The prevalence of antibiotics on farms for therapeutic and prophylactic use in animals can cause negative effects on biomethane production during anaerobic digestion. Previous literature has found decreased biomethane production rates from a variety of antibiotics, but biogas inhibition differs between studies of continuous and batch reactors and the type of antibiotic studied. Cephalosporin drugs are the most common antibiotic class used to treat mastitis in dairy cows and can retain most of their bioactivity after excretion. Ceftiofur is a commonly used cephalosporin drug but no previous study investigating the effect of Ceftiofur on biomethane during continuous anaerobic digestion has been performed. The aim of this study was to examine the effect on biomethane production when manure from cows treated with Ceftiofur was anaerobically digested. Laboratory sized anaerobic digesters (AD) were run at thermophilic (55°C) temperatures and a 10 day hydraulic retention time. Manure from cows treated with Ceftiofur were fed to the antibiotic treatment reactors for 50 days. The reactor performance was measured by i) biomethane production, ii) waste stabilization in terms of solids and chemical oxygen demand, iii) change in mass of Ceftiofur and iv) change in concentration of antibiotic resistant genes, specifically cfx(A), mef(A), and tet(Q). There was statistically significant decrease in cumulative gas production due to the addition of Ceftiofur into the reactors, but no significant difference between treatments in waste stabilization in terms of percent volatile solids (VS) and total chemical oxygen demand (TCOD) reduction. Anaerobic digestion decreased the amount of Ceftiofur in manure, and the amount of Ceftiofur in the reactors reduced over the time of the experiment. Change in antibiotic resistant genes (ARGs) were gene dependent over time. Concentrations of tet(Q) reduced significantly between feed and effluent of both treatments, and cfx(A) reduced significantly for the control treatment but not the Ceftiofur treatment. Concentrations of mef(A) increased over time in both treatments. Overall, the addition of Ceftiofur in continuously operated anaerobic digesters negatively affected biomethane production, a value-added product responsible for on-farm renewable energy. However, anaerobic digestion does decrease the mass of Ceftiofur within manure, thereby reducing the environmental loading from run-off from farms. / Master of Science / Anaerobic digestion is a biological treatment technology used on farms to treat manure. It can be used to reduce potential environmental damage from contaminants and manure, homogenize manure for fertilizer, and produce methane gas for renewable energy. An emerging challenge in manure management is the presence of antibiotics such as ceftiofur used in animal production to prevent and treat illnesses. When antibiotics are used on livestock, they are excreted from the animal in manure. When the manure is added to the digester, the antibiotic molecules within the manure can kill the bacteria responsible for manure homogenization and gas production. Ceftiofur is a type of cephalosporin antibiotic used to treat dairy cows for mastitis, a bacterial infection of the udder. When the cows are treated with Ceftiofur, it can remain in the excreted manure and enter the digester. The use of antibiotics on farms is also leading to a global phenomenon known as antibiotic resistance. The bacteria that are exposed to antibiotics can develop mutations to become immune to the antibiotic, and can spread the mutations through antibiotic resistant genes (ARGs). ARGs can spread to bacteria which have never been exposed to antibiotics, making them resistant. This causes a significant concern in regards to disease treatment across the world as the efficacy of antibiotics is threatened. Understanding how ARGs move and how they can be eliminated is crucial to preventing global antibiotic resistance. The purpose of this study was to assess the effect of anaerobic digestion on Ceftiofur and ARGs. Four continuous lab-scale anaerobic digesters, two using control manure and two using manure from cows treated with Ceftiofur, were run at 55˚C for a period of 50 days. Over time, the reactor with manure from cows treated with the Ceftiofur antibiotic produced less gas as compared to the control digesters. The amount of Ceftiofur within the digesters decreased over time, demonstrating anaerobic digestion’s ability to degrade the antibiotic molecule. The effect of anaerobic digestion on the ARG concentration was gene specific. The concentration of the tet(Q) gene, a gene responsible for resistance against the very common antibiotic tetracycline, was reduced by anaerobic digestion. These results demonstrate that anaerobic digestion is a technology which can reduce the environmental impact of manure from Ceftiofur-treated cows. This shows that manure treatment can be a first step in combating antibiotic resistance across the globe.

京都大学 / 新制・課程博士 / 博士(工学) / 甲第25269号 / 工博第5228号 / 新制||工||1997(附属図書館) / 京都大学大学院工学研究科都市環境工学専攻 / (主査)教授 西村 文武, 教授 米田 稔, 教授 松田 知成 / 学位規則第4条第1項該当 / Doctor of Agricultural Science / Kyoto University / DGAM

Food-borne illness outbreaks are occasionally associated with fresh-vegetable consumption, in part due to lack of a microbial inactivation step before consumption. Raw manure or improperly composted manure applied as soil amendments is an established source of pathogenic bacterial contamination. However, less is known about whether such soil amendments could serve as a source of transmission of antibiotic-resistant bacteria (ARB) or antibiotic-resistance genes (ARGs) via fresh produce. As such knowledge is developing, it is useful to identify strategies for mitigating ARGs and ARB on vegetable surfaces, especially those that are synergistic with known benefits in terms of general pathogen reduction on fresh produce. Sanitizers play an important role in post-harvest processing of vegetables, especially in terms of disinfecting the wash water and preventing cross-contamination. Further, temperature and time of storage of vegetables are critical to prevent the growth of microorganisms. To provide a background inoculum representing potential pre-harvest carryover of ARB and ARGs, carrots or romaine lettuce leaves were dipped in a slurry derived from composted manure from dairy cows previously dosed with antibiotics and further inoculated with multi-drug resistant E. coli O157:H7, a human pathogen, and a spoilage-associated and opportunistic pathogenic strain of Pseudomonas aeruginosa. Inoculated carrots (n=3, 25 g) were washed with water containing different sanitizers (sodium hypochlorite or peroxyacetic acid) or unwashed (control), packaged and stored at 10ºC for 7d or 2ºC for up to 60 d. Inoculated lettuce leaves (n=3, 100 g) were washed with sodium hypochlorite, packaged in modified atmosphere conditions (98% nitrogen), irradiated (1.0 kGy) and subsequently stored at 4ºC for 14 d. The effect of post-harvest treatment were compared at various times by enumeration on selective media. In addition, cultureindependent techniques were also performed to determine changes to the surficial carrot and lettuce microbiota by sequencing bacterial 16S rRNA gene amplicons. The effect of post-harvest treatments on the types and relative abundance of ARGs, also known as the “resistome,” were profiled by shotgun metagenomic sequencing and qPCR. Addition of a sanitizer during wash, storage temperature, and duration of storage affected the bacterial community structures on carrots, represented by the weighted Unifrac distance matrices (ANOSIM, R=0.465). Storage of sanitizer-washed carrots at 10ºC was associated with an increase in relative abundance of Pseudomonadaceae compared to 2ºC storage for 7 d (Wilcoxon, p<0.05). Increase in storage temperature from 2ºC (optimum) to 10ºC (temperature abuse) of sanitizer-washed carrots resulted in enrichment of ARGs conferring resistance to the following antibiotic classes: multidrug, peptide, polymyxin, quinolone, triclosan, aminoglycoside, bacitracin, β-lactam, and fosfomycin. Irradiation resulted in significant reductions (~3.5 log CFU/g) of inoculated antibiotic-resistant E. coli O157:H7 and Pseudomonas sp. on lettuce surfaces (ANOVA, p<0.05). The lettuce resistome, represented by the Bray-Curtis similarity of ARG occurrence, was affected by irradiation (ANOSIM, R=0.406). Irradiation of lettuce followed by 14 d of storage at 4ºC resulted in 2-4-fold reductions in relative abundance of ARGs encoding resistance to the following antibiotic classes: triclosan, quinolones, multidrug, polymyxin and β-lactam (Wilcoxon, p<0.05). No additional increase or reduction of the tet(A) gene present on inoculated P. aeruginosa was evident after 14d storage at 4ºC on irradiated samples. Results of this study suggest that inclusion of a sanitizer in wash water, irradiation, and storage at optimum refrigerated temperatures may offer effective strategies to combat proliferation of antibiotic resistant bacteria and antibiotic resistance genes on fresh produce. Further research is needed develop interventions that can mitigate tet(A) and other ARGs on produce that were not significantly reduced by irradiation. This study will guide future research on microbiome and metagenome of processed produce and assessment of critical control points to reduce the risk of antibiotic resistance from farm-to-fork. / PHD / Post-harvest interventions; such as washing, irradiation and cold storage, are employed to provide safe and wholesome fresh vegetables to consumers. Washing of vegetables in water that includes a sanitizing agent, such as chlorine or peroxyacetic acid (POAA), removes soil from the surface, reduces the bacteria in wash water and prevent cross-contamination between vegetables. It has an additional benefit to reduce microorganisms on produce surfaces that may cause the vegetables to spoil or result in illness in humans. Low temperature storage of produce, usually 0-5ºC, decreases the respiration rate of vegetables and reduces growth of microorganisms during storage. Some of the spoilage and/or pathogenic bacteria may also be antibiotic-resistant, which are commonly termed as antibiotic-resistant bacteria (ARB). Antibiotic resistance is a significant public health concern that leads to ineffective medical treatments, prolonged duration of illnesses and increased hospitalization costs. Antibiotic resistance is encoded by genes that confer resistance to wide range of antibiotic classes, including antibiotics used to treat human illnesses. These genes are termed as antibiotic resistance genes (ARGs). In this study we examined the effect of three common post-harvest interventions, washing with sanitizers, gamma irradiation, and cold storage to reduce antibiotic-resistant bacterial pathogens and antibiotic-resistant spoilage bacteria on carrots and lettuce. Storage temperature, inclusion of sanitizer in wash water, and length of chilled storage significantly influenced the diversity of bacteria found on carrot surface. Inclusion of either sanitizer in the wash water significantly reduced the populations of antibiotic-resistant E. coli O157:H7 (a pathogenic bacterium that causes a dangerous form of gastrointestinal illness) and Pseudomonas sp. (a bacterial species that commonly causes food spoilage). Storage at recommended temperature (2ºC) did not allow these bacteria to regrow and also reduced total ARGs on carrot surfaces. Washing of lettuce with sodium hypochlorite followed by irradiation (1.0 kGy) and storage at recommended temperature (4ºC) were effective in reducing the populations of antibiotic-resistant E. coli O157:H7 and Pseudomonas sp., and additionally reduced the number of some ARGs conferring resistance to select classes of antibiotics, including triclosan, quinolones, multidrug, polymyxin and β-lactam antibiotics on the lettuce surface. A novelty of this research is that it employed new, cutting-edge “metagenomic” DNA sequencing technique to identify and track antibiotic resistance through the various post-harvest interventions. Overall results of this research suggest that inclusion of sanitizer in wash water for fresh produce, followed by storage at refrigerated temperatures below 4ºC may reduce the risk posed by antibiotic resistant bacteria and antibiotic resistance genes on produce.

Tee PhD thesis presents the study of the response of Mycobacterium tuberculosis, the causative agent of tuberculosis, upon prolonged exposure to lethal concentrations of the first line anti-tuberculosis drug, rifampicin. The study shows that prolonged exposure to lethal concentration of rifampicin causes cell death initially by several log orders of cells, followed by a persistence phase, from where rifampicin resisters emerge carrying mutation in the RRDR locus of the rpoB gene. This phenomenon was found to occur even when the drug concentration is well above MBC levels. Luria-Delbruck experiment, in a modified format, showed that the resisters emerged as fresh mutants, and not due to the growth of pre-existing natural resisters to rifampicin. The per sister cells, which showed high levels of hydroxyl radical generation, were found to have thickened outer layer, unlike the mid-log phase cells, which restricts the permeability of a fluorescent-conjugate of rifampicin, 5-FAM-rifampicin, 10-fold less in per sister cells, as compared to mid-log phase cells. The thickened outer layer has high negative surface charge and is hydrophilic in nature. It is proposed that the hydrophilic-natured thickened outer layer might have restricted the permeability of lethal concentrations of hydrophobic-natured rifampicin. This, in turn, might have ensured the presence of sub-lethal concentration rifampicin inside the per sisters, which in turn might have generated the hydroxyl radical that caused mutagenesis to generate rifampicin resisters. The Chapter 1 is the Introduction to the thesis presented in 4 parts – Part 1.1, 1.2, 1.3 and 1.4, introducing briefly the history of antibiotics, antibiotic resistance, antibiotic persistence and a brief history of tuberculosis respectively. It is concluded with a rationale behind the present study. The Chapter 2 presents the entire Materials and Methods used in the experiments described in the thesis. The Chapter 3 presents the data on the response of M. tuberculosis to rifampicin upon extended exposure. Rifampicin exposure of susceptible M. tuberculosis H37Ra cells showed a decrease in their CFU/ml followed by a persistence phase wherein the CFU/ml remained constant. However, prolonged exposure of rifampicin even at higher concentrations showed regrowth in the culture, which was found to be due to the emergence of rifampicin-resistant bacteria. Screening of rifampicin-resistant mutants showed point mutations in the rifampicin resistance determining region (RRDR) of the rpoB gene in all the mutants. In parallel, using trans formants of M. tuberculosis expressing unstable GFP under the respective native ribosomal RNA promoter, the metabolic status of the per sister cells was determined. When actively growing highly fluorescing cells were exposed to lethal concentration of rifampicin, their metabolism diminished, as illustrated by the decrease in their fluorescence during persistence phase, followed by the emergence of a sub-population of bacteria which were again metabolically active. In order to verify whether the rifampicin resisters are freshly formed mutants or have come from the naturally existing resisters, Luria-Delbruck fluctuation test was performed in a modified manner. The number of rifampicin resisters that emerged from the persistent phase was found to vary amongst different cultures from different days and different times of exposure, showing fluctuation. However, the addition of theorem before persistence phase almost abolished the generation of the rifampicin-resistant bacilli, indicating the role of hydroxyl radical in the emergence of rifampicin resisters. The generation of hydroxyl radical in mycobacteria exposed to rifampicin was confirmed using electron para-magnetic resonance spectrometry (EPR), with the spin trap agent, 5,5- Dimethyl-1-pyrroline N-oxide (DMPO) specific for hydroxyl radical. An increase in the formation DMPO-OH adduct in the persistence phase cells was observed, in comparison to mid-log phase cells. Exposure to theorem significantly diminished the adduct formation. The persistence phase cells also showed significantly high levels of signal specific to the hydroxyl-specific fluorescent dye, hydroxyphenyl fluorescein (HPF), as compared to the mid-log phase cells. In addition we have determined the oxidative stress in the bacilli upon rifampicin exposure using a redox biosensor (Mrx1-roGFP) which also showed high oxidative stress in the persistent phase. These observations confirmed the presence of high levels of oxidative stress and hydroxyl radical in the rifampicin persistent cells, in comparison with mid-log phase cells. Whole genome sequencing of the four independently isolated rifampicin resistant M. tuberculosis showed genome wide mutations having less common mutations with respect to the wild type genome, indicative of the occurrence of random mutagenesis. In addition mutation frequencies were comparable between the samples with respect to the wild type sample. About 69% of the mutations were A-C or T-G, followed by A-T or T-A, which is known to be due to oxidative stress in the cells. Variations in the colony morphology were also observed on the persistent phase cells, indicating the occurrence of mutagenesis in the bacterial genome during rifampicin treatment. The Chapter 4 is on the morphological and ultrastructural studies on rifampicin-exposed M. tuberculosis cells. Transmission electron micrographs of rifampicin per sisters showed significant thickening of the outermost capsular layer (OL), as compared to the mid-log phase cells. This observation was verified by staining the cells with ruthenium red, which specifically stains anionic polysaccharide of the OL. Zeta potential (ZP) measurement of the surface charge of the persistent cells showed high negative ZP, as compared to the mid-log phase cells. The negative ZP value was found to gradually increase during the course of rifampicin treatment and to decrease during the regrowth phase. Hexadecane assay showed larger proportion of per sister cells being retained in the aqueous phase, as compared to the mid-log phase cells. This indicated the higher hydrophilicity of the per sister cells, which was in agreement with the higher surface negative charge of the cells. The permeability of rifampicin per sister cells to 5-FAM-rifampicin (rifampicin conjugated to 5-carboxy fluorescein, which is as hydrophobic as rifampicin) was found to be 10-fold less than that of the mid-log phase cells. However, removal of the thick OL by bead beating (BB) with 4 mm glass beads significantly improved the permeability of per sister cells to 5-FAM-rifampicin. On the contrary, no difference in the 5-FAM-rifampicin uptake was observed in mid-log phase cells, with or without BB. These observations implied that the thick hydrophilic-natured OL with high negative surface charge may be playing a significant role in limiting the permeability of hydrophobic-natured rifampicin entry into the persisted cells. This in turn may ensure the presence of sub-lethal concentration of rifampicin inside the persisted cells that are exposed to lethal concentration of the antibiotic. Exposure of bacteria to sub-lethal concentration of antibiotics has been reported to generate oxidative stress in the bacteria, leading to mutagenesis. A model has been proposed based on these observations in which the persistent mycobacteria are protected from lethal concentrations of the rifampicin by the thick OL which in turn ensures sub-lethal intracellular antibiotic concentration, leading to the generation of hydroxyl radical mediated mutagenesis and thereby emergence of rifampicin resisters. This thesis is concluded with the list of salient findings, publications and references.

No description available.

Bibliography / Thesis (MMed (Pathology. Medical Microbiology))--University of Stellenbosch, 2011. / ENGLISH ABSTRACT: Acinetobacter baumannii has emerged as one of the most troublesome nosocomial pathogens globally. This organism causes infections that are often extremely difficult to treat because of the widespread resistance to the major antibiotic groups. Colonization or infection with multidrugresistant A. baumannii is associated with the following risk factors: prolonged hospital stay, admission to an intensive care unit (ICU), mechanical ventilation, and exposure to broad spectrum antibiotics, recent surgery, invasive procedures, and severe underlying disease. A. baumannii has been isolated as part of the skin flora, mostly in moist regions such as axillae, groin and toe webs. It has also been isolated from the oral cavity and respiratory tract of healthy adults. Debilitated hospitalized patients have a high rate of colonization, especially during nosocomial Acinetobacter outbreaks. This organism is an opportunistic pathogen as it contains few virulence factors. Clinical manifestations of A. baumannii include nosocomial pneumonia, nosocomial bloodstream infections, traumatic battlefield and other wound infections, urinary tract infections, and post-neurological surgery meningitis. Fulminant community-acquired pneumonia has recently been reported, indicating that this organism can be highly pathogenic. The number of multidrug-resistant A. baumannii strains has been increasing worldwide in the past few years. Therefore the selection of empirical antibiotic treatment is very challenging. Antibiotic combinations are used mostly as empirical therapy in critically ill patients. One rationale for the use of combination therapy is to achieve synergy between agents. The checkerboard and time-kill methods are two traditional methods that have been used for synergy testing. These methods are labor intensive, cumbersome, costly, and time consuming. The E-test overlay method is a modification of the E-test method to determine synergy between the different antibiotics. This method is easy to perform, flexible and time efficient. The aim of this study was to assess the in vitro activity of different combinations of colistin, rifampicin, imipenem, and tobramycin against selected clinical strains of A. baumannii using the checkerboard and the E-test synergy methods. The MICs obtained with the E-test and broth microdilution method were compared. The results of the disk diffusion for imipenem and tobramycin as tested in the routine microbiology laboratory were presented for comparison. Overall good reproducibility was obtained with all three methods of sensitivity testing. The agreement of MICs between the broth dilution and E-test methods was good with not more than two dilution differences in MIC values for all isolates, except one in which the rifampicin E-test MIC differed with three dilutions from the MIC obtained with the microdilution method. However, the categorical agreement between the methods for rifampicin was poor. Although MICs did not differ with more than two dilutions in most cases, many major errors occurred because the MICs clustered around the breakpoints. The combinations of colistin + rifampicin, colistin + imipenem, colistin + tobramycin, rifampicin + tobramycin, and imipenem + tobramycin all showed indifferent or additive results by the E-test method. No results indicating synergy were obtained for all the above-mentioned combinations. There was one result indicating antagonistic effect for the combination of colistin + tobramycin. The results of the checkerboard method showed results indicating synergy in four of the six isolates for which the combination of colistin and rifampicin was tested. The other two isolates showed indifferent/additive results. All the other combinations showed indifferent/additive results for all isolates except isolate 30 (col + tob) and isolate 25 (rif + tob) which showed synergism. No antagonistic results were observed by the checkerboard method. When the results obtained with the E-test and checkerboard methods were compared, it was noted that for most antibiotic combinations an indifferent/additive result was obtained. However, for the colistin + rifampicin combination, the checkerboard method showed synergism for 4 of 6 isolates, whereas the E-test method showed indifference and an additive result in one. For the rifampicin + tobramycin, and colistin + tobramycin combinations, synergism was also shown with the checkerboard method in one isolate for each combination. The E-test method however showed an indifferent and additive result respectively. . The E-test method was found to be a rapid, reproducible, easy-to-perform, and flexible method to determine synergistic antibiotic activity. This study was however limited by low numbers of isolates. This might explain why no synergistic results were obtained with the E-test method and few synergistic results with the checkerboard method. Genotypic analysis using pulse-field gel electrophoresis (PFGE) may be considered in future studies to determine relatedness of the isolates which will facilitate the selection of different strains for synergy testing. Furthermore, clinical studies are needed to establish whether in vitro synergy testing is useful in the clinical setting and whether the results of synergy testing will have any bearing on the clinical outcome of patients infected with multidrug resistant A. baumannii. / AFRIKAANSE OPSOMMING: Acinetobacter baumannii het wêreldwyd as een van die mees problematiese nosokomiale patogene verskyn. Hierdie organisme veroorsaak infeksies wat dikwels baie moeilik is om te behandel weens wydverspreide weerstandigheid teen major antibiotikagroepe. Kolonisasie of infeksie met multi-weerstandige A. baumannii word geassosieer met die volgende riskofaktore: verlengde hospitaalverblyf, toelating tot ‘n intensiewe sorgeenheid (ICU), meganiese ventilasie, blootstelling aan breëspektrum antibiotika, onlangse chirurgie, indringende prosedures en ernstige onderliggende siekte. A. baumannii kan deel vorm van die normale velflora, veral in die axillae, inguinale area en tussen die tone. Dit is ook al vanuit die mondholte en die respiratoriese traktus van gesonde volwassenes geïsoleer. Verswakte gehospitaliseerde pasiënte word veral gekoloniseer gedurende nosokomiale Acinetobacter uitbrake. Hierdie organisme is ‘n opportunistiese patogeen en bevat min virulensie faktore. Kliniese manifestasies van A. baumannii sluit nosokomiale pneumonie, nosokomiale bloedstroom infeksies, troumatiese slagveld- en ander wondinfeksies, urienweginfeksies en meningitis wat volg op neurologiese chirurgie in. Fulminerende gemeenskapsverworwe pneumonie is onlangs beskryf en dui aan dat hierdie organisme hoogs patogenies kan wees. Die aantal multi-weerstandige A. baumannii stamme het wêreldwyd toegeneem oor die laaste paar jare. Daarom is die seleksie van empiriese antibiotiese behandeling ‘n uitdaging. Antibiotika kombinasies word meestal as empiriese behandeling in ernstige siek pasiënte gebruik. Die beginsel hiervan is om sinergistiese werking tussen agente te verkry. Die “checkerboard” en “time-kill” metodes is twee tradisionele metodes van sinergisme toetsing. Hierdie metodes is werksintensief, duur en tydrowend. Die E-toets sinergisme metode is gebaseer op die E-toets metode. Hierdie metode is maklik, buigbaar en tydseffektief. Die doel van hierdie studie was om die in vitro aktiwiteit tussen verskillende antibiotika kombinasies van colistin, rifampisien, imipenem, en tobramisien teen geselekteerde kliniese A. baumannii isolate te toets met die “checkerboard” en E-toets sinergisme toetsing metodes. Die minimum inhibitoriese konsentrasies (MIKs) verkry met die E-toets en “broth microdilution” metode is ook vergelyk. Die resultate van die skyfie diffusie metode (die metode wat in die roetiene mikrobiologie laboratorium gebruik word) vir imipenem en tobramisien word ook verskaf vir vergelyking van die resultate van verskillende sensitiwiteitsmetodes. In oorsig is goeie herhaalbaarheid van resultate verkry met al drie metodes van sensitiwiteitstoetsing. Die ooreenstemming van MIKs tussen die “broth dilution” en E-toets metodes was goed en resultate het met nie meer as twee verdunnings in MIK waardes verskil nie. Daar is een uitsondering waar die rifampisien E-toets MIK waarde met drie verdunnings van die MIK waarde verkry met die “microdilution” metode verskil. Die ooreenstemming tussen die sensitiwiteitskategorie resultate tussen die twee metodes was egter swak vir rifampisien. Alhoewel die MIKs in die meeste gevalle met nie meer as twee verdunnings in waarde verskil het nie, was daar baie major foute aangetoon omdat die MIKs rondom die breekpunte geval het. Die kombinasies van colistin + rifampisien, colistin + imipenem, colistin + tobramisien, rifampisien + tobramisien, en imipenem + tobramisien het oorwegend slegs matige interaksie met die E-toets metode getoon. Geen sinergisme is verkry met enige van die antibiotika kombinasies met hierdie metode nie. Daar was egter een resultaat wat antagonisme getoon het vir die kombinasie van colistin + tobramycin. Die resultate van die “checkerboard” metode het sinergisme getoon in vier van die ses isolate wat vir die kombinasie van colistin en rifampisien getoets was. Die ander twee isolate het slegs matige interaksie getoon. Al die ander kombinasies het ook slegs matige interaksie getoon, behalwe in isolaat 30 (col + tob) en isolaat 25 (rif + tob) waar die spesifieke kombinasies sinergisme getoon het. Geen antagonisme is waargeneem met die “checkerboard” metode nie. Met vergelyking van die E-toets en “checkerboard” metodes, is dit opmerklik dat vir die meeste van die antibiotika kombinasies slegs matige interaksie verkry is. Vir die colistin + rifampisien kombinasie toon die “checkerboard” metode egter sinergisme vir 4 uit 6 isolate, terwyl die E-toets metode slegs matige interaksie toon. Vir rifampisien + tobramisien, en colistin + tobramisien kombinasies is sinergisme getoon met die “checkerboard” metode in een isolaat vir elke kombinasie. Die E-toets metode het slegs matige interaksie getoon. Die E-toets sinergisme metode was vinnig, herhaalbaar en maklik om uit te voer. Hierdie studie word egter beperk deur lae getalle van isolate. Dit mag verklaar waarom geen sinergistiese resultate met die E-toets metode verkry is nie en die min sinergistiese resultate met die “checkerboard” metode. Genotipiese analiese met “pulse-field gel electrophoresis” mag in aanmerking geneem word in toekomstige studies om die verwantskap tussen isolate te bepaal wat die seleksie van verskillende stamme vir sinergisme toetsing sal vergemaklik. Verder, kliniese studies is nodig om te bepaal of in vitro sinergisme toetsing van waarde is en of die resultate van sinergisme toetsing ‘n rol speel in die kliniese uitkoms van pasënte geïnfekteer met multiweerstandige A. baumannii. / The National Health Laboratory Serivice

L'usage excessif et inapproprié des antibiotiques a été décrit dans le monde entier depuis 25ans, tant en ville qu'à l'hôpital. En plus des effets délétères sur les patients l'utilisation abusive des antibiotiques contribue à l'émergence de résistances bactériennes et à l'augmentation des dépenses hospitalières. Dans les années 1990 plusieurs organisations du monde de la santé ont publié des plans et des recommandations visant à contrôler les consommations en antibiotiques afin de limiter la pression de sélection sur les bactéries et d'en diminuer les coûts. Au CHU de Nancy une politique de bon usage des antibiotiques a été instaurée au milieu des années 1990 puis renforcée en 2006, avec une réorganisation complète du mode prescription et de la délivrance des antibiotiques dans tout l'établissement. Une équipe opérationnelle en infectiologie (EOI) composée d'un infectiologue et d'un pharmacien est intervenue dans une partie des services afin d'améliorer la qualité des prescriptions. Pour évaluer l'impact de l'intervention de l'EOI sur les consommations antibiotique et les coûts qui en découlent, une étude contrôlée en cluster avant/après a été réalisée .Nous avons comparé les consommations globale et par classes antibiotiques ainsi que les coûts « avant » et « après » dans 2 groupes (contrôle et intervention).Les résultats ont montré qu'après l'intervention de l'EIO les consommations globales avaient diminué de 34% dans le groupe intervention et de 3% dans le groupe contrôle ( P=0,003). Pour une même activité, la réduction du coût était 14 fois plus élevée dans le groupe intervention. Nous pouvons donc avancer que l'intervention d'une EOI constitue un moyen efficace pour réduire la consommation hospitalière en antibiotiques et les coûts qui en découlent. / Overuse and inappropriate use of antibiotics has been described worldwide for about 25 years, in both community and hospital settings. In addition to its deleterious effect on patients, antibiotic misuse can lead to the emergence of bacterial resistance and increased the cost of hospitalization. Indeed, during the 1990s several organizations published plans to control the costs of antibiotics and limit selective pressure on microorganisms through surveillance and interventions promoting rational use. An antimicrobial policy has been implemented at the University Hospitals of Nancy since the mid-1990s. This antibiotic policy was therefore reinforced the beginning of 2006, changes included complete reorganization of the methods of prescribing and delivering antibiotics in all wards of the University hospitals of Nancy. In addition, an Operational Multidisciplinary Antibiotic Team (OMAT) including an infectious disease physician and a clinical pharmacist was established in some wards. To evaluate the effectiveness of this OMAT, in reducing the hospital antimicrobial consumption and costs a cluster controlled "before-after" study was performed. We compared consumption of antibiotics overall and by therapeutic class and cost savings between "before" and "after" in both groups (control and intervention). The results of this study have shown that overall consumption of antibiotics decreased after implementation of the OMAT by 34% in the intervention group and by 3% in the control group (p = 0.003). For the same activity, the total cost savings were 14-fold higher in the intervention group. Establishment of an operational multidisciplinary team may be an effective way to reduce hospital antibiotic use and cost.

Instead of planktonic growth in nature, many species of bacteria form biofilm to survive in harsh conditions. Although many chronic bacterial infections are caused by bacterial species in a biofilm lifestyle, previous research has focused on studying antibiotic resistance in planktonic growth. Here we used a modified MBEC assay, i.e. biofilm growth on pegs, to determine Escherichia coli biofilm inhibitory concentrations (BIC) of ciprofloxacin, streptomycin and rifampicin and to study the minimal selective concentration (MSC) for ciprofloxacin in E. coli biofilm. We could observe high inhibitory concentrations for all antibiotics in the biofilm pre-formed in media without antibiotics compared to the biofilm formed in antibiotics. We also show preliminary result indicating that sublethal concentrations of ciprofloxacin lead to the selection of ciprofloxacin resistant mutants in biofilm and that the selection level is lower than what was observed in planktonic growing E. coli. With more knowledge in how the biofilm formation precedes in different antibiotic settings, the treatment for chronic biofilm infections used today could be evaluated and changed so that the infections could be eradicated.

Rising Antimicrobial Resistance is a threat faced all over the world. Bacterial infections that were treatable with antibiotics only a few years ago can now lead to life-threatening conditions. This thesis is part of the work of a large platform, PLATINEA, trying to reduce the rate of new resistances occurring in Sweden by preventing non optimal treatment. Due to shortages of the right antibiotics, suboptimal antibiotics are prescribed, which has shown to be accelerating the resistances among the bacterial populations. This study proposes an information exchange database and a central storage model for critical antibiotics to circumvent stock outs and inconveniences resulting from shortages of medically valuable antibiotics. Through interviewing prominent actors in the Swedish pharmaceutical supply chain an inside into the procurement of antibiotic in Sweden and what concerns are faced by the organs involved was created. Literature studies on occurred shortages of antibiotics in Sweden and the world were examined and possible reasons for these were identified. Examination of governmental efforts and assignments created the context in which gaps were identified that this thesis work could fill. A focus on Benzylpenicillin and Rifampicin were kept throughout the study. The collected data led to the implementation recommendation of two models by this study. An information platform suggested to allow better, faster and more accurate information exchange between all involved actors of the supply chain as well as a centralized storage model for the storage of antibiotics with medically high value in Sweden.  Through the implementation of the model systems shortages of critical antibiotics can be circumvented and better availability of information leads to quicker reactions ability to stock outs of other antibiotics.

Dans une perspective comparative entre la France et les États-Unis, ce travail analyse le processus de publicisation des liens entre l’antibiorésistance et l’alimentation, ainsi que ses implications en termes de contribution au développement de la production appelée sans antibiotique et de l’approche One Health. En partant de la prise de conscience des conséquences de l’usage des antibiotiques dans l’élevage, la recherche s’inscrit dans une réflexion pragmatiste de constitution des problèmes publics et s’appuie sur un corpus hybride composé de documents publiés entre 1980 et 2016 (presse écrite, littérature institutionnelle et entretiens semi-directifs). La méthode développée s’enrichit des outils de textométrie issus de l’analyse de discours et s’intéresse à l’émergence des dénominations et des formules qui nomment le problème, ses causes et ses solutions. La comparaison montre que le processus de publicisation de liens entre l’antibiorésistance et l’alimentation dévoile une trajectoire opposée dans les deux pays. Dans le cas français, ce processus s’inscrit dans un schéma top-down et se caractérise par une publicisation tardive faisant suite aux démarches des instances sanitaires européennes et internationales. L’appropriation du problème par des associations de consommateurs, ainsi que l’investissement des acteurs agroalimentaires dans le développement de la production sans antibiotique, n’émergent que récemment. En revanche, aux États-Unis, ce processus s’inscrit dans un modèle bottom-up suite à la constitution d’un public d’organisations non gouvernementales autour du problème. Leur mobilisation a contribué significativement au développement de programmes d’élevage sans antibiotique ainsi qu’à la mise à l’agenda gouvernemental du problème et le lancement d’un plan national dans une approche One Health. / In a cross-country perspective between France and the United States, this research analyses the process of publicizing the links between antibiotic resistance and food, as well as its contribution to the development of the antibiotic free production and the implementation of the One Health approach. Starting with the awareness of the antibiotic use in livestock consequences, the study relies on the pragmatist approach of the constitution of the public problems. It is based on wide corpora composed by documents published between 1980 and 2016 (written press, institutional literature and semi-directive interviews). The analysis method uses textometric tools derived from discourse analysis and focuses on the emergence of formulas that name the problem, its causes and its solutions. The comparison uncovers an opposite process between the two countries. In France, this process is part of a top-down approach and is characterized by a late publicization following the European and international health authorities’ initiatives. The consumer associations taking over the problem, as well as the agri-food actors’ commitment to the antibiotic free production, is very recent. In the United States, this process reveals a bottom-up model following a non-governmental organizations public constitution taking over the problem. Their mobilization has contributed to the development of the antibiotic free breeding programs, as well as to place the problem on the government agenda that launched a national plan in a One Health approach.