This thesis, directed by Fernando González-Candelas, explores the study of the bacterium T. pallidum, which causes various diseases such as syphilis, thanks to the development of new techniques for genomic and evolutionary analysis. Part of the results have been published in the journals Molecular Biology and Evolution, PLoS One and Current Biology. The thesis was defended on 18 September 2023.
Advances in sequencing technologies have increased the availability of complete genomes of Treponema pallidum, facilitating a better understanding of this bacterium that causes treponematosis, including syphilis. This PhD thesis, entitled "Genomic analysis of evolutionary processes and epidemiology of Treponema pallidum", includes four studies on both ancient and contemporary genomes of T. pallidum to improve our understanding of its evolution and epidemiology. A new method for recombination detection in T. pallidum genomes has been developed that improves previous tools for this essential component of bacterial phylogenomic analyses. Its application to 75 contemporary T. pallidum genomes revealed 19 recombination events at 12 loci that have contributed significantly to the current differentiation and variability of the syphilis-causing T. pallidum lineage. Further population genomic analyses have revealed that most of these loci are likely to be involved in the defence and virulence of the pathogen. Until recently, it was believed that it was not possible to obtain ancient T. pallidum genomes. In this thesis, two nearly complete genomes have been obtained: one from Poland, dated to the 17th century, and the other from Brazil, about 2000 years ago. This represents the first pre-Columbian genome of T. pallidum originating from the Americas. Incorporation of these genomes into different datasets has made it possible to describe new recombination events. The identification of the strains involved indicates the coexistence and circulation of several subspecies in the same region. Moreover, the inferred divergence data between lineages by adding ancient genomes are earlier than those obtained with modern genomes alone, increasing the accuracy of the evolutionary timeline through dating based on Bayesian molecular clock methods. Finally, to increase knowledge of the molecular epidemiology of treponematoses, a scheme was designed from 121 genomes of the three subspecies of T. pallidum. This scheme allows efficient discrimination between strains of the three subspecies, revealing their genetic diversity and prevalence of macrolide antibiotic resistance. Analysis of genetic diversity and population structure reveals localised transmission patterns and highlights the influence of regional factors on the spread of T. pallidum. Overall, this thesis represents a significant advance in our understanding of the evolution, genomics and epidemiology of T. pallidum.
Marta Pla-Diaz conducted her doctoral research in the Molecular Epidemiology group under the supervision of Fernando González-Candelas, professor of genetics at the University of Valencia and researcher at the Institute for Integrative Systems Biology I2SysBio (UV-CSIC) and at the joint unit of epidemiology and health (Fisabio-UV). During the development of the thesis, Marta Pla-Diaz made a stay in the laboratory of Verena Schuenemann (University of Zurich) and enjoyed a contract of the University Teacher Training Programme (FPU). The examining board was formed by Carmen Amaro (UV), Julio Rozas (Universitat de Barcelona) and Laura Gómez-Valero (Institut Pasteur, Paris), who graded the thesis as excellent.
