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Go with Your Gut. the Human Intestinal Microbiota, International Travel, Campylobacter and ESBL-Producing Enterobacteriaceae

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Go with Your Gut. the Human Intestinal Microbiota, International Travel, Campylobacter and ESBL-Producing Enterobacteriaceae Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Medicine 1735 Go with your gut The human intestinal microbiota, international travel, Campylobacter and ESBL-producing Enterobacteriaceae CHRISTIAN KAMPMANN ACTA UNIVERSITATIS UPSALIENSIS ISSN 1651-6206 ISBN 978-91-513-1171-5 UPPSALA urn:nbn:se:uu:diva-438449 2021 Dissertation presented at Uppsala University to be publicly examined in H:son- Holmdahlsalen, Akademiska Sjukhuset, Ingång 100/101, Dag Hammarskjölds väg 8, Uppsala, Wednesday, 19 May 2021 at 13:15 for the degree of Doctor of Philosophy (Faculty of Medicine). The examination will be conducted in Swedish. Faculty examiner: Docent Johan Ursing (Department of Clinical Sciences, Danderyd Hospital, Karolinska Institute). Abstract Kampmann, C. 2021. Go with your gut. The human intestinal microbiota, international travel, Campylobacter and ESBL-producing Enterobacteriaceae. Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Medicine 1735. 93 pp. Uppsala: Acta Universitatis Upsaliensis. ISBN 978-91-513-1171-5. Up to 100 million people travel annually from industrialized countries to resource-limited ones. Each traveller contains an internal ecosystem composed of tens of trillions of microbes, known as the intestinal microbiota, which has a large effect on health. The microbiota seems to be highly individual and mostly stable but can be significantly affected by several factors. Many international travellers are at high risk of getting infected by Campylobacter, the most common cause of bacterial enteritis worldwide. Campylobacter infection can cause a wide range of symptoms, with varying severity, for reasons largely unknown. Travel also radically increases the risk of colonization by antibiotic-resistant intestinal bacteria, notably Extended spectrum beta-lactamase (ESBL)-producing Enterobacteriaceae (EPE). To date, there are no therapies available for EPE-decolonization. In this thesis, it was investigated whether the bacterial intestinal microbiota affected susceptibility to Campylobacter and if international travel as such had an impact on the microbiota. In a prospective, observational study, 67 healthy Swedes, travelling in groups to countries with a high risk of Campylobacter infection, were followed. The travellers answered questionnaires and delivered two faecal samples before and three samples after the trip. These samples were cultured for enteropathogens and analysed for the microbiota composition. Low diversity of microbiota seemed to increase the risk of Campylobacter jejuni infection, whereas a high relative abundance of Lachnospiraceae might decrease the risk (Paper I). Furthermore, the overall bacterial diversity did not seem to change in connection with travelling. However, the bacterial family Enterobacteriaceae (otherwise connected with inflammation, infection and antibiotic-resistance) was shown to be dramatically increased in abundance immediately after travel, and the family Christensenellaceae (otherwise connected with beneficial health conditions) simultaneously decreased (Paper II). Eight travellers, from two different destinations, were infected with closely related C. jejuni isolates (ST353CC). The bacterial analysis of genomic and phenotypic characteristics revealed that the C. jejuni isolates of the travellers returning from one of the destinations and with more severe symptoms actually showed less pathogenic potential, compared to the isolates of travellers from the other destination and with milder symptoms. However, the travellers with more severe symptoms had much higher relative abundances of Bacteroidetes in their intestinal microbiota and, in contrast to the other travellers, excluded meat from their diet. (Paper III) Finally, we investigated in a randomized, placebo-controlled clinical trial of 80 established intestinal carriers of EPE, whether the oral probiotic product Vivomixx® could eradicate EPE. Vivomixx® was not superior to placebo (Paper IV). Keywords: travel, travellers´diarrhea, microbiota, Campylobacter, Campylobacter jejuni, ST353CC, colonization resistance, enteritis, infection, Enterobacteriaceae, Christensenellaceae, Lachnospiraceae, whole genome sequence, vegetarian, bacterial resistance, ESBL, Extended spectrum beta-lactamase, probiotics, intestinal decolonization, eradication treatment Christian Kampmann, Department of Medical Sciences, Clinical Microbiology, Akademiska sjukhuset, Uppsala University, SE-751 85 Uppsala, Sweden. © Christian Kampmann 2021 ISSN 1651-6206 ISBN 978-91-513-1171-5 urn:nbn:se:uu:diva-438449 (http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-438449) For Jonathan and Elliot “Bakterier på resa” Av: Jonathan Kampmann Olivares List of Papers I. Composition of human faecal microbiota in resistance to Campylo- bacter infection. C. Kampmann, J. Dicksved, L. Engstrand and H. Rautelin. Clinical Microbiology and Infection. 2016; 22 (1): 61.e1- 61.e8 II. Changes to human faecal microbiota after international travel. C. Kampmann, J. Dicksved, L. Engstrand and H. Rautelin. Submitted manuscript. III. Genomic and phenotypic differences in geographically separated clin- ical Campylobacter jejuni ST353CC isolates. C. Johansson, C. Kampmann, A. Nilsson, J. Dicksved, L. Engstrand and H. Rautelin. Manuscript. IV. Probiotics for intestinal decolonization of ESBL-producing Entero- bacteriaceae: a randomized, placebo-controlled clinical trial. O. Ljungquist, C. Kampmann, F. Resman, K. Riesbeck and J. Tham. Clinical Microbiology and Infection. 2020; 26 (4): 456-462. Contents Foreword ....................................................................................................... 11 Introduction ................................................................................................... 13 The intestinal microbiota .......................................................................... 13 Composition of the intestinal microbiota ............................................. 14 Influences on the composition of the intestinal microbiota ................. 15 Sequencing techniques to study microbiota composition ........................ 16 Amplicon sequencing of the 16S rRNA gene ...................................... 17 Data analysis ........................................................................................ 18 Travellers´ diarrhea (TD) ......................................................................... 19 Campylobacter ......................................................................................... 20 Epidemiology and clinical picture ....................................................... 20 Pathogenesis ........................................................................................ 22 Antibiotic resistance ............................................................................ 25 Laboratory diagnosis ........................................................................... 26 Multi Locus Sequence Typing (MLST)............................................... 26 Models for in vitro infection ................................................................ 27 Campylobacter and the microbiota .......................................................... 28 Colonization resistance ............................................................................ 29 Probiotics .................................................................................................. 30 Probiotics, the microbiota and colonization resistance ........................ 31 Properties, problems and clinical effects ............................................. 32 ESBL-producing Enterobacteriaceae (EPE) ........................................... 34 Global prevalence ................................................................................ 35 Colonization and infection ................................................................... 36 EPE and probiotics ................................................................................... 36 Aims .............................................................................................................. 41 Material and methods .................................................................................... 42 Paper I, II and III ...................................................................................... 42 Study persons ....................................................................................... 42 Faecal samples ..................................................................................... 44 Questionnaires ..................................................................................... 45 DNA extraction .................................................................................... 45 16S rRNA gene analysis ...................................................................... 46 PCR analysis of Campylobacter isolates and faecal samples .............. 46 Further analysis of C. jejuni isolates (Paper III) .................................. 46 Further genomic analyses of ST353CC isolates .................................. 47 In vitro analyses of ST353CC isolates ................................................. 48 Ethics ................................................................................................... 49 Paper IV ................................................................................................... 49 Study persons and method ................................................................... 49 Vivomixx® .........................................................................................
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