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PhD Doctor of Philosophy

Other, Biology
Microbiology, Molecular biology, Bacterial genomics, Bioinformatics, and Antibiotic resistance
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Project ideas

Investigation of antibiotic resistance in bacteria and how resistance genes can be detected and analyzed.

Bacterial resistance to antibiotics is nowadays a real concern worldwide and an area of interest for the scientist and medical community. This resistance is mediated by resistance genes within bacterial genomes and can be exchanged between bacteria; therefore it can be spread widely in hospital and non-hospital settings. In this project we aim : - To make an update on mode of actions of antibiotics on bacteria - To study the different resistance mechanisms developed by bacteria to fight against antibiotics - To learn how resistance to antibiotics can be detected and evaluated in laboratories - To learn how to investigate by bioinformatic analysis the presence of antibiotic resistance genes within genome sequences - And finally, to learn molecular sequence analyses including (sequence alignment, comparison, phylogenetic tree analysis, etc.)

Exploring whole genome sequences and genome analysis of multidrug resistant bacteria.

As well know today, antibiotic resistance in hospital and non-hospital settings has become a major public health issue worldwide. This antibiotic resistance issue is responsible of a huge deaths in hospitalized patients every year. So, as recommended by the international health organizations such as the World Health Organization (WHO), fighting antibiotic resistance has become a top priority for health settings. Therefore, for this purpose, we need, among other things, to understand and to study first the resistance mechanisms and the modes of transmission of the resistance genes between bacterial pathogens. Here, I purpose to initiate young students to how to investigate the antibiotic resistance in clinical isolates using the emerging high throughput sequencing technologies. Indeed, in this project, we will see basic bioinformatic ways to analyze raw data of a sequenced bacterial genome (by Illumina for example). How to assemble these data to reconstruct the genome sequences of the isolates. How to perform bacterial genome annotation, and finally how to perform an exhaustive analysis of genome sequences to identify the full repertoire of resistance genes. We can perform genotyping analysis based on genomic data to identify putative emerging clone multidrug resistant. The project will focus mainly in basic bioinformatic analyses using open access programs and tools to analyze genome sequences.

Coding skills

bash , py

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