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Whole genome sequencing of bacterial isolates of special interest: Salmonella, E. coli, Listeria and Campylobacter

Award Number: U18FD008944
ORGANIZATION: FOOD AND DRUG ADMINISTRATION
OPDIV: FDA
AWARD CLASS: COOPERATIVE AGREEMENT
AWARD ACTIVITY TYPE: KDA (KNOWLEDGE/DEVELOPMENT/APPLICATION)
PERIOD OF PERFORMANCE START DATE: 09/01/2026
PERIOD OF PERFORMANCE END DATE: 08/31/2027

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Whole genome sequencing of bacterial isolates of special interest: Salmonella, E. coli, Listeria and Campylobacter - Whole genome sequencing of bacterial isolates of special interest: Salmonella, E. coli, Listeria and Campylobacter Project Summary Bacteria from animal origin are a major source of food and feed contamination and are often identiﬁed as the potential cause of disease on animal or public health disease investigations. The Veterinary Laboratory Investigation and Response Network (Vet-LIRN) has identiﬁed the need to improve the bacterial genome information publicly available for several bacterial species, including Salmonella sp., E. coli, Listeria sp. and Campylobacter sp. We propose to sequence and publish the whole genome of bacteria of special interest for animal and public health. Speciﬁcally, this project will focus on Salmonella sp., E. coli, Listeria sp. and Campylobacter sp. The Minnesota Veterinary Diagnostic Laboratory (MVDL) maintains a large collection of isolates from the previous 2 years frozen at -80 C, including more than 1,000 Salmonella isolates, more than 1,000 E. coli isolates and a small number of Listeria sp. and Campylobacter sp. isolates. We will select 50 Salmonella sp. isolates and 50 E. coli isolates to sequence based on their antimicrobial resistance patterns, serotyping information and representativeness. In addition, we will sequence 20 Listeria isolates and 20 Campylobacter isolates. Bacterial whole genome sequencing will be performed by long read sequencing on an Oxford Nanopore Technology (ONT) sequencing platform. Brieﬂy, bacterial isolates will be resuspended, DNA will be extracted and ONT’s ligation-based library preparation will be performed. We will use MinION/GridION R10 ﬂow cells run on a GridION sequencer for 12-24 h. In the case that complete genomes could not be assembled with just ONT sequencing, the MVDL has the capability to sequence bacterial isolates by short read sequencing using Illumina and Element Biosciences platforms. Bacterial whole genomes will be assembled from raw reads using assemblers Fly and Autocycler. Sequencing will be performed to target a minimum genome depth of 30x. Raw sequencing reads and assembled genomes will be deposited in public databases, along with relevant metadata. Antimicrobial resistance prediction based on the antimicrobial genes found in each genome will be compared to the phenotypic antimicrobial resistance information available for each isolate. Genomes that show disagreements between genomic and phenotypic predicted antimicrobial resistance will be further investigated for potential new mechanisms of resistance.


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: 2026 ( Subtotal = $85,499 )
2026	2026	REGENTS OF THE UNIVERSITY OF MINNESOTA	2221 UNIVERSITY AVE SE STE 100	MINNEAPOLIS	MN	55414	HENNEPIN	USA	Food and Drug Administration Research	000	1	9/23/2026	NEW	$85,499
														Subtotal = $85,499

Grand Total All Awards = $85,499

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Whole genome sequencing of bacterial isolates of special interest: Salmonella, E. coli, Listeria and Campylobacter

Award Number: U18FD008944

ORGANIZATION: FOOD AND DRUG ADMINISTRATION

OPDIV: FDA

AWARD CLASS: COOPERATIVE AGREEMENT

AWARD ACTIVITY TYPE: KDA (KNOWLEDGE/DEVELOPMENT/APPLICATION)

PERIOD OF PERFORMANCE START DATE: 09/01/2026

PERIOD OF PERFORMANCE END DATE: 08/31/2027

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