A resistência bacteriana emergiu como importante problema de saúde pública no mundo. Nesta pesquisa, a distribuição das espécies e a evolução da sensibilidade aos antibióticos entre isolados clínicos obtidos em um hospital terciário foram analisadas no período de 2007 a 2012. As bactérias isoladas foram identificadas por análises bioquímicas convencionais. Segundo as recomendações do Clinical and Laboratory Standards Institute (CLSI) compatíveis ao ano do processamento microbiológico, o perfil de sensibilidade foi determinado pelo método de disco difusão, entretanto para a sensibilidade a vancomicina utilizou-se a concentração inibitória mínima (CIM). Durante o período da pesquisa totalizou-se 4.464 resultados de culturas distribuídos em 2007 (865), 2008 (981), 2009 (485), 2010 (539), 2011 (704) e 2012 (890). Com relação aos cocos Gram-positivos e as enterobactérias, Staphylococcus aureus e Eschericia coli foram as bactérias mais frequentemente isoladas, respectivamente. Dos antibióticos da classe dos beta-lactâmicos, piperacilina + tazobactam e aztreonam mostraram os melhores resultados de atividade antibacteriana. Todas as cepas isoladas de enterobactérias foram sensíveis aos carbapenêmicos. As cepas de Pseudomonas aeruginosa foram mais sensíveis ao imipenem do que ao meropenen, no entanto a redução dos perfis de sensibilidade foi evidenciada para ambos os antibióticos: imipenem (69,6% para 41,7%) e meropenem (63,3% para 25,0%). Todas Burkloderoderia cepacea e Acinetobacter baumanii demonstraram resistência ao meropenem, entretanto as cepas de Acinetobacter iuwoffi foram sensíveis aos carbapenêmicos. Aumentos semelhantes nos perfis de sensibilidade das cepas de Escherichia coli, Klebsiella pneumoniae e Klebsiella oxytoca (70% para 86,7%) foram observados para ciprofloxacina e levofloxacina. Da classe dos aminoglicosídeos, a amicacina mostrou melhor atividade antibacteriana do que a gentamicina. Nas amostras analisadas deste hospital não houve ocorrência de Enterococcus spp. resistente a vancomicina (VRE). Ainda, todas as cepas de cocos Gram-positivos foram sensíveis a vancomicina e teicoplamina. No geral os antibióticos apresentaram resultados preocupantes, uma vez que para as bactérias reconhecidas nos cenários das infecções hospitalares nenhuma foi sensível 100% a todas as classes de antibióticos. A situação da sensibilidade microbiana aos antibióticos é caótica tendo cada vez mais limitada a sua utilização na terapêutica / Bacterial resistance has emerged as an important public health problem in the world. In this study, the distribution of species and the evolution of antibiotic susceptibility among clinical isolates in a tertiary hospital were analyzed in the period from 2007 to 2012. Bacterial isolates were identified by conventional biochemical analyzes. According to the recommendations of the Clinical and Laboratory Standards Institute (CLSI) supported a year of microbiological processing, the sensitivity was determined by the disk diffusion method, however for sensitivity to vancomycin was used the minimum inhibitory concentration (MIC). During the research period, 4,464 culture results were obtained and distributed in 2007 (865), 2008 (981), 2009 (485), 2010 (539), 2011 (704) and 2012 (890). With respect to Gram-positive cocci and Enterobacteriaceae, Staphylococcus aureus and Escherichia coli were the most frequently isolated bacteria, respectively. From beta-lactams class, piperacillin + tazobactam and aztreonam showed the best results of antibacterial activity. All isolated strains of Enterobacteriaceae were susceptible to carbapenems. Pseudomonas aeruginosa strains were more sensitive to imipenem than the meropenen, however reducing the sensitivity profile was observed for both antibiotics imipenem (69.6% to 41.7%) and meropenem (63.3% for 25.0%). All Burkloderoderia cepacia and Acinetobacter baumannii were resistant to meropenem, however Acinetobacter iuwoffi strains were susceptible to carbapenems. Similar increases in the susceptibility of Escherichia coli, Klebsiella pneumoniae and Klebsiella oxytoca strains (70% to 86.7%) were observed for ciprofloxacin and levofloxacin. From aminoglycosides class, amikacin showed better antibacterial activity than gentamicin. In the samples analyzed in this hospital there was no occurrence of Enterococcus spp. resistant to vancomycin (VRE). Furthermore, all strains of Gram-positive cocci were susceptible to vancomycin and teicoplanin. Overall antibiotics showed worrying results, since none was recognized for bacteria in the nosocomial infection scenarios 100% sensitive to all classes of antibiotics. The situation of microbial sensitivity to antibiotics is becoming chaotic having limited their use in therapy

Orientador: Paola Castro Moraes / Coorientador: Andressa de Souza-Pollo / Banca: Alessandra Aparecida Medeiros-Ronchi / Banca: Janete Apparecida Desidério / Banca: José Geraldo Meirelles Palma Isola / Banca: Annelise Carla Camplesi dos Santos / Resumo: Lesões na pele podem resultar em feridas que, dependendo do tempo de reparação tissular podem ser classificadas como agudas ou crônicas, sendo crônicas aquelas que não apresentaram cicatrização dentro do período de quatro semanas. A ferida é contaminada por diferentes espécies bacterianas, sendo o sistema imunológico da pele o responsável por impedir que tais contaminações evoluam para infecções. No entanto, muitas vezes o quadro infeccioso é instalado, havendo necessidade de tratamento com antimicrobianos. Tendo em vista que o mau uso de antimicrobianos provoca resistência a multidrogas em estirpes bacterianas potencialmente patogênicas, este trabalho teve como objetivo identificar as bactérias prevalentes em feridas agudas e crônicas de cães por meio de sequenciamento da região 16S rRNA e testar a sensibilidade dos isolados a diferentes antimicrobianos. Para tanto, foram amostradas 20 feridas, sendo cada uma de um cão atendido no Hospital Veterinário da UNESP, Câmpus de Jaboticabal. De cada ferida foram obtidos dez isolados, os quais foram selecionados para o sequenciamento de DNA por meio de comparação entre os perfis genéticos obtidos pelo emprego de marcador molecular randômico. Foram sequenciados 74 isolados identificados como pertencentes a oito gêneros de bactérias gram-negativas, Proteus mirabilis, Escherichia coli, Pseudomonas aeruginosa, Enterobacter spp., Acinetobacter baumannii, Klebsiella spp., Kluyvera georgiana e Providencia stuartii, e três de gram-positivas,... (Resumo completo, clicar acesso eletrônico abaixo) / Abstract: Skin lesions can result in cutaneous wounds that may be classified as acute or chronic depending on the period of time spent in tissue repairment. Wounds that have not healed within four weeks are generally classified as chronic. The wound is contaminated by different bacterial species and the immune system of the skin is responsible for preventing infections. Nonetheless, the infectious process is often developed and antimicrobial treatment become necessary. Considering that the misuse of antimicrobials provokes multidrug resistance in potentially pathogenic bacterial strains, this work aimed to identify prevalent bacteria in acute and chronic wounds of dogs by 16S rRNA sequencing and to test the sensitivity of the isolates to different antimicrobials. For that, 20 wounds were sampled, each one from a dog admitted at the Veterinary Hospital of UNESP, Jaboticabal, São Paulo, Brazil. From each wound ten isolates were obtained, which were selected for DNA sequencing through genetic profiles comparison by applying a random molecular marker. Seventy-five isolates were identified as belonging to eight Gram-negative bacteria genera, Proteus mirabilis, Escherichia coli, Pseudomonas aeruginosa, Enterobacter spp., Acinetobacter baumannii, Klebsiella spp., Kluyvera georgiana and Providencia stuartii, and to three gram-positive bacteria genera, Enterococcus sp., Staphylococcus spp. and Bacillus spp. Cases of dogs with acute or chronic wounds associated to more than one bacterial genus w... (Complete abstract click electronic access below) / Doutor

Of the 22.5 million individuals infected with the human immunodeficiency virus (HIV) in sub-Saharan Africa, 62% of patients requiring treatment had access to highly active antiretroviral therapy (HAART) in 2011. The delivery of HAART and the appropriate laboratory monitoring of HIV positive individuals in sub-Saharan African countries has become a public health priority, an intervention which has and will continue to dramatically reduce HIV-related morbidity and mortality. Routine laboratory monitoring of HIV infected individuals should ideally include CD4+ T cell testing to assess when to start ART, viral load monitoring to assess virological failure on ART and when indicated, HIVDR genotyping.However, this is often not implemented in resource limited settings due to challenges such as inadequate infrastructure and laboratory capacity, amongst others. Thus the Affordable Resistance Testing for Africa (ART-A) initiative was established to develop an affordable HIV drug resistance testing (HIVDR) algorithm applicable to Africa. The objective of this study was to evaluate the role of in vitro HIVDR phenotyping in the context of HIV-1 subtype C (the most prevalent circulating subtype in sub-Saharan Africa), genotyping and genotypic interpretation tools using existing algorithms, as well as novel virological failure detection tools for clinical patient management. Current gold standard HIVDR phenotyping technologies use an HIV-1 subtype B backbone to create recombinant viruses with patient-derived polymerase (protease and partial reverse transcriptase). This backbone could impact on the in vitro phenotyping results of non-B subtypes, and therefore it was deemed necessary to establish the applicability of HIVDR phenotypic testing of subtype C polymerase when a commercially available subtype B backbone is used. One hundred and fourteen HIV-1 subtype C samples were HIVDR phenotyped against 17 antiretroviral drugs using both subtype B and C backbones and showed a high level of concordance between the two backbone phenotypic resistance profiles (95.8%; 1590 of 1660 fold change comparisons). Natural assay variability was largely responsible for discordant results. Results confirmed that HIV-1 phenotypic reverse transcriptase inhibitor drug resistance test interpretation is independent of the virus backbone subtype. No conclusions could be made for protease inhibitor resistance since limited samples from 2nd line failure were available. Subsequently, the HIVDR genotypic and phenotypic results of the 114 patient samples were compared to determine whether genotyping is a viable alternative to phenotyping. Results showed a 92.3% concordance between genotyping and phenotyping of individual drug comparisons for a number of HIVDR profiles. Discrepancies were attributed to phenotypic assay variability in addition to the role of mutation mixtures, which impacted genotypic interpretations. Overall, HIVDR genotyping is a reliable tool to detect and interpret antiretroviral drug resistance in HIV-1 subtype C infected patients, and can thus be used for clinical patient management. Once the accuracy of HIVDR genotyping was established, the development, validation and evaluation of a potential virological failure assay (ARTA-VFA) and a simplified HIVDR (ARTA-HIVDRultralight) assay was undertaken. A simplified and conceptually novel approach using a qualitative viral load assay with a pre-determined cut-off that gives a threshold above which virological failure (VF) could be confirmed and below which treatment success was likely, was tested. A real-time PCR (ARTA-VFA) assay was developed which involved the amplification of a short sequence of the HIV-1 LTR region from RNA extracted either from plasma and/or dried blood spots (DBS). The ARTA-VFA was tested on 409 patient samples,and successfully amplified samples from all major HIV-1 group M subtypes with equal specificity. The VF was qualitatively classified as a viral load >1000 RNA copies/ml in plasma samples, and >5000 RNA copies/ml in DBS samples. Comparative testing yielded accurate VF determination for therapy-switching in approximately 93% of clinical cases tested, compared to current gold standard quantitative viral load assays. A simplified HIVDR genotyping assay (ARTA-HIVDRultralight) targeting the region of RT harboring all major RT inhibitor resistance mutation positions, thus providing all relevant susceptibility data for first-line regimen failures was developed and assessed. The ARTAHIVDRultralight assay was designed to be practical, faster, and more affordable, show flexibility with respect to equipment (open platform), use DBS or plasma as starting material and amplify and sequence a smaller amplicon (RT). The assay performed well when compared to the in-house assay used in the laboratory at the time for both 212 plasma and 25 DBS samples, yielding identical mutations and subsequent resistant profiles. Furthermore, a theoretical in silico exercise to investigate the consequences of using 125,329 shortened RT genotype (ARTA-HIVDRultralight) as compared to full-length RT sequences showed >95% and >90% concordance when using the Stanford HIVdb algorithm and the virco®TYPE tool, respectively. Differences noted were minor and unlikely to have any impact on clinical decision-making. Overall, this study illustrated that the short RT sequences can be reliably used to generate HIVDR genotypes using the Stanford HIVdb and virco®TYPE algorithms and reduce sequencing costs substantially. A field evaluation using the ARTA-VFA and ARTA-HIVDRultralight on 288 clinical samples was conducted, showing that the accuracy and precision of both assays (using 248 plasma or 40 DBS sampling methods) compared well to the reference methodology, thereby extending access of testing to more remote settings.These assays were designed to either be used as a testing strategy of initially assessing VF,and once confirmed performing an HIVDR assay, or alternatively to be used separately as stand-alone, or within different laboratory tiers in resource limited settings. It is envisaged that the ARTA-VFA could be used in the middle laboratory tier, and if confirmatory, patient samples can be referred to a reference laboratory with the available infrastructure for HIVDR testing using the ARTA-HIVDRultralight. Lastly, an automated sequence analysis and editing software for use in correct base calling of nucleotide/mutation mixtures in HIVDR genotyping was validated on 1624 sequences. Compared to reference software, where interpretation is often operator dependent, this software performed extremely well, with minor discrepancies noted. The automated software can be used to reduce subjectivity, time taken for analysis which is often the rate-limiting step and thus improving the turn-around time and clinical relevance of HIVDR genotyping. Overall, the results obtained describe the validation of using HIVDR genotyping as an alternative tool to phenotyping, and the subsequent development and validation of simple, affordable, "open-platform" alternatives to currently used methods for virological failure monitoring, and accommodate a centralized approach to HIVDR with DBS testing in resource limited settings.

No description available.

The utility of focal-plane-array Fourier transform infrared (FPA-FTIR) spectroscopy as a rapid method for the differentiation of antibiotic resistant foodborne pathogens was studied. / Optimum spectral acquisition and processing parameters as well as appropriate film thickness of bacterial films were empirically established for the discrimination between two Shigella species (S. flexneri and S sonnei) in order to optimize the scanning parameters of an FPA-FTIR spectrometer. A detailed study of the potential of FPA-FTIR spectroscopy for the discrimination between antibiotic resistant and sensitive strains from two Salmonella species (S. Typhimurium and S. Heidelberg) was subsequently undertaken. The results of these studies demonstrated that the infrared spectra recorded by an FPA-FTIR spectrometer contained sufficient information to differentiate between antibiotic resistant and sensitive strains of Salmonella. Accordingly, FPA-FTIR spectroscopy may potentially serve as a high-throughput technique for the identification of foodborne as well as antibiotic resistant bacteria. / Interpretation of the regions selected in relation to the different resistance mechanisms would require more detailed studies. However, the identification of specific biochemical markers based on such spectral interpretation is generally not feasible owing to the complexity of the FTIR spectra of microorganisms.

Diss. (sammanfattning) Stockholm : Karol. inst., 2006. / Härtill 5 uppsatser.

Diss. (sammanfattning) Stockholm : Karol. inst., 2005. / Härtill 5 uppsatser.

Diss. (sammanfattning) Stockholm : Karol inst., 2004. / Härtill 5 uppsatser.

Diss. (sammanfattning) Stockholm : Karolinska institutet, 2007. / Härtill 5 uppsatser.

Thesis (M.Sc. (Maxillofacial Prosthetics))--Mahidol University, 2007. / LICL has E-Thesis 0024 ; please contact computer services. LIRV has E-Thesis 0024 ; please contact circulation services.