A consequence of antimicrobial use in food production systems is the potential for antimicrobial resistant (AMR) bacteria to develop and transfer to the human population via the food chain. Integrons have been identified as critical factors in the development of AMR. Despite Australia being amongst the world’s largest exporters of beef, there is a general lack of data on the prevalence of AMR in bacteria from Australian beef cattle. Consequently, the aim of this study has been to contribute to research strategies and knowledge of AMR by investigating integron-associated antimicrobial resistance in Australian beef cattle production systems. This study developed a protocol that targets resistance integrons. The protocol was trialled on 50 bovine faecal samples with a total of 39 integron-containing isolates recovered. Characterisation of the integrons was performed and it was determined that the majority of integrons harboured genes encoding resistance to trimethoprim (dfr) and streptomycin / spectinomycin (aad). The protocol provides an opportunity to rapidly interrogate populations of bacteria within a defined sample for resistance integrons. The protocol was used to investigate integron-associated AMR in Australian beef cattle production systems. Each production system was investigated for resistance integrons to determine if production practices were impacting on the prevalence and types of AMR present. The investigation found that the prevalence of integron-containing bacteria was higher in lot-fed cattle than grass-fed cattle which in turn were higher than organically produced cattle. However, the types of AMR differed very little across production systems and suggested that the higher prevalence of integrons in lot-fed samples may be a function of the intensive nature of this type of production system rather than a result of selective pressure caused by antibiotic use. Although there appeared to be no obvious trends in the types of gene cassettes carried by integrons from differing production systems, if lot-fed cattle continually arrive at slaughter with a higher prevalence of integron-containing bacteria then these cattle may be more likely to contribute to contamination of the final product. Samples from lot-fed, grass-fed and organically produced cattle at slaughter were collected. Despite the apparent unrelatedness of the cattle herds, there was little difference in the PCR prevalence of class 1 and class 2 integrase, the gene cassettes harboured by the integrons, and the host organism for the integron. Genes encoding resistance to streptomycin and chloramphenicol (catB8) dominated the majority of arrays regardless of production system, although two novel arrays were identified. One of the arrays, cmlA5-blaoxa-10-aadA1, was found in A. veronii biovar Sobria isolates from organic cattle thereby confirming the ability of multi-resistant integrons to persist in environments that have no obvious antimicrobial selection. The abattoir study revealed an unusually high prevalence of Aeromonas isolates carrying integrons. It appeared to implicate the abattoir environment as a direct contributor to the presence of integron-containing bacteria in each herd. Characterisation of each Aeromonas isolate determined that the isolates were not clonal in nature and not a result of persistent contamination at the abattoir. It seemed more probable that the Aeromonas isolates were present in the cattle prior to arrival and may have been acquired from the environment. To explore this further, soil samples from cattle associated and non-cattle associated areas were tested for the presence of resistance integrons. The prevalence of class 1 integrons was higher in cattle-associated soil samples than in non-cattle-associated soil samples, however the diversity of gene cassettes harboured by the integrons was greater in non-cattle-associated samples than cattle-associated samples. An array harbouring blaoxa-30 was isolated from a non-cattle-associated soil sample. Its presence continues to highlight the potential for multi-resistant integrons to exist in environments with no obvious antimicrobial selection pressure.The detection of seldom reported class 1 integron arrays in this study indicates the potential of the developed protocol to interrogate populations of bacteria for resistance integrons. This is highlighted further by the isolation of a novel class 2 integron. This novel class 2 integron from Providencia stuartii possesses a class 2 integrase that is predicted to be fully functional and has a variable region comprising nine ORFs that do not encode AMR genes. Overall, this study demonstrated that integrons are present in all cattle production systems employed in Australia and although the prevalence of integrons appeared to align with the anticipated use of antimicrobials in each system, differences in the integrons from each production system were not evident. As the similarities observed between integrons extend to isolates from organically produced cattle and from non-cattle associated soil samples it is suggested that the majority of integrons identified in this study are not present as a direct result of antimicrobial use in cattle production. Nevertheless, the potential of integrons to capture AMR genes remains and their presence in beef cattle highlights the need for the continued prudent use of antimicrobials.

Host defense peptides (HDPs) provide innate immune defense against invasive S. aureus infection. Recent studies suggest potential cross-resistance between HDPs and the lipopeptide antibiotic, daptomycin (DAP). Isolates that exhibit DAP non-susceptible phenotypes may have virulence advantages and pose challenges to effective treatment. The current studies were performed to compare the efficacies and mechanisms of action of native and engineered HDPs vs. clinical S. aureus strain pairs which differed in susceptibility to daptomycin in vitro. Ultrasensitive radial diffusion and multi-colored flow cytometry were employed to analyze distinctive susceptibilities and mechanisms of resistance, respectively. Overall efficacies were greater vs. DAP-susceptible (DSSA) vs. DAP non-susceptible (DNSA) S. aureus isolates for some but not all HDPs. Efficacy profiles of certain HDPs were influenced by pH, regardless of whether the particular isolate was DSSA or DNSA phenotype. Mechanistically, DSSA and DNSA isolates differed in responses to specific HDPs regarding cell energetics, membrane permeability, cytoplasm membrane turnover, and cell death protease induction. DSSA and DNSA strain pairs exhibited non-identical mechanisms of resistance to HDPs. At pH 7.5, as expected, HDPs hNP-1 and RP-1 exerted significantly greater efficacy on susceptible control strain ISP479C vs. its resistant counterpart ISP479R. These data suggest different mechanisms of HDP resistance are active in differing DNSA strains. These preliminary results are under further investigation, as are the genetic determinant(s) that may emerge during infection. If substantiated, these findings would imply multiple modes of survival of S. aureus in the face of DAP or HDPs.

How do microbes adapt to challenges from the environment? In this thesis, two distinct cases were examined through structural and biochemical methods. In the first, we followed a real-time protein evolution of HisA to a novel function. The second case was fusidic acid (FA) resistance mediated by the protein FusB in Staphylococcus aureus. In the first study, the aim was to understand how mutants of HisA from the histidine biosynthetic pathway could evolve a novel TrpF activity and further evolve to generalist or specialist enzymes. We solved the crystal structure of wild type Salmonella enterica HisA in its apo-state and the structures of the mutants D7N and D7N/D176A in complex with the substrate ProFAR. These two distinct complex structures showed us the coupled conformational changes of HisA and ProFAR before catalysis. We also solved crystal structures of ten mutants, some in complex with substrate or product. The structures indicate that bi-functional mutants adopt distinct loop conformations linked to the two functions and that mutations in specialist enzymes favor one of the conformations. We also observed biphasic relationships in which small changes in the activities of low-performance enzymes had large effects on fitness, until a threshold, above which large changes in enzyme performance had little effect on fitness. Fusidic acid blocks protein translation by locking elongation factor G (EF-G) to the ribosome after GTP hydrolysis in elongation and recycling of bacterial protein synthesis. To understand the rescue mechanism, we solved the crystal structure of FusB at 1.6Å resolution. The structure showed that FusB is a two-domain protein and C-terminal domain contains a treble clef zinc finger. Using hybrid constructs between S. aureus EF-G that binds to FusB, and E. coli EF-G that does not, the binding determinants were located to domain IV of EF-G. This was further supported by small-angle X-ray scattering studies of the FusB·EF-G complex. Using single-molecule methods, we observed FusB frequently binding to the ribosome and rescue of FA-inhibited elongation by effects on the non-rotated state ribosome. Ribosome binding of FusB was confirmed by isothermal titration calorimetry.

Thesis (MSc Food Sc)--Stellenbosch University, 2013. / ENGLISH ABSTRACT: Food-borne disease outbreaks caused by Escherichia coli have been linked to the use of faecally-polluted irrigation waters. Thus the overall aim of this research was to evaluate irrigation water and agricultural effluents as sources of antibiotic resistant E. coli in the Western Cape. The aim of the first study was to enumerate and characterise E. coli present in irrigation water and in potential contamination sources. Maximum total coliform and E. coli counts for irrigation sites was log 7.862 and log 5.364 MPN.100 mL-1, respectively. Five out of seven irrigation sites had E. coli counts exceeding national and international guidelines for ‘safe’ irrigation water (<1 000 counts.100 mL-1), making it unsafe for the irrigation of fresh produce. In this study, 46.6% of the E. coli strains were characterised in phylogenetic group B1. It has been shown that E. coli in group B1 have the ability to survive and persist in the external environment. Group B1 was also the most common group among isolates from irrigation sites (79.4%), while isolates from environmental sites grouped mainly in group A0 (54.1%). It was concluded that the wide variation of E. coli types present in irrigation water is a concern that should be further investigated. This raises human health implications since the increased exposure to faecal organisms increases the risk of food-borne outbreaks. The E. coli isolates (n = 120) and the marker (n = 37) and reference strains (n = 6), were evaluated for antibiotic resistance to seven medically-important antibiotics from different classes using the Kirby-Bauer disc diffusion method. Thirty-five strains (35/163 = 21.5%) exhibited resistance to one or more antibiotics. Piggery effluent was found to harbour the most antibiotic resistant E. coli isolates (9/35 = 25.7%). Among the resistant E. coli strains, the highest occurrence of antibiotic resistance was to trimethoprim (2.5 μg) (68.6%), tetracycline (30 μg) (57.1%), ampicillin (10 μg) (45.7%) and chloramphenicol (30 μg) (34.3%). Seventy-four percent (26/35) exhibited multiple antibiotic resistances to two or more antibiotics. The antibiotic resistant E. coli strains were evaluated for the presence of pathotypes using Polymerase Chain Reaction analysis to detect Intestinal Pathogenic E. coli (InPEC) and Extra-intestinal Pathogenic E. coli (ExPEC). Five InPEC strains were characterised as four Entero-Pathogenic E. coli (EPEC) strains resistant to three or four antibiotics and one Entero-Aggregative E. coli (EAEC) strain resistant to trimethoprim. The antibiotic resistant EAEC strain also possessed the ExPEC-related gene iutA. Two E. coli isolated from the Mosselbank River were both resistant to chloramphenicol and trimethoprim and also possessed the ExPEC-related gene iutA. It was concluded that the diverse antibiotic resistances of E. coli pathotypes present in irrigation water is a concern that should be further investigated. / AFRIKAANSE OPSOMMING: Voedselverwante siekte uitbrake wat deur Escherichia coli veroorsaak word, is gekoppel aan die gebruik van fekale besoedelde besproeiingswater. Dus was die hoof doel van die navorsing om besproeiingswater en landbou-afvalwater te evalueer as bronne van antibiotika-weerstandbiedende E. coli in die Wes-kaap. Die doel van die eerste studie was om die getalle en eienskappe van E. coli te bepaal wat in besproeiingswater en in ander potensiële besmettingsbronne teenwoordig is. Maksimum totale koliforme en E. coli-tellings vir besproeiingspunte was onderskeidelik log 7.862 en log 5.364 MPN.100 mL-1. Vyf uit sewe besproeiingspunte het E. coli-tellings gehad wat hoër is as die nasionale en internasionale riglyne vir ‘veilige’ besproeiingswater (<1 000 tellings.100 mL-1). Dit maak dit onveilig vir die besproeiing van vars produkte. In hierdie studie was 46.6% van die E. coli-stamme in filogenetiese groep B1 gegroepeer. Dit is reeds bewys dat E. coli in groep B1 oor die vermoë beskik om in die eksterne omgewing te oorleef en voort te bestaan. Groep B1 was ook die mees algemene groep onder die isolate van besproeiingspunte (79.4%), terwyl isolate van omgewingspunte meestal in groep A0 (54.1%) gegroepeer is. Die breë variasie E. coli tipes in die besproeiingswater is bekommerniswaardig en sal gevolglik verder ondersoek moet word. Dit bring gesondsheidsimplikasies mee vir mense aangesien die verhoogde blootstelling aan fekale organismes die risiko van voedselverwante uitbrake verhoog. Die E. coli isolate (n = 120) en die merker (n = 37) en verwysingsstamme (n = 6), is teen sewe medies belangrike antibiotikas uit verskillende klasse getoets vir antibiotika-weerstandbiedendheid. Die Kirby-Bauer skyfie diffusie metode is gebruik. Vyf-en-dertig stamme (35/163 = 21.5%) het weerstand teen een of meer antibiotika getoon. Dit is gevind dat vark-afvalwater die meeste antibiotika-weerstandbiedende E. coli-isolate (9/35 = 25.7%) bevat. Die weerstandbiedende E. coli-stamme het die hoogste antibiotika-weerstandheid getoon teen "trimethoprim" (2.5 μg) (68.6%), tetrasiklien (30 μg) (57.1%), ampisillien (10 μg) (45.7%) en chloramfenikol (30 μg) (34.3%). Vier-en-sewentig persent (26/35) het meervoudige weerstandbiedheid teen twee of meer antibiotikas getoon. Die antibiotika-weerstandbiedende E. Coli stamme is getoets vir die teenwoordigheid van patogene deur van Polimerase Ketting Reaksie analise gebruik te maak om ‘Intestinal Pathogenic’ E. coli (InPEC) en ‘Extra-intestinal Pathogenic’ E. coli (ExPEC) op te spoor. Vyf InPEC-stamme is geklassifiseer as vier ‘Entero-Pathogenic’ E. coli (EPEC)-stamme wat weerstandbiedend teen drie of vier antibiotika getoon het en een ‘Entero-Aggregative’ E. coli (EAEC)-stam wat weerstandbiedendheid getoon het teen "trimethoprim". Die antibiotika-weerstandbiedende EAEC-stam het ook die ExPEC-verwante geen, iutA, besit. Twee E. coli isolate van die Mosselbankrivier het weerstand teen beide chloramfenikol en "trimethoprim" getoon en het ook die ExPEC-verwante geen, iutA, besit. Daar is tot die gevolgtrekking gekom dat die diverse antibiotika-weerstandbiedenheid van E. coli patogene teenwoordig in besproeiingswaters bekommerniswaardig is en verder ondersoek behoort te word.

Made available in DSpace on 2014-06-11T19:32:52Z (GMT). No. of bitstreams: 0 Previous issue date: 2010-04-22Bitstream added on 2014-06-13T19:03:31Z : No. of bitstreams: 1 silva_rml_dr_jabo.pdf: 986300 bytes, checksum: 4a3600af533a0403550481d53c48eaae (MD5) / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) / Dentre os agentes bacterianos amplamente distribuídos no ecossistema aquático, destacam-se as famílias Aeromonadaceae e Enterobactereaceae. Os peixes são importantes veículos de infecções humanas causadas por essas bactérias. Com este enfoque, o estudo foi realizado com o objetivo de verificar a ocorrência de Aeromonas sp., coliformes termotolerantes e bactérias heterotróficas mesófilas em pisciculturas da Região da Baixada Ocidental Maranhense. Para tal, foram selecionadas no período de outubro de 2008 a março de 2009, doze propriedades nos municípios de Pinheiro, Palmeirândia e Perimirim e colhidas amostras de água dos viveiros e peixes de cada piscicultura, totalizando 96 amostras. Em 100% das amostras analisadas foi confirmada a presença de Aeromonas sp., classificadas em quatro espécies, A. hydrophila (87,03%), A. caviae (8,02%), A. veronii sobria (3,70%), A. schubertii (1,23%). Essas ainda apresentaram elevados percentuais de resistência e multiresistência a 12 antimicrobianos testados. As populações de bactérias heterotróficas mesófilas nas pisciculturas variaram de 102 UFC/mL a 104 UFC/mL de água. Das pisciculturas avaliadas, sete apresentaram pelo menos uma amostra em desacordo com o padrão para coliformes termotolerantes. As amostras analisadas revelaram - se como possíveis vias de transmissão de aeromonas potencialmente patogênicas para peixes e ser humano, representando risco para a saúde da população consumidora dos organismos cultivados nessas propriedades / Among widely distributed agents in the aquatic ecosystem can be outstanding the families Aeromonadaceae and Enterobacteriaceae. The fishs are very important vehicles of human infections caused for these bacteria. With the approach the study intended to verify the occurrence of Aeromonas sp., thermotolerant coliforms and heterotrophic mesophilic bacteria in fish farms located in Occidental Baixada Maranhense Region. Twelve properties in the Pinheiro, Palmeirândia and Perimirim’ s cities were selected in the period from October of 2008 to March of 2009, and harvested water pond and fish samples of each fish farm, with the total of 96 samples. Aeromonas sp. was confirmed in 100% of samples, classified in four species, A. hydrophila (87,03%), A. caviae (8,02%), A. veronii sobria (3,70%), A.schubertii (1,23%). These bacteria showed high resistance and multiple resistance to the 12 antibiotics tested. The populations of heterotrophic mesophilic bacteria varied between 1,4 x 102 UFC/mL to 7,2 x 103 UFC/mL/. Seven fish farms showed at least one sample in disagreement with the standard to termotholerant coliforms. The samples of water and fish revealed the possible sources of potentially pathogenic contamination of aeromonas for fish and human being representing risk for health of the population healthy that consume the organisms cultivated in these properties

Made available in DSpace on 2014-06-11T19:32:53Z (GMT). No. of bitstreams: 0 Previous issue date: 2006-10-03Bitstream added on 2014-06-13T19:22:44Z : No. of bitstreams: 1 rodolpho_d_dr_jabo.pdf: 299270 bytes, checksum: 8a1668550cacade414ec08c3350e51f4 (MD5) / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) / Escherichia coli Shigatoxigênica (STEC) tem sido implicada como agente causador de severas doenças humanas. Amostras de carne moída, moedor de carne e mãos de manipuladores de 23 estabelecimentos comerciais foram testadas para o isolamento de E. coli usando métodos microbiológicos padronizados. Um total de 287 cepas de E. coli isoladas destes diferentes locais foram submetidas ao PCR para detecção de genes stx 1, stx 2 e eae. As cepas positivas para o gene stx foram analisadas verificando se pertenciam ao sorogrupo 0157. Quatro cepas de STEC foram isoladas, sendo 2 de carne moída e 2 de moedor de carne, todas possuíam o gene stx 2, sendo negativas para a presença do gene eae e o sorogrupo 0157. Todas as E. coli isoladas, incluindo as 4 STEC, foram pesquisadas para sua resistência a 12 antibióticos. Altos níveis de resistência frente aos diferentes agentes antimicrobianos foram detectados; as resistências maiores foram observadas para a tetraciclina (76,6%), amoxicilina (64,1 %) e cefalotina (58,8%). Os altos níveis de resistência antimicrobiana salientam a necessidade para a utilização racional destes agentes em bovinos. Foram observadas índices elevados de sensibilidade frente a associação amoxicilina + ácido clavulânico (96,6%), ceftriaxona (92,7%) e gentamicina (90,3%). / Shiga toxigenic Escherichía colí (STEC) has been implicated as the causative agent of several human diseases. Samples from 23 retail meat stores (ground beef, grinding-machine and human hand) were assayed for E. calí isolation using microbiological standard methods. A total of 287 E. colí isolates from these different origins were submitted to polymerase chain reaction for the detection of stx 1, stx 2 and eae genes. The isolates positives for stx gene were serotyped for 0157. Four STEC isolates were recovered, 2 from ground beef and 2 from grinding-machine; ali harbored the stx 2 gene and were negative for the presence of the eae gene and the serogroup 0157. Ali E. colí isolates including the four STEC were screened for antibiotic resistance. High levels of resistance against different antimicrobial agents were detected; those most commonly observed were to tetracycline (76.6%), amoxicillin (64.1 %) and cephalothin (58.8%). Such high levels of antimicrobial agents' resistance highlight the need for a more rational use of these agents in cattle. Susceptibility was high for amoxicillin + clavulanic acid (96,6%), ceftriaxone (92,7%) and gentamicin (90,3%).

The work described in this thesis focused on the use of nuclear magnetic resonance spectroscopy (NMR) to study two classes of metallo enzymes - the Fe(II)- and 2oxoglutarate (2OG)-dependent dioxygenases and the metallo β-lactamases (MBLs). These enzymes are involved in clinically important biological processes, i.e. the hypoxic response and antimicrobial resistance, respectively. Both protein systems are interesting from an NMR perspective because they have dynamic regions involved in catalysis and ligand interactions. The work included mechanistic studies, protein-ligand interaction studies, and method development for inhibitor discovery. NMR was applied to study the human prolyl hydroxylase domain-containing protein 2 (PHD2), which is crucially involved in the chronic hypoxic response. The results reveal that binding of the C- and the N-terminus of the oxygen dependent degradation domains CODD and NODD, respectively, induce different interactions with PHD2. The substitution of a single amino acid, as occurs with PHD2 variants linked to erythrocytosis and breast cancer, can alter the selectivity of PHD2 towards its ODD substrates. Studies with the Trichoplax adhaerens PHD provide insights into the evolutionary substrate preference of the PHDs. Using ¹³C-labelled peptidyl-substrates; NMR was applied to investigate proposed 'alternative' PHD2 substrates/interaction partners. The product release mechanism of PHD2 was investigated using NMR; the results reveal that the presence of 2OG strongly discriminates between the binding of CODD and hydroxylated CODD to PHD2. NMR was also applied to monitor PHD2 kinetics and inhibition. Competition and displacement assays were designed and applied to investigate PHD inhibitor binding modes. Comparative studies on the activities and selectivities of PHD inhibitors in clinical trials should aid in the work on the therapeutic manipulation of the natural hypoxic response. Protein-observe ¹9F-NMR was used to study the São Paolo MBL (SPM-1). The results provide new structural insights into SPM-1 catalysis and the requirements for inhibitor development. They also reveal that the hydrolysed β-amino acid products of MBL catalysis can bind to SPM-1. They illustrate the utility of ¹⁹F-NMR for detecting metal chelation, which is not always readily tractable in studies on metallo enzyme inhibition, new binding modes, and stereoisomer binding/epimerisation in solution. The interaction of a cyclobutanone analogue, a broad-spectrum MBL inhibitor, with SPM-1 was investigated. A combination of ¹H, ¹⁹F, ¹³C-NMR and crystallographic analyses reveal that cyclobutanone binding may mimic formation of the oxyanion tetrahedral intermediate in β-lactam hydrolysis. The susceptibility of avibactam, the first clinically useful non-β-lactam β-lactamase inhibitor, to MBL-catalysed hydrolysis was studied. The results reveal that avibactam is not an MBL inhibitor and a poor substrate of most members of all three clinically relevant subclasses of MBLs. In some cases, avibactam undergoes slow hydrolysis in a process different from that observed with serine β-lactamases. Overall, the results illustrate the utility of NMR for studying dynamic aspects of enzyme catalysis and inhibitor binding.

Health Care Associated Infections (HCAIs) are a concern especially in regards to antibiotic resistance and effective treatments. Staphylococcus aureus is often the main focus for eradication and prevention procedures, however, other bacterial species are also problematic. These include Escherichia coli, Pseudomonas aeruginosa, Klebsiella pneumoniae, and Staphylococcus epidermidis amongst others. Chronic infections caused by these bacteria are often biofilm related, and include dental caries, otitis media, osteomyelitis, burns & chronic wounds, and device related & prosthetic joint infections. Prosthetic joints and indwelling devices, such as catheters, are a prime environment on which biofilms can develop. This thesis aims to look at biofilms, investigating how they are established, the development of resistance against individual antibiotics and the antibiotic concentrations required to reduce biofilm load. A novel biofilm system – the alginate bead method will be used for these experiments, The alginate bead method was developed by a previous student in the Gallagher Laboratory, due to a need to have a reliable, robust and inexpensive technique to examine formation of biofilms and antibiotic resistance. There are devices and assays available, such as the Calgary Biofilm Device, which are extensively used for these purposes. However, the cost is prohibitive. This thesis found that the development of biofilms occurs much earlier than expected, with stable, fixed formation after just four hours of growth. Depending upon the antibiotic, resistance can develop within the first two hours of growth and thereafter steadily increases. By 24 hours the biofilms are fully resistant to all the tested antibiotics. In mixed species biofilms, the two species act synergistically protecting each other against the antibiotics, resulting in a much higher antibiotic concentration required. Common antibiotics used to treat staphylococcal infections are often combined to enhance their destructive effect and prevent the development of resistance. The effects of these antibiotics, when combined was explored. Biofilm resistance against gentamicin, one of the most common antibiotics used to treat staphylococcal infections develops quickly. However, when combined with other antibiotics gentamicin resistance is delayed. As antibiotic concentrations have to be extremely high in order to have any effect on established biofilms, alternative methods need to be investigated. Any alternative approaches would be employed in conjunction with conventional therapies preventing stable biofilm formation and disrupting established biofilms. Such methods may include sugar metabolites, enzymatic disruption, D-amino acids and activation of the quorum sensing system. The main conclusion which can be taken from this work are that firstly the alginate bead method of a viable, suitable alternative to the Calgary Biofilm Device and supports biofilm formation and testing. Secondly that biofilms form and are resistant to antibiotics much earlier than expected, and extreme concentrations of antibiotics are required to have an effect. Thus the inclusion of alternative methods which disrupt biofilms would be beneficial to clinical practice. However, the alternative methods investigated within this thesis (D-amino acids and sugar metabolites) failed to show any inhibition of biofilms. There are other possible choices which would need to be investigated.

<b>Background</b> Antibiotic resistance is an important societal health issue. The greatest risk factor for developing a resistant infection is antibiotic use. Almost 75% of all antibiotics in the UK are prescribed in the community, and mostly for acute respiratory tract infections (RTIs). Yet, the majority of RTIs are self-limiting, viral and do not need antibiotic treatment, especially in young children. While the effects of antibiotic-resistant infections have been widely studied in hospitals (e.g. the MRSA 'superbug'), we know less about how antibiotic-resistant infections affect people in the community, even though this is where most antibiotics are prescribed. There is also widespread public misconception about antibiotic use and resistance despite several high-profile, multimillion antibiotic awareness campaigns. This is important to address because consultation behaviour and expectations for antibiotics are a significant determinant of antibiotic use in the community. <b>Methods</b> Three studies were conducted for this thesis. First, a systematic review and meta-analysis to assess the evidence of the impact of antibiotic resistance for patients with common infections in the community; second, a retrospective analysis of routinely collected primary care data to examine the relationship between antibiotic exposure and antibiotic 'response failure' in preschool children presenting with acute RTIs; third, a qualitative interview study to explore parents' perceptions and understanding of antibiotic use and resistance when they consider consulting in the community with their preschool child who has a respiratory tract infection. <b>Results</b> Antibiotic resistance significantly impacts on patients' illness burden for common infections in the community. Patients who presented in community health care settings with antibiotic-resistant E. coli urinary tract infections and S. pneumoniae respiratory tract infections were more likely to experience delays in recovery after antibiotic treatment. From routinely collected primary data (2009-2016), preschool children receiving two or more antibiotic courses in the previous year for acute RTIs had greater likelihood of antibiotic 'response failure' to treatment for subsequent acute RTIs compared to children that had received no previous antibiotics. When interviewing parents of young children, most parents were quite reticent about antibiotics for their children. However, very few considered antibiotic resistance as a possible harm of antibiotics. Parents thought their families were at low risk of antibiotic resistance because their families were 'low users' of antibiotics and did not perceive any association between their individual consumption of antibiotics and the development and spread of antibiotic-resistant bacteria in the community. They wanted future antibiotic awareness campaigns to have a universal message relevant to their families that fit into their daily lives. <b>Conclusions</b> The findings challenge the perception that antibiotic prescribing and resistance in the community poses little or no additional risk to patients in the community, or is remote from everyday prescribing decisions. Rapid diagnostic tests and other prognostic tools need to be promoted and evaluated to better identify patients who might need an antibiotic, and reduce the risk antibiotic response failures. Clinicians and parents should exercise caution about whether further antibiotics for acute RTIs are likely to be beneficial in those children who have received two or more antibiotic prescriptions for acute RTIs during the previous 12 months. Incorporating this into clinical practice guidelines and decision-support systems will help clinicians and parents consider a non-antibiotic strategy for acute RTIs. Future guidelines, campaigns and interventions around antibiotic resistance should tailor initiatives to outcomes that patients and clinicians in the community can relate to and slot into their daily lives. More research is needed to evaluate the impact of other common infections in primary care, and determine the relative contribution of antibiotic resistance to patients not responding to antibiotic treatment for common infections.

L'étape finale de biosynthèse du peptidoglycane est catalysée par les D,D-transpeptidases (PBPs), l'une des cibles principales des antibiotiques de type beta-lactame. Récemment, il a été montré qu'une nouvelle classe d'enzymes, les L,D-transpeptidases (LDts), permet de contourner l'inhibition des PBPs. Ces LDts ont été identifiées tant dans des bactéries résistantes aux beta-lactames que dans des formes dormantes de Mycobacterium tuberculosis. Les seuls beta-lactames capables de les inhiber, les carbapénèmes, forment une liaison covalente avec la cystéine catalytique des LDts. Ni le mécanisme de cette inactivation, ni la spécificité de ces enzymes pour les carbapénèmes ne sont toutefois expliqués à ce jour. Le but du présent travail consiste en l'investigation par RMN du mécanisme d'acylation des LDts par ces antibiotiques. Dans ce contexte, la première partie de cette thèse s'intéresse à la compréhension actuelle de l'émergence de ce phénomène de résistance. La seconde partie traite des principes de la RMN et des implémentations développées pour étudier la structure, la thermodynamique et la dynamique des LDts. La troisième et dernière partie démontre le succès de l'approche RMN dans l'étude des diverses étapes de la réaction d'acylation, à travers une étude détaillée de l'apoenzyme, de complexes non covalents avec différents beta-lactames, et de l'enzyme acylée par un carbapénème. Au cours de cette étude, la structure du site actif de l'apoenzyme de Bacillus subtilis a été affinée par rapport à une étude cristallographique antérieure. Pour cette enzyme et son pendant chez Enterococcus faecium, nous avons démontré que la spécificité pour les carbapénèmes n'intervient pas au stade de la formation du complexe non covalent. Pour finir, la formation de la liaison covalente entre LDt et carbapénème induit un réarrangement conformationnel substantiel et une augmentation de la flexibilité de l'enzyme. / The final cross-linking step of the peptidoglycan synthesis is usually catalyzed by D,D-transpeptidases (PBPs), one of the main targets of beta-lactam antibiotics. Recently, it was shown that these PBPs can be by-passed by a novel class of enzymes, the L,D-transpeptidases (LDts), identified in beta-lactam-resistant bacteria as well as in dormant forms of Mycobacterium tuberculosis. The only beta-lactams enable to inactivate these enzymes belong to the carbapenem class. The beta-lactam ring of this antibiotic family then covalently binds the catalytic cysteine of the LDt. Neither the mechanism of this reaction nor the specificity for carbapenems are yet understood. The aim of the present work is to investigate the acylation mechanism of LDts with carbapenems by NMR. In this context, the first part of this thesis focuses on the current biological understanding of the emergence of this resistance pathway. The second part deals with the NMR principles and the implementations developed to study the structure, thermodynamics and dynamics of LDts. The third part demonstrates that NMR is successful in studying all the steps of the acylation reaction. For this purpose, the LDt apoenzyme, the non-covalent complex with various beta-lactams, and the LDt-carbapenem acylenzyme were thoroughly investigated. The structure of the active site of the Bacillus subtilis apoenzyme was refined with respect to a previous crystallographic study. For the latter and the Enterococcus faecium enzymes, we showed that the carbapenem specificity does not occur at the stage of the non-covalent binding. In contrast to non-covalent interactions, the formation of the covalent bond between LDts and carbapenems induces substantial conformational rearrangement and increased flexibility in the enzyme.