Biology subjects

Petros, B.

Publications and source records attributed to Petros, B..

4 recordsLinked to original sources

bioRxiv2019

A molecular barcode and online tool to identify and map imported infection with Plasmodium vivax

Imported cases present a considerable challenge to the elimination of malaria. Traditionally, patient travel history has been used to identify imported cases, but the long-latency liver stages confound this approach in Plasmodium vivax. Molecular tools to identify and map imported cases offer a more robust approach, that can be combined with drug resistance and other surveillance markers in high-throughput, population-based genotyping frameworks. Using a machine learning approach incorporating hierarchical FST (HFST) and decision tree (DT) analysis applied to 831 P. vivax genomes from 20 countries, we identified a 28-Single Nucleotide Polymorphism (SNP) barcode with high capacity to predict the country of origin. The Matthews correlation coefficient (MCC), which provides a measure of the quality of the classifications, ranging from -1 (total disagreement) to 1 (perfect prediction), exceeded 0.9 in 15 countries in cross-validation evaluations. When combined with an existing 37-SNP P. vivax barcode, the 65-SNP panel exhibits MCC scores exceeding 0.9 in 17 countries with up to 30% missing data. As a secondary objective, several genes were identified with moderate MCC scores (median MCC range from 0.54-0.68), amenable as markers for rapid testing using low-throughput genotyping approaches. A likelihood-based classifier framework was established, that supports analysis of missing data and polyclonal infections. To facilitate investigator-lead analyses, the likelihood framework is provided as a web-based, open-access platform (vivaxGEN-geo) to support the analysis and interpretation of data produced either at the 28-SNP core or full 65-SNP barcode. These tools can be used by malaria control programs to identify the main reservoirs of infection so that resources can be focused to where they are needed most.

molecular biology↗

bioRxiv2019

Smear positive tuberculosis and genetic diversity of M. tuberculosis isolates in individuals visiting health facilities in South Gondar Zone, northwest Ethiopia

BackgroundTuberculosis (TB), a bacterial infectious disease, persisted to be a public health concern in many developing countries. However, lack of enough data concerning the public health burden and potential risk factors for the disease hampered control programs in target areas. Therefore, the present study aimed in determining the prevalence of TB and genetic diversity of M. tuberculosis isolates in South Gondar Zone, northwest Ethiopia.\n\nMethodsA cross-sectonal study was conducte between March 2015 and April 2017. Bacteriological examination, region of difference (RD) 9 based polymerase chain reaction (PCR) and spoligotyping were used to undertake the study.\n\nResultsThe overall prevalence of smear positive all forms TB was 6.3% (186/2953). Extra pulmonary TB (EPTB) was clinically characterized on about 62.4% (116/186) TB-positive cases. Some of the patients demographic characteristics such as [patients origin (chi-square ({chi}2) value; 62.8, p<0.001) were found to be significantly associated risk factors for the occurrence of TB in the study area. All the mycobacterial isolates were found to be M. tuberculosis. Among the 35 different spoligotype patterns identified, 22 patterns were shared types. The three dominantly identified families were T, CAS and Manu, each consisting of 46.9%, 24.0% and 10.4% of the isolates, respectively\n\nConclusionThe presented study revealed that TB continued to be a public health problem in South Gondar Zone which suggests a need of implementing effective disease control strategies.

epidemiology↗

bioRxiv2019

Tuberculosis at farmer-cattle interface in the rural villages of South Gondar Zone of northwest Ethiopia

BackgroundTuberculosis (TB) has been an important public health concern in Ethiopia, particularly at areas of human-animal intersection. However, limited epidemiological information is available in this respect in the country. Therefore, the present study was conducted to investigate the transmission of TB at human-cattle interface, associated risk factors and public awareness about the disease at South Gondar Zone, northwest Ethiopia.\n\nMethodsA cross sectional study was conducted between March 2015 and April 2018 on 186 farmers and 476 cattle in South Gondar Zone, northwest Ethiopia. Bacteriological examination, region of difference (RD) 9 based polymerase chain reaction (PCR), single intradermal comparative tuberculin test (SIDCTT) and questionnaire were used for undertaking this study.\n\nResultsCulture positivity in farmers was 59.7% (111/186) and all the culture positive isolates were M. tuberculosis. About 68% (74/111) of culture positive respondents did not know about the transmission of TB from cattle to human or vice versa. The animal and herd prevalence of bovine TB were 1.5% (7/476) and 7.4% (7/95) respectively. The odd of bovine TB in cattle owned by TB positive households was slightly higher than those owned by TB free households (adjusted odds ratio, AOR=1.39; 95% CI: 0.31-7.10; p = 0.76).\n\nConclusionAlthough SIDCTT reactivity was slightly higher in cattle owned by TB positive households, all the human isolates were M. tuberculosis and no M. bovis was isolated from farmers, which could be due to the low prevalence of bovine TB in the area.

epidemiology↗

bioRxiv2018

Molecular epidemiology and drug resistance patterns of Mycobacterium tuberculosis complex isolates from university students and the local community in Eastern Ethiopia

BackgroundPrevious studies suggest the burden of pulmonary tuberculosis (PTB) in Ethiopia may be greater in university students relative to the overall population. However, little is known about the transmission dynamics of PTB among students and members of the communities surrounding university campuses in Eastern Ethiopia.\n\nMethodsA cross sectional study was conducted in Eastern Ethiopia among culture-confirmed PTB cases from university students (n=36) and community members diagnosed at one of four hospitals (n=152) serving the surrounding area. Drug susceptibility testing (DST) was performed on Mycobacterium Tuberculosis Complex (MTBC) isolates using BD Bactec MGIT 960 and molecular genotyping was performed using spoligotyping and 24-loci MIRU-VNTR. MTBC strains with Identical genotyping patterns were assigned to molecular clusters as surrogate marker for recent transmission and further contact tracing was initiated among clustered patients.\n\nResultsAmong all study participants, four MTBC lineages and 11 sub-lineages were identified, with Ethiopia_3 being most common sub-lineage (29.4%) and associated with strain clustering (P= 0.016). We identified 13 (8.1%) strains phylogenetically related to the known Ethiopian sub-lineages with a distinct Spoligotyping patterns and designated as Ethiopia_4. The clustering rate of MTB strains was 52.9% for university students and 66.7% for community members with a Recent Transmission Index (RTI) of 17.6% and 48.4%, respectively. Female gender, urban residence, and new TB cases were significantly associated with strain clustering (p<0.05). Forty-eight (30%) of the study participants were resistant to one or more first line anti TB drugs, three patients were classified as multidrug resistant (MDR), defined by isoniazid and rifampicin resistance.\n\nConclusionWe found evidence of significant PTB cases clustering and recent transmission among Ethiopian university students and the local community in eastern Ethiopia; with Ethiopia_3 being the predominant circulating sub-lineage. A country wide comprehensive molecular surveillance and drug resistance profiling of MTBC strains and Implementation of TB control programs within universities and the surrounding community should be considered to decrease TB transmission.

epidemiology↗