Stage M1S2 (2019-2020)

The research activities of the Laboratory of Molecular Anthropology of the Strasbourg Institute of Legal Medicine have been articulated (for nearly 20 years) around the study of ancient and/or degraded genetic material, with the objective of reconstructing the history of ancient human populations or human pathogenic agents. Within this framework, this laboratory is developing a new research project: setting up a molecular biology testing method to detect and characterise treponemas in samples collected during the 19th and 20th centuries, from individuals suffering from syphilis, embedded in paraffin.

These samples, currently stored at the Strasbourg Institute of Anatomical Pathology (IAP), are complemented by histopathological microscope slides that were used for diagnosis. This presents a unique opportunity to implement a study of the phylogeny of the bacterium through the analysis of a large number of samples preserved before the use of penicillin. The proposed study of 19th and 20th century samples will allow us to give insight into ancient genetic diversity and the subsequent evolution of the pathogen.
Our work would consist in selecting cases where the diagnosis of syphilis is definite, as evidenced by the analysis of microscope slides, and developing a PCR amplification test, based on published works, targeting DNA fragments that have been described as characteristic of various strands of Treponema bacteria. Once these are characterised, their DNA sequences will be used to reconstruct the phylogeny of the pathogen.

This study implies the design of specific primers aimed at amplifying short DNA sequences, typical of degraded material. Preliminary work therefore entails gathering all complete and partial sequences in the scientific literature for Treponema bacteria and performing sequence alignments to identify stable and variable portions of the genome across species of Treponema and strains of T. pallidum in particular. This will include both the bioinformatic treatment of sequences and raw sequencing data, as well as phylogenetic and statistical analyses, before adapted primers can be designed and the resulting data analysed. These preliminary operations will be carried out by a M1 student under the supervision of junior and senior researchers.