Webinar 5: July 8th, 11.00-12.00 (SAST/CEST)

First talk:- Surveillance of Candida auris in Kenya

Speaker: Dr. med. Loice Achieng Ombajo (Center for Epidemiological Modelling and Analysis, University of Nairobi)

Abstract: Candida auris has emerged as a rapidly increasing cause of sepsis globally, but critical data gaps exist in understanding the situation in sub-Saharan Africa. There is limited data on the epidemiology, risk factors and outcomes of C. auris. There is also limited laboratory capacity for the isolation, identification and an6 fungal susceptibility testing of C.auris. In this talk, we will look at what we know regarding C.auris in Kenya, we will also present the results of an epidemiological and genomic investigation of a hospital outbreak and its successful control in Kenya. 

Second talk:- Development and evaluation of metagenomics approaches for pathogen surveillance at the human-animal interface in limited-resource countries

Speaker: Jean Claude Makangara (Multidisciplinary Center for Infectious Diseases, University of Bern)

Abstract: In the last two decades, the world has witnessed several emerging infectious diseases that led to severe health consequences, such as the Ebola outbreak in 2014 – 2016 and the emergence of Monkeypox virus (MPXV) and coronaviruses (MERS-CoV and SARS-CoV-2). In limited-resource countries like the Democratic Republic of Congo (DRC), many of these emerging viruses have a high endemicity; however, during past Ebola and MPXV outbreaks, not all symptomatic suspected cases tested positive for these viruses. However, since molecular diagnostics in low- and middle-income countries are often limited, many of these suspected symptomatic cases remain undiagnosed. An unbiased metagenomics approach, such as Sequence-Independent Single-Primer Amplification (SISPA), could help identify the potential etiological pathogens in these undiagnosed symptomatic cases. However, the disproportional abundance of host-derived nucleic acids over pathogen-associated nucleic acids reduces the overall sensitivity of metagenomic sequencing, including sequencing on the Oxford Nanopore Technology (ONT) platform, which is affordable for usage in limited-resource countries. Herein, we aim to increase the overall removal of host-derived nucleic acids during sample pre-processing by evaluating different enzymatic and chemical approaches that can be used in countries with limited resources. Using qRT-PCR and SISPA on the ONT sequencing platform we will determine the influence of these pre-processing approaches on the overall detection sensitivity and select the optimal condition for metagenomic-based identification of pathogens in clinical samples of previously undiagnosed symptomatic cases. Overall, we aim to develop a novel and optimized metagenomic approach that can be implemented for pathogen surveillance at the human-animal interface in limited-resource countries with high endemicity of emerging infectious diseases.

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