Chong, Kam Lin. / Thesis submitted in: December 2002. / Thesis (M.Phil.)--Chinese University of Hong Kong, 2003. / Includes bibliographical references (leaves 165-174). / Abstracts in English and Chinese. / ABSTRACT --- p.ii / ACKNOWLEDGEMENTS --- p.vii / TABLE OF CONTENTS --- p.viii / LIST OF ABBREVIATIONS --- p.xi / Chapter / Chapter 1. --- Introduction --- p.1 / Chapter 2. --- Literature review --- p.10 / Chapter 2.1 --- Prescribing patterns of antibiotics in hospital --- p.12 / Chapter 2.2 --- Worldwide problem of misuse of antibiotics --- p.15 / Chapter 2.2.1 --- Misuse of antibiotics in developed countries --- p.15 / Chapter 2.2.1.1 --- The United States of America --- p.16 / Chapter 2.2.1.2 --- The United Kingdom --- p.19 / Chapter 2.2.1.3 --- Australia --- p.23 / Chapter 2.2.1.4 --- Canada --- p.25 / Chapter 2.2.2 --- Misuse of antibiotics in African countries --- p.27 / Chapter 2.2.3 --- Misuse of antibiotics in Asian countries --- p.30 / Chapter 3. --- Objectives --- p.37 / Chapter 4. --- Methods --- p.39 / Chapter 4.1 --- Subjects --- p.39 / Chapter 4.2 --- Data --- p.41 / Chapter 4.3 --- Definition of terms --- p.44 / Chapter 4.3.1 --- Name of antibiotic --- p.44 / Chapter 4.3.2 --- Antibiotic course and antibiotic therapy --- p.44 / Chapter 4.3.3 --- Indications and types of antibiotic therapy --- p.47 / Chapter 4.3.4 --- Switch therapy --- p.50 / Chapter 4.3.5 --- Types of change --- p.50 / Chapter 4.3.6 --- Causes of change --- p.51 / Chapter 4.3.7 --- Clinical outcome of treatment --- p.53 / Chapter 4.3.8 --- Length of stay --- p.54 / Chapter 4.4 --- Determination of pattern of use --- p.54 / Chapter 4.5 --- Assessment of antibiotic therapies --- p.55 / Chapter 4.5.1 --- Assessment of indication and choice of agent --- p.59 / Chapter 4.5.2 --- Assessment of dosage --- p.60 / Chapter 4.5.3 --- Assessment of route of administration --- p.62 / Chapter 4.5.4 --- Assessment of duration of therapy --- p.62 / Chapter 4.6 --- Features of the guideline developed for the present study --- p.63 / Chapter 4.6.1 --- Ceftriaxone and cefotaxime are appropriate for treating serious infections --- p.72 / Chapter 4.6.2 --- Cefuroxime is not a first line agent --- p.72 / Chapter 4.6.3 --- Regimen for Helicobacter pylori eradication --- p.73 / Chapter 4.7 --- Statistical analysis --- p.73 / Chapter 5. --- Results --- p.74 / Chapter 5.1 --- Antibiotic courses and patients --- p.74 / Chapter 5.1.1 --- Inclusion and exclusion of antibiotic courses --- p.74 / Chapter 5.1.2 --- Patient sex and age --- p.76 / Chapter 5.1.3 --- Chronic disease/past medical history --- p.76 / Chapter 5.1.4 --- Length of stay --- p.78 / Chapter 5.2 --- Pattern of use --- p.79 / Chapter 5.2.1 --- Indications and sites of infection --- p.79 / Chapter 5.2.2 --- Types of antibiotic therapy --- p.83 / Chapter 5.2.3 --- Antibiotics prescribed in initial therapy --- p.84 / Chapter 5.2.4 --- Number of antibiotics in initial therapy --- p.87 / Chapter 5.2.5 --- Prescribing pattern of antibiotics in initial therapy --- p.88 / Chapter 5.2.5.1 --- Prescribing pattern of antibiotics in empirical treatment of lower respiratory tract infections --- p.89 / Chapter 5.2.5.2 --- Prescribing pattern of antibiotics in empirical treatment of sepsis --- p.90 / Chapter 5.2.6 --- Types of change --- p.92 / Chapter 5.2.7 --- Causes of change --- p.92 / Chapter 5.2.8 --- The relationship between causes of change and types of change --- p.93 / Chapter 5.2.9 --- Antibiotics prescribed in switch therapy --- p.96 / Chapter 5.2.10 --- Number of antibiotics in switch therapy --- p.99 / Chapter 5.3 --- Appropriateness of antibiotic therapy --- p.100 / Chapter 5.3.1 --- Appropriateness of empirical therapies --- p.101 / Chapter 5.3.2 --- Appropriateness of directed therapies --- p.102 / Chapter 5.3.3 --- Appropriateness of prophylactic therapies --- p.103 / Chapter 5.3.4 --- Appropriateness of unclassified therapies --- p.104 / Chapter 5.4 --- Clinical outcomes of treatment --- p.105 / Chapter 6. --- Discussion --- p.106 / Chapter 6.1 --- Limitations --- p.106 / Chapter 6.2 --- Method --- p.110 / Chapter 6.2.1 --- Symptom improved and not responded --- p.110 / Chapter 6.2.2 --- Grand round --- p.111 / Chapter 6.2.3 --- Susceptibility test result --- p.111 / Chapter 6.3 --- Results --- p.112 / Chapter 6.3.1 --- Patients --- p.112 / Chapter 6.3.2 --- Pattern of use --- p.113 / Chapter 6.3.2.1 --- Types of therapy --- p.113 / Chapter 6.3.2.2 --- Site of infection --- p.113 / Chapter 6.3.2.3 --- Prescribing pattern of antibiotics in initial therapy --- p.114 / Chapter 6.3.2.4 --- Relationship between types and causes of change --- p.115 / Chapter 6.3.3 --- Appropriateness of antibiotic therapies --- p.117 / Chapter 6.3.3.1 --- Misuse of empirical therapy --- p.118 / INAPPROPRIATE USE OF ANTIBIOTICS IN LOWER RESPIRATORY TRACT INFECTION --- p.118 / INAPPROPRIATE USE OF ANTIBIOTICS IN SEPSIS --- p.120 / MISUSE OF CEFUROXIME --- p.122 / MISUSE OF THIRD GENERATION CEPHALOSPORIN --- p.127 / Chapter 6.3.3.2 --- Appropriate use of directed therapy --- p.129 / Chapter 6.3.3.3 --- Appropriate use of prophylactic therapy --- p.130 / Chapter 6.3.3.4 --- Excessive use of unclassified therapy --- p.131 / Chapter 6.3.4 --- Clinical outcome of treatment --- p.133 / Chapter 6.4 --- Conclusion --- p.134 / Chapter 7. --- Summary --- p.136 / Chapter 8. --- Recommendations --- p.140 / APPENDICES --- p.143 / Chapter 1. --- Usual adult daily dose range of antibiotics --- p.144 / Chapter 2. --- Assessment of indications and choices of agent of initial therapies in an audit of 324 antibiotic courses in a medical ward --- p.146 / Chapter 3. --- Culture test results in an audit of use of antibiotics in a medical ward --- p.160 / Chapter 4. --- Generic to trade name conversion of antibiotics --- p.163 / REFERENCES --- p.165

Ko Mui Lam. / Thesis submitted in: December 2003. / Thesis (M.Phil.)--Chinese University of Hong Kong, 2004. / Includes bibliographical references (leaves 84-100). / Abstracts in English and Chinese. / Chapter Chapter 1 --- Introduction --- p.1 / Chapter A. --- Antibiotic use and resistance --- p.1 / Chapter B. --- Selection of resistant strains by antibiotics --- p.2 / Chapter C. --- Fluoroquinolones --- p.5 / Chapter D. --- β-Lactams --- p.8 / Chapter E. --- Aminoglycosides --- p.9 / Chapter F. --- Salmonella sp --- p.9 / Chapter a. --- Microbiology and clinical significance --- p.9 / Chapter b. --- Antimicrobial susceptibilities --- p.10 / Chapter G. --- Escherichia coli --- p.14 / Chapter a. --- Microbiology and clinical significance --- p.14 / Chapter b. --- Antimicrobial susceptibilities --- p.15 / Chapter H. --- Pseudomonas aeruginosa --- p.18 / Chapter a. --- Microbiology and clinical significance --- p.18 / Chapter b. --- Antimicrobial susceptibilities --- p.18 / Chapter I. --- Objectives --- p.22 / Chapter Chapter 2 --- Materials and Methods --- p.23 / Chapter A. --- Bacterial strains --- p.23 / Chapter B. --- Methods --- p.23 / Chapter a. --- Identification --- p.23 / Chapter i) --- Salmonella --- p.23 / Chapter ii) --- Escherichia coli --- p.24 / Chapter iii) --- Pseudomonas aeruginosa --- p.24 / Chapter b. --- Antimicrobial susceptibility testing --- p.24 / Chapter i) --- Determination of minimal inhibitory concentrations (MICs) of antibiotics --- p.24 / Chapter ii) --- "Determination of the antimicrobial susceptibility of Salmonella sp, Escherichia coli and Pseudomonas aeruginosa by the breakpoint method" --- p.28 / Chapter c. --- Effects of antimicrobial agents on the development of resistant mutants --- p.28 / Chapter Chapter 3 --- Results --- p.32 / Chapter A. --- Antimicrobial susceptibilities --- p.32 / Chapter B. --- Effects of fluoroquinolones on the development of resistance --- p.36 / Chapter a. --- Salmonella sp --- p.38 / Chapter b. --- Escherichia coli --- p.40 / Chapter c. --- Pseudomonas aeruginosa --- p.46 / Chapter C. --- Effects of β-lactams on the development of resistance --- p.49 / Chapter a. --- Salmonella sp --- p.49 / Chapter b. --- Escherichia coli --- p.53 / Chapter c. --- Pseudomonas aeruginosa --- p.56 / Chapter D. --- Effects of aminoglycosides on the development of resistance --- p.60 / Chapter a. --- Salmonella sp --- p.60 / Chapter b. --- Escherichia coli --- p.68 / Chapter c. --- Pseudomonas aeruginosa --- p.68 / Chapter Chapter 4 --- Discussion --- p.76 / References --- p.84 / List of Tables / Chapter I-1 --- Antimicrobial susceptibilities of salmonellae reported in the literature --- p.12 / Chapter I-2 --- Antimicrobial susceptibilities of Escherichia coli reported in the literature --- p.16 / Chapter I-3 --- Antimicrobial susceptibilities of Pseudomonas aeruginosa reported in the literature --- p.20 / Chapter II-1 --- Antibiotics and their solvents --- p.26 / Chapter II-2 --- Antibiotics and their concentrations tested --- p.27 / Chapter II-3 --- Antibiotics and their breakpoint concentration tested --- p.29 / Chapter III-1 --- Susceptibilities of 40 isolates of Salmonella sp to 12 antimicrobial agents --- p.33 / Chapter III-2 --- Susceptibilities of 40 isolates of Escherichia coli to 12 antimicrobial agents --- p.34

A high-performance liquid chromatography was developed to assay levofloxacin and vancomycin. Fluorescence polarization immunoassay was to assay amikacin. The oseltamivir carboxylate and telavancin concentrations were assayed by high-performance liquid chromatography coupled with tandem mass spectrometry. / An in vitro model was utilized to examine adsorption of antibiotics onto haemofilters. In order to test antibiotics from a range of classes, levofloxacin, amikacin, vancomycin, telavancin, and oseltamivir carboxylate were studied. / In summary, the antibiotic adsorption by haemofilters is a complex process. Both characteristics of antibiotics and haemofilters may determine adsorption. Among the studied antibiotics, in vitro adsorption of amikacin by PAN filters may have clinical significance, thus the routine monitoring of amikacin peak concentration in vivo during CRRT is recommended. / In the in vitro model, blood was pumped from an agitated, glass mixing chamber (heated using an automatic water bath), around a circuit and returned to the mixing chamber using a haemofiltration machine. Ultrafiltrate was also returned to the mixing chamber to constitute a closed circuit. As a result any decrease in drug concentration could only be due to adsorption to the filter and extracorporeal circuit, spontaneous degradation or metabolism by red cells. / The main findings were: (1) low adsorption of levofloxacin and vancomycin by haemofilters at clinically relevant concentrations; (2) significant absolute adsorption of amikacin by polyacrylonitrile haemofilters; (3) the adsorption of antibiotics was membrane-material dependent with greater adsorption by polyacrylonitrile filters; (4) lack of relationship between membrane surface area and amikacin adsorption; (5) the adsorption of levofloxacin is reversible, contrary to irreversibility of vancomycin and amikacin; (6) sieving coefficient of oseltamivir is very near to 1.0. / This thesis investigated: (1) the extent of antibiotic adsorption (levofloxacin, vancomycin, amikacin, telavancin and oseltamivir carboxylate) by haemofilters; (2) the time course of antibiotic adsorption by haemofilters; (3) the effects of plasma albumin concentration, initial dosage, pH, filter membrane material, filter membrane surface area and repeated dosing on adsorption; (4) the reversibility or irreversibility of adsorption; (5) clearance of oseltamivir carboxylate and telavancin by ultrafiltration. / Up to 25% of critically ill patients develop acute renal failure with sepsis being the most common cause. Outside of North and South America, these patients usually receive continuous renal replacement therapy (CRRT) which utilizes high flux haemofilter membranes. Thus it is common for these patients to be concurrently receiving antibiotics and CRRT. However, information about the adsorptive capacity of various haemofilters for most drugs is lacking. / "September 2007." / Advisers: Charles Gomersall; Tony Gin. / Source: Dissertation Abstracts International, Volume: 69-08, Section: B, page: 4659. / Thesis (Ph.D.)--Chinese University of Hong Kong, 2007. / Includes bibliographical references (p. 147-164). / Electronic reproduction. Hong Kong : Chinese University of Hong Kong, [2012] System requirements: Adobe Acrobat Reader. Available via World Wide Web. / Electronic reproduction. [Ann Arbor, MI] : ProQuest Information and Learning, [200-] System requirements: Adobe Acrobat Reader. Available via World Wide Web. / Abstract in English and Chinese. / School code: 1307.

INTRODUÇÃO: A Faringotonsilite é doença comum nos consultórios e prontosocorros de pediatria. OBJETIVOS: Avaliar o impacto da realização rotineira da prova rápida para pesquisa de estreptococo do grupo A (PRE) no diagnóstico e tratamento da faringotonsilite aguda em crianças e adolescentes atendidos em um Hospital Geral. MÉTODOS: Trata-se de um estudo prospectivo, observacional, de protocolo de atendimento, instituído no Pronto-Socorro do Hospital Universitário da Universidade de São Paulo para o atendimento de crianças e adolescentes com diagnóstico de faringotonsilite aguda. RESULTADOS: Foram estudadas 1039 crianças e adolescentes. Com base no quadro clínico, antibiótico seria prescrito em 530 pacientes (51%), e com o uso da PRE e/ou cultura de orofaringe foi prescrito em 268 (25,8%) pacientes. Das 509 crianças que não receberiam antibiótico pelo quadro clínico, 157 tiveram PRE e/ou cultura de orofaringe positiva. O diagnóstico baseado no quadro clínico apresentou sensibilidade de 63,06% (IC-95%:62,95-63,17%); especificidade de 57,33% (IC-95%:57,25-57,41%); valor preditivo positivo de 50,57% (IC-95%:50,47-50,66%) e valor preditivo negativo de 69,16% (IC-95%: 50,47-50,66%). CONCLUSÕES: Neste estudo o diagnóstico clínico da faringotonsilite estreptocócica mostrou baixa sensibilidade e especificidade. O uso rotineiro da prova rápida para pesquisa de estreptococo permitiu uma redução do uso de antibiótico e a identificação de crianças e adolescentes com faringotonsilite estreptocócicas que não receberiam antibiótico e estariam sob o risco das complicações da infecção estreptocócica / BACKGROUND: Sore throat is a common disease in the pediatric emergency room. OBJECTIVES: The objective of this study was to evaluate the impact of routine performance of rapid antigen detection test (RADT) in the diagnosis and treatment of acute pharyngitis in children treated at an academic hospital. METHODS: This is a prospective, observational, protocol compliance, established at the Emergency of Hospital Universitário - Universidade de São Paulo for the care of children and adolescents diagnosed with acute pharyngitis. RESULTS: We studied 1039 children and adolescents. Based on clinical findings, antibiotic would be prescribed in 530 patients (51%) and using the RADT or sore throat culture was prescribed in 268 patients. Of the 509 children who did not receive antibiotics for the clinical, 157 had positive RADT or sore throat culture. The diagnosis based on clinical sensitivity was 63,06% (IC 95% 62,95- 63,17%), specificity 57,3% (IC 95% 57,25-57,41%), positive predictive value of 50,57% (IC 95% 50,47-50,66%) and negative predictive value of 69,16% (IC 95% 50,47-50,66%). CONCLUSIONS: In this study the clinical diagnosis of streptococcal pharyngitis had low sensitivity and specificity. The routine use of rapid test for streptococcal research led to a reduction of antibiotic use and the identification of a risk group for complication of streptococcal infection

Ma, Hok Lun. / Thesis submitted in: December 2008. / Thesis (M.Phil.)--Chinese University of Hong Kong, 2009. / Includes bibliographical references (leaves 233-273). / Abstracts in English and Chinese. / Abstract --- p.i / Abstract (Chinese version) --- p.v / Tables of contents --- p.vi / Acknowledgement --- p.xvi / List of figures --- p.xvii / List of tables --- p.xxi / List of abbreviations and symbols --- p.xxviii / Chapter Chapter 1 --- Introduction --- p.1 / Chapter 1.1 --- Respiratory illnesses in children --- p.1 / Chapter 1.1.1 --- Worldwide burden of childhood pneumonia --- p.1 / Chapter 1.1.2 --- Further mortality related to childhood pneumonia --- p.4 / Chapter 1.2 --- Etiology agent of childhood respiratory illnesses --- p.5 / Chapter 1.2.1 --- Difficulties in determining etiological agent --- p.5 / Chapter 1.2.2 --- Overall situation of etiological agents in childhood pneumonia --- p.6 / Chapter 1.2.3 --- Relationship between age and pathogens --- p.9 / Chapter 1.2.4 --- "Relationship between serotypes, carriage and invasiveness" --- p.11 / Chapter 1.2.4.1 --- Carriage and Invasiveness --- p.12 / Chapter 1.2.4.2.1 --- Carriage of S. pneumoniae and H. influenzae in children in Hong Kong --- p.12 / Chapter 1.2.4.2.2 --- "Serotypes, carriage and invasiveness in S. pneumoniae" --- p.14 / Chapter 1.2.4.2.3 --- "Serotypes, carriage and invasiveness in H. influenzae" --- p.17 / Chapter 1.3 --- Epidemiology of antibiotic-resistant pathogens --- p.18 / Chapter 1.3.1 --- Molecular typing methods --- p.18 / Chapter 1.3.2 --- Spread of antibiotic-resistant pathogens --- p.20 / Chapter 1.3.2.1 --- Spread of antibiotic-resistant S. pneumoniae --- p.26 / Chapter 1.3.2.1.1 --- Spread of penicillin-resistant S. pneumoniae --- p.26 / Chapter 1.3.2.1.1.1 --- Spread of Spanish-23F-1 --- p.27 / Chapter 1.3.2.1.1.2 --- Spread of Spanish-6B-2 --- p.28 / Chapter 1.3.2.1.1.3 --- Spread of antibiotic-resistant S. pneumoniae clones in Hong Kong --- p.28 / Chapter 1.3.2.1.2 --- Spread of cephalosporin-resistant S. pneumoniae --- p.29 / Chapter 1.3.2.1.3 --- Spread of macrolide-resistant S. pneumoniae --- p.30 / Chapter 1.3.2.1.4 --- Spread of fluoroquinolone-resistant S. pneumoniae --- p.31 / Chapter 1.3.2.2 --- Spread of antibiotic-resistant H. influenzae --- p.32 / Chapter 1.3.2.2.1 --- Spread of β-lactam-resistant H. influenzae --- p.32 / Chapter 1.3.2.2.2 --- Spread of macrolide-resistant H. influenzae --- p.33 / Chapter 1.3.2.2.3 --- Spread of fluoroquinolone-resistant H. influenzae --- p.34 / Chapter 1.4 --- Mechanism of antibiotic-resistance in respiratory pathogens --- p.36 / Chapter 1.4.1 --- Mechanism of antibiotic-resistance in S. pneumoniae --- p.37 / Chapter 1.4.1.1 --- Mechanism of penicillin- and cephalosporin-resistance in S. pneumoniae --- p.37 / Chapter 1.4.1.1.1 --- Penicillin-binding protein (PBP)-mediated mechanism --- p.37 / Chapter 1.4.1.1.2 --- PBP-independent mechanisms --- p.49 / Chapter 1.4.1.1.2.1 --- "Murine peptide branching genes, murMN operon" --- p.49 / Chapter 1.4.1.1.2.2 --- "Two-component system, CiaRH" --- p.50 / Chapter 1.4.1.1.2.3 --- "Putative glycosyltransferase, CpoA" --- p.52 / Chapter 1.4.1.1.3 --- RNA and protein expression studies on S. pneumoniae for β-lactam-resistance --- p.52 / Chapter 1.4.1.1.3.1 --- RNA expression in penicillin-sensitive S. pneumoniae --- p.53 / Chapter 1.4.1.1.3.2 --- Protein expression in penicillin-resistant S. pneumoniae --- p.53 / Chapter 1.4.1.2 --- Mechanism of macrolide- and lincosamide- resistance in S. pneumoniae --- p.54 / Chapter 1.4.1.3 --- Mechanism of tetracycline-resistance in S. pneumoniae --- p.55 / Chapter 1.4.1.4 --- Mechanism of fluoroquinolone-resistance in S. pneumoniae --- p.55 / Chapter 1.4.2 --- Mechanism of antibiotic-resistant in H. influenzae --- p.56 / Chapter 1.4.2.1 --- Mechanism of β-lactam-resistance in H. influenzae --- p.56 / Chapter 1.4.2.1.1 --- β-lactamase-producing H. influenzae --- p.56 / Chapter 1.4.2.1.2 --- β-lactamase-negative ampicillin-resistant (BLNAR) H. influenzae --- p.58 / Chapter 1.4.2.1.2.1 --- Relationship between amino acid substitutions in PBP3 and β-lactam- resistance --- p.58 / Chapter 1.4.2.1.2.2 --- Relationship between amino acid substitutions in AcrR and β-lactam-resistance --- p.60 / Chapter 1.4.2.2 --- Mechanism of macrolide-resistance in H. influenzae --- p.61 / Chapter 1.4.2.3 --- Mechanism of fluoroquinolone-resistance in H. influenzae --- p.64 / Chapter 1.5 --- Impact of vaccination --- p.65 / Chapter 1.5.1 --- H. influenzae type b vaccination --- p.65 / Chapter 1.5.1.1 --- Efficacy of Hib conjugate vaccine --- p.66 / Chapter 1.5.1.2 --- Herd immunity related to Hib conjugate vaccine --- p.66 / Chapter 1.5.2 --- Pneumococcal vaccination --- p.66 / Chapter 1.5.2.1 --- Vaccine efficacy and herd immunity of pneumococcal vaccines --- p.67 / Chapter 1.5.2.2 --- Development of conjugate vaccines with higher valency --- p.67 / Chapter 1.5.2.3 --- Serotype replacement --- p.67 / Chapter 1.5.2.4 --- Development of pneumococcal vaccines with new targets --- p.69 / Chapter 1.6 --- Objectives of this study --- p.70 / Chapter Chapter 2 --- Materials and methods --- p.72 / Chapter 2.1 --- Collection and Identification of microorganisms --- p.72 / Chapter 2.1.1 --- Collection of S. pneumoniae and H. influenzae --- p.72 / Chapter 2.1.2 --- Identification of S. pneumoniae and H. influenzae --- p.73 / Chapter 2.2 --- Serotyping of S. pneumoniae and H. influenzae --- p.74 / Chapter 2.2.1 --- Serotyping by polymerase chain reaction (PCR) --- p.74 / Chapter 2.2.1.1 --- Preparation of crude DNA extract --- p.74 / Chapter 2.2.1.2 --- Screening for common serotypes by multiplex PCR --- p.74 / Chapter 2.2.1.3 --- Composition of PCR Mix --- p.77 / Chapter 2.2.1.4 --- Serotyping PCR conditions --- p.81 / Chapter 2.2.1.5 --- Gel Electrophoresis --- p.81 / Chapter 2.2.2 --- Serotyping by serum agglutination --- p.82 / Chapter 2.3 --- Antimicrobial susceptibility testing --- p.83 / Chapter 2.4 --- Clonal analysis of penicillin- and cephalosporin-resistant S. pneumoniae --- p.87 / Chapter 2.4.1 --- Pulsed-field Gel Electrophoresis (PFGE) --- p.87 / Chapter 2.4.1.1 --- Preparation of agarose plugs for PFGE --- p.87 / Chapter 2.4.1.2 --- Lysis of bacteria in agarose plugs --- p.89 / Chapter 2.4.1.3 --- Digestion of chromosomal DNA by restriction enzyme --- p.89 / Chapter 2.4.2 --- Multi-locus sequence typing (MLST) --- p.90 / Chapter 2.4.2.1 --- PCR amplification of house-keeping genes in MLST --- p.90 / Chapter 2.4.2.1.1 --- Preparation of DNA from agarose plugs --- p.92 / Chapter 2.4.2.1.2 --- Composition of PCR Mix --- p.92 / Chapter 2.4.2.1.3 --- MLST PCR conditions --- p.92 / Chapter 2.4.2.1.4 --- Gel Electrophoresis of MLST PCR products --- p.92 / Chapter 2.4.2.1.5 --- MLST PCR products purification --- p.93 / Chapter 2.4.2.2 --- Sequencing of housekeeping genes in MLST --- p.93 / Chapter 2.4.2.3 --- Sequencing analysis and sequence type (ST) determination in MLST --- p.94 / Chapter 2.4.3 --- Extended panel of antibiotic susceptibility testing on S. pneumoniae with known STs --- p.94 / Chapter 2.5 --- Analysis on potential penicillin- and cephalosporin-resistance mechanisms in S. pneumoniae --- p.96 / Chapter 2.5.1 --- Sequencing of potnetial penicillin- and cephalosporin- resistance determinants in S. pneumoniae --- p.96 / Chapter 2.5.1.1 --- Primer design of penicillin-binding protein (PBP) genes --- p.96 / Chapter 2.5.1.2 --- Primer design of non-PBP resistance determinants --- p.100 / Chapter 2.5.1.3 --- PCR amplification and sequencing of resistant determinants --- p.100 / Chapter 2.5.1.4 --- Sequence analysis --- p.100 / Chapter 2.5.2 --- Study on efflux mechanism of S. pneumoniae --- p.103 / Chapter 2.5.2.1 --- Modification of macrodilution for efflux assay --- p.103 / Chapter 2.5.2.2 --- Cefotaxime MIC determination with efflux inhibitors --- p.104 / Chapter 2.5.2.3 --- Determination of appropriate CCCP concentration --- p.105 / Chapter 2.5.2.4 --- Growth curve with efflux inhibitor --- p.105 / Chapter 2.5.3 --- Heteroresistance assay of S. pneumoniae --- p.106 / Chapter 2.5.4 --- "RNA expression study on penicillin- and cefotaxime-resistance determinants (pbp2x, pbpla and pbp2a) of S. pneumoniae" --- p.107 / Chapter 2.5.4.1 --- Growth of S. pneumoniae for RNA extraction --- p.107 / Chapter 2.5.4.2 --- RNA extraction and DNase digestion --- p.107 / Chapter 2.5.4.3 --- cDNA synthesis and real-time PCR --- p.108 / Chapter 2.6 --- Analysis on cephalosporin- and macrolide-resistance mechanisms in H. influenzae --- p.111 / Chapter 2.6.1 --- β-lactamase production of H. influenzae --- p.111 / Chapter 2.6.1.1 --- Nitrocefin Hydrolysis --- p.111 / Chapter 2.6.1.2 --- Screening for the presence of p-lactamase gene (blaTEM-1 and blaROB-1) by multiplex PCR --- p.111 / Chapter 2.6.2 --- PCR detection and sequencing of β-lactam- and macrolide- resistance determinants in H. influenzae --- p.113 / Chapter Chapter 3 --- Results of S. pneumoniae and H. influenzae children study --- p.116 / Chapter 3.1 --- Patient demographics of children study --- p.116 / Chapter 3.2 --- Serotype distributions --- p.117 / Chapter 3.2.1 --- Serotypes / serogroup distribution in S. pneumoniae --- p.117 / Chapter 3.2.2 --- Serotype distribution in H. influenzae children study --- p.120 / Chapter 3.3 --- Antibiotic susceptibilities and resistance antibiograms --- p.122 / Chapter 3.3.1 --- Antibiotic susceptibilities of S. pneumoniae --- p.122 / Chapter 3.3.2 --- Relationship between antibiotic resistance profiles and serotypes in S.pneumoniae --- p.126 / Chapter 3.3.3 --- Antibiotic susceptibilities of H. influenzae --- p.135 / Chapter 3.3.4 --- Antibiotic resistance profiles of H. influenzae --- p.138 / Chapter 3.4 --- Clonal analysis of penicillin- and cephalosporin-resistant S.pneumoniae --- p.139 / Chapter 3.4.1 --- Pulsed-field gel electrophoresis (PFGE) of S. pneumoniae --- p.139 / Chapter 3.4.2 --- Multi-locus sequence typing of S. pneumoniae --- p.141 / Chapter 3.5 --- Analysis of the penicillin- and cephalosporin-resistance determinants in S. pneumoniae --- p.143 / Chapter 3.5.1 --- "Sequence analysis of major pbp genes (pbp2x, pbpla and pbp2a)" --- p.143 / Chapter 3.5.2 --- "Sequence analysis of other potential penicillin- and cephalosporin- resistance determinants (pbp 1 b, pbp2b, pbp3, cpoA, ciaRH and murMN)" --- p.152 / Chapter 3.5.3 --- Sequence analysis of putative promoter sequences of pbp genes --- p.167 / Chapter 3.5.4 --- Efflux Inhibition Assay --- p.171 / Chapter 3.5.5 --- Heteroresistance Assay --- p.177 / Chapter 3.5.6 --- "RNA expression study on penicillin- and cephalosporin resistance determinants (pbp2x, pbpla and pbp2a)" --- p.179 / Chapter 3.6 --- Analysis of β-lactam-resistance determinants in H. influenzae --- p.185 / Chapter 3.6.1 --- β-lactamase production and blaTEM-1 promoter study --- p.185 / Chapter 3.6.2 --- "Sequence analysis of β-lactam-resistance determinants (ftsl, acrR genes, AcrAB-TolC efflux pump)" --- p.188 / Chapter 3.6.2.1 --- Sequence analysis offtsl --- p.188 / Chapter 3.6.2.2 --- Analysis of acrR and AcrAB-TolC efflux pump --- p.189 / Chapter 3.7 --- "Analysis of macrolide-resistance determinants in H, influenzae (AcrAB-TolC efflux pump, 23SrRNA, Ribosomal proteins L4 and L22)" --- p.199 / Chapter Chapter 4 --- Discussion on S. pneumoniae and H. influenzae children study --- p.204 / Chapter 4.1 --- Carriage rate of S. pneumoniae children collection --- p.204 / Chapter 4.2 --- Serotype distribution --- p.205 / Chapter 4.2.1 --- Serotype distribution and potential vaccine coverage in S. pneumoniae --- p.205 / Chapter 4.2.2 --- Serotype distribution in H. influenzae --- p.209 / Chapter 4.3 --- Antimicrobial resistance --- p.210 / Chapter 4.3.1 --- Antimicrobial resistance in S. pneumoniae --- p.210 / Chapter 4.3.2 --- Antimicrobial resistance in H. influenzae --- p.214 / Chapter 4.4 --- "Clonal analysis of high-level β-lactam-resistant S, pneumoniae" --- p.217 / Chapter 4.5 --- "β-lactam-resistance mechanisms in S, pneunomiae" --- p.220 / Chapter 4.6 --- Antimicrobial resistance mechanisms in H. influenzae --- p.224 / Chapter 4.6.1 --- β-lactam-resistance mechanism in β-lactamase-producing H. influenzae --- p.224 / Chapter 4.6.1.1 --- Variations in blaTEM-1 promoters in β-lactamase-producing H.influenzae --- p.224 / Chapter 4.6.1.2 --- β-lactam-resistance in β-lactamase-nonproducing H. influenzae --- p.225 / Chapter 4.6.2 --- Macrolide-resistance mechanisms in H. influenzae --- p.228 / Chapter Chapter 5 --- Conclusion and future studies --- p.230 / Chapter 5.1 --- "S, pneumoniae children study" --- p.230 / Chapter 5.2 --- H. influenzae children study --- p.231 / Chapter 5.3 --- Future studies --- p.232 / Bibliography --- p.233 / Appendix I 一 Sequence alignments and Tables --- p.274 / Appendix II 一 Materials and Methods --- p.313

Aquaculture is the fastest growing food industry in the world and it accounts for roughly half of the world's fish supply. The majority of global aquaculture production occurs in freshwater systems that are increasingly subject to multiple uses by different stakeholders. Given the overall scarcity of freshwater on a global scale, freshwater aquaculture will face increasing environmental constraints that will demand an ever better understanding of its potential impacts on the aquatic environment and human health. This thesis consists of a series of studies that, collectively, contribute to further our understanding on the effects of freshwater aquaculture effluents on aquatic ecosystems, on the effects and environmental safety of antibiotics used in freshwater aquaculture on aquatic bacterial communities and on the link between antibiotic pollution and antibiotic resistance. Chapter 2 reviews the effects of freshwater aquaculture effluents on stream ecosystems using land-based salmonid farms as a case study. In this chapter I discuss relevant considerations related to the temporal and spatial scales of effluent discharge and ecological effects that highlight the need to characterize the patterns of stressor discharge when assessing environmental impacts and designing ecological effects studies. I also discuss the potential role of multiple stressors - with an emphasis on veterinary medicines - in disrupting ecosystem structure and function. Overall, the critical analysis presented in this chapter indicates that further research on the effects of veterinary medicines using relevant exposure scenarios would significantly contribute to our understanding of their impact in relation to other effluent stressors. Chapter 3 is a general methods chapter that describes the stream microcosm system used to assess the effects of erythromycin thiocyanate (ERT) and florfenicol (FFC) on bacterial communities of stream biofilms. This chapter presents the results of preliminary experiments whose results provided relevant information on the overall operation of the microcosms and on the variability of major physical and biological variables. This information guided the experimental designs used to assess the effects of FFC and ERT on the bacterial community structure of stream biofilms. Chapter 4 presents the results of the experiment conducted to assess the effects of FFC on the bacterial community structure of developing biofilms. The objective was to assess changes in bacterial community structure along a gradient of FFC concentrations that could provide insight into the type and magnitude of effects that could be expected from episodic exposure of stream biofilms to FFC in headwater streams. At 10 and 20 days of biofilm development, bacterial community structure differentiated in a pattern consistent with the FFC concentration gradient and there was a positive relationship between bacterial richness and bacterial diversity with FFC concentration. At 15 days of biofilm development there was also a positive relationship between FFC concentration and the surface coverage of bacteria and extracellular polymeric substances. These trends declined as the biofilm developed a more complex architecture, in terms of thickness and in the surface coverage of algae. The results are consistent with an initial stimulatory effect of FFC on biofilm formation that triggered changes in bacterial community structure that were gradually compressed as the development of a complex biofilm architecture increased the relative importance of autogenic ecological processes. The results suggest that the co-occurrence of FFC with bacterial pathogens in effluents and wastewaters may favour their persistence in the environment by enhancing biofilm formation. Chapter 5 presents the results of the experiment conducted to assess the effects of ERT on the bacterial community structure of developing biofilms. Currently, Aquamycin® 100 - a Type A medicated article (i.e., Premix) containing 100 g ERT lb-1 and used to produce a Type C medicated feed - is a candidate drug for approval by the US FDA to control mortality associated with bacterial kidney disease in freshwater salmonids. The objective of this experiment was to assess the effects of ERT on the bacterial community structure of stream biofilms using an exposure period consistent with the 28-day treatment regime suggested for Aquamycin® 100. The results provide no evidence to suggest that a 30-day exposure to ERT concentrations in the range of 10 μg L-1 (i.e., 7.3 ± 3.9 μg L-1) would lead to changes in the bacterial community structure or overall bacterial abundance of stream biofilms, while they suggest that these effects may occur at concentrations in the range of 100 μg L-1 (i.e., 87.2 ± 31.1 μg L-1). Chapter 6 attempts to determine whether environmental concentrations of antibiotics and concentrations representing action limits used in environmental risk assessment may exert a selective pressure on clinically relevant bacteria in the environment. In this chapter I use bacterial inhibition as an assessment endpoint to link antibiotic selective pressures to the prevalence of resistance in bacterial populations. Species sensitivity distributions were derived for three antibiotics by fitting log-logistic models to endpoints calculated from minimum inhibitory concentration (MIC) distributions based on worldwide data collated by the European Committee on Antimicrobial Susceptibility Testing (EUCAST). Bacteria represented in these distributions were placed in a broader context by performing a brief phylogenetic analysis. The potentially affected fraction of bacterial genera at measured environmental concentrations of antibiotics and environmental risk assessment action limits was used as a proxy for antibiotic selective pressure. Measured environmental concentrations and environmental risk assessment action limits were also directly compared to wild-type cut-off values. Results suggest that measured environmental concentrations of antibiotics and concentrations representing environmental risk assessment action limits are high enough to exert a selective pressure on clinically relevant bacteria that may lead to an increase in the prevalence of resistance. Chapter 7 presents the results of an exploratory analysis conducted to assess the abundance of class 1 integrons in stream biofilms exposed to FFC and ERT. There was no pattern in the abundance of intI1 genes consistent with the treatment of FFC and ERT, suggesting either the absence of gene cassettes involved in dealing with selective pressures caused by these antibiotics or that the concentrations tested were below those required to give them a selective advantage. Chapter 8 is a brief general discussion that brings together the findings of the thesis and makes suggestions for future research. Key areas identified for future research include assessing in further detail the stimulatory effect of FFC on biofilm formation in complex bacterial communities, the interactive effects of multiple aquaculture effluent stressors on aquatic bacterial communities and their potential effects on the development of antibiotic resistance, the fate of FFC and ERT in stream ecosystems, and further developing the analysis based on MIC distributions presented in chapter 6 to assess the potential effects of antibiotic pollution on the selection of multi-drug resistance in the environment.

Diss. (sammanfattning) Stockholm : Karol inst., 2004. / Härtill 4 uppsatser.

Diss. (sammanfattning) Stockholm : Karol. inst., 2004. / Härtill 4 uppsatser.

Diss. (sammanfattning) Linköping : Univ., 2004. / Härtill 5 uppsatser.

Diss. (sammanfattning) Stockholm : Karolinska institutet, 2005. / Härtill 4 uppsatser.