Evaluation of direct colorimetric MTT assay for rapid detection of rifampicin and isoniazid resistance in Mycobacterium tuberculosis

With the spread of multidrug-resistant tuberculosis (MDR-TB) strains there is an increasing need for new accurate and cost-effective methods for a rapid diagnostic and drug susceptibility testing (DST), particularly in low-income countries where tuberculosis is hyperendemic. A colorimetric assay using 3-(4, 5-dimethylthiazol-2-yl)-2, 5-diphenyltetrazolium bromide (MTT) has been suggested as a promising method for DST, especially to rifampicin. In this study, we standardized and evaluated the MTT assay for a rapid direct detection of rifampicin and isoniazid resistant Mycobacterium tuberculosis strains from sputum specimens using Lowenstein-Jensen (LJ) culture medium as a gold standard. The MTT assay sensitivity, specificity, positive and negative predictive values for rifampicin were 100%, 86%, 100%, 99%, respectively. For isoniazid, the MTT assay had a 100% sensitivity, specificity, positive and negative predictive values. Interestingly, the MTT assay gave interpretable results within two weeks for 94% of the samples compared to 7-14 weeks for LJ media. Overall, an excellent agreement was observed between MTT assay and LJ proportion method (Kappa, 0.91 for rifampicin and 1.00 for isoniazid). In conclusion, the direct colorimetric MTT assay simultaneously detects susceptible and resistant strains of M. tuberculosis within three weeks. It significantly shortens the time required to obtain a DST result and could be a reliable alternative method for rapid detection of drug-resistant TB strains in high-TB-burden resource-limited settings

Genetic adaptation to high altitude in the Ethiopian highlands

Background: Genomic analysis of high-altitude populations residing in the Andes and Tibet has revealed several candidate loci for involvement in high-altitude adaptation, a subset of which have also been shown to be associated with hemoglobin levels, including EPAS1, EGLN1, and PPARA, which play a role in the HIF-1 pathway. Here, we have extended this work to high- and low-altitude populations living in Ethiopia, for which we have measured hemoglobin levels. We genotyped the Illumina 1M SNP array and employed several genome wide scans for selection and targeted association with hemoglobin levels to identify genes that play a role in adaptation to high altitude. Results: We have identified a set of candidate genes for positive selection in our high-altitude population sample, demonstrated significantly different hemoglobin levels between high- and low-altitude Ethiopians and have identified a subset of candidate genes for selection, several of which also show suggestive associations with hemoglobin levels. Conclusions: We highlight several candidate genes for involvement in high-altitude adaptation in Ethiopia, including CBARA1, VAV3, ARNT2 and THRB. Although most of these genes have not been identified in previous studies of high-altitude Tibetan or Andean population samples, two of these genes (THRB and ARNT2) play a role in the HIF-1 pathway, a pathway implicated in previous work reported in Tibetan and Andean studies. These combined results suggest that adaptation to high altitude arose independently due to convergent evolution in high-altitude Amhara populations in Ethiopia

Smallholder farmers’ legume technology adoption preferences and contributions to farmers’ performance: Evidences from N2Africa project

Bill & Melinda Gates Foundatio

Evaluating post-processing approaches for monthly and seasonal streamflow forecasts

Streamflow forecasting is prone to substantial uncertainty due to errors in meteorological forecasts, hydrological model structure, and parameterization, as well as in the observed rainfall and streamflow data used to calibrate the models. Statistical streamflow post-processing is an important technique available to improve the probabilistic properties of the forecasts. This study evaluates post-processing approaches based on three transformations – logarithmic (Log), log-sinh (Log-Sinh), and Box–Cox with λ=0.2 (BC0.2) – and identifies the best-performing scheme for post-processing monthly and seasonal (3-months-ahead) streamflow forecasts, such as those produced by the Australian Bureau of Meteorology. Using the Bureau's operational dynamic streamflow forecasting system, we carry out comprehensive analysis of the three post-processing schemes across 300 Australian catchments with a wide range of hydro-climatic conditions. Forecast verification is assessed using reliability and sharpness metrics, as well as the Continuous Ranked Probability Skill Score (CRPSS). Results show that the uncorrected forecasts (i.e. without post-processing) are unreliable at half of the catchments. Post-processing of forecasts substantially improves reliability, with more than 90 % of forecasts classified as reliable. In terms of sharpness, the BC0.2 scheme substantially outperforms the Log and Log-Sinh schemes. Overall, the BC0.2 scheme achieves reliable and sharper-than-climatology forecasts at a larger number of catchments than the Log and Log-Sinh schemes. The improvements in forecast reliability and sharpness achieved using the BC0.2 post-processing scheme will help water managers and users of the forecasting service make better-informed decisions in planning and management of water resources.Fitsum Woldemeskel, David McInerney, Julien Lerat, Mark Thyer, Dmitri Kavetski, Daehyok Shin, Narendra Tuteja and George Kuczer

Year Round Feed and Fodder Availability in Smallholder Dairy Farms across High and Low Altitude Areas in Eastern Africa

This research article published by the Journal of Experimental Agriculture International, 2020, Volume 42 [Issue 7]Feed-year strategies involve matching the cycles of dairy production with the changing availabilities of all sources of nutrients over time. Therefore, an understanding of seasonal variation in availability of forage resources is important in future planning and development of appropriate technologies to assure resilience of smallholder dairy systems to seasonal changes. This study was carried out to: 1) evaluate the current pattern of seasonal variation in forage availability in smallholder dairy farms, and 2) assess seasonal variation in year-round forage based feeding strategies in smallholder dairy farms in Eastern Africa. Data was collected from a purposive representative sample of 400 smallholder dairy farmers through cross-sectional and observational studies. The Feed Assessment Tool (FEAST) was used to capture the season’s effect (wet and dry) across high and low altitude areas in Kenya and Tanzania from 2016-2018. Data were analyzed using the generalized linear model (GLMM) procedure of SPSS 21.0 (Chicago, IL, USA), using models that included the fixed effects and random effects; and FEAST Version 2.21. Results showed that location (country), agro-ecological zone and season had a significant influence (p ≤ 0.05) on year-round rainfall variability. Availability and utilization of concentrate feeds, green and dry crop residues, improved fodder, pasture and legume forage throughout the year, were significantly influenced (p ≤ 0.05) by location, agro-ecological zone, seasons and production systems. Correlation between the forage resources revealed highly significant (p ≤ 0.001) and positive relationships in availability and usage across the two countries. From this study, rainfall variability was crucial in determining sources and year-round variation in availability and utilization of forages. Therefore, different seasonality driven site, region or country specific year-round feeding interventions and strategies could be applied depending upon type, source, quantity (availability) and quality of feeds to overcome seasonal milk fluctuations in smallholder dairy farms in Eastern Africa

Direct susceptibility testing for multi drug resistant tuberculosis: A meta-analysis

<p>Abstract</p> <p>Background</p> <p>One of the challenges facing the tuberculosis (TB) control programmes in resource-limited settings is lack of rapid techniques for detection of drug resistant TB, particularly multi drug resistant tuberculosis (MDR TB). Results obtained with the conventional indirect susceptibility testing methods come too late to influence a timely decision on patient management. More rapid tests directly applied on sputum samples are needed. This study compared the sensitivity, specificity and time to results of four direct drug susceptibility testing tests with the conventional indirect testing for detection of resistance to rifampicin and isoniazid in <it>M. tuberculosis</it>. The four direct tests included two in-house phenotypic assays – Nitrate Reductase Assay (NRA) and Microscopic Observation Drug Susceptibility (MODS), and two commercially available tests – Genotype^®MTBDR and Genotype^®MTBDR<it>plus </it>(Hain Life Sciences, Nehren, Germany).</p> <p>Methods</p> <p>A literature review and meta-analysis of study reports was performed. The Meta-Disc software was used to analyse the reports and tests for sensitivity, specificity, and area under the summary receiver operating characteristic (sROC) curves. Heterogeneity in accuracy estimates was tested with the Spearman correlation coefficient and Chi-square.</p> <p>Results</p> <p>Eighteen direct DST reports were analysed: NRA – 4, MODS- 6, Genotype MTBDR^®– 3 and Genotype^®MTBDR<it>plus </it>– 5. The pooled sensitivity and specificity for detection of resistance to rifampicin were 99% and 100% with NRA, 96% and 96% with MODS, 99% and 98% with Genotype^®MTBDR, and 99% and 99% with the new Genotype^®MTBDR<it>plus</it>, respectively. For isoniazid it was 94% and 100% for NRA, 92% and 96% for MODS, 71% and 100% for Genotype^®MTBDR, and 96% and 100% with the Genotype^®MTBDR<it>plus</it>, respectively. The area under the summary receiver operating characteristic (sROC) curves was in ranges of 0.98 to 1.00 for all the four tests. Molecular tests were completed in 1 – 2 days and also the phenotypic assays were much more rapid than conventional testing.</p> <p>Conclusion</p> <p>Direct testing of rifampicin and isoniazid resistance in <it>M. tuberculosis </it>was found to be highly sensitive and specific, and allows prompt detection of MDR TB.</p

Factors associated with bovine udder infections in smallholder dairy farms in EthiopiaFacteurs lies aux infections de la mamelle bovine dans les petites exploitations laitieres en Ethiopie

A cross sectional study to elucidate the prevalence and factors associated with udder infection was carried out from February 2002 to December 2002. A total of 336 milking cows of Arsi breed in Adame-Tulu district, Ethiopia were studied using California Mastitis Test (CMT) and clinical examination of udder. The study involved a multistage sampling with fifteen randomly selected villages from the district. Milking cows from six households selected randomly from each village were sampled by cluster sampling. Of the total milking cows examined, 131(38.9%) showed positive signs of mastitis; 41(12.2%) clinical and 90 (26.8%) sub clinical mastitis. Mastitis was reported to be significantly (&#967;2=10.5,

Yields and the nutritive value of early harvested common bean (Phaseolus vulgaris L.) crop residues for ruminants

The yields and nutritive value of haulm (stem and leaf) and pod wall (HPW) crop residues of common bean early-harvested atthe green pod fill stage were measured in nine genotypes grown in two dissimilar environments (Boricha and Mandura) inEthiopia. The concentrations of total N, neutral detergent fibre (NDF) and acid detergent fibre (ADF), and the in vitro DMdigestibility (IVDMD), in the HPW fractions (stem, leaf and pod wall) were measured. At Mandura the yields of seed and HPWaveraged 1.03 and 2.26 t/ha, respectively, and varied (p0.001) among genotypes (0.31-1.57 t/ha and 1.19-2.93 t/ha,respectively). However no such differences among genotypes (p0.05) were observed at Boricha. Stem, leaf and pod wallcomprised 52.4, 23.1 and 24.5% of HPW, respectively. The concentrations of N, NDF and ADF, and IVDMD in the HPW, andthe HPW fractions, generally varied (p0.05) among genotypes. The digestible DM (DDM) yields of HPW ranged amonggenotypes from 0.75-1.81 t/ ha at Mandura, and averaged 1.89 t/ha at Boricha. N yield ranged from 35.3-70.3 kg N/ha atBoricha and 18.3-43.4 kg N/ha at Mandura. Since yields of seed were positively correlated with yields of HPW DM, DDM andN, common bean genotypes can be selected concurrently for seed and HPW yields. Uses of high-yielding genotype can doublethe N and DDM yields without reducing seed yield. The N and IVDMD of HPW residue showed that early-harvested commonbean is a high nutritive value feedstuff for ruminants

Detection of asymptomatic renal infection in abattoir slaughtered cattle in southeastern Georgia, United States

Objectives: Leptospirosis is one of the most widespread zoonotic infectious diseases affecting humans and animals. Several animal species, including cattle, can act as potential asymptomatic carriers facilitating zoonotic transmission of Leptospira . This study was conducted to assess the occurrence of asymptomatic renal Leptospira carriers among cattle slaughtered in southeastern Georgia, United States. Methods: A battery of diagnostic tests, including dark field microscopy, direct fluorescent antibody staining, polymerase chain reaction, and culture, were performed on a set of bovine kidneys (n = 37) collected from an abattoir in southeastern Georgia, United States. Virulence of a field isolate obtained from this study was tested in a hamster experimental model. Results: Motile spirochete-like structures were observed by dark field microscopy in 23 (59%) out of 37 kidney samples tested. In all, 29 samples (78%) were positive by direct fluorescent antibody staining. Only 11 (29.7%) samples by polymerase chain reaction and 3 (8.1%) by culture were positive for Leptospira sp. The isolates obtained by culture were confirmed as Leptospira borgpetersenii . Hamsters experimentally infected with one of the Leptospira field isolates obtained from this study did not show clinical signs but developed renal infection with interstitial nephritis and tubular necrosis. Conclusions: This study confirms that asymptomatic Leptospira renal infection is present among cattle in the region. Our findings underscore the need for future studies to assess the potential environmental contamination and transmission to humans in contact with infected cattle