This thesis, supervised by Fernando González-Candelas, Rafael Sanjuán and Pilar Domingo-Calap, has studied how bacteria and their viruses interact and the ability to predict this interaction through genomic analysis. Part of the results have been published in the journal Cell Reports. The thesis was defended on July 21, 2023.
Bacteriophages play essential roles in bacterial ecology and evolution and are potential antimicrobial agents. However, the determinants of phage-host specificity remain elusive. The capsule enveloping some bacteria is the first barrier confronted by many phages. In this thesis, entitled "The effect of the genetic background on phage infectivity in an encapsulated host", we quantified the predictability of phage-bacteria interactions based on the type of host capsular locus (CLT) and the depolymerase domains (Dpos) specific for their receptor binding proteins. For this purpose, Klebsiella pneumoniae was used as a model due to its high capsular diversity and global health importance. A collection of 138 clinical strains of K. pneumoniae representative of the genomic diversity of the species was generated. These were challenged with 46 different environmental phages. Most of the phages exhibited capsular specificity, and their infection pattern could be accurately predicted from the host CLT. Thus, the Dpos encoded by phages, which have undergone horizontal transfer at large taxonomic scales, were key determinants of host tropism. In addition to capsule-specialist phages, some were discovered to have a broader host range. Notably, more than 90% of bacterial strains exhibit capsular heterogeneity, with both capsular and acapsular clones. This heterogeneity affects phage tropism, as broad-range phages preferentially infect bacteria with a higher proportion of acapsular clones, in contrast to capsule specialist phages. Acapsular mutants gain resistance in 286 out of 406 (70%) of the combinations tested. Neither phage capsule specificity nor infection of acapsular bacteria correlated with phage phylogenetic classification. Some 43% of the phages showed either obligate or facultative capsule binding behaviour depending on the bacterial strain and its capsular inactivation mechanism, which in turn leads to different compromises in resistance. These findings extend our understanding of the complex interactions between bacteria and their viruses and point to the possibility of predicting the early steps of phage infection using phage and bacterial genomic sequences.
Beatriz Beamud Aranguren carried out her doctoral research in the Molecular Epidemiology group under the supervision of Rafael Sanjuán Verdeguer, professor of genetics at the University of Valencia, Fernando González Candelas, professor of genetics at the UV and Pilar Domingo Calap, researcher of the Ramón y Cajal program at the UV, all of them researchers at the Institute of Integrative Systems Biology I2SysBio (UV-CSIC) and at the joint unit of epidemiology and health (Fisabio-UV). During the development of the thesis, Beatriz Beamud made a stay at the Synthetic Biology Unit of the Institut Pasteur (Paris) and enjoyed a contract within the University Teacher Training Program (FPU). The examining board was formed by Santiago F. Elena (I2SysBio, CSIC), Mária Džunková (I2SysBio, UV), and Olaya Rendueles (Institut Pasteur, Paris), who graded the thesis as outstanding.
