# Next-day whole genome sequencing and analysis using nanopore sequencing for real-time outbreak and transmission determination in healthcare facilities

> **NIH NIH R43** · DAY ZERO DIAGNOSTICS, INC. · 2021 · $300,000

## Abstract

The goal of this project is to develop an ultra-rapid, cost-effective whole genome sequencing based method to
determine if a healthcare associated infection (HAI) transmission event has occurred. HAIs, particularly those
caused by multidrug resistant organisms, are a recognized healthcare threat. Despite the potential of whole
genome sequencing technologies, there are no commercial offerings that can reliably detect an HAI transmission
event within 24 hours. Rapid turnaround times resulting in the confirmation of an HAI event promise to reduce
the spread of the HAI and has the potential to minimize the overuse and misuse of antimicrobial drugs. Likewise,
a technology with the sensitivity and precision to rule out an HAI event will reduce unnecessary and expensive
operational costs. To meet this medical and commercial need, Day Zero Diagnostics is developing a whole
genome sequencing and analysis workflow that leverages the speed and other advantages of third generation
sequencing technology (Oxford Nanopore) to demonstrate the feasibility of a 24 hour turnaround HAI service. In
addition to rapid read generation, the key features that differentiate this approach from existing pipelines (e.g.
Illumina technology) are that it overcomes the need for an external closely related reference genome and enables
full genome assembly including mobile genetic elements (plasmids) that are a source of antimicrobial resistance
and can be disseminated independently of the chromosomal genome. The goal of this Phase I effort is to develop
the necessary operational pipelines generating processing, assembly, and annotation of third generation
sequencing data for HAI. Aims are focused on the development of a single nucleotide polymorphism (SNP)
variant calling algorithm that is optimized for Oxford Nanopore data (Aim 1); developing a de novo assembly and
annotation pipeline for both chromosomal mobile element genomes (Aim 2), and demonstrating preliminary utility
as an HAI investigation service (Aim 3). The successful completion of the aims of this proposal will advance the
workflow towards further optimization and refinement, resulting in a commercial product with a “same day,” 24-
hour turnaround time. The final product will be offered as a service that has the potential for routine use in hospital
transmission investigations, therefore improving the capabilities of infection control and the management of HAIs.

## Key facts

- **NIH application ID:** 10136296
- **Project number:** 1R43AI156979-01
- **Recipient organization:** DAY ZERO DIAGNOSTICS, INC.
- **Principal Investigator:** Mohamad Sater
- **Activity code:** R43 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2021
- **Award amount:** $300,000
- **Award type:** 1
- **Project period:** 2020-12-01 → 2021-09-30

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10136296

## Citation

> US National Institutes of Health, RePORTER application 10136296, Next-day whole genome sequencing and analysis using nanopore sequencing for real-time outbreak and transmission determination in healthcare facilities (1R43AI156979-01). Retrieved via AI Analytics 2026-05-24 from https://api.ai-analytics.org/grant/nih/10136296. Licensed CC0.

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