Investigating drug resistance markers, evolution and co-infections of pathogens of public health concern using portable molecular detection and sequencing tools

Genome sequencing has become an important tool for characterization and surveillance of infectious diseases to guide public health measures. To complement pathogen sequencing, biological samples can be screened for the presence of distinct pathogens, specific genes or mutations by using rapid quantitative PCR (qPCR) based technologies.
The overall aim of this thesis was to develop and apply molecular detection and sequencing approaches as well as novel bioinformatic analysis tools for molecular surveillance of infectious diseases in Central Africa and the Middle East with high throughput and information depth.
The evolution of SARS-CoV-2 in Equatorial Guinea was monitored using a combination of reverse transcription qPCR (RT-qPCR) assays to detect mutations of interest and amplicon-based whole genome sequencing.
Molecular analysis of nucleic acids retained on malaria rapid diagnostic tests (RDTs) collected during a malaria indicator survey on Bioko Island, Equatorial Guinea found a high proportion of false-positive RDTs.
In addition, the extracted RDTs were screened for the presence of blood dwelling filarial nematodes Loa loa and Mansonella perstans.
A simplified protocol was developed to detect malaria parasite nucleic acids stored on dried blood spots using a portable and rapid qPCR platform.
A novel bioinformatic pipeline was developed for compositional profiling of antimalarial drug resistance markers in multiclonal Plasmodium falciparum infections collected from clinical malaria cases in Central Africa.
Whole genome sequencing of Campylobacter jejuni and Salmonella enterica was applied for the surveillance of foodborne bacteria in the poultry production chain in West Bank, Palestine using a One Health approach.
In summary, we successfully developed and applied tools for molecular surveillance of infectious diseases of high public health relevance caused by viruses, bacteria and parasites.