Publication Date

Spring 6-1-2021

Degree Type

Master's Project

Degree Name

Master of Science in Bioinformatics (MSBI)

Department

Computer Science

First Advisor

Wendy Lee

Abstract

The existential threat of emerging antibiotic resistance in microbial communities poses significant risks to public health. In particular, wastewater can serve as a point of confluence for pharmaceuticals and antibiotic-resistant bacteria from urban and agricultural settings. While this is a prime environment for genetic drift and horizontal transfer of antibiotic resistance genes (ARGs) and mobile genetic elements, it also presents an opportunity for resistome monitoring via shotgun metagenomic sequencing and downstream analysis. This project reports the application of a hybrid assembly approach for the detection of ARGs within DNA derived from a wastewater sample collected from the San José-Santa Clara Regional Wastewater Facility, which serves a significant portion of the San Francisco Bay Area. Hybrid assembly (with polishing) of Nanopore-derived long reads and Illumina-derived short reads resulted in detection of additional ARGs compared to a previously-performed short-read-based approach.

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