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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

Award Number: R16AI184350
ORGANIZATION: NATIONAL INSTITUTE OF ALLERGY & INFECTIOUS DISEASES
OPDIV: NIH
AWARD CLASS: DISCRETIONARY
AWARD ACTIVITY TYPE: SCIENTIFIC/HEALTH RESEARCH (INCLUDES SURVEYS)
PERIOD OF PERFORMANCE START DATE: 09/01/2024
PERIOD OF PERFORMANCE END DATE: 08/31/2028

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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 - 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.


Issue Date FY	Funding FY	Legal Entity Name	Legal Entity Address	Legal Entity City	Legal Entity State	Legal Entity Zip Code	Legal Entity COUNTY	Legal Entity COUNTRY	Assistance Listing	Award Code	Budget Year	Action Date	Action Type	Action Amount

Issue Date FY: 2025 ( Subtotal = $175,000 )
2025	2025	CALIFORNIA STATE UNIVERSITY FRESNO	5150 N MAPLE AVE	FRESNO	CA	93740	FRESNO	USA	Allergy and Infectious Diseases Research	000	2	9/9/2025	NON-COMPETING CONTINUATION	$175,000
														Subtotal = $175,000

Issue Date FY: 2024 ( Subtotal = $175,000 )
2024	2024	CALIFORNIA STATE UNIVERSITY, FRESNO	5150 N MAPLE AVE	FRESNO	CA	93740	FRESNO	USA	Allergy and Infectious Diseases Research	000	1	9/1/2024	NEW	$175,000
														Subtotal = $175,000

Grand Total All Awards = $350,000

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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

Award Number: R16AI184350

ORGANIZATION: NATIONAL INSTITUTE OF ALLERGY & INFECTIOUS DISEASES

OPDIV: NIH

AWARD CLASS: DISCRETIONARY

AWARD ACTIVITY TYPE: SCIENTIFIC/HEALTH RESEARCH (INCLUDES SURVEYS)

PERIOD OF PERFORMANCE START DATE: 09/01/2024

PERIOD OF PERFORMANCE END DATE: 08/31/2028

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