Project Abstract:
Surveillance of drug-resistant bacteria in resource-limited settings: a focus on cost-
effective long-read sequencing of eyedrop-associated P. aeruginosa and locally sourced metagenomic
samples
Antimicrobial resistance (AMR) poses a growing threat to global public health, rendering antibiotics
increasingly ineffective against drug-resistant bacteria. Recent episodes involving the contamination of
preservative-free eyedrops with extensively drug-resistant (XDR) Pseudomonas aeruginosa have resulted in
hundreds of infection cases and three fatalities. This outbreak underscores that superbug occurrences are no
longer confined to healthcare-associated settings, and we need a community-wide surveillance system that
monitors local infection outbreaks efficiently in terms of time, accuracy, and cost. Such a system is essential to
mitigate the adverse consequences of superbugs, encompassing a broad spectrum of sample types including
medicinal and agricultural products. To achieve this long-term goal, this project first aims to test a
decentralized AMR surveillance system in resource-limited settings by assessing the detection of drug-
resistant bacteria and antimicrobial bacteriophages with cost-efficient long-read sequencing. We will use
Flongle platforms that enable the sequencing of smaller assays (<$100 per run) to sequence the eyedrop-
associated samples to evaluate the accuracy and efficiency of XDR P. aeruginosa and bacteriophage genome
assembly. Through our collaborative efforts with the research team at UCSD (David Pride, Ph.D./M.D.), we
have the necessary data and expertise to conduct a comprehensive and quantitative evaluation of our
approach in contrast to their conventional sequencing methods. Next, we will conduct an exploratory study
involving the sequencing of locally sourced metagenomic samples from the farm units of CSU Fresno. This
exploratory study leverages the quantitative assessment of the low-cost AMR surveillance pipeline in the
previous aim to obtain metagenomic data that can reveal the extent of AMR presence within the Central Valley
region of Fresno with heavy agricultural activities and discover novel bacteria/phage pairs for future
biotherapeutic applications. The broader implication of this project extends to the empowerment of resource-
constraint institutes as proactive agents in the surveillance and investigation of antimicrobial resistance. By
monitoring local infection outbreaks throughout diverse segments of society, including underserved
communities, these institutes can effectively contribute to the rapid and efficient control and prevention of local
infection outbreaks, thereby bolstering public health on a broader scale.
