| 摘要 | 第8-11页 |
| ABSTRACT | 第11-14页 |
| LIST OF ABBREVIATIONS | 第15-17页 |
| CHAPTER 1 Introduction | 第17-47页 |
| 1.1 Antimicrobial resistance (AMR) | 第18-19页 |
| 1.2 Susceptibility testing | 第19-22页 |
| 1.2.1 Phenotype susceptibility testing methods | 第20-22页 |
| 1.2.2 Molecular characteristics of antimicrobial resistance | 第22页 |
| 1.3 How bacteria acquire resistance | 第22-27页 |
| 1.3.1 Mutation | 第22-24页 |
| 1.3.2 Horizontal and vertical transfer of resistance | 第24-25页 |
| 1.3.3 Mobile genetic elements | 第25-27页 |
| 1.4 How antimicrobials exert their effect | 第27-28页 |
| 1.5 How bacteria fight back against antimicrobials | 第28-30页 |
| 1.6 Main mechanisms of antibiotic resistance development to commonly used antibiotics in livestock (yak) herds | 第30-34页 |
| 1.6.1 Beta-lactams | 第31页 |
| 1.6.2 Tetracyclines | 第31-32页 |
| 1.6.3 Fluorquinolones and Quinolones | 第32页 |
| 1.6.4 Aminoglycosides and Aminocyclitols | 第32-33页 |
| 1.6.5 Chloramphenicol and Florfenicol | 第33页 |
| 1.6.6 Trimethoprim and Sulphonamides | 第33-34页 |
| 1.6.7 Co-resistance and cross-resistance | 第34页 |
| 1.7 Escherichia coli (E. coli) as an indicator organism | 第34-35页 |
| 1.8 Pathogenicity of E. coli and AMR | 第35-37页 |
| 1.9 Antibiotics usage: General considerations | 第37-41页 |
| 1.9.1 Reason for antimicrobial use in livestock | 第37-38页 |
| 1.9.2 Antimicrobial use and antimicrobial resistance | 第38-39页 |
| 1.9.3 Major multi-drug efflux pump and traditional Chinese medicine | 第39-40页 |
| 1.9.4 Challenges of antibiotic usage data collection | 第40-41页 |
| 1.10 Antimicrobial resistance in domestic yaks | 第41-43页 |
| 1.10.1 How this thesis will fill in the gaps demonstrated in this review | 第42-43页 |
| 1.11 Concluding statements | 第43-45页 |
| 1.12 Aims &Objectives | 第45-47页 |
| 1.12.1 Problem statement | 第45页 |
| 1.12.2 Aims | 第45-46页 |
| 1.12.3 Achieved goals | 第46页 |
| 1.12.4 Benefits from the project | 第46-47页 |
| CHAPTER 2 Antibiotic resistance of Escherichia coli in free-ranging healthy and diarrheic yaks (Bos grunniens) of Qinghai-Tibetan Plateau,China | 第47-83页 |
| 2.1 Objective of this study | 第47-48页 |
| 2.2 Materials and methods | 第48-55页 |
| 2.2.1 Sample collection, isolation, and identification | 第48页 |
| 2.2.2 Antibiotic sensitivity testing and screening of ESBL-producing strains | 第48-49页 |
| 2.2.3 DNA extraction | 第49页 |
| 2.2.4 Screening for resistance genes and virulence-associated genes | 第49-50页 |
| 2.2.5 Phylo groups of E. coli strains | 第50页 |
| 2.2.6 Sero-grouping | 第50-52页 |
| 2.2.7 Codon-based positive selection analysis | 第52-54页 |
| 2.2.8 Positive selection on amino acid positions | 第54页 |
| 2.2.9 Evolutionary analysis of diversifying selection | 第54-55页 |
| 2.2.10 Evolutionary finger printing of bla CTX-M gene | 第55页 |
| 2.2.11 Statistical analysis | 第55页 |
| 2.3 Results | 第55-75页 |
| 2.3.1 Isolation rate of E. coli | 第55页 |
| 2.3.2 Antibiotic resistance patterns of E. coli isolates | 第55-57页 |
| 2.3.3 Detection of resistance and virulence genes | 第57-59页 |
| 2.3.4 Occurrence of E. coli pathotypes | 第59-60页 |
| 2.3.5 Occurrence of phylogroups | 第60页 |
| 2.3.6 Association between antimicrobial resistance and virulence genes | 第60页 |
| 2.3.7 Occurrence of Serogroups | 第60-61页 |
| 2.3.8 Detection of ESBL genes | 第61页 |
| 2.3.9 Codon-based positive selection analysis in ESBL producing CTX-M gene | 第61-62页 |
| 2.3.10 Positive selection on amino acid positions | 第62页 |
| 2.3.11 Evolutionary analysis of diversifying selection | 第62-63页 |
| 2.3.12 Evolutionary finger printing of bla CTX-M gene | 第63-75页 |
| 2.4 Discussion | 第75-83页 |
| CHAPTER 3 Characteristics of integrons and associated gene cassettes in antibiotic resistant Escherichia coli isolated from free-ranging food animals in China | 第83-96页 |
| 3.1 Objective of this study | 第83页 |
| 3.2 Materials and Methods | 第83-87页 |
| 3.2.1 Ethics statement | 第83-84页 |
| 3.2.2 Study population and bacterial strains | 第84页 |
| 3.2.3 Characterization of the integrons | 第84-85页 |
| 3.2.4 Characterization of class 1 and 2 integron cassette arrays | 第85页 |
| 3.2.5 Restriction analysis of PCR products and DNA sequencing | 第85-86页 |
| 3.2.6 Sequence analysis and nucleotide accession number | 第86页 |
| 3.2.7 Conjugation studies and plasmid analysis | 第86页 |
| 3.2.8 Multilocus sequence typing of integrons positive E. coli | 第86-87页 |
| 3.3 Results | 第87-92页 |
| 3.3.1 Occurrence of class 1 and 2 integrons | 第87页 |
| 3.3.2 Characterization of integrons and transfer of class 1 integrons | 第87页 |
| 3.3.3 Multi-locus sequence analysis (MLSA) | 第87-91页 |
| 3.3.4 Conjugal transfer and plasmid profiling | 第91-92页 |
| 3.4 Discussion | 第92-96页 |
| CHAPTER 4 Experimental mouse lethality of Escherichia coli strains isolated from free ranging Tibetan Yaks | 第96-106页 |
| 4.1 Objective of this study | 第96页 |
| 4.2 Materials and Methods | 第96-98页 |
| 4.2.1 Ethics Statement | 第96-97页 |
| 4.2.2 Strains | 第97页 |
| 4.2.3 Serogrouping | 第97页 |
| 4.2.4 Mouse lethality assay | 第97-98页 |
| 4.2.5 Statistical analysis | 第98页 |
| 4.3 Results | 第98-103页 |
| 4.3.1 Lethality rate of E. coli strains | 第98页 |
| 4.3.2 Occurrence of Serogroups | 第98-99页 |
| 4.3.3 Mouse lethality assay | 第99-103页 |
| 4.4 Discussion | 第103-106页 |
| CHAPTER 5 Antibacterial effect and resistant regulation of Houttuynia cordata water extract against multi-drug resistant Escherichia coli | 第106-115页 |
| 5.1 Objective of this study | 第106页 |
| 5.2 Materials and Methods | 第106-109页 |
| 5.2.1 Materials and Reagents | 第106页 |
| 5.2.2 Water Extraction | 第106-107页 |
| 5.2.3 Bacterial Strains | 第107页 |
| 5.2.4 Antibacterial assay of H. cordata water extract | 第107-108页 |
| 5.2.5 Determination of minimum inhibitory concentration (MIC) and minimal bactericidal concentration (MBC) | 第108页 |
| 5.2.6 Reverse Transcription Quantitative-Real Time Polymerase Chain Reaction (RT-qPCR) | 第108-109页 |
| 5.2.7 Statistical analyses of the results | 第109页 |
| 5.3 Results | 第109-112页 |
| 5.3.1 Antibacterial effects of Houttuynia cordata water extract | 第109页 |
| 5.3.2 Transcriptional level of AcrA gene by RT-qPCR | 第109-112页 |
| 5.4 Discussion | 第112-115页 |
| CHAPTER 6 Conclusions and Future directions | 第115-118页 |
| 6.1 Study Ⅰ | 第115页 |
| 6.2 Study Ⅱ | 第115-116页 |
| 6.3 Study Ⅲ | 第116页 |
| 6.4 Study Ⅳ | 第116-117页 |
| 6.5 Future directions | 第117-118页 |
| References | 第118-139页 |
| Acknowledgements | 第139-140页 |
| List of Publications | 第140-141页 |
| Appendices | 第141-153页 |
| Appendix 1 | 第141-143页 |
| Appendix 2 | 第143-147页 |
| Appendix 3 | 第147-153页 |
