Thesis Occurrence and Dissemination of Micropollutants and Antibiotic Resistance in Aquatic Environment: A Prevalence Study across Geographical Location and Different Systems of Wastewater Management LAFFITE, Amandine Abstract The pollution of water is a major problem in many parts of the world. In many developing countries, aquatic systems are receiving untreated or partially treated effluents, containing anthropogenic pollutants whereas these rivers serve as a basic network for human and animal consumption. High values of toxic metals, persistent organic pollutants (POPs), faecal indicator bacteria (FIBs), antibiotic resistant bacteria (ARBs) and antibiotic resistance genes (ARGs) in rivers may pose a great risk to human health and aquatic living organisms. The main objective of the research is to assess the prevalence and dissemination of toxic metals, POPs, FIB, ARB and ARGs in the rivers of Kinshasa (Republic Democratic of the Congo) as a study case. Overall, the present work demonstrated that chemical and microbiological pollution can exceed, in many studied sites, the international recommendation for water quality and has the potential to affect ecosystem functions as well as human impact. Reference LAFFITE, Amandine. Occurrence and Dissemination of Micropollutants and Antibiotic Resistance in Aquatic Environment: A Prevalence Study across Geographical Location and Different Systems of Wastewater Management. Thèse de doctorat : Univ. Genève, 2019, no. Sc. 5355 DOI : 10.13097/archive-ouverte/unige:120648 URN : urn:nbn:ch:unige-1206485 Available at: http://archive-ouverte.unige.ch/unige:120648 Disclaimer: layout of this document may differ from the published version. 1 / 1 UNIVERSITÉ DE GENÈVE FACULTÉ DES SCIENCES Section des Sciences de la Terre et de l’Environnement Département F.-A. Forel des sciences de l’environnement et de l’eau Dr. John Poté Prof. Vera Slaveykova Occurrence and Dissemination of Micropollutants and Antibiotic Resistance in Aquatic Environment: A Prevalence Study across Geographical Location and Different Systems of Wastewater Management THÈSE présentée à la Faculté des Sciences de l’Université de Genève pour obtenir le grade de Docteur ès Sciences, mention Science de l’Environnement par Amandine LAFFITE de Perpignan (France) Thèse N°5355 GENÈVE 2019 UNIVERsITÉ DE CENÊVE FÂ{{JN-TÉ f}fis SflIEruf KS DOCTORAT ES SCIENCES, MENTION SCIENCES DE L'ENVIRONNEMENT Thèse de Madame Amandine LAFFITE intitulée : <<Occurrence and Dissemination of Micropollutants and Antibiotic Resistance in Aquatic Environment: A Prevalence study across Geographical Location and Different Systems of Wastewater Management>> La Faculté des sciences, sur le préavis de Monsieur J. POTE-WEMBONYAMA, docteur et directeur de thèse (Département F.-A. Forel des sciences de I'environnement et de I'eau), Madame V. SLAVEYKOVA, professeure ordinaire et codirectrice de thèse (Département F.-A. Forel des sciences de l'environnement et de I'eau), Monsieur B. W. IBELINGS, professeur ordinaire (Département F.-A. Forel des sciences de I'environnement et de l'eau), Monsieur S. J. HARBARTH, professeur ordinaire (Faculté de médecine, Service de prévention de I'infection) et Monsieur C. MULAJI KYELA, professeur (Département de chimie, Université de Kinshasa, République démocratique du Congo), autorise I'impression de la présente thèse, sans exprimer d'opinion sur les propositions qui y sont énoncées. Genève, le 6 juin 2019 Thèse - 5355 - Le Doyen N.B. - La thèse doit porter la déclaration précédente et remplir les conditions énumérées dans les "lnformations relatives aux thèses de doctorat à I'Université de Genève". Table des matières Abstract .................................................................................................................... VII Résumé .................................................................................................................. XIII Abbreviation lists .................................................................................................. XVII Figure caption ........................................................................................................ XXI Table caption ....................................................................................................... XXV .............................................................................................. 1 1.1 Anthropogenic impact on aquatic systems ....................................................... 3 1.1.1 Contamination sources ................................................................................ 3 1.1.2 Different types of pollutants ....................................................................... 4 1.1.3 Contamination variability ........................................................................... 7 1.1.4 Wastewater management systems .............................................................. 8 1.2 Antibiotic resistance genes as emerging pollutant ......................................... 10 1.2.1 A brief overview of antibiotic resistance .................................................. 11 1.2.2 General mechanisms of antibiotic resistance ............................................ 12 1.2.3 Β-lactams and β-lactam resistance ............................................................ 14 1.2.4 Genetic support and transfer mechanisms of antimicrobial resistance ..... 17 1.2.5 Link between AMR and virulence ............................................................ 21 1.2.6 The global spread of antibiotic resistance and the rise of superbugs ........ 22 1.2.7 Relevance of antibiotic resistance in the environment ............................. 23 1.3 Research objectives and chapters’ organization ............................................. 26 1.3.1 Research objectives ................................................................................... 26 1.3.2 Thesis outline ............................................................................................ 27 1.3.3 Study site implicated in the research ........................................................ 27 1.3.4 Institutional framework ............................................................................. 30 1.3.5 Funding ..................................................................................................... 31 I 1.3.6 List of publication relative to this research ............................................... 31 References ................................................................................................................ 34 .................. 41 Abstract ..................................................................................................................... 42 2.1 Introduction .................................................................................................... 43 2.2 Material and methods ..................................................................................... 44 2.2.1 Study sites and sampling procedure .......................................................... 44 2.2.2 Sediment grain size and organic matter, total organic carbon, total nitrogen and phosphorus analysis ........................................................................................ 45 2.2.3 Metal analysis in sediment samples .......................................................... 46 2.2.4 Geoaccumulation index and enrichment factor ........................................ 46 2.2.5 Chlorinated pesticides, PCBs, PAHs and PBDEs analysis ....................... 47 2.2.6 Data analysis ............................................................................................. 49 2.3 Results and discussion .................................................................................... 49 2.3.1 Physicochemical characteristics of sediments .......................................... 49 2.3.2 Metal concentrations in the surface sediments ......................................... 51 2.3.3 Enrichment factor (EF) and Geoaccumulation index (Igeo) .................... 52 2.3.4 Spatial distribution of persistent organic pollutants in sediments ............ 54 2.3.5 Correlation between parameters ............................................................... 63 2.4 Conclusion ...................................................................................................... 64 References ................................................................................................................ 65 .............................................................................. 71 Abstract ..................................................................................................................... 72 3.1 Introduction .................................................................................................... 73 3.2 Materials and Methods ................................................................................... 75 II 3.2.1 Study site description ................................................................................ 75 3.2.2 Sampling procedure .................................................................................. 76 3.2.3 Water physicochemical parameter analysis .............................................. 78 3.2.4 Faecal indicator bacteria (FIB) analysis in water and sediment samples . 78 3.2.5 Characterization of FIB strains ................................................................. 78 3.2.6 Data Analysis ............................................................................................ 79 3.3