Orientadores: Laura Maria Mariscal Ottoboni, Tatiana Teixeira Torres / Tese (doutorado) - Universidade Estadual de Campinas, Instituto de Biologia / Made available in DSpace on 2018-08-26T13:28:27Z (GMT). No. of bitstreams: 1 Stoppe_NancydeCastro_D.pdf: 4282286 bytes, checksum: f808229a92e702d707b4ebf6be210816 (MD5) Previous issue date: 2014 / Resumo: A contaminação fecal dos corpos hídricos é uma das principais causas de doenças entéricas veiculadas pela água no mundo, sendo importante efetuar a vigilância da água, a qual é feita utilizando-se micro-organismos indicadores de contaminação fecal. No entanto, os métodos tradicionais de detecção não são capazes de identificar a fonte de contaminação fecal. Este trabalho teve como objetivo a prospecção de marcadores moleculares nos hospedeiros e sua detecção em amostras de água de modo a permitir sua utilização na identificação de fontes de contaminação fecal em águas superficiais no Estado de São Paulo. Duas abordagens dependentes de biblioteca e cultivo, a classificação por meio de grupos filogenéticos e a técnica de MALDI-TOF/MS, foram utilizadas com linhagens de E. coli isoladas de diferentes hospedeiros e rios e reservatórios. O sequenciamento da região V3 do gene 16S ribossomal foi selecionado como o método independente de biblioteca e cultivo em DNA extraído de amostras de fezes humanas e bovinas e amostras de água. Os grupos filogenéticos foram utilizados na classificação dos hospedeiros utilizando análise de correspondência, onde foram observados agrupamentos por hábitos alimentares. A classificação das linhagens de E. coli isoladas de rios e reservatórios, sugere que a prevalência do subgrupo A1, seguido do subgrupo B23 está associada com contaminação de origem humana, enquanto o grupo B1 com contaminação de origem animal e os subgrupos D1 e D2 mais relacionados com ambientes prístinos. Na utilização de uma métrica de análise de rede social, w-clique, na distribuição dos grupos filogenéticos foi observado o agrupamento dos locais de amostragem associados ao grau de poluição, sugerindo seu uso como uma ferramenta complementar na avaliação da qualidade da água. Foram analisados os perfis proteicos de linhagens de E. coli de hospedeiros e amostras ambientais pela técnica de MALDI-TOF/MS. Foram identificados biomarcadores hospedeiro-específicos e sugerem sua utilização como potencial ferramenta na identificação da origem do hospedeiro. Os resultados da validação desses marcadores com perfis proteicos de linhagens de E. coli isoladas de rios e reservatórios mostraram que as amostras de água apresentaram marcadores de diferentes hospedeiros, sugerindo que esses rios possuam fontes de contaminação fecal mistas. No sequenciamento da região V3 do gene 16S ribossomal de amostras de fezes (humanas e bovinas) e águas foram identificadas 4.296 unidades taxonômicas operacionais (OTUs) . A maior diversidade foi observada nas amostras de fezes bovinas e a menor na amostra de água de ambiente prístino. Firmicutes foi o grupo predominante nas amostras de fezes humanas, enquanto que nas fezes bovinas foram os Firmicutes e Bacteroidetes. Nas amostras de água, o filo mais abundante foi Proteobacteria. A rede de interação entre as OTUs encontradas nas amostras também mostrou que as amostras de fezes apresentaram maior diversidade e entre as amostras de água, aquela com poluição de origem humana foi a que apresentou maior diversidade. Houve identificação de biomarcadores pelo método LEfSe para humanos (Actinobacteria, Betaproteobacteria e Firmicutes) e bovinos: (Bacteroidetes, Tenericutes e Spirochaetes). Marcadores hospedeiro-específicos foram identificados, mas esses não foram encontrados nas amostras de água sugerindo que as ferramentas utilizadas não apresentam a resolução para identificar os marcadores nas amostras ambientais ou que a contaminação nos corpos hídricos é mista. Adicionalmente, como os marcadores hospedeiro-específicos são oriundos de micro-organismos não autóctones, estes poderiam sofrer os efeitos adversos do ambiente, como fatores físico-químicos e competição com os organismos nativos / Abstract: The fecal contamination of water resources is the main cause of enteric waterborne diseases all over the world. Traditional indicator methods used in the water microbiological quality assessment are not able to identify fecal contamination source. This work intended to prospect molecular markers in hosts and track them in water samples to identify pollution sources in surface waters in the São Paulo State, Brazil. Two library-dependent methods with E. coli strains isolated from different hosts and water samples were used, a genotypic typing method (E. coli phylogenetic groups) and a phenotypic typing method (MALDI-TOF/MS). A library-independent method using 454 pyrosequencing of hypervariable16S rRNA gene V3 region was used in DNA from feces and water samples. Phylogenetic groups were used as a tool in host classification and correspondence analysis showed feeding habits clusters. The classification of environmental samples revealed higher frequencies of subgroups A1 and B23 in rivers impacted by human pollution sources, while subgroups D1 and D2 were associated with pristine sites, and subgroup B1 with domestic animal sources, indicating their use as a first screening for pollution source identification. A simple classification is proposed based on phylogenetic subgroup distribution using the w-clique metric, enabling differentiation of polluted and unpolluted sites. Protein profiles of E. coli strains isolated from host and water samples were analyzed by MALDI-TOF/MS. Specific host biomarkers were identified and their use was indicated as a potential tool for the source tracking. Validation with E. coli strains isolated from rivers and reservoirs showed that water samples presented markers from different hosts, suggesting these rivers have mixed sources of fecal contamination. Sequencing of the 16S rRNA V3 region in stool samples (human and bovine) and water showed 4296 operational taxonomic units (OTUs). The greatest diversity was observed in samples of cattle feces and the smallest one in the pristine water sample. Firmicutes was the predominant group in samples of human feces, while in the most common bovine feces are the Firmicutes and Bacteroidetes. The interaction network showed that the stool samples had the greatest diversity and, among them, the water sample with human pollution source showed the highest diversity. The LEfSe method was used to identify host biomarkers. As human biomarkers, Actinobacteria, Betaproteobacteria and Firmicutes were identified and for cattle the potential markers are Bacteroidetes, Tenericutes and Spirochaetes. Host-specific markers were identified, but they were not found in water samples suggesting that the used tools either do not have the resolution to identify markers in environmental samples or contamination in water bodies is mixed. Additionally, as the host-specific markers were isolated from non-autochthonous micro-organisms, they could be affected by the environmental adverse effects such as physical-chemical factors and competition with native organisms / Doutorado / Microbiologia / Doutora em Genética e Biologia Molecular

Orientador: Carlos Emílio Levy / Dissertação (mestrado) - Universidade Estadual de Campinas, Faculdade de Ciências Médicas / Made available in DSpace on 2018-08-27T01:21:38Z (GMT). No. of bitstreams: 1 CarvalhoFilho_ElioBarreto_M.pdf: 1484872 bytes, checksum: da445ed854a5a8f11143d06dd28aab5c (MD5) Previous issue date: 2015 / Resumo: Introdução: Bacilos gram-negativos não fermentadores (BGN-NFs) são microrganismos que se caracterizam pela incapacidade de utilizar a glicose como fonte de energia pela fermentação, degradando-a pela via oxidativa. A identificação dos BGN-NFs continua sendo um desafio para os laboratórios de rotina em microbiologia pela dificuldade de identificação, em virtude, da baixa ocorrência em amostras ambulatoriais, assim como, pela falta de recursos rápidos, eficientes e pela complexidade e alto custo dos testes de identificação. Estes microrganismos têm importância clínica para pacientes imunocomprometidos com infecções sistêmicas e pacientes com Fibrose Cística, com infecções oportunistas pulmonares. Nosso objetivo foi utilizar técnicas fenotípicas e de espectrometria de massas para identificar BGN-NFs pouco frequentes isolados em amostras clínicas de pacientes com FC e de pacientes internados no Hospital de Clínicas-Unicamp. Método: Foram analisados 71 isolados de amostras clínicas recuperadas do Banco de bactérias do Laboratório de Microbiologia do HC-Unicamp, envolvendo Chryseobacterium indologenes, Elizabethkingia meningoseptica, Cupriavidus pauculus, Ochrobactrum anthropi, Ralstonia pickettii, Ralstonia mannitolilytica, Ralstonia insidiosa, identificados por técnicas fenotípicas (provas bioquímicas manuais padronizadas pelo Laboratório de Microbiologia [método fenotípico manual] e automatizadas pelo Vitek®2, Phoenix¿) e por espectrometria de massa MALDI-TOF MS (BioMerieux®) e MALDI BD (Becton& Dickson®). Para 41 isolados de Ralstonia spp e Ochrobactrum anthropi estes métodos também foram comparados com PCR, pois não foram encontrados oligonucleotídeos específicos para os demais BGN-NFs estudados. Resultados: pelo método Fenotípico Manual foi possível identificar ao nível de espécie 54,9% dos isolados, apenas gênero 19,7% e 25,4% não puderam ser identificados. Houve uma baixa concordância entre as técnicas Fenotípica Manual e a Automatizada Vitek®2, sendo de 50,7%, quando considerada a concordância pelo menos ao nível de gênero. A maior concordância verificou-se entre os dois equipamentos de MALDI-TOF, de 87,3%, quando considerada a concordância pelo menos ao nível de gênero. Discussão: Quando comparamos todos os métodos utilizados para identificação dos 71 isolados encontramos uma concordância simultânea de 23,9% (17/71), quando considerado pelo menos ao nível de gênero e apenas 2 (2,8%) ao nível de espécie. Quando comparamos os métodos Fenotípico Manual, Vitek®2, Phoenix®, MALDI MS, MALDI BD e incluindo PCR para a identificação de 41 amostras de Ralstonia spp e Ochrobactrum anthropi, encontramos uma concordância simultânea de 19,5% (8/41) quando considerado pelo menos ao nível de gênero e 2 (2,8%) de espécie. Possíveis justificativas para a baixa concordância entre as metodologias seriam a diversidade de princípios, de acurácia e de bancos de dados dos métodos. Conclusão: É muito baixa a concordância entre as diferentes metodologias utilizadas, sendo que os equipamentos de MALDI-TOF possuem entre si uma correlação muito boa para identificação de BGN-NFs, porém mostram-se discordantes aos níveis de confiança dos resultados. Foi encontrada uma importante limitação na PCR apresentando reação cruzada com gêneros testados, sugerindo não ser confiável para este fim. Para os gêneros estudados e as metodologias empregadas, a discordância dos resultados sugerem cautela pela possibilidade de erro de identificação / Abstract: Introduction: Gram-negative non-fermenting (GN-NFB) are microorganisms that are characterized by the inability to use glucose by fermentation as an energy source, degrading it by the oxidative pathway. The identification of BGN-NFS remains a challenge for the routine of microbiology laboratories, due to the low occurrence in outpatient samples, the lack of fast and efficient resources and the complexity and high cost of the tests. These microorganisms are clinically important for immunocompromised patients with systemic infections and patients with Cystic Fibrosis, with opportunistic pulmonary infections. Our goal was to use phenotypic and mass spectrometry techniques to identify uncommon GN-NFB isolated in samples from CF patients and patients admitted to the Hospital de Clinicas Unicamp. Method: 71 isolates recovered from clinical specimens were selected from the from the Microbiology Laboratory bacteria collection, previously identified by fenotipic methods as Chryseobacterium indologenes, Elizabethkingia meningoseptica, Cupriavidus pauculus, Ochrobactrum anthropi, Ralstonia pickettii, Ralstonia mannitolilytica, Ralstonia insidiosa. The samples were identified by in house Phenotypic manual method, automated by Vitek®2, by Phoenix¿ and MALDI-TOF mass spectrometry MS (BioMerieux®) and MALDI BD (Becton Dickson®). These methods were also compared to PCR for only 41 isolates of Ralstonia spp and Ochrobactrum anthropi, because they were not found specific primers for the other GN-NFB analised. Results: the phenotypic Manual method identified to species level 54.9% of the isolates, 19.7% only to genera and 25.4% were not identified. There was a poor correlation between the techniques phenotypic Manual method and Automated Vitek®2, with 50.7% of agreement, when considering at least in terms of gender. The best agreement of 87.3% occurred between the results of the two MALDI-TOF equipment, when considering the correlation of at least at the level of genus. Discussion: When comparing all the methods used for the identification of 71 isolates were found simultaneous agreement of 23.9% (17/71) when considered at least to genus level and only 2 (2.8%) to species level. When analyzed the phenotypic Manual method, Vitek®2, Phoenix®, MALDI MS, MALDI BD and PCR applied to 41-GN-NFB samples, simultaneous agreement were found for 19.5% (8/41) when considered at least to genus level and 2 (2.8%) to species. Possible reasons for the low agreement between the methodologies could be the diversity of principles, accuracy and databases of the methods. Conclusion: The two methods of MALDI-TOF have a very good correlation for GN-NFB identification, however showed discordance for the confidence levels of results. With the primers tested one important limitation of the PCR is the cross-reaction among many genera, suggesting not to be safe for the discrimination of the analyzed genera. For the genera and methods analised the discrepancy of results suggests caution because of the possibility of wrong identification / Mestrado / Saude da Criança e do Adolescente / Mestre em Ciências

Fatty acids (FAs) represent an important class of metabolites, impacting on membrane building blocks and signaling compounds in cellular regulatory networks. In nature, prokaryotes are characterized with the most impressing FA structural diversity and the highest relative content of free fatty acids (FFAs). In this context, nitrogen-fixing bacteria (order Rhizobiales), the symbionts of legumes, are particularly interesting. Indeed, the FA profiles influence the structure of rhizobial nodulation factors, required for successful infection of plant root. Although FA patterns can be assessed by gas chromatography—(GC-) and liquid chromatography—mass spectrometry (LC-MS), sample preparation for these methods is time-consuming and quantification suffers from compromised sensitivity, low stability of derivatives and artifacts. In contrast, matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF-MS) represents an excellent platform for high-efficient metabolite fingerprinting, also applicable to FFAs. Therefore, here we propose a simple and straightforward protocol for high-throughput relative quantification of FFAs in rhizobia by combination of Langmuir technology and MALDI-TOF-MS featuring a high sensitivity, accuracy and precision of quantification. We describe a step-by-step procedure comprising rhizobia culturing, pre-cleaning, extraction, sample preparation, mass spectrometric analysis, data processing and post-processing. As a case study, a comparison of the FFA metabolomes of two rhizobia species—Rhizobium leguminosarum and Sinorhizobium meliloti, demonstrates the analytical potential of the protocol.

No / Several lines of evidence support an autoimmune basis for alopecia areata (AA), a common putative autoimmune hair loss disorder. However, definitive support is lacking largely because the identity of hair follicle (HF) autoantigen(s) involved in its pathogenesis remains unknown. Here, we isolated AA-reactive HF-specific antigens from normal human scalp anagen HF extracts by immunoprecipitation using serum antibodies from 10 AA patients. Samples were analyzed by LC-MALDI-TOF/TOF mass spectrometry, which indicated strong reactivity to the hair growth phase-specific structural protein trichohyalin in all AA sera. Keratin 16 (K16) was also identified as another potential AA-relevant target HF antigen. Double immunofluorescence studies using AA (and control sera) together with a monoclonal antibody to trichohyalin revealed that AA sera contained immunoreactivity that colocalized with trichohyalin in the growth phase-specific inner root sheath of HF. Furthermore, a partial colocalization of AA serum reactivity with anti-K16 antibody was observed in the outer root sheath of the HF. In summary, this study supports the involvement of an immune response to anagen-specific HFs antigens in AA and specifically suggests that an immune response to trichohyalin and K16 may have a role in the pathogenesis of the enigmatic disorder.

Antalet monoklonala antikroppar som används i läkemedel ökar kraftigt. Dessa läkemedel är dyra och risken för förfalskning är stor. Behovet att utveckla en metod för snabb och precis identifiering av monoklonala antikroppar är därför brådskande. För identifiering utfördes analyser med Matrix Assisted Laser Desorption/Ionization Time of Flight Mass Spectrometry (MALDI-ToF-MS), Capillary Gel Electrophoresis (CGE) and Capillary Zone Electrophoresis (CZE) på nio monoklonala antikroppar. Fokuset var att undersöka huruvida signifikanta fysiokemiska egenskaper och unika aminosyrasekvenser var närvarande och kunde urskiljas. Olika analyser med MALDI-ToF-MS användes till att både separera de monoklonala antikropparna baserat på dess fysiokemiska egenskaper, och annotera aminosyrasekvenser innehållande nyckelfragment. Med metoderna baserade på kapillärelektrofores uppnåddes också separation. CZE föredras framför CGE då mängden data som erhålls från CZE är större och provberedningen är enklare. Sammanfattningsvis utformades ett protokoll för identifieringsprocessen, vilket inleds med MALDI-ToF-MS-analyser av monoklonala antikroppar på reducerad form mot kända referenser. Därefter är en hypotes formulerad utifrån vilka antikroppar som ser mest lika ut. Slutligen analyseras dessa med CZE för fastställning av den monoklonala antikroppens identitet. / The number of monoclonal antibodies used in pharmaceuticals is increasing sharply. These medicines are expensive, and the risk of counterfeiting is high. The need to develop a method for rapid and precise identification of monoclonal antibodies is therefore urgent. For identification, analyses were performed with Matrix Assisted Laser Desorption/Ionization Time of Flight Mass Spectrometry (MALDI-ToF-MS), Capillary Gel Electrophoresis (CGE) and Capillary Zone Electrophoresis (CZE) on nine monoclonal antibodies. The focus was to investigate whether significant physiochemical features and unique amino acid sequences were present and could be distinguished. Various analyses with MALDI-ToF-MS were used to both separate the monoclonal antibodies based on their physicochemical properties and annotate amino acid sequences containing key fragments. With the methods based on capillary electrophoresis, separation was also achieved. CZE is preferred over CGE as the amount of data obtained from CZE is greater and sample preparation is simpler. In summary, an identification process protocol was designed and is initiated with MALDI-ToF-MS analyses of reduced-form monoclonal antibodies against known references. A hypothesis is then formulated based on which antibodies look the most similar. Finally, these are analysed by CZE to determine the identity of the monoclonal antibody.

The mechanochemical polycondensation between a diamine and a dialdehyde constitutes a sustainable alternative to classical solvent-based polymerization reactions. This process not only allows for a higher conversion and a shorter reaction time as compared to standard solvent-based syntheses of this conjugated polymer, but the reaction can also be adjusted by the energy introduced via the ball mill.

Phospholipids are dominant components of bacterial cell membranes, where they create double layers. Bacteria differ in their phospholipid composition determination of which can help in identification of important groups of microorganisms. Phospholipid composition of bacteria is influenced by many environmental factors, therefore its variation can be observed within one bacterial stem also. Because of its simplicity, thin layer chromatography is usually applied to identification and determination of bacterial phospholipids. Disadvantage of this method are the high demands of time, carefulness and skills of the analytical personnel. The increasing interest in the phospholipid double-layer promotes the detailed investigation of their fatty acid composition because the more detailed analyses allows for more information yield about bacteria. Gas chromatography hyphenated with mass spectrometry seems to be the best choice for these purposes. Fatty acid identity and total fatty acid content in phospholipid molecules could be determined by this method. Additionally, number, position and isomerism of double bonds and presence of other functional groups on hydrocarbon chain could be determined. Whereas a suitable and...

INTRODUÇÃO: As infecções por bactérias anaeróbias são geralmente de origem endógena, polimicrobianas e mistas. Devido a sua natureza fastidiosa, essas bactérias necessitam de uma prévia incubação em meios líquidos enriquecidos, como o caldo Thioglicolato (CT) para serem recuperadas, o isolamento desses microrganismos é trabalhoso e o tempo de resposta - TAT (turn around time) estendido desse exame pode estar associado a falhas terapêuticas e ao aumento da resistência bacteriana. A cultura de anaeróbios (CANA) ainda é um desafio para os laboratórios clínicos de rotina e novas estratégias para diminuir o TAT são fundamentais para que esse exame forneça um impacto clínico significativo. OBJETIVO: Otimizar o processo de triagem da CANA pela modificação do CT; comparar a identificação dos anaeróbios pelas metodologias fenotípicas ANC (Vitek 2- bioMérieux, France) e MALDI-TOF (Vitek MS - bioMérieux, France) e verificar o impacto econômico das ações propostas MÉTODOS: O caldo de triagem CT foi modificado eluindo individualmente discos comerciais de antibióticos (em concentrações fixas) selecionados por apresentarem baixa ou nenhuma ação contra microrganismos anaeróbios e com um bom espectro de ação para os principais aeróbios associados em culturas mistas e foram escolhidos aqueles que após uma bateria de testes frente a 15 cepas dos principais anaeróbios envolvidos em infecções humanas mantiveram a viabilidade inicial. O caldo Thioglicolato modificado (CTM) foi composto pela adição dos antibióticos que apresentaram a melhor \"performance\" acima descrita. A sensibilidade e especificidade do CTM foram avaliadas paralelamente com CT na rotina de CANA do HCFMUSP. Para a avaliar a identificação fenotípica, 421 anaeróbios isolados no período de seis meses foram submetidos a identificação pelo ANC (Vitek 2) e MALDI-TOF (Vitek MS). Os resultados discordantes ou com baixa discriminação da espécie foram avaliados pelo sequenciamento 16S rRNA. O impacto econômico da introdução do CTM bem como os custos diretos da identificação pelo MALDI-TOF foram avaliados. RESULTADOS: O CTM foi composto por amicacina, gentamicina e aztreonam. Das 159 amostras clínicas triadas pelo CT e CTM, 11 (7%) foram positivas para CANA com as mesmas espécies isoladas em ambos os meios. Utilizando o CTM, foi obtida uma redução dos falsos positivos de 97 (61%) para 69 (43%) quando comparado ao CT (p < 0,05). O TAT do resultado negativo da CANA com o CTM foi reduzido de 14 para sete dias em 28 (18%) amostras; o CTM permitiu a liberação do resultado positivo da CANA 48 horas à frente do CT. A sensibilidade do CTM foi igual ao CT, porém a especificidade foi superior em 19%. Das 421 cepas avaliadas, 35 foram identificadas somente pelo MALDI-TOF (Vitek MS) sendo que uma (Clostridium innocum) foi identificada somente pelo sequenciamento 16S rRNA. Das 386 avaliadas por ambas as metodologias, houve uma concordância de 97% e os resultados das 13 (3%) cepas submetidas ao sequenciamento foram concordantes em 92% com o MALDI-TOF (Vitek MS) que promoveu a redução do TAT do resultado positivo em cinco dias. A implementação do CTM possibilitou uma redução de custos nessa amostragem, de R$ 2.240,00 e a identificação pelo MALDI-TOF proporcionou uma economia de R$ 7.786,00. Considerando os valores econômicos encontrados nesse estudo e projetando-os nas estatísticas de CANA do HCFMUSP em 2017, o CTM poderia proporcionar uma economia de R$ 132.560,00 /ano e o MALDI-TOF uma redução nos gastos de R$ 13.579,00/ ano CONCLUSÕES: A padronização e implementação do CTM permitiu uma um aumento significativo de especificidade da cultura anaeróbia com redução do TAT e dos custos. A utilização do MALDI-TOF diminuiu o TAT das identificações aliado a uma melhor performance de forma custo efetiva / INTRODUCTION: Anaerobic bacterial infections are usually of endogenous origin, polymicrobial and mixed. Because of their fastidious nature, these bacteria require prior incubation in enriched liquid media, such as Thioglycolate broth (TB) to be recovered, the isolation of these microorganisms is laborious, and the TAT (turn around time) extended time of this examination may be associated with therapeutic failures and increased bacterial resistance. Anaerobic culture (AC) is still a challenge for routine clinical laboratories, and new strategies for lowering TAT are critical to provide a significant clinical impact. OBJECTIVE: To optimize the AC screening process by modifying the TB; Compare anaerobical identification between (Vitek 2- bioMérieux, France) and MALDI-TOF (Vitek MS - bioMérieux, France) and to verify the economic impact of the proposed actions. METHODS: TB broth was modified by eluting individually antibiotic commercial discs (at fixed concentrations) selected for low or no action against anaerobic microorganisms and with a good action spectrum for the main associated aerobes in mixed cultures. Those who maintained the initial viability after a battery of tests against 15 strains of the major anaerobes involved in human infections were selected. Modified Thioglycolate Broth (MTB) was composed of the antibiotics that presented the best performance described above. The sensitivity and specificity of MTB were evaluated in parallel with TB in the HCFMUSP AC routine. To evaluate the phenotypic identification, 421 anaerobes isolated in the six-month period were submitted to identification by ANC (Vitek 2) and MALDI-TOF (Vitek MS). Discordant results or those with low discrimination of the species were submitted to 16S rRNA sequencing. The economic impact of the introduction of MTB as well as the direct costs of MALDI-TOF identification were assessed. RESULTS: MTB was composed of amikacin, gentamicin and aztreonam. Of the 159 clinical samples screened by TB and MTB, 11 (7%) were positive for AC with the same species isolated in both media. Using MTB, a reduction of false positives was obtained from 97 (61%) to 69 (43%) when compared to TB (p < 0.05). The TAT of the negative result of the AC with the MTB was reduced from 14 to 7 days in 28 (18%) samples; the MTB allowed the release of the AC positive result 48 hours ahead of the TB. The sensitivity of MTB was equal to TB, but the specificity was higher in 19%. Of the 421 strains evaluated, 35 were identified only by MALDI-TOF (Vitek MS) and one (Clostridium innocum) was identified only by 16S rRNA sequencing. Of the 386 evaluated by both methodologies, there was a concordance of 97% and the results of the 13 (3%) strains submitted to the sequencing were concordant in 92% with the MALDI-TOF (Vitek MS) that promoted TAT of the positive result reduction in five days. The implementation of the MTB made possible a reduction of costs in this sampling, of US $ 677,00 and the identification by MALDI-TOF provided a saving of US $ 2354,00. Considering the economic values found in this study and projecting them in the HCFMUSP AC statistics in 2017, the MTB could provide savings of US $40,070.00 / year and MALDI-TOF a reduction in expenses of US $ 4,100.00 / year. CONCLUSIONS: Standardization and implementation of MTB allowed a significant increase of anaerobic culture specificity with TAT and costs reduction. The use of MALDI-TOF reduced the TAT of the identifications and also resulted in a better performance in a cost effective way

In this thesis, improved techniques for biomolecule analysis using capillary electrophoresis (CE) and matrix-assisted laser desorption/ionization-mass spectrometry (MALDI-MS) and hyphenations between those have been presented.A pre-concentration method which is possible to apply in both techniques, has also been investigated. In this work the off-line MS mode has been used either in the form of fractionation (Paper I) or by incorporating the MALDI target in the CE separation system (Paper II).In Paper I, a protocol for CE-MALDI analysis of cyanogen bromide digested bacteriorhodopsin (BR) peptides as model integral membrane protein peptides were established. Also, an improved protocol for partially automated manufacturing of a concentration MALDI-target plate is presented. The design of the targets was suitable for the fractions from the CE. A novel technique for the integration of CE to MALDI-MS using a closed-open-closed system is presented in Paper II, where the open part is a micro canal functioning as a MALDI target window. A protein separation was obtained and detected with MALDI-MS analysis in the micro canal. A method has been developed for detection of monosaccharides originating from hydrolysis of a single wood fiber performed in a micro channel, with an incorporated electromigration pre-concentration step preceding CE analysis in Paper III. The pre-concentration showed to be highly complex due to the fact that several parameters are included that affecting each other. In Paper IV a protocol using enzymatic digestion, MALDI-TOF-MS and CE with laser induced fluorescence (LIF) detection for the investigation of the degree of substitution of fluorescein isothiocyanate (FITC) to bovine serum albumin (BSA), as a contact allergen model system for protein-hapten binding in the skin, is presented. The intention of a further CE-MALDI hyphenation has been considered during the work. In Paper V 2,6-dihydroxyacetophenone (DHAP) was investigated, showing promising MALDI-MS matrix properties for hydrophobic proteins and peptides. 2,5-dihydroxybenzoic acid (DHB) was undoubtedly the better matrix for the hydrophilic proteins, but its performance for the larger and hydrophobic peptides was not optimal. Consequently, DHAP can be used as a compliment matrix for improved analysis of hydrophobic analytes. / QC 20101214

<p>Due to the hydrophobic nature of integral membrane proteins (IMP) they give rise to several difficulties concerning handling and analysis, which is not the case for the most water soluble proteins. New analysis methods are needed, where the insolubility problems of the hydrophobic proteins due to aggregation and adhesion are tackled. Those problems also affect digestion performance and equipment compatibility for the analysis.</p><p>Protocols for analysis and separation specified for IMP are presented in <b>Paper I</b> and<b> III</b>.</p><p>The instrumentation used in this work was capillary electrophoresis (CE) and matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS). Both instruments are suitable for peptide/proteins analysis.</p><p>In <b>Paper I</b>, protocols for a CE separation of bacteriorhodopsin (BR) peptides as model IMP peptides are established. Also, a partially automated manufacturing procedure of a concentration MALDI-target is presented, suitable for fractions from CE. The MS analysis detected 9 out of 10 cyanogen bromide (CNBr) digested BR peptides. A novel technique for the off-line integration of CE to MALDI-MS using a closed-open-closed system is presented in <b>Paper II</b>, where the open part is a microcanal functioning as a MALDI target window. Investigation of the microcanal electro-osmotic flow (EOF) properties and band broadening characteristics was performed. A protein separation was obtained and detected with MALDI-MS analysis in the microcanal. Different protein digestion methods were evaluated using BR in <b>Paper III</b> through MALDI-MS. Several digestion methods as well as MS media were investigated alongside different MALDI matrices. For example, matrices as the hydrophobic 2,6-dihydroxyacetophenone (DHAP) and 2-Hydroxy-3-methoxybenzoic acid (2H3MBA) or 2-Hydroxy-5-methoxybenzoic acid (2H5MBA) mixed with DHB, appeared to be promising matrices for analysis of BR.</p> / <p>Med anledning av integrala membranproteiners (IMP) hydrofoba egenskaper uppstår flera svårigheter vid hantering och analys av IMP, vilket inte är fallet för vattenlösliga proteiner. Nya analysmetoder krävs, som löser löslighetsproblemen för de hydrofoba proteinerna som tex flockning och adsorbtion. Dessa problem påverkar även klyvningsgrad och kompatibilitet med analysutrustningen.</p><p>I <b>Artikel I</b> och <b>Artikel III</b> presenteras protokoll för analys och separation specifikt för IMP. Instrumenteringen som har använts i detta arbete är kapillärelektrofores (CE) och matris-assisterad laserdesorptions-joniserings-masspektrometri (MALDI-MS). Båda instrumenten är lämpade för peptid/protein analyser.</p><p>I <b>Artikel I</b>, presenteras protokoll för en CE separation av peptider från bacteriorhodopsin (BR), som användes som modellpeptider för IMP. En delvis automatiserat tillverkningsprocedur för en koncentrerande MALDI-platta, som är anpassad för CE fraktionerna beskrivs också. MS-analysen detekterade 9 av 10 BR-peptider från cyanobromid-klyvning (CNBr). En ny teknik för off line-integrering av CE till MALDI-MS genom ett slutet-öppet-slutet system presenteras i <b>Artikel II</b>, där den öppna delen är en mikrokanal som fungerar som detektionsfönster i MALDI. Undersökning av mikrokanalens egenskaper som tex det elektroosmotiska flödet (EOF) och bandbreddningen utvärderades. En proteinseparation genomfördes och detekterades med MALDI–MS i mikrokanalen. Olika proteinklyvningsmetoder för BR undersöktes i <b>Artikel</b> <b>III</b> med MALDI-MS. Flera proteinklyvningsmetoder samt MS-medier utvärderades tillsammans med olika MALDI-matriser. Den hydrofoba matrisen 2,6-dihydroxyacetophenone (DHAP) och 2-Hydroxy-3-methoxybenzoic acid (2H3MBA) eller 2-Hydroxy-5-methoxybenzoic acid (2H5MBA) blandade med DHB, visade sig exempelvis vara lovande matriser för BR-analyser.</p>