth factor receptor EIA Enzyme immunoassays ELISA Enzyme-linked immunosorbent assay ENaC Epithelial sodium channel EPS Extracellular polymeric substance ERK Extracellular signal-regulated kinase ESBL Expanded-spectrum b-lactamase (ESBL)–producing EU European Union FAK Focal adhesion kinase Fed Flagellar co-expressed determinants FFEM Freeze fracture electron microscopy Abbreviations xv

FlaA Flagellin A FlaB Flagellin B FlaC Flagellin C FlgE Flagellar hook protein FlgR Two-component response regulator FlgS Two-component sensor kinase FliS Flagellar chaperone FlpA Fibronectin-like protein A FSA Food Standards Agency FSIS Food Safety and Inspection Service FspA2 Flagellar secreted protein A2 fT3SS Flagellar type III secretion system GalfNAc 2-acetamido-2-deoxy-D-galactofuranose GBS Guillain–Barré syndrome GEF Guanine nucleotide exchange factor GGT Gamma-glutamyltranspeptidase GS1 Genomospecies 1 GS2 Genomospecies 2 GWAS Genome-wide association studies HAAP Hazard analysis and critical control points HCF High conjugation frequency HGT Horizontal gene transfer hma Human microbiota-associated hpa Hours post-phage application HtrA High-temperature requirement A IBD Inflammatory bowel disease IBS Irritable bowel syndrome IFN Interferon Ig Immunoglobulin IL Interleukin IM Inner membrane IRF3 Interleukin regulatory factor 3 ISC Short-circuit current ISO International Organization for Standardization ISPC Internal sample process control IjBa Nuclear factor of kappa light polypeptide gene enhancer in B cells inhibitor alpha JAM Junctional adhesion molecule JlpA Jejuni lipoprotein A K+ Potassium ion Lamp1 Lysosomal-associated membrane protein 1 LDH Lactate dehydrogenase LFC Low frequency of conjugation LGT Lateral gene transfer LOS Lipooligosaccharide xvi Abbreviations

LPS Lipopolysaccharide MALDI–TOF MS Matrix-assisted laser desorption ionization (MALDI)– time-of-flight (TOF) mass spectroscopy (MS) MAMPs Microbe-associated molecular patterns MAP Modified atmosphere packaging mCCDA Modified charcoal-cefoperazone-deoxycholate agar MD-2 Myeloid differentiation protein -2 MDRGI Multidrug-resistant genomic island MeOPN O-methyl phosphoramidate MERS Middle East respiratory syndrome MFS Miller Fisher syndrome MIC Minimal inhibitory concentration MLCK Myosin light-chain kinase MLST Multi-locus sequence typing MOI Multiplicity of infection MOMP Major outer membrane protein MPI Ministry of Primary Industries, New Zealand mRNA Messenger ribonucleic acid mTOR Mammalian target of rapamycin MyD88 Myeloid differentiation primary response 88 Na+ Sodium ion NF-jB Nuclear factor kappa-light-chain-enhancer of activated B cells NGS Next-generation sequencing NHE Sodium–hydrogen antiporter NLR NOD-like receptor NLRP3 NLR family pyrin domain-containing protein 3 NOD Nucleotide–oligonucleotide domain NOD2 Nucleotide–oligonucleotide domain 2 OM Outer membrane OMV Outer membrane vesicle ONT Oxford Nanopore Technology ORS Oral rehydration solution PacBio Pacific Bioscience PAMP Pathogen-associated molecular pattern PCR Polymerase chain reaction pDC Plasmacytoid dendritic cell PDGFR Platelet-derived growth factor receptor PDZ Postsynaptic density protein PEB1 Periplasmic-binding protein 1 PFGE Pulsed-field gel electrophoresis PFU Plaque-forming units PGE2 Prostaglandin 2 PGL Protein glycosylation system PI3K Phosphatidylinositol 3-kinase PI3K-c Phosphatidylinositol 3-kinase-c Abbreviations xvii

PKC Protein kinase C PMA Propidium monoazide QALY Quality-adjusted life years qPCR Quantitative real-time polymerase chain reaction QQ Quorum quenching QS Quorum sensing RA Reactive arthritis Rac1 Ras-related C3 botulinum toxin substrate 1, a small Rho GTPase Repi Epithelial resistance Rsub Subepithelial resistance SAM S-adenosylmethionine SARS Severe acute respiratory syndrome SCFA Short-chain fatty acid SIGIRR Single Ig IL-1-related receptor Siglec Sialic acid-binding immunoglobulin-like lectin sm Soluble mouse SMRT Single-molecule real-time sequencing SNV Single-nucleotide variant SodB Superoxide dismutase B SPC Sample process control SPF Specific pathogen free SpoT ppGpp synthetase/pyrophosphohydrolase SRH S-ribosylhomocysteine ssDNA Single-stranded DNA ST Sequence type SVR Short variable region SYF Src−/−/Yes−/−/Fyn−/− triple knockout T3SS Type III secretion system T4SS Type IV secretion system TEM Transmission electron microscopy TER Transepithelial electrical resistance TIR Toll-Interleukin receptor domain TJ Tight junction Tlp Transducer-like protein TLR Toll-like receptor Tm Melting temperature TNF Tumor necrosis factor TracrRNA Trans-activating CRISPR RNA TRAM TRIF-related adapter molecule TRIF TIR-domain-containing adapter-inducing interferon-b UC Ulcerative colitis UI Uncertainty interval UK United Kingdom US United States xviii Abbreviations

UV Ultraviolet VBNC Viable but non-culturable VD Vitamin D VDR Vitamin D receptor wgMLST Whole-genome sequencing-based MLST WGS Whole-genome sequencing WHO World Health Organization YLD Years lost due to disability YLL Years of life lost YPLL Years of potential life lost ZO Zonula occludens Abbreviations xix