Molecular detection of Enteropathogens from diarrheic stool of HIV positive patients in Gondar, Ethiopia

Abstract Background Infectious diarrhea is a common problem in the developing world, especially among people living with HIV/AIDS. Traditional diagnostic methods such as stool culture and microscopic examination are limited by resources and poor sensitivity. The use of molecular diagnostics for enteropathogen detection in this region of sub-Saharan Africa has not been fully explored. We sought to identify risk factors and characterize enteropathogens from diarrheic stools of HIV-positive patients in Gondar, Ethiopia using multiplex molecular panels targeting key infectious agents. Methods A cross-sectional study of 100 stool samples was performed. Samples were collected consecutively from HIV- positive patients presenting with diarrhea at University of Gondar Hospital clinic, a major center in NW Ethiopia. Genomic DNA was extracted from stool and processed using a multiplex molecular panel Allplex™ [Seegene, Canada]. Correlations between patient characteristics, symptoms, public health risk factors, and enteropathogen type (s) were studied. Eighty-six samples were successfully analyzed by molecular methods. Results The mean age was 35 with 43% male. Eighty percent lived in an urban area, 18% had access to well water only, and 81% practiced proper hand hygiene. The majority of patients (72%) were receiving HAART with a median CD4 cell count of 362/μL. Multiple pathogens were detected in 94% of specimens, with an average of 5 enteropathogens per sample. Common bacteria, viruses, and parasites detected were Shigella spp./enteroinvasive E. coli (80%), enterotoxigenic E. coli (73%), Norovirus (16%) and B. hominis (62%). CD4 cell count < 500/ μL was associated with the presence of viruses (p = 0.004) and the absence of STEC (p = 0.010). The use of HAART or CD4 levels was not associated with the number of enteropathogens detected. Conclusions Diarrheic stool from HIV-positive outpatients in Gondar, Ethiopia had on average 5 enteropathogens present in their stool. Shigellaspp./enteroinvasive E. coli and enterotoxigenic E. coli are the major pathogens, not dissimilar to immunocompetent individuals in low income countries

Season and habitat affect diversity, abundance and reproductive state of small mammals near Lake Abaya, Ethiopia

This study investigated the spatio-temporal association of small mammals in human-modified habitats. Small mammals were sampled using Sherman traps along 200mtransects (with one trap at every 10minterval) in each of four habitats (cropland, forest patch, scrubland and wetland) replicated twice. Additional trapping was carried out in rural settlements comprising of eight homesteads, with five traps per homestead. Trapping was conducted in three sessions during the agricultural seasons: rainy (October), off-rain (December) and dry (February) over two years (2018 and 2019). In each session, trapping was carried out for three consecutive nights. A total of 497 small mammals belonging to 12 species from four families (Soricidae, Macroscelididae, Gliridae and Muridae) were captured. Murine rodents accounted for 99.4% of the animals with Mastomys erythroleucus (58%) being the dominant species. The scrubland had the highest small mammal species diversity while the cropland had the lowest. M. erythroleucus was not strongly associated with any spatio-temporal parameter and scored majority of seasonally reproducing individuals in the cropland, signifying its pest importance. Though disconnected from protected areas, habitats such as the scrubland harbor diverse small mammal species (including a vulnerable-endemic species, Grammomys minnae), suggesting the habitats’ significance for ecosystem functioning and conservation