Portrait of author

Zhuofeng Yu:
The wastewater plasmidome and its derived resistome: Insight into their dynamics in the urban water systems

Date: 16-05-2022    Supervisor: Søren Johannes Sørensen




My PhD work has been part of a European collaborative research project – DARWIN (JPI-AMR, 7044-00004B). The overall aim of my PhD work was to investigate the pool of plasmids (plasmidome) in the urban water systems (UWSs) and the associated antibiotic resistance encoded by these mobile genetic elements.

During my PhD, I have primarily evaluated the transfer and retransfer potential of wastewater derived extended-spectrum beta-lactamase genes encoding plasmids to an opportunistic pathogen and the wastewater communities, respectively. In addition, I have performed a sequence similarity search and metagenome investigation to reveal these transmissible resistance determinants' prevalence and abundance in the UWSs.

Furthermore, I studied the patterns and influential factors of the plasmidome and its derived antibiotic resistome in different stages of UWSs based on a direct plasmidome sequencing strategy and a rigorous bioinformatic workflow. Firstly, I focused on the circular contigs for the sake of studying ascertained plasmids. I discovered the UWS plasmidome compositions, richness, abundance, and dynamics during the UWS processing. Meanwhile, I investigated the persistent plasmids in the UWSs. On top of this, I have missed the message from those linear contigs produced from the dataset. Accordingly, I recruited the assembled putative plasmid contigs from both circular and linear modules in silico, removed chromosome associated contigs and studied antibiotic resistome regarding this 'full-version' plasmidome. I studied the diversity, richness, abundance, dynamics, and various factors of the plasmidome derived resistome. The common pool of shared resistome from different countries and the resistome persistence were also investigated. Finally, I linked the plasmidome derived resistome with the microbiome and the total resistome.

Overall, my PhD work demonstrates the necessity to implement regular surveillance and risk management for the plasmid-mediated antibiotic resistance, which should be appropriate for the different geographic regions and treatment compartments in the UWSs.