Biology subjects

Tafess, K.

Publications and source records attributed to Tafess, K..

3 recordsLinked to original sources

bioRxiv2024

Genomic characterization of a unique population of Leishmania tropica in a new emerging focus of cutaneous leishmaniasis in Somali region of Ethiopia

We sequenced Leishmania tropica genomes directly from eight human skin samples collected in a newly emerging focus of cutaneous leishmaniasis in Somali region, Ethiopia. We found a new variant with unique genomic signatures of drug resistance. Genomic homogeneity in the sampled population demonstrates the occurrence of a L. tropica outbreak.

microbiology↗

bioRxiv2020

Inadequate level of knowledge, mixed outlook and poor adherence to COVID-19 prevention guideline among Ethiopians

COVID-19 has a potential to cause chaos in Ethiopia due to the countrys already daunting economic and social challenges. Living and working conditions are highly conducive for transmission, as people live in crowded inter-generational households that often lack running water and other basic sanitary facilities. Thus, the aim of this study was to investigate the knowledge, attitudes and practices (KAP) of Ethiopians toward COVID-19 following the introduction of state of emergency by the Ethiopian government to curb the spread of the disease. A cross-sectional study design was conducted in nine reginal states and two chartered cities. Data for demographic, Knowledge, attitude and practice toward COVID-19 were collected through telephone interview from 1570 participants. Descriptive and bivariate analyses using chi-square test, t-test or analysis of variance were performed as appropriate. Binary and multiple logistic regression analysis were used to measure the relationship between the categorical dependent variables and one or more socio-demographic independent variables with two-tailed at =0.05 significance level and 95% of confidence interval. The level of good knowledge, favourable attitude and good practice among the respondents were 42%, 53.8% and 24.3% respectively. Being rural resident, older than 50 years, having at least primary education, being resident of Amhara and Oromia regions were independent predictors of knowledge level. While being rural resident, married, employed, having at least basic education, being residents of Afar, Amhara, Gambela, Oromia and Somali regions were found to be the best predictors of the attitude, being rural resident, government employee, having at least basic education, and living outside of the capital were the independent predictors of practice level of the respondents. The finding revealed that Ethiopians have inadequate level of knowledge and are generally have a mixed outlook on overcoming the pandemic with poor adherence to COVID-19 prevention practice. reinforcing preventive measures and intensifying sensitization campaigns to fill the knowledge gap and persuading people to follow the preventive measures set by the government with concurrent evaluation of the impacts of these measures on knowledge and practice is highly recommended to mitigate the disease.

animal behavior and cognition↗

bioRxiv2019

Targeted Sequencing Workflows for Comprehensive Drug Resistance Profiling of Mycobacterium tuberculosis cultures using Illumina MiSeq and Nanopore MinION: Comparison of analytical and diagnostic performance, turnaround time and cost

The emergence of Mycobacterium tuberculosis strains with complex drug resistance profiles necessitates a rapid and extensive drug susceptibility test for comprehensive guidance of patient treatment. Here, we developed two targeted-sequencing workflows based on Illumina MiSeq and Nanopore MinION for the prediction of drug resistance in M. tuberculosis towards 12 anti-tuberculous agents.\n\nA total of 163 M. tuberculosis cultured isolates collected from Hong Kong and Ethiopia were subjected to a multiplex PCR for simultaneous amplification of 19 drug-resistance associated genetic regions. The amplicons were then barcoded and sequenced in parallel on MiSeq and MinION in respective batch sizes of 24 and 12 samples. Both platforms successfully sequenced all samples with average depths of coverage of 1,127x and 1,649x respectively. Utilizing a self-developed Web-based bioinformatics pipeline, Bacteriochek-TB, for variant analysis, we found that the MiSeq and MinION result could achieve 100% agreement if variants with an allele frequency of <40% reported by MinION were excluded. For drug resistance prediction, both workflows achieved an average sensitivity of 94.8% and specificity of 98.0% when compared with phenotypic drug susceptibility test. The turnaround times for the MiSeq and MinION workflows were 38 and 15 hours, facilitating the delivery of treatment guidance at least 17-18 days earlier than pDST respectively. The higher cost per sample on the MinION platform (US$71.56) versus the MiSeq platform (US$67.83) was attributed to differences in batching capabilities.\n\nOur study demonstrated the interchangeability of MiSeq and MinION sequencing workflows for generation of accurate and actionable results for the treatment of tuberculosis.\n\nImportanceTB therapy involving different combinations of antibiotics have been introduced to address the issue of drug resistance. However, this practice has led to increasing numbers of M. tuberculosis with complex drug resistance profiles. Molecular assays for rapid and comprehensive drug resistance profiling of M. tuberculosis are lacking.\n\nHere, we described targeted-sequencing workflows based on Illumina MiSeq and Nanopore MinION for the detection of drug resistance mutations scattered across 19 genetic regions in M. tuberculosis. A bioinformatics pipeline was also developed to translate raw datasets into clinician-friendly reports that provide comprehensive genetic information for the prediction of drug resistance towards 12 antibiotics.\n\nThis is the first study to evaluate and compare the uses of Illumina and Nanopore platforms for diagnosis of drug-resistant tuberculosis. Remarkably, our diagnostic strategy is compatible with different sequencing platforms that can be applied in diagnostic centres with different levels of throughput and financial support for TB diagnosis.

microbiology↗