The performance of an in-house nested-PCR technique for pleural tuberculosis diagnoses

Introduction This study evaluated the performance of an in-house nested-PCR system for the detection of the Mycobacterium tuberculosis complex in pleural fluid, blood and urine samples from pleural effusion tuberculosis patients by health services physicians in Pernambuco, Brazil. Methods A prospective double-blind study with 37 hospitalized patients of both sexes, aged over 15, was used to investigate the diagnosis of pleural effusion. The criteria used to define the cases included the demonstration of bacillus in biological samples by smear or culture or by a granulomatous finding in the histopathological examination, associated with an evident response to specific treatments to each clinical situation. Pleural fluid, blood and urine samples were collected and subjected to routine tests and the nested PCR technique to assess for M. tuberculosis amplification. Results In total, 37 pleural effusion patients took part in the study, of whom 19 (51.3%) had tubercular etiologies and 18 (48.7%) had etiologies from other causes. When the pleural fluid, blood and/or urine sample in-house nested-PCR sensitivities were evaluated simultaneously, the results were positive regardless of the biological specimen (the sensitivity was 84.2%); however, when the blood and/or urine samples were analyzed together, the sensitivity was 72.2%. When the pleural fluid samples were evaluated alone, the sensitivity was only 33.3%. Conclusions The performance of the diagnostic pleural tuberculosis nested-PCR was directly related to the diversity of the samples collected from the same patient. Additionally, this study may identify a need to prioritize non-invasive blood and urine collection for this diagnosis.

Modeling microbes: New methods for integrated metabolic and regulatory network reconstruction

PhD Thesis in Bioengineering

Deterioração bacteriológica do jaraqui Semaprochilodus spp. capturado no estado do Amazonas e conservado em gelo

Neste trabalho foram analisados 73 espécimes de jaraqui Semaprochilodus spp. conservados em caixas de poliestireno expandido entre camadas de gelo. Foram realizadas as seguintes análises: avaliação sensorial pela tabela de Torry modificada e pelo índice de qualidade por deméritos; determinação do pH e das bases voláteis totais (N-BVT); contagem total dos microrganismos aeróbios psicrófilos a 20 ºC por 4 dias, psicrotróficos a 7 ºC por 10 dias, dos mesófilos a 37 ºC por 2 dias; contagem, isolamento e identificação das bactérias Aeromonas sp. Bacillus sp. e Pseudomonas sp. a 20 ºC por 24 horas e de Plesiomonas sp. a 37 ºC por 2 dias. O jaraqui se manteve em condições de consumo, pela avaliação sensorial, por 18 e 21 dias. O pH e as bases voláteis totais não foram bons indicadores de qualidade; as contagens totais de psicrófilos, psicrotróficos e mesófilos não apresentaram diferença significativa e as bactérias não apresentaram comportamento deteriorador pela ausência da produção de H2S.

Diversity and capacity to promote maize growth of bacteria isolated from the Amazon region

ABSTRACT Maize plants can establish beneficial associations with plant growth-promoting bacteria. However, few studies have been conducted on the characterization and inoculation of these bacteria in the Amazon region. This study aimed to characterize endophytic bacteria isolated from maize in the Amazon region and to assess their capacity to promote plant growth. Fifty-five bacterial isolates were obtained from maize grown in two types of ecosystems, i.e., a cerrado (savanna) and a forest area. The isolates were characterized by the presence of the nifH gene, their ability to synthesize indole-3-acetic acid (IAA) and solubilize calcium phosphate (CaHPO4), and 16S rRNA partial gene sequencing. Twenty-four bacteria contained the nifH gene, of which seven were isolated from maize plants cultivated in a cerrado area and seventeen from a forest area. Fourteen samples showed the capacity to synthesize IAA and only four solubilized calcium phosphate. The following genera were found among these isolates: Pseudomonas; Acinetobacter; Enterobacter; Pantoea; Burkholderia and Bacillus. In addition, eight isolates with plant growth-promoting capacity were selected for a glasshouse experiment involving the inoculation of two maize genotypes (a hybrid and a variety) grown in pots containing soil. Inoculation promoted the development of the maize plants but no significant interaction between maize cultivar and bacterial inoculation was found. A high diversity of endophytic bacteria is present in the Amazon region and these bacteria have potential to promote the development of maize plants.

PEGylated ofloxacin nanoparticles render strong antibacterial activity against many clinically important human pathogens.

The rise of bacterial resistance against important drugs threatens their clinical utility. Fluoroquinones, one of the most important classes of contemporary antibiotics has also reported to suffer bacterial resistance. Since the general mechanism of bacterial resistance against fluoroquinone antibiotics (e.g. ofloxacin) consists of target mutations resulting in reduced membrane permeability and increased efflux by the bacteria, strategies that could increase bacterial uptake and reduce efflux of the drug would provide effective treatment. In the present study, we have compared the efficiencies of ofloxacin delivered in the form of free drug (OFX) and as nanoparticles on bacterial uptake and antibacterial activity. Although both poly(lactic-co-glycolic acid) (OFX-PLGA) and methoxy poly(ethylene glycol)-b-poly(lactic-co-glycolic acid) (OFX-mPEG-PLGA) nanoformulations presented improved bacterial uptake and antibacterial activity against all the tested human bacterial pathogens, namely, Escherichia coli, Proteus vulgaris, Salmonella typhimurium, Pseudomonas aeruginosa, Klebsiella pneumoniae and Staphylococcus aureus, OFX-mPEG-PLGA showed significantly higher bacterial uptake and antibacterial activity compared to OFX-PLGA. We have also found that mPEG-PLGA nanoencapsulation could significantly inhibit Bacillus subtilis resistance development against OFX.

Biodegradable drug-eluting stents: Targeting urothelial tumors of upper urinary tract

INTRODUCTION & OBJECTIVES: Urothelial tumors of upper urinary tract are ranked among the most common types of cancers worldwide. The current standard therapy to prevent recurrence is intravesical Bacillus Calmetteâ Guerin (BCG) immunotherapy, but it presents several disadvantages such as BCG failure and intolerance. Another way is to use chemotherapy, which is generally better tolerated that BCG. In this case, drugs such as epirubicin, doxorubicin, paclitaxel and gemcitabine are used. Nevertheless, intravesical chemotherapy only prevents recurrence in the short-term. These failings can be partially attributed to the short residence time and low bioavailability of the drug within the upper urinary tract and the cancer cells, resulting in a need for frequent drug instillation. To avoid these problems, biodegradable ureteral stents impregnated by supercritical fluid CO2 (SCF) with each of the four anti-cancer drugs were produced. MATERIAL & METHODS: Four formulations with different concentrations of gelatin and alginate and crosslink agent were tested and bismuth was added to confer radiopaque properties to the stent. The preliminary in vivo validation studies in female domestic pigs was conducted at the University of Minho, Braga, after formal approval by the institutionâ s review board and in accordance with its internal ethical protocol for animal experiments. Paclitaxel, epirubicin, doxorubicin and gemcitabine were impregnated in the stents and the release kinetics was measured in artificial urine solution (AUS) for 9 days by UV spectroscopy in a microplate reader. The anti-tumoral effect of the developed stents in transitional cell carcinoma (TCC) and HUVEC primary cells, used as control, was evaluated. RESULTS: The in vivo validation of this second-generation of ureteral stents performed was herein demonstrated. Biodegradable ureteral stents were placed in the ureters of a female pigs, following the normal surgical procedure. The animals remained asymptomatic, with normal urine flow. The in vitro release study in AUS of the stent impregnated showed a higher release in the first 72h for the four anti-cancer drugs impregnated after this time the plateau was achieved and the stent degraded after 9 days. The direct and indirect contact of the anti-cancer biodegradable stents with the TCC and HUVEC cell lines confirm the anti-tumor effect of the stents impregnated with the four anti-cancer drugs, reducing around 75% of the viability of the TCC cell line after 72h and no killing effect in the HUVEC cells. CONCLUSIONS: The use of biodegradable ureteral stent in urology clinical practice not only reduce the stent-related symptoms but also open new treatment therapyâ s, like in urothelial tumors of upper urinary tract. Furthermore, we have demonstrated the clinical validation in vivo pig model. This study has thus shown the killing efficacy of the anti-cancer drug eluting biodegradable stents in vitro for the TCC cell line, with no toxicity observed in the control, non-cancerous cells.The direct and indirect contact of the anti-cancer biodegradable stents with the TCC and HUVEC cell lines confirm the anti-tumor effect of the stents impregnated with the four anti-cancer drugs, reducing around 75% of the viability of the TCC cell line after 72h and no killing effect in the HUVEC cells. This study has thus shown the killing efficacy of the anti-cancer drug eluting biodegradable stents in vitro for the TCC cell line, with no toxicity observed in the control, non-cancerous cells.

Optimization of peptide nucleic acid fluorescence in situ hybridization (PNA-FISH) for the detection of bacteria: the effect of pH, dextran sulfate and probe concentration

Fluorescence in situ hybridization (FISH) is a molecular technique widely used for the detection and characterization of microbial populations. FISH is affected by a wide variety of abiotic and biotic variables and the way they interact with each other. This is translated into a wide variability of FISH procedures found in the literature. The aim of this work is to systematically study the effects of pH, dextran sulfate and probe concentration in the FISH protocol, using a general peptide nucleic acid (PNA) probe for the Eubacteria domain. For this, response surface methodology was used to optimize these 3 PNA-FISH parameters for Gram-negative (Escherichia coli and Pseudomonas fluorescens) and Gram-positive species (Listeria innocua, Staphylococcus epidermidis and Bacillus cereus). The obtained results show that a probe concentration higher than 300 nM is favorable for both groups. Interestingly, a clear distinction between the two groups regarding the optimal pH and dextran sulfate concentration was found: a high pH (approx. 10), combined with lower dextran sulfate concentration (approx. 2% [w/v]) for Gram-negative species and near-neutral pH (approx. 8), together with higher dextran sulfate concentrations (approx. 10% [w/v]) for Gram-positive species. This behavior seems to result from an interplay between pH and dextran sulfate and their ability to influence probe concentration and diffusion towards the rRNA target. This study shows that, for an optimum hybridization protocol, dextran sulfate and pH should be adjusted according to the target bacteria.

An evaluation of septic tank effluent movement in soil and groundwater systems

Recent studies have shown that septic tank systems are a major source of groundwater pollution. Many public health workers feel that the most cri^cal aspect of the use of septic tanks as a means of sewage disposal is the contamination of private water wells with attendant human health hazards. In this study the movement and attenuation of septic tank effluents in a range of soil/overburden types and hydrogeological situations was investigated. The suitability of a number of chemical and biological tracer materials to monitor the movement of septic tank effluent constituents to groundwater sources was also examined. The investigation was divided into three separate but inteiTelated sections. In the first section of the study the movement of septic tank effluent from two soil treatment systems was investigated by direct measurements of soil nutrient concentrations and enteric bacterial numbers in the soil beneath and downgradient of the test systems. Two sites with different soil types and hydrogeological characteristics were used. The results indicated that the attenuation of the effluent in both of the treatment systems was incomplete. Migration of nitrate, ammonium, phosphate and fecal bacteria to a depth of 50 cm beneath the inverts of the distribution tiles was demonstrated on all sampling occasions. The lateral migration of the pollutants was less pronounced, although on occasions high nutrients levels and fecal bacterial numbers were detected at a lateral distance of 4.0 m downgradient of the test systems. There was evidence that the degree and extent of effluent migration was increased after periods of heavy or prolonged rainfall when the attenuating properties of the treatment systems were reduced as a result of saturation of the soil. The second part of the study examined the contamination of groundwaters downgradient of septic tank soil treatment systems. Three test sites were used in the investigation. The sites were chosen because of differences in the thicknesses and nature of the unsaturated zone available for effluent attenuation at each of the locations. A series of groundwater monitoring boreholes were installed downgradient of the test systems at each of the sites and these were sampled regularly to assess the efficiency of the overburden material in reducing the polluting potential of the wastewater. Effluent attenuation in the septic tank treatment systems was shown to be incomplete, resulting in chemical and microbiological contamination of the groundwaters downgradient of the systems. The nature and severity of groundwater contamination was dependent on the composition and thickness of the unsaturated zone and the extent of weathering in the underlying saturated bedrock. The movement of septic tank effluent through soil/overburdens to groundwater sources was investigated by adding a range of chemical and biological tracer materials to the three septic tank systems used in section two of the study. The results demonstrated that a single tracer type cannot be used to accurately monitor the movement of all effluent constituents through soils to groundwater. The combined use of lithium bromide and endospores of Bacillus globigii was found to give an accurate indication of the movement of both the chemical and biological effluent constituents.

Nematódeos e bactérias em fôlhas de alcachôfra

Diseased plants of artichoke (Cynara scolimus L.) from the Instituto Agronômico, Campinas, Brazil, harboured nematodes in the leaves. The nematodes proved to belong to the species Protorhabditis oxyuris (Claus, 1862) Dougherty, 1955. As it could not be charged as the primary agent of the disease, a study of the bacteria found in the material was made. This disclosed that 4 different bacterial forms were present, namely Bacillus subtilis, Bacterium udum, Xanthomonas beticola var. cynarae n. var., and Cory neb acterium fascians var. cynarae n. var. The typical forms of X. beticola and of C. fascians are known as pathogenic to a number of plants: but, in the present case, unfortunately no inoculation trial could be made as an attempt to clear up the possible pathogenicity of any of them also to Cynara scolimus. The nematode P. oxyuris is the secondary agent, which however possibly play an important part in the distribution of the bacteria, as it has been repeatedly pointed out by previous writers with reference to closely related species. The symptoms of the disease are described. The main injuries found on leaves were necrotic areas progressing from the distal part of the limb, resulting in a great reduction of the leaf superficies.

Protozoários intestinais de vertebrados observados em Salobra

Protozoa were collected by means of dry smears and cultures in Cleveland's medium contained in 2cm3 ampules. The isolation and subsequent cultivation of trichomonad organisms in ampules were generally successfull; but the cultures went down, when transferred to test-tubes in the same medium, apparently because of the liberation of characteristic pigment by Bacillus pyocyaneus.

Poderá o carrapato transmitir a lepra?: isolamento e cultura dum bacilo acido-álcool resistente de sedimento de "Amblyomma cajennense" capturado em leproso: 2ª nota

In this 2nd note upon the possibility of transmission of human leprosy by ticks, the A. relates his stepps to obtain the collaboration of his colleagues working in leprosaria in various States of Brazil, Argentina and Paraguay in such studies. Firstly the A. describes the positive results of examination of sediment of ticks, the cattle tick Boophilus microplus (Canestrini, 1888), received from Paraná (Leprosário São Roque) , which were put on active lepers, two of them sucking during 9 days and one during 7 days. Two out of three were killed for examination and were very strongly positive for acid-fast bacilli. A series of tubes of Loewenstein medium was smeared with the sediment of such ticks. Secondly the A. relates his personnal experiment, carried out in Rio de Janeiro, trying to infect normal ticks in lepers. The experiment with Boophilus microplus was negative and was twicely positive the experiment with Amblyomma cajennense Fabricius, 1794. The experiment is being in progress and will be continued in other places of Brazil. Finally, after being given the general characteristics of Boophilus microplus, the A. describes the non-chromogenic culture of a acid-fast bacillus isolated by him from sediment of ticks (Amblyomma cajennense) captured in lepers from Colônia Santa Isabel (Minas gerais), which parasitism was spontaneous. The first isolation was obtained in Loewenstein medium after 62 days incubation at 37°C. The culture is pure and the bacillus is permanent acid-fast. The plate1, in full color, represents this culture in its four generations. The colonies are pearl-white in color, dry, elevated and rough, developing slowly and beginning as white pinhead points scattered upon the surface of the medium. The culture is not yet rich enough to be inoculated into laboratory animals, which will be done when possible.

Infecção experimental de carrapatos (Amblyomma cajennense) em ratos com lepra Stefansky

The A. succeeded, after various experiments, to infect ticks (Amblyoma cajennense) with STEFANSKY bacillus, upon feeding them in rats suffering from murine leprosy, in advanced stages. The A. thinks that will be ease to transfer the sickness from rat to rat by means of inoculation of triturate of infected ticks, as did MARCHOUX with Laelaps echdninus.

A lepra tuberculoide, ou melhor, a lesão tuberculoide na lepra, representa uma fase de transição desta dermatose e não uma forma clínica autônoma: novos achados bacterioscópicos na linfa subcutânea de leprosos

The A., after an intorductory history of his experience in leprosy, discusses the more convinient routine method of classification of leprosy cases, basing it in the facte that every case is mixt, i. e. when the skin shows any lesion the nerves of that region are also affected by the bacilli. Studying by a new thecnics, which he baptised before as "Lleras' method", the scarching of the agent of leprosy in tuberculoid cases, by examination of sub-corium lymph obtained from the lesion, he discovered new forms of the Hansen bacillus, which describes briefly, arriving at the following conclusions: 1. The A., after discussing about the evolution and clinical classification of leprosy, describes new forms of the HANSIN bacillus, discoverd in the lymph extracted from subcutis of leprosy lesion. 2. In 100 % of tuberculoid cases (total studied 29) the A. found, in the subcutis lymph, bacilli, granules, clubs or other forms of HANSEN bacillus. 3. Such bacteriological findigs and the proved mutation of tuberculoid leprosy into lepromatous type, demolished the basis of the so-called "polar" classification of leprosy. 4. Considering the proved facts already referred to, the A. arrived at the conclusion that 50 % of all papers published about tuberculoid leprosy, within the last ten years, are fanciful. 5. The presence, in the subcutis of lepers, of metamorphosic forms of HANSEN bacillus, is the cause of common relapses of negativated cases by treatment, which fact suggests a new therapeutics method to destroy such elements in loco, and exiges more strict examination before release of interned patients.

Verificação, em condiçoes naturais, da infecção de mais três hematófagos (Anophelineos, Flebótomos e Simulídeos) em leprosos

The A. went last August to the State of Minas Gerais to continue his studies on transmission of leprosy by insects. He selected ten lepers (all L3 cases) for his experiments. It happened in the middle of August, a few day after freezing temperature. Practically there were no day mosquitoes, even near a river where in March there were very many. Bringing the patients to a wood, near the Peixe River (Fish River), at the dawn they were attacked by very many Anopheles, some flebotomus, a few Simulium and very rare Culex scapularis. All these insects became infected, in different degrees, by biting such patients. CONCLUSIONS. 1. Two species of Anopheles (A. albitarsis and A. tarsimaculatus) became strongly infected by Hansen bacilli. 2. By dissection done by Dr. Oliveira Castro were found lepra bacilli in various points of the proboscis of two Flebotomus (F. intermedius) and in their stomachs. 3. By smearing were found lepra bacilli in two specimens of Simulium sp. (probably pertinax). 4. It was confirmed also the verification done last March, at the same Leper Colony, that Phthirius pubis can be also a carrier of lepra bacillus. 5. There was confirmed also natural infection of nymphs of Amblyomma cajennense in lepers. Dr. Oliveira Castro is dissecting the Anopheles to locate the bacilli in their organisms and he started, with the cooperation of the Director of Colonia Santa Fé, Dr. José Mariano, attenpts to re-infect a group of negative-nerve cases of leprosy with infected mosquitoes.

Culturas de bacilos ácido-álcool resistentes isolados de hematófagos infectados em leprosos: evidências de se tratar do bacilo de Hansen

The A. summarises the history of his first culture of acidfast bacillus isolated directly from leprosy lesions (Sample José) and refers about two samples recovered from guinea pig and white rat inoculated with said culture. Then the A. completes his previous descriptions of four cultures of acidfast bacilli isolated by him from ticks (Amblyomma cajaennense and Boophilus microplus, two cultures from each species) infected experimentally in lepers. The A. having found specimens of two species of Triatomidae (Triatoma infestans and Panstrongylus megistus) naturally infected with HANSEN bacillus in huts habited by lepers in the State of Minas Gerais (Dec. 1942), started a series of experiments, using larvae and nymphs of T. infestans bred in laboratory at the Instituto Oswaldo Cruz, to infect in active cases of leprosy, in the city of Rio de Janeiro, could obtain two new samples of cultures of acid-fast bacilli (Ns. 6 and 7 of his set). In this papaer the A. studies the biological properties of said cultures, proving that Penicilin has not effect upon them, like other substances. The sulphuric and acetic acids were used to purify some of the cultures, with good results, the cultures becoming more rich and growing faster. Potassium hydroxide Sodium (10% solution) was also used with success to isolate and to purify the cultures, but it seems that it affects the bacilli in some way. In flud glycerinated media the majority of such cultures produce velum suitable for the preparation of antigens for skin tests and for therapeutical use. At last the A. says that he is becoming convinced that the HANSEN bacillus is in cause, especially after thee evidences of culturing the bacillus from one patient, in different opportunities.