Biology subjects

Kepha, S.

Publications and source records attributed to Kepha, S..

3 recordsLinked to original sources

bioRxiv2021

Mobile microscopy and telemedicine platform assisted by deep learning for quantification of Trichuris trichiura infection.

Soil-transmitted helminths (STH) are the most prevalent pathogens among the group of neglected tropical diseases (NTDs). Kato-Katz technique is the diagnosis method recommended by WHO and although is generally more sensitive than other microscopic methods in high transmission settings, it often presents a decreased sensitivity in low transmission settings and it is labour intensive. Digitizing the samples could provide a solution which allows to store the samples in a digital database and perform remote analysis. Artificial intelligence methods based on digitized samples can support diagnostics efforts by support diagnostics efforts by performing an automatic and objective quantification of disease infection. In this work, we propose an end-to-end pipeline for microscopy image digitization and automatic analysis of digitized images of soil-transmitted helminths. Our solution includes (1) a digitalization system based on a mobile app that digitizes the microscope samples using a low-cost 3D-printed microscope adapter, (2) a telemedicine platform for remote analysis and labelling and (3) novel deep learning algorithms for automatic assessment and quantification of parasitological infection of STH. This work has been evaluated by comparing the STH quantification using both a manual remote analysis based on the digitized images and the AI-assisted quantification against the reference method based on conventional microscopy. The deep learning algorithm has been trained and tested on 41 slides of stool samples containing 949 eggs from 6 different subjects using a cross-validation strategy obtaining a mean precision of 98,44% and mean recall of 80,94%. The results also proved the potential of generalization capability of the method at identifying different types of helminth eggs. In conclusion, this work has presented a comprehensive pipeline using smartphone-based microscopy integrated with a telemedicine platform for automatic image analysis and quantification of STH infection using artificial intelligence models.

microbiology↗

bioRxiv2020

Extensive hybridization between pig and human Ascaris identifies a highly interbred species complex infecting humans

Human ascariasis is a major neglected tropical disease caused by the nematode Ascaris lumbricoides. We report a 296 megabase (Mb) reference quality genome comprised of 17902 protein-coding genes derived from a single, representative Ascaris worm collected from 60 human hosts in Kenyan villages where pig husbandry is rare. Notably, the majority of human isolates (63/68) possessed mitochondrial genomes that clustered closer to the pig parasite Ascaris suum than to A. lumbricoides. Comparative phylogenomic analyses identified over 11 million nuclear-encoded SNPs but just two distinct genetic types that had recombined across the genomes analysed. The nuclear genomes had extensive heterozygosity and all samples existed as genetic mosaics with either A. suum-like or A. lumbricoides-like inheritance patterns supporting a highly interbred Ascaris species genetic complex. As no barriers appear to exist for anthroponotic transmission of these "hybrid" worms, a one-health approach to control the spread of human ascariasis will be necessary.

genomics↗

bioRxiv2019

Domains of transmission and association of community, school, and household sanitation with soil-transmitted helminth infections among children in coastal Kenya

IntroductionFew studies have simultaneously examined the role of sanitation conditions at the home, school, and community on soil-transmitted helminth (STH) infection. We examined the contribution of each domain that children inhabit (home, village, and school) and estimated the association of sanitation in each domain with STH infection.\n\nMethodsUsing data from 4,104 children from Kwale County, Kenya, who reported attending school, we used logistic regression models with cross-classified random effects to calculate measures of general contextual effects and estimate associations of village, school, and household sanitation with STH infection.\n\nFindingsWe found reported use of a sanitation facility by households was associated with reduced prevalence of hookworm infection but not with reduced prevalence of T. trichiura infection. School sanitation coverage > 3 toilets per 100 pupils was associated with lower prevalence of hookworm infection. School sanitation was not associated with T. trichiura infection. Village sanitation coverage > 81% was associated with reduced prevalence of T. trichiura infection, but no protective association was detected for hookworm infection. General contextual effects represented by residual heterogeneity between village and school domains had comparable impact upon likelihood of hookworm and T. trichiura infection as sanitation coverage in either of these domains.\n\nConclusionFindings support the importance of providing good sanitation facilities to support mass drug administration in reducing the burden of STH infection in children.\n\nAuthor SummaryInfection by whipworm and hookworm results from either ingestion of eggs or larvae or through skin exposure to larvae. These eggs and larvae develop in suitable soils contaminated with openly-deposited human faeces. Safe disposal of faeces should reduce transmission of these soil-transmitted helminths (STH), yet evidence of the impact of sanitation on STH transmission remains limited. We used data collected during a large, community-wide survey to measure prevalence of STH infections in coastal Kenya in 2015 to examine the relationship between sanitation conditions at home, school, and village and the presence of STH infection among 4,104 children who reported attending schools. We found that sanitation access at home and school sanitation coverage, but not the overall level of village sanitation coverage, was protective against hookworm infection. In contrast, only high village sanitation coverage, but not home or school sanitation, was protective against whipworm infection. Current STH control strategies emphasise periodic deworming through mass drug administration (MDA) of at-risk populations, including school-age children. Our findings highlight the need for continued efforts, alongside MDA, to extend access to good sanitation facilities at homes, schools, and across communities.

epidemiology↗