Comparison of the Proportion Method With Mycobacteria Growth Indicator Tube and E-test for Susceptibility Testing of Mycobacterium tuberculosis

The aim of this study was to investigate the correlation between proportion method with mycobacteria growth indicator tube (MGIT) and E-test for Mycobacterium tuberculosis. Forty clinical isolates were tested. MGIT and E-test with the first line antituberculous drugs correlated with the proportion method. Our results suggested that MGIT and E-test methods can be routinely used instead of the proportion method.

Drug susceptibility testing of Mycobacterium tuberculosis by the broth microdilution method with 7H9 broth

In this study, we have evaluated the broth microdilution method (BMM) for susceptibility testing of Mycobacterium tuberculosis. A total of 43 clinical isolates of M. tuberculosis and H37Rv as a control strain were studied. All isolates were tested by the proportion method and the BMM for isoniazid (INH), rifampicin (RIF), streptomycin (STR), and ethambutol (ETM). The proportion method was carried out according to the National Committee for Clinical Laboratory Standards (NCCLS) on Löwenstein-Jensen (LJ) medium. The BMM was carried out using 7H9 broth with 96 well-plates. All strains were tested at 3.2-0.05 µg/ml, 16-0.25 µg/ml, 32-0.5 µg/ml, and 32-0.5 µg/ml concentrations for INH, RIF, STR, and ETM, respectively. When the BMM was compared with the proportion method, sensitivity was 100, 100, 96.9, and 90.2%, while specificity was 100, 85.7, 90.9, and 100% for INH, RIF, STR, and ETM, respectively. The plates were examined 7, 10, 14, and 21 days after incubation. The majority of the result were obtained at 14th days after incubation, while the proportion method result were ended in 21-28 days. According to our results, it may be suggested that the BMM is suitable for early determining of multidrug-resistance-M. tuberculosis strains in developed or developing countries.

New records of calyptrate dipterans (Fanniidae, Muscidae and Sarcophagidae) associated with the decomposition of domestic pigs in Brazil

The calyptrate dipterans are the most important decomposers of human cadavers. Knowledge of their species and distribution are of great importance to forensic entomology, especially because of the enormous diversity in Brazil. Carcasses of domestic pigs (Sus scrofa, L) were the experimental models used to attract calyptrates of forensic interest during the winters of 2006 and 2007 and the summers of 2006 and 2008. A total of 24,423 specimens from 44 species were collected (19 Muscidae, 2 Fanniidae and 23 Sarcophagidae), three of which were new records of occurrence and 20 of which were new forensic records for the state of Rio de Janeiro. Fourteen of these species were newly identified as forensically important in Brazil.

A sensitive and robust lc-ms/ms method with monolithic column and electrospray ionization for the quantitation of efavirenz in human plasma: application to a bioequivalence study

An LC-MS/MS method has been developed for the determination of efavirenz (EFZ) in human plasma using hydrochlorothiazide as internal standard (I.S.). An ESI negative mode with multiple reaction-monitoring was used monitoring the transitions m/z 313.88→69.24 (EFZ) and 296.02→204.76 (I.S.). Samples were extracted using liquid-liquid extraction. The total run time was 2.0 min. The separation was achieved with HPLC-RP using a monolithic column. The assay was linear in the concentration range of 100 - 5000 ng mL-1. The mean recovery was 83%. Intra- and inter-day precision were < 9.5% and < 8.9%, respectively and accuracy was in the range ± 8.33%. The method was successfully applied to a bioequivalence study.

Turbulent shallow-water model for orographic subgrid-scale perturbations

A parallel pseudo-spectral method for the simulation in distributed memory computers of the shallow-water equations in primitive form was developed and used on the study of turbulent shallow-waters LES models for orographic subgrid-scale perturbations. The main characteristics of the code are: momentum equations integrated in time using an accurate pseudo-spectral technique; Eulerian treatment of advective terms; and parallelization of the code based on a domain decomposition technique. The parallel pseudo-spectral code is efficient on various architectures. It gives high performance onvector computers and good speedup on distributed memory systems. The code is being used for the study of the interaction mechanisms in shallow-water ows with regular as well as random orography with a prescribed spectrum of elevations. Simulations show the evolution of small scale vortical motions from the interaction of the large scale flow and the small-scale orographic perturbations. These interactions transfer energy from the large-scale motions to the small (usually unresolved) scales. The possibility of including the parametrization of this effects in turbulent LES subgrid-stress models for the shallow-water equations is addressed.

Start-up of horizontal anaerobic reactors with sludge blanket and fixed bed for wastewater treatment from coffee processing by wet method

In this study it was evaluated the start-up procedures of anaerobic treatment system with three horizontal anaerobic reactors (R1, R2 and R3), installed in series, with volume of 1.2 L each. R1 had sludge blanket, and R2 and R3 had half supporter of bamboo and coconut fiber, respectively. As an affluent, it was synthesized wastewater from mechanical pulping of the coffee fruit by wet method, with a mean value of total chemical oxygen demand (CODtotal) of 16,003 mg L-1. The hydraulic retention time (HRT) in each reactor was 30 h. The volumetric organic loading (VOL) applied in R1 varied from 8.9 to 25.0 g of CODtotal (L d)-1. The mean removal efficiencies of CODtotal varied from 43 to 97% in the treatment system (R1+R2+R3), stabilizing above 80% after 30 days of operation. The mean content of methane in the biogas were of 70 to 76%, the mean volumetric production was 1.7 L CH4 (L reactor d)-1 in the system, and the higher conversions were around at 0.20 L CH4 (g CODremoved)-1 in R1 and R2. The mean values of pH in the effluents ranged from 6.8 to 8.3 and the mean values of total volatile acids remained below 200 mg L-1 in the effluent of R3. The concentrations of total phenols of the affluent ranged from 45 to 278 mg L-1, and the mean removal efficiency was of 52%. The start-up of the anaerobic treatment system occurred after 30 days of operation as a result of inoculation with anaerobic sludge with active microbiota.

Heat Source Estimation with the Conjugate Gradient Method in Inverse Linear Diffusive Problems

In this work, we present the solution of a class of linear inverse heat conduction problems for the estimation of unknown heat source terms, with no prior information of the functional forms of timewise and spatial dependence of the source strength, using the conjugate gradient method with an adjoint problem. After describing the mathematical formulation of a general direct problem and the procedure for the solution of the inverse problem, we show applications to three transient heat transfer problems: a one-dimensional cylindrical problem; a two-dimensional cylindrical problem; and a one-dimensional problem with two plates.

In-house ELISA method to analyze anti-Trypanosoma cruzi IgG reactivity for differential diagnosis and evaluation of Chagas disease morbidity

INTRODUCTION: The goal was to develop an in-house serological method with high specificity and sensitivity for diagnosis and monitoring of Chagas disease morbidity. METHODS: With this purpose, the reactivities of anti-T. cruzi IgG and subclasses were tested in successive serum dilutions of patients from Berilo municipality, Jequitinhonha Valley, Minas Gerais, Brazil. The performance of the in-house ELISA was also evaluated in samples from other relevant infectious diseases, including HIV, hepatitis C (HCV), syphilis (SYP), visceral leishmaniasis (VL), and American tegumentary leishmaniasis (ATL), and noninfected controls (NI). Further analysis was performed to evaluate the applicability of this in-house methodology for monitoring Chagas disease morbidity into three groups of patients: indeterminate (IND), cardiac (CARD), and digestive/mixed (DIG/Mix), based on their clinical status. RESULTS: The analysis of total IgG reactivity at serum dilution 1:40 was an excellent approach to Chagas disease diagnosis (100% sensitivity and specificity). The analysis of IgG subclasses showed cross-reactivity, mainly with NI, VL, and ATL, at all selected serum dilutions. Based on the data analysis, the IND group displayed higher IgG3 levels and the DIG/Mix group presented higher levels of total IgG as compared with the IND and CARD groups. CONCLUSIONS: These findings demonstrated that methodology presents promising applicability in the analysis of anti-T. cruzi IgG reactivity for the differential diagnosis and evaluation of Chagas disease morbidity.

Evaluation of DNA Recombinant Methodologies for the Diagnosis of Plasmodium falciparum and their Comparison with the Microscopy Assay

Since 1984, DNA tests based on the highly repeated subtelomeric sequences of Plasmodium falciparum (rep 20) have been frequently used in malaria diagnosis. Rep 20 is very specific for this parasite, and is made of 21 bp units, organized in repeated blocks with direct and inverted orientation. Based in this particular organization, we selected a unique consensus oligonucleotide (pf-21) to drive a PCR reaction coupled to hybridization to non-radioactive labeled probes. The pf-21 unique oligo PCR (pf-21-I) assay produced DNA amplification fingerprints when was applied on purified P. falciparum DNA samples (Brazil and Colombia), as well as in patient's blood samples from a large area of Venezuela. The performance of the Pf-21-I assay was compared against Giemsa stained thick blood smears from samples collected at a malaria endemic area of the Bolívar State, Venezuela, at the field station of Malariología in Tumeremo. Coupled to non-radioactive hybridization the pf-21-I performed better than the traditional microscopic method with a r=1.7:1. In the case of mixed infections the r value of P. falciparum detection increased to 2.5:1. The increased diagnostic sensitivity of the test produced with this homologous oligonucleotide could provide an alternative to the epidemiological diagnosis of P. falciparum being currently used in Venezuela endemic areas, where low parasitemia levels and asymptomatic malaria are frequent. In addition, the DNA fingerprint could be tested in molecular population studies

Standartization of broth microdilution method for Mycobacterium tuberculosis

Indirect drug susceptibility tests of Mycobacterium tuberculosis was done to investigate the accuracy and feasibility of a broth microdilution method (BMM) for determining minimal inhibitory concentrations of conventional drugs against M. tuberculosis. Test drugs included isoniazid (H), rifampicin (R), ethambutol (E), streptomycin (S) and pyrazinamide (Z). Fifty isolates of M. tuberculosis from patients who had never received drug therapy, and H37Rv strain for control, were evaluated in the system. When comparing this method with the gold standard proportional method in Lowenstein-Jensen medium, sensitivity of 100% for all drugs and specifities of 91, 100, 96, 98 and 85% were observed respectively for H, R, E, S and Z. The BMM was read faster (14-20 days) than the proportional method (20-28 days). The microdilution method evaluated allows the testing of multiple drugs in multiple concentrations. It is easy to perform and does not require special equipment or expensive supplies. In contrast to radiometric method it does not use radioactive material.

Factors associated with schistosomiasis mansoni in a population from the municipality of Jaboticatubas, State of Minas Gerais, Brazil

Jaboticatubas is a municipality in the metropolitan region of Belo Horizonte which has been a target of a wide media release as "the capital of schistosomiasis" since the 1960's. In order to give support to a work based on an integrated control, we sought to identify the disease determinants at the site. A transversal study was carried out aimed at identifying prevalence rates of the disease and factors associated with the infection in the district of São José de Almeida, and two close localities, Cipó Velho and São José da Serra, all of them located in the municipality of Jaboticatubas. A parasitological survey was performed, applying the Kato-Katz method with two slides per sample in 1186 schoolchildren which represents 77% of all registered pupils in four public schools in 2001. Among these schoolchildren a number of 101 (8.6%) prooved positive for Schistosoma mansoni eggs in their stool samples. A total of 64 families, whose schoolchildren had shown to be positive for schistosomiasis, also undertook examinations. As negative control, a random sample was collected from the 206 families, whose children had proven negative for schistosomiasis. The prevalence among 270 families (1304 people) was 12%. To assess those who continued to have contact with possibly contaminated water, 1061 (81.4%) people of the 270 families were interviewed. A multivariate analysis identified the following factors associated with the infection: time of residence in the area (short period), garbage disposal (use of deserted areas), gender (male), age (from 10 to 29 years), and water contact (daily and weekly). Further analysis of these factors revealed a close correlation between water contact and the disease, with a positive significant frequency concerning almost all those items. Depending on gender and age significant variations of water contact patterns associated with leisure and professional activities were found. A malacological survey on water collections in the area identified snails of the species Biomphalaria straminea and B. glabrata. The latter showed 17 (0.6%) specimens positive for S. mansoni. Qualitative studies have complemented such evidences, which allowed us to design a reference picture and specific indicators of the disease for the local population. Those data provided the essential information to continue the development of an already ongoing educative process, as well as projects on environmental improvements.

An in-house real-time polymerase chain reaction: standardisation and comparison with the Cobas Amplicor HBV monitor and Cobas AmpliPrep/Cobas TaqMan HBV tests for the quantification of hepatitis B virus DNA

This study aimed to standardise an in-house real-time polymerase chain reaction (rtPCR) to allow quantification of hepatitis B virus (HBV) DNA in serum or plasma samples, and to compare this method with two commercial assays, the Cobas Amplicor HBV monitor and the Cobas AmpliPrep/Cobas TaqMan HBV test. Samples from 397 patients from the state of São Paulo were analysed by all three methods. Fifty-two samples were from patients who were human immunodeficiency virus and hepatitis C virus positive, but HBV negative. Genotypes were characterised, and the viral load was measure in each sample. The in-house rtPCR showed an excellent success rate compared with commercial tests; inter-assay and intra-assay coefficients correlated with commercial tests (r = 0.96 and r = 0.913, p < 0.001) and the in-house test showed no genotype-dependent differences in detection and quantification rates. The in-house assay tested in this study could be used for screening and quantifying HBV DNA in order to monitor patients during therapy.

Insects associated with the composting process of solid urban waste separated at the source

Sarcosaprophagous macroinvertebrates (earthworms, termites and a number of Diptera larvae) enhance changes in the physical and chemical properties of organic matter during degradation and stabilization processes in composting, causing a decrease in the molecular weights of compounds. This activity makes these organisms excellent recyclers of organic matter. This article evaluates the succession of insects associated with the decomposition of solid urban waste separated at the source. The study was carried out in the city of Medellin, Colombia. A total of 11,732 individuals were determined, belonging to the classes Insecta and Arachnida. Species of three orders of Insecta were identified, Diptera, Coleoptera and Hymenoptera. Diptera corresponding to 98.5% of the total, was the most abundant and diverse group, with 16 families (Calliphoridae, Drosophilidae, Psychodidae, Fanniidae, Muscidae, Milichiidae, Ulidiidae, Scatopsidae, Sepsidae, Sphaeroceridae, Heleomyzidae, Stratiomyidae, Syrphidae, Phoridae, Tephritidae and Curtonotidae) followed by Coleoptera with five families (Carabidae, Staphylinidae, Ptiliidae, Hydrophilidae and Phalacaridae). Three stages were observed during the composting process, allowing species associated with each stage to be identified. Other species were also present throughout the whole process. In terms of number of species, Diptera was the most important group observed, particularly Ornidia obesa, considered a highly invasive species, and Hermetia illuscens, both reported as beneficial for decomposition of organic matter.

Necrophagous diptera associated with wild animal carcasses in southern Brazil

Necrophagous Diptera associated with wild animal carcasses in southern Brazil. The aim of this study was to acquire a better knowledge concerning the diversity of necrophagous Diptera that develop on wild animal carcasses. For this purpose, the decomposition of six wild animal carcasses was observed in order to collect and identify the main species of necrophagous flies associated with the decomposition process. The carcasses were found on highways near the cities of Pelotas and Capão do Leão in the initial stage of decomposition, with no significant injuries or prior larval activity. Four wild animal models were represented in this study: two specimens of Didelphis albiventris Lund, 1840; two Tupinambis merianae Linnaeus, 1758; one Nothura maculosa Temminck, 1815; and one Cerdocyon thous Linnaeus, 1766. A total of 16,242 flies from 14 species were reared in the laboratory, where Muscidae presented the greatest diversity of necrophagous species. Overall, (i) carcasses with larger biomass developed a higher abundance of flies and (ii) the necrophagous community was dominated by Calliphoridae, two patterns that were predicted from published literature; and (iii) the highest diversity was observed on the smaller carcasses exposed to the lowest temperatures, a pattern that may have been caused by the absence of the generalist predator Chrysomya albiceps (Wiedemann, 1819). (iv) An UPGMA analysis revealed a similar pattern of clusters of fly communities, where the same species were structuring the groupings.

Long-term C-CO2 emissions and carbon crop residue mineralization in an oxisol under different tillage and crop rotation systems

Soil C-CO2 emissions are sensitive indicators of management system impacts on soil organic matter (SOM). The main soil C-CO2 sources at the soil-plant interface are the decomposition of crop residues, SOM turnover, and respiration of roots and soil biota. The objectives of this study were to evaluate the impacts of tillage and cropping systems on long-term soil C-CO2 emissions and their relationship with carbon (C) mineralization of crop residues. A long-term experiment was conducted in a Red Oxisol in Cruz Alta, RS, Brazil, with subtropical climate Cfa (Köppen classification), mean annual precipitation of 1,774 mm and mean annual temperature of 19.2 ºC. Treatments consisted of two tillage systems: (a) conventional tillage (CT) and (b) no tillage (NT) in combination with three cropping systems: (a) R0- monoculture system (soybean/wheat), (b) R1- winter crop rotation (soybean/wheat/soybean/black oat), and (c) R2- intensive crop rotation (soybean/ black oat/soybean/black oat + common vetch/maize/oilseed radish/wheat). The soil C-CO2 efflux was measured every 14 days for two years (48 measurements), by trapping the CO2 in an alkaline solution. The soil gravimetric moisture in the 0-0.05 m layer was determined concomitantly with the C-CO2 efflux measurements. The crop residue C mineralization was evaluated with the mesh-bag method, with sampling 14, 28, 56, 84, 112, and 140 days after the beginning of the evaluation period for C measurements. Four C conservation indexes were used to assess the relation between C-CO2 efflux and soil C stock and its compartments. The crop residue C mineralization fit an exponential model in time. For black oat, wheat and maize residues, C mineralization was higher in CT than NT, while for soybean it was similar. Soil moisture was higher in NT than CT, mainly in the second year of evaluation. There was no difference in tillage systems for annual average C-CO2 emissions, but in some individual evaluations, differences between tillage systems were noticed for C-CO2 evolution. Soil C-CO2 effluxes followed a bi-modal pattern, with peaks in October/November and February/March. The highest emission was recorded in the summer and the lowest in the winter. The C-CO2 effluxes were weakly correlated to air temperature and not correlated to soil moisture. Based on the soil C conservation indexes investigated, NT associated to intensive crop rotation was more C conserving than CT with monoculture.