IIntrodução A utilização excessiva de antimicrobianos na medicina humana, veterinária e agricultura resultou no aparecimento da resistência bacteriana. Este fenômeno gera problemas de saúde pública que podem resultar na reemergência de doenças infecciosas. O uso de antibióticos, principalmente de forma profilática, tornou-se prática na aquicultura, como ocorre no Brasil, onde a regulamentação para o uso de medicamentos veterinários é ineficiente. Além disso, há evidências da transferência de organismos resistentes para humanos por meio do consumo de produtos de origem animal, quando, durante a fase de criação e produção destes foram administrados antibióticos. Objetivo Pesquisar a ocorrência de genes de resistência a antibióticos em filés de tilápia comercializados em supermercados do município de São Paulo SP. Material e Métodos Foram coletadas 10 amostras de filé de tilápia e realizada a pesquisa de coliformes termotolerantes como indicadores das condições higiênico-sanitárias do alimento. Em seguida, as amostras foram inoculadas em Caldo Lúria 0,5 por cento e o DNA total das bactérias cultivadas nesse meio foi extraído por meio de choque térmico para pesquisa de genes de resistência aos antibióticos -lactâmicos e tetraciclinas pela PCR. Os genes identificados pela PCR foram confirmados pelo sequenciamento. Resultados Em 100 por cento das amostras analisadas o resultado para coliformes termotolerantes foi < 3 NMP.g-1. Na pesquisa de genes de resistência a -lactâmicos, o gene blaOXY-5 foi detectado em 90 por cento das amostras, blaTEM-1b em 20 por cento , blaLEN-16 em 10 por cento , blaSHV-28 em 10 por cento , blaKPC-2 em 20 por cento , blaMOX-6 em 10 por cento e blaCphA em 60 por cento . Os genes de resistência a tetraciclinas identificados foram tetB em 10 por cento das amostras, tetC em 20 por cento , tetD em 80 por cento , tetE em 50 por cento , tetG em 60 por cento , tetO e tetS em 10 por cento cada e tetW em 20 por cento . Conclusões Em 90 por cento das amostras foi identificada a presença de genes de resistência aos antibióticos -lactâmicos e tetraciclinas, demonstrando uma grande circulação de resistência bacteriana na aquicultura e verificando a necessidade de legislação e fiscalização mais atuantes no controle do uso de antibióticos na aquicultura / IIntroduction The excessive use of antimicrobials in human medicine, veterinary medicine and agriculture has resulted in the emergence of bacterial resistance. This phenomenon creates public health problems that may result in the re-emergence of infectious diseases. The use of antibiotics, mainly prophylactically, has become a practice in aquaculture, including Brazil, where the legislation for the use of veterinary drugs is inefficient. Furthermore, there is evidence of transmission of resistant organisms to humans through consumption of animal products, especially when the antibiotics have been administered during the raising and production of these animals. Objective To search for the occurrence of antibiotics resistance genes in tilapia fillets commercialized in supermarkets in São Paulo city - SP. Material and Methods 10 tilapia fillet samples were collected and submitted to fecal coliform search as an indicator of the sanitary conditions of the food. Then, the samples were inoculated into Luria broth 0,5 per cent and the total DNA was extracted from growing bacteria by thermal shock for the search of resistance genes to -lactam and tetracyclines antibiotics by PCR. The genes identified by PCR were confirmed by sequencing. Results In 100 per cent of samples the result was < 3 NMP.g-1 for fecal coliform organisms. In the study of -lactam resistance genes, blaOXY-5 gene was detected in 90 per cent of samples, blaTEM-1b in 20 per cent , blaLEN-16 in 10 per cent , blaSHV-28 in 10 per cent , blaKPC-2 in 20 per cent , blaMOX-6 in 10 per cent and blaCphA in 60 per cent . The tetracyclines resistance genes identified were tetB in 10 per cent of samples, tetC in 20 per cent , tetD in 80 per cent , tetE in 50 per cent , tetG in 60 per cent , tetO and tetS in 10 per cent each and tetW in 20 per cent . Conclusions 90 per cent of the samples showed the presence of -lactam and tetracyclines resistance genes, demonstrating a high circulation of bacterial resistance in aquaculture and verifying the need for more active law and surveillance in controlling the use of antibiotics in aquaculture.

Introdução. A introdução dos antimicrobianos na prática clínica no século XX foi um grande avanço para a medicina. Entretanto, seu uso indiscriminado, tanto na medicina (humana e animal) quanto na agricultura e pecuária, possibilitou a seleção e disseminação de microrganismos resistentes. A transferência genética horizontal é um dos principais mecanismos responsáveis pela disseminação de genes que codificam resistência aos antimicrobianos, pois possibilita a transmissão da resistência de uma célula bacteriana (comensal ou patogênica) para outra. Genes codificadores de resistência a antimicrobianos de importância clínica são encontrados em microrganismos de origem ambiental, clínica e alimentar. Objetivo. O objetivo do presente estudo foi detectar genes que codificam resistência aos antibióticos -lactâmicos, Tetraciclinas e Quinolonas, em amostras de carne de frango, visando estudar a ocorrência da resistência antimicrobiana nesse produto considerado um alimento comum na dieta do homem. Materiais e Métodos. Foram utilizadas 30 amostras de carne de frango. Após a inoculação da carne de frango em caldo Luria 0,5 por cento , o DNA total das bactérias cultivadas nesse meio foi extraído por choque térmico e utilizado na pesquisa de genes de resistência pela técnica de PCR seguida de eletroforese em gel de agarose. Foi também realizada a pesquisa de Coliformes Termotolerantes por meio da técnica dos tubos múltiplos para estimar a qualidade higiênico sanitária das amostras. Resultados: Oito (26,7 por cento ) amostras apresentaram um ou mais genes codificadores de resistência à antimicrobianos -Lactâmicos, 28 (93,3 por cento ) amostras apresentaram um ou mais genes codificadores de resistência às Tetraciclinas e 28 (93,3 por cento ) amostras apresentaram um ou mais genes codificadores de resistência às Quinolonas. Conclusões: A realização deste estudo contribuiu com informações a respeito da circulação de genes de resistência na carne de frango e alerta as autoridades de Saúde Pública do Brasil quanto à disseminação da resistência bacteriana e a necessidade de mais estudos a respeito desse problema, já que esses são raros ou inexistentes no País. / Introduction. The introduction of antibiotics in clinical practice in the twentieth century was a breakthrough for medicine. However, their indiscriminate use in both medicine (human and animal) as in agriculture and livestock, enabled the selection and spread of resistant microorganisms. Horizontal gene transfer is a major mechanism responsible for the spread of genes encoding antimicrobial resistance, since it allows the transmission of resistance from one bacteria to another. Genes encoding resistance to antimicrobials of clinical importance are found in microorganisms present in food, environment and clinical sources. Objective. The aim of this study was to detect genes encoding resistance to -lactam antibiotics, tetracyclines and quinolones in meat samples from chicken samples, to study the occurrence of antimicrobial resistance in this product considered a common food in human diet. Materials and Methods. Thirty samples of chicken were used. After inoculation of chicken meat in Luria broth 0.5 per cent , the total DNA of the bacteria cultured was extracted by heat shock and used to search resistance genes by PCR followed by agarose gel electrophoresis. The search for thermotolerant coliforms was also conducted using the technique of multiple tubes in order to estimate the sanitary quality of the samples. Results: Eight (26,7 per cent ) of the samples had one or more genes encoding for resistance to -lactam antimicrobials, 28 (93,3 per cent ) had one or more genes encoding resistance to tetracyclines and 27 (93,3 per cent ) samples had one or more genes encoding resistance to quinolones. Conclusions: This study contributes to the scientific community and sanitary agencies, bringing information regarding the occurrence and distribution of resistance genes in chicken, alerting the Public Health authorities in Brazil about the spread of bacterial resistance and the need for more studies in this field, as these are rare or nonexistent in the country.

In this thesis we modify an existing model for the spread of resistant bacteria in a hospital. The existing model does not account for some of the trends seen in the data found in literature. The new model takes some of these trends into account. For the new model, we examine issues relating to identifiability, sensitivity analysis, parameter estimation, uncertainty analysis, and equilibrium stability.

Antibiotic resistance is an ever-growing topic of concern within the medical field causing researchers to examine the mechanisms of resistance to develop new antimicrobials. Bacteria’s ability to form biofilms is one mechanism which aids in antimicrobial resistance. Staphylococcus aureus is of special interest as it is one of the most frequent biofilm-forming bacteria found on medical devices causing infections and posing dangerous threats in a clinical setting. A recently developed antimicrobial gel has been shown to have profound effects on treating bacterial infections and wound healing. This research is centered upon examining the antimicrobial effects of this gel on the three different stages of biofilm formation in clinical and laboratory strains of S. aureus. Through a series of experiments examining the effects this gel has on S. aureus at the stages of biofilm attachment, maturation, and dispersion, the gel has shown significant levels of inhibition. These findings indicate that the novel gel disrupts biofilm forming processes of S. aureus, which provides useful information for fighting infections in the medical field. Further research on the uses and effects of this new gel could lead possibility using the antimicrobial compound for a variety of clinical purposes.

Unregulated use of growth promoting antibiotics like Tetracyclines in agricultural feeds is becoming an increasing problem in antibiotic resistance. Undigested antibiotics leads to significant concentrations in livestock waste. These concentrations provide continuous selection pressure for the development of antibiotic resistance genes in the environment. Antibiotic resistance related deaths are projected to surpass cancer related deaths by 2050 making antibiotic resistance a pressing public health issue. The purpose of this study is to determine the abundance and persistence of tetracycline (tet) resistance genes in swine waste over a period of 100 days in an anaerobic digester system. Tet(A), tet(B), tet(G), tet(M), tet(O), tet(Q), and tet(W) were quantified by quantitative polymerase chain reaction after DNA extraction. Primers that target ribosomal protection proteins and efflux proteins were used. Antibiotic resistance genes decreased from day one but were found to be present throughout the study.

In urban karst areas, such as the City of Bowling Green, Kentucky and the Tampa Bay Metropolitan Area, groundwater quality faces a variety of threats. The development of residential, commercial, and industrial landuse types allows for a wide variety of groundwater pollutants to enter the karst groundwater systems. Various different models and indices have attempted evaluative approaches to identify issues in urban karst areas, but the methods vary by location and lack a focus on urban karst groundwater quality. There also exists a lack of a data-driven approach that is able to capture short- and long-term changes in threats to groundwater quality as a result of urbanization. The overall purpose of this study was to develop a holistic, data-driven evaluation toolbox with threat, vulnerability, and monitoring assessment tools for urban karst groundwater systems to better determine the possible threats, data collection needs, monitoring parameters, and analytical approaches needed to ensure groundwater quality is maintained in urban karst regions. This study focused on: 1) determining what indicators, parameters, resolution, and data quality need to be prioritized to create an effective, holistic monitoring framework for urban karst groundwater, and 2) developing an effective assessment and evaluative tools for urban karst groundwater quality sites using historic and modern data in an urban karst setting. The outcomes include an Urban Karst Aquifer Resource Evaluation (UKARE) Toolbox with a Threat, Vulnerability, and Monitoring evaluation tools that were applied and validated through application of the Toolbox using case studies in the City of Bowling Green, Kentucky and the Tampa Bay Metropolitan Area in Florida. The results demonstrate the universal applicability of the UKARE Toolbox to different urban karst sites and its effectiveness at scoring for threats and vulnerabilities, as well as identifying potential monitoring sites through primary data collection of water quality parameters and emerging pathogens at over 150 sites between both study areas. The final results of this study are useful to develop monitoring and management plans through a standardized scoring and evaluation tool in order to influence urban karst groundwater monitoring and management.

New antibiotics with novel targets or mechanisms of action are needed to counter the steady emergence of bacterial pathogens that are resistant to antibiotics used in the clinic. MraY, a promising novel target for antibiotic development, initiates the lipid cycle for the biosynthesis of peptidoglycan cell wall, which is essential for the survival of most, if-not-all, bacteria. MraY is an enzyme that catalyzes the transfer and attachment of phospho-MurNAc-pentapeptide to a lipid carrier, undecaprenylphosphate. Muraymycins are recently discovered lipopeptidyl nucleoside antibiotics that exhibit remarkable antibiotic activity against Gram-positive as well as Gram-negative bacteria by inhibiting MraY. We conducted a thorough examination of the metabolic profile of Streptomyces sp. strain NRRL 30473, a known producer of muraymycins. Eight muraymycins were isolated and characterized by a suite of spectroscopic methods, including three new members of muraymycin family named B8, B9 and C5. Muraymycins B8 and B9, which differ from other muraymycins by having an elongated fatty acid side chain, showed potent antibacterial activity against Escherichia coli ∆tolC mutant and pM IC50 against Staphylococcus aureus MraY. Muraymycin C5, which is characterized by an N-acetyl modification of the disaccharide’s primary amine, greatly reduced its antibacterial activity, which possibly indicates this modification is used for self-resistance. In addition to the discovery of new muraymycins, eleven enzymes from the biosynthetic pathway were functionally assigned and characterized in vitro. Six enzymes involved in the biosynthesis of amino ribofuranosylated uronic acid moiety of muraymycin were characterized: Mur16, a non-heme, Fe(II)-dependent α-ketoglutarate: UMP dioxygenase; Mur17, an L-threonine: uridine-5′-aldehyde transaldolase; Mur20, an L-methionine:1-aminotransferase; Mur26, a low specificity pyrimidine nucleoside phosphorylase; Mur18, a primary amine-requiring nucleotidylyltransferase; Mur19, a 5-amino-5-deoxyribosyltransferase. A one-pot enzyme reaction was utilized to produce this disaccharide moiety and its 2′′-deoxy analogue. Two muraymycin-modifying enzymes that confer self-resistance were functionally assigned and characterized: Mur28, a TmrB-like ATP-dependent muraymycin phosphotransferase, and Mur29, a muraymycin nucleotidyltransferase. Notably, Mur28 preferentially phosphorylates the intermediate, aminoribofuranosylated uronic acid, in the muraymycin biosynthetic pathway to produce a cryptic phosphorylated-dissacharide intermediate. Mur23 and Mur24 were assigned as two enzymes that modify the cryptic phosphorylated intermediate by attachment of an aminopropyl group. Mur24 catalyzes the incorporation of butyric acid into the phosphorylated-disaccharide. Following the incorporation, Mur23 catalyzes a PLP-dependent decarboxylation. Finally, Mur15, which belongs to the cupin family, is functionally assigned as a non-heme, Fe(II)-dependent α-ketoglutarate dioxygenase that catalyzes the β-hydroxylation of a leucine moiety in muraymycin D1 to form muraymycin C1. Mur15 can also hydroxylate the γ-position of leucine moiety to muraymycins with fatty acid chain in β-position.

L’anthropisation médicamenteuse des eaux usées favorise l’émergence et la diffusion dans l’environnement de microorganismes résistants aux antibiotiques. Les effluents hospitaliers pourraient être doublement impliqués en véhiculant antibiotiques et bactéries multirésistantes. L’objectif de ce travail est de caractériser les effluents hospitaliers d’un Centre Hospitalo-Universitaire en évaluant simultanément les concentrations d’antibiotiques (fluoroquinolones et imipénème) et la diversité des bactéries résistantes à ces antibiotiques au sein de biofilms constitués in situ. Les concentrations en antibiotiques mesurées par chromatographie en phase liquide - spectrométrie de masse après collecte via un échantillonnage passif pendant 15 jours sont égales à 2,08±0,88μg/L (ciprofloxacine), 101,06±18.47 μg/L (ofloxacine), 6,43±0.56 μg/L (norfloxacine) et indétectable pour l’imipénème. Comparées aux données de consommation à l’hôpital pendant cette même période, les concentrations estimées sont 5,84±1,78μg/L (ciprofloxacine), 11.22±1.09μg/L (ofloxacine), 7.68±3,7μg/L (norfloxacine) et 3,61±0,24ug/L (imipénème). La mesure du risque potentiel écotoxicologique s’est avérée positive pour la ciprofloxacine et la norfloxacine (hazard quotient >1). En parallèle, des bactéries résistantes aux fluoroquinolones (n=115) ou aux carbapénèmes (n=38) ont été isolées de biofilms formés dans les effluents hospitaliers. 60 % des isolats, constitués majoritairement de bacilles à Gram négatif, notamment Aeromonas spp et Klebsiella spp, sont résistants à plusieurs familles d’antibiotiques dont certains sont exclusivement utilisés à l’hôpital. La majorité des souches hébergent des éléments génétiques mobiles dont des plasmides conjugatifs porteurs de la résistance à l’imipénème ou aux fluoroquinolones. La présence combinée de bactéries résistantes aux antibiotiques hébergeant des éléments génétiques mobiles en lien avec ces résistances et de faibles concentrations en antibiotiques permet de qualifier l’interface hôpital-environnement comme un lieu propice au transfert des résistances. / The presence of pharmaceutical compounds in waste water favors the emergence and the spreading of antibiotic resistant microorganisms. The hospital effluents could be involved gathering antibiotics and multiresistant bacteria. The aim of this work is to characterize the hospital effluents of a teaching hospital measuring simultaneously the concentrations of antibiotics (fluoroquinolones and imipenem) and the diversity of the bacteria resistant to these antibiotics within hospital effluent biofilms.The antibiotics concentrations were measured by liquid-phase chromatography - mass spectrometry via a passive sampling during 15 days. The measured environmental concentrations were 2.08 ± 0.88μg/L (ciprofloxacin), 101.06 ± 18.47 μg/L (ofloxacine), 6.43 ± 0.56 μg/L (norfloxacine). Imipenem was not detected. Compared with the data of hospital consumption during the same period, the predicted estimated concentrations are 5.84±1.78µg/L(ciprofloxacin), 11.22 ± 1.09µg/L (ofloxacin), 7.68 ± 3.7µg/L, 7.68 ± 3.7μg/L (norfloxacin) and 3.61 ± 0.24ug/L (imipenem). The ecotoxicological risk was confirmed for the ciprofloxacin and the ofloxacin (hazard quotient > 1).In parallel, fluoroquinolones (n=115) and carbapenem (n=38) resistant bacteria were isolated from hospital effluent biofilm. Sixty % of isolates, mainly composed by Gram negative bacilli in particular Aeromona spp and Klebsiella spp, are resistant to several antibiotics among which some are exclusively used at the hospital. The majority of these strains have mobile genetic elements such as conjugative plasmids harboring imipenem or fluoroquinolones resistances.The presences of both antibiotics resistant bacteria harboring mobile genetic elements in connection with these resistances and low antibiotics concentrations make the hospital effluent a convenient place for the transfer of resistance between the hospital and the environment.

Background: Antibiotic overuse/misuse has been documented in several reports to increase the risk of Clostridioides difficile (C.diff) infection and antibiotic resistance. The older adult population is more prone to use antibiotic medications than any other age group due to decreased immune function, use of urinary catheters, ventilation during hospitalization and other factors. Antibiotic resistance and C.diff are major public health problems. However, studies examining the trends of antibiotic use and the association between the antibiotic use and negative health outcomes among older adults in the outpatient and emergency department settings are limited. Objectives: The main objectives of this dissertation were to: 1) calculate the national antibiotic trends among community-dwelling older adults in the United State; 2) evaluate the antibiotic trends and antibiotic appropriateness among older adult patients visiting the geriatrics clinic and adult internal ambulatory care clinic at VCU Health; and 3) examine the antibiotic trends and antibiotic appropriateness among older adult patients and middle-aged patients visiting the emergency department at VCU Health. Methods: For the first objective, data were obtained from Medical Expenditure Panel survey (MEPS) a nationally representative dataset (2011-2015). Descriptive analyses were conducted and multiple logistic regression was performed to assess the association between the antibiotic use and demographic and sociodemographic characteristics. In the second objective, data were obtained from VCU Health outpatient clinics (geriatrics, and Internal medicine ambulatory care clinic only). Descriptive statistics were calculated and multiple logistic regression was performed to assess the association between antibiotic appropriateness and type of clinics and other demographic characteristics. In the third objective, the emergency department electronic medical records at VCU were used. Trend analysis was performed across the dissertation studies using the Cochran–Armitage test. All variables were considered statistically significant at an α level of 0.05. All the statistical analyses were conducted using the Statistical Analysis Software Version 9.4 (SAS v.9.4), (SAS Institute Inc, Cary, NC). Results: There were 105,762,134 prescriptions dispensed to older adults in the outpatient setting in the US from 2011 to 2015. Antibiotic prescriptions were more common among women (18%) compared to men (12%). White participants received more antibiotics (27%) than African Americans (1.77%) and others (1.4%). Among the 3,515 patients who visited either Geriatrics or Internal Medicine ambulatory clinic at VCU Health from 2012-2017, 1,534 antibiotics were prescribed. Potentially inappropriate antibiotic prescriptions were similar between the two clinics (30% in Geriatrics clinic and 28% in Internal Medicine ambulatory clinic) with p-value of 0.08. In addition, 6,343 middle-aged or older adult patients were dispensed and prescribed an antibiotic in the ED at VCU Health from (2012 to 2017). Eighteen percent of the antibiotic prescriptions received by middle age group were considered potentially inappropriate, compared to 9% among the older adult patient (p < 0.0001). Conclusions: The rate of antibiotic use overall remains unchanged despite the national and international efforts to reduce antibiotic prescriptions and eventually to reduce antibiotic resistance. The changes in the patterns of use in some of the antibiotic categories appear to be driven more by the safety concerns rather than reducing overall use. Future research is needed to strengthen antibiotic stewardship programs for older adults in outpatient settings.

Urinary tract infections are diagnosed in female populations primarily in ambulatory care settings in the United States. Yet, published evidence documents that many of the antibiotics prescribed in these settings are unnecessary, erroneous, or, inappropriately prescribed. Improper management of uncomplicated urinary tract infections in nonpregnant women has resulted in higher morbidity rates due to antibiotic resistance. The purpose of this retrospective observational cohort study was to explore a current national database for associations between nonpregnant American female patients who were exposed to poverty and at risk for urinary tract infection antibiotic resistance in an ambulatory care setting. Krieger's ecosocial theory was utilized as the study's theoretical foundation to complement current public health social change priorities. Data from the National Ambulatory Medical Care Survey were analyzed to explore potential associations with urinary tract infections and antibiotic resistance. The sample consisted of ambulatory patients with urinary tract infection symptoms (n=45). The independent variables selected were antibiotics prescribed initially in 3 months or less after the onset of urinary tract infection symptoms, the continuation of antibiotics prescribed in 12 months or less after recurrence, and three classes of antibiotics prescribed for urinary tract infection symptoms known as broad-spectrum, narrow-spectrum, and combined broad- and narrow-spectrum antibiotics, while the dependent variable was urinary tract infection antibiotic resistance. Relationships between the variables were analyzed using binary logistic regression, however, there were no statistically significant outcomes. Promoting antibiotic stewardship programs in all health care settings in the U.S. can effect positive social changes that will prevent further antibiotic resistance.