Resumen de Application of high-throughput sequencing to the genomic epidemiology of bacterial pathogens
The genomic revolution, through the development of the high-throughput, sequencing (HTS) technologies, has greatly benefited Microbiology. Thanks to the possibilities offered by HTS, in recent years the number of studies in clinical microbiology and epidemiology that apply it has increased. However, its routine implementation in the clinic is still far from being a reality in many countries, so more research is required to mature its use and solve the obstacles it presents.
In this work, the main objective is to show the usefulness of this technology for the study of three bacterial pathogens and their epidemiology, through its application in four different cases.
The first chapter addresses the study of the genomic epidemiology of Neisseria gonorrhoeae in three Spanish regions. Thanks to obtaining the complete genomes, it was possible to delve into its population structure and its epidemiology. Likewise, it was possible to carry out the detection of determinants of resistance to antibiotics present in the gonococcal population in Spain.
In the second chapter, HTS is applied for the first time to solve a case of transmission of gonorrhea in the context of a forensic case of possible abuse of a minor. Thanks to its resolution power, it was possible to discriminate between isolates from those involved in the case and those from control patients. This was not possible with the classical molecular biology techniques. These results show the usefulness of HTS in this type of cases.
The third chapter investigates the genetic relationship between the isolates of two nosocomial outbreaks produced by Serratia marcescens. On this occasion, we evaluate the impact of choosing a reference genome to investigate an outbreak. If the reference used is too close genetically to the isolates of the outbreak, the outbreak cannot be defined as such.
Finally, the fourth chapter investigates the recombination of Lactococcus garvieae at different taxonomic levels. Its sequencing using long reads technology allowed the complete assembly of its genome, allowing a more complete analysis.
