From the clinic to the farm: applying sequencing and de novo assembly to characterize One-Health bacterial pathogens

Abstract

Multi-drug resistant bacteria infections are a threat to animal and human health due to the limitation in treatment, which can lead to severe clinical complications, longer hospital stays, or even death. Multi-drug resistant bacteria can be transmitted to the environment, other animals, or humans via different ways, such as fecal contamination or food-chain. In this scenario, One-Health is an approach that considers health as a global entity, including human, animal, and the environment._x000D_ _x000D_ _x000D_ _x000D_ The aim of this thesis is to optimize the use of long reads in whole-genome sequencing approaches for characterizing the bacterial genome and plasmids, including the presence of antibiotic resistance genes, mobile genetic elements, and virulence factors._x000D_ _x000D_ _x000D_ _x000D_ By using long-read whole-genome sequencing, we de novo assembled complete chromosomes and plasmids as single contigs for Staphylococcus pseudintermedius from dogs, Escherichia coli from livestock and the farmer, and Klebsiella pneumoniae from humans. This approach located the antibiotic resistance genes in plasmids or chromosomes and spanned mobile genetic elements, thus overcoming the pitfalls associated with short reads. Moreover, we unraveled the transmission of similar plasmids harboring antibiotic resistance genes for colistin-resistant Escherichia coli in a mixed farm and for carbapenem-resistant Klebsiella pneumoniae in an inter-hospital outbreak._x000D_ _x000D_ _x000D_ _x000D_ The antibiotic resistance and virulence factor genes profiles of Staphylococcus pseudintermedius from dogs and Escherichia coli from livestock highlight the role of domestic animals as a reservoir of pathogens with highly zoonotic potential.

Date of Award	29 Jun 2021
Original language	English
Supervisor	Olga Francino Martí (Director)