The growing threat of antimicrobial resistance is among the largest concerns in the world today. One method under development to combat this issue is the encapsulation of microbes in microfluidic droplets for single-cell testing. This method may be able to circumvent the need for a traditional positive cell culture which consumes the majority of the testing time using current diagnostic methods. This dissertation presents a method by which to deterministically encapsulate microbes using an artificial intelligence object detection algorithm and a Droplet-On-Demand microfluidic device. To accomplish this, the Droplet-On-Demand microfluidic device was first developed using a unique 3D-printing manufacturing method. An annular Channel-in-Channel droplet generator was developed which produced droplets within the hydrophobic 3D-printed polymeric microfluidic device. Supporting microfluidic unit operations were also developed including pumps, a 3-way flow-thru valve, and a detection window used for visualizing microfluidic particles. Control software was developed using python which controlled pneumatically-actuated membranes within the microfluidic device, the imaging system, and the object detection algorithm. 20-μm and 2-μm test particles were used as non-biological test particles while red blood cells and fluorescent E.coli baceria were used as biological test particles. All test particles were identified and encapsulated and show the flexibility of the system overall and the ability to identify a variety of particles of interest in microfluidic systems. Growth tests were conducted using E.coli bacteria encapsulated within microfluidic droplets with a fluorescent metabolic indicator. The fluorescence of droplets containing actively growing encapsulated bacteria was quantified using a unique first-principles model paired with an image processing protocol to provide relative concentration data to quantify the growth of the E.coli over time. These growth results indicated that bacterial growth in droplets could be detected and quickly quantified in 4 hours and thus provide practical results to clinicians on the susceptibility of bacteria to an antibiotic. This Droplet-On-Demand technology has the capability of providing clinically applicable data from the most basic and fundamental biological source, an individual cell; and that can be done with low concentrations and on any cell that can be visually identified.

Orientadoesr: Angela Maria Moraes, Silvia Yuko Eguchi / Dissertação (mestrado) - Universidade Estadual de Campinas, Faculdade de Engenharia Quimica / Made available in DSpace on 2018-08-07T08:22:07Z (GMT). No. of bitstreams: 1 Lucchesi_ElianeGama_M.pdf: 1203175 bytes, checksum: 28d918ad922300d0066ef3f03d052bdd (MD5) Previous issue date: 2006 / Resumo: Biofilme microbiano é definido como uma associação de células microbianas, fixadas a superfícies, bióticas ou abióticas, envolta por uma complexa matriz extracelular de substâncias poliméricas. Os biofilmes representam mais de 90% dos contaminantes existentes em sistemas aquosos, industriais, clínicos e ambientais. A resistência de microrganismos em biofilmes (sésseis) a biocidas é muito maior que a resistência de células livres (planctônicas), quando se compara seus antibiogramas. A rápida e correta avaliação do efeito de agentes antimicrobianos sobre os microrganismos sésseis é muito importante para a adequada seleção das ações corretivas a serem aplicadas em sistemas industriais contaminados. Atualmente, o sistema in vitro mais indicado para gerar, quantificar e erradicar biofilmes é o dispositivo MBECTM, de alto custo, desenvolvido por pesquisadores canadenses. O presente estudo visou o desenvolvimento de um sistema alternativo que fornecesse resultados análogos ao MBECTM, empregando esferas de vidro como suporte para o crescimento de biofilmes ao invés de placas de poliestíreno. Em amostras de três segmentos industriais diferentes (óleo de corte usado na usinagem de metais, amaciante ,. de roupas e caldo de cana) contaminados com microrganismos formadores de biofilmes, foram testadas sete formulações de biocidas em diversas concentrações, tanto no sistema desenvolvido quanto no dispositivo MBECTM. Os biocidas utilizados foram fomecidos pela IPEL Itibanyl Produtos Especiais Ltda, formulados com os seguintes princípios ativos: 2-bromo-2nitropropano-1 ,3-diol (BNP-115); 2-n-octíl-4isotiazolin-3-ona, 2-tiocianometiltiobenzotiazol, dimetílolurea, 5-cloro-2 metil-4isotiazolin-3-ona, 2-metil-4-isotiazolin-3-ona (FBP-124); 2-n-octil-4 isotiazolin-3-ona, dimetilolurea, 1,2-benzisotiazolin-3-ona (FBP-128); sódio-2-piridinatiol-n-óxido (FBP-140); hexahidro-1,3,5-tris(2-hidroxietil) s-triazina (BP-180); 2-bromo-2nitropropano-1,3-diol, 5cloJo-2metíl-4-isotiazolin-3-ona, 2-metil-4-isotiazolin-3-ona (BP-509);e 2-n-octil-4isotiazolin-3-ona, dimethylolurea, 3-iodo-2-propinil butil carbamato (FBP-417). A concentração inibitória mínima. (MIe) dos biocidas e suas concentrações mínimas de morte (CMM) foram determinadas para as bactérias planctônicas do fluido de corte, e a melhor relação custo/benefício foi observada para o biocida BNP-11,5, que apresentou MIC e CMM de 0,014% (v/v). Quanto às células sésseis, formadas em ambos os dispositivos utilizando-se fluido de corte contaminado como inóculo, o biocida de melhor relação custo/benefício foi o BP180. Nos ensaios com amaciante de roupas e caldo de cana, as melhores relações custo/benefício foram verificadas para os biocidas BNP-115, BP-180 e BP-509. A maturidade do biofilme foi muito importante para avaliar a eficácia dos biocidas. Verificou-se, durante o desenvolvimento. do trabalho, que para a concentração de erradicação (CE) do biofílme formado no dispositivo MBECTM ser semelhante às concentrações determinadas nas esferas de vidro, houve a necessidade de um periodo de incubação maior (72 horas) no MBECTM do que no sistema de esferas (48 horas). Os valores de CE determinados para o dispositivo MBEC TM, com 48 horas e 72 horas de incubação foram, respectivamente, 12 vezes maior que a concentração tradicional recomendada e de 30 a 125 vezes tal concentração, dependendo do biocida testado. Estes resultados evidenciaram que a maturidade do biofilme formado a partir do óleo de corte contaminado é atingida mais rapidarTIente no sistema de esferas de vidro do que no dispositivo MBEC TM, mostrando que é possível gerar um biofilme representativo da contaminação industrial em 48 horas no sistema alternativo desenvolvido, agilizando as ações corretivas e evitando ou minimizando principalmente os custos com o descarte das emulsões / Abstract: A microbial biofilm is defined as an association of microbial cells adhered to surfaces, biotic or abiotic, wrapped up in a complex extracellular polymeric matrix. Biofilms represent more than 90% of the existent contaminants in aqueous, industrial, and clinical systems, as well as in the environment. The resistance to biocides of microorganisms in biofilms (sessile cells) is much larger than that observed for cells in suspension (planktonic) when their antibiograms are compared. The fast and correct evaluation of the effect of antimicrobial agents on sessile microorganisms is very important for the appropriate selection of the corrective adions to be applied in contaminated industrial systems. Nowadays, the most indicated system to generate, quantify and eradicate biofilms is the MBECTM device, developed by Canadian researchers. The present study seeked the development of an altemative system to supply results similar to those obtained with the MBEC TM device, employing glass spheres as a support for biofilm growth instead of polystyrene plates. In samples of three different industrial segments (metal working cutting fluid, liquid fabric softener and sugar cane extract), seven commercial biocide formulations were tested in several concentrations, on "'rboth the developed system using glass spheres as support, and on the MBECTM device. The biocides employed were provided by IPEL ltibanyl Produtos Especiais Ltda, and were formulated with the following active agents: 2-brome-2nitropropane-1,3-diol (BNP-115); 2-n-octil-4isotiazolin-3-0ne, 2-tiocianometiltiobenzotiazol, dimethyilolurea, 5cloro-2metil-4-isotiazolin-3-one, 2-metil-4-isotiazolin-3-one (FBP-124); 2-n-octil-4 isotiazolin-3-0ne, dimethylolurea, 1,2-benzisotiazolin-3-0ne (FBP-128); sodium-2piridinatiol-n-oxide (FBP-140); hexahidro-1,3,5-tris(2-hidroxietil) s-triazine (BP-180); 2brome-2nitropropane-1 ,3-diol, 5-cloro-2metil-4-isotiazolin-3-one, 2-metil-4-isotiazolin-3-0ne (BP-509);e 2-n-octil-4-isotiazolin-3-0ne, dimethylolurea, 3-iodo-2-propinil butil carbamate (FBP-417). . The minimum inhibitory concentration (MIC) and minimum concentration of death (CMM) of the different biocides were determined for the cutting fluid planktonic bacteria and the best costlbenefit ratio was observed for BNP-115 biocide, which presented MIC and CMM values equal to 0,014% (v/v). Referring to sessile cells formed on both systems, when the contaminated cutting fluid was used as inoculum, the biocide presenting the best costlbenefit ratio was BP-180. In the tests with liquid fabric softener and sugar cane extract, the best costlbenefit ratios were verified when using BNP-115, BP-180 and BP-509 biocides. The maturity of the biofilm was very important to evaluate the effectiveness of the biocides. It was verified, during the development of the work, that for the eradication concentration (CE) of the biofilm formed in the MBEC TM device to be similar to the concentrations determined in the glass spheres, a larger incubation period was required (72 hours) in MBECTM than in the system constituted of spheres (48 hours). The determined values of CE using the MBECTM device, after incubation periods of 48 hours and 72 hours, were, respedively, 12 times higher than the traditional recommended concentration and from 30 to 125 times such concentration, depending on the tested biocide. These results evidenced that the biofilm formed trom the cutting oil reached its maturity more quickly in the glass spheres system than in the MBEC TM device, showing that it is possible to generate a representative biofilm starting from an industrial contaminated sample in 48 hours in the developed system, accelerating the proper corrective actions and avoiding or minimizing mainly the costs related to emulsion disposal / Mestrado / Desenvolvimento de Processos Biotecnologicos / Mestre em Engenharia Química

Introduction: Les efforts globaux pour contrôler la tuberculose sont présentement restreints par la prévalence croissante du VIH/SIDA. Quoique les éclosions de la tuberculose multi résistante (TB-MDR) soient fréquemment rapportées parmi les populations atteintes du SIDA, le lien entre VIH/SIDA et le développement de résistance n’est pas clair. Objectifs: Cette recherche visait à : (1) développer une base de connaissances concernant les facteurs associés à des éclosions de la TB-MDR parmi les patients atteints du VIH/SIDA; (2) utiliser ce cadre de connaissances pour accroître des mesures préliminaires pour mieux contrôler la tuberculose pulmonaire chez les patients atteints du VIH/SIDA; et (3) afin d’améliorer l’application des ces mesures, affiner les techniques bactériologiques existantes pour Mycobacterium tuberculosis. Méthodologie: Quatre études ont été réalisées : (1) Une étude longitudinale pour identifier les facteurs associés avec une éclosion de la TB-MDR parmi les patients atteints du SIDA qui ont reçu le traitement directement supervisé de courte durée (DOTS) pour la tuberculose pulmonaire au Lima et au Pérou entre 1999 et 2005; (2) Une étude transversale pour décrire différentes étapes de l’histoire naturelle de la tuberculose, la prévalence et les facteurs associés avec la mycobactérie qu’on retrouve dans les selles des patients atteints du SIDA; (3) Un projet pilote pour développer des stratégies de dépistage pour la tuberculose pulmonaire parmi les patients hospitalisés atteints du SIDA, en utilisant l’essaie Microscopic Observation Drug Susceptibility (MODS); et (4) Une étude laboratoire pour identifier les meilleures concentrations critiques pour détecter les souches MDR de M. tuberculosis en utilisant l’essaie MODS. Résultats : Étude 1 démontre qu’une épidémie de TB-MDR parmi les patients atteints du SIDA qui ont reçu DOTS pour la tuberculose pulmonaire ait été causée par la superinfection du clone de M. tuberculosis plutôt que le développement de la résistance secondaire. Bien que ce clone ait été plus commun parmi la cohorte de patients atteints du SIDA, il n’avait aucune différence de risque pour superinfection entre les patients avec ou sans SIDA. Ces résultats suggèrent qu’un autre facteur, possiblement associé à la diarrhée, peu contribuer à la prévalence élevée de ce clone chez les patients atteints du SIDA. Étude 2 suggère que chez la plupart des patients atteints du SIDA il a été retrouvé une mycobactérie dans leurs selles alors qu’ils étaient en phase terminale au niveau de la tuberculose pulmonaire. Or, les patients atteints du SIDA ayant été hospitalisés pendant les deux dernières années pour une autre condition médicale sont moins à risque de se retrouver avec une mycobactérie dans leurs selles. Étude 3 confirme que la tuberculose pulmonaire a été commune à tous les patients hospitalisés atteints du SIDA, mais diagnostiquée incorrectement en utilisant les critères cliniques présentement recommandés pour la tuberculose. Or, l’essaie MODS a détecté pour la plupart de ces cas. De plus, MODS a été également efficace quand la méthode a été dirigée aux patients soupçonnés d’avoir la tuberculose, à cause de leurs symptômes. Étude 4 démontre les difficultés de détecter les souches de M. tuberculosis avec une faible résistance contre ethambutol et streptomycine en utilisant l’essai MODS avec les concentrations de drogue présentement recommandées pour un milieu de culture. Cependant, l’utilité diagnostique de MODS peut être améliorée ; modifier les concentrations critiques et utiliser deux plaques et non une, pour des tests réguliers. Conclusion: Nos études soulèvent la nécessité d’améliorer le diagnostic et le traitement de la tuberculose parmi les patients atteints du SIDA, en particulier ceux qui vivent dans des régions avec moins de ressources. Par ailleurs, nos résultats font ressortir les effets indirects que les soins de santé ont sur les patients infectés par le VIH et qu’ils peuvent avoir sur le développement de la tuberculose. / Background: Global efforts to control tuberculosis are currently being hampered by a continuing rise in the prevalence of HIV/AIDS. Although outbreaks of multidrug resistant tuberculosis (MDR-TB) are commonly reported among AIDS populations, the link between HIV/AIDS and the development of drug-resistance remains unclear. Objectives: This thesis aimed to: (1) build a knowledge foundation regarding underlying factors associated with outbreaks of MDR-TB among HIV/AIDS patients; (2) use this knowledge framework to develop preliminary health measures for controlling pulmonary tuberculosis among HIV/AIDS patients; and (3) in an effort to better implement these health measures, refine existing culture-based diagnostics for Mycobacterium tuberculosis. Methods: Four studies were conducted: (1) a longitudinal study to identify the underlying factors associated with an epidemic of MDR-TB among AIDS patients receiving Directly- Observed Therapy Short-course (DOTS) for pulmonary tuberculosis in Lima, Peru between 1999 and 2005; (2) a cross-sectional study to characterize the prevalence and factors associated with gastrointestinal shedding with mycobacteria among AIDS patients at different stages in the natural history of tuberculosis; (3) a pilot study to develop screening strategies for pulmonary tuberculosis among hospitalized HIV/AIDS patients using the Microscopic Observation Drug Susceptibility (MODS) assay; and (4) a laboratory-based study to define the optimal critical concentrations needed for detecting drug resistance in M. tuberculosis using MODS. Results: Study 1 revealed that an epidemic of MDR-TB among AIDS patients receiving DOTS for pulmonary tuberculosis was due to super-infection with a specific clone of M. tuberculosis rather than the development of secondary drug-resistance. Although this epidemic clone was more common among patients in the AIDS cohort, risk of superinfection did not differ between AIDS and non-AIDS patients after adjusting for baseline risk of exposure, suggesting that another factor possibly associated with diarrhea may be contributing to the strain’s high prevalence among AIDS patients. Study 2 showed that the majority of AIDS patients in the later stages of pulmonary tuberculosis exhibited gastrointestinal shedding with mycobacteria. Stool shedding was rare in the absence of pulmonary tuberculosis. AIDS patients were also less likely to shed mycobacteria if they had been hospitalized during the previous two years for another medical condition. Study 3 confirmed that pulmonary tuberculosis was common among hospitalized AIDS patients but frequently misdiagnosed using currently recommended diagnostic algorithms. The MODS assay detected most cases and was equally effective when targeted to patients clinically suspicious for tuberculosis. Study 4 demonstrated that low grade drug resistance in M. tuberculosis to ethambutol and streptomycin was difficult to detect with MODS using currently recommended drug-concentration standards in broth. Its diagnostic utility could be improved by modifying drug-concentration standards, and including two versus one critical concentration well for standardized testing. Conclusion: Our studies underscore the need to improve the diagnosis and treatment of tuberculosis among AIDS patients living in resource-constrained settings, all in an effort to prevent morbidity, mortality and the transmission of drug-resistant strains. They also highlight the indirect effect that general health care among HIV-infected patients can have on the development of tuberculosis.

Introduction: Les efforts globaux pour contrôler la tuberculose sont présentement restreints par la prévalence croissante du VIH/SIDA. Quoique les éclosions de la tuberculose multi résistante (TB-MDR) soient fréquemment rapportées parmi les populations atteintes du SIDA, le lien entre VIH/SIDA et le développement de résistance n’est pas clair. Objectifs: Cette recherche visait à : (1) développer une base de connaissances concernant les facteurs associés à des éclosions de la TB-MDR parmi les patients atteints du VIH/SIDA; (2) utiliser ce cadre de connaissances pour accroître des mesures préliminaires pour mieux contrôler la tuberculose pulmonaire chez les patients atteints du VIH/SIDA; et (3) afin d’améliorer l’application des ces mesures, affiner les techniques bactériologiques existantes pour Mycobacterium tuberculosis. Méthodologie: Quatre études ont été réalisées : (1) Une étude longitudinale pour identifier les facteurs associés avec une éclosion de la TB-MDR parmi les patients atteints du SIDA qui ont reçu le traitement directement supervisé de courte durée (DOTS) pour la tuberculose pulmonaire au Lima et au Pérou entre 1999 et 2005; (2) Une étude transversale pour décrire différentes étapes de l’histoire naturelle de la tuberculose, la prévalence et les facteurs associés avec la mycobactérie qu’on retrouve dans les selles des patients atteints du SIDA; (3) Un projet pilote pour développer des stratégies de dépistage pour la tuberculose pulmonaire parmi les patients hospitalisés atteints du SIDA, en utilisant l’essaie Microscopic Observation Drug Susceptibility (MODS); et (4) Une étude laboratoire pour identifier les meilleures concentrations critiques pour détecter les souches MDR de M. tuberculosis en utilisant l’essaie MODS. Résultats : Étude 1 démontre qu’une épidémie de TB-MDR parmi les patients atteints du SIDA qui ont reçu DOTS pour la tuberculose pulmonaire ait été causée par la superinfection du clone de M. tuberculosis plutôt que le développement de la résistance secondaire. Bien que ce clone ait été plus commun parmi la cohorte de patients atteints du SIDA, il n’avait aucune différence de risque pour superinfection entre les patients avec ou sans SIDA. Ces résultats suggèrent qu’un autre facteur, possiblement associé à la diarrhée, peu contribuer à la prévalence élevée de ce clone chez les patients atteints du SIDA. Étude 2 suggère que chez la plupart des patients atteints du SIDA il a été retrouvé une mycobactérie dans leurs selles alors qu’ils étaient en phase terminale au niveau de la tuberculose pulmonaire. Or, les patients atteints du SIDA ayant été hospitalisés pendant les deux dernières années pour une autre condition médicale sont moins à risque de se retrouver avec une mycobactérie dans leurs selles. Étude 3 confirme que la tuberculose pulmonaire a été commune à tous les patients hospitalisés atteints du SIDA, mais diagnostiquée incorrectement en utilisant les critères cliniques présentement recommandés pour la tuberculose. Or, l’essaie MODS a détecté pour la plupart de ces cas. De plus, MODS a été également efficace quand la méthode a été dirigée aux patients soupçonnés d’avoir la tuberculose, à cause de leurs symptômes. Étude 4 démontre les difficultés de détecter les souches de M. tuberculosis avec une faible résistance contre ethambutol et streptomycine en utilisant l’essai MODS avec les concentrations de drogue présentement recommandées pour un milieu de culture. Cependant, l’utilité diagnostique de MODS peut être améliorée ; modifier les concentrations critiques et utiliser deux plaques et non une, pour des tests réguliers. Conclusion: Nos études soulèvent la nécessité d’améliorer le diagnostic et le traitement de la tuberculose parmi les patients atteints du SIDA, en particulier ceux qui vivent dans des régions avec moins de ressources. Par ailleurs, nos résultats font ressortir les effets indirects que les soins de santé ont sur les patients infectés par le VIH et qu’ils peuvent avoir sur le développement de la tuberculose. / Background: Global efforts to control tuberculosis are currently being hampered by a continuing rise in the prevalence of HIV/AIDS. Although outbreaks of multidrug resistant tuberculosis (MDR-TB) are commonly reported among AIDS populations, the link between HIV/AIDS and the development of drug-resistance remains unclear. Objectives: This thesis aimed to: (1) build a knowledge foundation regarding underlying factors associated with outbreaks of MDR-TB among HIV/AIDS patients; (2) use this knowledge framework to develop preliminary health measures for controlling pulmonary tuberculosis among HIV/AIDS patients; and (3) in an effort to better implement these health measures, refine existing culture-based diagnostics for Mycobacterium tuberculosis. Methods: Four studies were conducted: (1) a longitudinal study to identify the underlying factors associated with an epidemic of MDR-TB among AIDS patients receiving Directly- Observed Therapy Short-course (DOTS) for pulmonary tuberculosis in Lima, Peru between 1999 and 2005; (2) a cross-sectional study to characterize the prevalence and factors associated with gastrointestinal shedding with mycobacteria among AIDS patients at different stages in the natural history of tuberculosis; (3) a pilot study to develop screening strategies for pulmonary tuberculosis among hospitalized HIV/AIDS patients using the Microscopic Observation Drug Susceptibility (MODS) assay; and (4) a laboratory-based study to define the optimal critical concentrations needed for detecting drug resistance in M. tuberculosis using MODS. Results: Study 1 revealed that an epidemic of MDR-TB among AIDS patients receiving DOTS for pulmonary tuberculosis was due to super-infection with a specific clone of M. tuberculosis rather than the development of secondary drug-resistance. Although this epidemic clone was more common among patients in the AIDS cohort, risk of superinfection did not differ between AIDS and non-AIDS patients after adjusting for baseline risk of exposure, suggesting that another factor possibly associated with diarrhea may be contributing to the strain’s high prevalence among AIDS patients. Study 2 showed that the majority of AIDS patients in the later stages of pulmonary tuberculosis exhibited gastrointestinal shedding with mycobacteria. Stool shedding was rare in the absence of pulmonary tuberculosis. AIDS patients were also less likely to shed mycobacteria if they had been hospitalized during the previous two years for another medical condition. Study 3 confirmed that pulmonary tuberculosis was common among hospitalized AIDS patients but frequently misdiagnosed using currently recommended diagnostic algorithms. The MODS assay detected most cases and was equally effective when targeted to patients clinically suspicious for tuberculosis. Study 4 demonstrated that low grade drug resistance in M. tuberculosis to ethambutol and streptomycin was difficult to detect with MODS using currently recommended drug-concentration standards in broth. Its diagnostic utility could be improved by modifying drug-concentration standards, and including two versus one critical concentration well for standardized testing. Conclusion: Our studies underscore the need to improve the diagnosis and treatment of tuberculosis among AIDS patients living in resource-constrained settings, all in an effort to prevent morbidity, mortality and the transmission of drug-resistant strains. They also highlight the indirect effect that general health care among HIV-infected patients can have on the development of tuberculosis.